From yanwong at pub.open-bio.org  Tue Feb  1 03:52:17 2005
From: yanwong at pub.open-bio.org (Yan Wong)
Date: Tue Feb  1 03:42:49 2005
Subject: [MOBY-guts] biomoby commit
Message-ID: <200502010852.j118qHHl013127@pub.open-bio.org>


yanwong
Tue Feb  1 03:52:17 EST 2005
Update of /home/repository/moby/moby-live/Python/bioMoby/webservice
In directory pub.open-bio.org:/tmp/cvs-serv12609/webservice

Modified Files:
	Dispatcher.py Invocators.py TCBioMoby.py __init__.py 
Log Message:


moby-live/Python/bioMoby/webservice Dispatcher.py,1.2,1.3 Invocators.py,1.2,1.3 TCBioMoby.py,1.2,1.3 __init__.py,1.2,1.3
===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/webservice/Dispatcher.py,v
retrieving revision 1.2
retrieving revision 1.3
diff -u -r1.2 -r1.3
--- /home/repository/moby/moby-live/Python/bioMoby/webservice/Dispatcher.py	2005/01/18 13:46:24	1.2
+++ /home/repository/moby/moby-live/Python/bioMoby/webservice/Dispatcher.py	2005/02/01 08:52:17	1.3
@@ -76,7 +76,7 @@
     def __str__(self):
         return "An error occurs during the Dispatcher process: "
 
-	
+        
 class AbstractDispatcher:
     """ Subclass this one to create your own dispatcher class
         a Dispatcher class must have a execute method
@@ -91,16 +91,16 @@
 
         from bioMoby import MobyUnmarshaller
 
-	self._isbase64=False
-	self._workdir=workdir
-	self.answers={}
-	
-	#First see if we have a MobyContent Object or a string
-	mc=mobyContentXML
-	self._isString=False
-	
-	if not hasattr(mobyContentXML, 'queryData'):
-	    self._isString=True
+        self._isbase64=False
+        self._workdir=workdir
+        self.answers={}
+        
+        #First see if we have a MobyContent Object or a string
+        mc=mobyContentXML
+        self._isString=False
+        
+        if not hasattr(mobyContentXML, 'queryData'):
+            self._isString=True
             try:
                 #Do some cleaning on the XML Document before proceeding...
                 #Remove all \t|\n from the <a>\n\t</a>
@@ -110,117 +110,117 @@
                 mc=um.loads("><".join(r.split(mobyContentXML)))
             except:
                 try:
-		    mc=um.loads(base64.decodestring(mobyContentXML))
-	            self._isbase64=True
-	        except binascii.Error:
-	            raise  EDispatchError, "Invalid types in the moby Content object"
+                    mc=um.loads(base64.decodestring(mobyContentXML))
+                    self._isbase64=True
+                except binascii.Error:
+                    raise  EDispatchError, "Invalid types in the moby Content object"
 
         self.queryData=mc.queryData
         self.invocator=Invocator
-	self._invocatorParameters=invocatorParameters
+        self._invocatorParameters=invocatorParameters
         self.commandBuilder=CommandBuilder
         self.formatter=formatter
-	
-	del MobyUnmarshaller
+        
+        del MobyUnmarshaller
 
     def execute(self):
-	""" Override this method
-	"""
-	pass
+        """ Override this method
+        """
+        pass
 
     def _toMoby(self):
-	"""Return the results as a MobyContent Object
-	"""
-	from bioMoby import MobyContent
-	
-	if self._isbase64:
-	    return base64.encodestring(str(MobyContent(self.answers)))
-	
+        """Return the results as a MobyContent Object
+        """
+        from bioMoby import MobyContent
+        
+        if self._isbase64:
+            return base64.encodestring(str(MobyContent(self.answers)))
+        
         return str(MobyContent(self.answers))
 
-	
+        
 class SimpleDispatcher(AbstractDispatcher):
     """ A simple dispatcher execute sequentially the treatments
     """
     def __init__(self, mobyContentXML, Invocator, InvocatorParameters, CommandBuilder, formatter=None, workdir="/tmp"):
-	AbstractDispatcher.__init__(self, mobyContentXML, Invocator, InvocatorParameters, CommandBuilder, formatter, workdir)
-	
-	from bioMoby import MobyObject
-	
-	if 'JOBSESSION' in self.queryData.keys():
-	    self._sessionid=self.queryData['JOBSESSION'][0].id
-	else:
-	    self._sessionid=`random.randint(0,sys.maxint-1)`
-	    
-	    while "session"+self._sessionid in os.listdir(self._workdir):
-		self._sessionid=`random.randint(0,sys.maxint-1)`
-		
+        AbstractDispatcher.__init__(self, mobyContentXML, Invocator, InvocatorParameters, CommandBuilder, formatter, workdir)
+        
+        from bioMoby import MobyObject
+        
+        if 'JOBSESSION' in self.queryData.keys():
+            self._sessionid=self.queryData['JOBSESSION'][0].id
+        else:
+            self._sessionid=`random.randint(0,sys.maxint-1)`
+            
+            while "session"+self._sessionid in os.listdir(self._workdir):
+                self._sessionid=`random.randint(0,sys.maxint-1)`
+                
             os.mkdir(self._workdir+"/session"+self._sessionid)
-	
-	os.chdir(self._workdir+"/session"+self._sessionid)
-	
+        
+        os.chdir(self._workdir+"/session"+self._sessionid)
+        
         self.answers={'JOBSESSION':[MobyObject(namespace="SESSIONID", id=self._sessionid)]}
 
     def _clean(self):
-	"""Clean the session directory
-	"""
+        """Clean the session directory
+        """
         #Clean the session directory
         os.chdir(self._workdir)
         shutil.rmtree(self._workdir+"/session"+self._sessionid)
-	    
+            
     def _fetchAnswers(self):
-	""" Fetch the answers and clean the session directory
-	"""
-	from bioMoby import GeneralInvocator
-	
-	answers={}
+        """ Fetch the answers and clean the session directory
+        """
+        from bioMoby import GeneralInvocator
+        
+        answers={}
 
-	ruserdir="session"+self._sessionid
+        ruserdir="session"+self._sessionid
         try:
-	    l=os.listdir(self._workdir+"/"+ruserdir)
-	except:
-	    l=[]
-	
-	if len(l)>0:
-	    #There is a session directory
+            l=os.listdir(self._workdir+"/"+ruserdir)
+        except:
+            l=[]
+        
+        if len(l)>0:
+            #There is a session directory
             for querykey in l:
-		if querykey[:8]=="results-":
-		    aQueryName=querykey[8:]
-	            gi=GeneralInvocator(aQueryName ,userdir=self._workdir+"/"+ruserdir)
-	            answers[aQueryName]=[gi.getResults()]
+                if querykey[:8]=="results-":
+                    aQueryName=querykey[8:]
+                    gi=GeneralInvocator(aQueryName ,userdir=self._workdir+"/"+ruserdir)
+                    answers[aQueryName]=[gi.getResults()]
 
                     if self.formatter != None:
                         answers[aQueryName]=self.formatter(answers[aQueryName][0])
-			
+                        
             if len(answers.keys())>0:
-	        self.answers=answers
-		
-                self._clean()	
+                self.answers=answers
+                
+                self._clean()        
 
-	del GeneralInvocator
-		
+        del GeneralInvocator
+                
     def execute(self):
-	"""Execute the queries sequentially
-	"""
+        """Execute the queries sequentially
+        """
 
-	try:
+        try:
             for key in self.queryData.keys():
-	        query=self.queryData[key]
-	        r=self.invocator(key, self.commandBuilder(query), userdir=self._workdir+"/session"+self._sessionid)
-	        r.execute()
-	    
-	    self._fetchAnswers()
-	except:
-	    import traceback
-	    import StringIO
-	    from bioMoby import MobyString
-	    sio=StringIO.StringIO()
-	    traceback.print_exc(file=sio)
-	    
-	    self.answers['JOBSESSION']=[MobyString(content=sio.getvalue())]
-	    self._clean()
-	
-	return self._toMoby()
+                query=self.queryData[key]
+                r=self.invocator(key, self.commandBuilder(query), userdir=self._workdir+"/session"+self._sessionid)
+                r.execute()
+            
+            self._fetchAnswers()
+        except:
+            import traceback
+            import StringIO
+            from bioMoby import MobyString
+            sio=StringIO.StringIO()
+            traceback.print_exc(file=sio)
+            
+            self.answers['JOBSESSION']=[MobyString(content=sio.getvalue())]
+            self._clean()
+        
+        return self._toMoby()
 
 class MultiThreadDispatcher(SimpleDispatcher):
     """ Use a MultiThread to execute a query
@@ -231,114 +231,114 @@
         from bioMoby import MobyString
 
         query=self.queryData[queryKey]
-	
-	#Execute the query
+        
+        #Execute the query
         try:
             r=self.invocator(queryKey, self.commandBuilder(query), userdir=self._workdir+"/session"+self._sessionid)
-	    r.execute()
+            r.execute()
             time.sleep(0)
-	    
+            
         except:
-	    #If there is a problem, we return the generated exception
-	    import traceback
-	    import StringIO
-	    sio=StringIO.StringIO()
-	    traceback.print_exc(file=sio)
-	    
-	    self.answers['JOBSESSION']=[MobyString(content=sio.getvalue())]
-	    self._clean()
+            #If there is a problem, we return the generated exception
+            import traceback
+            import StringIO
+            sio=StringIO.StringIO()
+            traceback.print_exc(file=sio)
+            
+            self.answers['JOBSESSION']=[MobyString(content=sio.getvalue())]
+            self._clean()
 
 
         del MobyString
 
     
     def execute(self):
-	""" Execute the queries with threads
-	"""
-	
-	try:
+        """ Execute the queries with threads
+        """
+        
+        try:
             os.chdir(self._workdir+"/session"+self._sessionid)
             mt=MultiThread(self._execute, self.queryData.keys())
             mt.start()
             mt.join()
 
-	    self._fetchAnswers()
+            self._fetchAnswers()
         except:
-	    self._clean()
-	    
-	return self._toMoby()
+            self._clean()
+            
+        return self._toMoby()
 
-	
+        
 class PBSDispatcher(SimpleDispatcher):
     """Dispatcher for PBS jobs
     """
 
     def __init__(self, mobyContentXML, InvocatorParameters, CommandBuilder, formatter=None, workdir="/tmp"):
-	""" PBS Dispatcher work with PBSInvocator
-	    it uses a session directory, a session file (where the queries IDs are stored)
-	    when the execute method is call with an session id, it reads all entries from the session file and
-	    make a qstat on each ids.
-	"""
-	from bioMoby.webservice import PBSInvocator
-	
-	SimpleDispatcher.__init__(self, mobyContentXML, PBSInvocator, InvocatorParameters, CommandBuilder, formatter, workdir)
+        """ PBS Dispatcher work with PBSInvocator
+            it uses a session directory, a session file (where the queries IDs are stored)
+            when the execute method is call with an session id, it reads all entries from the session file and
+            make a qstat on each ids.
+        """
+        from bioMoby.webservice import PBSInvocator
+        
+        SimpleDispatcher.__init__(self, mobyContentXML, PBSInvocator, InvocatorParameters, CommandBuilder, formatter, workdir)
     
     def _getResults(self):
-	""" Do a qstat and check availability of results
-	"""
-	from bioMoby import GeneralInvocator
-	
-	answers={}
-	outputfiles={}
-	queryKeys=[]
-	
-	#Read the sessions file, in which there are all queries identifiers
-	
-	fp=file("sessions","r")
-	for queryInformation in fp.readlines():
-	    #for each queries, retrieve the qsub ids, and associated output files.
-	    #delete the CR at the end of the line before proceding
-	    queryInformation=queryInformation[:-1] 
-	    #Get the IDs
-	    qsubId=queryInformation.split(";")[1].split(".")[0]
-	    qk=queryInformation.split(";")[0]
-	    #Get the query key
-	    queryKeys.append(qk)
+        """ Do a qstat and check availability of results
+        """
+        from bioMoby import GeneralInvocator
+        
+        answers={}
+        outputfiles={}
+        queryKeys=[]
+        
+        #Read the sessions file, in which there are all queries identifiers
+        
+        fp=file("sessions","r")
+        for queryInformation in fp.readlines():
+            #for each queries, retrieve the qsub ids, and associated output files.
+            #delete the CR at the end of the line before proceding
+            queryInformation=queryInformation[:-1] 
+            #Get the IDs
+            qsubId=queryInformation.split(";")[1].split(".")[0]
+            qk=queryInformation.split(";")[0]
+            #Get the query key
+            queryKeys.append(qk)
             #get the associated Outputfiles
-	    outputfiles[qk]=queryInformation.split(";")[2].split("::")
+            outputfiles[qk]=queryInformation.split(";")[2].split("::")
 
-	    #Do a qstat and check if the job is still running or on queue
-	    i, o, e = os.popen3("qstat %s"%qsubId)
+            #Do a qstat and check if the job is still running or on queue
+            i, o, e = os.popen3("qstat %s"%qsubId)
 
-	    orl=o.readlines()
-	    erl=e.readlines()
-	    
-	    if len(orl)>0:
-		#if one job is not finished, exit the _getResults function
-		#The dispatcher will give all the results or none 
-		return None
-	
-	fp.close()
-	
-	# At this step, all jobs are done
-	tdir=self._workdir+"/session"+self._sessionid
-	
-	
-	for querykey in queryKeys:
-	    #check the results-query.out:
-	    if "results-"+querykey+".out" in os.listdir(tdir):
+            orl=o.readlines()
+            erl=e.readlines()
+            
+            if len(orl)>0:
+                #if one job is not finished, exit the _getResults function
+                #The dispatcher will give all the results or none 
+                return None
+        
+        fp.close()
+        
+        # At this step, all jobs are done
+        tdir=self._workdir+"/session"+self._sessionid
+        
+        
+        for querykey in queryKeys:
+            #check the results-query.out:
+            if "results-"+querykey+".out" in os.listdir(tdir):
                 fp=file(tdir+"/results-"+querykey+".out")
-	        s=fp.readlines()
-	        fp.close()
+                s=fp.readlines()
+                fp.close()
 
                 if len(s)==0:
-	            os.remove(tdir+"/results-"+querykey+".out")
-	        else:
-		    if len(outputfiles.keys())>0:
-		        shutil.copy(tdir+"/results-"+querykey+".out", tdir+"/results-"+querykey+"/results.out")
+                    os.remove(tdir+"/results-"+querykey+".out")
+                else:
+                    if len(outputfiles.keys())>0:
+                        shutil.copy(tdir+"/results-"+querykey+".out", tdir+"/results-"+querykey+"/results.out")
 
             for f in outputfiles[querykey]:
-	        ruserdir=tdir+"/results-"+querykey
+                ruserdir=tdir+"/results-"+querykey
                 # if it is a file then retrieve the file
                 if os.path.isfile(f):
                     aTemp=f.split('/')
@@ -351,48 +351,48 @@
                         os.remove(f+"/"+fs)
                     os.removedirs(f)
 
-	#retrieve all the results
+        #retrieve all the results
         try:
-	    l=os.listdir(tdir)
-	except:
-	    l=[]
-	
-	if len(l)>0:
+            l=os.listdir(tdir)
+        except:
+            l=[]
+        
+        if len(l)>0:
             for querykey in l:
-		if querykey[:8]=="results-":
-		    aQueryName=querykey[8:]
-	            gi=GeneralInvocator(aQueryName, userdir=tdir)
-	            answers[aQueryName]=[gi.getResults()]
+                if querykey[:8]=="results-":
+                    aQueryName=querykey[8:]
+                    gi=GeneralInvocator(aQueryName, userdir=tdir)
+                    answers[aQueryName]=[gi.getResults()]
 
                     if self.formatter != None:
                         answers[aQueryName]=self.formatter(answers[aQueryName][0])
-			
+                        
             if len(answers.keys())>0:
-	        self.answers=answers
-		
+                self.answers=answers
+                
                 self._clean()
-	
-	del GeneralInvocator
+        
+        del GeneralInvocator
 
-	
+        
     def execute(self):
-	"""Execute the command in a PBS script using the PBSInvocator
-	"""
+        """Execute the command in a PBS script using the PBSInvocator
+        """
 
         if 'JOBSESSION' in self.queryData.keys():
-	    self.answers=self.queryData
+            self.answers=self.queryData
 
-	    self._getResults()
-	else:
-	    #we need to store informations in a file
-	    #query id, qsubid, outputfiles
-	    fp=file("sessions","w")
-	    for queryKey in self.queryData.keys():
-		query=self.queryData[queryKey]
-	        r=self.invocator(queryKey, self.commandBuilder(query), fp, userdir=self._workdir+"/session"+self._sessionid)
-		r.setParameters(self._invocatorParameters)
-		r.execute()
-	    fp.close()
+            self._getResults()
+        else:
+            #we need to store informations in a file
+            #query id, qsubid, outputfiles
+            fp=file("sessions","w")
+            for queryKey in self.queryData.keys():
+                query=self.queryData[queryKey]
+                r=self.invocator(queryKey, self.commandBuilder(query), fp, userdir=self._workdir+"/session"+self._sessionid)
+                r.setParameters(self._invocatorParameters)
+                r.execute()
+            fp.close()
 
         return self._toMoby()
 
@@ -405,18 +405,18 @@
             The commandBuilder function shall return  a command, arguments, and a set of temporary files
             [queryData]-->("commandName","commandArgs", ["tempfiles"])
         """
-	SimpleDispatcher.__init__(self, mobyContentXML, Invocator, None, CommandBuilder, formatter, workdir)
-	
-	import pyipc
-	
-	#Create a Jobsession ID, a semaphore and a session directory
-	if 'JOBSESSION' in self.queryData.keys():
-	    self._sem=pyipc.SemaphoreGroup(int(self._sessionid))
-	else:
+        SimpleDispatcher.__init__(self, mobyContentXML, Invocator, None, CommandBuilder, formatter, workdir)
+        
+        import pyipc
+        
+        #Create a Jobsession ID, a semaphore and a session directory
+        if 'JOBSESSION' in self.queryData.keys():
+            self._sem=pyipc.SemaphoreGroup(int(self._sessionid))
+        else:
             self._sem=pyipc.SemaphoreGroup(int(self._sessionid))
             self._sem.wait()
-	
-	del pyipc
+        
+        del pyipc
 
     def _execute(self, queryKey):
         """ Execute a single query, store the result in the answers attribute
@@ -424,99 +424,99 @@
         from bioMoby import MobyString
 
         query=self.queryData[queryKey]
-	
-	#Execute the query
+        
+        #Execute the query
         try:
             r=self.invocator(queryKey, self.commandBuilder(query), userdir=self._workdir+"/session"+self._sessionid)
-	    r.execute()
+            r.execute()
             time.sleep(0)
         except:
-	    #If there is a problem, we return the generated exception
-	    import traceback
-	    fp=file(self._workdir+"/session"+self._sessionid+"/results-"+queryKey,"w")
-	    fp.write("The query: "+queryKey+" has not been processed")
-	    traceback.print_exc(file=fp)
-	    fp.close()
+            #If there is a problem, we return the generated exception
+            import traceback
+            fp=file(self._workdir+"/session"+self._sessionid+"/results-"+queryKey,"w")
+            fp.write("The query: "+queryKey+" has not been processed")
+            traceback.print_exc(file=fp)
+            fp.close()
 
         del MobyString
 
     def _getSem(self):
-	try:
-	    #Wait for answers of all queries
-	    self._sem.wait()
-	    self._fetchAnswers()
+        try:
+            #Wait for answers of all queries
+            self._sem.wait()
+            self._fetchAnswers()
 
-	    #Remove the IPC
+            #Remove the IPC
             import pyipc
-	    pyipc.removeIPC(self._sem)
-	    del pyipc
+            pyipc.removeIPC(self._sem)
+            del pyipc
         except:
-	    pass
-	
+            pass
+        
     def execute(self, timeout=120):
         """Execute the queries with a pool of threads, store the results in a mobyContent Object
         """
-	import signal
-	
-	#Do a fetchAnswers if the user has a sessionid
-	if 'JOBSESSION' in self.queryData.keys():
-	    self.answers=self.queryData
-
-	    t=threading.Thread(target=self._getSem)
-	    t.start()
-	    t.join(timeout)
+        import signal
+        
+        #Do a fetchAnswers if the user has a sessionid
+        if 'JOBSESSION' in self.queryData.keys():
+            self.answers=self.queryData
+
+            t=threading.Thread(target=self._getSem)
+            t.start()
+            t.join(timeout)
 
             return self._toMoby()
         else:
-	    #A MobyContent without jobsession id has been received
-	    try:
-		#make a fork
-	        pid=os.fork()
-	    except:
-		raise Exception, "Cannot treat any further request, please retry"
-
-	    if pid>0:
-		#try to get the results
-#		os.wait()
-	        t=threading.Thread(target=self._getSem)
-	        t.start()
-	        t.join(timeout)
+            #A MobyContent without jobsession id has been received
+            try:
+                #make a fork
+                pid=os.fork()
+            except:
+                raise Exception, "Cannot treat any further request, please retry"
+
+            if pid>0:
+                #try to get the results
+#                os.wait()
+                t=threading.Thread(target=self._getSem)
+                t.start()
+                t.join(timeout)
 
                 return self._toMoby()
-	    else:
+            else:
                 #do second fork
                 try: 
                     pid = os.fork()
-		except:
-		    raise Exception, "Cannot treat any further request, please retry"
-		    
+                except:
+                    raise Exception, "Cannot treat any further request, please retry"
+                    
                 if pid>0:
-		    #it it is too long, kill the process
-		    time.sleep(1.05*timeout)
+                    #it it is too long, kill the process
+                    time.sleep(1.05*timeout)
                     os.kill(os.getppid(), signal.SIGKILL)
-		    os._exit(0)
-		else:
-		    #execute the treatment
+                    os._exit(0)
+                else:
+                    #execute the treatment
                     os.setpgrp()
-		    
-		    try:
-		        os.chdir(self._workdir+"/session"+self._sessionid)
-	                mt=MultiThread(self._execute, self.queryData.keys())
+                    
+                    try:
+                        os.chdir(self._workdir+"/session"+self._sessionid)
+                        mt=MultiThread(self._execute, self.queryData.keys())
                         mt.start()
                         mt.join()
-		    except:
-			self._clean()
+                    except:
+                        self._clean()
 
-		    try:
-	                self._sem.signal()
+                    try:
+                        self._sem.signal()
                     finally:
-			if os.getppid()>1:
-                  	    try:
-			        os.kill(os.getppid(), signal.SIGKILL)
-		            except:
-			        pass
-			    
-		        os._exit(0)
+                        if os.getppid()>1:
+                              try:
+                                  os.kill(os.getppid(), signal.SIGKILL)
+                              except:
+                                  pass
+                            
+                        os._exit(0)
 
-	#if nothing works return nothing
-	return {}
+        #if nothing works return nothing
+        return {}

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/webservice/Invocators.py,v
retrieving revision 1.2
retrieving revision 1.3
diff -u -r1.2 -r1.3
--- /home/repository/moby/moby-live/Python/bioMoby/webservice/Invocators.py	2005/01/18 13:46:24	1.2
+++ /home/repository/moby/moby-live/Python/bioMoby/webservice/Invocators.py	2005/02/01 08:52:17	1.3
@@ -18,34 +18,34 @@
     """
     
     def __init__(self, queryid, userdir="/tmp", timeout=None):
-	"""queryid is the identifier of a query, userdir is the session directory, timeout the limit time of execution of the query
-	"""
+        """queryid is the identifier of a query, userdir is the session directory, timeout the limit time of execution of the query
+        """
         self.command=""
         from bioMoby import MobyObject
 
         self.results=[]
         self.queryid=queryid
-	
+        
         del MobyObject
         self.errors=""
         self.userdir=userdir
         
 
     def getResults(self):
-	"""retrieve the results if available
-	"""
+        """retrieve the results if available
+        """
         import os
             
         fname=self.userdir+"/results-"+self.queryid
 
         if os.path.isfile(fname):
-	    #if it is a single file
+            #if it is a single file
             fp=file(fname,"r")
             self.results=[fp.read()]
             fp.close()
 #            os.remove(fname)
         else:
-	    #or a directory
+            #or a directory
             self.results=[]
             for fs in os.listdir(fname):
                 if os.path.isfile(fname+"/"+fs):
@@ -87,32 +87,32 @@
 
         results=[]
 
-	ruserdir=self.userdir+"/results-"+self.queryid
-	
+        ruserdir=self.userdir+"/results-"+self.queryid
+        
         #if there are some output files then retrieve them as results
         if len(self.outputfiles) !=0:
             i,o,e=os.popen3(self.command)
 
-	    #read error first and then standard output
-	    
+            #read error first and then standard output
+            
             try:
                 et=e.read()
-		fp=file(self.userdir+"/"+self.queryid+".err")
-		fp.write(et)
-		fp.close()
+                fp=file(self.userdir+"/"+self.queryid+".err")
+                fp.write(et)
+                fp.close()
             except:
-		pass
-	    
-	    try:
+                pass
+            
+            try:
                 ot=o.read()
-		fp=file(self.userdir+"/"+self.queryid+".out")
-		fp.write(ot)
-		fp.close()
-	    except:
-		pass
+                fp=file(self.userdir+"/"+self.queryid+".out")
+                fp.write(ot)
+                fp.close()
+            except:
+                pass
 
-	    #wait unfinished sub process
-		
+            #wait unfinished sub process
+                
             try:
                 os.wait()
             except:
@@ -123,7 +123,7 @@
             for f in self.outputfiles:
                 # if it is a file then retrieve the file
                 if os.path.isfile(f):
-		    aTemp=f.split('/')
+                    aTemp=f.split('/')
                     shutil.copy(f, ruserdir+"/"+aTemp[len(aTemp)-1])
                     os.remove(f)
                 elif os.path.isdir(f):
@@ -135,20 +135,20 @@
         else:
             stdin, stdout, stderr=os.popen3(self.command)
             results=stdout.read()
-	    
-	    fp=file(self.userdir+"/results-"+self.queryid,"w")
-	    fp.write(results)
-	    fp.close()
-	    
-#	    t=stderr.read()
+            
+            fp=file(self.userdir+"/results-"+self.queryid,"w")
+            fp.write(results)
+            fp.close()
+            
+#            t=stderr.read()
 
             stdin.close()
             stdout.close()
             stderr.close()
             os.wait()    
 
-	#Make all the cleaning wipe the session directory
-	    
+        #Make all the cleaning wipe the session directory
+            
         for tmpfile in self.tempfiles:
             try:
                 if os.path.isfile(tmpfile):
@@ -163,71 +163,71 @@
     """Parameters for the qsub command
     """
     def __init__(self, queueName, qsubParameters):
-	""" queueName: name of the PBS queue
-	    qsubParameters: a list of parameters for the -l option: ['ncpus=4', 'walltime=01:00:00']
-	"""
-	self.queueName=queueName
-	self.qsubParameters=qsubParameters
-	
-	
+        """ queueName: name of the PBS queue
+            qsubParameters: a list of parameters for the -l option: ['ncpus=4', 'walltime=01:00:00']
+        """
+        self.queueName=queueName
+        self.qsubParameters=qsubParameters
+        
+        
 class PBSInvocator(LocalInvocator):
     """Invokes a command in a qsub
     """
     
     def __init__(self, queryKey, command, aFile, userdir="/tmp"):
-	"""The file is needed here to keep the generated outputfiles
-	"""
-	LocalInvocator.__init__(self, queryKey, command, userdir)
-	self._queueName=""
-	self._PBSparameters=[]
-	self._aFile=aFile
+        """The file is needed here to keep the generated outputfiles
+        """
+        LocalInvocator.__init__(self, queryKey, command, userdir)
+        self._queueName=""
+        self._PBSparameters=[]
+        self._aFile=aFile
 
     def setParameters(self, invocatorParameters):
-	"""Set parameters of qsub
-	"""
-	self._queueName=invocatorParameters.queueName
-	self._PBSparameters=invocatorParameters.qsubParameters
-	
+        """Set parameters of qsub
+        """
+        self._queueName=invocatorParameters.queueName
+        self._PBSparameters=invocatorParameters.qsubParameters
+        
     def execute(self):
-	"""execute the command in a qsub script
-	"""
-	
-	#we write in the session directory a small script
-	fp=file(self.userdir+"/"+self.queryid+".sh","w")
-	fp.write("#!/bin/bash\n")
-	fp.write("#PBS -S /bin/bash\n")
-	fp.write("#PBS -o "+self.userdir+"/results-"+self.queryid+".out\n")
-	fp.write("#PBS -e "+self.userdir+"/"+self.queryid+".err\n")
-	fp.write("#PBS -q %s\n"%self._queueName)
-	fp.write("#PBS -l %s\n"%":".join(self._PBSparameters))
-	
-	#we add to the script the cd command in order to be in the session directory
-	fp.write("cd %s\n"%self.userdir)
-	fp.write("%s\n"%self.command)
-	fp.close()
-	
-	import os
-	
-	#execute the qsub command
-	i, o, e=os.popen3("qsub "+self.userdir+"/"+self.queryid+".sh")
-	
-	#see if there are mistakes
-	erl=e.read()
-	
-	if erl!="":
-	    raise Exception, "".join(erl)
+        """execute the command in a qsub script
+        """
+        
+        #we write in the session directory a small script
+        fp=file(self.userdir+"/"+self.queryid+".sh","w")
+        fp.write("#!/bin/bash\n")
+        fp.write("#PBS -S /bin/bash\n")
+        fp.write("#PBS -o "+self.userdir+"/results-"+self.queryid+".out\n")
+        fp.write("#PBS -e "+self.userdir+"/"+self.queryid+".err\n")
+        fp.write("#PBS -q %s\n"%self._queueName)
+        fp.write("#PBS -l %s\n"%":".join(self._PBSparameters))
+        
+        #we add to the script the cd command in order to be in the session directory
+        fp.write("cd %s\n"%self.userdir)
+        fp.write("%s\n"%self.command)
+        fp.close()
+        
+        import os
+        
+        #execute the qsub command
+        i, o, e=os.popen3("qsub "+self.userdir+"/"+self.queryid+".sh")
+        
+        #see if there are mistakes
+        erl=e.read()
+        
+        if erl!="":
+            raise Exception, "".join(erl)
 
-	#write in the session file the queries, qsub identifiers and the output files
-	orl=o.readlines()
+        #write in the session file the queries, qsub identifiers and the output files
+        orl=o.readlines()
         anId=orl[0].split('\n')[0]
 
-	if len(self.outputfiles) !=0:
-	    self._aFile.write(self.queryid+";"+anId+";"+"::".join(self.outputfiles)+"\n")
-	    os.mkdir(self.userdir+"/results-"+self.queryid)
-	    
-	del os
-	#return the qsub identifier
-	return anId
+        if len(self.outputfiles) !=0:
+            self._aFile.write(self.queryid+";"+anId+";"+"::".join(self.outputfiles)+"\n")
+            os.mkdir(self.userdir+"/results-"+self.queryid)
+            
+        del os
+        #return the qsub identifier
+        return anId
 
 class CGIPostMInvocator(GeneralInvocator):
     """Functions for multipart post
@@ -241,9 +241,9 @@
         files is a sequence of (name, filename, value) elements for data to be uploaded as files
         Return the server's response page.
         """
-	    
+            
         import httplib    
-	
+        
         content_type, body = self.encode_multipart_formdata()
         print content_type, body
         h = httplib.HTTP(host)
@@ -253,9 +253,9 @@
         h.endheaders()
         h.send(body)
         errcode, errmsg, headers = h.getreply()
-	    
+            
         del httplib
-	
+        
         return h.file.readlines()
 
     def encode_multipart_formdata(self):

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/webservice/TCBioMoby.py,v
retrieving revision 1.2
retrieving revision 1.3
diff -u -r1.2 -r1.3
--- /home/repository/moby/moby-live/Python/bioMoby/webservice/TCBioMoby.py	2005/01/18 13:46:24	1.2
+++ /home/repository/moby/moby-live/Python/bioMoby/webservice/TCBioMoby.py	2005/02/01 08:52:17	1.3
@@ -53,4 +53,4 @@
         from xml.dom.minidom import parseString
      
         print >>sw, '''<%s><![CDATA[%s]]></%s>''' % (self.tag, parseString(toReturn).toprettyxml(), self.tag)
-	
+        

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/webservice/__init__.py,v
retrieving revision 1.2
retrieving revision 1.3
diff -u -r1.2 -r1.3
--- /home/repository/moby/moby-live/Python/bioMoby/webservice/__init__.py	2005/01/18 13:46:24	1.2
+++ /home/repository/moby/moby-live/Python/bioMoby/webservice/__init__.py	2005/02/01 08:52:17	1.3
@@ -35,7 +35,7 @@
     l=filter(filterfunc, setOfParameters)
     
     if l:
-	return l[0]
+        return l[0]
 
     return 
     
@@ -56,6 +56,6 @@
     l=filter(filterfunc, setOfParameters)
     
     if l:
-	return l[0]
-	
+        return l[0]
+        
     return
\ No newline at end of file

From yanwong at pub.open-bio.org  Tue Feb  1 03:59:44 2005
From: yanwong at pub.open-bio.org (Yan Wong)
Date: Tue Feb  1 03:49:03 2005
Subject: [MOBY-guts] biomoby commit
Message-ID: <200502010859.j118xiLU013177@pub.open-bio.org>


yanwong
Tue Feb  1 03:59:44 EST 2005
Update of /home/repository/moby/moby-live/Python/utils/wx
In directory pub.open-bio.org:/tmp/cvs-serv13152

Modified Files:
	objectBrowser.py 
Log Message:


moby-live/Python/utils/wx objectBrowser.py,1.5,1.6
===================================================================
RCS file: /home/repository/moby/moby-live/Python/utils/wx/objectBrowser.py,v
retrieving revision 1.5
retrieving revision 1.6
diff -u -r1.5 -r1.6
--- /home/repository/moby/moby-live/Python/utils/wx/objectBrowser.py	2005/01/27 08:44:06	1.5
+++ /home/repository/moby/moby-live/Python/utils/wx/objectBrowser.py	2005/02/01 08:59:44	1.6
@@ -65,7 +65,7 @@
                 obj=obj[len(obj)-1]
             else:
                 obj="None"
-	    
+        
             if obj in self._ISARelations:
                 self._ISARelations[obj].append(objectName)
             else:
@@ -102,7 +102,7 @@
 
         self.staticText1 = wxStaticText(id=wxID_WXFRAME1STATICTEXT1,
               label='Description', name='staticText1', parent=self.panel1,
-              pos=wxPoint(16, 0), size=wxSize(64, 16), style=0)
+              pos=wxPoint(16, 0), size=wxSize(70, 16), style=0)
 
         self.textCtrl1 = wxTextCtrl(id=wxID_WXFRAME1TEXTCTRL1, name='textCtrl1',
               parent=self.panel1, pos=wxPoint(16, 16), size=wxSize(400, 56),
@@ -110,7 +110,7 @@
 
         self.staticText2 = wxStaticText(id=wxID_WXFRAME1STATICTEXT2,
               label='Contact Email', name='staticText2', parent=self.panel1,
-              pos=wxPoint(16, 80), size=wxSize(80, 16), style=0)
+              pos=wxPoint(16, 80), size=wxSize(90, 16), style=0)
 
         self.textCtrl2 = wxTextCtrl(id=wxID_WXFRAME1TEXTCTRL2, name='textCtrl2',
               parent=self.panel1, pos=wxPoint(16, 96), size=wxSize(400, 22),
@@ -118,7 +118,7 @@
 
         self.staticText3 = wxStaticText(id=wxID_WXFRAME1STATICTEXT3,
               label='Authority URI', name='staticText3', parent=self.panel1,
-              pos=wxPoint(16, 128), size=wxSize(80, 16), style=0)
+              pos=wxPoint(16, 128), size=wxSize(90, 16), style=0)
 
         self.textCtrl3 = wxTextCtrl(id=wxID_WXFRAME1TEXTCTRL3, name='textCtrl3',
               parent=self.panel1, pos=wxPoint(16, 144), size=wxSize(400, 24),
@@ -126,7 +126,7 @@
 
         self.staticText4 = wxStaticText(id=wxID_WXFRAME1STATICTEXT4,
               label='HAS', name='staticText4', parent=self.panel1,
-              pos=wxPoint(16, 184), size=wxSize(32, 16), style=0)
+              pos=wxPoint(16, 184), size=wxSize(40, 16), style=0)
 
         self.listBox1 = wxListBox(choices=[], id=wxID_WXFRAME1LISTBOX1,
               name='listBox1', parent=self.panel1, pos=wxPoint(16, 200),
@@ -134,7 +134,7 @@
 
         self.staticText5 = wxStaticText(id=wxID_WXFRAME1STATICTEXT5,
               label='HASA', name='staticText5', parent=self.panel1,
-              pos=wxPoint(16, 264), size=wxSize(56, 16), style=0)
+              pos=wxPoint(16, 264), size=wxSize(60, 16), style=0)
 
         self.listBox2 = wxListBox(choices=[], id=wxID_WXFRAME1LISTBOX2,
               name='listBox2', parent=self.panel1, pos=wxPoint(16, 280),
@@ -143,7 +143,7 @@
         self.staticText6 = wxStaticText(id=wxID_WXFRAME1STATICTEXT6,
               label='Services that take this data type as input:',
               name='staticText6', parent=self.panel1, pos=wxPoint(16, 352),
-              size=wxSize(230, 16), style=0)
+              size=wxSize(250, 16), style=0)
 
         self.listBox3 = wxListBox(choices=[], id=wxID_WXFRAME1LISTBOX3,
               name='listBox3', parent=self.panel1, pos=wxPoint(16, 368),
@@ -156,15 +156,15 @@
 
         self.staticText7 = wxStaticText(id=wxID_WXFRAME1STATICTEXT7,
               label='URL', name='staticText7', parent=self, pos=wxPoint(8, 16),
-              size=wxSize(24, 16), style=0)
+              size=wxSize(30, 16), style=0)
 
         self.staticText8 = wxStaticText(id=wxID_WXFRAME1STATICTEXT8, label='NS',
               name='staticText8', parent=self, pos=wxPoint(8, 56),
-              size=wxSize(16, 16), style=0)
+              size=wxSize(20, 16), style=0)
 
         self.button2 = wxButton(id=wxID_WXFRAME1BUTTON2,
               label='Retrieve objects', name='button2', parent=self,
-              pos=wxPoint(8, 136), size=wxSize(120, 22), style=0)
+              pos=wxPoint(8, 136), size=wxSize(120, 24), style=0)
         EVT_BUTTON(self.button2, wxID_WXFRAME1BUTTON2, self.OnButton2Button)
 
         self.gauge1 = wxGauge(id=wxID_WXFRAME1GAUGE1, name='gauge1',
@@ -174,7 +174,7 @@
         self.staticText9 = wxStaticText(id=wxID_WXFRAME1STATICTEXT9,
               label='Services that take this data type as output:',
               name='staticText9', parent=self.panel1, pos=wxPoint(16, 440),
-              size=wxSize(237, 16), style=0)
+              size=wxSize(260, 16), style=0)
 
         self.listBox4 = wxListBox(choices=[], id=wxID_WXFRAME1LISTBOX4,
               name='listBox4', parent=self.panel1, pos=wxPoint(16, 456),
@@ -194,7 +194,7 @@
 
         self.checkBox1 = wxCheckBox(id=wxID_WXFRAME1CHECKBOX1,
               label='Fetch data from cache (if there is any)', name='checkBox1',
-              parent=self, pos=wxPoint(8, 104), size=wxSize(248, 24), style=0)
+              parent=self, pos=wxPoint(8, 104), size=wxSize(260, 24), style=0)
         self.checkBox1.SetValue(False)
 
     def __init__(self, parent):

From yanwong at pub.open-bio.org  Tue Feb  1 06:25:53 2005
From: yanwong at pub.open-bio.org (Yan Wong)
Date: Tue Feb  1 06:16:29 2005
Subject: [MOBY-guts] biomoby commit
Message-ID: <200502011125.j11BPrpK013895@pub.open-bio.org>


yanwong
Tue Feb  1 06:25:53 EST 2005
Update of /home/repository/moby/moby-live/Python/bioMoby
In directory pub.open-bio.org:/tmp/cvs-serv13870

Modified Files:
	mobyDataTypes.py 
Log Message:


moby-live/Python/bioMoby mobyDataTypes.py,1.6,1.7
===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/mobyDataTypes.py,v
retrieving revision 1.6
retrieving revision 1.7
diff -u -r1.6 -r1.7
--- /home/repository/moby/moby-live/Python/bioMoby/mobyDataTypes.py	2005/02/01 08:52:15	1.6
+++ /home/repository/moby/moby-live/Python/bioMoby/mobyDataTypes.py	2005/02/01 11:25:53	1.7
@@ -149,7 +149,7 @@
         #Put the raw content of the object
         #If you want to put your special object, then then you should write 
         #a __str__ method
-        if hasattr(self, "content") and self.content:
+        if hasattr(self, "content") and self.content!=none and self.content!="":
             result.append("%s"%(self.content))
         
         result.append("</%s:%s>"%(self.__prefix__, self.__tag__))

From yanwong at pub.open-bio.org  Tue Feb  1 06:31:22 2005
From: yanwong at pub.open-bio.org (Yan Wong)
Date: Tue Feb  1 06:26:13 2005
Subject: [MOBY-guts] biomoby commit
Message-ID: <200502011131.j11BVMog013947@pub.open-bio.org>


yanwong
Tue Feb  1 06:31:22 EST 2005
Update of /home/repository/moby/moby-live/Python/bioMoby
In directory pub.open-bio.org:/tmp/cvs-serv13922

Modified Files:
	mobyDataTypes.py 
Log Message:


moby-live/Python/bioMoby mobyDataTypes.py,1.7,1.8
===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/mobyDataTypes.py,v
retrieving revision 1.7
retrieving revision 1.8
diff -u -r1.7 -r1.8
--- /home/repository/moby/moby-live/Python/bioMoby/mobyDataTypes.py	2005/02/01 11:25:53	1.7
+++ /home/repository/moby/moby-live/Python/bioMoby/mobyDataTypes.py	2005/02/01 11:31:22	1.8
@@ -149,7 +149,7 @@
         #Put the raw content of the object
         #If you want to put your special object, then then you should write 
         #a __str__ method
-        if hasattr(self, "content") and self.content!=none and self.content!="":
+        if hasattr(self, "content") and self.content!=None and self.content!="":
             result.append("%s"%(self.content))
         
         result.append("</%s:%s>"%(self.__prefix__, self.__tag__))

From yanwong at pub.open-bio.org  Tue Feb  1 09:20:46 2005
From: yanwong at pub.open-bio.org (Yan Wong)
Date: Tue Feb  1 09:11:13 2005
Subject: [MOBY-guts] biomoby commit
Message-ID: <200502011420.j11EKkG9014847@pub.open-bio.org>


yanwong
Tue Feb  1 09:20:46 EST 2005
Update of /home/repository/moby/moby-live/Python/utils
In directory pub.open-bio.org:/tmp/cvs-serv14364/utils

Modified Files:
	moby2python.py 
Log Message:


moby-live/Python/utils moby2python.py,1.4,1.5
===================================================================
RCS file: /home/repository/moby/moby-live/Python/utils/moby2python.py,v
retrieving revision 1.4
retrieving revision 1.5
diff -u -r1.4 -r1.5
--- /home/repository/moby/moby-live/Python/utils/moby2python.py	2005/01/18 13:44:04	1.4
+++ /home/repository/moby/moby-live/Python/utils/moby2python.py	2005/02/01 14:20:46	1.5
@@ -53,7 +53,9 @@
     res=["    def fromMoby(self, value):\n"]
     res.append("        \"\"\" Load the attributes from an XML string\n        \"\"\"")
     res.append("        from bioMoby.mobyMarshal import MobyUnmarshaller")
-    res.append("        doc=parseString(value).firstChild")
+    res.append("        doc=value")
+    res.append("        if isinstance(value, str):")
+    res.append("            doc=parseString(value).firstChild")
     res.append("        um=MobyUnmarshaller()")
     res.append("        self.content=\"\"")
     
@@ -83,7 +85,7 @@
     res.append("            if elt.nodeName==\"CrossReference\" or elt.nodeName==\"moby:CrossReference\":")
     res.append("                self.__cross__=[]")
     res.append("                for ref in elt.childNodes:")
-    res.append("                    self.__cross__.append(ref.toxml())")        
+    res.append("                    self.__cross__.append(um.loads(ref))")        
 
 
     for parameter in parameters:
@@ -92,7 +94,7 @@
             
             if parameter[2]=='Integer' or parameter[2]=='Float' or parameter[2]=='String':
                 res.append("                t="+makeMobyName(parameter[2])+"()")
-                res.append("                t.fromMoby(elt.toxml())")
+                res.append("                t.fromMoby(elt)")
                 if parameter[1]!="[]":
                     res.append("                self."+cleanName(parameter[0])+"=t.content")
                 else:
@@ -100,7 +102,7 @@
                     
             elif parameter[0]!='content':
                 res.append("                self."+cleanName(parameter[0])+"="+makeMobyName(parameter[2])+"()")
-                res.append("                self."+cleanName(parameter[0])+".fromMoby(elt.toxml())")
+                res.append("                self."+cleanName(parameter[0])+".fromMoby(elt)")
                     
     return "\n".join(res)
 
@@ -133,7 +135,7 @@
 
         if ancestor not in paramDict.keys():
             makeInterface(ancestor, path)
-	
+    
         for aProp in getPropertiesFromAncestor(ancestor):
             properties.append(aProp)
    
@@ -150,7 +152,7 @@
                 
             properties.append((articleName,"None",articleType))
 
-	    
+        
     if "HAS" in objectDefinition["Relationship"].keys():
         for hasRelationship in objectDefinition["Relationship"]["HAS"]:
             articleName=hasRelationship[0]
@@ -197,9 +199,9 @@
         pyResult.append("class "+mObjectName+":\n")
 
     if "Description" in objectDefinition:
-	description=objectDefinition["Description"]
+        description=objectDefinition["Description"]
     if "authURI" in objectDefinition:
-	author=objectDefinition["authURI"]
+        author=objectDefinition["authURI"]
     if "contactEmail" in objectDefinition:
         contact=objectDefinition["contactEmail"]
     

From yanwong at pub.open-bio.org  Tue Feb  1 09:20:44 2005
From: yanwong at pub.open-bio.org (Yan Wong)
Date: Tue Feb  1 09:11:52 2005
Subject: [MOBY-guts] biomoby commit
Message-ID: <200502011420.j11EKi83014390@pub.open-bio.org>


yanwong
Tue Feb  1 09:20:44 EST 2005
Update of /home/repository/moby/moby-live/Python/bioMoby
In directory pub.open-bio.org:/tmp/cvs-serv14364/bioMoby

Modified Files:
	mobyDataTypes.py 
Log Message:


moby-live/Python/bioMoby mobyDataTypes.py,1.8,1.9
===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/mobyDataTypes.py,v
retrieving revision 1.8
retrieving revision 1.9
diff -u -r1.8 -r1.9
--- /home/repository/moby/moby-live/Python/bioMoby/mobyDataTypes.py	2005/02/01 11:31:22	1.8
+++ /home/repository/moby/moby-live/Python/bioMoby/mobyDataTypes.py	2005/02/01 14:20:44	1.9
@@ -209,10 +209,10 @@
                     #if there is already an object, then store it inside a list and 
                     #append the other objects in the list 
                     if hasattr(self, associatedObjectName):
-                        if type(getattr(self, associatedObjectName)) is list:
+                        if isinstance(getattr(self, associatedObjectName), list):
                             getattr(self, associatedObjectName).append(o)
                         else:
-                            setattr(self, associatedObjectName, [o])
+                            setattr(self, associatedObjectName, o)
                     else:
                         setattr(self, associatedObjectName, o)
             else:

From yanwong at pub.open-bio.org  Tue Feb  1 09:33:49 2005
From: yanwong at pub.open-bio.org (Yan Wong)
Date: Tue Feb  1 09:23:19 2005
Subject: [MOBY-guts] biomoby commit
Message-ID: <200502011433.j11EXn74014904@pub.open-bio.org>


yanwong
Tue Feb  1 09:33:49 EST 2005
Update of /home/repository/moby/moby-live/Python/bioMoby
In directory pub.open-bio.org:/tmp/cvs-serv14879/bioMoby

Modified Files:
	mobyDataTypes.py 
Log Message:


moby-live/Python/bioMoby mobyDataTypes.py,1.9,1.10
===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/mobyDataTypes.py,v
retrieving revision 1.9
retrieving revision 1.10
diff -u -r1.9 -r1.10
--- /home/repository/moby/moby-live/Python/bioMoby/mobyDataTypes.py	2005/02/01 14:20:44	1.9
+++ /home/repository/moby/moby-live/Python/bioMoby/mobyDataTypes.py	2005/02/01 14:33:49	1.10
@@ -107,7 +107,7 @@
         mobyObjects=filter(filterFunc, dir(self))
         
         #If none, return the tag closed
-        if len(mobyObjects)==0 and (not hasattr(self, "__cross__") or len(self.__cross__)==0) and (not hasattr(self, "__PIB__") or len(self.__PIB__)==0) and (not hasattr(self, "content") or not self.content):
+        if len(mobyObjects)==0 and (not hasattr(self, "__cross__") or len(self.__cross__)==0) and (not hasattr(self, "__PIB__") or len(self.__PIB__)==0) and (not hasattr(self, "content") or self.content==None or self.content==""):
             beginTag.append("/>")
             return " ".join(beginTag)
 

From yanwong at pub.open-bio.org  Wed Feb  2 10:08:34 2005
From: yanwong at pub.open-bio.org (Yan Wong)
Date: Wed Feb  2 09:57:45 2005
Subject: [MOBY-guts] biomoby commit
Message-ID: <200502021508.j12F8YLi020349@pub.open-bio.org>


yanwong
Wed Feb  2 10:08:34 EST 2005
Update of /home/repository/moby/moby-live/Python/bioMoby/ontology
In directory pub.open-bio.org:/tmp/cvs-serv20328

Added Files:
	MSF.py 
Log Message:


moby-live/Python/bioMoby/ontology MSF.py,NONE,1.1
From yanwong at pub.open-bio.org  Wed Feb  2 10:18:06 2005
From: yanwong at pub.open-bio.org (Yan Wong)
Date: Wed Feb  2 10:07:55 2005
Subject: [MOBY-guts] biomoby commit
Message-ID: <200502021518.j12FI6DL020441@pub.open-bio.org>


yanwong
Wed Feb  2 10:18:06 EST 2005
Update of /home/repository/moby/moby-live/Python/bioMoby/ontology
In directory pub.open-bio.org:/tmp/cvs-serv20420

Added Files:
	Alignment.py 
Log Message:


moby-live/Python/bioMoby/ontology Alignment.py,NONE,1.1
From yanwong at pub.open-bio.org  Wed Feb  2 10:20:55 2005
From: yanwong at pub.open-bio.org (Yan Wong)
Date: Wed Feb  2 10:10:11 2005
Subject: [MOBY-guts] biomoby commit
Message-ID: <200502021520.j12FKtBS020499@pub.open-bio.org>


yanwong
Wed Feb  2 10:20:55 EST 2005
Update of /home/repository/moby/moby-live/Python/bioMoby/ontology
In directory pub.open-bio.org:/tmp/cvs-serv20478

Added Files:
	FASTA_NA_multi.py Gene_Expression_data.py 
Log Message:


moby-live/Python/bioMoby/ontology FASTA_NA_multi.py,NONE,1.1 Gene_Expression_data.py,NONE,1.1
From kawas at pub.open-bio.org  Wed Feb  2 11:49:18 2005
From: kawas at pub.open-bio.org (Eddie Kawas)
Date: Wed Feb  2 11:38:27 2005
Subject: [MOBY-guts] biomoby commit
Message-ID: <200502021649.j12GnHCr020760@pub.open-bio.org>


kawas
Wed Feb  2 11:49:17 EST 2005
Update of /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/gui/objectCreationTool
In directory pub.open-bio.org:/tmp/cvs-serv20735/org/biomoby/client/gui/objectCreationTool

Modified Files:
	Construct.java 
Log Message:
Changed the declaration that creates an empty rdf model. Hopefully helps get rid of the logging issues.

moby-live/Java/src/main/org/biomoby/client/gui/objectCreationTool Construct.java,1.1,1.2
===================================================================
RCS file: /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/gui/objectCreationTool/Construct.java,v
retrieving revision 1.1
retrieving revision 1.2
diff -u -r1.1 -r1.2
--- /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/gui/objectCreationTool/Construct.java	2004/09/27 22:15:13	1.1
+++ /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/gui/objectCreationTool/Construct.java	2005/02/02 16:49:17	1.2
@@ -8,6 +8,7 @@
 
 import com.hp.hpl.jena.mem.ModelMem;
 import com.hp.hpl.jena.rdf.model.Model;
+import com.hp.hpl.jena.rdf.model.ModelFactory;
 import com.hp.hpl.jena.rdf.model.Statement;
 import com.hp.hpl.jena.rdf.model.StmtIterator;
 
@@ -52,7 +53,7 @@
 		HashMap homes = new HashMap(); // (key=parent,val=household)
 		try {
 			// create an empty model
-			Model model = new ModelMem();
+			Model model = ModelFactory.createDefaultModel();
 
 			InputStream in =
 				new URL(url)

From yanwong at pub.open-bio.org  Wed Feb  2 11:52:31 2005
From: yanwong at pub.open-bio.org (Yan Wong)
Date: Wed Feb  2 11:41:41 2005
Subject: [MOBY-guts] biomoby commit
Message-ID: <200502021652.j12GqVgK020799@pub.open-bio.org>


yanwong
Wed Feb  2 11:52:31 EST 2005
Update of /home/repository/moby/moby-live/Python/bioMoby
In directory pub.open-bio.org:/tmp/cvs-serv20774

Modified Files:
	mobyDataTypes.py 
Log Message:


moby-live/Python/bioMoby mobyDataTypes.py,1.10,1.11
===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/mobyDataTypes.py,v
retrieving revision 1.10
retrieving revision 1.11
diff -u -r1.10 -r1.11
--- /home/repository/moby/moby-live/Python/bioMoby/mobyDataTypes.py	2005/02/01 14:33:49	1.10
+++ /home/repository/moby/moby-live/Python/bioMoby/mobyDataTypes.py	2005/02/02 16:52:31	1.11
@@ -87,7 +87,7 @@
         
         self.content=content
         
-                
+    
     def toMoby(self):
         """Deserializes the content in XML api
         """
@@ -98,7 +98,7 @@
         for attribute in __ATTRIBUTES__:
             if hasattr(self, attribute) and getattr(self, attribute):
                 beginTag.append("%s:%s=\"%s\""%(self.__prefix__, attribute, getattr(self,attribute)))
-
+            
         #Retrieve only object's attributes that are public.
         filterFunc=lambda x: x[0] != "_" and not callable(getattr(self, x)) and x !="content" and x not in __ATTRIBUTES__
         
@@ -107,13 +107,13 @@
         mobyObjects=filter(filterFunc, dir(self))
         
         #If none, return the tag closed
-        if len(mobyObjects)==0 and (not hasattr(self, "__cross__") or len(self.__cross__)==0) and (not hasattr(self, "__PIB__") or len(self.__PIB__)==0) and (not hasattr(self, "content") or self.content==None or self.content==""):
+        if len(mobyObjects)==0 and (not hasattr(self, "__cross__") or len(self.__cross__)==0) and (not hasattr(self, "__PIB__") or len(self.__PIB__)==0) and (not hasattr(self, "content") or self.content is None or self.content==""):
             beginTag.append("/>")
             return " ".join(beginTag)
-
+        
         #Else, end begin tag and serialize the associated objects
         beginTag.append(">")
-
+        
         result=[" ".join(beginTag)]
         
         #Serialize Cross references
@@ -162,8 +162,8 @@
         elem=xml
         
         if isinstance(xml, str):
-            doc=parseString(xmlstring)
-        
+            doc=parseString(xml)
+            
             elem=doc.firstChild
         
         self.__tag__=elem.localName
@@ -195,10 +195,10 @@
                 else:
                     #Do the same for the other objects
                     associatedObjectName=child.getAttribute("moby:articleName")
-                
+                    
                     if not associatedObjectName:
                         associatedObjectName=child.getAttribute("articleName")
-                
+                        
                     if not associatedObjectName:
                         associatedObjectName="associated"
                     
@@ -252,7 +252,7 @@
         doc=xml
         
         uri=doc.namespaceURI
-    
+        
         MobyObject.fromMoby(self, doc)
         
         self.authURI=doc.getAttributeNS(uri, "authURI")
@@ -260,7 +260,6 @@
         self.evidenceCode=doc.getAttributeNS(uri, "evidenceCode")
         self.xrefType=doc.getAttributeNS(uri, "xrefType")
 
-        
 class MobyInteger(MobyObject):
     """Use this object to serialize/deserialize integers
     """
@@ -311,30 +310,30 @@
         """
         from mobyMarshal import MobyMarshaller
         m=MobyMarshaller()        
-
+        
         result=['<?xml version="1.0" encoding="UTF-8"?><moby:MOBY xmlns:moby="http://www.biomoby.org/moby"><moby:mobyContent']
-                
+        
         if self.authority !="":
             result.append(' moby:authority="'+self.authority+'"')
-                    
+        
         result.append('>')
-                    
+        
         if self.servicenotes !="":
             result.append('<moby:serviceNotes>'+self.servicenotes+'</moby:serviceNotes>')
-
+        
         for queryKey in self.queryData:
             result.append("<moby:mobyData moby:queryID='"+queryKey+"'>")
-
+            
             #For serialization, use the MobyMarshaller object
             
             for queryObject in self.queryData[queryKey]:
                 #if the Collection ('CollectionName',[MobyObjects])
                 if queryObject.__class__ is tuple:
                     result.append("<moby:Collection moby:articleName='"+queryObject[0]+"'>")
-
+                    
                     for aSimple in queryObject[1]:
                         result.append('<moby:Simple>'+m.dumps(aSimple)+'</moby:Simple>')
-                    
+                        
                     result.append("</moby:Collection>")
                 #If it is a parameter
                 elif queryObject.__class__ is Parameter:
@@ -342,13 +341,13 @@
                 #Or a simple object
                 else: 
                     result.append("<moby:Simple>"+m.dumps(queryObject)+"</moby:Simple>")
-
+                
             result.append("</moby:mobyData>")
-
+            
         result.append('</moby:mobyContent></moby:MOBY>')
-
+        
         del MobyMarshaller
-
+        
         return "".join(result)
 
     def fromMoby(self, xmlObject):
@@ -357,7 +356,7 @@
         from bioMoby import MobyUnmarshaller
         
         um=MobyUnmarshaller()
-
+        
         self.queryData={}
         
         doc=xmlObject
@@ -366,35 +365,35 @@
             doc=parseString(xmlObject)
         
         mdl=doc.getElementsByTagName('mobyData')
-
+        
         if not mdl:
             mdl=doc.getElementsByTagName('moby:mobyData')
-
+        
         #For each query            
         for elt in mdl:
             #Get the ID
             queryID=str(elt.getAttribute('queryID'))
-
+            
             if not queryID:
                 queryID=str(elt.getAttribute('moby:queryID'))
-
+            
             #Collect the data
             data=[]
-
+            
             #for each datum translate it in MobyObject, and put it in the list
             for datum in elt.childNodes:
                 #If it is a collection
                 if datum.nodeType==datum.ELEMENT_NODE and datum.localName=="Collection":
                     articleName=datum.getAttribute('moby:articleName')
-        
+                    
                     articles=[]
-        
+                    
                     for article in datum.childNodes:
                         if article.nodeType==article.ELEMENT_NODE and article.localName=="Simple":
                             for child in article.childNodes:
                                 if child.nodeType==child.ELEMENT_NODE:
                                     articles.append(um.loadn(child))
-
+                                    
                     data.append((articleName, articles))
                 #if it is a Simple object
                 elif datum.nodeType==datum.ELEMENT_NODE and datum.localName=="Simple":
@@ -442,7 +441,6 @@
             queries["%s-%s"%(queryName, queryID)]=aSimple
             
         return queries
-                
         
     def getObject(self, queryName, objectName):
         """Get an object from a query with its name
@@ -451,8 +449,7 @@
         
         for obj in filter(filterfunc, self.queryData[queryName]):
             return obj
-
-                
+            
     def getObjects(self, queryName):
         """Retrieve objects from a query
         """
@@ -470,7 +467,7 @@
             result[param.articleName]=param.value
                 
         return result
-
+        
     def getParameter(self, queryName, parameterName):
         """Retrieve a parameter from a query and his name
         """
@@ -484,4 +481,4 @@
     def __repr__(self):
         """put the xml of the Content
         """
-        return self.__str__()
+        return self.__str__()
\ No newline at end of file

From gordonp at pub.open-bio.org  Thu Feb  3 17:37:31 2005
From: gordonp at pub.open-bio.org (Paul Gordon)
Date: Thu Feb  3 17:26:35 2005
Subject: [MOBY-guts] biomoby commit
Message-ID: <200502032237.j13MbV1o027017@pub.open-bio.org>


gordonp
Thu Feb  3 17:37:30 EST 2005
Update of /home/repository/moby/moby-live/Java/src/main/org/biomoby/client
In directory pub.open-bio.org:/tmp/cvs-serv26992

Modified Files:
	MobyRequest.java 
Log Message:
Updated response Vector creation to fix spurious Java array run-time type safety check issues

moby-live/Java/src/main/org/biomoby/client MobyRequest.java,1.5,1.6
===================================================================
RCS file: /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/MobyRequest.java,v
retrieving revision 1.5
retrieving revision 1.6
diff -u -r1.5 -r1.6
--- /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/MobyRequest.java	2004/09/03 20:28:16	1.5
+++ /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/MobyRequest.java	2005/02/03 22:37:30	1.6
@@ -206,6 +206,8 @@
     }
 
     /**
+     * @return a vector of MobyDataInstance[], each element of the vector is the collection of response objects for the correspondingly indexed input request.
+     *
      * @throws MobyException if you try to get the results before calling InvokeService
      */
     public Vector getOutput() throws MobyException{
@@ -679,7 +681,8 @@
 
 	    // What we're building is a Vector, where each element represents
 	    // a Response's DataInstance Output (i.e. Simple and Collection return values)
-	    responsesOutput.add(out.toArray());
+            MobyDataInstance[] mdis = new MobyDataInstance[out.size()];
+	    responsesOutput.add(out.toArray(mdis));
 
 	    releaseXPath(response);
 	}

From yanwong at pub.open-bio.org  Fri Feb  4 07:58:25 2005
From: yanwong at pub.open-bio.org (Yan Wong)
Date: Fri Feb  4 07:47:28 2005
Subject: [MOBY-guts] biomoby commit
Message-ID: <200502041258.j14CwPFg029623@pub.open-bio.org>


yanwong
Fri Feb  4 07:58:24 EST 2005
Update of /home/repository/moby/moby-live/Python/bioMoby/webservice
In directory pub.open-bio.org:/tmp/cvs-serv29563/webservice

Modified Files:
	Dispatcher.py 
Log Message:


moby-live/Python/bioMoby/webservice Dispatcher.py,1.3,1.4
===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/webservice/Dispatcher.py,v
retrieving revision 1.3
retrieving revision 1.4
diff -u -r1.3 -r1.4
--- /home/repository/moby/moby-live/Python/bioMoby/webservice/Dispatcher.py	2005/02/01 08:52:17	1.3
+++ /home/repository/moby/moby-live/Python/bioMoby/webservice/Dispatcher.py	2005/02/04 12:58:24	1.4
@@ -88,9 +88,9 @@
             formatter: a function that transforms raw results from the Invocator into Moby Objects
             workdir: the session directory
         """
-
+        
         from bioMoby import MobyUnmarshaller
-
+        
         self._isbase64=False
         self._workdir=workdir
         self.answers={}
@@ -105,7 +105,7 @@
                 #Do some cleaning on the XML Document before proceeding...
                 #Remove all \t|\n from the <a>\n\t</a>
                 um=MobyUnmarshaller()
-
+                
                 r=re.compile("\>[\n|\t]+\<")
                 mc=um.loads("><".join(r.split(mobyContentXML)))
             except:
@@ -114,7 +114,7 @@
                     self._isbase64=True
                 except binascii.Error:
                     raise  EDispatchError, "Invalid types in the moby Content object"
-
+        
         self.queryData=mc.queryData
         self.invocator=Invocator
         self._invocatorParameters=invocatorParameters
@@ -137,7 +137,7 @@
             return base64.encodestring(str(MobyContent(self.answers)))
         
         return str(MobyContent(self.answers))
-
+        
         
 class SimpleDispatcher(AbstractDispatcher):
     """ A simple dispatcher execute sequentially the treatments
@@ -167,14 +167,14 @@
         #Clean the session directory
         os.chdir(self._workdir)
         shutil.rmtree(self._workdir+"/session"+self._sessionid)
-            
+    
     def _fetchAnswers(self):
         """ Fetch the answers and clean the session directory
         """
         from bioMoby import GeneralInvocator
         
         answers={}
-
+        
         ruserdir="session"+self._sessionid
         try:
             l=os.listdir(self._workdir+"/"+ruserdir)
@@ -188,7 +188,7 @@
                     aQueryName=querykey[8:]
                     gi=GeneralInvocator(aQueryName ,userdir=self._workdir+"/"+ruserdir)
                     answers[aQueryName]=[gi.getResults()]
-
+                    
                     if self.formatter != None:
                         answers[aQueryName]=self.formatter(answers[aQueryName][0])
                         
@@ -196,13 +196,13 @@
                 self.answers=answers
                 
                 self._clean()        
-
+        
         del GeneralInvocator
-                
+    
     def execute(self):
         """Execute the queries sequentially
         """
-
+        
         try:
             for key in self.queryData.keys():
                 query=self.queryData[key]
@@ -229,7 +229,7 @@
         """ Execute a single query, store the result in the answers attribute
         """
         from bioMoby import MobyString
-
+        
         query=self.queryData[queryKey]
         
         #Execute the query
@@ -247,8 +247,7 @@
             
             self.answers['JOBSESSION']=[MobyString(content=sio.getvalue())]
             self._clean()
-
-
+        
         del MobyString
 
     
@@ -261,14 +260,13 @@
             mt=MultiThread(self._execute, self.queryData.keys())
             mt.start()
             mt.join()
-
+            
             self._fetchAnswers()
         except:
             self._clean()
-            
+        
         return self._toMoby()
 
-        
 class PBSDispatcher(SimpleDispatcher):
     """Dispatcher for PBS jobs
     """
@@ -306,10 +304,10 @@
             queryKeys.append(qk)
             #get the associated Outputfiles
             outputfiles[qk]=queryInformation.split(";")[2].split("::")
-
+            
             #Do a qstat and check if the job is still running or on queue
             i, o, e = os.popen3("qstat %s"%qsubId)
-
+            
             orl=o.readlines()
             erl=e.readlines()
             
@@ -330,13 +328,13 @@
                 fp=file(tdir+"/results-"+querykey+".out")
                 s=fp.readlines()
                 fp.close()
-
+                
                 if len(s)==0:
                     os.remove(tdir+"/results-"+querykey+".out")
                 else:
                     if len(outputfiles.keys())>0:
                         shutil.copy(tdir+"/results-"+querykey+".out", tdir+"/results-"+querykey+"/results.out")
-
+            
             for f in outputfiles[querykey]:
                 ruserdir=tdir+"/results-"+querykey
                 # if it is a file then retrieve the file
@@ -350,7 +348,7 @@
                         shutil.copy(f+"/"+fs, ruserdir+"/"+fs)
                         os.remove(f+"/"+fs)
                     os.removedirs(f)
-
+        
         #retrieve all the results
         try:
             l=os.listdir(tdir)
@@ -363,7 +361,7 @@
                     aQueryName=querykey[8:]
                     gi=GeneralInvocator(aQueryName, userdir=tdir)
                     answers[aQueryName]=[gi.getResults()]
-
+                    
                     if self.formatter != None:
                         answers[aQueryName]=self.formatter(answers[aQueryName][0])
                         
@@ -374,14 +372,13 @@
         
         del GeneralInvocator
 
-        
     def execute(self):
         """Execute the command in a PBS script using the PBSInvocator
         """
-
+        
         if 'JOBSESSION' in self.queryData.keys():
             self.answers=self.queryData
-
+            
             self._getResults()
         else:
             #we need to store informations in a file
@@ -393,7 +390,7 @@
                 r.setParameters(self._invocatorParameters)
                 r.execute()
             fp.close()
-
+        
         return self._toMoby()
 
 class Dispatcher(SimpleDispatcher):
@@ -422,7 +419,7 @@
         """ Execute a single query, store the result in the answers attribute
         """
         from bioMoby import MobyString
-
+        
         query=self.queryData[queryKey]
         
         #Execute the query
@@ -437,7 +434,7 @@
             fp.write("The query: "+queryKey+" has not been processed")
             traceback.print_exc(file=fp)
             fp.close()
-
+        
         del MobyString
 
     def _getSem(self):
@@ -445,14 +442,14 @@
             #Wait for answers of all queries
             self._sem.wait()
             self._fetchAnswers()
-
+            
             #Remove the IPC
             import pyipc
             pyipc.removeIPC(self._sem)
             del pyipc
         except:
             pass
-        
+    
     def execute(self, timeout=120):
         """Execute the queries with a pool of threads, store the results in a mobyContent Object
         """
@@ -461,11 +458,11 @@
         #Do a fetchAnswers if the user has a sessionid
         if 'JOBSESSION' in self.queryData.keys():
             self.answers=self.queryData
-
+            
             t=threading.Thread(target=self._getSem)
             t.start()
             t.join(timeout)
-
+            
             return self._toMoby()
         else:
             #A MobyContent without jobsession id has been received
@@ -474,14 +471,14 @@
                 pid=os.fork()
             except:
                 raise Exception, "Cannot treat any further request, please retry"
-
+            
             if pid>0:
                 #try to get the results
 #                os.wait()
                 t=threading.Thread(target=self._getSem)
                 t.start()
                 t.join(timeout)
-
+                
                 return self._toMoby()
             else:
                 #do second fork
@@ -506,7 +503,7 @@
                         mt.join()
                     except:
                         self._clean()
-
+                    
                     try:
                         self._sem.signal()
                     finally:

From yanwong at pub.open-bio.org  Fri Feb  4 07:58:25 2005
From: yanwong at pub.open-bio.org (Yan Wong)
Date: Fri Feb  4 07:47:34 2005
Subject: [MOBY-guts] biomoby commit
Message-ID: <200502041258.j14CwPk7029604@pub.open-bio.org>


yanwong
Fri Feb  4 07:58:24 EST 2005
Update of /home/repository/moby/moby-live/Python/bioMoby
In directory pub.open-bio.org:/tmp/cvs-serv29563

Modified Files:
	mobyClient.py mobyDataTypes.py mobyMarshal.py mobyRegister.py 
	mobyService.py 
Log Message:


moby-live/Python/bioMoby mobyClient.py,1.3,1.4 mobyDataTypes.py,1.11,1.12 mobyMarshal.py,1.4,1.5 mobyRegister.py,1.3,1.4 mobyService.py,1.3,1.4
===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/mobyClient.py,v
retrieving revision 1.3
retrieving revision 1.4
diff -u -r1.3 -r1.4
--- /home/repository/moby/moby-live/Python/bioMoby/mobyClient.py	2005/02/01 08:52:15	1.3
+++ /home/repository/moby/moby-live/Python/bioMoby/mobyClient.py	2005/02/04 12:58:24	1.4
@@ -32,7 +32,7 @@
     def call_method(self, method, arguments):
         """It invokes a remote method of the bioMoby server
         """
-
+        
         #soapaction is necessary, if not, remote calls don't work
         self.server.soapaction=self.ns+"#"+method
         
@@ -48,21 +48,21 @@
             it returns a dictionary {'name':descriptions', ...}
         """
         result={}
-
+        
         #Remote call of the method on the Moby server
         xmlt=self.call_method("retrieveObjectNames", None)
-
+        
         doc=parseString(xmlt)
         
         for node in doc.getElementsByTagName("Object"):
             objectName=node.getAttribute("name")
-
+            
             for subNode in node.childNodes:
                 if subNode.nodeType==subNode.ELEMENT_NODE:
                     for ssNode in subNode.childNodes:
                         if ssNode.nodeType==ssNode.CDATA_SECTION_NODE:
                             result[objectName]=ssNode.nodeValue
-
+        
         return result
 
     def retrieveObjectDefinition(self, objectName):
@@ -72,10 +72,10 @@
         "urn:lsid:biomoby.org:objectrelation:hasa":"HASA",
         "urn:lsid:biomoby.org:objectrelation:has":"HAS"
         }
-
+        
         definition={}
         definition["Relationship"]={}
-
+        
         xmlinput="<retrieveObjectDefinition><objectType>"+objectName+"</objectType></retrieveObjectDefinition>"
         doc=parseString(self.call_method("retrieveObjectDefinition", xmlinput))
         
@@ -85,7 +85,7 @@
                 for elem in child.childNodes:
                     if elem.nodeType==elem.ELEMENT_NODE and elem.nodeName=="objectType" and elem.firstChild:
                         definition["Relationship"][dc[child.getAttribute("relationshipType")]].append((elem.getAttribute("articleName"), elem.firstChild.nodeValue))
-
+            
             elif child.nodeType==child.ELEMENT_NODE:
                 if child.firstChild:
                         definition[str(child.nodeName)]=child.firstChild.nodeValue
@@ -104,23 +104,22 @@
         result=[]
         
         xmlt=self.call_method("retrieveServiceProviders", None)
-
+        
         doc=parseString(xmlt)
         
         for node in doc.getElementsByTagName("serviceProvider"):
             serviceProviderName= node.getAttribute("name")
             result.append(serviceProviderName)
-            
-        return result
-
         
+        return result
+    
     def retrieveNamespaces(self):
         """Retrieves a list of namespaces as a dictionary
         """
         result={}
         
         xmlt=self.call_method("retrieveNamespaces", None)
-
+        
         doc=parseString(xmlt)
         
         for node in doc.getElementsByTagName("Namespace"):
@@ -130,9 +129,8 @@
                     for ssNode in subNode.childNodes:
                         if ssNode.nodeType==ssNode.CDATA_SECTION_NODE:
                             result[ns]=ssNode.nodeValue
-
+        
         return result
-            
 
     def retrieveServiceNames(self):
         """Retrieves a list of service's names as a dictionary {'name':'URI'}
@@ -148,87 +146,84 @@
             authURI=node.getAttribute("authURI")
             
             result[serviceName]=authURI
-   
+        
         return result
 
-
     def retrieveServiceTypes(self):
         """Retrieves a list of service's types as a dictionary {'Name':'Description'}
         """        
         result={}
         
         xmlt=self.call_method("retrieveServiceTypes", None)
-
+        
         doc=parseString(xmlt)
         
         for node in doc.getElementsByTagName("serviceType"):
             st=node.getAttribute("name")      
-
+            
             for subNode in node.childNodes:
                 if subNode.nodeType==subNode.ELEMENT_NODE:
                     for ssNode in subNode.childNodes:
                         if ssNode.nodeType==ssNode.CDATA_SECTION_NODE:
                             result[st]=ssNode.nodeValue
-    
+        
         return result
-
-
+        
     def retrieveServiceWSDLByAuthority(self, serviceName, authority):
         """Retrieves a WSDL from moby from a service name and a URI
         """
         xmlinput="<retrieveService><Service authURI=\"" + authority + "\" serviceName=\"" + serviceName + "\"/></retrieveService>"
         
         xmlt=self.call_method("retrieveService", xmlinput)
-
+        
         doc=parseString(xmlt)
         
         service=doc.firstChild
         wsdl=service.firstChild.nodeValue
-
+        
         return wsdl
-
-
+        
     def retrieveServiceWSDL(self, serviceName):
         """Retrieves a WSDL from the name of a service
         """
         m=self.retrieveServiceNames()
         return self.retrieveServiceWSDLByAuthority(serviceName, m[serviceName])
-
+        
     def retrieveServiceTypesRelationships(self, serviceType, expand):
         """Retrieves the list of service's type's relationships
         """
         result=[]
         
-
+        
         xmlinput="<Relationship><serviceType>" + serviceType + "</serviceType><relationshipType>ISA</relationshipType><expandRelationship>" + `expand` + "</expandRelationship></Relationship>"
         
         xmlt=self.call_method("Relationships", xmlinput)
-
+        
         doc=parseString(xmlt)
         
         for node in doc.getElementsByTagName("Relationship"):
             for serviceType in node.childNodes:
                 if serviceType.nodeType==serviceType.ELEMENT_NODE:
                     result.append(serviceType.firstChild.nodeValue)
-                    
+        
         return result
-    
+        
     def retrieveDataTypesRelationships(self, dataTypeName):
         """Retrieves only ISA relationships
         """
-
+        
         return self.retrieveDataTypesRelationsByType(dataTypeName, 'ISA')
-
+        
     def retrieveDataTypesRelationsByType(self, dataTypeName, relationType):
         """Retrieves data types relationships
         """
-
+        
         result={}
         
         xmlinput="<Relationship><objectType>" + dataTypeName + "</objectType><relationshipType>"+relationType+"</relationshipType><relationshipType>HASA</relationshipType><relationshipType>HAS</relationshipType><expandRelationship>1</expandRelationship></Relationship>"
-
+        
         xmlt=self.call_method("Relationships", xmlinput)
-
+        
         doc=parseString(xmlt)
         
         for node in doc.getElementsByTagName("Relationship"):
@@ -239,15 +234,14 @@
                     relationTypeResults.append(ssNode.firstChild.nodeValue)
                     
             result[relationType]=relationTypeResults
-
-        return result
         
+        return result
         
     def findService(self, mobyQuery):
         """Finds a service from a set of queries
         """
         from mobyService import ServiceQuery ,ServiceList
-
+        
         if mobyQuery.__class__==ServiceQuery:
             xmlInput="<findService>"+str(mobyQuery)+"</findService>"
             
@@ -262,4 +256,4 @@
     def __init__(self, url="http://mobycentral.cbr.nrc.ca/cgi-bin/MOBY05/mobycentral.pl", ns="http://mobycentral.cbr.nrc.ca/MOBY/Central"):
         """Constructor for class Client
         """
-        Central.__init__(self, url, ns)
+        Central.__init__(self, url, ns)
\ No newline at end of file

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/mobyDataTypes.py,v
retrieving revision 1.11
retrieving revision 1.12
diff -u -r1.11 -r1.12
--- /home/repository/moby/moby-live/Python/bioMoby/mobyDataTypes.py	2005/02/02 16:52:31	1.11
+++ /home/repository/moby/moby-live/Python/bioMoby/mobyDataTypes.py	2005/02/04 12:58:24	1.12
@@ -27,12 +27,12 @@
         self.articleName=articleName
         self.value=value
         self.__isSecondary__=True
-        
+    
     def toMoby(self):
         """Returns the object as a XML
         """
         return "<moby:Parameter moby:articleName='"+self.articleName+"'><moby:value>"+str(self.value)+"</moby:value></moby:Parameter>"
-            
+    
     def __str__(self):
         """Return the Parameter in its XML form
         """
@@ -42,7 +42,7 @@
         """Print the XML on the python command line.
         """
         return self.toMoby()
-            
+    
     def fromMoby(self, xml):
         """Get the attributes from a XML string
         """
@@ -55,9 +55,9 @@
         l=xmlelt.getElementsByTagName("value")
         if len(l)==0:
             l=xmlelt.getElementsByTagName("moby:value")
-
+            
             self.value=l[0].firstChild.nodeValue
-        
+
 class MobyGeneric(object):
     """A Generic object (to use with the Marshaller)
     """
@@ -71,7 +71,7 @@
         
         for name, value in kw.items():
             setattr(self, name, value)
-        
+
 class MobyObject(MobyGeneric):
     """Define a Moby XML Object
        It has methods toMoby and fromMoby 
@@ -86,7 +86,7 @@
         self.__PIB__=[]
         
         self.content=content
-        
+
     
     def toMoby(self):
         """Deserializes the content in XML api
@@ -155,7 +155,7 @@
         result.append("</%s:%s>"%(self.__prefix__, self.__tag__))
         
         return "".join(result)
-        
+    
     def fromMoby(self, xml):
         """Deserialization method
         """
@@ -219,14 +219,14 @@
                 self.content.append(child.nodeValue)
                 
         self.content="".join(self.content)
-        
+    
 
     def __str__(self):
         return self.toMoby()
-        
+    
     def __repr__(self):
         return self.toMoby()
-        
+    
 
 class MobyXref(MobyObject):
     """Describes an Xref
@@ -237,7 +237,7 @@
         self.serviceName=serviceName
         self.evidenceCode=evidenceCode
         self.xrefType=xrefType
-        
+    
     def toMoby(self):
         """Serialize the Xref object
         """
@@ -269,7 +269,7 @@
     def fromMoby(self, xml):
         MobyObject.fromMoby(self, xml)
         self.content = int(self.content)
-        
+
 class MobyFloat(MobyObject):
     """Serialize/deserialize floating point numbers
     """
@@ -279,7 +279,7 @@
     def fromMoby(self, xml):
         MobyObject.fromMoby(self, xml)
         self.content=float(self.content)
-        
+
 
 class MobyString(MobyObject):
     """String Moby object
@@ -304,7 +304,7 @@
         """return the XML form of the Moby Content object
         """
         return self.toMoby()
-        
+    
     def toMoby(self):
         """The XML reprentation of the content
         """
@@ -408,12 +408,12 @@
                     data.append(p)
                     
             self.queryData[queryID]=data
-            
+    
     def __getitem__(self, key):
         """Get a query from his name
         """
         return self.queryData[key]
-        
+    
     def __setitem__(self, key, item):
         """Store a query in the dictionary
         """
@@ -423,12 +423,12 @@
         """Return the number of elements inside the dictionary
         """
         return len(self.queryData)
-        
+    
     def keys(self):
         """Return all queries's name
         """
         return self.queryData.keys()
-        
+    
     def collectionToQueries(self, aCollection):
         """Turn a collection of object into a set of queries
         """
@@ -441,7 +441,7 @@
             queries["%s-%s"%(queryName, queryID)]=aSimple
             
         return queries
-        
+    
     def getObject(self, queryName, objectName):
         """Get an object from a query with its name
         """
@@ -449,14 +449,14 @@
         
         for obj in filter(filterfunc, self.queryData[queryName]):
             return obj
-            
+    
     def getObjects(self, queryName):
         """Retrieve objects from a query
         """
         filterfunc=lambda obj: not hasattr(obj, "__isSecondary__")
         
         return filter(filterfunc, self.queryData[queryName])
-        
+    
     def getParameters(self, queryName):
         """Retrieve parameters from a query
         """
@@ -467,7 +467,7 @@
             result[param.articleName]=param.value
                 
         return result
-        
+    
     def getParameter(self, queryName, parameterName):
         """Retrieve a parameter from a query and his name
         """
@@ -477,7 +477,7 @@
         
         if l:
             return l[0]
-        
+    
     def __repr__(self):
         """put the xml of the Content
         """

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/mobyMarshal.py,v
retrieving revision 1.4
retrieving revision 1.5
diff -u -r1.4 -r1.5
--- /home/repository/moby/moby-live/Python/bioMoby/mobyMarshal.py	2005/02/01 08:52:15	1.4
+++ /home/repository/moby/moby-live/Python/bioMoby/mobyMarshal.py	2005/02/04 12:58:24	1.5
@@ -24,11 +24,11 @@
         """
         if type(value).__name__=='NoneType':
             return ""
-
+        
         tvalue=type(value).__name__
-
+        
         method="m_"+tvalue
-
+        
         if hasattr(value, "toMoby"):
             return value.toMoby()
         
@@ -36,15 +36,16 @@
             return getattr(self,method)(value,articleName=articleName)
         
         return self._compoundObject(value, articleName=articleName)
-            
-        
+    
+    
     def m_str(self, value, articleName=""):
         """Return a string as itself"""
         from bioMoby.mobyDataTypes  import MobyString
         m=MobyString(content=value, articleName=articleName)
         del MobyString
-        return str(m)
         
+        return str(m)
+    
     def m_unicode(self, value, articleName=""):
         """Turn a unicode string into a mobyString object
         """
@@ -54,7 +55,7 @@
         """Return a string object into a mobyString object
         """
         return self.m_str(value, articleName)
-        
+    
     def m_int(self, value, namespace="", id="", articleName=""):
         """Turn an integer into a Moby XML object
         """
@@ -62,7 +63,7 @@
         m=MobyInteger(value, namespace=namespace, id=id, articleName=articleName)
         
         return m.toMoby()
-        
+    
     def m_float(self, value, namespace="", id="", articleName=""):
         """Turn a float into a Moby XML object
         """
@@ -70,7 +71,7 @@
         m=MobyFloat(value, namespace=namespace, id=id, articleName=articleName)
         
         return m.toMoby()
-        
+    
     def m_list(self, value, articleName=""):
         """Turn a list into a Moby XML object
         """
@@ -96,8 +97,7 @@
         result.append('</moby:Dict>')
         
         return "".join(result)
-
-            
+    
     def m_tuple(self, value, namespace="", articleName=""):
         """Define a tuple as a Moby Object
         """
@@ -109,7 +109,7 @@
         result.append('</moby:Tuple>')
         
         return "".join(result)
-
+    
     def _compoundObject(self, value, articleName=""):
         """transforms an object and all properties into a XML
         """
@@ -140,7 +140,7 @@
             header.append(">")
             
         result.append(" ".join(header))
-
+        
         if properties:
             result.append("".join(properties))            
         
@@ -149,16 +149,14 @@
         
         if properties:
             result.append("</%s>"%tagName)
-
-
-        return r"".join(result)
-        
         
+        return r"".join(result)
+    
     def dumps(self, value, articleName=""):
         """Serialize the object into a Moby XML object
         """
         return self._marshal(value, articleName)
-        
+    
 
 class MobyUnmarshaller:
     """Transform an XML into a Moby Python Object
@@ -168,24 +166,24 @@
         """ Cleaning the name of the object
         """
         import re
-
+        
         aName=str(aName)
         
         if aName=="":
             return ""
-
+        
         if aName=="namespace" or aName=="id" or aName=='content':
             return aName
-
+        
         r=re.compile("\W")
-    
+        
         t=r.split(aName)
-    
+        
         for i in range(0,len(t)):
             t[i]=str.upper(t[i][0])+t[i][1:]
-
+        
         del re
-
+        
         return "".join(t)
 
     def loadn(self, xmlNode):
@@ -198,7 +196,7 @@
         
         #Try to see if this object got a deserializer
         object2build=self._cleanName(nn)
-
+        
         objectName=str.upper(object2build[0])+object2build[1:]
         
         if hasattr(bioMoby.mobyDataTypes, "Moby%s"%objectName):
@@ -224,14 +222,12 @@
 #            from bioMoby.mobyExceptions import EInvalidMobyXML    
             
 #            raise EInvalidMobyXML
-
-        
+    
     def loads(self, xmlString):
         """ Deserializes an xml string and return a bioMoby-Python object
         """
         if xmlString=="":
             return None    
-
 #        _typesmodule=["bioMoby.mobyDataTypes", "bioMoby.ontology"]
             
         doc=parseString(xmlString)
@@ -254,15 +250,16 @@
             return int(value.firstChild.nodeValue.replace("\n","").replace("\t","").replace(" ",""))
         else:
             return 0
-            
+    
     def m_Float(self, value):
         """Turn a Float XML element into a float number
         """
         value.normalize()
         if value.firstChild:
             return float(value.firstChild.nodeValue.replace("\n","").replace("\t","").replace(" ",""))
+        
         return 0.0
-            
+    
     def m_String(self, value):
         """Turn a Moby XML String element into a String object
         """
@@ -273,9 +270,8 @@
         for aChild in value.childNodes:
             if aChild.nodeType==aChild.TEXT_NODE or aChild.nodeType==aChild.CDATA_SECTION_NODE:
                 cnt.append(aChild.wholeText)
-                
-        return        r"".join(cnt)
         
+        return        r"".join(cnt)
 
     def m_Object(self, value):
         """Turn any XML into a generic object
@@ -283,7 +279,7 @@
         filterFunc= lambda x: x.nodeType==x.ELEMENT_NODE
         
         typeName="GMoby%s"%str(value.localName)
-
+        
         from bioMoby.mobyDataTypes import MobyGeneric
         
         NewType=type(typeName, (MobyGeneric,), {})
@@ -296,24 +292,24 @@
         for tupleAttribute in value.attributes.itemsNS():
             #First item, second field:
             setattr(anObject, str(tupleAttribute[0][1]), str(tupleAttribute[1]))
-
+        
         i=0    
         for elem in filter(filterFunc, value.childNodes):
             methodName="m_%s"%str(elem.localName)
-
+            
             articleName=elem.getAttribute("moby:articleName")
             
             if not articleName:
                 articleName=elem.getAttribute("articleName")
-                
+            
             if not articleName:
                 articleName="attribute_%s"%i
-                
+            
             if hasattr(self, methodName):
                 prop=getattr(self, methodName)(elem)
             else:
-                    prop=self.m_Object(elem)
-                
+                prop=self.m_Object(elem)
+            
             if hasattr(anObject, articleName):
                 t=prop
                 if not type(getattr(anObject, articleName)) is list:
@@ -323,17 +319,17 @@
             else:
                 setattr(anObject, articleName, prop)
             i+=1
-
+        
         content=[]
-
+        
         isContentNode= lambda x: x.nodeType==x.TEXT_NODE or x.nodeType==x.CDATA_SECTION_NODE
         
         for elem in filter(isContentNode, value.childNodes):
             content.append(str(elem.nodeValue))
-            
+        
         if content:
             anObject.content(r"".join(content))
-            
+        
         return anObject
 
     def m_MobyContent(self, value):
@@ -347,5 +343,4 @@
         
         del MobyContent
         
-        return mc
-        
+        return mc
\ No newline at end of file

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/mobyRegister.py,v
retrieving revision 1.3
retrieving revision 1.4
diff -u -r1.3 -r1.4
--- /home/repository/moby/moby-live/Python/bioMoby/mobyRegister.py	2005/02/01 08:52:15	1.3
+++ /home/repository/moby/moby-live/Python/bioMoby/mobyRegister.py	2005/02/04 12:58:24	1.4
@@ -20,10 +20,10 @@
         self.id=""
         self.message=""
         self.RDF=""
-
+        
         #Parse the document, retrieve the success, id, message and RDF fields
         doc=parseString(xmlInput)
-
+        
         if len(doc.getElementsByTagName("success")[0].childNodes)>0:
             self.success=int(doc.getElementsByTagName("success")[0].childNodes[0].nodeValue)
         if len(doc.getElementsByTagName("id")[0].childNodes)>0:
@@ -35,17 +35,17 @@
                 self.RDF=doc.getElementsByTagName("RDF")[0].firstChild.toprettyxml()
         except:
             pass
-
+    
     def __str__(self):
         """Return the moby xml of the instance
         """
         return "<MOBYRegistration><id>"+self.id+"</id><success>"+`self.success`+"</success><message><![CDATA["+self.message+"]]></message><RDF>"+self.RDF+"</RDF></MOBYRegistration>"
-        
+    
     def toTuple(self):
         """return the  tuple form of  the instance
         """
         return (self.id, self.success,  self.message, self.RDF)
-        
+    
     def isSuccess(self):
         """Indicate whether the registration was successful or not
         """
@@ -79,7 +79,7 @@
         GeneralInformations.__init__(self, contact=contactEmail, authURI=authURI, description=description)
         self.relationship=relationship
         self.serviceType=serviceType
-        
+    
     def __str__(self):
         """Return the instance as a Moby XML
         """
@@ -88,22 +88,21 @@
         result.append("<authURI>"+self.authURI+"</authURI>")
         result.append("<Description><![CDATA["+self.description+"]]></Description>")
         result.append('<Relationship relationshipType="'+self.relationship[0]+'">')
-    
+        
         for serviceType in self.relationship[1]:
             result.append('<serviceType>'+serviceType+'</serviceType>')
-
+        
         result.append("</Relationship>")
-            
-
-        return "".join(result)
-
         
+        
+        return "".join(result)
+    
     def register(self):
         """Register the service's type on the moby server
         """
         xmlinput="<registerServiceType>"+str(self)+"</registerServiceType>"
         return RegistrationObject(self.central.call_method("registerServiceType", xmlinput))
-        
+    
     def deregister(self):
         """Deregister the service's Type on moby
         """
@@ -126,7 +125,7 @@
         """
         result=["<objectType>"+self.objectType+"</objectType>"]
         result.append("<Description><![CDATA["+self.description+"]]></Description>")
-                
+        
         for relationship in self.relationships:
             result.append('<Relationship relationshipType="'+relationship[0]+'">')
             
@@ -134,12 +133,11 @@
                 result.append('<objectType articleName="'+objectTypeKey+'">'+relationship[1][objectTypeKey]+'</objectType>')
                 
             result.append("</Relationship>")
-
+        
         result.append("<authURI>"+self.authURI+"</authURI>")
         result.append("<contactEmail>"+self.contact+"</contactEmail>")
-
+        
         return "".join(result)
-
     
     def register(self):
         """Register the  object's class
@@ -160,12 +158,12 @@
     def __init__(self, namespaceType="", contact="", authURI="", description=""):
         GeneralInformations.__init__(self, contact=contact, authURI=authURI,description=description)
         self.namespaceType=namespaceType
-
+    
     def __str__(self):
         """return the XML of the name space
         """
         return "<namespaceType>"+self.namespaceType+"</namespaceType><contactEmail>"+self.contact+"</contactEmail><authURI>"+self.authURI+"</authURI><Description><![CDATA["+self.description+"]]></Description>"
-
+    
     def register(self):
         """Register the namespace on a Moby server
         """
@@ -176,4 +174,4 @@
         """Deregister the namespace
         """
         xmlinput="<deregisterNamespace>"+self.namespaceType+"</deregisterNamespace>"
-        return RegistrationObject(self.central.call_method("deregisterNamespace", xmlinput))
+        return RegistrationObject(self.central.call_method("deregisterNamespace", xmlinput))
\ No newline at end of file

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/mobyService.py,v
retrieving revision 1.3
retrieving revision 1.4
diff -u -r1.3 -r1.4
--- /home/repository/moby/moby-live/Python/bioMoby/mobyService.py	2005/02/01 08:52:15	1.3
+++ /home/repository/moby/moby-live/Python/bioMoby/mobyService.py	2005/02/04 12:58:24	1.4
@@ -33,16 +33,16 @@
         
         for namespace in self.namespaces:
             result.append('<Namespace>'+namespace+'</Namespace>')
-    
+        
         result.append('</Simple>')
         
         return "".join(result)
-
+    
     def fromXML(self, xml):
         """Return an article from a xml node
         """
         node=parseString(xml)
-
+        
         self.name=node.getAttribute("articleName")
         for otns in node.childNodes:
             if otns.nodeName=="objectType":
@@ -63,12 +63,11 @@
         
         self.enums=enums
 
-    
     def toTuple(self):
         """Return the object as a tuple
         """
         return (self.name, self.type, self.default, self.min, self.max, self.enums)
-            
+    
     def __str__(self):
         """Return the xml form of the object
         """
@@ -83,23 +82,23 @@
             
         if self.max !='':
             result.append('<max>'+self.max+'</max>')
-
+        
         for enum in self.enums:
             result.append('<enum>'+enum+'</enum>')
-
+        
         result.append('</Parameter>')
-
+        
         return "".join(result)
-
+    
     def fromXML(self, xml):
         """Return a parameter from a xml
         """
         
         node=parseString(xml)        
-
+        
         self.enums=[]
         self.name=node.getAttribute("articleName")
-
+        
         for childNode in node.childNodes:
             if childNode.nodeName=="datatype":
                 self.type=childNode.firstChild.nodeValue
@@ -129,11 +128,11 @@
         self.protocol="moby"
         self.authURI=""
         self.serviceName=""
-
+        
         self.expandObjects=0
         self.expandServices=1
         self.authoritative=0
-
+        
         if 'serviceName' in kw:
             self.serviceName=kw['serviceName']
         if 'serviceType' in kw:
@@ -148,15 +147,15 @@
             self.outputObjects=kw['outputObjects']
         if 'keywords' in kw:
             self.keywords=kw['keywords']
-            
+    
     def submits2XML(self, entries):
         """Tranforms inputs/outputs into xml
         """
-
+        
         import string
         result=[]
         for submit in entries:
-
+            
             #first look if it is an article or a collection
             #first case
             if submit[1].__class__ is string or submit[1].__class__ is str:
@@ -165,42 +164,41 @@
                 #otns[1] namespace
                 for namespace in submit[2]:
                     result.append("<Namespace>"+namespace+"</Namespace>")
-
+                
                 result.append("</Simple>")
                 #it is a collection
             else:
                 result.append('<Collection articleName="'+submit[0]+'">')
-
+                
                 for simpleArticle in submit[1]:
                     result.append('<Simple articleName="'+simpleArticle[0]+'"><objectType>'+simpleArticle[1]+'</objectType>')
                     for namespace in simpleArticle[2]:
                         result.append("<Namespace>"+namespace+"</namespace>")
-
+                    
                     result.append("</Simple>")
                         
                 result.append("</Collection>")
-
+        
         del string                    
         return "".join(result)
-
-
+    
     def keywords2XML(self, keywords):
         """Transform keywords into xml
         """
         result=[]
+        
         for keyword in keywords:
             result.append("<keyword>"+keyword+"</keyword>")
-            
-
+        
+        
         return "".join(result)
-
-
+    
     def __str__(self):
         """Give the xml form of the query
         """
         result=["<inputObjects><Input>"]
         result.append(self.submits2XML(self.inputObjects))
-
+        
         result.append("</Input></inputObjects><outputObjects><output>")
         result.append(self.submits2XML(self.outputObjects))
         result.append("</output></outputObjects>")
@@ -208,18 +206,18 @@
         result.append("<serviceType>"+self.serviceType+"</serviceType>")
         result.append("<Protocol>moby</Protocol>")
         result.append("<authURI>"+self.authURI+"</authURI>")
-
+        
         if self.serviceName != "" and self.serviceName !="dummy":
             result.append("<serviceName>"+self.serviceName+"</serviceName>")
-
+        
         result.append("<expandObjects>"+`self.expandObjects`+"</expandObjects>")
         result.append("<expandServices>"+`self.expandServices`+"</expandServices>")
         result.append("<authoritative>"+`self.authoritative`+"</authoritative>")
         result.append("<keywords>")
         result.append(self.keywords2XML(self.keywords))
         result.append("</keywords>")
-
-
+        
+        
         return "".join(result)
 
 
@@ -236,10 +234,10 @@
             
             -A WSDL
         """
-
+        
         GeneralInformations.__init__(self)
         self.namespace="http://biomoby.org/"
-
+        
         self.name=""
         self.type=""
         self.category=""
@@ -251,7 +249,7 @@
         self.secondaryArticles=[]
         self.methods=[]
         self.results=""
-
+        
         if len(arg)==1 and arg[0].__class__ is dict:
             arg=arg[0]
             for key in arg.keys():
@@ -291,11 +289,11 @@
         """
         self.methods=[]
         doc=parseString(wsdl)
-
+        
         for method in doc.getElementsByTagName("operation"):
             if method.getAttribute("name") not in self.methods:
                 self.methods.append(method.getAttribute("name"))
-
+        
         if self.url=="":
             for url in doc.getElementsByTagName("soap:address"):
                 self.url=url.getAttribute("location")
@@ -310,7 +308,7 @@
         """
         
         from SOAPpy import SOAPProxy
-
+        
         webservice=SOAPProxy(self.url,namespace=self.namespace)
         
         if method=="":
@@ -318,34 +316,34 @@
                 method=self.name
             else:
                 method=self.methods[0]
-
+        
         if method not in self.methods:
             from bioMoby.mobyExceptions import ENotAWSMethod
             raise ENotAWSMethod
-
+        
         webservice.soapaction=self.namespace+"#"+method
-
+        
         if debug:
             webservice.config.debug=1
         
         toQuery=str(query)
-
+        
         del  SOAPProxy
-
+        
         result=webservice.invoke(method, toQuery)
         
         if returnXml:
             return result
-            
+        
         #try to return a MobyContent Object instead
         from bioMoby.mobyDataTypes import MobyContent
         mc=MobyContent()
         mc.fromMoby(result)
         
         del MobyContent
-
+        
         return mc
-            
+    
     def __str__(self):
         """Returns The moby xml form of the web service
         """
@@ -358,7 +356,7 @@
         result.append("<contactEmail>"+self.contact+"</contactEmail>")
         result.append("<authoritativeService>"+`self.authoritative`+"</authoritativeService>")
         result.append("<Description><![CDATA["+self.description+"]]></Description>")
-
+        
         result.append("<Input>")
         
         for inputObject in self.inputObjects:
@@ -366,25 +364,25 @@
                 result.append(str(inputObject))
             elif inputObject.__class__ is dict:
                 result.append('<Collection articleName="'+inputObject.keys()[0]+'">')
-
+                
                 for aSimple in inputObject[inputObject.keys()[0]]:
                     result.append(str(aSimple))
-
+                
                 result.append("</Collection>")
             else:
                 from mobyExceptions import EInvalidArgument
                 raise EInvalidArgument, "Bad input object"
-            
+        
         result.append("</Input>")
-
+        
         result.append("<Output>")
-
+        
         for output in self.outputObjects:
             if output.__class__ is ServiceArticle:
                 result.append(str(output))
             elif output.__class__ is dict:
                 result.append('<Collection articleName="'+output.keys()[0]+'">')
-
+                
                 for aSimple in output[output.keys()[0]]:
                     result.append(str(aSimple))
                     
@@ -392,19 +390,18 @@
             else:
                 from mobyExceptions import EInvalidArgument
                 raise EInvalidArgument, "Bad output object"
-                    
-
+        
+        
         result.append("</Output>")
-
+        
         result.append("<secondaryArticles>")
         
         for secondaryArticle in self.secondaryArticles:
             result.append(str(secondaryArticle))
-
+        
         result.append("</secondaryArticles>")
-
+        
         return "".join(result)
-    
 
     def register(self):
         """Register the service on the Moby server    
@@ -435,8 +432,7 @@
         """
         
         self.results=self.execute(mobyContent, returnXml=(mobyContent.__class__ is str))
-                
-        
+    
     def start(self, mobycontent, timeout=-1):
         """Start the service as it was a thread
         """
@@ -447,16 +443,14 @@
             self._execThread=Thread(target=self._executeThread, args=(mobycontent,))
         else:
             self._execThread=Thread(target=self._executeThread, args=(mobycontent,), timeout=timeout)
-
-        self._execThread.start()
         
+        self._execThread.start()
+    
     def join(self):
         """Same as Thread.join
         """
         self._execThread.join()
-        
-        
-        
+    
 class ServiceList:
     """Class representing a service's list
     """
@@ -466,16 +460,16 @@
         """
         
         simpleArticle=ServiceArticle(name='',type='',namespaces=[])
-
+        
         simpleArticle.name=node.getAttribute("articleName")
         for otns in node.childNodes:
             if otns.nodeName=="objectType":
                 simpleArticle.type=otns.firstChild.nodeValue
             elif otns.nodeName=="Namespace":
                 simpleArticle.namespaces.append(otns.firstChild.nodeValue)
-                
+        
         return simpleArticle
-
+    
     def toCollection(self, node):
         """Return a collection of articles
         """
@@ -485,21 +479,20 @@
         for simpleArticle in node.childNodes:
             if simpleArticle.nodeName=="Simple":
                 collection.append(self.toSimpleArticle(simpleArticle))
-            
+        
         result[collectionName]=collection
         
         return result
     
-
     def toSecondary(self, node):
         """Return a parameter from a xml
         """
         secondary=ServiceSecondary(name="", type="", default="", min="", max="", enums=[])
-
+        
         secondary.enums=[]
-
+        
         secondary.name=node.getAttribute("articleName")
-
+        
         for childNode in node.childNodes:
             if childNode.nodeName=="datatype":
                 if childNode.firstChild:
@@ -516,18 +509,18 @@
             elif childNode.nodeName=="enum":
                 if childNode.firstChild:
                     secondary.enums.append(childNode.firstChild.nodeValue)
-
+        
         return secondary
 
     def __init__(self, xmlt):
         """Give the instance of an object from xml
         """
         self.list=[]
-
+        
         doc=parseString(xmlt)
         #for each service
         for node in doc.getElementsByTagName("Service"):
-
+            
             service=Service()
             service.name=node.getAttribute("serviceName")
             service.methods=[service.name]
@@ -565,7 +558,7 @@
                     for secondary in child.childNodes:
                         if secondary.nodeName=="Parameter":
                             service.secondaryArticles.append(self.toSecondary(secondary))
-                            
+            
             self.list.append(service)
 
     def getServiceByName(self, nameOfService):
@@ -574,7 +567,7 @@
         for service in self.list:
             if service.name==nameOfService:
                 return service
-                
+        
         return None
     
     def getServiceByAuthURI(self, authURI):
@@ -583,7 +576,7 @@
         for service in self.list:
             if service.authURI==authURI:
                 return service
-                
+        
         return None
 
     def __getitem__(self, key):

From yanwong at pub.open-bio.org  Fri Feb  4 10:58:37 2005
From: yanwong at pub.open-bio.org (Yan Wong)
Date: Fri Feb  4 10:47:40 2005
Subject: [MOBY-guts] biomoby commit
Message-ID: <200502041558.j14Fwbbt030084@pub.open-bio.org>


yanwong
Fri Feb  4 10:58:37 EST 2005
Update of /home/repository/moby/moby-live/Python/bioMoby
In directory pub.open-bio.org:/tmp/cvs-serv30059

Modified Files:
	mobyDataTypes.py 
Log Message:


moby-live/Python/bioMoby mobyDataTypes.py,1.12,1.13
===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/mobyDataTypes.py,v
retrieving revision 1.12
retrieving revision 1.13
diff -u -r1.12 -r1.13
--- /home/repository/moby/moby-live/Python/bioMoby/mobyDataTypes.py	2005/02/04 12:58:24	1.12
+++ /home/repository/moby/moby-live/Python/bioMoby/mobyDataTypes.py	2005/02/04 15:58:37	1.13
@@ -438,7 +438,7 @@
         queryID=1
         
         for aSimple in aCollection[1]:
-            queries["%s-%s"%(queryName, queryID)]=aSimple
+            queries["%s-%s"%(queryName, queryID)]=[aSimple]
             
         return queries
     

From yanwong at pub.open-bio.org  Fri Feb  4 11:03:40 2005
From: yanwong at pub.open-bio.org (Yan Wong)
Date: Fri Feb  4 10:52:35 2005
Subject: [MOBY-guts] biomoby commit
Message-ID: <200502041603.j14G3eqD030127@pub.open-bio.org>


yanwong
Fri Feb  4 11:03:40 EST 2005
Update of /home/repository/moby/moby-live/Python/bioMoby
In directory pub.open-bio.org:/tmp/cvs-serv30102

Modified Files:
	mobyDataTypes.py 
Log Message:


moby-live/Python/bioMoby mobyDataTypes.py,1.13,1.14
===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/mobyDataTypes.py,v
retrieving revision 1.13
retrieving revision 1.14
diff -u -r1.13 -r1.14
--- /home/repository/moby/moby-live/Python/bioMoby/mobyDataTypes.py	2005/02/04 15:58:37	1.13
+++ /home/repository/moby/moby-live/Python/bioMoby/mobyDataTypes.py	2005/02/04 16:03:40	1.14
@@ -439,6 +439,7 @@
         
         for aSimple in aCollection[1]:
             queries["%s-%s"%(queryName, queryID)]=[aSimple]
+            queryID+=1
             
         return queries
     

From mwilkinson at pub.open-bio.org  Sun Feb  6 16:58:36 2005
From: mwilkinson at pub.open-bio.org (Mark Wilkinson)
Date: Sun Feb  6 16:47:18 2005
Subject: [MOBY-guts] biomoby commit
Message-ID: <200502062158.j16LwaE7014950@pub.open-bio.org>


mwilkinson
Sun Feb  6 16:58:36 EST 2005
Update of /home/repository/moby/moby-live/Perl/MOBY
In directory pub.open-bio.org:/tmp/cvs-serv14931

Modified Files:
	Central.pm 
Log Message:
should fiux problem with servicd registration

moby-live/Perl/MOBY Central.pm,1.146,1.147
===================================================================
RCS file: /home/repository/moby/moby-live/Perl/MOBY/Central.pm,v
retrieving revision 1.146
retrieving revision 1.147
diff -u -r1.146 -r1.147
--- /home/repository/moby/moby-live/Perl/MOBY/Central.pm	2004/12/14 20:55:11	1.146
+++ /home/repository/moby/moby-live/Perl/MOBY/Central.pm	2005/02/06 21:58:35	1.147
@@ -3220,7 +3220,7 @@
 		  && &_LOG( $_->nodeType, "\t", $_->toString, "\n" );
 
 		#next unless $_->nodeType == TEXT_NODE;
-		$content .= $_->toString;
+		$content .= $_->textContent;
 	}
 	return $content;
 }
@@ -3243,7 +3243,7 @@
 		if ($_->toString =~ /<!\[CDATA\[((?>[^\]]+))\]\]>/) {
 			$content .= $1;
 		} else {
-			$content .= $_->toString;
+			$content .= $_->textContent;
 		}
 	}
 	return $content;

From mwilkinson at pub.open-bio.org  Sun Feb  6 17:24:48 2005
From: mwilkinson at pub.open-bio.org (Mark Wilkinson)
Date: Sun Feb  6 17:15:37 2005
Subject: [MOBY-guts] biomoby commit
Message-ID: <200502062224.j16MOmFc015075@pub.open-bio.org>


mwilkinson
Sun Feb  6 17:24:47 EST 2005
Update of /home/repository/moby/moby-live/Perl/MOBY/Client
In directory pub.open-bio.org:/tmp/cvs-serv15056/MOBY/Client

Modified Files:
	Central.pm 
Log Message:
fixing at teh client side as well

moby-live/Perl/MOBY/Client Central.pm,1.87,1.88
===================================================================
RCS file: /home/repository/moby/moby-live/Perl/MOBY/Client/Central.pm,v
retrieving revision 1.87
retrieving revision 1.88
diff -u -r1.87 -r1.88
--- /home/repository/moby/moby-live/Perl/MOBY/Client/Central.pm	2004/12/15 19:37:12	1.87
+++ /home/repository/moby/moby-live/Perl/MOBY/Client/Central.pm	2005/02/06 22:24:47	1.88
@@ -1863,7 +1863,7 @@
 
 		#print getNodeTypeName($_), "\t", $_->toString,"\n";
 		next unless $_->nodeType == TEXT_NODE;
-		$content = $_->toString;
+		$content = $_->textContent;
 	}
     $content ||="";
 	$content =~ s/<!\[CDATA\[((?>[^\]]+))\]\]>/$1/gs;
@@ -1883,14 +1883,14 @@
 
 		#print getNodeTypeName($_), "\t", $_->toString,"\n";
 		next unless $_->nodeType == TEXT_NODE;
-		$content = $_->toString;
+		$content = $_->textContent;
 	}
 	return $content;
 }
 
 sub _nodeRawContent {
 
-	# will get text of **all** child $node from the given $DOM
+	# will get XML of **all** child $node from the given $DOM
 	# regardless of their depth!!
 	my ( $DOM, $node ) = @_;
 	my $x = $DOM->getElementsByTagName( $node );
@@ -1923,7 +1923,7 @@
 
 			#print getNodeTypeName($_), "\t", $_->toString,"\n";
 			next unless $_->nodeType == TEXT_NODE;
-			push @result, $_->toString;
+			push @result, $_->textContent;
 		}
 	}
 	return @result;

From mwilkinson at pub.open-bio.org  Sun Feb  6 17:46:45 2005
From: mwilkinson at pub.open-bio.org (Mark Wilkinson)
Date: Sun Feb  6 17:35:44 2005
Subject: [MOBY-guts] biomoby commit
Message-ID: <200502062246.j16MkjAO015335@pub.open-bio.org>


mwilkinson
Sun Feb  6 17:46:45 EST 2005
Update of /home/repository/moby/moby-live/Perl/MOBY/Client
In directory pub.open-bio.org:/tmp/cvs-serv15316

Modified Files:
	Central.pm 
Log Message:
fixing the registration object output

moby-live/Perl/MOBY/Client Central.pm,1.88,1.89
===================================================================
RCS file: /home/repository/moby/moby-live/Perl/MOBY/Client/Central.pm,v
retrieving revision 1.88
retrieving revision 1.89
diff -u -r1.88 -r1.89
--- /home/repository/moby/moby-live/Perl/MOBY/Client/Central.pm	2005/02/06 22:24:47	1.88
+++ /home/repository/moby/moby-live/Perl/MOBY/Client/Central.pm	2005/02/06 22:46:45	1.89
@@ -1829,6 +1829,7 @@
 	my $id      = &_nodeTextContent( $Object,  'id' );
 	my $success = &_nodeTextContent( $Object,  'success' );
 	my $message = &_nodeCDATAContent( $Object, 'message' );
+print STDERR "******$message******\n";
 	my $RDF     = &_nodeRawContent( $Object,   'RDF' );
 	my $reg = MOBY::Client::Registration->new(
 											   success         => $success,
@@ -1862,7 +1863,7 @@
 	foreach ( @child ) {
 
 		#print getNodeTypeName($_), "\t", $_->toString,"\n";
-		next unless $_->nodeType == TEXT_NODE;
+		next unless (($_->nodeType == TEXT_NODE) || ($_->nodeType == CDATA_SECTION_NODE));
 		$content = $_->textContent;
 	}
     $content ||="";
@@ -1882,7 +1883,7 @@
 	foreach ( @child ) {
 
 		#print getNodeTypeName($_), "\t", $_->toString,"\n";
-		next unless $_->nodeType == TEXT_NODE;
+		next unless (($_->nodeType == TEXT_NODE) || ($_->nodeType == CDATA_SECTION_NODE));
 		$content = $_->textContent;
 	}
 	return $content;
@@ -1922,7 +1923,7 @@
 		foreach ( @child2 ) {
 
 			#print getNodeTypeName($_), "\t", $_->toString,"\n";
-			next unless $_->nodeType == TEXT_NODE;
+			next unless (($_->nodeType == TEXT_NODE) || ($_->nodeType == CDATA_SECTION_NODE));
 			push @result, $_->textContent;
 		}
 	}

From yanwong at pub.open-bio.org  Mon Feb  7 09:23:13 2005
From: yanwong at pub.open-bio.org (Yan Wong)
Date: Mon Feb  7 09:12:47 2005
Subject: [MOBY-guts] biomoby commit
Message-ID: <200502071423.j17ENDn9018500@pub.open-bio.org>


yanwong
Mon Feb  7 09:23:13 EST 2005
Update of /home/repository/moby/moby-live/Python/utils
In directory pub.open-bio.org:/tmp/cvs-serv18475

Modified Files:
	moby2python.py 
Log Message:


moby-live/Python/utils moby2python.py,1.5,1.6
===================================================================
RCS file: /home/repository/moby/moby-live/Python/utils/moby2python.py,v
retrieving revision 1.5
retrieving revision 1.6
diff -u -r1.5 -r1.6
--- /home/repository/moby/moby-live/Python/utils/moby2python.py	2005/02/01 14:20:46	1.5
+++ /home/repository/moby/moby-live/Python/utils/moby2python.py	2005/02/07 14:23:13	1.6
@@ -85,7 +85,8 @@
     res.append("            if elt.nodeName==\"CrossReference\" or elt.nodeName==\"moby:CrossReference\":")
     res.append("                self.__cross__=[]")
     res.append("                for ref in elt.childNodes:")
-    res.append("                    self.__cross__.append(um.loads(ref))")        
+    res.append("                    if ref.nodeType==ref.ELEMENT_NODE:")    
+    res.append("                        self.__cross__.append(um.loadn(ref))")        
 
 
     for parameter in parameters:

From kawas at pub.open-bio.org  Mon Feb  7 20:50:32 2005
From: kawas at pub.open-bio.org (Eddie Kawas)
Date: Mon Feb  7 20:39:13 2005
Subject: [MOBY-guts] biomoby commit
Message-ID: <200502080150.j181oWm1020725@pub.open-bio.org>


kawas
Mon Feb  7 20:50:31 EST 2005
Update of /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/gui/serviceInstanceCreationTool
In directory pub.open-bio.org:/tmp/cvs-serv20700/org/biomoby/client/gui/serviceInstanceCreationTool

Modified Files:
	MobyUtilities.java 
Log Message:
Fixed GetRelations so that the name argument can be an LSID - Eddie

moby-live/Java/src/main/org/biomoby/client/gui/serviceInstanceCreationTool MobyUtilities.java,1.1,1.2
===================================================================
RCS file: /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/gui/serviceInstanceCreationTool/MobyUtilities.java,v
retrieving revision 1.1
retrieving revision 1.2
diff -u -r1.1 -r1.2
--- /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/gui/serviceInstanceCreationTool/MobyUtilities.java	2004/09/27 21:29:14	1.1
+++ /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/gui/serviceInstanceCreationTool/MobyUtilities.java	2005/02/08 01:50:31	1.2
@@ -7,6 +7,8 @@
 import java.util.Iterator;
 import java.util.LinkedList;
 import java.util.StringTokenizer;
+import java.util.regex.Matcher;
+import java.util.regex.Pattern;
 
 import javax.swing.tree.TreePath;
 
@@ -19,147 +21,160 @@
  */
 
 public class MobyUtilities {
-	// strings that when concatenated return the attributes, articlename, etc of an object
-	final private static String MURL = new String("http://mobycentral.cbr.nrc.ca/cgi-bin/types/Objects?name=");
-	final private static String MURL2 = new String("&lsid_name");
-
-	/**
-	 * PRE: None.<p>
-	 * POST: a linked list of all the relations is returned, such that:<p>
-	 * => The first item in the list is a string representation of the parent<p>
-	 * => The second item is a linked list of all the 'HAS' container relationships<p>
-	 * => The third item is a linked list of all the 'HASA' container relationships
-	 * @param name, the name of the object to query for.
-	 * @return returns a linked list {String, LinkedList, LinkedList} of relationships
-	 */
-	public static LinkedList GetRelations(String name) throws IOException {
-		URL url = null;
-		url = new URL(MURL + name + MURL2);
-		BufferedReader in = new BufferedReader(new InputStreamReader(url.openStream()));
-		String input;
-		String parent = "";
-		LinkedList llHas = new LinkedList();
-		LinkedList llHasa = new LinkedList();
-
-		while ((input = in.readLine()) != null) {
-			StringTokenizer st = new StringTokenizer(input, "\t");
-			if (st.countTokens() > 2) {
-				st.nextToken(); // object name that was queried
-				StringTokenizer lsid = new StringTokenizer(st.nextToken(), ":");
-				String relation = "";
-				while (lsid.hasMoreTokens())
-					relation = lsid.nextToken(); // isa, hasa, etc
-				if (relation.equalsIgnoreCase("isa"))
-					parent = st.nextToken();
-				else if (relation.equalsIgnoreCase("has"))
-					llHas.add(st.nextToken());
-				else if (relation.equalsIgnoreCase("hasa"))
-					llHasa.add(st.nextToken());
-			}
-		}
-		if (parent.equals("")) {
-			return null;
-		}
-		LinkedList listToReturn = new LinkedList();
-		listToReturn.addFirst(parent);
-		listToReturn.add(llHas);
-		listToReturn.add(llHasa);
-		return listToReturn;
-	}
-
-	/**
-	 * 
-	 * PRE: None.<p>
-	 * POST: a Pair object is returned if the String could be parsed, otherwise, null is returned.
-	 * @param rel - the string representation of the relation in the form Attribute(articleName), i.e. Integer(Count).
-	 * @return returns a fully constructed Pair object if the relation was valid, otherwise, null is returned. 
-	 */
-	public static Pair ParseRelation(String rel) {
-		// integer(length) == attribute(articlename)
-		Pair p = null;
-		int x = -1;
-		String attribute, articleName;
-		if ((x = rel.indexOf("(")) >= 0) {
-			attribute = rel.substring(0, x);
-			articleName = rel.substring(x + 1, rel.length() - 1);
-			p = new Pair(articleName, attribute);
-		}
-
-		return p;
-	}
-
-	/**
-	 * 
-	 * PRE: None.<p>
-	 * POST: Returns the leaf object in a TreePath if path is not null, otherwise, null is returned.
-	 * @param path - a TreePath containing the object of interest.
-	 * @return returns the name of the leaf object contained in the path.
-	 */
-	public static String GetObject(TreePath path) {
-		if (path == null)
-			return null;
-		String s = path.toString();
-		int start = s.lastIndexOf(", ");
-		int end = s.indexOf("]");
-		if (start < 0) {
-			start = 0;
-		}
-		int space = -1;
-		if ((space = s.lastIndexOf(" ")) >= 0) {
-			s = s.substring(space + 1, end);
-		} else
-			s = s.substring(start + 1, end);
-		return s;
-	}
-
-	/**
-	 * 
-	 * PRE: ll is a valid linkedlist, panelDetails is a valid MobyUserPanel.<p>
-	 * POST: All the relations of child are outputted to the MobyUserPanel panelDetails.
-	 * @param ll - a linked list created via GetRelations()
-	 * @param panelDetails - the MobyUserPanel to output the relationships
-	 * @param child - the object that GetRelations() was called with.
-	 */
-	public static String WriteToPanel(LinkedList ll, String child) {
-		//System.out.println(ll);
-		StringBuffer sb = new StringBuffer("");
-		sb.append(child + System.getProperty("line.separator") + "ISA: " + System.getProperty("line.separator") + "\t");
-		String parent = (String) ll.removeFirst();
-		sb.append(parent + System.getProperty("line.separator"));
-		LinkedList llhas = (LinkedList) ll.removeFirst();
-		if (llhas != null) {
-			sb.append("Has: ");
-			Iterator i = llhas.iterator();
-			while (i.hasNext()) {
-				Pair p = MobyUtilities.ParseRelation((String) i.next());
-				if (p != null)
-					sb.append(
-						System.getProperty("line.separator")
-							+ "\t"
-							+ p.getAttribute()
-							+ " - "
-							+ p.getArticlename()
-							+ " ");
-			}
-			sb.append(System.getProperty("line.separator"));
-		}
-		LinkedList llhasa = (LinkedList) ll.removeFirst();
-		if (llhasa != null) {
-			sb.append("Hasa: ");
-			Iterator i = llhasa.iterator();
-			while (i.hasNext()) {
-				Pair p = MobyUtilities.ParseRelation((String) i.next());
-				if (p != null)
-					sb.append(
-						System.getProperty("line.separator")
-							+ "\t"
-							+ p.getAttribute()
-							+ "->"
-							+ p.getArticlename()
-							+ " ");
-			}
-		}
-		return sb.toString();
-	}
-
-}
+    // strings that when concatenated return the attributes, articlename, etc of an object
+    final private static String URL_OBJECT = new String(
+            "http://mobycentral.cbr.nrc.ca/cgi-bin/types/Objects?name=");
+
+    final private static String URL_LSID = new String(
+            "http://mobycentral.cbr.nrc.ca/cgi-bin/types/Objects?lsid_name=");
+
+    /**
+     * PRE: None.<p>
+     * POST: a linked list of all the relations is returned, such that:<p>
+     * => The first item in the list is a string representation of the parent<p>
+     * => The second item is a linked list of all the 'HAS' container relationships<p>
+     * => The third item is a linked list of all the 'HASA' container relationships
+     * @param name, the name of the object to query for - can be an Moby Object LSID.
+     * @return returns a linked list {String, LinkedList, LinkedList} of relationships
+     */
+    public static LinkedList GetRelations(String name) throws IOException {
+        URL url = null;
+        boolean isLSID = false;
+        // TODO check if name == lsid
+        Pattern p = Pattern.compile("(^urn:lsid:biomoby.org:objectclass:\\S+)",
+                Pattern.CASE_INSENSITIVE);
+        Matcher m = p.matcher(name);
+        isLSID = m.matches();
+
+        if (!isLSID)
+            url = new URL(URL_OBJECT + name);
+        else
+            url = new URL(URL_LSID + name);
+        BufferedReader in = new BufferedReader(new InputStreamReader(url
+                .openStream()));
+        String input;
+        String parent = "Object";
+        LinkedList llHas = new LinkedList();
+        LinkedList llHasa = new LinkedList();
+
+        while ((input = in.readLine()) != null) {
+            StringTokenizer st = new StringTokenizer(input, "\t");
+            if (st.countTokens() > 2) {
+                st.nextToken(); // object name that was queried
+                StringTokenizer lsid = new StringTokenizer(st.nextToken(), ":");
+                String relation = "";
+                while (lsid.hasMoreTokens())
+                    relation = lsid.nextToken(); // isa, hasa, etc
+                if (relation.equalsIgnoreCase("isa"))
+                    parent = st.nextToken();
+                else if (relation.equalsIgnoreCase("has"))
+                    llHas.add(st.nextToken());
+                else if (relation.equalsIgnoreCase("hasa"))
+                    llHasa.add(st.nextToken());
+            }
+        }
+        if (parent.equals("")) {
+            return null;
+        }
+        LinkedList listToReturn = new LinkedList();
+        listToReturn.addFirst(parent);
+        listToReturn.add(llHas);
+        listToReturn.add(llHasa);
+        return listToReturn;
+    }
+
+    /**
+     * 
+     * PRE: None.<p>
+     * POST: a Pair object is returned if the String could be parsed, otherwise, null is returned.
+     * @param rel - the string representation of the relation in the form Attribute(articleName), i.e. Integer(Count).
+     * @return returns a fully constructed Pair object if the relation was valid, otherwise, null is returned. 
+     */
+    public static Pair ParseRelation(String rel) {
+        // integer(length) == attribute(articlename)
+        Pair p = null;
+        int x = -1;
+        String attribute, articleName;
+        if ((x = rel.indexOf("(")) >= 0) {
+            attribute = rel.substring(0, x);
+            articleName = rel.substring(x + 1, rel.length() - 1);
+            p = new Pair(articleName, attribute);
+        }
+
+        return p;
+    }
+
+    /**
+     * 
+     * PRE: None.<p>
+     * POST: Returns the leaf object in a TreePath if path is not null, otherwise, null is returned.
+     * @param path - a TreePath containing the object of interest.
+     * @return returns the name of the leaf object contained in the path.
+     */
+    public static String GetObject(TreePath path) {
+        if (path == null)
+            return null;
+        String s = path.toString();
+        int start = s.lastIndexOf(", ");
+        int end = s.indexOf("]");
+        if (start < 0) {
+            start = 0;
+        }
+        int space = -1;
+        if ((space = s.lastIndexOf(" ")) >= 0) {
+            s = s.substring(space + 1, end);
+        } else
+            s = s.substring(start + 1, end);
+        return s;
+    }
+
+    /**
+     * 
+     * PRE: ll is a valid linkedlist, panelDetails is a valid MobyUserPanel.<p>
+     * POST: All the relations of child are outputted to the MobyUserPanel panelDetails.
+     * @param ll - a linked list created via GetRelations()
+     * @param panelDetails - the MobyUserPanel to output the relationships
+     * @param child - the object that GetRelations() was called with.
+     */
+    public static String WriteToPanel(LinkedList ll, String child) {
+        //System.out.println(ll);
+        StringBuffer sb = new StringBuffer("");
+        sb.append(child + System.getProperty("line.separator") + "ISA: "
+                + System.getProperty("line.separator") + "\t");
+        String parent = (String) ll.removeFirst();
+        sb.append(parent + System.getProperty("line.separator"));
+        LinkedList llhas = (LinkedList) ll.removeFirst();
+        if (llhas != null) {
+            sb.append("Has: ");
+            Iterator i = llhas.iterator();
+            while (i.hasNext()) {
+                Pair p = MobyUtilities.ParseRelation((String) i.next());
+                if (p != null)
+                    sb.append(System.getProperty("line.separator") + "\t"
+                            + p.getAttribute() + " - " + p.getArticlename()
+                            + " ");
+            }
+            sb.append(System.getProperty("line.separator"));
+        }
+        LinkedList llhasa = (LinkedList) ll.removeFirst();
+        if (llhasa != null) {
+            sb.append("Hasa: ");
+            Iterator i = llhasa.iterator();
+            while (i.hasNext()) {
+                Pair p = MobyUtilities.ParseRelation((String) i.next());
+                if (p != null)
+                    sb.append(System.getProperty("line.separator") + "\t"
+                            + p.getAttribute() + "->" + p.getArticlename()
+                            + " ");
+            }
+        }
+        return sb.toString();
+    }
+
+    public static void main(String[] args) throws IOException {
+        LinkedList ll = MobyUtilities.GetRelations("genbank-flatfile");
+        System.out.println(ll.toString());
+        ll = MobyUtilities.GetRelations("urn:lsid:biomoby.org:objectclass:Object");
+        System.out.println(ll.toString());
+    }
+}
\ No newline at end of file

From mwilkinson at pub.open-bio.org  Tue Feb  8 11:49:16 2005
From: mwilkinson at pub.open-bio.org (Mark Wilkinson)
Date: Tue Feb  8 11:37:57 2005
Subject: [MOBY-guts] biomoby commit
Message-ID: <200502081649.j18GnGgD024562@pub.open-bio.org>


mwilkinson
Tue Feb  8 11:49:16 EST 2005
Update of /home/repository/moby/moby-live/Perl/MOBY
In directory pub.open-bio.org:/tmp/cvs-serv24543/MOBY

Modified Files:
	CommonSubs.pm 
Log Message:
thanks to Sophie for squashing this bug.  Crossreferences were not being detected if prefixed by moby: 

moby-live/Perl/MOBY CommonSubs.pm,1.58,1.59
===================================================================
RCS file: /home/repository/moby/moby-live/Perl/MOBY/CommonSubs.pm,v
retrieving revision 1.58
retrieving revision 1.59
diff -u -r1.58 -r1.59
--- /home/repository/moby/moby-live/Perl/MOBY/CommonSubs.pm	2004/12/15 17:49:44	1.58
+++ /home/repository/moby/moby-live/Perl/MOBY/CommonSubs.pm	2005/02/08 16:49:15	1.59
@@ -1617,7 +1617,7 @@
 	$ns = $xref->getAttributeNode( 'moby:namespace' ) unless $ns;
 	return undef unless $ns;
 	my $id = $xref->getAttributeNode( 'id' );
-	$id = $xref->getAttributeNode( 'moby:id' ) unless $ns;
+	$id = $xref->getAttributeNode( 'moby:id' ) unless $id;
 	return undef unless $id;
 	my $XREF = MOBY::CrossReference->new(
 										  type      => "object",

From nopushneva at pub.open-bio.org  Tue Feb  8 18:32:15 2005
From: nopushneva at pub.open-bio.org (Nina Opushneva)
Date: Tue Feb  8 18:20:54 2005
Subject: [MOBY-guts] biomoby commit
Message-ID: <200502082332.j18NWFpI026780@pub.open-bio.org>


nopushneva
Tue Feb  8 18:32:14 EST 2005
Update of /home/repository/moby/moby-live/Perl/MOBY
In directory pub.open-bio.org:/tmp/cvs-serv26754

Modified Files:
	Central.pm 
Log Message:
add the RDFagent call

moby-live/Perl/MOBY Central.pm,1.147,1.148
===================================================================
RCS file: /home/repository/moby/moby-live/Perl/MOBY/Central.pm,v
retrieving revision 1.147
retrieving revision 1.148
diff -u -r1.147 -r1.148
--- /home/repository/moby/moby-live/Perl/MOBY/Central.pm	2005/02/06 21:58:35	1.147
+++ /home/repository/moby/moby-live/Perl/MOBY/Central.pm	2005/02/08 23:32:14	1.148
@@ -1234,6 +1234,26 @@
 		 $OUTPUTS,      $SECONDARY,   $signatureURL
 	  )
 	  = &_registerServicePayload( $payload );
+
+#--------RDFagent call----------------------------------------
+
+if (defined $signatureURL){
+  my $ch = 0;
+  my $i;
+  foreach $i ($serviceName, $serviceType, $AuthURI, $contactEmail, $URL, $desc, $Category){
+       if (defined $i){
+          $ch = 1;
+        }        
+  }
+
+  if ($ch == 0){
+    my $rez = system("/export/home/nina/rdfagent/run-RDFagent ".$signatureURL);
+
+    return &_error("The RDFagent call was successful.  Report will send to you by E-mail","") if ($rez == 0);
+    return &_error("Some problem with a connection or RDF model building","") if ($rez != 0);
+  }
+}
+#---------------------------------------------------------------
 	$authoritativeService = defined( $authoritativeService ) ? 1 : 0;
 	my $error;
 	$error .= "missing serviceName \n" unless defined $serviceName;
@@ -1368,15 +1388,16 @@
 			""
 		);
 	}
-	use MOBY::Client::Central;
-	my $services         = MOBY::Client::Central::_parseServices( '', '', $si );
-	my $service_instance = shift @{$services};
-	my $storage          = new RDF::Core::Storage::Memory;
-	my $model            = new RDF::Core::Model( Storage => $storage );
-	my $RDF_MODEL = MOBY::RDF::ServiceInstanceRDF->new(
-										   model            => $model,
-										   service_instance => $service_instance );
-	my $RDF_XML = $RDF_MODEL->serialize;
+#	use MOBY::Client::Central;
+#	my $services         = MOBY::Client::Central::_parseServices( '', '', $si );
+#	my $service_instance = shift @{$services};
+#	my $storage          = new RDF::Core::Storage::Memory;
+#	my $model            = new RDF::Core::Model( Storage => $storage );
+#	my $RDF_MODEL = MOBY::RDF::ServiceInstanceRDF->new(
+										   #model            => $model,
+										   #service_instance => $service_instance );
+#	my $RDF_XML = $RDF_MODEL->serialize;
+        my $RDF_XML = "";
 	return &_success( "Registration successful",
 					  $SVC->service_instance_id, $RDF_XML );
 }
@@ -3757,4 +3778,39 @@
 	my $XSD;
 	return $XSD;
 }
+
+#=head2 runRDFagent
+
+#Title     :	runRDFagent
+#Usage     :	$MOBY->runRDFagent($inputXML)
+#Function  :	run RDFagent for signatureURL
+#Returns   :	
+#Args      :	
+      
+#inputXML  :
+#<runRDFagent>
+# <RDFfileURL>rdfFileURL</RDFfileURL>
+#</runRDFagent>
+			      
+#=cut
+		
+#sub _runRDFagent{
+		   
+# my ($self)=@_; 
+# my $Parser = new XML::DOM::Parser;
+# my $doc = $Parser->parse($payload);
+# my $Object      = $doc->getDocumentElement();
+# my $obj         = $Object->nodeName;
+# return undef unless ( $obj eq 'runRDFagent' );
+# my $url = &_nodeTextContent( $Object, "RDFfileURL" );
+# my $l = $url->getLength;
+# if ($l == 0){
+#   print "The RDFagent can't run without a parameter";
+# }else{
+#   system("/home/rdfagent/run-RDFagent"+ $url);
+#   print "The RDFagent run saccessfully. A result will sent to you by E-mail";
+# }
+										
+}
 1;
+`

From nopushneva at pub.open-bio.org  Tue Feb  8 18:43:06 2005
From: nopushneva at pub.open-bio.org (Nina Opushneva)
Date: Tue Feb  8 18:31:38 2005
Subject: [MOBY-guts] biomoby commit
Message-ID: <200502082343.j18Nh6I8026858@pub.open-bio.org>


nopushneva
Tue Feb  8 18:43:06 EST 2005
Update of /home/repository/moby/moby-live/Perl/MOBY/Client
In directory pub.open-bio.org:/tmp/cvs-serv26832

Modified Files:
	Central.pm 
Log Message:
added a check for RDFagent call, and call a new RDFbuilder

moby-live/Perl/MOBY/Client Central.pm,1.89,1.90
===================================================================
RCS file: /home/repository/moby/moby-live/Perl/MOBY/Client/Central.pm,v
retrieving revision 1.89
retrieving revision 1.90
diff -u -r1.89 -r1.90
--- /home/repository/moby/moby-live/Perl/MOBY/Client/Central.pm	2005/02/06 22:46:45	1.89
+++ /home/repository/moby/moby-live/Perl/MOBY/Client/Central.pm	2005/02/08 23:43:06	1.90
@@ -778,6 +778,36 @@
 	my $Category = lc( $a{category} );
 	chomp $Category;
 	$Category ||= "";
+
+#____________call RDFagent__________________________________________________
+if (defined $signatureURL){
+  my $ch = 0;
+  my $sign_req;
+    foreach $sign_req ($name, $type, $authURI, $email, $URL, $desc, $Category){
+      if ($sign_req ne ""){
+        $ch = 1;
+
+        }        
+    }  
+     if ($ch == 0){
+ print "call Agent\n";
+	     my $message = "
+		<registerService>
+			<Category></Category>
+			<serviceName></serviceName>
+			<serviceType></serviceType>
+			<Description></Description>
+                        <signatureURL>$signatureURL</signatureURL>
+			<URL></URL>
+			<authURI></authURI>
+			<contactEmail></contactEmail>
+	       </registerService>";		
+         my   ( $return ) = $self->_call( 'default', 'registerService', $message );
+	    return ( $self->parseRegXML( $return ) );
+
+    }
+}
+#____________________________________________________________________________________________
 	return $self->errorRegXML(
 "Only 'moby' and 'wsdl' Service Categories are currently allowed - you gave me $Category"
 	  )
@@ -798,7 +828,7 @@
 			<serviceName>$name</serviceName>
 			<serviceType>$type</serviceType>
 			<Description><![CDATA[$desc]]></Description>
-            <signatureURL>$signatureURL</signatureURL>
+                        <signatureURL>$signatureURL</signatureURL>
 			<URL>$URL</URL>
 			<authURI>$authURI</authURI>
 			<contactEmail>$email</contactEmail>";
@@ -950,7 +980,22 @@
 
 #	my $return = $self->SOAP_connection->call(registerService => ($message))->paramsall;
 	my ( $return ) = $self->_call( 'default', 'registerService', $message );
-	return ( $self->parseRegXML( $return ) );
+#	return ( $self->parseRegXML( $return ) );
+#_______call a new version RDFbuilder (by Eddie Kawas) _________________________________________
+  my $reg = $self->parseRegXML( $return );
+  if ($reg->success == 1){
+  require LWP::UserAgent;
+     
+     my $ua = LWP::UserAgent->new;
+         my $url='http://mobycentral.cbr.nrc.ca:8090/DemoServlet/forms/getSignatureResponse?domain='.$authURI.'&serviceName='.$name;
+	 
+	 my $response = $ua->get($url);
+	 my $rdf = $response->content;
+	 print "$rdf\n"; 
+}	 
+   return $reg;
+#_______________________________________________________________________________________________
+
 }
 
 =head2 registerServiceWSDL
@@ -970,6 +1015,7 @@
 
 #	my $return = $self->SOAP_connection->call(registerServiceWSDL => ($message))->paramsall;
 	my ( $return ) = $self->_call( 'default', 'registerServiceWSDL', $message );
+
 	return ( $self->parseRegXML( $return ) );
 }
 

From gordonp at pub.open-bio.org  Wed Feb  9 12:17:25 2005
From: gordonp at pub.open-bio.org (Paul Gordon)
Date: Wed Feb  9 12:06:39 2005
Subject: [MOBY-guts] biomoby commit
Message-ID: <200502091717.j19HHPY1030820@pub.open-bio.org>


gordonp
Wed Feb  9 12:17:25 EST 2005
Update of /home/repository/moby/moby-live/Java/src/main/org/biomoby/shared
In directory pub.open-bio.org:/tmp/cvs-serv30799/org/biomoby/shared

Added Files:
	MobyDataDateTime.java 
Log Message:
Utility class to deal with painful parsing and creation of ISO 8601 dates (as used by MOBY's DateTime objects)

moby-live/Java/src/main/org/biomoby/shared MobyDataDateTime.java,NONE,1.1
From gordonp at pub.open-bio.org  Wed Feb  9 12:20:38 2005
From: gordonp at pub.open-bio.org (Paul Gordon)
Date: Wed Feb  9 12:09:23 2005
Subject: [MOBY-guts] biomoby commit
Message-ID: <200502091720.j19HKcQQ030874@pub.open-bio.org>


gordonp
Wed Feb  9 12:20:38 EST 2005
Update of /home/repository/moby/moby-live/Java/src/main/org/biomoby/shared
In directory pub.open-bio.org:/tmp/cvs-serv30837/org/biomoby/shared

Modified Files:
	MobyDataFloat.java MobyDataInt.java 
	MobyDataSimpleInstance.java MobyDataString.java 
Log Message:
Updates to correct javadoc errors, plus addition of underlying object accessibility for MOBY Data Instances

moby-live/Java/src/main/org/biomoby/shared MobyDataFloat.java,1.1,1.2 MobyDataInt.java,1.1,1.2 MobyDataSimpleInstance.java,1.3,1.4 MobyDataString.java,1.1,1.2
===================================================================
RCS file: /home/repository/moby/moby-live/Java/src/main/org/biomoby/shared/MobyDataFloat.java,v
retrieving revision 1.1
retrieving revision 1.2
diff -u -r1.1 -r1.2
--- /home/repository/moby/moby-live/Java/src/main/org/biomoby/shared/MobyDataFloat.java	2004/09/03 20:28:16	1.1
+++ /home/repository/moby/moby-live/Java/src/main/org/biomoby/shared/MobyDataFloat.java	2005/02/09 17:20:38	1.2
@@ -61,6 +61,13 @@
 	return copy;
     }
 
+    /**
+     * @return a BigDecimal 
+     */
+    public Object getObject(){
+	return value;
+    }
+
     public String getValue(){
 	return ""+value;
     }

===================================================================
RCS file: /home/repository/moby/moby-live/Java/src/main/org/biomoby/shared/MobyDataInt.java,v
retrieving revision 1.1
retrieving revision 1.2
diff -u -r1.1 -r1.2
--- /home/repository/moby/moby-live/Java/src/main/org/biomoby/shared/MobyDataInt.java	2004/09/03 20:28:16	1.1
+++ /home/repository/moby/moby-live/Java/src/main/org/biomoby/shared/MobyDataInt.java	2005/02/09 17:20:38	1.2
@@ -3,10 +3,10 @@
 import java.math.*;
 
 /**
- * A class representing a MOBY Float primitive.  Note that the 
- * Float notion in MOBY does not define a specific bit precision.
- * All values in this class are stored as Java BigDecimal, which is 
- * arbitary precision to avoid loss of data integrity.
+ * A class representing a MOBY Integer primitive.  Note that the 
+ * Integer notion in MOBY does not define a specific bit precision.
+ * All values in this class are stored as Java BigInteger, which has no 
+ * minmum or maximum value, to avoid loss of data integrity.
  */
 
 public class MobyDataInt extends MobyDataSimpleInstance{
@@ -15,7 +15,8 @@
     
     /**
      * Constructor to use if the incoming value is a number object such as 
-     * Float, Double, Integer, BigDecimal, etc.
+     * Float, Double, Integer, BigInteger, BigDecimal, etc.
+     * Real numbers will be converted to their integer equivalents. 
      */
     public MobyDataInt(String articleName, Number n){
 	super(articleName);
@@ -33,7 +34,7 @@
 
     /**
      * Constructor to use if the incoming value is a primitive.
-     * If you want to pass in a float or int, cast it to a double.
+     * If you want to pass in a float or double, cast it to an int.
      */
     public MobyDataInt(String articleName, int i){
 	super(articleName);
@@ -42,10 +43,10 @@
     }
 
     /**
-     * Constructor to use if the incoming value is a string representing a number 
-     * (including mantissa/exponent format).
+     * Constructor to use if the incoming value is a string representing an integer number. 
+     * 
      *
-     * @throws NumberFormatException if the string does not represent a number
+     * @throws NumberFormatException if the string does not represent an integer number
      */
     public MobyDataInt(String articleName, String stringNumber) throws NumberFormatException{
 	super(articleName);
@@ -61,6 +62,13 @@
 	return copy;
     }
 
+    /**
+     * @return a BigInteger
+     */
+    public Object getObject(){
+	return value;
+    }
+
     public String getValue(){
 	return ""+value;
     }

===================================================================
RCS file: /home/repository/moby/moby-live/Java/src/main/org/biomoby/shared/MobyDataSimpleInstance.java,v
retrieving revision 1.3
retrieving revision 1.4
diff -u -r1.3 -r1.4
--- /home/repository/moby/moby-live/Java/src/main/org/biomoby/shared/MobyDataSimpleInstance.java	2004/09/23 10:20:29	1.3
+++ /home/repository/moby/moby-live/Java/src/main/org/biomoby/shared/MobyDataSimpleInstance.java	2005/02/09 17:20:38	1.4
@@ -132,6 +132,16 @@
     }
 
     /**
+     * Gives access to the Java object instance underlying the MobyData instance.  
+     * For example, to increment a MOBY integer object, call ((BigInteger) (data.getObject()).add(BigInteger.ONE)
+     *
+     * Not yet fully implemented for base objects whose setValue() method has been called.
+     */
+    public Object getObject(){
+	return dataValue;
+    }
+
+    /**
      * Convenience method to get the basic XML representation
      * @return the raw XML representation of the object
      */

===================================================================
RCS file: /home/repository/moby/moby-live/Java/src/main/org/biomoby/shared/MobyDataString.java,v
retrieving revision 1.1
retrieving revision 1.2
diff -u -r1.1 -r1.2
--- /home/repository/moby/moby-live/Java/src/main/org/biomoby/shared/MobyDataString.java	2004/09/03 20:28:16	1.1
+++ /home/repository/moby/moby-live/Java/src/main/org/biomoby/shared/MobyDataString.java	2005/02/09 17:20:38	1.2
@@ -3,10 +3,7 @@
 import java.math.*;
 
 /**
- * A class representing a MOBY Float primitive.  Note that the 
- * Float notion in MOBY does not define a specific bit precision.
- * All values in this class are stored as Java BigDecimal, which is 
- * arbitary precision to avoid loss of data integrity.
+ * A class representing a MOBY String primitive. 
  */
 
 public class MobyDataString extends MobyDataSimpleInstance{
@@ -44,17 +41,33 @@
 	return copy;
     }
 
+    /**
+     * @return a String
+     */
+    public Object getObject(){
+	return value;
+    }
+
     public String getValue(){
 	return value;
     }
 
+    /**
+     * This class sanitizes strings of XML escape characters such as the ampersand (&amp;) and the 
+     * less-than sign (&lt;).  WARNING: this method will not escape ampersand in the string "&amp;amp;", 
+     * or '&amp;#x26;' style character references.  We will assume that is this case you've probably 
+     * already written the string as XML. 
+     *
+     * WARNING: As of yet, we do not deal with the false escaping of strings containg already-escaped 
+     * CDATA sections!
+     */
     public String toXML(){
 	MobyNamespace[] ns = getNamespaces();
 	if(xmlMode == SERVICE_XML_MODE){
 	    String tmpValue = value;
 	    if(tmpValue != null){
 		tmpValue = tmpValue.replaceAll("<", "&lt;");
-		tmpValue = tmpValue.replaceAll("&", "&amp;");
+		tmpValue = tmpValue.replaceAll("&(?!(amp|#x\\d+);)", "&amp;");
 	    }
 	    
 	    return "<moby:String moby:namespace=\""+ 

From gordonp at pub.open-bio.org  Wed Feb  9 12:39:17 2005
From: gordonp at pub.open-bio.org (Paul Gordon)
Date: Wed Feb  9 12:27:40 2005
Subject: [MOBY-guts] biomoby commit
Message-ID: <200502091739.j19HdHEF030977@pub.open-bio.org>


gordonp
Wed Feb  9 12:39:17 EST 2005
Update of /home/repository/moby/moby-live/Java/src/main/org/biomoby/shared
In directory pub.open-bio.org:/tmp/cvs-serv30952/org/biomoby/shared

Modified Files:
	MobyPrefixResolver.java 
Log Message:
Changed attribute namespace conditional to check for both empty string and null, as different parsers can use one or the other to represent the fact that an attribute is not bound to a namespace

moby-live/Java/src/main/org/biomoby/shared MobyPrefixResolver.java,1.2,1.3
===================================================================
RCS file: /home/repository/moby/moby-live/Java/src/main/org/biomoby/shared/MobyPrefixResolver.java,v
retrieving revision 1.2
retrieving revision 1.3
diff -u -r1.2 -r1.3
--- /home/repository/moby/moby-live/Java/src/main/org/biomoby/shared/MobyPrefixResolver.java	2004/07/07 16:02:47	1.2
+++ /home/repository/moby/moby-live/Java/src/main/org/biomoby/shared/MobyPrefixResolver.java	2005/02/09 17:39:17	1.3
@@ -45,7 +45,7 @@
      */
     public static String getAttr(org.w3c.dom.Element e, String attrName){
 	String value = e.getAttributeNS(MOBY_XML_NAMESPACE, attrName);
-	if(value == null){
+	if(value == null || "".equals(value)){
 	    value = e.getAttributeNS(null, attrName);
 	}
 	return value;

From kawas at pub.open-bio.org  Wed Feb  9 13:26:41 2005
From: kawas at pub.open-bio.org (Eddie Kawas)
Date: Wed Feb  9 13:16:37 2005
Subject: [MOBY-guts] biomoby commit
Message-ID: <200502091826.j19IQfEA031153@pub.open-bio.org>


kawas
Wed Feb  9 13:26:41 EST 2005
Update of /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/gui/serviceInstanceCreationTool
In directory pub.open-bio.org:/tmp/cvs-serv31128/org/biomoby/client/gui/serviceInstanceCreationTool

Modified Files:
	MobyUtilities.java 
Log Message:
Fixed GetRelations so that it executes quickly and doesnt spin off
into infinite loops with bad input - Eddie

moby-live/Java/src/main/org/biomoby/client/gui/serviceInstanceCreationTool MobyUtilities.java,1.2,1.3
===================================================================
RCS file: /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/gui/serviceInstanceCreationTool/MobyUtilities.java,v
retrieving revision 1.2
retrieving revision 1.3
diff -u -r1.2 -r1.3
--- /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/gui/serviceInstanceCreationTool/MobyUtilities.java	2005/02/08 01:50:31	1.2
+++ /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/gui/serviceInstanceCreationTool/MobyUtilities.java	2005/02/09 18:26:41	1.3
@@ -4,6 +4,7 @@
 import java.io.IOException;
 import java.io.InputStreamReader;
 import java.net.URL;
+import java.util.ArrayList;
 import java.util.Iterator;
 import java.util.LinkedList;
 import java.util.StringTokenizer;
@@ -12,6 +13,9 @@
 
 import javax.swing.tree.TreePath;
 
+import org.biomoby.client.gui.util.MobyObjectPrimitiveExtractor;
+import org.biomoby.client.gui.util.Triples;
+
 /**
  * Utilities that are useful for retrieving information about certain objects, parsing objects, etc.
  * @author Eddie Kawas
@@ -21,12 +25,6 @@
  */
 
 public class MobyUtilities {
-    // strings that when concatenated return the attributes, articlename, etc of an object
-    final private static String URL_OBJECT = new String(
-            "http://mobycentral.cbr.nrc.ca/cgi-bin/types/Objects?name=");
-
-    final private static String URL_LSID = new String(
-            "http://mobycentral.cbr.nrc.ca/cgi-bin/types/Objects?lsid_name=");
 
     /**
      * PRE: None.<p>
@@ -40,44 +38,31 @@
     public static LinkedList GetRelations(String name) throws IOException {
         URL url = null;
         boolean isLSID = false;
-        // TODO check if name == lsid
-        Pattern p = Pattern.compile("(^urn:lsid:biomoby.org:objectclass:\\S+)",
+        Pattern p = Pattern.compile("(^urn:lsid:biomoby.org:objectclass:\\S+$)",
                 Pattern.CASE_INSENSITIVE);
         Matcher m = p.matcher(name);
         isLSID = m.matches();
+        if (isLSID) {
+            int x = name.lastIndexOf(":")+1;
+            name = name.substring(x);
+        }
 
-        if (!isLSID)
-            url = new URL(URL_OBJECT + name);
-        else
-            url = new URL(URL_LSID + name);
-        BufferedReader in = new BufferedReader(new InputStreamReader(url
-                .openStream()));
-        String input;
-        String parent = "Object";
         LinkedList llHas = new LinkedList();
         LinkedList llHasa = new LinkedList();
-
-        while ((input = in.readLine()) != null) {
-            StringTokenizer st = new StringTokenizer(input, "\t");
-            if (st.countTokens() > 2) {
-                st.nextToken(); // object name that was queried
-                StringTokenizer lsid = new StringTokenizer(st.nextToken(), ":");
-                String relation = "";
-                while (lsid.hasMoreTokens())
-                    relation = lsid.nextToken(); // isa, hasa, etc
-                if (relation.equalsIgnoreCase("isa"))
-                    parent = st.nextToken();
-                else if (relation.equalsIgnoreCase("has"))
-                    llHas.add(st.nextToken());
-                else if (relation.equalsIgnoreCase("hasa"))
-                    llHasa.add(st.nextToken());
+        MobyObjectPrimitiveExtractor mope = new MobyObjectPrimitiveExtractor();
+        ArrayList al = mope.getPrimitives(name);
+        for (Iterator x = al.iterator(); x.hasNext();) {
+            Triples t = (Triples)x.next();
+            if (t.getType() == Triples.HAS) {
+                llHas.add(t.getPrimitive());
+            }
+            if (t.getType() == Triples.HASA) {
+                llHasa.add(t.getPrimitive());
             }
         }
-        if (parent.equals("")) {
-            return null;
-        }
+        // set up the return list
         LinkedList listToReturn = new LinkedList();
-        listToReturn.addFirst(parent);
+        listToReturn.addFirst("Object");
         listToReturn.add(llHas);
         listToReturn.add(llHasa);
         return listToReturn;
@@ -172,9 +157,9 @@
     }
 
     public static void main(String[] args) throws IOException {
-        LinkedList ll = MobyUtilities.GetRelations("genbank-flatfile");
+        LinkedList ll = MobyUtilities.GetRelations("DNASequence");
         System.out.println(ll.toString());
-        ll = MobyUtilities.GetRelations("urn:lsid:biomoby.org:objectclass:Object");
+        ll = MobyUtilities.GetRelations("urn:lsid:biomoby.org:objectclass:DNASequence");
         System.out.println(ll.toString());
     }
 }
\ No newline at end of file

From nopushneva at pub.open-bio.org  Wed Feb  9 19:17:45 2005
From: nopushneva at pub.open-bio.org (Nina Opushneva)
Date: Wed Feb  9 19:06:31 2005
Subject: [MOBY-guts] biomoby commit
Message-ID: <200502100017.j1A0HjbZ032063@pub.open-bio.org>


nopushneva
Wed Feb  9 19:17:45 EST 2005
Update of /home/repository/moby/moby-live/Perl/MOBY
In directory pub.open-bio.org:/tmp/cvs-serv32037

Modified Files:
	Central.pm 
Log Message:
delete some typo

moby-live/Perl/MOBY Central.pm,1.148,1.149
===================================================================
RCS file: /home/repository/moby/moby-live/Perl/MOBY/Central.pm,v
retrieving revision 1.148
retrieving revision 1.149
diff -u -r1.148 -r1.149
--- /home/repository/moby/moby-live/Perl/MOBY/Central.pm	2005/02/08 23:32:14	1.148
+++ /home/repository/moby/moby-live/Perl/MOBY/Central.pm	2005/02/10 00:17:45	1.149
@@ -3779,38 +3779,6 @@
 	return $XSD;
 }
 
-#=head2 runRDFagent
 
-#Title     :	runRDFagent
-#Usage     :	$MOBY->runRDFagent($inputXML)
-#Function  :	run RDFagent for signatureURL
-#Returns   :	
-#Args      :	
-      
-#inputXML  :
-#<runRDFagent>
-# <RDFfileURL>rdfFileURL</RDFfileURL>
-#</runRDFagent>
-			      
-#=cut
-		
-#sub _runRDFagent{
-		   
-# my ($self)=@_; 
-# my $Parser = new XML::DOM::Parser;
-# my $doc = $Parser->parse($payload);
-# my $Object      = $doc->getDocumentElement();
-# my $obj         = $Object->nodeName;
-# return undef unless ( $obj eq 'runRDFagent' );
-# my $url = &_nodeTextContent( $Object, "RDFfileURL" );
-# my $l = $url->getLength;
-# if ($l == 0){
-#   print "The RDFagent can't run without a parameter";
-# }else{
-#   system("/home/rdfagent/run-RDFagent"+ $url);
-#   print "The RDFagent run saccessfully. A result will sent to you by E-mail";
-# }
-										
-}
 1;
-`
+

From gordonp at pub.open-bio.org  Tue Feb 15 12:47:40 2005
From: gordonp at pub.open-bio.org (Paul Gordon)
Date: Tue Feb 15 12:35:24 2005
Subject: [MOBY-guts] biomoby commit
Message-ID: <200502151747.j1FHlevD006970@pub.open-bio.org>


gordonp
Tue Feb 15 12:47:40 EST 2005
Update of /home/repository/moby/moby-live/Java/src/main/org/biomoby/client
In directory pub.open-bio.org:/tmp/cvs-serv6945

Modified Files:
	MobyRequest.java 
Log Message:
Added conveinece method to create XML envelope when you only have one input request to process

moby-live/Java/src/main/org/biomoby/client MobyRequest.java,1.6,1.7
===================================================================
RCS file: /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/MobyRequest.java,v
retrieving revision 1.6
retrieving revision 1.7
diff -u -r1.6 -r1.7
--- /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/MobyRequest.java	2005/02/03 22:37:30	1.6
+++ /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/MobyRequest.java	2005/02/15 17:47:39	1.7
@@ -543,6 +543,11 @@
 	return domDoc.getDocumentElement();
     }
 
+    public String convertMOBYDataToMOBYRequest(MobyDataInstance data, MobyDataSecondaryInstance[] secondary) throws MobyException{
+        MobyDataInstance[] mdsis = new MobyDataInstance[1];
+        mdsis[0] = data;
+        return convertMOBYDataToMOBYRequest(mdsis, secondary);
+    }
 
     /**
      * @param data the array of input parameters to put in a MOBY XML request

From kawas at pub.open-bio.org  Wed Feb 16 10:38:28 2005
From: kawas at pub.open-bio.org (Eddie Kawas)
Date: Wed Feb 16 10:26:25 2005
Subject: [MOBY-guts] biomoby commit
Message-ID: <200502161538.j1GFcSic011487@pub.open-bio.org>


kawas
Wed Feb 16 10:38:28 EST 2005
Update of /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/gui/util
In directory pub.open-bio.org:/tmp/cvs-serv11466/org/biomoby/client/gui/util

Added Files:
	MobyObjectPrimitiveExtractor.java Triples.java 
Log Message:
Adding MobyObjectPrimitiveExtractor and Triples. May be duplicating code, but are necessary to ensure that other classes compile.

moby-live/Java/src/main/org/biomoby/client/gui/util MobyObjectPrimitiveExtractor.java,NONE,1.1 Triples.java,NONE,1.1
From yanwong at pub.open-bio.org  Wed Feb 16 10:38:46 2005
From: yanwong at pub.open-bio.org (Yan Wong)
Date: Wed Feb 16 10:26:31 2005
Subject: [MOBY-guts] biomoby commit
Message-ID: <200502161538.j1GFck0o011539@pub.open-bio.org>


yanwong
Wed Feb 16 10:38:46 EST 2005
Update of /home/repository/moby/moby-live/Python/bioMoby
In directory pub.open-bio.org:/tmp/cvs-serv11495/bioMoby

Modified Files:
	mobyDataTypes.py 
Log Message:


moby-live/Python/bioMoby mobyDataTypes.py,1.14,1.15
===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/mobyDataTypes.py,v
retrieving revision 1.14
retrieving revision 1.15
diff -u -r1.14 -r1.15
--- /home/repository/moby/moby-live/Python/bioMoby/mobyDataTypes.py	2005/02/04 16:03:40	1.14
+++ /home/repository/moby/moby-live/Python/bioMoby/mobyDataTypes.py	2005/02/16 15:38:46	1.15
@@ -172,7 +172,7 @@
         
         self.content=[]
         
-        if elem.nodeName.split(":")>1:
+        if elem.nodeName.split(":")==2:
             self.__prefix__=elem.nodeName.split(":")[0]
         
         #Set the object's attributes
@@ -406,8 +406,11 @@
                     p=Parameter()
                     p.fromMoby(datum)
                     data.append(p)
-                    
-            self.queryData[queryID]=data
+            
+            if not queryID in self.queryData.keys():
+                self.queryData[queryID]=data
+            else:
+                self.queryData[str(len(self.queryData.keys())+1)]=data
     
     def __getitem__(self, key):
         """Get a query from his name

From yanwong at pub.open-bio.org  Wed Feb 16 10:38:46 2005
From: yanwong at pub.open-bio.org (Yan Wong)
Date: Wed Feb 16 10:26:54 2005
Subject: [MOBY-guts] biomoby commit
Message-ID: <200502161538.j1GFckEr011520@pub.open-bio.org>


yanwong
Wed Feb 16 10:38:46 EST 2005
Update of /home/repository/moby/moby-live/Python
In directory pub.open-bio.org:/tmp/cvs-serv11495

Modified Files:
	changelog 
Log Message:


moby-live/Python changelog,1.5,1.6
===================================================================
RCS file: /home/repository/moby/moby-live/Python/changelog,v
retrieving revision 1.5
retrieving revision 1.6
diff -u -r1.5 -r1.6
--- /home/repository/moby/moby-live/Python/changelog	2005/01/27 08:44:04	1.5
+++ /home/repository/moby/moby-live/Python/changelog	2005/02/16 15:38:46	1.6
@@ -63,3 +63,4 @@
      The objectBrowser serializes the results in a file in order to save time of retrieval :p 
 
      Some cosmetic changes on the code.
+0.8p1: Changed some code about serialization/deserialization

From yanwong at pub.open-bio.org  Thu Feb 17 08:20:38 2005
From: yanwong at pub.open-bio.org (Yan Wong)
Date: Thu Feb 17 08:11:30 2005
Subject: [MOBY-guts] biomoby commit
Message-ID: <200502171320.j1HDKcGc017174@pub.open-bio.org>


yanwong
Thu Feb 17 08:20:37 EST 2005
Update of /home/repository/moby/moby-live/Python/bioMoby
In directory pub.open-bio.org:/tmp/cvs-serv17142/bioMoby

Modified Files:
	mobyDataTypes.py 
Log Message:

Corrected a bug in Mobycontent that prevent it to fill the properties servicenotes and authority

moby-live/Python/bioMoby mobyDataTypes.py,1.15,1.16
===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/mobyDataTypes.py,v
retrieving revision 1.15
retrieving revision 1.16
diff -u -r1.15 -r1.16
--- /home/repository/moby/moby-live/Python/bioMoby/mobyDataTypes.py	2005/02/16 15:38:46	1.15
+++ /home/repository/moby/moby-live/Python/bioMoby/mobyDataTypes.py	2005/02/17 13:20:37	1.16
@@ -364,6 +364,27 @@
         if isinstance(xmlObject, str):
             doc=parseString(xmlObject)
         
+        #Get the authority
+        authnode=doc.getElementsByTagName("mobyContent")
+        
+        if not authnode:
+            authnode=doc.getElementsByTagName("moby:mobyContent")
+            
+        if authnode:
+            self.authority=authnode[0].getAttribute("authority")
+        
+        if self.authority=="":
+            self.authority=authnode[0].getAttribute("moby:authority")
+        
+        #Get the service notes
+        servicenodes=doc.getElementsByTagName("serviceNotes")
+        
+        if not servicenodes:
+            servicenodes=doc.getElementsByTagName("moby:serviceNotes")
+        
+        if servicenodes and servicenodes[0].firstChild:
+            self.servicenotes=servicenodes[0].firstChild.nodeValue
+        
         mdl=doc.getElementsByTagName('mobyData')
         
         if not mdl:

From mwilkinson at pub.open-bio.org  Fri Feb 18 10:21:03 2005
From: mwilkinson at pub.open-bio.org (Mark Wilkinson)
Date: Fri Feb 18 10:09:24 2005
Subject: [MOBY-guts] biomoby commit
Message-ID: <200502181521.j1IFL3cd026610@pub.open-bio.org>


mwilkinson
Fri Feb 18 10:21:03 EST 2005
Update of /home/repository/moby/moby-live/Perl
In directory pub.open-bio.org:/tmp/cvs-serv26591

Modified Files:
	Makefile.PL 
Log Message:
switching from XML DOM to XML LibXML in the Makefile depedencies

moby-live/Perl Makefile.PL,1.6,1.7
===================================================================
RCS file: /home/repository/moby/moby-live/Perl/Makefile.PL,v
retrieving revision 1.6
retrieving revision 1.7
diff -u -r1.6 -r1.7
--- /home/repository/moby/moby-live/Perl/Makefile.PL	2003/11/12 22:33:09	1.6
+++ /home/repository/moby/moby-live/Perl/Makefile.PL	2005/02/18 15:21:03	1.7
@@ -76,7 +76,7 @@
 	      'VERSION'	      => $VERSION, 
 	      'PREREQ_PM'     => {
               'SOAP::Lite' => 0.55,
-              'XML::DOM' => 1.42,
+              'XML::LibXML' => 1.58,
 	      }, # e.g., Module::Name => 1.1
 	      #'PM_FILTER'     => "", 
 	      ($] >= 5.005 ?    ## Add these new keywords supported since 5.005

From yanwong at pub.open-bio.org  Fri Feb 18 10:54:10 2005
From: yanwong at pub.open-bio.org (Yan Wong)
Date: Fri Feb 18 10:41:36 2005
Subject: [MOBY-guts] biomoby commit
Message-ID: <200502181554.j1IFsAvZ026720@pub.open-bio.org>


yanwong
Fri Feb 18 10:54:10 EST 2005
Update of /home/repository/moby/moby-live/Python/bioMoby
In directory pub.open-bio.org:/tmp/cvs-serv26689

Modified Files:
	mobyDataTypes.py mobyMarshal.py 
Log Message:
The code has been modified in order to implement Provision Information Block
Actually, PIB is only a set of string :

  o.__PIB__=["<Remarks author= \"an Author\">this small remark will appear in the PIB</Remarks>"]

moby-live/Python/bioMoby mobyDataTypes.py,1.16,1.17 mobyMarshal.py,1.5,1.6
===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/mobyDataTypes.py,v
retrieving revision 1.16
retrieving revision 1.17
diff -u -r1.16 -r1.17
--- /home/repository/moby/moby-live/Python/bioMoby/mobyDataTypes.py	2005/02/17 13:20:37	1.16
+++ /home/repository/moby/moby-live/Python/bioMoby/mobyDataTypes.py	2005/02/18 15:54:10	1.17
@@ -130,7 +130,9 @@
             result.append("<ProvisionInformation>")
             
             for aPIB in self.__PIB__:
-                result.append(aPIB.toMoby())
+                #Decide that a PIB will be a string where people can put its
+                #own stuff
+                result.append(str(aPIB))
                 
             result.append("</ProvisionInformation>")
         
@@ -192,6 +194,9 @@
                             anObj=MobyObject()
                             anObj.fromMoby(aCross)
                             self.__cross__.append(anObj)
+                elif child.localName=="ProvisionInformation":
+                    for aPIB in child.childNodes:
+                        self.__PIB__.append(aPIB.toxml())
                 else:
                     #Do the same for the other objects
                     associatedObjectName=child.getAttribute("moby:articleName")

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/mobyMarshal.py,v
retrieving revision 1.5
retrieving revision 1.6
diff -u -r1.5 -r1.6
--- /home/repository/moby/moby-live/Python/bioMoby/mobyMarshal.py	2005/02/04 12:58:24	1.5
+++ /home/repository/moby/moby-live/Python/bioMoby/mobyMarshal.py	2005/02/18 15:54:10	1.6
@@ -280,55 +280,13 @@
         
         typeName="GMoby%s"%str(value.localName)
         
-        from bioMoby.mobyDataTypes import MobyGeneric
+        from bioMoby.mobyDataTypes import MobyObject
         
-        NewType=type(typeName, (MobyGeneric,), {})
+        NewType=type(typeName, (MobyObject,), {})
         
         anObject=NewType()
         
-        anObject.__prefix__="moby"
-        anObject.__tag__=str(value.localName)
-        
-        for tupleAttribute in value.attributes.itemsNS():
-            #First item, second field:
-            setattr(anObject, str(tupleAttribute[0][1]), str(tupleAttribute[1]))
-        
-        i=0    
-        for elem in filter(filterFunc, value.childNodes):
-            methodName="m_%s"%str(elem.localName)
-            
-            articleName=elem.getAttribute("moby:articleName")
-            
-            if not articleName:
-                articleName=elem.getAttribute("articleName")
-            
-            if not articleName:
-                articleName="attribute_%s"%i
-            
-            if hasattr(self, methodName):
-                prop=getattr(self, methodName)(elem)
-            else:
-                prop=self.m_Object(elem)
-            
-            if hasattr(anObject, articleName):
-                t=prop
-                if not type(getattr(anObject, articleName)) is list:
-                    t=getattr(anObject, articleName)
-                    setattr(anObject, articleName, [])
-                getattr(anObject, articleName).append(t)
-            else:
-                setattr(anObject, articleName, prop)
-            i+=1
-        
-        content=[]
-        
-        isContentNode= lambda x: x.nodeType==x.TEXT_NODE or x.nodeType==x.CDATA_SECTION_NODE
-        
-        for elem in filter(isContentNode, value.childNodes):
-            content.append(str(elem.nodeValue))
-        
-        if content:
-            anObject.content(r"".join(content))
+        anObject.fromMoby(value)
         
         return anObject
 

From yanwong at pub.open-bio.org  Fri Feb 18 10:58:21 2005
From: yanwong at pub.open-bio.org (Yan Wong)
Date: Fri Feb 18 10:45:49 2005
Subject: [MOBY-guts] biomoby commit
Message-ID: <200502181558.j1IFwL3R026773@pub.open-bio.org>


yanwong
Fri Feb 18 10:58:21 EST 2005
Update of /home/repository/moby/moby-live/Python
In directory pub.open-bio.org:/tmp/cvs-serv26740

Modified Files:
	PKG-INFO README changelog 
Log Message:
Implementation of the PIB

moby-live/Python PKG-INFO,1.5,1.6 README,1.4,1.5 changelog,1.6,1.7
===================================================================
RCS file: /home/repository/moby/moby-live/Python/PKG-INFO,v
retrieving revision 1.5
retrieving revision 1.6
diff -u -r1.5 -r1.6
--- /home/repository/moby/moby-live/Python/PKG-INFO	2005/01/27 08:44:04	1.5
+++ /home/repository/moby/moby-live/Python/PKG-INFO	2005/02/18 15:58:21	1.6
@@ -1,6 +1,6 @@
 Metadata-Version: 1.0
 Name: bioMoby
-Version: 0.8
+Version: 0.9
 Summary: Python interface for bioMoby
 Home-page: http://bioserv.rpbs.jussieu.fr
 Author: Yan Wong

===================================================================
RCS file: /home/repository/moby/moby-live/Python/README,v
retrieving revision 1.4
retrieving revision 1.5
diff -u -r1.4 -r1.5
--- /home/repository/moby/moby-live/Python/README	2004/12/08 14:57:28	1.4
+++ /home/repository/moby/moby-live/Python/README	2005/02/18 15:58:21	1.5
@@ -49,5 +49,5 @@
 +tutorials: Some scripts in order to show some of the functions
 +webservice: Example of webservice in Python using bioMoby-python's API
 +utils: moby2python is a program that convert mobyObject definitions into Python files (all derived from MobyObject and has a personalized fromMoby method)
-+ZSI-1.5.0-patched: the patched version of ZSI 1.5.0 
++ZSI-1.6.0 
 Suggestions welcome!

===================================================================
RCS file: /home/repository/moby/moby-live/Python/changelog,v
retrieving revision 1.6
retrieving revision 1.7
diff -u -r1.6 -r1.7
--- /home/repository/moby/moby-live/Python/changelog	2005/02/16 15:38:46	1.6
+++ /home/repository/moby/moby-live/Python/changelog	2005/02/18 15:58:21	1.7
@@ -63,4 +63,7 @@
      The objectBrowser serializes the results in a file in order to save time of retrieval :p 
 
      Some cosmetic changes on the code.
+
 0.8p1: Changed some code about serialization/deserialization
+
+0.9: PIB implemented as a set of string in the __PIB__ field

From kawas at pub.open-bio.org  Wed Feb 23 10:39:07 2005
From: kawas at pub.open-bio.org (Eddie Kawas)
Date: Wed Feb 23 10:26:03 2005
Subject: [MOBY-guts] biomoby commit
Message-ID: <200502231539.j1NFd7HO027915@pub.open-bio.org>


kawas
Wed Feb 23 10:39:06 EST 2005
Update of /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/gui/serviceInstanceCreationTool
In directory pub.open-bio.org:/tmp/cvs-serv27890/org/biomoby/client/gui/serviceInstanceCreationTool

Modified Files:
	MobyUtilities.java 
Log Message:
Fixed imports and removed getRelations() - see getPrimitives(...)
in MobyObjectPrimitiveExtractor instead.
Eddie

moby-live/Java/src/main/org/biomoby/client/gui/serviceInstanceCreationTool MobyUtilities.java,1.3,1.4
===================================================================
RCS file: /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/gui/serviceInstanceCreationTool/MobyUtilities.java,v
retrieving revision 1.3
retrieving revision 1.4
diff -u -r1.3 -r1.4
--- /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/gui/serviceInstanceCreationTool/MobyUtilities.java	2005/02/09 18:26:41	1.3
+++ /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/gui/serviceInstanceCreationTool/MobyUtilities.java	2005/02/23 15:39:06	1.4
@@ -1,21 +1,11 @@
 package org.biomoby.client.gui.serviceInstanceCreationTool;
 
-import java.io.BufferedReader;
 import java.io.IOException;
-import java.io.InputStreamReader;
-import java.net.URL;
-import java.util.ArrayList;
 import java.util.Iterator;
 import java.util.LinkedList;
-import java.util.StringTokenizer;
-import java.util.regex.Matcher;
-import java.util.regex.Pattern;
 
 import javax.swing.tree.TreePath;
 
-import org.biomoby.client.gui.util.MobyObjectPrimitiveExtractor;
-import org.biomoby.client.gui.util.Triples;
-
 /**
  * Utilities that are useful for retrieving information about certain objects, parsing objects, etc.
  * @author Eddie Kawas
@@ -27,45 +17,11 @@
 public class MobyUtilities {
 
     /**
-     * PRE: None.<p>
-     * POST: a linked list of all the relations is returned, such that:<p>
-     * => The first item in the list is a string representation of the parent<p>
-     * => The second item is a linked list of all the 'HAS' container relationships<p>
-     * => The third item is a linked list of all the 'HASA' container relationships
-     * @param name, the name of the object to query for - can be an Moby Object LSID.
-     * @return returns a linked list {String, LinkedList, LinkedList} of relationships
+     * @deprecated please see MobyObjectPrimitiveExtractor.java
      */
     public static LinkedList GetRelations(String name) throws IOException {
-        URL url = null;
-        boolean isLSID = false;
-        Pattern p = Pattern.compile("(^urn:lsid:biomoby.org:objectclass:\\S+$)",
-                Pattern.CASE_INSENSITIVE);
-        Matcher m = p.matcher(name);
-        isLSID = m.matches();
-        if (isLSID) {
-            int x = name.lastIndexOf(":")+1;
-            name = name.substring(x);
-        }
-
-        LinkedList llHas = new LinkedList();
-        LinkedList llHasa = new LinkedList();
-        MobyObjectPrimitiveExtractor mope = new MobyObjectPrimitiveExtractor();
-        ArrayList al = mope.getPrimitives(name);
-        for (Iterator x = al.iterator(); x.hasNext();) {
-            Triples t = (Triples)x.next();
-            if (t.getType() == Triples.HAS) {
-                llHas.add(t.getPrimitive());
-            }
-            if (t.getType() == Triples.HASA) {
-                llHasa.add(t.getPrimitive());
-            }
-        }
-        // set up the return list
-        LinkedList listToReturn = new LinkedList();
-        listToReturn.addFirst("Object");
-        listToReturn.add(llHas);
-        listToReturn.add(llHasa);
-        return listToReturn;
+        
+        return new LinkedList();
     }
 
     /**

From kawas at pub.open-bio.org  Wed Feb 23 10:41:03 2005
From: kawas at pub.open-bio.org (Eddie Kawas)
Date: Wed Feb 23 10:28:05 2005
Subject: [MOBY-guts] biomoby commit
Message-ID: <200502231541.j1NFf3iM028054@pub.open-bio.org>


kawas
Wed Feb 23 10:41:03 EST 2005
Update of /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/gui/util
In directory pub.open-bio.org:/tmp/cvs-serv28029/org/biomoby/client/gui/util

Modified Files:
	MobyObjectPrimitiveExtractor.java 
Log Message:
Corrected the use of Dom from JDOM to w3c DOM to make class compatible
with other jMoby classes.
Eddie

moby-live/Java/src/main/org/biomoby/client/gui/util MobyObjectPrimitiveExtractor.java,1.1,1.2
===================================================================
RCS file: /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/gui/util/MobyObjectPrimitiveExtractor.java,v
retrieving revision 1.1
retrieving revision 1.2
diff -u -r1.1 -r1.2
--- /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/gui/util/MobyObjectPrimitiveExtractor.java	2005/02/16 15:38:28	1.1
+++ /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/gui/util/MobyObjectPrimitiveExtractor.java	2005/02/23 15:41:03	1.2
@@ -5,60 +5,91 @@
 package org.biomoby.client.gui.util;
 
 import java.io.BufferedReader;
-import java.io.ByteArrayInputStream;
 import java.io.ByteArrayOutputStream;
 import java.io.IOException;
 import java.io.InputStreamReader;
+import java.io.OutputStream;
+import java.io.StringReader;
 import java.net.MalformedURLException;
 import java.net.URL;
 import java.util.ArrayList;
 import java.util.Iterator;
-import java.util.List;
 
+import javax.xml.parsers.DocumentBuilder;
+import javax.xml.parsers.DocumentBuilderFactory;
 import javax.xml.parsers.ParserConfigurationException;
+import javax.xml.transform.Transformer;
+import javax.xml.transform.TransformerConfigurationException;
+import javax.xml.transform.TransformerException;
+import javax.xml.transform.TransformerFactory;
+import javax.xml.transform.dom.DOMSource;
+import javax.xml.transform.stream.StreamResult;
 
-import org.jdom.Attribute;
-import org.jdom.Document;
-import org.jdom.Element;
-import org.jdom.JDOMException;
-import org.jdom.Namespace;
-import org.jdom.input.SAXBuilder;
+import org.biomoby.shared.MobyDataFloat;
+import org.biomoby.shared.MobyDataInt;
+import org.biomoby.shared.MobyDataSimpleInstance;
+import org.biomoby.shared.MobyDataString;
+import org.biomoby.shared.MobyDataType;
+import org.jdom.input.DOMBuilder;
 import org.jdom.output.Format;
 import org.jdom.output.XMLOutputter;
+import org.w3c.dom.Document;
+import org.w3c.dom.Element;
+import org.w3c.dom.Node;
+import org.w3c.dom.NodeList;
+import org.xml.sax.InputSource;
 import org.xml.sax.SAXException;
 
-import com.hp.hpl.jena.vocabulary.RDF;
-import com.hp.hpl.jena.vocabulary.RDFS;
-
 /**
  * @author Eddie Kawas
- * <p>Created for
  * <p>This class was created to ...
  * <p>For questions, comments, or bugs
  * <p>email me at edward.kawas@gmail.com
  */
 public class MobyObjectPrimitiveExtractor {
     final private static String URL_OBJECT = new String(
-    	"http://mobycentral.cbr.nrc.ca:8090/authority/metadata?lsid=");
-    final static Namespace HAS = Namespace.getNamespace("has","http://biomoby.org/RESOURCES/MOBY-S/Predicates#");
-    final static Namespace HASA = Namespace.getNamespace("hasa","http://biomoby.org/RESOURCES/MOBY-S/Predicates#");
-    final static Namespace ARTICLE = Namespace.getNamespace("articleName","http://biomoby.org/RESOURCES/MOBY-S/Predicates#");
-    final static String[] PRIMITIVES = {"String", "Float", "Integer", "Object", "DateTime"};
+            "http://mobycentral.cbr.nrc.ca:8090/authority/metadata?lsid=");
+
+    final static String[] PRIMITIVES = {
+            "String",
+            "Float",
+            "Integer",
+            "Object",
+            "DateTime" };
+
+    final static String MOBY = "http://www.biomoby.org/moby";
+
+    /**
+     *  
+     * <b>PRE:</b><p>
+     * <b>POST:</b><p>
+     * @param MobyElement - The Element containing the MOBY Object to find primitives for
+     * @return an array of MobyDataSimpleInstances that are the primitives for MobyElement.
+     */
+    public MobyDataSimpleInstance[] getPrimitives(Element MobyElement) {
+        return getPrimitivesHelper(MobyElement.getTagName());
+    }
+
     /**
      *  
      * <b>PRE:</b><p>
      * <b>POST:</b><p>
-     * @param name - name of the Moby Object to decompose
-     * @return Triples[] - an array of Triples or null if an error occured
-     * @throws ParserConfigurationException
-     * @throws IOException
-     * @throws SAXException
+     * @param Object - The object to find primitives for
+     * @return an array of MobyDataSimpleInstances that are the primitives for Object.
+     */
+    public MobyDataSimpleInstance[] getPrimitives(String object) {
+        return getPrimitivesHelper(object);
+    }
+
+    /*
+     * getPrimitives helper.
      */
-    public ArrayList getPrimitives(String name) {
+    private MobyDataSimpleInstance[] getPrimitivesHelper(String name) {
         ArrayList list = new ArrayList();
         if (isPrimitive(name)) {
-            list.add(new Triples(name, name, Triples.HASA));
-            return list;
+            MobyDataSimpleInstance mdsi = new MobyDataSimpleInstance("");
+            mdsi.setDataType(new MobyDataType(name));
+            return new MobyDataSimpleInstance[] { mdsi };
         }
         String lsid = "urn:lsid:biomoby.org:objectclass:" + name;
         String rdf = getObjectRDF(lsid);
@@ -69,121 +100,130 @@
         // create a DOM document
         Document doc = getDOMDocument(rdf);
         // start parsing
-        List rdfsClassList = doc.getRootElement().getContent();
-        Iterator it = rdfsClassList.iterator();
-        while (it.hasNext()) {
-            Object obj = it.next();
-            Element hasa = null, has = null;
-            if (obj instanceof Element) {
-                Element classElement = (Element) obj;
-                // set up appropriate iterators
-                Iterator hasIterator = classElement.getChildren("has", HAS).iterator();
-                Iterator hasaIterator = classElement.getChildren("hasa",HASA).iterator();
-                Iterator subClassIterator = classElement.getChildren("subClassOf", Namespace.getNamespace(RDFS.getURI())).iterator();
-                // iterate through the lists
-                while (hasIterator.hasNext()) {
-                    Element hasElement = (Element) hasIterator.next();
-                    List hasInnerElementList = hasElement.getChildren();
-                    if (!hasInnerElementList.isEmpty()) {
-                        Element mobyObject = (Element) hasInnerElementList.get(0);
-                        String primitive = mobyObject.getName();
-                        int type = Triples.HAS;
-                        String articleName = mobyObject.getChildText("articleName", ARTICLE);
-                        // check if primitive is a primitive
-                        if (isPrimitive(primitive)) {
-                            Triples t =  new Triples(articleName, primitive, type);
-                            list.add(t);
-                        } else {
-                            // recurse
-                            ArrayList recurse = getPrimitives(primitive);
-                            if (recurse == null) {
-                                return null;
-                            }
-                            processRecursionList(list, recurse);
+        Element root = doc.getDocumentElement();
+        NodeList rdfsClassList = root.getElementsByTagName("rdfs:Class");
+        for (int x = 0; x < rdfsClassList.getLength(); x++) {
+            // process each class:
+            Element _class = ((Element) rdfsClassList.item(x));
+            NodeList has = _class.getElementsByTagName("mobyPred:has");
+            NodeList hasa = _class.getElementsByTagName("mobyPred:hasa");
+            // subClassOf can contain attributes or just an element
+            NodeList subClassOf = _class
+                    .getElementsByTagName("rdfs:subClassOf");
+            for (int i = 0; i < has.getLength(); i++) {
+                NodeList children = ((Element) has.item(i)).getChildNodes();
+                for (int j = 0; j < children.getLength(); j++) {
+                    if (!(children.item(j) instanceof Element))
+                        continue;
+                    Element child = (Element) children.item(j);
+                    Node articleNode = child.getElementsByTagName(
+                            "mobyPred:articleName").item(0);
+                    String localName = child.getLocalName();
+                    String articleName = (articleNode == null) ? ""
+                            : articleNode.getTextContent();
+                    //                  TODO - recurse if object is not a primitive
+                    if (isPrimitive(localName)) {
+                        MobyDataSimpleInstance mdsi = createPrimitiveType(localName, articleName);
+                        list.add(mdsi);
+                    } else {
+                        MobyDataSimpleInstance[] recurseArray = getPrimitives(localName);
+                        for (int k = 0; k < recurseArray.length; k++) {
+                            list.add(recurseArray[k]);
                         }
                     }
                 }
-                hasIterator = null;
-                while (hasaIterator.hasNext()) {
-                    Element hasaElement = (Element) hasaIterator.next();
-                    List hasaInnerElementList = hasaElement.getChildren();
-                    if (!hasaInnerElementList.isEmpty()) {
-                        Element mobyObject = (Element) hasaInnerElementList.get(0);
-                        String primitive = mobyObject.getName();
-                        int type = Triples.HASA;
-                        String articleName = mobyObject.getChildText("articleName", ARTICLE);
-                        // check if primitive is a primitive
-                        if (isPrimitive(primitive)) {
-                            Triples t =  new Triples(articleName, primitive, type);
-                            list.add(t);
+            }
+            for (int i = 0; i < hasa.getLength(); i++) {
+                NodeList children = ((Element) hasa.item(i)).getChildNodes();
+                for (int j = 0; j < children.getLength(); j++) {
+                    if (children.item(j) instanceof Element) {
+                        Element child = (Element) children.item(j);
+                        Node articleNode = child.getElementsByTagName(
+                                "mobyPred:articleName").item(0);
+                        String localName = child.getLocalName();
+                        String articleName = (articleNode == null) ? ""
+                                : articleNode.getTextContent();
+                        //                      TODO - recurse if object is not a primitive
+                        if (isPrimitive(localName)) {
+                            MobyDataSimpleInstance mdsi = createPrimitiveType(localName, articleName);
+                            list.add(mdsi);
                         } else {
-                            // recurse
-                            ArrayList recurse = getPrimitives(primitive);
-                            if (recurse == null) {
-                                return null;
+                            MobyDataSimpleInstance[] recurseArray = getPrimitives(localName);
+                            for (int k = 0; k < recurseArray.length; k++) {
+                                list.add(recurseArray[k]);
                             }
-                            processRecursionList(list, recurse);
                         }
                     }
                 }
-                hasaIterator = null;
-                /*
-                 * iterate through subClassOf
-                 * checking to see if the object is
-                 * a subclass of a primitive
-                 */
-                while (subClassIterator.hasNext()) {
-                    Element sub = (Element)subClassIterator.next();
-                    
-                    // check if we have an element called Class
-                    Element rdfsClass = sub.getChild("Class", Namespace.getNamespace(RDFS.getURI()));
-                    if (rdfsClass != null) {
-                        // get the rdf:about attribute
-                        String attr = rdfsClass.getAttributeValue("about", Namespace.getNamespace(RDF.getURI()));
-                        if (attr != null) {
-                            // i.e. http://biomoby.org/RESOURCES/MOBY-S/Objects#text-plain
-                            if (attr.indexOf("#") > 0) {
-                                attr = attr.substring(attr.indexOf("#")+1);
-                            }
-                            if (isPrimitive(attr)&& !attr.equals("Object")) {
-                                // assume if you are something, it means you have it (singular)
-                                Triples t =  new Triples(name, attr, Triples.HASA);
-                                list.add(t);
-                            }
-                        }
+            }
+
+            for (int i = 0; i < subClassOf.getLength(); i++) {
+                Element subClass = (Element) subClassOf.item(i);
+                // check for attributes
+                if (subClass.hasAttributes()) {
+                    String object = subClass.getAttribute("rdf:resource");
+                    if (object.indexOf("#") > 0) {
+                        object = object.substring(object.indexOf("#") + 1);
                     }
-                    /* process <rdfs:subClassOf rdf:resource="..."/> */
-                    String attr = sub.getAttributeValue("resource", Namespace.getNamespace(RDF.getURI()));
-                    if (attr != null) {
-                        if (attr.indexOf("#") > 0) {
-                            attr = attr.substring(attr.indexOf("#") + 1);
-                        }
-                        if (isPrimitive(attr) && !attr.equals("Object")) {
-                            // assume if you are something, it means you have it (singular)
-                            Triples t = new Triples(name, attr, Triples.HASA);
-                            list.add(t);
-                        }
+                    if (isPrimitive(object) && !object.equals("Object")) {
+                        MobyDataSimpleInstance mdsi = new MobyDataSimpleInstance(
+                                object);
+                        mdsi.setDataType(new MobyDataType(object));
+                        list.add(mdsi);
+                    }
+                } else {
+                    String object = ((Element) ((Element) subClass)
+                            .getElementsByTagName("rdfs:Class").item(0))
+                            .getAttribute("rdf:about");
+                    if (object.indexOf("#") > 0) {
+                        object = object.substring(object.indexOf("#") + 1);
+                    }
+                    if (isPrimitive(object) && !object.equals("Object")) {
+                        MobyDataSimpleInstance mdsi = new MobyDataSimpleInstance(
+                                object);
+                        mdsi.setDataType(new MobyDataType(object));
+                        list.add(mdsi);
                     }
                 }
+
             }
         }
-        
-        return list;
+
+        return convertArrayList(list);
     }
-    
-    private void processRecursionList(ArrayList list, ArrayList recurse) {
-        for (Iterator x = recurse.iterator(); x.hasNext();) {
-            Triples t = (Triples) x.next();
-            list.add(t);
+
+
+    /*
+     * method to create default DataTypes.
+     */
+    private MobyDataSimpleInstance createPrimitiveType(String localName, String articleName) {
+        if (localName.equalsIgnoreCase("Float")) {
+            return new MobyDataFloat(articleName, 0.0);
+        } else if (localName.equalsIgnoreCase("String")) {
+            return new MobyDataString(articleName, "");
+        } else if (localName.equalsIgnoreCase("Integer")) {
+            return new MobyDataInt(articleName, 0);
+        } else if(localName.equalsIgnoreCase("DateTime")) {
+            MobyDataSimpleInstance mdsi = new MobyDataSimpleInstance(articleName);
+            mdsi.setDataType(new MobyDataType(localName));
+            return mdsi;
         }
+        // error
+        return null;
     }
 
-    /**
-     *  
-     * <b>PRE:</b><p>
-     * <b>POST:</b><p>
-     * @param test - the test Moby object name to test with
-     * @return true if test is a primitive, false otherwise
+    private MobyDataSimpleInstance[] convertArrayList(ArrayList list) {
+        int size = list.size();
+        MobyDataSimpleInstance[] mdsi = new MobyDataSimpleInstance[size];
+        size = 0;
+        for (Iterator x = list.iterator(); x.hasNext(); size++) {
+            mdsi[size] = (MobyDataSimpleInstance) x.next();
+        }
+        return mdsi;
+    }
+
+    /*
+     * simply tests whether a string is a primitive
      */
     private boolean isPrimitive(String test) {
         for (int x = 0; x < PRIMITIVES.length; x++) {
@@ -192,94 +232,106 @@
         }
         return false;
     }
+
     /*
      * given an xml string, create a DOM document
      */
     private Document getDOMDocument(String rdfXML) {
-        // start creating the triples
-        SAXBuilder builder = new SAXBuilder();
-        Document doc = null;
         try {
-            // Create the document
-            doc = builder.build(new ByteArrayInputStream(rdfXML.getBytes()));
-        } catch (JDOMException e) {
-            System.err.println("Error in getPrimitives:1 - JDOMException.\n" + e.getMessage());
-            return null;
-        } catch (IOException e) {
-            System.err.println("Error in getPrimitives:2 - IOException.\n"+ e.getMessage());
-            return null;
-        }
-        return doc;
+            // Create a builder factory
+            DocumentBuilderFactory factory = DocumentBuilderFactory
+                    .newInstance();
+            factory.setNamespaceAware(true);
+            // Create the builder and parse the file
+            Document doc = factory.newDocumentBuilder().parse(
+                    new InputSource(new StringReader(rdfXML)));
+            return doc;
+        } catch (SAXException e) {
+            // A parsing error occurred; the xml input is not valid
+        } catch (ParserConfigurationException e) {} catch (IOException e) {}
+        return null;
     }
-    
+
     /*
      * given an lsdi, get the moby object rdf document
      */
     private String getObjectRDF(String lsid) {
         URL url;
         try {
-            url = new URL(URL_OBJECT+lsid);
+            url = new URL(URL_OBJECT + lsid);
         } catch (MalformedURLException e) {
-            System.err.println("Error in getObjectRDF:1 - MalformedURLException.");
+            System.err
+                    .println("Error in getObjectRDF:1 - MalformedURLException.");
             return null;
         }
         BufferedReader in = null;
         try {
             in = new BufferedReader(new InputStreamReader(url.openStream()));
         } catch (IOException e1) {
-            System.err.println("Error in getObjectRDF:2 - IOException. \n- Can't read from URL");
+            System.err
+                    .println("Error in getObjectRDF:2 - IOException. \n- Can't read from URL");
             return null;
         }
         String input;
         StringBuffer sb = new StringBuffer();
         try {
             while ((input = in.readLine()) != null) {
-                sb.append(input+System.getProperty("line.separator"));
+                sb.append(input + System.getProperty("line.separator"));
             }
         } catch (IOException e2) {
-            System.err.println("Error in getObjectRDF:3 - IOException.\n-Problems reading from URL");
+            System.err
+                    .println("Error in getObjectRDF:3 - IOException.\n-Problems reading from URL");
             return null;
         }
 
         return sb.toString();
     }
-    
+
     /**
      *  
      * <b>PRE:</b> Object is a valid Moby Object<p>
      * <b>POST:</b> An element representing the moby class structure is created.</br>>
      * @link http://www.biomoby.org/twiki/bin//view/Moby/MobySAPI#ObjectStructure
      * @param object - the Moby object to create a structure for
-     * @param triples - the primitives in Triples format to add to this structure 
-     * @return an Element representing the Moby Class Structure
+     * @param mdsi - an array of MobyDataSimpleInstances to add to the element 
+     * @return an Element representing the Moby Class Structure containing the MobyDataSimpleInstances
      */
-    public Element getElementContainingTriples(String object, ArrayList triples) {
+    public Element getElementContainingPrimitives(String object,
+            MobyDataSimpleInstance[] mdsi) {
         /*
-<moby:GenericSequence namespace='AGI_LocusCode' id='At2g42410'>   
-	<CrossReference>    
-		<Object namespace='Global_Keyword' id='superman'/> 
-	</CrossReference>
-	<moby:Integer namespace='' id='' articleName='Length'>214</moby:Integer> 
-	<moby:String namespace='' id=''articleName='SequenceString'>MKRTHLASFSNRDKTRLGYL</moby:String>
-</moby:GenericSequence>
+         <moby:GenericSequence namespace='AGI_LocusCode' id='At2g42410'>   
+         <CrossReference>    
+         <Object namespace='Global_Keyword' id='superman'/> 
+         </CrossReference>
+         <moby:Integer namespace='' id='' articleName='Length'>214</moby:Integer> 
+         <moby:String namespace='' id=''articleName='SequenceString'>MKRTHLASFSNRDKTRLGYL</moby:String>
+         </moby:GenericSequence>
          */
         /*root element*/
         Element root = null;
-        Namespace ns = Namespace.getNamespace("moby", "http://www.biomoby.org/moby");
-        root = new Element(object);
-        root.setNamespace(ns);
-        
+        Document doc = createDomDocument();
+        root = doc.createElementNS(MOBY, object);
         /*iterate through triples, create elements and add to root*/
-        Iterator it = triples.iterator();
-        while (it.hasNext()) {
-            Triples t = (Triples)it.next();
-            Element e = new Element(t.getPrimitive(), ns);
-            e.setAttribute(new Attribute("id", ""));
-            e.setAttribute(new Attribute("articleName", t.getArticleName()));
-            root.addContent(e);
+        for (int x = 0; x < mdsi.length; x++) {
+            MobyDataSimpleInstance mds = mdsi[x];
+            Element e = doc.createElementNS(MOBY, mds.getDataType().getName());
+            e.setAttribute("id", "");
+            e.setAttribute("articleName", mds.getName());
+            root.appendChild(e);
         }
         return root;
     }
+
+    private Document createDomDocument() {
+        try {
+            DocumentBuilder builder = DocumentBuilderFactory.newInstance()
+                    .newDocumentBuilder();
+            Document doc = builder.newDocument();
+            return doc;
+        } catch (ParserConfigurationException e) {}
+        return null;
+    }
+
     /**
      *  
      * <b>PRE:</b>Element e exists and Class, namespace, and id are valid.<p>
@@ -290,30 +342,33 @@
      * @param id - the identifier within that namespace that specifies the precise resource represented in the object
      * @return Element - the root element containing the CRIB just added.
      */
-    public Element addCrossReferenceToElement(Element e, String Class, String namespace, String id) {
+    public Element addCrossReferenceToElement(Element e, String Class,
+            String namespace, String id) {
         /* first make sure that the element doesnt already contain
          * the CrossReference child
          */
-        Iterator it = e.getChildren("CrossReference").iterator();
+        NodeList it = e.getElementsByTagName("CrossReference");
         Element cross = null;
-        if (it.hasNext()) {
+        if (it.getLength() > 0) {
             /*There is a pre-existing tag*/
-            cross = (Element)it.next();
-            Element object = new Element(Class);
-            object.setAttribute(new Attribute("namespace", namespace));
-            object.setAttribute(new Attribute("id", id));
-            cross.addContent(object);
+            cross = (Element) it.item(0);
+            Document doc = createDomDocument();
+            Element object = doc.createElement(Class);
+            object.setAttribute("namespace", namespace);
+            object.setAttribute("id", id);
+            cross.appendChild(object);
         } else {
-            cross = new Element ("CrossReference");
-            Element object = new Element(Class);
-            object.setAttribute(new Attribute("namespace", namespace));
-            object.setAttribute(new Attribute("id", id));
-            cross.addContent(object);
-            e.addContent(cross);
+            Document doc = e.getOwnerDocument();
+            Element object = doc.createElement(Class);
+            cross = doc.createElement("CrossReference");
+            object.setAttribute("namespace", namespace);
+            object.setAttribute("id", id);
+            cross.appendChild(object);
+            e.appendChild(cross);
         }
         return e;
     }
-    
+
     /**
      *  
      * <b>PRE:</b><p>
@@ -328,49 +383,55 @@
      * @param description - this is the textual content of the XML element, and contains a human-readable description of the intended interpretation of this cross-reference.
      * @return - the root object Element with the Xref cross reference added to it.
      */
-    public Element addXrefCrossReferenceToElement(Element e, String id, String namespace, String authURI, String serviceName, String evidenceCode, String XrefType, String description) {
+
+    public Element addXrefCrossReferenceToElement(Element e, String id,
+            String namespace, String authURI, String serviceName,
+            String evidenceCode, String XrefType, String description) {
         /*
          * everything is required other than description
          */
-        if (namespace == null || id == null || authURI == null || serviceName == null || evidenceCode == null || XrefType == null)
+        if (namespace == null || id == null || authURI == null
+                || serviceName == null || evidenceCode == null
+                || XrefType == null)
             return e;
         /* 
          * make sure that the element doesnt already contain
          * the CrossReference child
          */
-        Iterator it = e.getChildren("CrossReference").iterator();
+        NodeList it = e.getElementsByTagName("CrossReference");
         Element cross = null;
-        if (it.hasNext()) {
+        if (it.getLength() > 0) {
+            Document doc = e.getOwnerDocument();
             /*There is a pre-existing tag*/
-            cross = (Element)it.next();
-            Element object = new Element("Xref");
-            object.setAttribute(new Attribute("namespace", namespace));
-            object.setAttribute(new Attribute("id", id));
-            object.setAttribute(new Attribute("authURI", authURI));
-            object.setAttribute(new Attribute("serviceName", serviceName));
-            object.setAttribute(new Attribute("evidenceCode", evidenceCode));
-            object.setAttribute(new Attribute("XrefType", XrefType));
+            cross = (Element) it.item(0);
+            Element object = doc.createElement("Xref");
+            object.setAttribute("namespace", namespace);
+            object.setAttribute("id", id);
+            object.setAttribute("authURI", authURI);
+            object.setAttribute("serviceName", serviceName);
+            object.setAttribute("evidenceCode", evidenceCode);
+            object.setAttribute("XrefType", XrefType);
             if (description != null)
-                object.setText(description);
-            cross.addContent(object);
+                object.setNodeValue(description);
+            cross.appendChild(object);
         } else {
-            cross = new Element ("CrossReference");
-            Element object = new Element("Xref");
-            object.setAttribute(new Attribute("namespace", namespace));
-            object.setAttribute(new Attribute("id", id));
-            object.setAttribute(new Attribute("authURI", authURI));
-            object.setAttribute(new Attribute("serviceName", serviceName));
-            object.setAttribute(new Attribute("evidenceCode", evidenceCode));
-            object.setAttribute(new Attribute("XrefType", XrefType));
+            Document doc = e.getOwnerDocument();
+            cross = doc.createElement("CrossReference");
+            Element object = doc.createElement("Xref");
+            object.setAttribute("namespace", namespace);
+            object.setAttribute("id", id);
+            object.setAttribute("authURI", authURI);
+            object.setAttribute("serviceName", serviceName);
+            object.setAttribute("evidenceCode", evidenceCode);
+            object.setAttribute("XrefType", XrefType);
             if (description != null)
-                object.setText(description);
-            cross.addContent(object);
-            e.addContent(cross);
+                object.setNodeValue(description);
+            cross.appendChild(object);
+            e.appendChild(cross);
         }
         return e;
     }
-    
-    
+
     /**
      *  
      * <b>PRE:</b><p>
@@ -381,27 +442,30 @@
      */
     /*
      * <ProvisionInformation>
-              ... one or more of the provision elements (below) ...
-       </ProvisionInformation>
-       
-       <serviceSoftware software_name="" software_version="" software_comment=""/>
-       <serviceDatabase database_name="" database_version="" database_comment=""/>
-       <serviceComment>comment here</serviceComment>
+     ... one or more of the provision elements (below) ...
+     </ProvisionInformation>
+     
+     <serviceSoftware software_name="" software_version="" software_comment=""/>
+     <serviceDatabase database_name="" database_version="" database_comment=""/>
+     <serviceComment>comment here</serviceComment>
      */
-    public Element addProvisionInformationBlock(Element root, Element[] elements){
+    public Element addProvisionInformationBlock(Element root, Element[] elements) {
         if (elements == null || root == null || elements.length < 1)
             return root;
         /* only add PIB to a root element with no PIB child*/
-        if (!root.getChildren("ProvisionInformation").isEmpty()) {
+        if (root.getElementsByTagName("ProvisionInformation").item(0) != null) {
             return root;
         }
-        Element pib = new Element("ProvisionInformation");
-        for (int x=0; x < elements.length; x++)
-            pib.addContent(elements[x]);
-        root.addContent(pib);
+        Document doc = root.getOwnerDocument();
+        Element pib = doc.createElement("ProvisionInformation");
+        for (int x = 0; x < elements.length; x++) {
+            doc.adoptNode(elements[x]);
+            pib.appendChild(elements[x]);
+        }
+        root.appendChild(pib);
         return root;
     }
-    
+
     /**
      *  
      * <b>PRE:</b><p>
@@ -411,15 +475,18 @@
      * @param comment - any applicable comments
      * @return - a serviceSoftware Element with its attributes appropriately set.
      */
-    public Element createPIBServiceSoftwareElement(String name, String version, String comment) {
+    public Element createPIBServiceSoftwareElement(String name, String version,
+            String comment) {
         if (name == null || version == null || comment == null)
             return null;
-        Element e = new Element("serviceSoftware");
-        e.setAttribute(new Attribute("software_name", name));
-        e.setAttribute(new Attribute("software_version", version));
-        e.setAttribute(new Attribute("software_comment", comment));
+        Document doc = createDomDocument();
+        Element e = doc.createElement("serviceSoftware");
+        e.setAttribute("software_name", name);
+        e.setAttribute("software_version", version);
+        e.setAttribute("software_comment", comment);
         return e;
     }
+
     /**
      *  
      * <b>PRE:</b><p>
@@ -429,16 +496,18 @@
      * @param comment - any applicable comments
      * @return - a serviceDatabase Element with its attributes appropriately set.
      */
-    public Element createPIBServiceDatabaseElement(String name, String version, String comment) {
+    public Element createPIBServiceDatabaseElement(String name, String version,
+            String comment) {
         if (name == null || version == null || comment == null)
             return null;
-        Element e = new Element("serviceDatabase");
-        e.setAttribute(new Attribute("database_name", name));
-        e.setAttribute(new Attribute("database_version", version));
-        e.setAttribute(new Attribute("database_comment", comment));
+        Document doc = createDomDocument();
+        Element e = doc.createElement("serviceDatabase");
+        e.setAttribute("database_name", name);
+        e.setAttribute("database_version", version);
+        e.setAttribute("database_comment", comment);
         return e;
     }
-    
+
     /**
      *  
      * <b>PRE:</b><p>
@@ -449,24 +518,12 @@
     public Element createPIBServiceCommentElement(String comment) {
         if (comment == null)
             return null;
-        Element e = new Element("serviceComment");
-        e.setText(comment);
+
+        Element e = createDomDocument().createElement("serviceComment");
+        e.setTextContent(comment);
         return e;
     }
-    
-    public static void main(String[] args) {
-        MobyObjectPrimitiveExtractor g = new MobyObjectPrimitiveExtractor();
-        ArrayList l = g.getPrimitives("GenericSequence");
-        Element e = g.getElementContainingTriples("GenericSequence", l);
-        System.out.println(output(e));
-        e = g.addCrossReferenceToElement(e, "Object","NCBI_gi", "bob");
-        System.out.println(output(e));
-        e = g.addXrefCrossReferenceToElement(e, "myNamespace", "545454", "www.illuminae.com", "myServiceName", "myCode", "myXtype", "bob is your description");
-        System.out.println(output(e));
-        //g.getPrimitives("DNASequence");
-        //g.getPrimitives("CommentedRNASequence");
-    }
-    
+
     /**
      *  
      * <b>PRE:</b><p>
@@ -474,7 +531,7 @@
      * @param e - the dom element to stringify.
      * @return - a string representation of the element
      */
-    public static String output(Element e) {
+    public String createStringFromElement(Element e) {
         ByteArrayOutputStream buf = new ByteArrayOutputStream();
         // Create the document
         XMLOutputter fmt = new XMLOutputter();
@@ -483,10 +540,36 @@
         format.setIndent("     ");
         fmt.setFormat(format);
         try {
-            fmt.output(e, buf);
+            fmt.output(convert(e), buf);
         } catch (IOException ex) {
             System.out.println("Error: " + ex.getLocalizedMessage());
         }
-        return "Document: \n" + buf.toString();
+        return buf.toString();
     }
-}
+
+    private void outputDocumentToStream(Document doc, OutputStream s) {
+        // Use a Transformer for output
+        TransformerFactory tFactory = TransformerFactory.newInstance();
+        Transformer transformer;
+        try {
+            transformer = tFactory.newTransformer();
+            DOMSource source = new DOMSource(doc);
+            StreamResult result = new StreamResult(s);
+            transformer.transform(source, result);
+        } catch (TransformerConfigurationException e1) {
+            System.err.println("Couldnt print out DOM Doc.1 "
+                    + e1.getLocalizedMessage());
+        } catch (TransformerException e) {
+            System.err.println("Couldnt print out DOM Doc.2 "
+                    + e.getLocalizedMessage());
+        }
+    }
+
+    private static org.jdom.Element convert(Element domDoc) throws IOException {
+        // Create new DOMBuilder, using default parser
+        DOMBuilder builder = new DOMBuilder();
+        org.jdom.Element jdomDoc = builder.build(domDoc);
+        return jdomDoc;
+    }
+    
+}
\ No newline at end of file

From kawas at pub.open-bio.org  Thu Feb 24 18:55:59 2005
From: kawas at pub.open-bio.org (Eddie Kawas)
Date: Thu Feb 24 18:42:47 2005
Subject: [MOBY-guts] biomoby commit
Message-ID: <200502242355.j1ONtxKU002191@pub.open-bio.org>


kawas
Thu Feb 24 18:55:59 EST 2005
Update of /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/gui/util
In directory pub.open-bio.org:/tmp/cvs-serv2169

Removed Files:
	MobyObjectPrimitiveExtractor.java 
Log Message:
removed this class because it required 'extra' work to get it to compile properly.
once everyone is using java 1.5.0 or has extra time on their hands, i will put it back.
Sorry.

moby-live/Java/src/main/org/biomoby/client/gui/util MobyObjectPrimitiveExtractor.java,1.2,NONE
rcsdiff: /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/gui/util/RCS/MobyObjectPrimitiveExtractor.java,v: No such file or directory

From kawas at pub.open-bio.org  Thu Feb 24 18:56:15 2005
From: kawas at pub.open-bio.org (Eddie Kawas)
Date: Thu Feb 24 18:42:59 2005
Subject: [MOBY-guts] biomoby commit
Message-ID: <200502242356.j1ONuFpp002222@pub.open-bio.org>


kawas
Thu Feb 24 18:56:15 EST 2005
Update of /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/gui/util
In directory pub.open-bio.org:/tmp/cvs-serv2200

Removed Files:
	Triples.java 
Log Message:
removed this class because it required 'extra' work to get it to compile properly.
once everyone is using java 1.5.0 or has extra time on their hands, i will put it back.
Sorry.

moby-live/Java/src/main/org/biomoby/client/gui/util Triples.java,1.1,NONE
rcsdiff: /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/gui/util/RCS/Triples.java,v: No such file or directory

From yanwong at pub.open-bio.org  Tue Feb  1 03:41:38 2005
From: yanwong at pub.open-bio.org (Yan Wong)
Date: Thu Apr 14 12:22:43 2005
Subject: [MOBY-guts] biomoby commit
Message-ID: <200502010852.j118qGxG012654@pub.open-bio.org>


yanwong
Tue Feb  1 03:52:15 EST 2005
Update of /home/repository/moby/moby-live/Python/bioMoby
In directory pub.open-bio.org:/tmp/cvs-serv12609

Modified Files:
	mobyClient.py mobyDataTypes.py mobyExceptions.py 
	mobyMarshal.py mobyRegister.py mobyService.py 
Log Message:


moby-live/Python/bioMoby mobyClient.py,1.2,1.3 mobyDataTypes.py,1.5,1.6 mobyExceptions.py,1.2,1.3 mobyMarshal.py,1.3,1.4 mobyRegister.py,1.2,1.3 mobyService.py,1.2,1.3
===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/mobyClient.py,v
retrieving revision 1.2
retrieving revision 1.3
diff -u -r1.2 -r1.3
--- /home/repository/moby/moby-live/Python/bioMoby/mobyClient.py	2005/01/18 13:46:22	1.2
+++ /home/repository/moby/moby-live/Python/bioMoby/mobyClient.py	2005/02/01 08:52:15	1.3
@@ -22,10 +22,10 @@
         
         from SOAPpy import SOAPProxy        
         self.server=SOAPProxy(self.url, namespace=self.ns)
-	
-	if debug:
-	    self.server.config.debug=1
-	    
+        
+        if debug:
+            self.server.config.debug=1
+            
         del SOAPProxy
 
 
@@ -68,28 +68,28 @@
     def retrieveObjectDefinition(self, objectName):
         """Retrieves a list of object's definitions
         """
-	dc={"urn:lsid:biomoby.org:objectrelation:isa":"ISA",
-	"urn:lsid:biomoby.org:objectrelation:hasa":"HASA",
-	"urn:lsid:biomoby.org:objectrelation:has":"HAS"
-	}
+        dc={"urn:lsid:biomoby.org:objectrelation:isa":"ISA",
+        "urn:lsid:biomoby.org:objectrelation:hasa":"HASA",
+        "urn:lsid:biomoby.org:objectrelation:has":"HAS"
+        }
 
-	definition={}
-	definition["Relationship"]={}
+        definition={}
+        definition["Relationship"]={}
 
         xmlinput="<retrieveObjectDefinition><objectType>"+objectName+"</objectType></retrieveObjectDefinition>"
         doc=parseString(self.call_method("retrieveObjectDefinition", xmlinput))
-	
-	for child in doc.firstChild.childNodes:
-	    if child.nodeType==child.ELEMENT_NODE and child.nodeName=="Relationship":
-		definition["Relationship"][dc[child.getAttribute("relationshipType")]]=[]
-		for elem in child.childNodes:
-	            if elem.nodeType==elem.ELEMENT_NODE and elem.nodeName=="objectType" and elem.firstChild:
-			definition["Relationship"][dc[child.getAttribute("relationshipType")]].append((elem.getAttribute("articleName"), elem.firstChild.nodeValue))
-
-	    elif child.nodeType==child.ELEMENT_NODE:
-		if child.firstChild:
-			definition[str(child.nodeName)]=child.firstChild.nodeValue
-	
+        
+        for child in doc.firstChild.childNodes:
+            if child.nodeType==child.ELEMENT_NODE and child.nodeName=="Relationship":
+                definition["Relationship"][dc[child.getAttribute("relationshipType")]]=[]
+                for elem in child.childNodes:
+                    if elem.nodeType==elem.ELEMENT_NODE and elem.nodeName=="objectType" and elem.firstChild:
+                        definition["Relationship"][dc[child.getAttribute("relationshipType")]].append((elem.getAttribute("articleName"), elem.firstChild.nodeValue))
+
+            elif child.nodeType==child.ELEMENT_NODE:
+                if child.firstChild:
+                        definition[str(child.nodeName)]=child.firstChild.nodeValue
+        
         return definition
 
     def retrieveObjectSchema(self, objectName):
@@ -260,6 +260,6 @@
             raise ETypeMismatch
             
     def __init__(self, url="http://mobycentral.cbr.nrc.ca/cgi-bin/MOBY05/mobycentral.pl", ns="http://mobycentral.cbr.nrc.ca/MOBY/Central"):
-	"""Constructor for class Client
-	"""
+        """Constructor for class Client
+        """
         Central.__init__(self, url, ns)

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/mobyDataTypes.py,v
retrieving revision 1.5
retrieving revision 1.6
diff -u -r1.5 -r1.6
--- /home/repository/moby/moby-live/Python/bioMoby/mobyDataTypes.py	2005/01/27 13:46:57	1.5
+++ /home/repository/moby/moby-live/Python/bioMoby/mobyDataTypes.py	2005/02/01 08:52:15	1.6
@@ -26,7 +26,7 @@
     def __init__(self, articleName="", value=""):
         self.articleName=articleName
         self.value=value
-	self.__isSecondary__=True
+        self.__isSecondary__=True
         
     def toMoby(self):
         """Returns the object as a XML
@@ -34,199 +34,199 @@
         return "<moby:Parameter moby:articleName='"+self.articleName+"'><moby:value>"+str(self.value)+"</moby:value></moby:Parameter>"
             
     def __str__(self):
-	"""Return the Parameter in its XML form
-	"""
+        """Return the Parameter in its XML form
+        """
         return self.toMoby()
 
     def __repr__(self):
-	"""Print the XML on the python command line.
-	"""
+        """Print the XML on the python command line.
+        """
         return self.toMoby()
             
     def fromMoby(self, xml):
         """Get the attributes from a XML string
         """
-	xmlelt=xml
-	
-	if isinstance(xml, str):
-	    xmlelt=parseString(xml).firstChild
-	    
+        xmlelt=xml
+        
+        if isinstance(xml, str):
+            xmlelt=parseString(xml).firstChild
+            
         self.articleName=xmlelt.getAttribute('moby:articleName')
-	l=xmlelt.getElementsByTagName("value")
-	if len(l)==0:
-	    l=xmlelt.getElementsByTagName("moby:value")
+        l=xmlelt.getElementsByTagName("value")
+        if len(l)==0:
+            l=xmlelt.getElementsByTagName("moby:value")
 
-       	self.value=l[0].firstChild.nodeValue
-	
+            self.value=l[0].firstChild.nodeValue
+        
 class MobyGeneric(object):
     """A Generic object (to use with the Marshaller)
     """
     def __init__(self, namespace="", id="", articleName="", *args, **kw):
-	"""Class constructor, basic attributes are namespace, 
-	   identifier and the article's name
-	"""
-	self.namespace=namespace
-	self.id=id
-	self.articleName=articleName
-	
-	for name, value in kw.items():
+        """Class constructor, basic attributes are namespace, 
+           identifier and the article's name
+        """
+        self.namespace=namespace
+        self.id=id
+        self.articleName=articleName
+        
+        for name, value in kw.items():
             setattr(self, name, value)
-	
+        
 class MobyObject(MobyGeneric):
     """Define a Moby XML Object
        It has methods toMoby and fromMoby 
     """
     def __init__(self, prefix="moby", tag="Object", content="", *args, **kw):
-	"""Class constructor for a bioMoby Object
-	"""
-	MobyGeneric.__init__(self, *args, **kw)
-	self.__prefix__=prefix
-	self.__tag__=tag
-	self.__cross__=[]
-	self.__PIB__=[]
-	
-	self.content=content
-	
-		
+        """Class constructor for a bioMoby Object
+        """
+        MobyGeneric.__init__(self, *args, **kw)
+        self.__prefix__=prefix
+        self.__tag__=tag
+        self.__cross__=[]
+        self.__PIB__=[]
+        
+        self.content=content
+        
+                
     def toMoby(self):
-	"""Deserializes the content in XML api
-	"""
-	
-	beginTag=["<%s:%s"%(self.__prefix__,self.__tag__)]
-	
-	#First see if the object has an  identifier, a namepsace and a name
-	for attribute in __ATTRIBUTES__:
-	    if hasattr(self, attribute) and getattr(self, attribute):
-		beginTag.append("%s:%s=\"%s\""%(self.__prefix__, attribute, getattr(self,attribute)))
-
-	#Retrieve only object's attributes that are public.
-	filterFunc=lambda x: x[0] != "_" and not callable(getattr(self, x)) and x !="content" and x not in __ATTRIBUTES__
-	
-	#Retrieve the associated objects
-	#In MobyObject, associated objects are object's attributes
-	mobyObjects=filter(filterFunc, dir(self))
-	
-	#If none, return the tag closed
-	if len(mobyObjects)==0 and (not hasattr(self, "__cross__") or len(self.__cross__)==0) and (not hasattr(self, "__PIB__") or len(self.__PIB__)==0) and (not hasattr(self, "content") or not self.content):
-	    beginTag.append("/>")
-	    return " ".join(beginTag)
+        """Deserializes the content in XML api
+        """
+        
+        beginTag=["<%s:%s"%(self.__prefix__,self.__tag__)]
+        
+        #First see if the object has an  identifier, a namepsace and a name
+        for attribute in __ATTRIBUTES__:
+            if hasattr(self, attribute) and getattr(self, attribute):
+                beginTag.append("%s:%s=\"%s\""%(self.__prefix__, attribute, getattr(self,attribute)))
 
-	#Else, end begin tag and serialize the associated objects
+        #Retrieve only object's attributes that are public.
+        filterFunc=lambda x: x[0] != "_" and not callable(getattr(self, x)) and x !="content" and x not in __ATTRIBUTES__
+        
+        #Retrieve the associated objects
+        #In MobyObject, associated objects are object's attributes
+        mobyObjects=filter(filterFunc, dir(self))
+        
+        #If none, return the tag closed
+        if len(mobyObjects)==0 and (not hasattr(self, "__cross__") or len(self.__cross__)==0) and (not hasattr(self, "__PIB__") or len(self.__PIB__)==0) and (not hasattr(self, "content") or not self.content):
+            beginTag.append("/>")
+            return " ".join(beginTag)
+
+        #Else, end begin tag and serialize the associated objects
         beginTag.append(">")
 
-	result=[" ".join(beginTag)]
-	
-	#Serialize Cross references
-	if hasattr(self, "__cross__") and self.__cross__:
-	    result.append("<CrossReference>")
-	    
-	    for aCross in self.__cross__:
-		result.append(aCross.toMoby())
-		
-	    result.append("</CrossReference>")
-	
+        result=[" ".join(beginTag)]
+        
+        #Serialize Cross references
+        if hasattr(self, "__cross__") and self.__cross__:
+            result.append("<CrossReference>")
+            
+            for aCross in self.__cross__:
+                result.append(aCross.toMoby())
+                
+            result.append("</CrossReference>")
+        
         #Serialize PIB
-	if hasattr(self, "__PIB__") and self.__PIB__:
-	    result.append("<ProvisionInformation>")
-	    
-	    for aPIB in self.__PIB__:
-		result.append(aPIB.toMoby())
-		
-	    result.append("</ProvisionInformation>")
-	
-	#Serialize the other attibutes
-	#If the attributes has a toMoby method, then use it
-	#Else, use a MobyMarshaller object to serialize
-	for mobyObject in mobyObjects:
-	    if hasattr(getattr(self,mobyObject), "toMoby"):
+        if hasattr(self, "__PIB__") and self.__PIB__:
+            result.append("<ProvisionInformation>")
+            
+            for aPIB in self.__PIB__:
+                result.append(aPIB.toMoby())
+                
+            result.append("</ProvisionInformation>")
+        
+        #Serialize the other attibutes
+        #If the attributes has a toMoby method, then use it
+        #Else, use a MobyMarshaller object to serialize
+        for mobyObject in mobyObjects:
+            if hasattr(getattr(self,mobyObject), "toMoby"):
                 getattr(self, mobyObject).__articleName__=mobyObject
                 result.append(getattr(self, mobyObject).toMoby())
-	    else:
-		from bioMoby import MobyMarshaller
-		m=MobyMarshaller()
-		result.append(m.dumps(getattr(self, mobyObject), articleName=mobyObject))
-	
-	#Put the raw content of the object
-	#If you want to put your special object, then then you should write 
-	#a __str__ method
-	if hasattr(self, "content") and self.content:
-	    result.append("%s"%(self.content))
-	
-	result.append("</%s:%s>"%(self.__prefix__, self.__tag__))
-	
-	return "".join(result)
-	
+            else:
+                from bioMoby import MobyMarshaller
+                m=MobyMarshaller()
+                result.append(m.dumps(getattr(self, mobyObject), articleName=mobyObject))
+        
+        #Put the raw content of the object
+        #If you want to put your special object, then then you should write 
+        #a __str__ method
+        if hasattr(self, "content") and self.content:
+            result.append("%s"%(self.content))
+        
+        result.append("</%s:%s>"%(self.__prefix__, self.__tag__))
+        
+        return "".join(result)
+        
     def fromMoby(self, xml):
-	"""Deserialization method
-	"""
-	elem=xml
-	
-	if isinstance(xml, str):
-	    doc=parseString(xmlstring)
-	
-	    elem=doc.firstChild
-	
-	self.__tag__=elem.localName
-	
-	self.__prefix__="moby"
-	
-	self.content=[]
-	
-	if elem.nodeName.split(":")>1:
-	    self.__prefix__=elem.nodeName.split(":")[0]
-	
-	#Set the object's attributes
-	for attribute in elem.attributes.values():
-	    setattr(self, attribute.localName, str(attribute.nodeValue))
-
-	for child in elem.childNodes:
-	    if child.nodeType==child.ELEMENT_NODE:
-		#deserializes the cross references
-		if child.localName=="CrossReference":
-		    for aCross in child.childNodes:
-			if aCross.localName=="Xref":
-			    aXref=MobyXref()
-			    aXref.fromMoby(aCross)
-			    self.__cross__.append(aXref)
-			if aCross.localName=="Object":
-			    anObj=MobyObject()
-			    anObj.fromMoby(aCross)
-			    self.__cross__.append(anObj)
-		else:
-		    #Do the same for the other objects
-		    associatedObjectName=child.getAttribute("moby:articleName")
-		
-		    if not associatedObjectName:
-		        associatedObjectName=child.getAttribute("articleName")
-		
-		    if not associatedObjectName:
-		        associatedObjectName="associated"
-		    
-		    #Create an object
-		    o=MobyObject()
-		    o.fromMoby(child)
-		    
-		    #if there is already an object, then store it inside a list and 
-		    #append the other objects in the list 
-		    if hasattr(self, associatedObjectName):
-		        if type(getattr(self, associatedObjectName)) is list:
-			    getattr(self, associatedObjectName).append(o)
-		        else:
-			    setattr(self, associatedObjectName, [o])
-		    else:
+        """Deserialization method
+        """
+        elem=xml
+        
+        if isinstance(xml, str):
+            doc=parseString(xmlstring)
+        
+            elem=doc.firstChild
+        
+        self.__tag__=elem.localName
+        
+        self.__prefix__="moby"
+        
+        self.content=[]
+        
+        if elem.nodeName.split(":")>1:
+            self.__prefix__=elem.nodeName.split(":")[0]
+        
+        #Set the object's attributes
+        for attribute in elem.attributes.values():
+            setattr(self, attribute.localName, str(attribute.nodeValue))
+
+        for child in elem.childNodes:
+            if child.nodeType==child.ELEMENT_NODE:
+                #deserializes the cross references
+                if child.localName=="CrossReference":
+                    for aCross in child.childNodes:
+                        if aCross.localName=="Xref":
+                            aXref=MobyXref()
+                            aXref.fromMoby(aCross)
+                            self.__cross__.append(aXref)
+                        if aCross.localName=="Object":
+                            anObj=MobyObject()
+                            anObj.fromMoby(aCross)
+                            self.__cross__.append(anObj)
+                else:
+                    #Do the same for the other objects
+                    associatedObjectName=child.getAttribute("moby:articleName")
+                
+                    if not associatedObjectName:
+                        associatedObjectName=child.getAttribute("articleName")
+                
+                    if not associatedObjectName:
+                        associatedObjectName="associated"
+                    
+                    #Create an object
+                    o=MobyObject()
+                    o.fromMoby(child)
+                    
+                    #if there is already an object, then store it inside a list and 
+                    #append the other objects in the list 
+                    if hasattr(self, associatedObjectName):
+                        if type(getattr(self, associatedObjectName)) is list:
+                            getattr(self, associatedObjectName).append(o)
+                        else:
+                            setattr(self, associatedObjectName, [o])
+                    else:
                         setattr(self, associatedObjectName, o)
             else:
-		self.content.append(child.nodeValue)
-		
-	self.content="".join(self.content)
-	
+                self.content.append(child.nodeValue)
+                
+        self.content="".join(self.content)
+        
 
     def __str__(self):
-	return self.toMoby()
-	
+        return self.toMoby()
+        
     def __repr__(self):
-	return self.toMoby()
-	
+        return self.toMoby()
+        
 
 class MobyXref(MobyObject):
     """Describes an Xref
@@ -246,48 +246,48 @@
     def fromMoby(self, xml):
         """Deserialize the Xref Object
         """
-	if isinstance(xml, str):
-	    doc=parseString(xml).firstChild
-	
-	doc=xml
-	
+        if isinstance(xml, str):
+            doc=parseString(xml).firstChild
+        
+        doc=xml
+        
         uri=doc.namespaceURI
     
-	MobyObject.fromMoby(self, doc)
+        MobyObject.fromMoby(self, doc)
         
         self.authURI=doc.getAttributeNS(uri, "authURI")
         self.serviceName=doc.getAttributeNS(uri, "serviceName")
         self.evidenceCode=doc.getAttributeNS(uri, "evidenceCode")
         self.xrefType=doc.getAttributeNS(uri, "xrefType")
 
-	
+        
 class MobyInteger(MobyObject):
     """Use this object to serialize/deserialize integers
     """
     def __init__(self, value=0, *args, **kw):
-	MobyObject.__init__(self, content=value, tag="Integer", *args, **kw)
+        MobyObject.__init__(self, content=value, tag="Integer", *args, **kw)
 
     def fromMoby(self, xml):
-	MobyObject.fromMoby(self, xml)
-	self.content = int(self.content)
-	
+        MobyObject.fromMoby(self, xml)
+        self.content = int(self.content)
+        
 class MobyFloat(MobyObject):
     """Serialize/deserialize floating point numbers
     """
     def __init__(self, value=0, *args, **kw):
-	MobyObject.__init__(self, content=value, tag="Float", *args, **kw)
-	
+        MobyObject.__init__(self, content=value, tag="Float", *args, **kw)
+        
     def fromMoby(self, xml):
-	MobyObject.fromMoby(self, xml)
-	self.content=float(self.content)
-	
+        MobyObject.fromMoby(self, xml)
+        self.content=float(self.content)
+        
 
 class MobyString(MobyObject):
     """String Moby object
     """
     def __init__(self, content="", *args, **kw):
-	MobyObject.__init__(self, content=content, *args, **kw)
-	self.__tag__="String"
+        MobyObject.__init__(self, content=content, *args, **kw)
+        self.__tag__="String"
 
 class MobyContent:
     """The class describes a Moby Content (for queries or answers)
@@ -302,10 +302,10 @@
         self.queryData=queryData
 
     def __str__(self):
-	"""return the XML form of the Moby Content object
-	"""
-	return self.toMoby()
-	
+        """return the XML form of the Moby Content object
+        """
+        return self.toMoby()
+        
     def toMoby(self):
         """The XML reprentation of the content
         """
@@ -325,8 +325,8 @@
         for queryKey in self.queryData:
             result.append("<moby:mobyData moby:queryID='"+queryKey+"'>")
 
-	    #For serialization, use the MobyMarshaller object
-	    
+            #For serialization, use the MobyMarshaller object
+            
             for queryObject in self.queryData[queryKey]:
                 #if the Collection ('CollectionName',[MobyObjects])
                 if queryObject.__class__ is tuple:
@@ -352,19 +352,19 @@
         return "".join(result)
 
     def fromMoby(self, xmlObject):
-	"""fill the properties from an XML
+        """fill the properties from an XML
         """
         from bioMoby import MobyUnmarshaller
-	
-	um=MobyUnmarshaller()
+        
+        um=MobyUnmarshaller()
 
         self.queryData={}
-	
-	doc=xmlObject
-	
-	if isinstance(xmlObject, str):
-	    doc=parseString(xmlObject)
-	
+        
+        doc=xmlObject
+        
+        if isinstance(xmlObject, str):
+            doc=parseString(xmlObject)
+        
         mdl=doc.getElementsByTagName('mobyData')
 
         if not mdl:
@@ -373,115 +373,115 @@
         #For each query            
         for elt in mdl:
             #Get the ID
-	    queryID=str(elt.getAttribute('queryID'))
+            queryID=str(elt.getAttribute('queryID'))
 
             if not queryID:
                 queryID=str(elt.getAttribute('moby:queryID'))
 
-	    #Collect the data
+            #Collect the data
             data=[]
 
-	    #for each datum translate it in MobyObject, and put it in the list
+            #for each datum translate it in MobyObject, and put it in the list
             for datum in elt.childNodes:
-		#If it is a collection
+                #If it is a collection
                 if datum.nodeType==datum.ELEMENT_NODE and datum.localName=="Collection":
-		    articleName=datum.getAttribute('moby:articleName')
+                    articleName=datum.getAttribute('moby:articleName')
         
                     articles=[]
         
                     for article in datum.childNodes:
                         if article.nodeType==article.ELEMENT_NODE and article.localName=="Simple":
-			    for child in article.childNodes:
-				if child.nodeType==child.ELEMENT_NODE:
+                            for child in article.childNodes:
+                                if child.nodeType==child.ELEMENT_NODE:
                                     articles.append(um.loadn(child))
 
                     data.append((articleName, articles))
-		#if it is a Simple object
+                #if it is a Simple object
                 elif datum.nodeType==datum.ELEMENT_NODE and datum.localName=="Simple":
-		    for elt in datum.childNodes:
+                    for elt in datum.childNodes:
                         if elt.nodeType==elt.ELEMENT_NODE:
-		            o=um.loadn(elt)
-		            data.append(o)
-	        elif datum.nodeType==datum.ELEMENT_NODE and datum.localName=="Parameter":
-		    #It is a Parameter
-		    p=Parameter()
-		    p.fromMoby(datum)
-		    data.append(p)
+                            o=um.loadn(elt)
+                            data.append(o)
+                elif datum.nodeType==datum.ELEMENT_NODE and datum.localName=="Parameter":
+                    #It is a Parameter
+                    p=Parameter()
+                    p.fromMoby(datum)
+                    data.append(p)
                     
             self.queryData[queryID]=data
-	    
+            
     def __getitem__(self, key):
-	"""Get a query from his name
+        """Get a query from his name
         """
         return self.queryData[key]
         
     def __setitem__(self, key, item):
-	"""Store a query in the dictionary
-	"""
+        """Store a query in the dictionary
+        """
         self.queryData[key]=item
 
     def __len__(self):
-	"""Return the number of elements inside the dictionary
-	"""
+        """Return the number of elements inside the dictionary
+        """
         return len(self.queryData)
         
     def keys(self):
-	"""Return all queries's name
-	"""
+        """Return all queries's name
+        """
         return self.queryData.keys()
-	
+        
     def collectionToQueries(self, aCollection):
-	"""Turn a collection of object into a set of queries
-	"""
-	queries={}
-	queryName=aCollection[0]
-	
-	queryID=1
-	
-	for aSimple in aCollection[1]:
-	    queries["%s-%s"%(queryName, queryID)]=aSimple
-	    
-	return queries
-		
-	
+        """Turn a collection of object into a set of queries
+        """
+        queries={}
+        queryName=aCollection[0]
+        
+        queryID=1
+        
+        for aSimple in aCollection[1]:
+            queries["%s-%s"%(queryName, queryID)]=aSimple
+            
+        return queries
+                
+        
     def getObject(self, queryName, objectName):
-	"""Get an object from a query with its name
-	"""
-	filterfunc=lambda obj: not hasattr(obj,'__isSecondary__') and hasattr(obj, "articleName") and obj.articleName==objectName
-	
-	for obj in filter(filterfunc, self.queryData[queryName]):
+        """Get an object from a query with its name
+        """
+        filterfunc=lambda obj: not hasattr(obj,'__isSecondary__') and hasattr(obj, "articleName") and obj.articleName==objectName
+        
+        for obj in filter(filterfunc, self.queryData[queryName]):
             return obj
 
-		
+                
     def getObjects(self, queryName):
-	"""Retrieve objects from a query
-	"""
-	filterfunc=lambda obj: not hasattr(obj, "__isSecondary__")
-	
-	return filter(filterfunc, self.queryData[queryName])
-	
+        """Retrieve objects from a query
+        """
+        filterfunc=lambda obj: not hasattr(obj, "__isSecondary__")
+        
+        return filter(filterfunc, self.queryData[queryName])
+        
     def getParameters(self, queryName):
-	"""Retrieve parameters from a query
-	"""
-	filterfunc=lambda param: hasattr(param, "__isSecondary__")
-	
-	result={}
-	for param in filter(filterfunc, self.queryData[queryName]):
-	    result[param.articleName]=param.value
-		
-	return result
+        """Retrieve parameters from a query
+        """
+        filterfunc=lambda param: hasattr(param, "__isSecondary__")
+        
+        result={}
+        for param in filter(filterfunc, self.queryData[queryName]):
+            result[param.articleName]=param.value
+                
+        return result
 
     def getParameter(self, queryName, parameterName):
-	"""Retrieve a parameter from a query and his name
-	"""
-	filterfunc=lambda param: hasattr(param, "__isSecondary__") and hasattr(param, "articleName") and param.articleName==parameterName
-	
-	l=filter(filterfunc, self.queryData[queryName])
-	
-	if l:
-	    return l[0]
-	
+        """Retrieve a parameter from a query and his name
+        """
+        filterfunc=lambda param: hasattr(param, "__isSecondary__") and hasattr(param, "articleName") and param.articleName==parameterName
+        
+        l=filter(filterfunc, self.queryData[queryName])
+        
+        if l:
+            return l[0]
+        
     def __repr__(self):
-	"""put the xml of the Content
-	"""
-	return self.__str__()
+        """put the xml of the Content
+        """
+        return self.__str__()

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/mobyExceptions.py,v
retrieving revision 1.2
retrieving revision 1.3
diff -u -r1.2 -r1.3
--- /home/repository/moby/moby-live/Python/bioMoby/mobyExceptions.py	2005/01/18 13:46:22	1.2
+++ /home/repository/moby/moby-live/Python/bioMoby/mobyExceptions.py	2005/02/01 08:52:15	1.3
@@ -41,4 +41,4 @@
     """A XML input is not a Moby XML Object.
     """
     def __str__(self):
-	return "The bioMoby XML object couldn't be parsed"
\ No newline at end of file
+        return "The bioMoby XML object couldn't be parsed"
\ No newline at end of file

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/mobyMarshal.py,v
retrieving revision 1.3
retrieving revision 1.4
diff -u -r1.3 -r1.4
--- /home/repository/moby/moby-live/Python/bioMoby/mobyMarshal.py	2005/01/27 08:44:05	1.3
+++ /home/repository/moby/moby-live/Python/bioMoby/mobyMarshal.py	2005/02/01 08:52:15	1.4
@@ -10,7 +10,7 @@
     
     01/17/2005: MobyMarshaller and MobyUnmarshaller can operate on all objects
                 serialisation and deserialisation are done only on public (no _ prefix) non callable attributes
-		The serialisation and deserialisation is recursive.
+                The serialisation and deserialisation is recursive.
 """
 
 from xml.dom.minidom import parseString
@@ -20,8 +20,8 @@
     """
     
     def _marshal(self, value, articleName=""):
-	"""this method do the serialization of the object
-	"""
+        """this method do the serialization of the object
+        """
         if type(value).__name__=='NoneType':
             return ""
 
@@ -29,9 +29,9 @@
 
         method="m_"+tvalue
 
-	if hasattr(value, "toMoby"):
-	    return value.toMoby()
-	
+        if hasattr(value, "toMoby"):
+            return value.toMoby()
+        
         if hasattr(self, method):
             return getattr(self,method)(value,articleName=articleName)
         
@@ -46,8 +46,8 @@
         return str(m)
         
     def m_unicode(self, value, articleName=""):
-	"""Turn a unicode string into a mobyString object
-	"""
+        """Turn a unicode string into a mobyString object
+        """
         return self.m_str(str(value), articleName)
 
     def m_string(self, value, articleName=""):
@@ -59,18 +59,18 @@
         """Turn an integer into a Moby XML object
         """
         from bioMoby.mobyDataTypes import MobyInteger
-	m=MobyInteger(value, namespace=namespace, id=id, articleName=articleName)
-	
-	return m.toMoby()
-	
+        m=MobyInteger(value, namespace=namespace, id=id, articleName=articleName)
+        
+        return m.toMoby()
+        
     def m_float(self, value, namespace="", id="", articleName=""):
         """Turn a float into a Moby XML object
         """
         from bioMoby.mobyDataTypes import MobyFloat
-	m=MobyFloat(value, namespace=namespace, id=id, articleName=articleName)
-	
-	return m.toMoby()
-	
+        m=MobyFloat(value, namespace=namespace, id=id, articleName=articleName)
+        
+        return m.toMoby()
+        
     def m_list(self, value, articleName=""):
         """Turn a list into a Moby XML object
         """
@@ -113,50 +113,50 @@
     def _compoundObject(self, value, articleName=""):
         """transforms an object and all properties into a XML
         """
-	
-	result=[]
-	
-	properties=[]
-	
-	filterfunc=lambda x: x[0] != "_" and not callable(getattr(value, x)) and x !="content" and x not in ["id", "namespace", "articleName", "content"]
-	attribfunc= lambda x: hasattr(value, x)
-	
-	tagName="moby:%s"%type(value).__name__
-	
-	if hasattr(value, "__tag__") and value.__tag__:
-	    tagName="moby:%s"%value.__tag__
-	
-	header=["<%s"%tagName]
-	
-	for attribute in filter(attribfunc, ["id", "namespace", "articleName"]):
-	    header.append("moby:%s=\"%s\""%(attribute,getattr(value,attribute)))
-	
-	for prop in filter(filterfunc, dir(value)):
-	    properties.append(self._marshal(getattr(value, prop), articleName=prop))
-	    
-	if not properties and not (hasattr(value, "content") and value.content):
-	    header.append("/>")
-	else:
-	    header.append(">")
-	    
-	result.append(" ".join(header))
-
-	if properties:
-	    result.append("".join(properties))	    
-	
-	if hasattr(value, "content") and value.content:
-	    result.append("<![CDATA[%s]]>"%value.content)
-	
-	if properties:
-	    result.append("</%s>"%tagName)
-
-
-	return r"".join(result)
-	
-	
+        
+        result=[]
+        
+        properties=[]
+        
+        filterfunc=lambda x: x[0] != "_" and not callable(getattr(value, x)) and x !="content" and x not in ["id", "namespace", "articleName", "content"]
+        attribfunc= lambda x: hasattr(value, x)
+        
+        tagName="moby:%s"%type(value).__name__
+        
+        if hasattr(value, "__tag__") and value.__tag__:
+            tagName="moby:%s"%value.__tag__
+        
+        header=["<%s"%tagName]
+        
+        for attribute in filter(attribfunc, ["id", "namespace", "articleName"]):
+            header.append("moby:%s=\"%s\""%(attribute,getattr(value,attribute)))
+        
+        for prop in filter(filterfunc, dir(value)):
+            properties.append(self._marshal(getattr(value, prop), articleName=prop))
+            
+        if not properties and not (hasattr(value, "content") and value.content):
+            header.append("/>")
+        else:
+            header.append(">")
+            
+        result.append(" ".join(header))
+
+        if properties:
+            result.append("".join(properties))            
+        
+        if hasattr(value, "content") and value.content:
+            result.append("<![CDATA[%s]]>"%value.content)
+        
+        if properties:
+            result.append("</%s>"%tagName)
+
+
+        return r"".join(result)
+        
+        
     def dumps(self, value, articleName=""):
-	"""Serialize the object into a Moby XML object
-	"""
+        """Serialize the object into a Moby XML object
+        """
         return self._marshal(value, articleName)
         
 
@@ -169,8 +169,8 @@
         """
         import re
 
-	aName=str(aName)
-	
+        aName=str(aName)
+        
         if aName=="":
             return ""
 
@@ -189,51 +189,51 @@
         return "".join(t)
 
     def loadn(self, xmlNode):
-	"""Deserializes an XML node and return a Python Object
-	"""
-	import bioMoby.mobyDataTypes
-	import bioMoby.ontology
-	
-	nn=xmlNode.localName
-	
+        """Deserializes an XML node and return a Python Object
+        """
+        import bioMoby.mobyDataTypes
+        import bioMoby.ontology
+        
+        nn=xmlNode.localName
+        
         #Try to see if this object got a deserializer
         object2build=self._cleanName(nn)
 
         objectName=str.upper(object2build[0])+object2build[1:]
-	
-	if hasattr(bioMoby.mobyDataTypes, "Moby%s"%objectName):
-	    o=getattr(bioMoby.mobyDataTypes, "Moby%s"%objectName)()
-	    if hasattr(o, "fromMoby"):
-		o.fromMoby(xmlNode)
-	    return o
-	elif hasattr(bioMoby.ontology, "Moby%s"%objectName):
-	    o=getattr(bioMoby.ontology, "Moby%s"%objectName)()
-	    if hasattr(o, "fromMoby"):
-		o.fromMoby(xmlNode)
-	    return o
-	    
+        
+        if hasattr(bioMoby.mobyDataTypes, "Moby%s"%objectName):
+            o=getattr(bioMoby.mobyDataTypes, "Moby%s"%objectName)()
+            if hasattr(o, "fromMoby"):
+                o.fromMoby(xmlNode)
+            return o
+        elif hasattr(bioMoby.ontology, "Moby%s"%objectName):
+            o=getattr(bioMoby.ontology, "Moby%s"%objectName)()
+            if hasattr(o, "fromMoby"):
+                o.fromMoby(xmlNode)
+            return o
+            
         methodName=str('m_'+nn)
-	    
-	if not hasattr(self, methodName):
+            
+        if not hasattr(self, methodName):
             methodName="m_Object"
-		
-#	try:
+                
+#        try:
         return getattr(self,methodName)(xmlNode)
 #        except:
-#	    #if not, Raise an invalid moby XML :-(
-#	    from bioMoby.mobyExceptions import EInvalidMobyXML    
-	    
+#            #if not, Raise an invalid moby XML :-(
+#            from bioMoby.mobyExceptions import EInvalidMobyXML    
+            
 #            raise EInvalidMobyXML
 
-	
+        
     def loads(self, xmlString):
-	""" Deserializes an xml string and return a bioMoby-Python object
-	"""
+        """ Deserializes an xml string and return a bioMoby-Python object
+        """
         if xmlString=="":
             return None    
 
-#	_typesmodule=["bioMoby.mobyDataTypes", "bioMoby.ontology"]
-	    
+#        _typesmodule=["bioMoby.mobyDataTypes", "bioMoby.ontology"]
+            
         doc=parseString(xmlString)
         
         mcl=doc.getElementsByTagNameNS('http://www.biomoby.org/moby','mobyContent')
@@ -243,109 +243,109 @@
             
         element=doc.firstChild
         
-	self.loadn(element)
+        self.loadn(element)
 
     def m_Integer(self, value):
-	"""Turn a Integer XML element into an integer
-	"""
-	value.normalize()
-	
-	if value.firstChild:
-	    return int(value.firstChild.nodeValue.replace("\n","").replace("\t","").replace(" ",""))
-	else:
-	    return 0
-	    
+        """Turn a Integer XML element into an integer
+        """
+        value.normalize()
+        
+        if value.firstChild:
+            return int(value.firstChild.nodeValue.replace("\n","").replace("\t","").replace(" ",""))
+        else:
+            return 0
+            
     def m_Float(self, value):
-	"""Turn a Float XML element into a float number
-	"""
-	value.normalize()
-	if value.firstChild:
-	    return float(value.firstChild.nodeValue.replace("\n","").replace("\t","").replace(" ",""))
+        """Turn a Float XML element into a float number
+        """
+        value.normalize()
+        if value.firstChild:
+            return float(value.firstChild.nodeValue.replace("\n","").replace("\t","").replace(" ",""))
         return 0.0
-	    
+            
     def m_String(self, value):
-	"""Turn a Moby XML String element into a String object
-	"""
-	
-	cnt=[]
-	value.normalize()
-	
-	for aChild in value.childNodes:
-	    if aChild.nodeType==aChild.TEXT_NODE or aChild.nodeType==aChild.CDATA_SECTION_NODE:
-		cnt.append(aChild.wholeText)
-		
-	return	r"".join(cnt)
-	
+        """Turn a Moby XML String element into a String object
+        """
+        
+        cnt=[]
+        value.normalize()
+        
+        for aChild in value.childNodes:
+            if aChild.nodeType==aChild.TEXT_NODE or aChild.nodeType==aChild.CDATA_SECTION_NODE:
+                cnt.append(aChild.wholeText)
+                
+        return        r"".join(cnt)
+        
 
     def m_Object(self, value):
-	"""Turn any XML into a generic object
-	"""
-	filterFunc= lambda x: x.nodeType==x.ELEMENT_NODE
-	
-	typeName="GMoby%s"%str(value.localName)
-
-	from bioMoby.mobyDataTypes import MobyGeneric
-	
-	NewType=type(typeName, (MobyGeneric,), {})
-	
-	anObject=NewType()
-	
-	anObject.__prefix__="moby"
-	anObject.__tag__=str(value.localName)
-	
-	for tupleAttribute in value.attributes.itemsNS():
-	    #First item, second field:
-	    setattr(anObject, str(tupleAttribute[0][1]), str(tupleAttribute[1]))
-
-	i=0    
-	for elem in filter(filterFunc, value.childNodes):
-	    methodName="m_%s"%str(elem.localName)
-
-	    articleName=elem.getAttribute("moby:articleName")
-	    
-	    if not articleName:
-		articleName=elem.getAttribute("articleName")
-		
-	    if not articleName:
-		articleName="attribute_%s"%i
-		
-	    if hasattr(self, methodName):
-		prop=getattr(self, methodName)(elem)
-	    else:
-	    	prop=self.m_Object(elem)
-		
-	    if hasattr(anObject, articleName):
-	        t=prop
-	        if not type(getattr(anObject, articleName)) is list:
-		    t=getattr(anObject, articleName)
-		    setattr(anObject, articleName, [])
-		getattr(anObject, articleName).append(t)
-	    else:
-	        setattr(anObject, articleName, prop)
-	    i+=1
-
-	content=[]
-
-	isContentNode= lambda x: x.nodeType==x.TEXT_NODE or x.nodeType==x.CDATA_SECTION_NODE
-	
-	for elem in filter(isContentNode, value.childNodes):
-	    content.append(str(elem.nodeValue))
-	    
-	if content:
-	    anObject.content(r"".join(content))
-	    
-	return anObject
+        """Turn any XML into a generic object
+        """
+        filterFunc= lambda x: x.nodeType==x.ELEMENT_NODE
+        
+        typeName="GMoby%s"%str(value.localName)
+
+        from bioMoby.mobyDataTypes import MobyGeneric
+        
+        NewType=type(typeName, (MobyGeneric,), {})
+        
+        anObject=NewType()
+        
+        anObject.__prefix__="moby"
+        anObject.__tag__=str(value.localName)
+        
+        for tupleAttribute in value.attributes.itemsNS():
+            #First item, second field:
+            setattr(anObject, str(tupleAttribute[0][1]), str(tupleAttribute[1]))
+
+        i=0    
+        for elem in filter(filterFunc, value.childNodes):
+            methodName="m_%s"%str(elem.localName)
+
+            articleName=elem.getAttribute("moby:articleName")
+            
+            if not articleName:
+                articleName=elem.getAttribute("articleName")
+                
+            if not articleName:
+                articleName="attribute_%s"%i
+                
+            if hasattr(self, methodName):
+                prop=getattr(self, methodName)(elem)
+            else:
+                    prop=self.m_Object(elem)
+                
+            if hasattr(anObject, articleName):
+                t=prop
+                if not type(getattr(anObject, articleName)) is list:
+                    t=getattr(anObject, articleName)
+                    setattr(anObject, articleName, [])
+                getattr(anObject, articleName).append(t)
+            else:
+                setattr(anObject, articleName, prop)
+            i+=1
+
+        content=[]
+
+        isContentNode= lambda x: x.nodeType==x.TEXT_NODE or x.nodeType==x.CDATA_SECTION_NODE
+        
+        for elem in filter(isContentNode, value.childNodes):
+            content.append(str(elem.nodeValue))
+            
+        if content:
+            anObject.content(r"".join(content))
+            
+        return anObject
 
     def m_MobyContent(self, value):
-	"""Turn an MobyContentXML into a MobyContent object
-	"""
-	from bioMoby.mobyDataTypes import MobyContent
-	
-	mc=MobyContent({})
-	
-	mc.fromMoby(value)
-	
-	del MobyContent
-	
-	return mc
-	
+        """Turn an MobyContentXML into a MobyContent object
+        """
+        from bioMoby.mobyDataTypes import MobyContent
+        
+        mc=MobyContent({})
+        
+        mc.fromMoby(value)
+        
+        del MobyContent
+        
+        return mc
+        

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/mobyRegister.py,v
retrieving revision 1.2
retrieving revision 1.3
diff -u -r1.2 -r1.3
--- /home/repository/moby/moby-live/Python/bioMoby/mobyRegister.py	2005/01/18 13:46:22	1.2
+++ /home/repository/moby/moby-live/Python/bioMoby/mobyRegister.py	2005/02/01 08:52:15	1.3
@@ -19,9 +19,9 @@
         self.success=0
         self.id=""
         self.message=""
-	self.RDF=""
+        self.RDF=""
 
-	#Parse the document, retrieve the success, id, message and RDF fields
+        #Parse the document, retrieve the success, id, message and RDF fields
         doc=parseString(xmlInput)
 
         if len(doc.getElementsByTagName("success")[0].childNodes)>0:
@@ -32,9 +32,9 @@
             self.message=doc.getElementsByTagName("message")[0].childNodes[0].nodeValue
         try:
             if len(doc.getElementsByTagName("RDF"))>0:
-	        self.RDF=doc.getElementsByTagName("RDF")[0].firstChild.toprettyxml()
-	except:
-	    pass
+                self.RDF=doc.getElementsByTagName("RDF")[0].firstChild.toprettyxml()
+        except:
+            pass
 
     def __str__(self):
         """Return the moby xml of the instance
@@ -63,7 +63,7 @@
         self.authURI=authURI
         self.description=description
         #it uses a central object for registration
-    	from mobyClient import Central
+        from mobyClient import Central
         self.central=Central()
         del Central
 
@@ -78,8 +78,8 @@
         self.serviceType=serviceType
         GeneralInformations.__init__(self, contact=contactEmail, authURI=authURI, description=description)
         self.relationship=relationship
-	self.serviceType=serviceType
-	
+        self.serviceType=serviceType
+        
     def __str__(self):
         """Return the instance as a Moby XML
         """

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/mobyService.py,v
retrieving revision 1.2
retrieving revision 1.3
diff -u -r1.2 -r1.3
--- /home/repository/moby/moby-live/Python/bioMoby/mobyService.py	2005/01/18 13:46:22	1.2
+++ /home/repository/moby/moby-live/Python/bioMoby/mobyService.py	2005/02/01 08:52:15	1.3
@@ -6,7 +6,7 @@
     Author: Wong Yan
     
     01/17/2004: Service can be executed as a Thread, thus several queries can be made
-    		in the same time.
+                    in the same time.
 """
 
 from mobyRegister import GeneralInformations
@@ -244,7 +244,7 @@
         self.type=""
         self.category=""
         self.url=""
-	self.signatureURL=""
+        self.signatureURL=""
         self.authoritative=0
         self.inputObjects=[]
         self.outputObjects=[]
@@ -264,8 +264,8 @@
                     self.type=arg[key]
                 elif key=='url':
                     self.url=arg['url']
-		elif key=='signatureURL':
-		    self.signatureURL=arg['signatureURL']
+                elif key=='signatureURL':
+                    self.signatureURL=arg['signatureURL']
                 elif key=='authoritative':
                     self.authoritative=arg[key]
                 elif key=='contactEmail':
@@ -311,7 +311,7 @@
         
         from SOAPpy import SOAPProxy
 
-	webservice=SOAPProxy(self.url,namespace=self.namespace)
+        webservice=SOAPProxy(self.url,namespace=self.namespace)
         
         if method=="":
             if len(self.methods)==0:
@@ -325,9 +325,9 @@
 
         webservice.soapaction=self.namespace+"#"+method
 
-	if debug:
-	    webservice.config.debug=1
-	
+        if debug:
+            webservice.config.debug=1
+        
         toQuery=str(query)
 
         del  SOAPProxy
@@ -339,13 +339,13 @@
             
         #try to return a MobyContent Object instead
         from bioMoby.mobyDataTypes import MobyContent
-	mc=MobyContent()
-	mc.fromMoby(result)
+        mc=MobyContent()
+        mc.fromMoby(result)
         
         del MobyContent
 
         return mc
-    	
+            
     def __str__(self):
         """Returns The moby xml form of the web service
         """
@@ -354,7 +354,7 @@
         result.append("<serviceType>"+self.type+"</serviceType>")
         result.append("<authURI>"+self.authURI+"</authURI>")
         result.append("<URL>"+self.url+"</URL>")
-	result.append("<signatureURL>"+self.signatureURL+"</signatureURL>")
+        result.append("<signatureURL>"+self.signatureURL+"</signatureURL>")
         result.append("<contactEmail>"+self.contact+"</contactEmail>")
         result.append("<authoritativeService>"+`self.authoritative`+"</authoritativeService>")
         result.append("<Description><![CDATA["+self.description+"]]></Description>")
@@ -367,10 +367,10 @@
             elif inputObject.__class__ is dict:
                 result.append('<Collection articleName="'+inputObject.keys()[0]+'">')
 
-		for aSimple in inputObject[inputObject.keys()[0]]:
+                for aSimple in inputObject[inputObject.keys()[0]]:
                     result.append(str(aSimple))
 
-		result.append("</Collection>")
+                result.append("</Collection>")
             else:
                 from mobyExceptions import EInvalidArgument
                 raise EInvalidArgument, "Bad input object"
@@ -385,10 +385,10 @@
             elif output.__class__ is dict:
                 result.append('<Collection articleName="'+output.keys()[0]+'">')
 
-		for aSimple in output[output.keys()[0]]:
+                for aSimple in output[output.keys()[0]]:
                     result.append(str(aSimple))
-		    
-		result.append("</Collection>")
+                    
+                result.append("</Collection>")
             else:
                 from mobyExceptions import EInvalidArgument
                 raise EInvalidArgument, "Bad output object"
@@ -410,10 +410,10 @@
         """Register the service on the Moby server    
            has been added  here a code to verify that signatureURL is not empty :)
         """
-	if self.signatureURL=="":
-	    from mobyExceptions import EInvalidArgument
-	    raise EInvalidArgument, "field signatureURL cannot be empty"
-	
+        if self.signatureURL=="":
+            from mobyExceptions import EInvalidArgument
+            raise EInvalidArgument, "field signatureURL cannot be empty"
+        
         xmlinput="<registerService>"+str(self)+"</registerService>"
         
         from mobyRegister import RegistrationObject
@@ -431,32 +431,32 @@
         return result
 
     def _executeThread(self, mobyContent):
-	"""Execute the service, store the result in a field
-	"""
-	
-	self.results=self.execute(mobyContent, returnXml=(mobyContent.__class__ is str))
-		
-	
+        """Execute the service, store the result in a field
+        """
+        
+        self.results=self.execute(mobyContent, returnXml=(mobyContent.__class__ is str))
+                
+        
     def start(self, mobycontent, timeout=-1):
-	"""Start the service as it was a thread
-	"""
-	from threading import Thread
-	
-	
-	if timeout != -1:
-	    self._execThread=Thread(target=self._executeThread, args=(mobycontent,))
-	else:
-	    self._execThread=Thread(target=self._executeThread, args=(mobycontent,), timeout=timeout)
+        """Start the service as it was a thread
+        """
+        from threading import Thread
+        
+        
+        if timeout != -1:
+            self._execThread=Thread(target=self._executeThread, args=(mobycontent,))
+        else:
+            self._execThread=Thread(target=self._executeThread, args=(mobycontent,), timeout=timeout)
 
-	self._execThread.start()
-	
+        self._execThread.start()
+        
     def join(self):
-	"""Same as Thread.join
-	"""
-	self._execThread.join()
-	
-	
-	
+        """Same as Thread.join
+        """
+        self._execThread.join()
+        
+        
+        
 class ServiceList:
     """Class representing a service's list
     """
@@ -502,17 +502,17 @@
 
         for childNode in node.childNodes:
             if childNode.nodeName=="datatype":
-		if childNode.firstChild:
+                if childNode.firstChild:
                     secondary.type=childNode.firstChild.nodeValue
             elif childNode.nodeName=="default":
                 if childNode.firstChild:
-		    secondary.default=childNode.firstChild.nodeValue
+                    secondary.default=childNode.firstChild.nodeValue
             elif childNode.nodeName=="min":
                 if childNode.firstChild:
-		    secondary.min=childNode.firstChild.nodeValue
+                    secondary.min=childNode.firstChild.nodeValue
             elif childNode.nodeName=="max":
                 if childNode.firstChild:
-		    secondary.max=childNode.firstChild.nodeValue
+                    secondary.max=childNode.firstChild.nodeValue
             elif childNode.nodeName=="enum":
                 if childNode.firstChild:
                     secondary.enums.append(childNode.firstChild.nodeValue)
@@ -547,7 +547,7 @@
                     service.contact=child.firstChild.nodeValue
                 elif child.nodeName=="URL" and child.firstChild:
                     service.url=child.firstChild.nodeValue
-		elif child.nodeName=="signatureURL" and child.firstChild:
+                elif child.nodeName=="signatureURL" and child.firstChild:
                     service.signatureURL=child.firstChild.nodeValue
                 elif child.nodeName=="Input":
                     for article in child.childNodes:

From yanwong at pub.open-bio.org  Tue Feb  1 03:42:57 2005
From: yanwong at pub.open-bio.org (Yan Wong)
Date: Thu Apr 14 12:22:52 2005
Subject: [MOBY-guts] biomoby commit
Message-ID: <200502010852.j118qHRx013096@pub.open-bio.org>


yanwong
Tue Feb  1 03:52:16 EST 2005
Update of /home/repository/moby/moby-live/Python/bioMoby/ontology
In directory pub.open-bio.org:/tmp/cvs-serv12609/ontology

Modified Files:
	AlleleAssociation.py Allele_freq.py AminoAcidSequence.py 
	B64_Encoded_PNG.py B64_Encoded_Postscript.py 
	B64_encoded_PDB.py B64_encoded_gif.py B64_encoded_jpeg.py 
	BLASTText.py BasicGFFSequenceFeature.py 
	ClustalAlnFormattedText.py ClustalMsfFormattedText.py 
	CommentedAASequence.py CommentedDNASequence.py 
	CommentedRNASequence.py DNASequence.py 
	DNASequenceWithGFFFeatures.py DateTime.py Decypher_Text.py 
	Edge.py EmblFlatfile.py FASTA.py FASTA_AA.py FASTA_NA.py 
	FASTA_Text.py GFF.py GFF1.py GFF2.py GFF2_5.py GFF3.py 
	GO_Term.py GenbankFlatfile.py GenericSequence.py 
	GeneticElement.py Genotype.py Germplasm_Details.py 
	Germplasm_List.py Global_Keyword.py HBond_Pair.py 
	HFormatText.py Haplotyping_Study_obj.py ICIS_Query.py 
	ICIS_Query2.py ICIS_Query3.py IntAct_XML.py Interaction.py 
	InteractionMethod.py Interaction_partner.py Interactor.py 
	MEME_Text.py MGIS_ACCESSION.py MMP_Locus.py MO_Term_Test.py 
	MmCIFText.py Multi_key_value_pair.py 
	MyTestingDataType_11024145298313.py MyTree.py 
	NCBI_BLAST_Text.py NCBI_Blast_XML.py NCBI_Blast_XML_Gif.py 
	NCBI_Blast_XML_Gif_Map.py NCBI_MEME_Text.py 
	NucleotideSequence.py PDBFormattedText.py PDBText.py PDGJOB.py 
	PHDText.py PMUTText.py PSeaTextFormatted.py 
	PhenotypeDescription.py PubMedMEDLINE.py RNASequence.py 
	SINGER_ACCESSION.py Sample.py SchematikonMotifID.py 
	SchematikonMotifSupport.py SchematikonSegmentAttributes.py 
	SchematikonSegmentID.py SchematikonStructureAnnotation.py 
	SchematikonVorocodeName.py Scored_acronym_string.py 
	SimpleAnnotatedGIFImage.py SimpleAnnotatedJPEGImage.py 
	Simple_key_value_pair.py Snp_allele.py Snp_genotype.py 
	Study.py TEST.py TargetP_result.py Testout.py TextBase64.py 
	TextFormatted.py TextHtml.py TextPlain.py TextUuencoded.py 
	TextXml.py Text_plain.py Trait_Details.py Tree.py 
	TropGENE_ACCESSION.py TropGENE_Diversity_Matrix.py 
	TropGENE_LOCUS.py VirtualSequence.py WU_BLAST_Text.py 
	Wildcard_Query.py __init__.py 
Log Message:


moby-live/Python/bioMoby/ontology AlleleAssociation.py,1.3,1.4 Allele_freq.py,1.3,1.4 AminoAcidSequence.py,1.3,1.4 B64_Encoded_PNG.py,1.3,1.4 B64_Encoded_Postscript.py,1.3,1.4 B64_encoded_PDB.py,1.3,1.4 B64_encoded_gif.py,1.3,1.4 B64_encoded_jpeg.py,1.3,1.4 BLASTText.py,1.3,1.4 BasicGFFSequenceFeature.py,1.3,1.4 ClustalAlnFormattedText.py,1.3,1.4 ClustalMsfFormattedText.py,1.3,1.4 CommentedAASequence.py,1.3,1.4 CommentedDNASequence.py,1.3,1.4 CommentedRNASequence.py,1.3,1.4 DNASequence.py,1.3,1.4 DNASequenceWithGFFFeatures.py,1.3,1.4 DateTime.py,1.3,1.4 Decypher_Text.py,1.3,1.4 Edge.py,1.3,1.4 EmblFlatfile.py,1.3,1.4 FASTA.py,1.3,1.4 FASTA_AA.py,1.3,1.4 FASTA_NA.py,1.3,1.4 FASTA_Text.py,1.3,1.4 GFF.py,1.3,1.4 GFF1.py,1.3,1.4 GFF2.py,1.3,1.4 GFF2_5.py,1.3,1.4 GFF3.py,1.3,1.4 GO_Term.py,1.3,1.4 GenbankFlatfile.py,1.3,1.4 GenericSequence.py,1.3,1.4 GeneticElement.py,1.3,1.4 Genotype.py,1.3,1.4 Germplasm_Details.py,1.3,1.4 Germplasm_List.py,1.3,1.4 Global_Keyword.py,1.3,1.4 HBon!
d_Pair.py,1.3,1.4 HFormatText.py,1.3,1.4 Haplotyping_Study_obj.py,1.3,1.4 ICIS_Query.py,1.3,1.4 ICIS_Query2.py,1.3,1.4 ICIS_Query3.py,1.3,1.4 IntAct_XML.py,1.3,1.4 Interaction.py,1.3,1.4 InteractionMethod.py,1.3,1.4 Interaction_partner.py,1.3,1.4 Interactor.py,1.3,1.4 MEME_Text.py,1.3,1.4 MGIS_ACCESSION.py,1.3,1.4 MMP_Locus.py,1.3,1.4 MO_Term_Test.py,1.3,1.4 MmCIFText.py,1.3,1.4 Multi_key_value_pair.py,1.3,1.4 MyTestingDataType_11024145298313.py,1.3,1.4 MyTree.py,1.3,1.4 NCBI_BLAST_Text.py,1.3,1.4 NCBI_Blast_XML.py,1.3,1.4 NCBI_Blast_XML_Gif.py,1.3,1.4 NCBI_Blast_XML_Gif_Map.py,1.3,1.4 NCBI_MEME_Text.py,1.3,1.4 NucleotideSequence.py,1.3,1.4 PDBFormattedText.py,1.3,1.4 PDBText.py,1.3,1.4 PDGJOB.py,1.3,1.4 PHDText.py,1.3,1.4 PMUTText.py,1.3,1.4 PSeaTextFormatted.py,1.3,1.4 PhenotypeDescription.py,1.3,1.4 PubMedMEDLINE.py,1.3,1.4 RNASequence.py,1.3,1.4 SINGER_ACCESSION.py,1.3,1.4 Sample.py,1.3,1.4 SchematikonMotifID.py,1.3,1.4 SchematikonMotifSupport.py,1.3,1.4 SchematikonSegme!
ntAttributes.py,1.3,1.4 SchematikonSegmentID.py,1.3,1.4 Schem!
atikonStructureAnnotation.py,1.3,1.4 SchematikonVorocodeName.py,1.3,1.4 Scored_acronym_string.py,1.3,1.4 SimpleAnnotatedGIFImage.py,1.3,1.4 SimpleAnnotatedJPEGImage.py,1.3,1.4 Simple_key_value_pair.py,1.3,1.4 Snp_allele.py,1.3,1.4 Snp_genotype.py,1.3,1.4 Study.py,1.3,1.4 TEST.py,1.3,1.4 TargetP_result.py,1.3,1.4 Testout.py,1.3,1.4 TextBase64.py,1.3,1.4 TextFormatted.py,1.3,1.4 TextHtml.py,1.3,1.4 TextPlain.py,1.3,1.4 TextUuencoded.py,1.3,1.4 TextXml.py,1.3,1.4 Text_plain.py,1.3,1.4 Trait_Details.py,1.3,1.4 Tree.py,1.3,1.4 TropGENE_ACCESSION.py,1.3,1.4 TropGENE_Diversity_Matrix.py,1.3,1.4 TropGENE_LOCUS.py,1.3,1.4 VirtualSequence.py,1.3,1.4 WU_BLAST_Text.py,1.3,1.4 Wildcard_Query.py,1.3,1.4 __init__.py,1.2,1.3
===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/ontology/AlleleAssociation.py,v
retrieving revision 1.3
retrieving revision 1.4
diff -u -r1.3 -r1.4
--- /home/repository/moby/moby-live/Python/bioMoby/ontology/AlleleAssociation.py	2005/01/27 08:44:05	1.3
+++ /home/repository/moby/moby-live/Python/bioMoby/ontology/AlleleAssociation.py	2005/02/01 08:52:15	1.4
@@ -50,8 +50,7 @@
             if elt.nodeName=="CrossReference" or elt.nodeName=="moby:CrossReference":
                 self.__cross__=[]
                 for ref in elt.childNodes:
-                    if ref.nodeType==ref.ELEMENT_NODE:
-                        self.__cross__.append(um.loads(ref.toxml()))
+                    self.__cross__.append(ref.toxml())
             if elt.nodeType==elt.ELEMENT_NODE and (elt.nodeName=="String" or elt.nodeName=="moby:String") and (elt.getAttribute("articleName")=="snp" or elt.getAttribute("moby:articleName")=="snp"):
                 t=MobyString()
                 t.fromMoby(elt.toxml())

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/ontology/Allele_freq.py,v
retrieving revision 1.3
retrieving revision 1.4
diff -u -r1.3 -r1.4
--- /home/repository/moby/moby-live/Python/bioMoby/ontology/Allele_freq.py	2005/01/27 08:44:05	1.3
+++ /home/repository/moby/moby-live/Python/bioMoby/ontology/Allele_freq.py	2005/02/01 08:52:15	1.4
@@ -44,8 +44,7 @@
             if elt.nodeName=="CrossReference" or elt.nodeName=="moby:CrossReference":
                 self.__cross__=[]
                 for ref in elt.childNodes:
-                    if ref.nodeType==ref.ELEMENT_NODE:
-                        self.__cross__.append(um.loads(ref.toxml()))
+                    self.__cross__.append(ref.toxml())
             if elt.nodeType==elt.ELEMENT_NODE and (elt.nodeName=="Object" or elt.nodeName=="moby:Object") and (elt.getAttribute("articleName")=="panel_lsid" or elt.getAttribute("moby:articleName")=="panel_lsid"):
                 self.Panel_lsid=MobyObject()
                 self.Panel_lsid.fromMoby(elt.toxml())

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/ontology/AminoAcidSequence.py,v
retrieving revision 1.3
retrieving revision 1.4
diff -u -r1.3 -r1.4
--- /home/repository/moby/moby-live/Python/bioMoby/ontology/AminoAcidSequence.py	2005/01/27 08:44:05	1.3
+++ /home/repository/moby/moby-live/Python/bioMoby/ontology/AminoAcidSequence.py	2005/02/01 08:52:15	1.4
@@ -49,8 +49,7 @@
             if elt.nodeName=="CrossReference" or elt.nodeName=="moby:CrossReference":
                 self.__cross__=[]
                 for ref in elt.childNodes:
-                    if ref.nodeType==ref.ELEMENT_NODE:
-                        self.__cross__.append(um.loads(ref.toxml()))
+                    self.__cross__.append(ref.toxml())
             if elt.nodeType==elt.ELEMENT_NODE and (elt.nodeName=="Integer" or elt.nodeName=="moby:Integer") and (elt.getAttribute("articleName")=="Length" or elt.getAttribute("moby:articleName")=="Length"):
                 t=MobyInteger()
                 t.fromMoby(elt.toxml())

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/ontology/B64_Encoded_PNG.py,v
retrieving revision 1.3
retrieving revision 1.4
diff -u -r1.3 -r1.4
--- /home/repository/moby/moby-live/Python/bioMoby/ontology/B64_Encoded_PNG.py	2005/01/27 08:44:05	1.3
+++ /home/repository/moby/moby-live/Python/bioMoby/ontology/B64_Encoded_PNG.py	2005/02/01 08:52:15	1.4
@@ -46,5 +46,4 @@
             if elt.nodeName=="CrossReference" or elt.nodeName=="moby:CrossReference":
                 self.__cross__=[]
                 for ref in elt.childNodes:
-                    if ref.nodeType==ref.ELEMENT_NODE:
-                        self.__cross__.append(um.loads(ref.toxml()))
\ No newline at end of file
+                    self.__cross__.append(ref.toxml())
\ No newline at end of file

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/ontology/B64_Encoded_Postscript.py,v
retrieving revision 1.3
retrieving revision 1.4
diff -u -r1.3 -r1.4
--- /home/repository/moby/moby-live/Python/bioMoby/ontology/B64_Encoded_Postscript.py	2005/01/27 08:44:05	1.3
+++ /home/repository/moby/moby-live/Python/bioMoby/ontology/B64_Encoded_Postscript.py	2005/02/01 08:52:15	1.4
@@ -46,5 +46,4 @@
             if elt.nodeName=="CrossReference" or elt.nodeName=="moby:CrossReference":
                 self.__cross__=[]
                 for ref in elt.childNodes:
-                    if ref.nodeType==ref.ELEMENT_NODE:
-                        self.__cross__.append(um.loads(ref.toxml()))
\ No newline at end of file
+                    self.__cross__.append(ref.toxml())
\ No newline at end of file

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/ontology/B64_encoded_PDB.py,v
retrieving revision 1.3
retrieving revision 1.4
diff -u -r1.3 -r1.4
--- /home/repository/moby/moby-live/Python/bioMoby/ontology/B64_encoded_PDB.py	2005/01/27 08:44:05	1.3
+++ /home/repository/moby/moby-live/Python/bioMoby/ontology/B64_encoded_PDB.py	2005/02/01 08:52:15	1.4
@@ -46,5 +46,4 @@
             if elt.nodeName=="CrossReference" or elt.nodeName=="moby:CrossReference":
                 self.__cross__=[]
                 for ref in elt.childNodes:
-                    if ref.nodeType==ref.ELEMENT_NODE:
-                        self.__cross__.append(um.loads(ref.toxml()))
\ No newline at end of file
+                    self.__cross__.append(ref.toxml())
\ No newline at end of file

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/ontology/B64_encoded_gif.py,v
retrieving revision 1.3
retrieving revision 1.4
diff -u -r1.3 -r1.4
--- /home/repository/moby/moby-live/Python/bioMoby/ontology/B64_encoded_gif.py	2005/01/27 08:44:05	1.3
+++ /home/repository/moby/moby-live/Python/bioMoby/ontology/B64_encoded_gif.py	2005/02/01 08:52:15	1.4
@@ -46,5 +46,4 @@
             if elt.nodeName=="CrossReference" or elt.nodeName=="moby:CrossReference":
                 self.__cross__=[]
                 for ref in elt.childNodes:
-                    if ref.nodeType==ref.ELEMENT_NODE:
-                        self.__cross__.append(um.loads(ref.toxml()))
\ No newline at end of file
+                    self.__cross__.append(ref.toxml())
\ No newline at end of file

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/ontology/B64_encoded_jpeg.py,v
retrieving revision 1.3
retrieving revision 1.4
diff -u -r1.3 -r1.4
--- /home/repository/moby/moby-live/Python/bioMoby/ontology/B64_encoded_jpeg.py	2005/01/27 08:44:05	1.3
+++ /home/repository/moby/moby-live/Python/bioMoby/ontology/B64_encoded_jpeg.py	2005/02/01 08:52:15	1.4
@@ -46,5 +46,4 @@
             if elt.nodeName=="CrossReference" or elt.nodeName=="moby:CrossReference":
                 self.__cross__=[]
                 for ref in elt.childNodes:
-                    if ref.nodeType==ref.ELEMENT_NODE:
-                        self.__cross__.append(um.loads(ref.toxml()))
\ No newline at end of file
+                    self.__cross__.append(ref.toxml())
\ No newline at end of file

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/ontology/BLASTText.py,v
retrieving revision 1.3
retrieving revision 1.4
diff -u -r1.3 -r1.4
--- /home/repository/moby/moby-live/Python/bioMoby/ontology/BLASTText.py	2005/01/27 08:44:05	1.3
+++ /home/repository/moby/moby-live/Python/bioMoby/ontology/BLASTText.py	2005/02/01 08:52:15	1.4
@@ -46,5 +46,4 @@
             if elt.nodeName=="CrossReference" or elt.nodeName=="moby:CrossReference":
                 self.__cross__=[]
                 for ref in elt.childNodes:
-                    if ref.nodeType==ref.ELEMENT_NODE:
-                        self.__cross__.append(um.loads(ref.toxml()))
\ No newline at end of file
+                    self.__cross__.append(ref.toxml())
\ No newline at end of file

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/ontology/BasicGFFSequenceFeature.py,v
retrieving revision 1.3
retrieving revision 1.4
diff -u -r1.3 -r1.4
--- /home/repository/moby/moby-live/Python/bioMoby/ontology/BasicGFFSequenceFeature.py	2005/01/27 08:44:05	1.3
+++ /home/repository/moby/moby-live/Python/bioMoby/ontology/BasicGFFSequenceFeature.py	2005/02/01 08:52:15	1.4
@@ -60,8 +60,7 @@
             if elt.nodeName=="CrossReference" or elt.nodeName=="moby:CrossReference":
                 self.__cross__=[]
                 for ref in elt.childNodes:
-                    if ref.nodeType==ref.ELEMENT_NODE:
-                        self.__cross__.append(um.loads(ref.toxml()))
+                    self.__cross__.append(ref.toxml())
             if elt.nodeType==elt.ELEMENT_NODE and (elt.nodeName=="String" or elt.nodeName=="moby:String") and (elt.getAttribute("articleName")=="reference" or elt.getAttribute("moby:articleName")=="reference"):
                 t=MobyString()
                 t.fromMoby(elt.toxml())

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/ontology/ClustalAlnFormattedText.py,v
retrieving revision 1.3
retrieving revision 1.4
diff -u -r1.3 -r1.4
--- /home/repository/moby/moby-live/Python/bioMoby/ontology/ClustalAlnFormattedText.py	2005/01/27 08:44:05	1.3
+++ /home/repository/moby/moby-live/Python/bioMoby/ontology/ClustalAlnFormattedText.py	2005/02/01 08:52:15	1.4
@@ -46,5 +46,4 @@
             if elt.nodeName=="CrossReference" or elt.nodeName=="moby:CrossReference":
                 self.__cross__=[]
                 for ref in elt.childNodes:
-                    if ref.nodeType==ref.ELEMENT_NODE:
-                        self.__cross__.append(um.loads(ref.toxml()))
\ No newline at end of file
+                    self.__cross__.append(ref.toxml())
\ No newline at end of file

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/ontology/ClustalMsfFormattedText.py,v
retrieving revision 1.3
retrieving revision 1.4
diff -u -r1.3 -r1.4
--- /home/repository/moby/moby-live/Python/bioMoby/ontology/ClustalMsfFormattedText.py	2005/01/27 08:44:05	1.3
+++ /home/repository/moby/moby-live/Python/bioMoby/ontology/ClustalMsfFormattedText.py	2005/02/01 08:52:15	1.4
@@ -46,5 +46,4 @@
             if elt.nodeName=="CrossReference" or elt.nodeName=="moby:CrossReference":
                 self.__cross__=[]
                 for ref in elt.childNodes:
-                    if ref.nodeType==ref.ELEMENT_NODE:
-                        self.__cross__.append(um.loads(ref.toxml()))
\ No newline at end of file
+                    self.__cross__.append(ref.toxml())
\ No newline at end of file

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/ontology/CommentedAASequence.py,v
retrieving revision 1.3
retrieving revision 1.4
diff -u -r1.3 -r1.4
--- /home/repository/moby/moby-live/Python/bioMoby/ontology/CommentedAASequence.py	2005/01/27 08:44:05	1.3
+++ /home/repository/moby/moby-live/Python/bioMoby/ontology/CommentedAASequence.py	2005/02/01 08:52:15	1.4
@@ -50,8 +50,7 @@
             if elt.nodeName=="CrossReference" or elt.nodeName=="moby:CrossReference":
                 self.__cross__=[]
                 for ref in elt.childNodes:
-                    if ref.nodeType==ref.ELEMENT_NODE:
-                        self.__cross__.append(um.loads(ref.toxml()))
+                    self.__cross__.append(ref.toxml())
             if elt.nodeType==elt.ELEMENT_NODE and (elt.nodeName=="Integer" or elt.nodeName=="moby:Integer") and (elt.getAttribute("articleName")=="Length" or elt.getAttribute("moby:articleName")=="Length"):
                 t=MobyInteger()
                 t.fromMoby(elt.toxml())

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/ontology/CommentedDNASequence.py,v
retrieving revision 1.3
retrieving revision 1.4
diff -u -r1.3 -r1.4
--- /home/repository/moby/moby-live/Python/bioMoby/ontology/CommentedDNASequence.py	2005/01/27 08:44:05	1.3
+++ /home/repository/moby/moby-live/Python/bioMoby/ontology/CommentedDNASequence.py	2005/02/01 08:52:15	1.4
@@ -50,8 +50,7 @@
             if elt.nodeName=="CrossReference" or elt.nodeName=="moby:CrossReference":
                 self.__cross__=[]
                 for ref in elt.childNodes:
-                    if ref.nodeType==ref.ELEMENT_NODE:
-                        self.__cross__.append(um.loads(ref.toxml()))
+                    self.__cross__.append(ref.toxml())
             if elt.nodeType==elt.ELEMENT_NODE and (elt.nodeName=="Integer" or elt.nodeName=="moby:Integer") and (elt.getAttribute("articleName")=="Length" or elt.getAttribute("moby:articleName")=="Length"):
                 t=MobyInteger()
                 t.fromMoby(elt.toxml())

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/ontology/CommentedRNASequence.py,v
retrieving revision 1.3
retrieving revision 1.4
diff -u -r1.3 -r1.4
--- /home/repository/moby/moby-live/Python/bioMoby/ontology/CommentedRNASequence.py	2005/01/27 08:44:05	1.3
+++ /home/repository/moby/moby-live/Python/bioMoby/ontology/CommentedRNASequence.py	2005/02/01 08:52:15	1.4
@@ -50,8 +50,7 @@
             if elt.nodeName=="CrossReference" or elt.nodeName=="moby:CrossReference":
                 self.__cross__=[]
                 for ref in elt.childNodes:
-                    if ref.nodeType==ref.ELEMENT_NODE:
-                        self.__cross__.append(um.loads(ref.toxml()))
+                    self.__cross__.append(ref.toxml())
             if elt.nodeType==elt.ELEMENT_NODE and (elt.nodeName=="Integer" or elt.nodeName=="moby:Integer") and (elt.getAttribute("articleName")=="Length" or elt.getAttribute("moby:articleName")=="Length"):
                 t=MobyInteger()
                 t.fromMoby(elt.toxml())

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/ontology/DNASequence.py,v
retrieving revision 1.3
retrieving revision 1.4
diff -u -r1.3 -r1.4
--- /home/repository/moby/moby-live/Python/bioMoby/ontology/DNASequence.py	2005/01/27 08:44:05	1.3
+++ /home/repository/moby/moby-live/Python/bioMoby/ontology/DNASequence.py	2005/02/01 08:52:15	1.4
@@ -49,8 +49,7 @@
             if elt.nodeName=="CrossReference" or elt.nodeName=="moby:CrossReference":
                 self.__cross__=[]
                 for ref in elt.childNodes:
-                    if ref.nodeType==ref.ELEMENT_NODE:
-                        self.__cross__.append(um.loads(ref.toxml()))
+                    self.__cross__.append(ref.toxml())
             if elt.nodeType==elt.ELEMENT_NODE and (elt.nodeName=="Integer" or elt.nodeName=="moby:Integer") and (elt.getAttribute("articleName")=="Length" or elt.getAttribute("moby:articleName")=="Length"):
                 t=MobyInteger()
                 t.fromMoby(elt.toxml())

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/ontology/DNASequenceWithGFFFeatures.py,v
retrieving revision 1.3
retrieving revision 1.4
diff -u -r1.3 -r1.4
--- /home/repository/moby/moby-live/Python/bioMoby/ontology/DNASequenceWithGFFFeatures.py	2005/01/27 08:44:05	1.3
+++ /home/repository/moby/moby-live/Python/bioMoby/ontology/DNASequenceWithGFFFeatures.py	2005/02/01 08:52:15	1.4
@@ -52,8 +52,7 @@
             if elt.nodeName=="CrossReference" or elt.nodeName=="moby:CrossReference":
                 self.__cross__=[]
                 for ref in elt.childNodes:
-                    if ref.nodeType==ref.ELEMENT_NODE:
-                        self.__cross__.append(um.loads(ref.toxml()))
+                    self.__cross__.append(ref.toxml())
             if elt.nodeType==elt.ELEMENT_NODE and (elt.nodeName=="Integer" or elt.nodeName=="moby:Integer") and (elt.getAttribute("articleName")=="Length" or elt.getAttribute("moby:articleName")=="Length"):
                 t=MobyInteger()
                 t.fromMoby(elt.toxml())

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/ontology/DateTime.py,v
retrieving revision 1.3
retrieving revision 1.4
diff -u -r1.3 -r1.4
--- /home/repository/moby/moby-live/Python/bioMoby/ontology/DateTime.py	2005/01/27 08:44:05	1.3
+++ /home/repository/moby/moby-live/Python/bioMoby/ontology/DateTime.py	2005/02/01 08:52:15	1.4
@@ -46,5 +46,4 @@
             if elt.nodeName=="CrossReference" or elt.nodeName=="moby:CrossReference":
                 self.__cross__=[]
                 for ref in elt.childNodes:
-                    if ref.nodeType==ref.ELEMENT_NODE:
-                        self.__cross__.append(um.loads(ref.toxml()))
\ No newline at end of file
+                    self.__cross__.append(ref.toxml())
\ No newline at end of file

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/ontology/Decypher_Text.py,v
retrieving revision 1.3
retrieving revision 1.4
diff -u -r1.3 -r1.4
--- /home/repository/moby/moby-live/Python/bioMoby/ontology/Decypher_Text.py	2005/01/27 08:44:05	1.3
+++ /home/repository/moby/moby-live/Python/bioMoby/ontology/Decypher_Text.py	2005/02/01 08:52:15	1.4
@@ -46,5 +46,4 @@
             if elt.nodeName=="CrossReference" or elt.nodeName=="moby:CrossReference":
                 self.__cross__=[]
                 for ref in elt.childNodes:
-                    if ref.nodeType==ref.ELEMENT_NODE:
-                        self.__cross__.append(um.loads(ref.toxml()))
\ No newline at end of file
+                    self.__cross__.append(ref.toxml())
\ No newline at end of file

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/ontology/Edge.py,v
retrieving revision 1.3
retrieving revision 1.4
diff -u -r1.3 -r1.4
--- /home/repository/moby/moby-live/Python/bioMoby/ontology/Edge.py	2005/01/27 08:44:05	1.3
+++ /home/repository/moby/moby-live/Python/bioMoby/ontology/Edge.py	2005/02/01 08:52:15	1.4
@@ -49,8 +49,7 @@
             if elt.nodeName=="CrossReference" or elt.nodeName=="moby:CrossReference":
                 self.__cross__=[]
                 for ref in elt.childNodes:
-                    if ref.nodeType==ref.ELEMENT_NODE:
-                        self.__cross__.append(um.loads(ref.toxml()))
+                    self.__cross__.append(ref.toxml())
             if elt.nodeType==elt.ELEMENT_NODE and (elt.nodeName=="String" or elt.nodeName=="moby:String") and (elt.getAttribute("articleName")=="partner" or elt.getAttribute("moby:articleName")=="partner"):
                 t=MobyString()
                 t.fromMoby(elt.toxml())

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/ontology/EmblFlatfile.py,v
retrieving revision 1.3
retrieving revision 1.4
diff -u -r1.3 -r1.4
--- /home/repository/moby/moby-live/Python/bioMoby/ontology/EmblFlatfile.py	2005/01/27 08:44:05	1.3
+++ /home/repository/moby/moby-live/Python/bioMoby/ontology/EmblFlatfile.py	2005/02/01 08:52:15	1.4
@@ -46,5 +46,4 @@
             if elt.nodeName=="CrossReference" or elt.nodeName=="moby:CrossReference":
                 self.__cross__=[]
                 for ref in elt.childNodes:
-                    if ref.nodeType==ref.ELEMENT_NODE:
-                        self.__cross__.append(um.loads(ref.toxml()))
\ No newline at end of file
+                    self.__cross__.append(ref.toxml())
\ No newline at end of file

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/ontology/FASTA.py,v
retrieving revision 1.3
retrieving revision 1.4
diff -u -r1.3 -r1.4
--- /home/repository/moby/moby-live/Python/bioMoby/ontology/FASTA.py	2005/01/27 08:44:05	1.3
+++ /home/repository/moby/moby-live/Python/bioMoby/ontology/FASTA.py	2005/02/01 08:52:15	1.4
@@ -46,5 +46,4 @@
             if elt.nodeName=="CrossReference" or elt.nodeName=="moby:CrossReference":
                 self.__cross__=[]
                 for ref in elt.childNodes:
-                    if ref.nodeType==ref.ELEMENT_NODE:
-                        self.__cross__.append(um.loads(ref.toxml()))
\ No newline at end of file
+                    self.__cross__.append(ref.toxml())
\ No newline at end of file

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/ontology/FASTA_AA.py,v
retrieving revision 1.3
retrieving revision 1.4
diff -u -r1.3 -r1.4
--- /home/repository/moby/moby-live/Python/bioMoby/ontology/FASTA_AA.py	2005/01/27 08:44:05	1.3
+++ /home/repository/moby/moby-live/Python/bioMoby/ontology/FASTA_AA.py	2005/02/01 08:52:15	1.4
@@ -46,5 +46,4 @@
             if elt.nodeName=="CrossReference" or elt.nodeName=="moby:CrossReference":
                 self.__cross__=[]
                 for ref in elt.childNodes:
-                    if ref.nodeType==ref.ELEMENT_NODE:
-                        self.__cross__.append(um.loads(ref.toxml()))
\ No newline at end of file
+                    self.__cross__.append(ref.toxml())
\ No newline at end of file

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/ontology/FASTA_NA.py,v
retrieving revision 1.3
retrieving revision 1.4
diff -u -r1.3 -r1.4
--- /home/repository/moby/moby-live/Python/bioMoby/ontology/FASTA_NA.py	2005/01/27 08:44:05	1.3
+++ /home/repository/moby/moby-live/Python/bioMoby/ontology/FASTA_NA.py	2005/02/01 08:52:15	1.4
@@ -46,5 +46,4 @@
             if elt.nodeName=="CrossReference" or elt.nodeName=="moby:CrossReference":
                 self.__cross__=[]
                 for ref in elt.childNodes:
-                    if ref.nodeType==ref.ELEMENT_NODE:
-                        self.__cross__.append(um.loads(ref.toxml()))
\ No newline at end of file
+                    self.__cross__.append(ref.toxml())
\ No newline at end of file

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/ontology/FASTA_Text.py,v
retrieving revision 1.3
retrieving revision 1.4
diff -u -r1.3 -r1.4
--- /home/repository/moby/moby-live/Python/bioMoby/ontology/FASTA_Text.py	2005/01/27 08:44:05	1.3
+++ /home/repository/moby/moby-live/Python/bioMoby/ontology/FASTA_Text.py	2005/02/01 08:52:15	1.4
@@ -46,5 +46,4 @@
             if elt.nodeName=="CrossReference" or elt.nodeName=="moby:CrossReference":
                 self.__cross__=[]
                 for ref in elt.childNodes:
-                    if ref.nodeType==ref.ELEMENT_NODE:
-                        self.__cross__.append(um.loads(ref.toxml()))
\ No newline at end of file
+                    self.__cross__.append(ref.toxml())
\ No newline at end of file

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/ontology/GFF.py,v
retrieving revision 1.3
retrieving revision 1.4
diff -u -r1.3 -r1.4
--- /home/repository/moby/moby-live/Python/bioMoby/ontology/GFF.py	2005/01/27 08:44:05	1.3
+++ /home/repository/moby/moby-live/Python/bioMoby/ontology/GFF.py	2005/02/01 08:52:15	1.4
@@ -46,5 +46,4 @@
             if elt.nodeName=="CrossReference" or elt.nodeName=="moby:CrossReference":
                 self.__cross__=[]
                 for ref in elt.childNodes:
-                    if ref.nodeType==ref.ELEMENT_NODE:
-                        self.__cross__.append(um.loads(ref.toxml()))
\ No newline at end of file
+                    self.__cross__.append(ref.toxml())
\ No newline at end of file

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/ontology/GFF1.py,v
retrieving revision 1.3
retrieving revision 1.4
diff -u -r1.3 -r1.4
--- /home/repository/moby/moby-live/Python/bioMoby/ontology/GFF1.py	2005/01/27 08:44:05	1.3
+++ /home/repository/moby/moby-live/Python/bioMoby/ontology/GFF1.py	2005/02/01 08:52:15	1.4
@@ -46,5 +46,4 @@
             if elt.nodeName=="CrossReference" or elt.nodeName=="moby:CrossReference":
                 self.__cross__=[]
                 for ref in elt.childNodes:
-                    if ref.nodeType==ref.ELEMENT_NODE:
-                        self.__cross__.append(um.loads(ref.toxml()))
\ No newline at end of file
+                    self.__cross__.append(ref.toxml())
\ No newline at end of file

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/ontology/GFF2.py,v
retrieving revision 1.3
retrieving revision 1.4
diff -u -r1.3 -r1.4
--- /home/repository/moby/moby-live/Python/bioMoby/ontology/GFF2.py	2005/01/27 08:44:05	1.3
+++ /home/repository/moby/moby-live/Python/bioMoby/ontology/GFF2.py	2005/02/01 08:52:15	1.4
@@ -46,5 +46,4 @@
             if elt.nodeName=="CrossReference" or elt.nodeName=="moby:CrossReference":
                 self.__cross__=[]
                 for ref in elt.childNodes:
-                    if ref.nodeType==ref.ELEMENT_NODE:
-                        self.__cross__.append(um.loads(ref.toxml()))
\ No newline at end of file
+                    self.__cross__.append(ref.toxml())
\ No newline at end of file

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/ontology/GFF2_5.py,v
retrieving revision 1.3
retrieving revision 1.4
diff -u -r1.3 -r1.4
--- /home/repository/moby/moby-live/Python/bioMoby/ontology/GFF2_5.py	2005/01/27 08:44:05	1.3
+++ /home/repository/moby/moby-live/Python/bioMoby/ontology/GFF2_5.py	2005/02/01 08:52:15	1.4
@@ -46,5 +46,4 @@
             if elt.nodeName=="CrossReference" or elt.nodeName=="moby:CrossReference":
                 self.__cross__=[]
                 for ref in elt.childNodes:
-                    if ref.nodeType==ref.ELEMENT_NODE:
-                        self.__cross__.append(um.loads(ref.toxml()))
\ No newline at end of file
+                    self.__cross__.append(ref.toxml())
\ No newline at end of file

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/ontology/GFF3.py,v
retrieving revision 1.3
retrieving revision 1.4
diff -u -r1.3 -r1.4
--- /home/repository/moby/moby-live/Python/bioMoby/ontology/GFF3.py	2005/01/27 08:44:05	1.3
+++ /home/repository/moby/moby-live/Python/bioMoby/ontology/GFF3.py	2005/02/01 08:52:15	1.4
@@ -46,5 +46,4 @@
             if elt.nodeName=="CrossReference" or elt.nodeName=="moby:CrossReference":
                 self.__cross__=[]
                 for ref in elt.childNodes:
-                    if ref.nodeType==ref.ELEMENT_NODE:
-                        self.__cross__.append(um.loads(ref.toxml()))
\ No newline at end of file
+                    self.__cross__.append(ref.toxml())
\ No newline at end of file

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/ontology/GO_Term.py,v
retrieving revision 1.3
retrieving revision 1.4
diff -u -r1.3 -r1.4
--- /home/repository/moby/moby-live/Python/bioMoby/ontology/GO_Term.py	2005/01/27 08:44:05	1.3
+++ /home/repository/moby/moby-live/Python/bioMoby/ontology/GO_Term.py	2005/02/01 08:52:15	1.4
@@ -48,8 +48,7 @@
             if elt.nodeName=="CrossReference" or elt.nodeName=="moby:CrossReference":
                 self.__cross__=[]
                 for ref in elt.childNodes:
-                    if ref.nodeType==ref.ELEMENT_NODE:
-                        self.__cross__.append(um.loads(ref.toxml()))
+                    self.__cross__.append(ref.toxml())
             if elt.nodeType==elt.ELEMENT_NODE and (elt.nodeName=="String" or elt.nodeName=="moby:String") and (elt.getAttribute("articleName")=="Term" or elt.getAttribute("moby:articleName")=="Term"):
                 t=MobyString()
                 t.fromMoby(elt.toxml())

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/ontology/GenbankFlatfile.py,v
retrieving revision 1.3
retrieving revision 1.4
diff -u -r1.3 -r1.4
--- /home/repository/moby/moby-live/Python/bioMoby/ontology/GenbankFlatfile.py	2005/01/27 08:44:05	1.3
+++ /home/repository/moby/moby-live/Python/bioMoby/ontology/GenbankFlatfile.py	2005/02/01 08:52:15	1.4
@@ -46,5 +46,4 @@
             if elt.nodeName=="CrossReference" or elt.nodeName=="moby:CrossReference":
                 self.__cross__=[]
                 for ref in elt.childNodes:
-                    if ref.nodeType==ref.ELEMENT_NODE:
-                        self.__cross__.append(um.loads(ref.toxml()))
\ No newline at end of file
+                    self.__cross__.append(ref.toxml())
\ No newline at end of file

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/ontology/GenericSequence.py,v
retrieving revision 1.3
retrieving revision 1.4
diff -u -r1.3 -r1.4
--- /home/repository/moby/moby-live/Python/bioMoby/ontology/GenericSequence.py	2005/01/27 08:44:05	1.3
+++ /home/repository/moby/moby-live/Python/bioMoby/ontology/GenericSequence.py	2005/02/01 08:52:15	1.4
@@ -49,8 +49,7 @@
             if elt.nodeName=="CrossReference" or elt.nodeName=="moby:CrossReference":
                 self.__cross__=[]
                 for ref in elt.childNodes:
-                    if ref.nodeType==ref.ELEMENT_NODE:
-                        self.__cross__.append(um.loads(ref.toxml()))
+                    self.__cross__.append(ref.toxml())
             if elt.nodeType==elt.ELEMENT_NODE and (elt.nodeName=="Integer" or elt.nodeName=="moby:Integer") and (elt.getAttribute("articleName")=="Length" or elt.getAttribute("moby:articleName")=="Length"):
                 t=MobyInteger()
                 t.fromMoby(elt.toxml())

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/ontology/GeneticElement.py,v
retrieving revision 1.3
retrieving revision 1.4
diff -u -r1.3 -r1.4
--- /home/repository/moby/moby-live/Python/bioMoby/ontology/GeneticElement.py	2005/01/27 08:44:05	1.3
+++ /home/repository/moby/moby-live/Python/bioMoby/ontology/GeneticElement.py	2005/02/01 08:52:15	1.4
@@ -47,8 +47,7 @@
             if elt.nodeName=="CrossReference" or elt.nodeName=="moby:CrossReference":
                 self.__cross__=[]
                 for ref in elt.childNodes:
-                    if ref.nodeType==ref.ELEMENT_NODE:
-                        self.__cross__.append(um.loads(ref.toxml()))
+                    self.__cross__.append(ref.toxml())
             if elt.nodeType==elt.ELEMENT_NODE and (elt.nodeName=="String" or elt.nodeName=="moby:String") and (elt.getAttribute("articleName")=="GeneticElement" or elt.getAttribute("moby:articleName")=="GeneticElement"):
                 t=MobyString()
                 t.fromMoby(elt.toxml())

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/ontology/Genotype.py,v
retrieving revision 1.3
retrieving revision 1.4
diff -u -r1.3 -r1.4
--- /home/repository/moby/moby-live/Python/bioMoby/ontology/Genotype.py	2005/01/27 08:44:05	1.3
+++ /home/repository/moby/moby-live/Python/bioMoby/ontology/Genotype.py	2005/02/01 08:52:15	1.4
@@ -49,8 +49,7 @@
             if elt.nodeName=="CrossReference" or elt.nodeName=="moby:CrossReference":
                 self.__cross__=[]
                 for ref in elt.childNodes:
-                    if ref.nodeType==ref.ELEMENT_NODE:
-                        self.__cross__.append(um.loads(ref.toxml()))
+                    self.__cross__.append(ref.toxml())
             if elt.nodeType==elt.ELEMENT_NODE and (elt.nodeName=="String" or elt.nodeName=="moby:String") and (elt.getAttribute("articleName")=="snp" or elt.getAttribute("moby:articleName")=="snp"):
                 t=MobyString()
                 t.fromMoby(elt.toxml())

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/ontology/Germplasm_Details.py,v
retrieving revision 1.3
retrieving revision 1.4
diff -u -r1.3 -r1.4
--- /home/repository/moby/moby-live/Python/bioMoby/ontology/Germplasm_Details.py	2005/01/27 08:44:05	1.3
+++ /home/repository/moby/moby-live/Python/bioMoby/ontology/Germplasm_Details.py	2005/02/01 08:52:15	1.4
@@ -55,8 +55,7 @@
             if elt.nodeName=="CrossReference" or elt.nodeName=="moby:CrossReference":
                 self.__cross__=[]
                 for ref in elt.childNodes:
-                    if ref.nodeType==ref.ELEMENT_NODE:
-                        self.__cross__.append(um.loads(ref.toxml()))
+                    self.__cross__.append(ref.toxml())
             if elt.nodeType==elt.ELEMENT_NODE and (elt.nodeName=="Integer" or elt.nodeName=="moby:Integer") and (elt.getAttribute("articleName")=="date" or elt.getAttribute("moby:articleName")=="date"):
                 t=MobyInteger()
                 t.fromMoby(elt.toxml())

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/ontology/Germplasm_List.py,v
retrieving revision 1.3
retrieving revision 1.4
diff -u -r1.3 -r1.4
--- /home/repository/moby/moby-live/Python/bioMoby/ontology/Germplasm_List.py	2005/01/27 08:44:05	1.3
+++ /home/repository/moby/moby-live/Python/bioMoby/ontology/Germplasm_List.py	2005/02/01 08:52:16	1.4
@@ -55,8 +55,7 @@
             if elt.nodeName=="CrossReference" or elt.nodeName=="moby:CrossReference":
                 self.__cross__=[]
                 for ref in elt.childNodes:
-                    if ref.nodeType==ref.ELEMENT_NODE:
-                        self.__cross__.append(um.loads(ref.toxml()))
+                    self.__cross__.append(ref.toxml())
             if elt.nodeType==elt.ELEMENT_NODE and (elt.nodeName=="Integer" or elt.nodeName=="moby:Integer") and (elt.getAttribute("articleName")=="germplasm_id" or elt.getAttribute("moby:articleName")=="germplasm_id"):
                 t=MobyInteger()
                 t.fromMoby(elt.toxml())

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/ontology/Global_Keyword.py,v
retrieving revision 1.3
retrieving revision 1.4
diff -u -r1.3 -r1.4
--- /home/repository/moby/moby-live/Python/bioMoby/ontology/Global_Keyword.py	2005/01/27 08:44:05	1.3
+++ /home/repository/moby/moby-live/Python/bioMoby/ontology/Global_Keyword.py	2005/02/01 08:52:16	1.4
@@ -45,5 +45,4 @@
             if elt.nodeName=="CrossReference" or elt.nodeName=="moby:CrossReference":
                 self.__cross__=[]
                 for ref in elt.childNodes:
-                    if ref.nodeType==ref.ELEMENT_NODE:
-                        self.__cross__.append(um.loads(ref.toxml()))
\ No newline at end of file
+                    self.__cross__.append(ref.toxml())
\ No newline at end of file

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/ontology/HBond_Pair.py,v
retrieving revision 1.3
retrieving revision 1.4
diff -u -r1.3 -r1.4
--- /home/repository/moby/moby-live/Python/bioMoby/ontology/HBond_Pair.py	2005/01/27 08:44:05	1.3
+++ /home/repository/moby/moby-live/Python/bioMoby/ontology/HBond_Pair.py	2005/02/01 08:52:16	1.4
@@ -49,8 +49,7 @@
             if elt.nodeName=="CrossReference" or elt.nodeName=="moby:CrossReference":
                 self.__cross__=[]
                 for ref in elt.childNodes:
-                    if ref.nodeType==ref.ELEMENT_NODE:
-                        self.__cross__.append(um.loads(ref.toxml()))
+                    self.__cross__.append(ref.toxml())
             if elt.nodeType==elt.ELEMENT_NODE and (elt.nodeName=="String" or elt.nodeName=="moby:String") and (elt.getAttribute("articleName")=="A" or elt.getAttribute("moby:articleName")=="A"):
                 t=MobyString()
                 t.fromMoby(elt.toxml())

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/ontology/HFormatText.py,v
retrieving revision 1.3
retrieving revision 1.4
diff -u -r1.3 -r1.4
--- /home/repository/moby/moby-live/Python/bioMoby/ontology/HFormatText.py	2005/01/27 08:44:05	1.3
+++ /home/repository/moby/moby-live/Python/bioMoby/ontology/HFormatText.py	2005/02/01 08:52:16	1.4
@@ -46,5 +46,4 @@
             if elt.nodeName=="CrossReference" or elt.nodeName=="moby:CrossReference":
                 self.__cross__=[]
                 for ref in elt.childNodes:
-                    if ref.nodeType==ref.ELEMENT_NODE:
-                        self.__cross__.append(um.loads(ref.toxml()))
\ No newline at end of file
+                    self.__cross__.append(ref.toxml())
\ No newline at end of file

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/ontology/Haplotyping_Study_obj.py,v
retrieving revision 1.3
retrieving revision 1.4
diff -u -r1.3 -r1.4
--- /home/repository/moby/moby-live/Python/bioMoby/ontology/Haplotyping_Study_obj.py	2005/01/27 08:44:05	1.3
+++ /home/repository/moby/moby-live/Python/bioMoby/ontology/Haplotyping_Study_obj.py	2005/02/01 08:52:16	1.4
@@ -45,5 +45,4 @@
             if elt.nodeName=="CrossReference" or elt.nodeName=="moby:CrossReference":
                 self.__cross__=[]
                 for ref in elt.childNodes:
-                    if ref.nodeType==ref.ELEMENT_NODE:
-                        self.__cross__.append(um.loads(ref.toxml()))
\ No newline at end of file
+                    self.__cross__.append(ref.toxml())
\ No newline at end of file

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/ontology/ICIS_Query.py,v
retrieving revision 1.3
retrieving revision 1.4
diff -u -r1.3 -r1.4
--- /home/repository/moby/moby-live/Python/bioMoby/ontology/ICIS_Query.py	2005/01/27 08:44:05	1.3
+++ /home/repository/moby/moby-live/Python/bioMoby/ontology/ICIS_Query.py	2005/02/01 08:52:16	1.4
@@ -50,8 +50,7 @@
             if elt.nodeName=="CrossReference" or elt.nodeName=="moby:CrossReference":
                 self.__cross__=[]
                 for ref in elt.childNodes:
-                    if ref.nodeType==ref.ELEMENT_NODE:
-                        self.__cross__.append(um.loads(ref.toxml()))
+                    self.__cross__.append(ref.toxml())
             if elt.nodeType==elt.ELEMENT_NODE and (elt.nodeName=="Integer" or elt.nodeName=="moby:Integer") and (elt.getAttribute("articleName")=="end_row" or elt.getAttribute("moby:articleName")=="end_row"):
                 t=MobyInteger()
                 t.fromMoby(elt.toxml())

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/ontology/ICIS_Query2.py,v
retrieving revision 1.3
retrieving revision 1.4
diff -u -r1.3 -r1.4
--- /home/repository/moby/moby-live/Python/bioMoby/ontology/ICIS_Query2.py	2005/01/27 08:44:05	1.3
+++ /home/repository/moby/moby-live/Python/bioMoby/ontology/ICIS_Query2.py	2005/02/01 08:52:16	1.4
@@ -52,8 +52,7 @@
             if elt.nodeName=="CrossReference" or elt.nodeName=="moby:CrossReference":
                 self.__cross__=[]
                 for ref in elt.childNodes:
-                    if ref.nodeType==ref.ELEMENT_NODE:
-                        self.__cross__.append(um.loads(ref.toxml()))
+                    self.__cross__.append(ref.toxml())
             if elt.nodeType==elt.ELEMENT_NODE and (elt.nodeName=="String" or elt.nodeName=="moby:String") and (elt.getAttribute("articleName")=="search_text1" or elt.getAttribute("moby:articleName")=="search_text1"):
                 t=MobyString()
                 t.fromMoby(elt.toxml())

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/ontology/ICIS_Query3.py,v
retrieving revision 1.3
retrieving revision 1.4
diff -u -r1.3 -r1.4
--- /home/repository/moby/moby-live/Python/bioMoby/ontology/ICIS_Query3.py	2005/01/27 08:44:05	1.3
+++ /home/repository/moby/moby-live/Python/bioMoby/ontology/ICIS_Query3.py	2005/02/01 08:52:16	1.4
@@ -50,8 +50,7 @@
             if elt.nodeName=="CrossReference" or elt.nodeName=="moby:CrossReference":
                 self.__cross__=[]
                 for ref in elt.childNodes:
-                    if ref.nodeType==ref.ELEMENT_NODE:
-                        self.__cross__.append(um.loads(ref.toxml()))
+                    self.__cross__.append(ref.toxml())
             if elt.nodeType==elt.ELEMENT_NODE and (elt.nodeName=="Integer" or elt.nodeName=="moby:Integer") and (elt.getAttribute("articleName")=="search_text1" or elt.getAttribute("moby:articleName")=="search_text1"):
                 t=MobyInteger()
                 t.fromMoby(elt.toxml())

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/ontology/IntAct_XML.py,v
retrieving revision 1.3
retrieving revision 1.4
diff -u -r1.3 -r1.4
--- /home/repository/moby/moby-live/Python/bioMoby/ontology/IntAct_XML.py	2005/01/27 08:44:05	1.3
+++ /home/repository/moby/moby-live/Python/bioMoby/ontology/IntAct_XML.py	2005/02/01 08:52:16	1.4
@@ -46,5 +46,4 @@
             if elt.nodeName=="CrossReference" or elt.nodeName=="moby:CrossReference":
                 self.__cross__=[]
                 for ref in elt.childNodes:
-                    if ref.nodeType==ref.ELEMENT_NODE:
-                        self.__cross__.append(um.loads(ref.toxml()))
\ No newline at end of file
+                    self.__cross__.append(ref.toxml())
\ No newline at end of file

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/ontology/Interaction.py,v
retrieving revision 1.3
retrieving revision 1.4
diff -u -r1.3 -r1.4
--- /home/repository/moby/moby-live/Python/bioMoby/ontology/Interaction.py	2005/01/27 08:44:05	1.3
+++ /home/repository/moby/moby-live/Python/bioMoby/ontology/Interaction.py	2005/02/01 08:52:16	1.4
@@ -51,8 +51,7 @@
             if elt.nodeName=="CrossReference" or elt.nodeName=="moby:CrossReference":
                 self.__cross__=[]
                 for ref in elt.childNodes:
-                    if ref.nodeType==ref.ELEMENT_NODE:
-                        self.__cross__.append(um.loads(ref.toxml()))
+                    self.__cross__.append(ref.toxml())
             if elt.nodeType==elt.ELEMENT_NODE and (elt.nodeName=="String" or elt.nodeName=="moby:String") and (elt.getAttribute("articleName")=="result" or elt.getAttribute("moby:articleName")=="result"):
                 t=MobyString()
                 t.fromMoby(elt.toxml())

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/ontology/InteractionMethod.py,v
retrieving revision 1.3
retrieving revision 1.4
diff -u -r1.3 -r1.4
--- /home/repository/moby/moby-live/Python/bioMoby/ontology/InteractionMethod.py	2005/01/27 08:44:05	1.3
+++ /home/repository/moby/moby-live/Python/bioMoby/ontology/InteractionMethod.py	2005/02/01 08:52:16	1.4
@@ -49,8 +49,7 @@
             if elt.nodeName=="CrossReference" or elt.nodeName=="moby:CrossReference":
                 self.__cross__=[]
                 for ref in elt.childNodes:
-                    if ref.nodeType==ref.ELEMENT_NODE:
-                        self.__cross__.append(um.loads(ref.toxml()))
+                    self.__cross__.append(ref.toxml())
             if elt.nodeType==elt.ELEMENT_NODE and (elt.nodeName=="String" or elt.nodeName=="moby:String") and (elt.getAttribute("articleName")=="shortlabel" or elt.getAttribute("moby:articleName")=="shortlabel"):
                 t=MobyString()
                 t.fromMoby(elt.toxml())

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/ontology/Interaction_partner.py,v
retrieving revision 1.3
retrieving revision 1.4
diff -u -r1.3 -r1.4
--- /home/repository/moby/moby-live/Python/bioMoby/ontology/Interaction_partner.py	2005/01/27 08:44:05	1.3
+++ /home/repository/moby/moby-live/Python/bioMoby/ontology/Interaction_partner.py	2005/02/01 08:52:16	1.4
@@ -49,8 +49,7 @@
             if elt.nodeName=="CrossReference" or elt.nodeName=="moby:CrossReference":
                 self.__cross__=[]
                 for ref in elt.childNodes:
-                    if ref.nodeType==ref.ELEMENT_NODE:
-                        self.__cross__.append(um.loads(ref.toxml()))
+                    self.__cross__.append(ref.toxml())
             if elt.nodeType==elt.ELEMENT_NODE and (elt.nodeName=="Integer" or elt.nodeName=="moby:Integer") and (elt.getAttribute("articleName")=="direction" or elt.getAttribute("moby:articleName")=="direction"):
                 t=MobyInteger()
                 t.fromMoby(elt.toxml())

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/ontology/Interactor.py,v
retrieving revision 1.3
retrieving revision 1.4
diff -u -r1.3 -r1.4
--- /home/repository/moby/moby-live/Python/bioMoby/ontology/Interactor.py	2005/01/27 08:44:05	1.3
+++ /home/repository/moby/moby-live/Python/bioMoby/ontology/Interactor.py	2005/02/01 08:52:16	1.4
@@ -47,8 +47,7 @@
             if elt.nodeName=="CrossReference" or elt.nodeName=="moby:CrossReference":
                 self.__cross__=[]
                 for ref in elt.childNodes:
-                    if ref.nodeType==ref.ELEMENT_NODE:
-                        self.__cross__.append(um.loads(ref.toxml()))
+                    self.__cross__.append(ref.toxml())
             if elt.nodeType==elt.ELEMENT_NODE and (elt.nodeName=="String" or elt.nodeName=="moby:String") and (elt.getAttribute("articleName")=="role" or elt.getAttribute("moby:articleName")=="role"):
                 t=MobyString()
                 t.fromMoby(elt.toxml())

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/ontology/MEME_Text.py,v
retrieving revision 1.3
retrieving revision 1.4
diff -u -r1.3 -r1.4
--- /home/repository/moby/moby-live/Python/bioMoby/ontology/MEME_Text.py	2005/01/27 08:44:05	1.3
+++ /home/repository/moby/moby-live/Python/bioMoby/ontology/MEME_Text.py	2005/02/01 08:52:16	1.4
@@ -46,5 +46,4 @@
             if elt.nodeName=="CrossReference" or elt.nodeName=="moby:CrossReference":
                 self.__cross__=[]
                 for ref in elt.childNodes:
-                    if ref.nodeType==ref.ELEMENT_NODE:
-                        self.__cross__.append(um.loads(ref.toxml()))
\ No newline at end of file
+                    self.__cross__.append(ref.toxml())
\ No newline at end of file

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/ontology/MGIS_ACCESSION.py,v
retrieving revision 1.3
retrieving revision 1.4
diff -u -r1.3 -r1.4
--- /home/repository/moby/moby-live/Python/bioMoby/ontology/MGIS_ACCESSION.py	2005/01/27 08:44:05	1.3
+++ /home/repository/moby/moby-live/Python/bioMoby/ontology/MGIS_ACCESSION.py	2005/02/01 08:52:16	1.4
@@ -66,8 +66,7 @@
             if elt.nodeName=="CrossReference" or elt.nodeName=="moby:CrossReference":
                 self.__cross__=[]
                 for ref in elt.childNodes:
-                    if ref.nodeType==ref.ELEMENT_NODE:
-                        self.__cross__.append(um.loads(ref.toxml()))
+                    self.__cross__.append(ref.toxml())
             if elt.nodeType==elt.ELEMENT_NODE and (elt.nodeName=="String" or elt.nodeName=="moby:String") and (elt.getAttribute("articleName")=="Biotic_stress_Yellowsig" or elt.getAttribute("moby:articleName")=="Biotic_stress_Yellowsig"):
                 t=MobyString()
                 t.fromMoby(elt.toxml())

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/ontology/MMP_Locus.py,v
retrieving revision 1.3
retrieving revision 1.4
diff -u -r1.3 -r1.4
--- /home/repository/moby/moby-live/Python/bioMoby/ontology/MMP_Locus.py	2005/01/27 08:44:05	1.3
+++ /home/repository/moby/moby-live/Python/bioMoby/ontology/MMP_Locus.py	2005/02/01 08:52:16	1.4
@@ -45,5 +45,4 @@
             if elt.nodeName=="CrossReference" or elt.nodeName=="moby:CrossReference":
                 self.__cross__=[]
                 for ref in elt.childNodes:
-                    if ref.nodeType==ref.ELEMENT_NODE:
-                        self.__cross__.append(um.loads(ref.toxml()))
\ No newline at end of file
+                    self.__cross__.append(ref.toxml())
\ No newline at end of file

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/ontology/MO_Term_Test.py,v
retrieving revision 1.3
retrieving revision 1.4
diff -u -r1.3 -r1.4
--- /home/repository/moby/moby-live/Python/bioMoby/ontology/MO_Term_Test.py	2005/01/27 08:44:05	1.3
+++ /home/repository/moby/moby-live/Python/bioMoby/ontology/MO_Term_Test.py	2005/02/01 08:52:16	1.4
@@ -50,8 +50,7 @@
             if elt.nodeName=="CrossReference" or elt.nodeName=="moby:CrossReference":
                 self.__cross__=[]
                 for ref in elt.childNodes:
-                    if ref.nodeType==ref.ELEMENT_NODE:
-                        self.__cross__.append(um.loads(ref.toxml()))
+                    self.__cross__.append(ref.toxml())
             if elt.nodeType==elt.ELEMENT_NODE and (elt.nodeName=="String" or elt.nodeName=="moby:String") and (elt.getAttribute("articleName")=="class_name" or elt.getAttribute("moby:articleName")=="class_name"):
                 t=MobyString()
                 t.fromMoby(elt.toxml())

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/ontology/MmCIFText.py,v
retrieving revision 1.3
retrieving revision 1.4
diff -u -r1.3 -r1.4
--- /home/repository/moby/moby-live/Python/bioMoby/ontology/MmCIFText.py	2005/01/27 08:44:05	1.3
+++ /home/repository/moby/moby-live/Python/bioMoby/ontology/MmCIFText.py	2005/02/01 08:52:16	1.4
@@ -46,5 +46,4 @@
             if elt.nodeName=="CrossReference" or elt.nodeName=="moby:CrossReference":
                 self.__cross__=[]
                 for ref in elt.childNodes:
-                    if ref.nodeType==ref.ELEMENT_NODE:
-                        self.__cross__.append(um.loads(ref.toxml()))
\ No newline at end of file
+                    self.__cross__.append(ref.toxml())
\ No newline at end of file

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/ontology/Multi_key_value_pair.py,v
retrieving revision 1.3
retrieving revision 1.4
diff -u -r1.3 -r1.4
--- /home/repository/moby/moby-live/Python/bioMoby/ontology/Multi_key_value_pair.py	2005/01/27 08:44:05	1.3
+++ /home/repository/moby/moby-live/Python/bioMoby/ontology/Multi_key_value_pair.py	2005/02/01 08:52:16	1.4
@@ -49,8 +49,7 @@
             if elt.nodeName=="CrossReference" or elt.nodeName=="moby:CrossReference":
                 self.__cross__=[]
                 for ref in elt.childNodes:
-                    if ref.nodeType==ref.ELEMENT_NODE:
-                        self.__cross__.append(um.loads(ref.toxml()))
+                    self.__cross__.append(ref.toxml())
             if elt.nodeType==elt.ELEMENT_NODE and (elt.nodeName=="String" or elt.nodeName=="moby:String") and (elt.getAttribute("articleName")=="key" or elt.getAttribute("moby:articleName")=="key"):
                 t=MobyString()
                 t.fromMoby(elt.toxml())

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/ontology/MyTestingDataType_11024145298313.py,v
retrieving revision 1.3
retrieving revision 1.4
diff -u -r1.3 -r1.4
--- /home/repository/moby/moby-live/Python/bioMoby/ontology/MyTestingDataType_11024145298313.py	2005/01/27 08:44:05	1.3
+++ /home/repository/moby/moby-live/Python/bioMoby/ontology/MyTestingDataType_11024145298313.py	2005/02/01 08:52:16	1.4
@@ -46,5 +46,4 @@
             if elt.nodeName=="CrossReference" or elt.nodeName=="moby:CrossReference":
                 self.__cross__=[]
                 for ref in elt.childNodes:
-                    if ref.nodeType==ref.ELEMENT_NODE:
-                        self.__cross__.append(um.loads(ref.toxml()))
\ No newline at end of file
+                    self.__cross__.append(ref.toxml())
\ No newline at end of file

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/ontology/MyTree.py,v
retrieving revision 1.3
retrieving revision 1.4
diff -u -r1.3 -r1.4
--- /home/repository/moby/moby-live/Python/bioMoby/ontology/MyTree.py	2005/01/27 08:44:05	1.3
+++ /home/repository/moby/moby-live/Python/bioMoby/ontology/MyTree.py	2005/02/01 08:52:16	1.4
@@ -46,5 +46,4 @@
             if elt.nodeName=="CrossReference" or elt.nodeName=="moby:CrossReference":
                 self.__cross__=[]
                 for ref in elt.childNodes:
-                    if ref.nodeType==ref.ELEMENT_NODE:
-                        self.__cross__.append(um.loads(ref.toxml()))
\ No newline at end of file
+                    self.__cross__.append(ref.toxml())
\ No newline at end of file

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/ontology/NCBI_BLAST_Text.py,v
retrieving revision 1.3
retrieving revision 1.4
diff -u -r1.3 -r1.4
--- /home/repository/moby/moby-live/Python/bioMoby/ontology/NCBI_BLAST_Text.py	2005/01/27 08:44:05	1.3
+++ /home/repository/moby/moby-live/Python/bioMoby/ontology/NCBI_BLAST_Text.py	2005/02/01 08:52:16	1.4
@@ -46,5 +46,4 @@
             if elt.nodeName=="CrossReference" or elt.nodeName=="moby:CrossReference":
                 self.__cross__=[]
                 for ref in elt.childNodes:
-                    if ref.nodeType==ref.ELEMENT_NODE:
-                        self.__cross__.append(um.loads(ref.toxml()))
\ No newline at end of file
+                    self.__cross__.append(ref.toxml())
\ No newline at end of file

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/ontology/NCBI_Blast_XML.py,v
retrieving revision 1.3
retrieving revision 1.4
diff -u -r1.3 -r1.4
--- /home/repository/moby/moby-live/Python/bioMoby/ontology/NCBI_Blast_XML.py	2005/01/27 08:44:05	1.3
+++ /home/repository/moby/moby-live/Python/bioMoby/ontology/NCBI_Blast_XML.py	2005/02/01 08:52:16	1.4
@@ -46,5 +46,4 @@
             if elt.nodeName=="CrossReference" or elt.nodeName=="moby:CrossReference":
                 self.__cross__=[]
                 for ref in elt.childNodes:
-                    if ref.nodeType==ref.ELEMENT_NODE:
-                        self.__cross__.append(um.loads(ref.toxml()))
\ No newline at end of file
+                    self.__cross__.append(ref.toxml())
\ No newline at end of file

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/ontology/NCBI_Blast_XML_Gif.py,v
retrieving revision 1.3
retrieving revision 1.4
diff -u -r1.3 -r1.4
--- /home/repository/moby/moby-live/Python/bioMoby/ontology/NCBI_Blast_XML_Gif.py	2005/01/27 08:44:05	1.3
+++ /home/repository/moby/moby-live/Python/bioMoby/ontology/NCBI_Blast_XML_Gif.py	2005/02/01 08:52:16	1.4
@@ -48,8 +48,7 @@
             if elt.nodeName=="CrossReference" or elt.nodeName=="moby:CrossReference":
                 self.__cross__=[]
                 for ref in elt.childNodes:
-                    if ref.nodeType==ref.ELEMENT_NODE:
-                        self.__cross__.append(um.loads(ref.toxml()))
+                    self.__cross__.append(ref.toxml())
             if elt.nodeType==elt.ELEMENT_NODE and (elt.nodeName=="b64_encoded_gif" or elt.nodeName=="moby:b64_encoded_gif") and (elt.getAttribute("articleName")=="hitGraph" or elt.getAttribute("moby:articleName")=="hitGraph"):
                 self.HitGraph=MobyB64_encoded_gif()
                 self.HitGraph.fromMoby(elt.toxml())
\ No newline at end of file

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/ontology/NCBI_Blast_XML_Gif_Map.py,v
retrieving revision 1.3
retrieving revision 1.4
diff -u -r1.3 -r1.4
--- /home/repository/moby/moby-live/Python/bioMoby/ontology/NCBI_Blast_XML_Gif_Map.py	2005/01/27 08:44:05	1.3
+++ /home/repository/moby/moby-live/Python/bioMoby/ontology/NCBI_Blast_XML_Gif_Map.py	2005/02/01 08:52:16	1.4
@@ -50,8 +50,7 @@
             if elt.nodeName=="CrossReference" or elt.nodeName=="moby:CrossReference":
                 self.__cross__=[]
                 for ref in elt.childNodes:
-                    if ref.nodeType==ref.ELEMENT_NODE:
-                        self.__cross__.append(um.loads(ref.toxml()))
+                    self.__cross__.append(ref.toxml())
             if elt.nodeType==elt.ELEMENT_NODE and (elt.nodeName=="b64_encoded_gif" or elt.nodeName=="moby:b64_encoded_gif") and (elt.getAttribute("articleName")=="hitGraph" or elt.getAttribute("moby:articleName")=="hitGraph"):
                 self.HitGraph=MobyB64_encoded_gif()
                 self.HitGraph.fromMoby(elt.toxml())

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/ontology/NCBI_MEME_Text.py,v
retrieving revision 1.3
retrieving revision 1.4
diff -u -r1.3 -r1.4
--- /home/repository/moby/moby-live/Python/bioMoby/ontology/NCBI_MEME_Text.py	2005/01/27 08:44:05	1.3
+++ /home/repository/moby/moby-live/Python/bioMoby/ontology/NCBI_MEME_Text.py	2005/02/01 08:52:16	1.4
@@ -46,5 +46,4 @@
             if elt.nodeName=="CrossReference" or elt.nodeName=="moby:CrossReference":
                 self.__cross__=[]
                 for ref in elt.childNodes:
-                    if ref.nodeType==ref.ELEMENT_NODE:
-                        self.__cross__.append(um.loads(ref.toxml()))
\ No newline at end of file
+                    self.__cross__.append(ref.toxml())
\ No newline at end of file

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/ontology/NucleotideSequence.py,v
retrieving revision 1.3
retrieving revision 1.4
diff -u -r1.3 -r1.4
--- /home/repository/moby/moby-live/Python/bioMoby/ontology/NucleotideSequence.py	2005/01/27 08:44:05	1.3
+++ /home/repository/moby/moby-live/Python/bioMoby/ontology/NucleotideSequence.py	2005/02/01 08:52:16	1.4
@@ -49,8 +49,7 @@
             if elt.nodeName=="CrossReference" or elt.nodeName=="moby:CrossReference":
                 self.__cross__=[]
                 for ref in elt.childNodes:
-                    if ref.nodeType==ref.ELEMENT_NODE:
-                        self.__cross__.append(um.loads(ref.toxml()))
+                    self.__cross__.append(ref.toxml())
             if elt.nodeType==elt.ELEMENT_NODE and (elt.nodeName=="Integer" or elt.nodeName=="moby:Integer") and (elt.getAttribute("articleName")=="Length" or elt.getAttribute("moby:articleName")=="Length"):
                 t=MobyInteger()
                 t.fromMoby(elt.toxml())

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/ontology/PDBFormattedText.py,v
retrieving revision 1.3
retrieving revision 1.4
diff -u -r1.3 -r1.4
--- /home/repository/moby/moby-live/Python/bioMoby/ontology/PDBFormattedText.py	2005/01/27 08:44:05	1.3
+++ /home/repository/moby/moby-live/Python/bioMoby/ontology/PDBFormattedText.py	2005/02/01 08:52:16	1.4
@@ -46,5 +46,4 @@
             if elt.nodeName=="CrossReference" or elt.nodeName=="moby:CrossReference":
                 self.__cross__=[]
                 for ref in elt.childNodes:
-                    if ref.nodeType==ref.ELEMENT_NODE:
-                        self.__cross__.append(um.loads(ref.toxml()))
\ No newline at end of file
+                    self.__cross__.append(ref.toxml())
\ No newline at end of file

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/ontology/PDBText.py,v
retrieving revision 1.3
retrieving revision 1.4
diff -u -r1.3 -r1.4
--- /home/repository/moby/moby-live/Python/bioMoby/ontology/PDBText.py	2005/01/27 08:44:05	1.3
+++ /home/repository/moby/moby-live/Python/bioMoby/ontology/PDBText.py	2005/02/01 08:52:16	1.4
@@ -46,5 +46,4 @@
             if elt.nodeName=="CrossReference" or elt.nodeName=="moby:CrossReference":
                 self.__cross__=[]
                 for ref in elt.childNodes:
-                    if ref.nodeType==ref.ELEMENT_NODE:
-                        self.__cross__.append(um.loads(ref.toxml()))
\ No newline at end of file
+                    self.__cross__.append(ref.toxml())
\ No newline at end of file

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/ontology/PDGJOB.py,v
retrieving revision 1.3
retrieving revision 1.4
diff -u -r1.3 -r1.4
--- /home/repository/moby/moby-live/Python/bioMoby/ontology/PDGJOB.py	2005/01/27 08:44:05	1.3
+++ /home/repository/moby/moby-live/Python/bioMoby/ontology/PDGJOB.py	2005/02/01 08:52:16	1.4
@@ -52,8 +52,7 @@
             if elt.nodeName=="CrossReference" or elt.nodeName=="moby:CrossReference":
                 self.__cross__=[]
                 for ref in elt.childNodes:
-                    if ref.nodeType==ref.ELEMENT_NODE:
-                        self.__cross__.append(um.loads(ref.toxml()))
+                    self.__cross__.append(ref.toxml())
             if elt.nodeType==elt.ELEMENT_NODE and (elt.nodeName=="String" or elt.nodeName=="moby:String") and (elt.getAttribute("articleName")=="answerService" or elt.getAttribute("moby:articleName")=="answerService"):
                 t=MobyString()
                 t.fromMoby(elt.toxml())

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/ontology/PHDText.py,v
retrieving revision 1.3
retrieving revision 1.4
diff -u -r1.3 -r1.4
--- /home/repository/moby/moby-live/Python/bioMoby/ontology/PHDText.py	2005/01/27 08:44:05	1.3
+++ /home/repository/moby/moby-live/Python/bioMoby/ontology/PHDText.py	2005/02/01 08:52:16	1.4
@@ -46,5 +46,4 @@
             if elt.nodeName=="CrossReference" or elt.nodeName=="moby:CrossReference":
                 self.__cross__=[]
                 for ref in elt.childNodes:
-                    if ref.nodeType==ref.ELEMENT_NODE:
-                        self.__cross__.append(um.loads(ref.toxml()))
\ No newline at end of file
+                    self.__cross__.append(ref.toxml())
\ No newline at end of file

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/ontology/PMUTText.py,v
retrieving revision 1.3
retrieving revision 1.4
diff -u -r1.3 -r1.4
--- /home/repository/moby/moby-live/Python/bioMoby/ontology/PMUTText.py	2005/01/27 08:44:05	1.3
+++ /home/repository/moby/moby-live/Python/bioMoby/ontology/PMUTText.py	2005/02/01 08:52:16	1.4
@@ -46,5 +46,4 @@
             if elt.nodeName=="CrossReference" or elt.nodeName=="moby:CrossReference":
                 self.__cross__=[]
                 for ref in elt.childNodes:
-                    if ref.nodeType==ref.ELEMENT_NODE:
-                        self.__cross__.append(um.loads(ref.toxml()))
\ No newline at end of file
+                    self.__cross__.append(ref.toxml())
\ No newline at end of file

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/ontology/PSeaTextFormatted.py,v
retrieving revision 1.3
retrieving revision 1.4
diff -u -r1.3 -r1.4
--- /home/repository/moby/moby-live/Python/bioMoby/ontology/PSeaTextFormatted.py	2005/01/27 08:44:05	1.3
+++ /home/repository/moby/moby-live/Python/bioMoby/ontology/PSeaTextFormatted.py	2005/02/01 08:52:16	1.4
@@ -46,5 +46,4 @@
             if elt.nodeName=="CrossReference" or elt.nodeName=="moby:CrossReference":
                 self.__cross__=[]
                 for ref in elt.childNodes:
-                    if ref.nodeType==ref.ELEMENT_NODE:
-                        self.__cross__.append(um.loads(ref.toxml()))
\ No newline at end of file
+                    self.__cross__.append(ref.toxml())
\ No newline at end of file

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/ontology/PhenotypeDescription.py,v
retrieving revision 1.3
retrieving revision 1.4
diff -u -r1.3 -r1.4
--- /home/repository/moby/moby-live/Python/bioMoby/ontology/PhenotypeDescription.py	2005/01/27 08:44:05	1.3
+++ /home/repository/moby/moby-live/Python/bioMoby/ontology/PhenotypeDescription.py	2005/02/01 08:52:16	1.4
@@ -47,8 +47,7 @@
             if elt.nodeName=="CrossReference" or elt.nodeName=="moby:CrossReference":
                 self.__cross__=[]
                 for ref in elt.childNodes:
-                    if ref.nodeType==ref.ELEMENT_NODE:
-                        self.__cross__.append(um.loads(ref.toxml()))
+                    self.__cross__.append(ref.toxml())
             if elt.nodeType==elt.ELEMENT_NODE and (elt.nodeName=="String" or elt.nodeName=="moby:String") and (elt.getAttribute("articleName")=="Phenotype" or elt.getAttribute("moby:articleName")=="Phenotype"):
                 t=MobyString()
                 t.fromMoby(elt.toxml())

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/ontology/PubMedMEDLINE.py,v
retrieving revision 1.3
retrieving revision 1.4
diff -u -r1.3 -r1.4
--- /home/repository/moby/moby-live/Python/bioMoby/ontology/PubMedMEDLINE.py	2005/01/27 08:44:05	1.3
+++ /home/repository/moby/moby-live/Python/bioMoby/ontology/PubMedMEDLINE.py	2005/02/01 08:52:16	1.4
@@ -46,5 +46,4 @@
             if elt.nodeName=="CrossReference" or elt.nodeName=="moby:CrossReference":
                 self.__cross__=[]
                 for ref in elt.childNodes:
-                    if ref.nodeType==ref.ELEMENT_NODE:
-                        self.__cross__.append(um.loads(ref.toxml()))
\ No newline at end of file
+                    self.__cross__.append(ref.toxml())
\ No newline at end of file

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/ontology/RNASequence.py,v
retrieving revision 1.3
retrieving revision 1.4
diff -u -r1.3 -r1.4
--- /home/repository/moby/moby-live/Python/bioMoby/ontology/RNASequence.py	2005/01/27 08:44:05	1.3
+++ /home/repository/moby/moby-live/Python/bioMoby/ontology/RNASequence.py	2005/02/01 08:52:16	1.4
@@ -49,8 +49,7 @@
             if elt.nodeName=="CrossReference" or elt.nodeName=="moby:CrossReference":
                 self.__cross__=[]
                 for ref in elt.childNodes:
-                    if ref.nodeType==ref.ELEMENT_NODE:
-                        self.__cross__.append(um.loads(ref.toxml()))
+                    self.__cross__.append(ref.toxml())
             if elt.nodeType==elt.ELEMENT_NODE and (elt.nodeName=="Integer" or elt.nodeName=="moby:Integer") and (elt.getAttribute("articleName")=="Length" or elt.getAttribute("moby:articleName")=="Length"):
                 t=MobyInteger()
                 t.fromMoby(elt.toxml())

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/ontology/SINGER_ACCESSION.py,v
retrieving revision 1.3
retrieving revision 1.4
diff -u -r1.3 -r1.4
--- /home/repository/moby/moby-live/Python/bioMoby/ontology/SINGER_ACCESSION.py	2005/01/27 08:44:05	1.3
+++ /home/repository/moby/moby-live/Python/bioMoby/ontology/SINGER_ACCESSION.py	2005/02/01 08:52:16	1.4
@@ -50,8 +50,7 @@
             if elt.nodeName=="CrossReference" or elt.nodeName=="moby:CrossReference":
                 self.__cross__=[]
                 for ref in elt.childNodes:
-                    if ref.nodeType==ref.ELEMENT_NODE:
-                        self.__cross__.append(um.loads(ref.toxml()))
+                    self.__cross__.append(ref.toxml())
             if elt.nodeType==elt.ELEMENT_NODE and (elt.nodeName=="String" or elt.nodeName=="moby:String") and (elt.getAttribute("articleName")=="ACCNO" or elt.getAttribute("moby:articleName")=="ACCNO"):
                 t=MobyString()
                 t.fromMoby(elt.toxml())

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/ontology/Sample.py,v
retrieving revision 1.3
retrieving revision 1.4
diff -u -r1.3 -r1.4
--- /home/repository/moby/moby-live/Python/bioMoby/ontology/Sample.py	2005/01/27 08:44:05	1.3
+++ /home/repository/moby/moby-live/Python/bioMoby/ontology/Sample.py	2005/02/01 08:52:16	1.4
@@ -49,8 +49,7 @@
             if elt.nodeName=="CrossReference" or elt.nodeName=="moby:CrossReference":
                 self.__cross__=[]
                 for ref in elt.childNodes:
-                    if ref.nodeType==ref.ELEMENT_NODE:
-                        self.__cross__.append(um.loads(ref.toxml()))
+                    self.__cross__.append(ref.toxml())
             if elt.nodeType==elt.ELEMENT_NODE and (elt.nodeName=="String" or elt.nodeName=="moby:String") and (elt.getAttribute("articleName")=="code" or elt.getAttribute("moby:articleName")=="code"):
                 t=MobyString()
                 t.fromMoby(elt.toxml())

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/ontology/SchematikonMotifID.py,v
retrieving revision 1.3
retrieving revision 1.4
diff -u -r1.3 -r1.4
--- /home/repository/moby/moby-live/Python/bioMoby/ontology/SchematikonMotifID.py	2005/01/27 08:44:05	1.3
+++ /home/repository/moby/moby-live/Python/bioMoby/ontology/SchematikonMotifID.py	2005/02/01 08:52:16	1.4
@@ -47,8 +47,7 @@
             if elt.nodeName=="CrossReference" or elt.nodeName=="moby:CrossReference":
                 self.__cross__=[]
                 for ref in elt.childNodes:
-                    if ref.nodeType==ref.ELEMENT_NODE:
-                        self.__cross__.append(um.loads(ref.toxml()))
+                    self.__cross__.append(ref.toxml())
             if elt.nodeType==elt.ELEMENT_NODE and (elt.nodeName=="String" or elt.nodeName=="moby:String") and (elt.getAttribute("articleName")=="ID" or elt.getAttribute("moby:articleName")=="ID"):
                 t=MobyString()
                 t.fromMoby(elt.toxml())

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/ontology/SchematikonMotifSupport.py,v
retrieving revision 1.3
retrieving revision 1.4
diff -u -r1.3 -r1.4
--- /home/repository/moby/moby-live/Python/bioMoby/ontology/SchematikonMotifSupport.py	2005/01/27 08:44:05	1.3
+++ /home/repository/moby/moby-live/Python/bioMoby/ontology/SchematikonMotifSupport.py	2005/02/01 08:52:16	1.4
@@ -48,8 +48,7 @@
             if elt.nodeName=="CrossReference" or elt.nodeName=="moby:CrossReference":
                 self.__cross__=[]
                 for ref in elt.childNodes:
-                    if ref.nodeType==ref.ELEMENT_NODE:
-                        self.__cross__.append(um.loads(ref.toxml()))
+                    self.__cross__.append(ref.toxml())
             if elt.nodeType==elt.ELEMENT_NODE and (elt.nodeName=="Integer" or elt.nodeName=="moby:Integer") and (elt.getAttribute("articleName")=="UniqueSupport" or elt.getAttribute("moby:articleName")=="UniqueSupport"):
                 t=MobyInteger()
                 t.fromMoby(elt.toxml())

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/ontology/SchematikonSegmentAttributes.py,v
retrieving revision 1.3
retrieving revision 1.4
diff -u -r1.3 -r1.4
--- /home/repository/moby/moby-live/Python/bioMoby/ontology/SchematikonSegmentAttributes.py	2005/01/27 08:44:05	1.3
+++ /home/repository/moby/moby-live/Python/bioMoby/ontology/SchematikonSegmentAttributes.py	2005/02/01 08:52:16	1.4
@@ -52,8 +52,7 @@
             if elt.nodeName=="CrossReference" or elt.nodeName=="moby:CrossReference":
                 self.__cross__=[]
                 for ref in elt.childNodes:
-                    if ref.nodeType==ref.ELEMENT_NODE:
-                        self.__cross__.append(um.loads(ref.toxml()))
+                    self.__cross__.append(ref.toxml())
             if elt.nodeType==elt.ELEMENT_NODE and (elt.nodeName=="Integer" or elt.nodeName=="moby:Integer") and (elt.getAttribute("articleName")=="Length" or elt.getAttribute("moby:articleName")=="Length"):
                 t=MobyInteger()
                 t.fromMoby(elt.toxml())

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/ontology/SchematikonSegmentID.py,v
retrieving revision 1.3
retrieving revision 1.4
diff -u -r1.3 -r1.4
--- /home/repository/moby/moby-live/Python/bioMoby/ontology/SchematikonSegmentID.py	2005/01/27 08:44:05	1.3
+++ /home/repository/moby/moby-live/Python/bioMoby/ontology/SchematikonSegmentID.py	2005/02/01 08:52:16	1.4
@@ -47,8 +47,7 @@
             if elt.nodeName=="CrossReference" or elt.nodeName=="moby:CrossReference":
                 self.__cross__=[]
                 for ref in elt.childNodes:
-                    if ref.nodeType==ref.ELEMENT_NODE:
-                        self.__cross__.append(um.loads(ref.toxml()))
+                    self.__cross__.append(ref.toxml())
             if elt.nodeType==elt.ELEMENT_NODE and (elt.nodeName=="String" or elt.nodeName=="moby:String") and (elt.getAttribute("articleName")=="ID" or elt.getAttribute("moby:articleName")=="ID"):
                 t=MobyString()
                 t.fromMoby(elt.toxml())

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/ontology/SchematikonStructureAnnotation.py,v
retrieving revision 1.3
retrieving revision 1.4
diff -u -r1.3 -r1.4
--- /home/repository/moby/moby-live/Python/bioMoby/ontology/SchematikonStructureAnnotation.py	2005/01/27 08:44:05	1.3
+++ /home/repository/moby/moby-live/Python/bioMoby/ontology/SchematikonStructureAnnotation.py	2005/02/01 08:52:16	1.4
@@ -50,8 +50,7 @@
             if elt.nodeName=="CrossReference" or elt.nodeName=="moby:CrossReference":
                 self.__cross__=[]
                 for ref in elt.childNodes:
-                    if ref.nodeType==ref.ELEMENT_NODE:
-                        self.__cross__.append(um.loads(ref.toxml()))
+                    self.__cross__.append(ref.toxml())
             if elt.nodeType==elt.ELEMENT_NODE and (elt.nodeName=="String" or elt.nodeName=="moby:String") and (elt.getAttribute("articleName")=="PROMOTIF gamma-turn" or elt.getAttribute("moby:articleName")=="PROMOTIF gamma-turn"):
                 t=MobyString()
                 t.fromMoby(elt.toxml())

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/ontology/SchematikonVorocodeName.py,v
retrieving revision 1.3
retrieving revision 1.4
diff -u -r1.3 -r1.4
--- /home/repository/moby/moby-live/Python/bioMoby/ontology/SchematikonVorocodeName.py	2005/01/27 08:44:05	1.3
+++ /home/repository/moby/moby-live/Python/bioMoby/ontology/SchematikonVorocodeName.py	2005/02/01 08:52:16	1.4
@@ -47,8 +47,7 @@
             if elt.nodeName=="CrossReference" or elt.nodeName=="moby:CrossReference":
                 self.__cross__=[]
                 for ref in elt.childNodes:
-                    if ref.nodeType==ref.ELEMENT_NODE:
-                        self.__cross__.append(um.loads(ref.toxml()))
+                    self.__cross__.append(ref.toxml())
             if elt.nodeType==elt.ELEMENT_NODE and (elt.nodeName=="String" or elt.nodeName=="moby:String") and (elt.getAttribute("articleName")=="VorocodeName" or elt.getAttribute("moby:articleName")=="VorocodeName"):
                 t=MobyString()
                 t.fromMoby(elt.toxml())

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/ontology/Scored_acronym_string.py,v
retrieving revision 1.3
retrieving revision 1.4
diff -u -r1.3 -r1.4
--- /home/repository/moby/moby-live/Python/bioMoby/ontology/Scored_acronym_string.py	2005/01/27 08:44:05	1.3
+++ /home/repository/moby/moby-live/Python/bioMoby/ontology/Scored_acronym_string.py	2005/02/01 08:52:16	1.4
@@ -50,8 +50,7 @@
             if elt.nodeName=="CrossReference" or elt.nodeName=="moby:CrossReference":
                 self.__cross__=[]
                 for ref in elt.childNodes:
-                    if ref.nodeType==ref.ELEMENT_NODE:
-                        self.__cross__.append(um.loads(ref.toxml()))
+                    self.__cross__.append(ref.toxml())
             if elt.nodeType==elt.ELEMENT_NODE and (elt.nodeName=="Float" or elt.nodeName=="moby:Float") and (elt.getAttribute("articleName")=="score" or elt.getAttribute("moby:articleName")=="score"):
                 t=MobyFloat()
                 t.fromMoby(elt.toxml())

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/ontology/SimpleAnnotatedGIFImage.py,v
retrieving revision 1.3
retrieving revision 1.4
diff -u -r1.3 -r1.4
--- /home/repository/moby/moby-live/Python/bioMoby/ontology/SimpleAnnotatedGIFImage.py	2005/01/27 08:44:05	1.3
+++ /home/repository/moby/moby-live/Python/bioMoby/ontology/SimpleAnnotatedGIFImage.py	2005/02/01 08:52:16	1.4
@@ -48,8 +48,7 @@
             if elt.nodeName=="CrossReference" or elt.nodeName=="moby:CrossReference":
                 self.__cross__=[]
                 for ref in elt.childNodes:
-                    if ref.nodeType==ref.ELEMENT_NODE:
-                        self.__cross__.append(um.loads(ref.toxml()))
+                    self.__cross__.append(ref.toxml())
             if elt.nodeType==elt.ELEMENT_NODE and (elt.nodeName=="String" or elt.nodeName=="moby:String") and (elt.getAttribute("articleName")=="Description" or elt.getAttribute("moby:articleName")=="Description"):
                 t=MobyString()
                 t.fromMoby(elt.toxml())

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/ontology/SimpleAnnotatedJPEGImage.py,v
retrieving revision 1.3
retrieving revision 1.4
diff -u -r1.3 -r1.4
--- /home/repository/moby/moby-live/Python/bioMoby/ontology/SimpleAnnotatedJPEGImage.py	2005/01/27 08:44:05	1.3
+++ /home/repository/moby/moby-live/Python/bioMoby/ontology/SimpleAnnotatedJPEGImage.py	2005/02/01 08:52:16	1.4
@@ -49,8 +49,7 @@
             if elt.nodeName=="CrossReference" or elt.nodeName=="moby:CrossReference":
                 self.__cross__=[]
                 for ref in elt.childNodes:
-                    if ref.nodeType==ref.ELEMENT_NODE:
-                        self.__cross__.append(um.loads(ref.toxml()))
+                    self.__cross__.append(ref.toxml())
             if elt.nodeType==elt.ELEMENT_NODE and (elt.nodeName=="String" or elt.nodeName=="moby:String") and (elt.getAttribute("articleName")=="Description" or elt.getAttribute("moby:articleName")=="Description"):
                 t=MobyString()
                 t.fromMoby(elt.toxml())

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/ontology/Simple_key_value_pair.py,v
retrieving revision 1.3
retrieving revision 1.4
diff -u -r1.3 -r1.4
--- /home/repository/moby/moby-live/Python/bioMoby/ontology/Simple_key_value_pair.py	2005/01/27 08:44:05	1.3
+++ /home/repository/moby/moby-live/Python/bioMoby/ontology/Simple_key_value_pair.py	2005/02/01 08:52:16	1.4
@@ -48,8 +48,7 @@
             if elt.nodeName=="CrossReference" or elt.nodeName=="moby:CrossReference":
                 self.__cross__=[]
                 for ref in elt.childNodes:
-                    if ref.nodeType==ref.ELEMENT_NODE:
-                        self.__cross__.append(um.loads(ref.toxml()))
+                    self.__cross__.append(ref.toxml())
             if elt.nodeType==elt.ELEMENT_NODE and (elt.nodeName=="String" or elt.nodeName=="moby:String") and (elt.getAttribute("articleName")=="value" or elt.getAttribute("moby:articleName")=="value"):
                 t=MobyString()
                 t.fromMoby(elt.toxml())

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/ontology/Snp_allele.py,v
retrieving revision 1.3
retrieving revision 1.4
diff -u -r1.3 -r1.4
--- /home/repository/moby/moby-live/Python/bioMoby/ontology/Snp_allele.py	2005/01/27 08:44:05	1.3
+++ /home/repository/moby/moby-live/Python/bioMoby/ontology/Snp_allele.py	2005/02/01 08:52:16	1.4
@@ -37,8 +37,7 @@
             if elt.nodeName=="CrossReference" or elt.nodeName=="moby:CrossReference":
                 self.__cross__=[]
                 for ref in elt.childNodes:
-                    if ref.nodeType==ref.ELEMENT_NODE:
-                        self.__cross__.append(um.loads(ref.toxml()))
+                    self.__cross__.append(ref.toxml())
             if elt.nodeType==elt.ELEMENT_NODE and (elt.nodeName=="DNASequence" or elt.nodeName=="moby:DNASequence") and (elt.getAttribute("articleName")=="snp_allele" or elt.getAttribute("moby:articleName")=="snp_allele"):
                 self.Snp_allele=MobyDNASequence()
                 self.Snp_allele.fromMoby(elt.toxml())
\ No newline at end of file

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/ontology/Snp_genotype.py,v
retrieving revision 1.3
retrieving revision 1.4
diff -u -r1.3 -r1.4
--- /home/repository/moby/moby-live/Python/bioMoby/ontology/Snp_genotype.py	2005/01/27 08:44:05	1.3
+++ /home/repository/moby/moby-live/Python/bioMoby/ontology/Snp_genotype.py	2005/02/01 08:52:16	1.4
@@ -38,8 +38,7 @@
             if elt.nodeName=="CrossReference" or elt.nodeName=="moby:CrossReference":
                 self.__cross__=[]
                 for ref in elt.childNodes:
-                    if ref.nodeType==ref.ELEMENT_NODE:
-                        self.__cross__.append(um.loads(ref.toxml()))
+                    self.__cross__.append(ref.toxml())
             if elt.nodeType==elt.ELEMENT_NODE and (elt.nodeName=="snp_allele" or elt.nodeName=="moby:snp_allele") and (elt.getAttribute("articleName")=="allele1" or elt.getAttribute("moby:articleName")=="allele1"):
                 self.Allele1=MobySnp_allele()
                 self.Allele1.fromMoby(elt.toxml())

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/ontology/Study.py,v
retrieving revision 1.3
retrieving revision 1.4
diff -u -r1.3 -r1.4
--- /home/repository/moby/moby-live/Python/bioMoby/ontology/Study.py	2005/01/27 08:44:05	1.3
+++ /home/repository/moby/moby-live/Python/bioMoby/ontology/Study.py	2005/02/01 08:52:16	1.4
@@ -50,8 +50,7 @@
             if elt.nodeName=="CrossReference" or elt.nodeName=="moby:CrossReference":
                 self.__cross__=[]
                 for ref in elt.childNodes:
-                    if ref.nodeType==ref.ELEMENT_NODE:
-                        self.__cross__.append(um.loads(ref.toxml()))
+                    self.__cross__.append(ref.toxml())
             if elt.nodeType==elt.ELEMENT_NODE and (elt.nodeName=="String" or elt.nodeName=="moby:String") and (elt.getAttribute("articleName")=="study_name" or elt.getAttribute("moby:articleName")=="study_name"):
                 t=MobyString()
                 t.fromMoby(elt.toxml())

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/ontology/TEST.py,v
retrieving revision 1.3
retrieving revision 1.4
diff -u -r1.3 -r1.4
--- /home/repository/moby/moby-live/Python/bioMoby/ontology/TEST.py	2005/01/27 08:44:05	1.3
+++ /home/repository/moby/moby-live/Python/bioMoby/ontology/TEST.py	2005/02/01 08:52:16	1.4
@@ -46,5 +46,4 @@
             if elt.nodeName=="CrossReference" or elt.nodeName=="moby:CrossReference":
                 self.__cross__=[]
                 for ref in elt.childNodes:
-                    if ref.nodeType==ref.ELEMENT_NODE:
-                        self.__cross__.append(um.loads(ref.toxml()))
\ No newline at end of file
+                    self.__cross__.append(ref.toxml())
\ No newline at end of file

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/ontology/TargetP_result.py,v
retrieving revision 1.3
retrieving revision 1.4
diff -u -r1.3 -r1.4
--- /home/repository/moby/moby-live/Python/bioMoby/ontology/TargetP_result.py	2005/01/27 08:44:05	1.3
+++ /home/repository/moby/moby-live/Python/bioMoby/ontology/TargetP_result.py	2005/02/01 08:52:16	1.4
@@ -52,8 +52,7 @@
             if elt.nodeName=="CrossReference" or elt.nodeName=="moby:CrossReference":
                 self.__cross__=[]
                 for ref in elt.childNodes:
-                    if ref.nodeType==ref.ELEMENT_NODE:
-                        self.__cross__.append(um.loads(ref.toxml()))
+                    self.__cross__.append(ref.toxml())
             if elt.nodeType==elt.ELEMENT_NODE and (elt.nodeName=="Float" or elt.nodeName=="moby:Float") and (elt.getAttribute("articleName")=="o_score" or elt.getAttribute("moby:articleName")=="o_score"):
                 t=MobyFloat()
                 t.fromMoby(elt.toxml())

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/ontology/Testout.py,v
retrieving revision 1.3
retrieving revision 1.4
diff -u -r1.3 -r1.4
--- /home/repository/moby/moby-live/Python/bioMoby/ontology/Testout.py	2005/01/27 08:44:05	1.3
+++ /home/repository/moby/moby-live/Python/bioMoby/ontology/Testout.py	2005/02/01 08:52:16	1.4
@@ -51,8 +51,7 @@
             if elt.nodeName=="CrossReference" or elt.nodeName=="moby:CrossReference":
                 self.__cross__=[]
                 for ref in elt.childNodes:
-                    if ref.nodeType==ref.ELEMENT_NODE:
-                        self.__cross__.append(um.loads(ref.toxml()))
+                    self.__cross__.append(ref.toxml())
             if elt.nodeType==elt.ELEMENT_NODE and (elt.nodeName=="Integer" or elt.nodeName=="moby:Integer") and (elt.getAttribute("articleName")=="gid" or elt.getAttribute("moby:articleName")=="gid"):
                 t=MobyInteger()
                 t.fromMoby(elt.toxml())

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/ontology/TextBase64.py,v
retrieving revision 1.3
retrieving revision 1.4
diff -u -r1.3 -r1.4
--- /home/repository/moby/moby-live/Python/bioMoby/ontology/TextBase64.py	2005/01/27 08:44:05	1.3
+++ /home/repository/moby/moby-live/Python/bioMoby/ontology/TextBase64.py	2005/02/01 08:52:16	1.4
@@ -46,5 +46,4 @@
             if elt.nodeName=="CrossReference" or elt.nodeName=="moby:CrossReference":
                 self.__cross__=[]
                 for ref in elt.childNodes:
-                    if ref.nodeType==ref.ELEMENT_NODE:
-                        self.__cross__.append(um.loads(ref.toxml()))
\ No newline at end of file
+                    self.__cross__.append(ref.toxml())
\ No newline at end of file

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/ontology/TextFormatted.py,v
retrieving revision 1.3
retrieving revision 1.4
diff -u -r1.3 -r1.4
--- /home/repository/moby/moby-live/Python/bioMoby/ontology/TextFormatted.py	2005/01/27 08:44:05	1.3
+++ /home/repository/moby/moby-live/Python/bioMoby/ontology/TextFormatted.py	2005/02/01 08:52:16	1.4
@@ -46,5 +46,4 @@
             if elt.nodeName=="CrossReference" or elt.nodeName=="moby:CrossReference":
                 self.__cross__=[]
                 for ref in elt.childNodes:
-                    if ref.nodeType==ref.ELEMENT_NODE:
-                        self.__cross__.append(um.loads(ref.toxml()))
\ No newline at end of file
+                    self.__cross__.append(ref.toxml())
\ No newline at end of file

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/ontology/TextHtml.py,v
retrieving revision 1.3
retrieving revision 1.4
diff -u -r1.3 -r1.4
--- /home/repository/moby/moby-live/Python/bioMoby/ontology/TextHtml.py	2005/01/27 08:44:05	1.3
+++ /home/repository/moby/moby-live/Python/bioMoby/ontology/TextHtml.py	2005/02/01 08:52:16	1.4
@@ -46,5 +46,4 @@
             if elt.nodeName=="CrossReference" or elt.nodeName=="moby:CrossReference":
                 self.__cross__=[]
                 for ref in elt.childNodes:
-                    if ref.nodeType==ref.ELEMENT_NODE:
-                        self.__cross__.append(um.loads(ref.toxml()))
\ No newline at end of file
+                    self.__cross__.append(ref.toxml())
\ No newline at end of file

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/ontology/TextPlain.py,v
retrieving revision 1.3
retrieving revision 1.4
diff -u -r1.3 -r1.4
--- /home/repository/moby/moby-live/Python/bioMoby/ontology/TextPlain.py	2005/01/27 08:44:05	1.3
+++ /home/repository/moby/moby-live/Python/bioMoby/ontology/TextPlain.py	2005/02/01 08:52:16	1.4
@@ -46,5 +46,4 @@
             if elt.nodeName=="CrossReference" or elt.nodeName=="moby:CrossReference":
                 self.__cross__=[]
                 for ref in elt.childNodes:
-                    if ref.nodeType==ref.ELEMENT_NODE:
-                        self.__cross__.append(um.loads(ref.toxml()))
\ No newline at end of file
+                    self.__cross__.append(ref.toxml())
\ No newline at end of file

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/ontology/TextUuencoded.py,v
retrieving revision 1.3
retrieving revision 1.4
diff -u -r1.3 -r1.4
--- /home/repository/moby/moby-live/Python/bioMoby/ontology/TextUuencoded.py	2005/01/27 08:44:05	1.3
+++ /home/repository/moby/moby-live/Python/bioMoby/ontology/TextUuencoded.py	2005/02/01 08:52:16	1.4
@@ -46,5 +46,4 @@
             if elt.nodeName=="CrossReference" or elt.nodeName=="moby:CrossReference":
                 self.__cross__=[]
                 for ref in elt.childNodes:
-                    if ref.nodeType==ref.ELEMENT_NODE:
-                        self.__cross__.append(um.loads(ref.toxml()))
\ No newline at end of file
+                    self.__cross__.append(ref.toxml())
\ No newline at end of file

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/ontology/TextXml.py,v
retrieving revision 1.3
retrieving revision 1.4
diff -u -r1.3 -r1.4
--- /home/repository/moby/moby-live/Python/bioMoby/ontology/TextXml.py	2005/01/27 08:44:05	1.3
+++ /home/repository/moby/moby-live/Python/bioMoby/ontology/TextXml.py	2005/02/01 08:52:16	1.4
@@ -46,5 +46,4 @@
             if elt.nodeName=="CrossReference" or elt.nodeName=="moby:CrossReference":
                 self.__cross__=[]
                 for ref in elt.childNodes:
-                    if ref.nodeType==ref.ELEMENT_NODE:
-                        self.__cross__.append(um.loads(ref.toxml()))
\ No newline at end of file
+                    self.__cross__.append(ref.toxml())
\ No newline at end of file

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/ontology/Text_plain.py,v
retrieving revision 1.3
retrieving revision 1.4
diff -u -r1.3 -r1.4
--- /home/repository/moby/moby-live/Python/bioMoby/ontology/Text_plain.py	2005/01/27 08:44:05	1.3
+++ /home/repository/moby/moby-live/Python/bioMoby/ontology/Text_plain.py	2005/02/01 08:52:16	1.4
@@ -46,5 +46,4 @@
             if elt.nodeName=="CrossReference" or elt.nodeName=="moby:CrossReference":
                 self.__cross__=[]
                 for ref in elt.childNodes:
-                    if ref.nodeType==ref.ELEMENT_NODE:
-                        self.__cross__.append(um.loads(ref.toxml()))
\ No newline at end of file
+                    self.__cross__.append(ref.toxml())
\ No newline at end of file

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/ontology/Trait_Details.py,v
retrieving revision 1.3
retrieving revision 1.4
diff -u -r1.3 -r1.4
--- /home/repository/moby/moby-live/Python/bioMoby/ontology/Trait_Details.py	2005/01/27 08:44:05	1.3
+++ /home/repository/moby/moby-live/Python/bioMoby/ontology/Trait_Details.py	2005/02/01 08:52:16	1.4
@@ -52,8 +52,7 @@
             if elt.nodeName=="CrossReference" or elt.nodeName=="moby:CrossReference":
                 self.__cross__=[]
                 for ref in elt.childNodes:
-                    if ref.nodeType==ref.ELEMENT_NODE:
-                        self.__cross__.append(um.loads(ref.toxml()))
+                    self.__cross__.append(ref.toxml())
             if elt.nodeType==elt.ELEMENT_NODE and (elt.nodeName=="String" or elt.nodeName=="moby:String") and (elt.getAttribute("articleName")=="trait_desc" or elt.getAttribute("moby:articleName")=="trait_desc"):
                 t=MobyString()
                 t.fromMoby(elt.toxml())

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/ontology/Tree.py,v
retrieving revision 1.3
retrieving revision 1.4
diff -u -r1.3 -r1.4
--- /home/repository/moby/moby-live/Python/bioMoby/ontology/Tree.py	2005/01/27 08:44:05	1.3
+++ /home/repository/moby/moby-live/Python/bioMoby/ontology/Tree.py	2005/02/01 08:52:16	1.4
@@ -46,5 +46,4 @@
             if elt.nodeName=="CrossReference" or elt.nodeName=="moby:CrossReference":
                 self.__cross__=[]
                 for ref in elt.childNodes:
-                    if ref.nodeType==ref.ELEMENT_NODE:
-                        self.__cross__.append(um.loads(ref.toxml()))
\ No newline at end of file
+                    self.__cross__.append(ref.toxml())
\ No newline at end of file

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/ontology/TropGENE_ACCESSION.py,v
retrieving revision 1.3
retrieving revision 1.4
diff -u -r1.3 -r1.4
--- /home/repository/moby/moby-live/Python/bioMoby/ontology/TropGENE_ACCESSION.py	2005/01/27 08:44:05	1.3
+++ /home/repository/moby/moby-live/Python/bioMoby/ontology/TropGENE_ACCESSION.py	2005/02/01 08:52:16	1.4
@@ -66,8 +66,7 @@
             if elt.nodeName=="CrossReference" or elt.nodeName=="moby:CrossReference":
                 self.__cross__=[]
                 for ref in elt.childNodes:
-                    if ref.nodeType==ref.ELEMENT_NODE:
-                        self.__cross__.append(um.loads(ref.toxml()))
+                    self.__cross__.append(ref.toxml())
             if elt.nodeType==elt.ELEMENT_NODE and (elt.nodeName=="TropGENE_LOCUS" or elt.nodeName=="moby:TropGENE_LOCUS") and (elt.getAttribute("articleName")=="RFLP" or elt.getAttribute("moby:articleName")=="RFLP"):
                 self.RFLP=MobyTropGENE_LOCUS()
                 self.RFLP.fromMoby(elt.toxml())

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/ontology/TropGENE_Diversity_Matrix.py,v
retrieving revision 1.3
retrieving revision 1.4
diff -u -r1.3 -r1.4
--- /home/repository/moby/moby-live/Python/bioMoby/ontology/TropGENE_Diversity_Matrix.py	2005/01/27 08:44:05	1.3
+++ /home/repository/moby/moby-live/Python/bioMoby/ontology/TropGENE_Diversity_Matrix.py	2005/02/01 08:52:16	1.4
@@ -46,5 +46,4 @@
             if elt.nodeName=="CrossReference" or elt.nodeName=="moby:CrossReference":
                 self.__cross__=[]
                 for ref in elt.childNodes:
-                    if ref.nodeType==ref.ELEMENT_NODE:
-                        self.__cross__.append(um.loads(ref.toxml()))
\ No newline at end of file
+                    self.__cross__.append(ref.toxml())
\ No newline at end of file

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/ontology/TropGENE_LOCUS.py,v
retrieving revision 1.3
retrieving revision 1.4
diff -u -r1.3 -r1.4
--- /home/repository/moby/moby-live/Python/bioMoby/ontology/TropGENE_LOCUS.py	2005/01/27 08:44:05	1.3
+++ /home/repository/moby/moby-live/Python/bioMoby/ontology/TropGENE_LOCUS.py	2005/02/01 08:52:16	1.4
@@ -45,5 +45,4 @@
             if elt.nodeName=="CrossReference" or elt.nodeName=="moby:CrossReference":
                 self.__cross__=[]
                 for ref in elt.childNodes:
-                    if ref.nodeType==ref.ELEMENT_NODE:
-                        self.__cross__.append(um.loads(ref.toxml()))
\ No newline at end of file
+                    self.__cross__.append(ref.toxml())
\ No newline at end of file

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/ontology/VirtualSequence.py,v
retrieving revision 1.3
retrieving revision 1.4
diff -u -r1.3 -r1.4
--- /home/repository/moby/moby-live/Python/bioMoby/ontology/VirtualSequence.py	2005/01/27 08:44:05	1.3
+++ /home/repository/moby/moby-live/Python/bioMoby/ontology/VirtualSequence.py	2005/02/01 08:52:16	1.4
@@ -47,8 +47,7 @@
             if elt.nodeName=="CrossReference" or elt.nodeName=="moby:CrossReference":
                 self.__cross__=[]
                 for ref in elt.childNodes:
-                    if ref.nodeType==ref.ELEMENT_NODE:
-                        self.__cross__.append(um.loads(ref.toxml()))
+                    self.__cross__.append(ref.toxml())
             if elt.nodeType==elt.ELEMENT_NODE and (elt.nodeName=="Integer" or elt.nodeName=="moby:Integer") and (elt.getAttribute("articleName")=="Length" or elt.getAttribute("moby:articleName")=="Length"):
                 t=MobyInteger()
                 t.fromMoby(elt.toxml())

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/ontology/WU_BLAST_Text.py,v
retrieving revision 1.3
retrieving revision 1.4
diff -u -r1.3 -r1.4
--- /home/repository/moby/moby-live/Python/bioMoby/ontology/WU_BLAST_Text.py	2005/01/27 08:44:05	1.3
+++ /home/repository/moby/moby-live/Python/bioMoby/ontology/WU_BLAST_Text.py	2005/02/01 08:52:16	1.4
@@ -46,5 +46,4 @@
             if elt.nodeName=="CrossReference" or elt.nodeName=="moby:CrossReference":
                 self.__cross__=[]
                 for ref in elt.childNodes:
-                    if ref.nodeType==ref.ELEMENT_NODE:
-                        self.__cross__.append(um.loads(ref.toxml()))
\ No newline at end of file
+                    self.__cross__.append(ref.toxml())
\ No newline at end of file

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/ontology/Wildcard_Query.py,v
retrieving revision 1.3
retrieving revision 1.4
diff -u -r1.3 -r1.4
--- /home/repository/moby/moby-live/Python/bioMoby/ontology/Wildcard_Query.py	2005/01/27 08:44:05	1.3
+++ /home/repository/moby/moby-live/Python/bioMoby/ontology/Wildcard_Query.py	2005/02/01 08:52:16	1.4
@@ -50,8 +50,7 @@
             if elt.nodeName=="CrossReference" or elt.nodeName=="moby:CrossReference":
                 self.__cross__=[]
                 for ref in elt.childNodes:
-                    if ref.nodeType==ref.ELEMENT_NODE:
-                        self.__cross__.append(um.loads(ref.toxml()))
+                    self.__cross__.append(ref.toxml())
             if elt.nodeType==elt.ELEMENT_NODE and (elt.nodeName=="Integer" or elt.nodeName=="moby:Integer") and (elt.getAttribute("articleName")=="end_row" or elt.getAttribute("moby:articleName")=="end_row"):
                 t=MobyInteger()
                 t.fromMoby(elt.toxml())

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/ontology/__init__.py,v
retrieving revision 1.2
retrieving revision 1.3
diff -u -r1.2 -r1.3
--- /home/repository/moby/moby-live/Python/bioMoby/ontology/__init__.py	2005/01/18 13:46:22	1.2
+++ /home/repository/moby/moby-live/Python/bioMoby/ontology/__init__.py	2005/02/01 08:52:16	1.3
@@ -6,6 +6,7 @@
 from MO_Term_Test import MobyMO_Term_Test
 from CommentedDNASequence import MobyCommentedDNASequence
 from BasicGFFSequenceFeature import MobyBasicGFFSequenceFeature
+from MSF import MobyMSF
 from MyTestingDataType_11024145298313 import MobyMyTestingDataType_11024145298313
 from PDBFormattedText import MobyPDBFormattedText
 from Testout import MobyTestout
@@ -24,6 +25,7 @@
 from BLASTText import MobyBLASTText
 from Allele_freq import MobyAllele_freq
 from GenericSequence import MobyGenericSequence
+from Alignment import MobyAlignment
 from ICIS_Query import MobyICIS_Query
 from PHDText import MobyPHDText
 from WU_BLAST_Text import MobyWU_BLAST_Text
@@ -33,6 +35,7 @@
 from GFF3 import MobyGFF3
 from PDGJOB import MobyPDGJOB
 from CommentedAASequence import MobyCommentedAASequence
+from FASTA_NA_multi import MobyFASTA_NA_multi
 from ClustalMsfFormattedText import MobyClustalMsfFormattedText
 from Multi_key_value_pair import MobyMulti_key_value_pair
 from AlleleAssociation import MobyAlleleAssociation

From yanwong at pub.open-bio.org  Tue Feb  1 09:11:12 2005
From: yanwong at pub.open-bio.org (Yan Wong)
Date: Thu Apr 14 12:22:55 2005
Subject: [MOBY-guts] biomoby commit
Message-ID: <200502011420.j11EKksT014828@pub.open-bio.org>


yanwong
Tue Feb  1 09:20:44 EST 2005
Update of /home/repository/moby/moby-live/Python/bioMoby/ontology
In directory pub.open-bio.org:/tmp/cvs-serv14364/bioMoby/ontology

Modified Files:
	AlleleAssociation.py Allele_freq.py AminoAcidSequence.py 
	B64_Encoded_PNG.py B64_Encoded_Postscript.py 
	B64_encoded_PDB.py B64_encoded_gif.py B64_encoded_jpeg.py 
	BLASTText.py BasicGFFSequenceFeature.py 
	ClustalAlnFormattedText.py ClustalMsfFormattedText.py 
	CommentedAASequence.py CommentedDNASequence.py 
	CommentedRNASequence.py DNASequence.py 
	DNASequenceWithGFFFeatures.py DateTime.py Decypher_Text.py 
	Edge.py EmblFlatfile.py FASTA.py FASTA_AA.py FASTA_NA.py 
	FASTA_Text.py GFF.py GFF1.py GFF2.py GFF2_5.py GFF3.py 
	GO_Term.py GenbankFlatfile.py GenericSequence.py 
	GeneticElement.py Genotype.py Germplasm_Details.py 
	Germplasm_List.py Global_Keyword.py HBond_Pair.py 
	HFormatText.py Haplotyping_Study_obj.py ICIS_Query.py 
	ICIS_Query2.py ICIS_Query3.py IntAct_XML.py Interaction.py 
	InteractionMethod.py Interaction_partner.py Interactor.py 
	MEME_Text.py MGIS_ACCESSION.py MMP_Locus.py MO_Term_Test.py 
	MmCIFText.py Multi_key_value_pair.py 
	MyTestingDataType_11024145298313.py MyTree.py 
	NCBI_BLAST_Text.py NCBI_Blast_XML.py NCBI_Blast_XML_Gif.py 
	NCBI_Blast_XML_Gif_Map.py NCBI_MEME_Text.py 
	NucleotideSequence.py PDBFormattedText.py PDBText.py PDGJOB.py 
	PHDText.py PMUTText.py PSeaTextFormatted.py 
	PhenotypeDescription.py PubMedMEDLINE.py RNASequence.py 
	SINGER_ACCESSION.py Sample.py SchematikonMotifID.py 
	SchematikonMotifSupport.py SchematikonSegmentAttributes.py 
	SchematikonSegmentID.py SchematikonStructureAnnotation.py 
	SchematikonVorocodeName.py Scored_acronym_string.py 
	SimpleAnnotatedGIFImage.py SimpleAnnotatedJPEGImage.py 
	Simple_key_value_pair.py Snp_allele.py Snp_genotype.py 
	Study.py TEST.py TargetP_result.py Testout.py TextBase64.py 
	TextFormatted.py TextHtml.py TextPlain.py TextUuencoded.py 
	TextXml.py Text_plain.py Trait_Details.py Tree.py 
	TropGENE_ACCESSION.py TropGENE_Diversity_Matrix.py 
	TropGENE_LOCUS.py VirtualSequence.py WU_BLAST_Text.py 
	Wildcard_Query.py 
Log Message:


moby-live/Python/bioMoby/ontology AlleleAssociation.py,1.4,1.5 Allele_freq.py,1.4,1.5 AminoAcidSequence.py,1.4,1.5 B64_Encoded_PNG.py,1.4,1.5 B64_Encoded_Postscript.py,1.4,1.5 B64_encoded_PDB.py,1.4,1.5 B64_encoded_gif.py,1.4,1.5 B64_encoded_jpeg.py,1.4,1.5 BLASTText.py,1.4,1.5 BasicGFFSequenceFeature.py,1.4,1.5 ClustalAlnFormattedText.py,1.4,1.5 ClustalMsfFormattedText.py,1.4,1.5 CommentedAASequence.py,1.4,1.5 CommentedDNASequence.py,1.4,1.5 CommentedRNASequence.py,1.4,1.5 DNASequence.py,1.4,1.5 DNASequenceWithGFFFeatures.py,1.4,1.5 DateTime.py,1.4,1.5 Decypher_Text.py,1.4,1.5 Edge.py,1.4,1.5 EmblFlatfile.py,1.4,1.5 FASTA.py,1.4,1.5 FASTA_AA.py,1.4,1.5 FASTA_NA.py,1.4,1.5 FASTA_Text.py,1.4,1.5 GFF.py,1.4,1.5 GFF1.py,1.4,1.5 GFF2.py,1.4,1.5 GFF2_5.py,1.4,1.5 GFF3.py,1.4,1.5 GO_Term.py,1.4,1.5 GenbankFlatfile.py,1.4,1.5 GenericSequence.py,1.4,1.5 GeneticElement.py,1.4,1.5 Genotype.py,1.4,1.5 Germplasm_Details.py,1.4,1.5 Germplasm_List.py,1.4,1.5 Global_Keyword.py,1.4,1.5 HBon!
d_Pair.py,1.4,1.5 HFormatText.py,1.4,1.5 Haplotyping_Study_obj.py,1.4,1.5 ICIS_Query.py,1.4,1.5 ICIS_Query2.py,1.4,1.5 ICIS_Query3.py,1.4,1.5 IntAct_XML.py,1.4,1.5 Interaction.py,1.4,1.5 InteractionMethod.py,1.4,1.5 Interaction_partner.py,1.4,1.5 Interactor.py,1.4,1.5 MEME_Text.py,1.4,1.5 MGIS_ACCESSION.py,1.4,1.5 MMP_Locus.py,1.4,1.5 MO_Term_Test.py,1.4,1.5 MmCIFText.py,1.4,1.5 Multi_key_value_pair.py,1.4,1.5 MyTestingDataType_11024145298313.py,1.4,1.5 MyTree.py,1.4,1.5 NCBI_BLAST_Text.py,1.4,1.5 NCBI_Blast_XML.py,1.4,1.5 NCBI_Blast_XML_Gif.py,1.4,1.5 NCBI_Blast_XML_Gif_Map.py,1.4,1.5 NCBI_MEME_Text.py,1.4,1.5 NucleotideSequence.py,1.4,1.5 PDBFormattedText.py,1.4,1.5 PDBText.py,1.4,1.5 PDGJOB.py,1.4,1.5 PHDText.py,1.4,1.5 PMUTText.py,1.4,1.5 PSeaTextFormatted.py,1.4,1.5 PhenotypeDescription.py,1.4,1.5 PubMedMEDLINE.py,1.4,1.5 RNASequence.py,1.4,1.5 SINGER_ACCESSION.py,1.4,1.5 Sample.py,1.4,1.5 SchematikonMotifID.py,1.4,1.5 SchematikonMotifSupport.py,1.4,1.5 SchematikonSegme!
ntAttributes.py,1.4,1.5 SchematikonSegmentID.py,1.4,1.5 Schem!
atikonStructureAnnotation.py,1.4,1.5 SchematikonVorocodeName.py,1.4,1.5 Scored_acronym_string.py,1.4,1.5 SimpleAnnotatedGIFImage.py,1.4,1.5 SimpleAnnotatedJPEGImage.py,1.4,1.5 Simple_key_value_pair.py,1.4,1.5 Snp_allele.py,1.4,1.5 Snp_genotype.py,1.4,1.5 Study.py,1.4,1.5 TEST.py,1.4,1.5 TargetP_result.py,1.4,1.5 Testout.py,1.4,1.5 TextBase64.py,1.4,1.5 TextFormatted.py,1.4,1.5 TextHtml.py,1.4,1.5 TextPlain.py,1.4,1.5 TextUuencoded.py,1.4,1.5 TextXml.py,1.4,1.5 Text_plain.py,1.4,1.5 Trait_Details.py,1.4,1.5 Tree.py,1.4,1.5 TropGENE_ACCESSION.py,1.4,1.5 TropGENE_Diversity_Matrix.py,1.4,1.5 TropGENE_LOCUS.py,1.4,1.5 VirtualSequence.py,1.4,1.5 WU_BLAST_Text.py,1.4,1.5 Wildcard_Query.py,1.4,1.5
===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/ontology/AlleleAssociation.py,v
retrieving revision 1.4
retrieving revision 1.5
diff -u -r1.4 -r1.5
--- /home/repository/moby/moby-live/Python/bioMoby/ontology/AlleleAssociation.py	2005/02/01 08:52:15	1.4
+++ /home/repository/moby/moby-live/Python/bioMoby/ontology/AlleleAssociation.py	2005/02/01 14:20:44	1.5
@@ -30,7 +30,9 @@
         """ Load the attributes from an XML string
         """
         from bioMoby.mobyMarshal import MobyUnmarshaller
-        doc=parseString(value).firstChild
+        doc=value
+        if isinstance(value, str):
+            doc=parseString(value).firstChild
         um=MobyUnmarshaller()
         self.content=""
         self.namespace=doc.getAttribute("moby:namespace")
@@ -50,16 +52,16 @@
             if elt.nodeName=="CrossReference" or elt.nodeName=="moby:CrossReference":
                 self.__cross__=[]
                 for ref in elt.childNodes:
-                    self.__cross__.append(ref.toxml())
+                    self.__cross__.append(um.loads(ref))
             if elt.nodeType==elt.ELEMENT_NODE and (elt.nodeName=="String" or elt.nodeName=="moby:String") and (elt.getAttribute("articleName")=="snp" or elt.getAttribute("moby:articleName")=="snp"):
                 t=MobyString()
-                t.fromMoby(elt.toxml())
+                t.fromMoby(elt)
                 self.Snp=t.content
             if elt.nodeType==elt.ELEMENT_NODE and (elt.nodeName=="Float" or elt.nodeName=="moby:Float") and (elt.getAttribute("articleName")=="pValue" or elt.getAttribute("moby:articleName")=="pValue"):
                 t=MobyFloat()
-                t.fromMoby(elt.toxml())
+                t.fromMoby(elt)
                 self.PValue=t.content
             if elt.nodeType==elt.ELEMENT_NODE and (elt.nodeName=="String" or elt.nodeName=="moby:String") and (elt.getAttribute("articleName")=="validity" or elt.getAttribute("moby:articleName")=="validity"):
                 t=MobyString()
-                t.fromMoby(elt.toxml())
+                t.fromMoby(elt)
                 self.Validity=t.content
\ No newline at end of file

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/ontology/Allele_freq.py,v
retrieving revision 1.4
retrieving revision 1.5
diff -u -r1.4 -r1.5
--- /home/repository/moby/moby-live/Python/bioMoby/ontology/Allele_freq.py	2005/02/01 08:52:15	1.4
+++ /home/repository/moby/moby-live/Python/bioMoby/ontology/Allele_freq.py	2005/02/01 14:20:44	1.5
@@ -28,7 +28,9 @@
         """ Load the attributes from an XML string
         """
         from bioMoby.mobyMarshal import MobyUnmarshaller
-        doc=parseString(value).firstChild
+        doc=value
+        if isinstance(value, str):
+            doc=parseString(value).firstChild
         um=MobyUnmarshaller()
         self.content=""
 
@@ -44,17 +46,17 @@
             if elt.nodeName=="CrossReference" or elt.nodeName=="moby:CrossReference":
                 self.__cross__=[]
                 for ref in elt.childNodes:
-                    self.__cross__.append(ref.toxml())
+                    self.__cross__.append(um.loads(ref))
             if elt.nodeType==elt.ELEMENT_NODE and (elt.nodeName=="Object" or elt.nodeName=="moby:Object") and (elt.getAttribute("articleName")=="panel_lsid" or elt.getAttribute("moby:articleName")=="panel_lsid"):
                 self.Panel_lsid=MobyObject()
-                self.Panel_lsid.fromMoby(elt.toxml())
+                self.Panel_lsid.fromMoby(elt)
             if elt.nodeType==elt.ELEMENT_NODE and (elt.nodeName=="Object" or elt.nodeName=="moby:Object") and (elt.getAttribute("articleName")=="snp_lsid" or elt.getAttribute("moby:articleName")=="snp_lsid"):
                 self.Snp_lsid=MobyObject()
-                self.Snp_lsid.fromMoby(elt.toxml())
+                self.Snp_lsid.fromMoby(elt)
             if elt.nodeType==elt.ELEMENT_NODE and (elt.nodeName=="snp_allele" or elt.nodeName=="moby:snp_allele") and (elt.getAttribute("articleName")=="allele_freq" or elt.getAttribute("moby:articleName")=="allele_freq"):
                 self.Allele_freq=MobySnp_allele()
-                self.Allele_freq.fromMoby(elt.toxml())
+                self.Allele_freq.fromMoby(elt)
             if elt.nodeType==elt.ELEMENT_NODE and (elt.nodeName=="Integer" or elt.nodeName=="moby:Integer") and (elt.getAttribute("articleName")=="frequency" or elt.getAttribute("moby:articleName")=="frequency"):
                 t=MobyInteger()
-                t.fromMoby(elt.toxml())
+                t.fromMoby(elt)
                 self.Frequency.append(t.content)
\ No newline at end of file

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/ontology/AminoAcidSequence.py,v
retrieving revision 1.4
retrieving revision 1.5
diff -u -r1.4 -r1.5
--- /home/repository/moby/moby-live/Python/bioMoby/ontology/AminoAcidSequence.py	2005/02/01 08:52:15	1.4
+++ /home/repository/moby/moby-live/Python/bioMoby/ontology/AminoAcidSequence.py	2005/02/01 14:20:44	1.5
@@ -29,7 +29,9 @@
         """ Load the attributes from an XML string
         """
         from bioMoby.mobyMarshal import MobyUnmarshaller
-        doc=parseString(value).firstChild
+        doc=value
+        if isinstance(value, str):
+            doc=parseString(value).firstChild
         um=MobyUnmarshaller()
         self.content=""
         self.namespace=doc.getAttribute("moby:namespace")
@@ -49,12 +51,12 @@
             if elt.nodeName=="CrossReference" or elt.nodeName=="moby:CrossReference":
                 self.__cross__=[]
                 for ref in elt.childNodes:
-                    self.__cross__.append(ref.toxml())
+                    self.__cross__.append(um.loads(ref))
             if elt.nodeType==elt.ELEMENT_NODE and (elt.nodeName=="Integer" or elt.nodeName=="moby:Integer") and (elt.getAttribute("articleName")=="Length" or elt.getAttribute("moby:articleName")=="Length"):
                 t=MobyInteger()
-                t.fromMoby(elt.toxml())
+                t.fromMoby(elt)
                 self.Length=t.content
             if elt.nodeType==elt.ELEMENT_NODE and (elt.nodeName=="String" or elt.nodeName=="moby:String") and (elt.getAttribute("articleName")=="SequenceString" or elt.getAttribute("moby:articleName")=="SequenceString"):
                 t=MobyString()
-                t.fromMoby(elt.toxml())
+                t.fromMoby(elt)
                 self.SequenceString=t.content
\ No newline at end of file

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/ontology/B64_Encoded_PNG.py,v
retrieving revision 1.4
retrieving revision 1.5
diff -u -r1.4 -r1.5
--- /home/repository/moby/moby-live/Python/bioMoby/ontology/B64_Encoded_PNG.py	2005/02/01 08:52:15	1.4
+++ /home/repository/moby/moby-live/Python/bioMoby/ontology/B64_Encoded_PNG.py	2005/02/01 14:20:44	1.5
@@ -26,7 +26,9 @@
         """ Load the attributes from an XML string
         """
         from bioMoby.mobyMarshal import MobyUnmarshaller
-        doc=parseString(value).firstChild
+        doc=value
+        if isinstance(value, str):
+            doc=parseString(value).firstChild
         um=MobyUnmarshaller()
         self.content=""
         self.namespace=doc.getAttribute("moby:namespace")
@@ -46,4 +48,4 @@
             if elt.nodeName=="CrossReference" or elt.nodeName=="moby:CrossReference":
                 self.__cross__=[]
                 for ref in elt.childNodes:
-                    self.__cross__.append(ref.toxml())
\ No newline at end of file
+                    self.__cross__.append(um.loads(ref))
\ No newline at end of file

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/ontology/B64_Encoded_Postscript.py,v
retrieving revision 1.4
retrieving revision 1.5
diff -u -r1.4 -r1.5
--- /home/repository/moby/moby-live/Python/bioMoby/ontology/B64_Encoded_Postscript.py	2005/02/01 08:52:15	1.4
+++ /home/repository/moby/moby-live/Python/bioMoby/ontology/B64_Encoded_Postscript.py	2005/02/01 14:20:44	1.5
@@ -26,7 +26,9 @@
         """ Load the attributes from an XML string
         """
         from bioMoby.mobyMarshal import MobyUnmarshaller
-        doc=parseString(value).firstChild
+        doc=value
+        if isinstance(value, str):
+            doc=parseString(value).firstChild
         um=MobyUnmarshaller()
         self.content=""
         self.namespace=doc.getAttribute("moby:namespace")
@@ -46,4 +48,4 @@
             if elt.nodeName=="CrossReference" or elt.nodeName=="moby:CrossReference":
                 self.__cross__=[]
                 for ref in elt.childNodes:
-                    self.__cross__.append(ref.toxml())
\ No newline at end of file
+                    self.__cross__.append(um.loads(ref))
\ No newline at end of file

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/ontology/B64_encoded_PDB.py,v
retrieving revision 1.4
retrieving revision 1.5
diff -u -r1.4 -r1.5
--- /home/repository/moby/moby-live/Python/bioMoby/ontology/B64_encoded_PDB.py	2005/02/01 08:52:15	1.4
+++ /home/repository/moby/moby-live/Python/bioMoby/ontology/B64_encoded_PDB.py	2005/02/01 14:20:44	1.5
@@ -26,7 +26,9 @@
         """ Load the attributes from an XML string
         """
         from bioMoby.mobyMarshal import MobyUnmarshaller
-        doc=parseString(value).firstChild
+        doc=value
+        if isinstance(value, str):
+            doc=parseString(value).firstChild
         um=MobyUnmarshaller()
         self.content=""
         self.namespace=doc.getAttribute("moby:namespace")
@@ -46,4 +48,4 @@
             if elt.nodeName=="CrossReference" or elt.nodeName=="moby:CrossReference":
                 self.__cross__=[]
                 for ref in elt.childNodes:
-                    self.__cross__.append(ref.toxml())
\ No newline at end of file
+                    self.__cross__.append(um.loads(ref))
\ No newline at end of file

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/ontology/B64_encoded_gif.py,v
retrieving revision 1.4
retrieving revision 1.5
diff -u -r1.4 -r1.5
--- /home/repository/moby/moby-live/Python/bioMoby/ontology/B64_encoded_gif.py	2005/02/01 08:52:15	1.4
+++ /home/repository/moby/moby-live/Python/bioMoby/ontology/B64_encoded_gif.py	2005/02/01 14:20:44	1.5
@@ -26,7 +26,9 @@
         """ Load the attributes from an XML string
         """
         from bioMoby.mobyMarshal import MobyUnmarshaller
-        doc=parseString(value).firstChild
+        doc=value
+        if isinstance(value, str):
+            doc=parseString(value).firstChild
         um=MobyUnmarshaller()
         self.content=""
         self.namespace=doc.getAttribute("moby:namespace")
@@ -46,4 +48,4 @@
             if elt.nodeName=="CrossReference" or elt.nodeName=="moby:CrossReference":
                 self.__cross__=[]
                 for ref in elt.childNodes:
-                    self.__cross__.append(ref.toxml())
\ No newline at end of file
+                    self.__cross__.append(um.loads(ref))
\ No newline at end of file

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/ontology/B64_encoded_jpeg.py,v
retrieving revision 1.4
retrieving revision 1.5
diff -u -r1.4 -r1.5
--- /home/repository/moby/moby-live/Python/bioMoby/ontology/B64_encoded_jpeg.py	2005/02/01 08:52:15	1.4
+++ /home/repository/moby/moby-live/Python/bioMoby/ontology/B64_encoded_jpeg.py	2005/02/01 14:20:44	1.5
@@ -26,7 +26,9 @@
         """ Load the attributes from an XML string
         """
         from bioMoby.mobyMarshal import MobyUnmarshaller
-        doc=parseString(value).firstChild
+        doc=value
+        if isinstance(value, str):
+            doc=parseString(value).firstChild
         um=MobyUnmarshaller()
         self.content=""
         self.namespace=doc.getAttribute("moby:namespace")
@@ -46,4 +48,4 @@
             if elt.nodeName=="CrossReference" or elt.nodeName=="moby:CrossReference":
                 self.__cross__=[]
                 for ref in elt.childNodes:
-                    self.__cross__.append(ref.toxml())
\ No newline at end of file
+                    self.__cross__.append(um.loads(ref))
\ No newline at end of file

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/ontology/BLASTText.py,v
retrieving revision 1.4
retrieving revision 1.5
diff -u -r1.4 -r1.5
--- /home/repository/moby/moby-live/Python/bioMoby/ontology/BLASTText.py	2005/02/01 08:52:15	1.4
+++ /home/repository/moby/moby-live/Python/bioMoby/ontology/BLASTText.py	2005/02/01 14:20:44	1.5
@@ -26,7 +26,9 @@
         """ Load the attributes from an XML string
         """
         from bioMoby.mobyMarshal import MobyUnmarshaller
-        doc=parseString(value).firstChild
+        doc=value
+        if isinstance(value, str):
+            doc=parseString(value).firstChild
         um=MobyUnmarshaller()
         self.content=""
         self.namespace=doc.getAttribute("moby:namespace")
@@ -46,4 +48,4 @@
             if elt.nodeName=="CrossReference" or elt.nodeName=="moby:CrossReference":
                 self.__cross__=[]
                 for ref in elt.childNodes:
-                    self.__cross__.append(ref.toxml())
\ No newline at end of file
+                    self.__cross__.append(um.loads(ref))
\ No newline at end of file

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/ontology/BasicGFFSequenceFeature.py,v
retrieving revision 1.4
retrieving revision 1.5
diff -u -r1.4 -r1.5
--- /home/repository/moby/moby-live/Python/bioMoby/ontology/BasicGFFSequenceFeature.py	2005/02/01 08:52:15	1.4
+++ /home/repository/moby/moby-live/Python/bioMoby/ontology/BasicGFFSequenceFeature.py	2005/02/01 14:20:44	1.5
@@ -39,7 +39,9 @@
         """ Load the attributes from an XML string
         """
         from bioMoby.mobyMarshal import MobyUnmarshaller
-        doc=parseString(value).firstChild
+        doc=value
+        if isinstance(value, str):
+            doc=parseString(value).firstChild
         um=MobyUnmarshaller()
         self.content=""
         self.namespace=doc.getAttribute("moby:namespace")
@@ -60,43 +62,43 @@
             if elt.nodeName=="CrossReference" or elt.nodeName=="moby:CrossReference":
                 self.__cross__=[]
                 for ref in elt.childNodes:
-                    self.__cross__.append(ref.toxml())
+                    self.__cross__.append(um.loads(ref))
             if elt.nodeType==elt.ELEMENT_NODE and (elt.nodeName=="String" or elt.nodeName=="moby:String") and (elt.getAttribute("articleName")=="reference" or elt.getAttribute("moby:articleName")=="reference"):
                 t=MobyString()
-                t.fromMoby(elt.toxml())
+                t.fromMoby(elt)
                 self.Reference=t.content
             if elt.nodeType==elt.ELEMENT_NODE and (elt.nodeName=="String" or elt.nodeName=="moby:String") and (elt.getAttribute("articleName")=="source" or elt.getAttribute("moby:articleName")=="source"):
                 t=MobyString()
-                t.fromMoby(elt.toxml())
+                t.fromMoby(elt)
                 self.Source=t.content
             if elt.nodeType==elt.ELEMENT_NODE and (elt.nodeName=="String" or elt.nodeName=="moby:String") and (elt.getAttribute("articleName")=="method" or elt.getAttribute("moby:articleName")=="method"):
                 t=MobyString()
-                t.fromMoby(elt.toxml())
+                t.fromMoby(elt)
                 self.Method=t.content
             if elt.nodeType==elt.ELEMENT_NODE and (elt.nodeName=="Integer" or elt.nodeName=="moby:Integer") and (elt.getAttribute("articleName")=="start" or elt.getAttribute("moby:articleName")=="start"):
                 t=MobyInteger()
-                t.fromMoby(elt.toxml())
+                t.fromMoby(elt)
                 self.Start=t.content
             if elt.nodeType==elt.ELEMENT_NODE and (elt.nodeName=="Integer" or elt.nodeName=="moby:Integer") and (elt.getAttribute("articleName")=="stop" or elt.getAttribute("moby:articleName")=="stop"):
                 t=MobyInteger()
-                t.fromMoby(elt.toxml())
+                t.fromMoby(elt)
                 self.Stop=t.content
             if elt.nodeType==elt.ELEMENT_NODE and (elt.nodeName=="Float" or elt.nodeName=="moby:Float") and (elt.getAttribute("articleName")=="score" or elt.getAttribute("moby:articleName")=="score"):
                 t=MobyFloat()
-                t.fromMoby(elt.toxml())
+                t.fromMoby(elt)
                 self.Score=t.content
             if elt.nodeType==elt.ELEMENT_NODE and (elt.nodeName=="String" or elt.nodeName=="moby:String") and (elt.getAttribute("articleName")=="strand" or elt.getAttribute("moby:articleName")=="strand"):
                 t=MobyString()
-                t.fromMoby(elt.toxml())
+                t.fromMoby(elt)
                 self.Strand=t.content
             if elt.nodeType==elt.ELEMENT_NODE and (elt.nodeName=="String" or elt.nodeName=="moby:String") and (elt.getAttribute("articleName")=="frame" or elt.getAttribute("moby:articleName")=="frame"):
                 t=MobyString()
-                t.fromMoby(elt.toxml())
+                t.fromMoby(elt)
                 self.Frame=t.content
             if elt.nodeType==elt.ELEMENT_NODE and (elt.nodeName=="String" or elt.nodeName=="moby:String") and (elt.getAttribute("articleName")=="phase" or elt.getAttribute("moby:articleName")=="phase"):
                 t=MobyString()
-                t.fromMoby(elt.toxml())
+                t.fromMoby(elt)
                 self.Phase=t.content
             if elt.nodeType==elt.ELEMENT_NODE and (elt.nodeName=="multi_key_value_pair" or elt.nodeName=="moby:multi_key_value_pair") and (elt.getAttribute("articleName")=="column9_tag_value" or elt.getAttribute("moby:articleName")=="column9_tag_value"):
                 self.Column9_tag_value=MobyMulti_key_value_pair()
-                self.Column9_tag_value.fromMoby(elt.toxml())
\ No newline at end of file
+                self.Column9_tag_value.fromMoby(elt)
\ No newline at end of file

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/ontology/ClustalAlnFormattedText.py,v
retrieving revision 1.4
retrieving revision 1.5
diff -u -r1.4 -r1.5
--- /home/repository/moby/moby-live/Python/bioMoby/ontology/ClustalAlnFormattedText.py	2005/02/01 08:52:15	1.4
+++ /home/repository/moby/moby-live/Python/bioMoby/ontology/ClustalAlnFormattedText.py	2005/02/01 14:20:44	1.5
@@ -26,7 +26,9 @@
         """ Load the attributes from an XML string
         """
         from bioMoby.mobyMarshal import MobyUnmarshaller
-        doc=parseString(value).firstChild
+        doc=value
+        if isinstance(value, str):
+            doc=parseString(value).firstChild
         um=MobyUnmarshaller()
         self.content=""
         self.namespace=doc.getAttribute("moby:namespace")
@@ -46,4 +48,4 @@
             if elt.nodeName=="CrossReference" or elt.nodeName=="moby:CrossReference":
                 self.__cross__=[]
                 for ref in elt.childNodes:
-                    self.__cross__.append(ref.toxml())
\ No newline at end of file
+                    self.__cross__.append(um.loads(ref))
\ No newline at end of file

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/ontology/ClustalMsfFormattedText.py,v
retrieving revision 1.4
retrieving revision 1.5
diff -u -r1.4 -r1.5
--- /home/repository/moby/moby-live/Python/bioMoby/ontology/ClustalMsfFormattedText.py	2005/02/01 08:52:15	1.4
+++ /home/repository/moby/moby-live/Python/bioMoby/ontology/ClustalMsfFormattedText.py	2005/02/01 14:20:44	1.5
@@ -26,7 +26,9 @@
         """ Load the attributes from an XML string
         """
         from bioMoby.mobyMarshal import MobyUnmarshaller
-        doc=parseString(value).firstChild
+        doc=value
+        if isinstance(value, str):
+            doc=parseString(value).firstChild
         um=MobyUnmarshaller()
         self.content=""
         self.namespace=doc.getAttribute("moby:namespace")
@@ -46,4 +48,4 @@
             if elt.nodeName=="CrossReference" or elt.nodeName=="moby:CrossReference":
                 self.__cross__=[]
                 for ref in elt.childNodes:
-                    self.__cross__.append(ref.toxml())
\ No newline at end of file
+                    self.__cross__.append(um.loads(ref))
\ No newline at end of file

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/ontology/CommentedAASequence.py,v
retrieving revision 1.4
retrieving revision 1.5
diff -u -r1.4 -r1.5
--- /home/repository/moby/moby-live/Python/bioMoby/ontology/CommentedAASequence.py	2005/02/01 08:52:15	1.4
+++ /home/repository/moby/moby-live/Python/bioMoby/ontology/CommentedAASequence.py	2005/02/01 14:20:44	1.5
@@ -30,7 +30,9 @@
         """ Load the attributes from an XML string
         """
         from bioMoby.mobyMarshal import MobyUnmarshaller
-        doc=parseString(value).firstChild
+        doc=value
+        if isinstance(value, str):
+            doc=parseString(value).firstChild
         um=MobyUnmarshaller()
         self.content=""
         self.namespace=doc.getAttribute("moby:namespace")
@@ -50,16 +52,16 @@
             if elt.nodeName=="CrossReference" or elt.nodeName=="moby:CrossReference":
                 self.__cross__=[]
                 for ref in elt.childNodes:
-                    self.__cross__.append(ref.toxml())
+                    self.__cross__.append(um.loads(ref))
             if elt.nodeType==elt.ELEMENT_NODE and (elt.nodeName=="Integer" or elt.nodeName=="moby:Integer") and (elt.getAttribute("articleName")=="Length" or elt.getAttribute("moby:articleName")=="Length"):
                 t=MobyInteger()
-                t.fromMoby(elt.toxml())
+                t.fromMoby(elt)
                 self.Length=t.content
             if elt.nodeType==elt.ELEMENT_NODE and (elt.nodeName=="String" or elt.nodeName=="moby:String") and (elt.getAttribute("articleName")=="SequenceString" or elt.getAttribute("moby:articleName")=="SequenceString"):
                 t=MobyString()
-                t.fromMoby(elt.toxml())
+                t.fromMoby(elt)
                 self.SequenceString=t.content
             if elt.nodeType==elt.ELEMENT_NODE and (elt.nodeName=="String" or elt.nodeName=="moby:String") and (elt.getAttribute("articleName")=="Description" or elt.getAttribute("moby:articleName")=="Description"):
                 t=MobyString()
-                t.fromMoby(elt.toxml())
+                t.fromMoby(elt)
                 self.Description=t.content
\ No newline at end of file

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/ontology/CommentedDNASequence.py,v
retrieving revision 1.4
retrieving revision 1.5
diff -u -r1.4 -r1.5
--- /home/repository/moby/moby-live/Python/bioMoby/ontology/CommentedDNASequence.py	2005/02/01 08:52:15	1.4
+++ /home/repository/moby/moby-live/Python/bioMoby/ontology/CommentedDNASequence.py	2005/02/01 14:20:44	1.5
@@ -30,7 +30,9 @@
         """ Load the attributes from an XML string
         """
         from bioMoby.mobyMarshal import MobyUnmarshaller
-        doc=parseString(value).firstChild
+        doc=value
+        if isinstance(value, str):
+            doc=parseString(value).firstChild
         um=MobyUnmarshaller()
         self.content=""
         self.namespace=doc.getAttribute("moby:namespace")
@@ -50,16 +52,16 @@
             if elt.nodeName=="CrossReference" or elt.nodeName=="moby:CrossReference":
                 self.__cross__=[]
                 for ref in elt.childNodes:
-                    self.__cross__.append(ref.toxml())
+                    self.__cross__.append(um.loads(ref))
             if elt.nodeType==elt.ELEMENT_NODE and (elt.nodeName=="Integer" or elt.nodeName=="moby:Integer") and (elt.getAttribute("articleName")=="Length" or elt.getAttribute("moby:articleName")=="Length"):
                 t=MobyInteger()
-                t.fromMoby(elt.toxml())
+                t.fromMoby(elt)
                 self.Length=t.content
             if elt.nodeType==elt.ELEMENT_NODE and (elt.nodeName=="String" or elt.nodeName=="moby:String") and (elt.getAttribute("articleName")=="SequenceString" or elt.getAttribute("moby:articleName")=="SequenceString"):
                 t=MobyString()
-                t.fromMoby(elt.toxml())
+                t.fromMoby(elt)
                 self.SequenceString=t.content
             if elt.nodeType==elt.ELEMENT_NODE and (elt.nodeName=="String" or elt.nodeName=="moby:String") and (elt.getAttribute("articleName")=="Description" or elt.getAttribute("moby:articleName")=="Description"):
                 t=MobyString()
-                t.fromMoby(elt.toxml())
+                t.fromMoby(elt)
                 self.Description=t.content
\ No newline at end of file

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/ontology/CommentedRNASequence.py,v
retrieving revision 1.4
retrieving revision 1.5
diff -u -r1.4 -r1.5
--- /home/repository/moby/moby-live/Python/bioMoby/ontology/CommentedRNASequence.py	2005/02/01 08:52:15	1.4
+++ /home/repository/moby/moby-live/Python/bioMoby/ontology/CommentedRNASequence.py	2005/02/01 14:20:44	1.5
@@ -30,7 +30,9 @@
         """ Load the attributes from an XML string
         """
         from bioMoby.mobyMarshal import MobyUnmarshaller
-        doc=parseString(value).firstChild
+        doc=value
+        if isinstance(value, str):
+            doc=parseString(value).firstChild
         um=MobyUnmarshaller()
         self.content=""
         self.namespace=doc.getAttribute("moby:namespace")
@@ -50,16 +52,16 @@
             if elt.nodeName=="CrossReference" or elt.nodeName=="moby:CrossReference":
                 self.__cross__=[]
                 for ref in elt.childNodes:
-                    self.__cross__.append(ref.toxml())
+                    self.__cross__.append(um.loads(ref))
             if elt.nodeType==elt.ELEMENT_NODE and (elt.nodeName=="Integer" or elt.nodeName=="moby:Integer") and (elt.getAttribute("articleName")=="Length" or elt.getAttribute("moby:articleName")=="Length"):
                 t=MobyInteger()
-                t.fromMoby(elt.toxml())
+                t.fromMoby(elt)
                 self.Length=t.content
             if elt.nodeType==elt.ELEMENT_NODE and (elt.nodeName=="String" or elt.nodeName=="moby:String") and (elt.getAttribute("articleName")=="SequenceString" or elt.getAttribute("moby:articleName")=="SequenceString"):
                 t=MobyString()
-                t.fromMoby(elt.toxml())
+                t.fromMoby(elt)
                 self.SequenceString=t.content
             if elt.nodeType==elt.ELEMENT_NODE and (elt.nodeName=="String" or elt.nodeName=="moby:String") and (elt.getAttribute("articleName")=="Description" or elt.getAttribute("moby:articleName")=="Description"):
                 t=MobyString()
-                t.fromMoby(elt.toxml())
+                t.fromMoby(elt)
                 self.Description=t.content
\ No newline at end of file

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/ontology/DNASequence.py,v
retrieving revision 1.4
retrieving revision 1.5
diff -u -r1.4 -r1.5
--- /home/repository/moby/moby-live/Python/bioMoby/ontology/DNASequence.py	2005/02/01 08:52:15	1.4
+++ /home/repository/moby/moby-live/Python/bioMoby/ontology/DNASequence.py	2005/02/01 14:20:44	1.5
@@ -29,7 +29,9 @@
         """ Load the attributes from an XML string
         """
         from bioMoby.mobyMarshal import MobyUnmarshaller
-        doc=parseString(value).firstChild
+        doc=value
+        if isinstance(value, str):
+            doc=parseString(value).firstChild
         um=MobyUnmarshaller()
         self.content=""
         self.namespace=doc.getAttribute("moby:namespace")
@@ -49,12 +51,12 @@
             if elt.nodeName=="CrossReference" or elt.nodeName=="moby:CrossReference":
                 self.__cross__=[]
                 for ref in elt.childNodes:
-                    self.__cross__.append(ref.toxml())
+                    self.__cross__.append(um.loads(ref))
             if elt.nodeType==elt.ELEMENT_NODE and (elt.nodeName=="Integer" or elt.nodeName=="moby:Integer") and (elt.getAttribute("articleName")=="Length" or elt.getAttribute("moby:articleName")=="Length"):
                 t=MobyInteger()
-                t.fromMoby(elt.toxml())
+                t.fromMoby(elt)
                 self.Length=t.content
             if elt.nodeType==elt.ELEMENT_NODE and (elt.nodeName=="String" or elt.nodeName=="moby:String") and (elt.getAttribute("articleName")=="SequenceString" or elt.getAttribute("moby:articleName")=="SequenceString"):
                 t=MobyString()
-                t.fromMoby(elt.toxml())
+                t.fromMoby(elt)
                 self.SequenceString=t.content
\ No newline at end of file

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/ontology/DNASequenceWithGFFFeatures.py,v
retrieving revision 1.4
retrieving revision 1.5
diff -u -r1.4 -r1.5
--- /home/repository/moby/moby-live/Python/bioMoby/ontology/DNASequenceWithGFFFeatures.py	2005/02/01 08:52:15	1.4
+++ /home/repository/moby/moby-live/Python/bioMoby/ontology/DNASequenceWithGFFFeatures.py	2005/02/01 14:20:44	1.5
@@ -31,7 +31,9 @@
         """ Load the attributes from an XML string
         """
         from bioMoby.mobyMarshal import MobyUnmarshaller
-        doc=parseString(value).firstChild
+        doc=value
+        if isinstance(value, str):
+            doc=parseString(value).firstChild
         um=MobyUnmarshaller()
         self.content=""
         self.namespace=doc.getAttribute("moby:namespace")
@@ -52,15 +54,15 @@
             if elt.nodeName=="CrossReference" or elt.nodeName=="moby:CrossReference":
                 self.__cross__=[]
                 for ref in elt.childNodes:
-                    self.__cross__.append(ref.toxml())
+                    self.__cross__.append(um.loads(ref))
             if elt.nodeType==elt.ELEMENT_NODE and (elt.nodeName=="Integer" or elt.nodeName=="moby:Integer") and (elt.getAttribute("articleName")=="Length" or elt.getAttribute("moby:articleName")=="Length"):
                 t=MobyInteger()
-                t.fromMoby(elt.toxml())
+                t.fromMoby(elt)
                 self.Length=t.content
             if elt.nodeType==elt.ELEMENT_NODE and (elt.nodeName=="String" or elt.nodeName=="moby:String") and (elt.getAttribute("articleName")=="SequenceString" or elt.getAttribute("moby:articleName")=="SequenceString"):
                 t=MobyString()
-                t.fromMoby(elt.toxml())
+                t.fromMoby(elt)
                 self.SequenceString=t.content
             if elt.nodeType==elt.ELEMENT_NODE and (elt.nodeName=="BasicGFFSequenceFeature" or elt.nodeName=="moby:BasicGFFSequenceFeature") and (elt.getAttribute("articleName")=="DNASequenceWithGFFFeatures" or elt.getAttribute("moby:articleName")=="DNASequenceWithGFFFeatures"):
                 self.DNASequenceWithGFFFeatures=MobyBasicGFFSequenceFeature()
-                self.DNASequenceWithGFFFeatures.fromMoby(elt.toxml())
\ No newline at end of file
+                self.DNASequenceWithGFFFeatures.fromMoby(elt)
\ No newline at end of file

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/ontology/DateTime.py,v
retrieving revision 1.4
retrieving revision 1.5
diff -u -r1.4 -r1.5
--- /home/repository/moby/moby-live/Python/bioMoby/ontology/DateTime.py	2005/02/01 08:52:15	1.4
+++ /home/repository/moby/moby-live/Python/bioMoby/ontology/DateTime.py	2005/02/01 14:20:44	1.5
@@ -26,7 +26,9 @@
         """ Load the attributes from an XML string
         """
         from bioMoby.mobyMarshal import MobyUnmarshaller
-        doc=parseString(value).firstChild
+        doc=value
+        if isinstance(value, str):
+            doc=parseString(value).firstChild
         um=MobyUnmarshaller()
         self.content=""
         self.namespace=doc.getAttribute("moby:namespace")
@@ -46,4 +48,4 @@
             if elt.nodeName=="CrossReference" or elt.nodeName=="moby:CrossReference":
                 self.__cross__=[]
                 for ref in elt.childNodes:
-                    self.__cross__.append(ref.toxml())
\ No newline at end of file
+                    self.__cross__.append(um.loads(ref))
\ No newline at end of file

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/ontology/Decypher_Text.py,v
retrieving revision 1.4
retrieving revision 1.5
diff -u -r1.4 -r1.5
--- /home/repository/moby/moby-live/Python/bioMoby/ontology/Decypher_Text.py	2005/02/01 08:52:15	1.4
+++ /home/repository/moby/moby-live/Python/bioMoby/ontology/Decypher_Text.py	2005/02/01 14:20:44	1.5
@@ -26,7 +26,9 @@
         """ Load the attributes from an XML string
         """
         from bioMoby.mobyMarshal import MobyUnmarshaller
-        doc=parseString(value).firstChild
+        doc=value
+        if isinstance(value, str):
+            doc=parseString(value).firstChild
         um=MobyUnmarshaller()
         self.content=""
         self.namespace=doc.getAttribute("moby:namespace")
@@ -46,4 +48,4 @@
             if elt.nodeName=="CrossReference" or elt.nodeName=="moby:CrossReference":
                 self.__cross__=[]
                 for ref in elt.childNodes:
-                    self.__cross__.append(ref.toxml())
\ No newline at end of file
+                    self.__cross__.append(um.loads(ref))
\ No newline at end of file

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/ontology/Edge.py,v
retrieving revision 1.4
retrieving revision 1.5
diff -u -r1.4 -r1.5
--- /home/repository/moby/moby-live/Python/bioMoby/ontology/Edge.py	2005/02/01 08:52:15	1.4
+++ /home/repository/moby/moby-live/Python/bioMoby/ontology/Edge.py	2005/02/01 14:20:44	1.5
@@ -29,7 +29,9 @@
         """ Load the attributes from an XML string
         """
         from bioMoby.mobyMarshal import MobyUnmarshaller
-        doc=parseString(value).firstChild
+        doc=value
+        if isinstance(value, str):
+            doc=parseString(value).firstChild
         um=MobyUnmarshaller()
         self.content=""
         self.namespace=doc.getAttribute("moby:namespace")
@@ -49,12 +51,12 @@
             if elt.nodeName=="CrossReference" or elt.nodeName=="moby:CrossReference":
                 self.__cross__=[]
                 for ref in elt.childNodes:
-                    self.__cross__.append(ref.toxml())
+                    self.__cross__.append(um.loads(ref))
             if elt.nodeType==elt.ELEMENT_NODE and (elt.nodeName=="String" or elt.nodeName=="moby:String") and (elt.getAttribute("articleName")=="partner" or elt.getAttribute("moby:articleName")=="partner"):
                 t=MobyString()
-                t.fromMoby(elt.toxml())
+                t.fromMoby(elt)
                 self.Partner=t.content
             if elt.nodeType==elt.ELEMENT_NODE and (elt.nodeName=="Integer" or elt.nodeName=="moby:Integer") and (elt.getAttribute("articleName")=="direction" or elt.getAttribute("moby:articleName")=="direction"):
                 t=MobyInteger()
-                t.fromMoby(elt.toxml())
+                t.fromMoby(elt)
                 self.Direction=t.content
\ No newline at end of file

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/ontology/EmblFlatfile.py,v
retrieving revision 1.4
retrieving revision 1.5
diff -u -r1.4 -r1.5
--- /home/repository/moby/moby-live/Python/bioMoby/ontology/EmblFlatfile.py	2005/02/01 08:52:15	1.4
+++ /home/repository/moby/moby-live/Python/bioMoby/ontology/EmblFlatfile.py	2005/02/01 14:20:44	1.5
@@ -26,7 +26,9 @@
         """ Load the attributes from an XML string
         """
         from bioMoby.mobyMarshal import MobyUnmarshaller
-        doc=parseString(value).firstChild
+        doc=value
+        if isinstance(value, str):
+            doc=parseString(value).firstChild
         um=MobyUnmarshaller()
         self.content=""
         self.namespace=doc.getAttribute("moby:namespace")
@@ -46,4 +48,4 @@
             if elt.nodeName=="CrossReference" or elt.nodeName=="moby:CrossReference":
                 self.__cross__=[]
                 for ref in elt.childNodes:
-                    self.__cross__.append(ref.toxml())
\ No newline at end of file
+                    self.__cross__.append(um.loads(ref))
\ No newline at end of file

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/ontology/FASTA.py,v
retrieving revision 1.4
retrieving revision 1.5
diff -u -r1.4 -r1.5
--- /home/repository/moby/moby-live/Python/bioMoby/ontology/FASTA.py	2005/02/01 08:52:15	1.4
+++ /home/repository/moby/moby-live/Python/bioMoby/ontology/FASTA.py	2005/02/01 14:20:44	1.5
@@ -26,7 +26,9 @@
         """ Load the attributes from an XML string
         """
         from bioMoby.mobyMarshal import MobyUnmarshaller
-        doc=parseString(value).firstChild
+        doc=value
+        if isinstance(value, str):
+            doc=parseString(value).firstChild
         um=MobyUnmarshaller()
         self.content=""
         self.namespace=doc.getAttribute("moby:namespace")
@@ -46,4 +48,4 @@
             if elt.nodeName=="CrossReference" or elt.nodeName=="moby:CrossReference":
                 self.__cross__=[]
                 for ref in elt.childNodes:
-                    self.__cross__.append(ref.toxml())
\ No newline at end of file
+                    self.__cross__.append(um.loads(ref))
\ No newline at end of file

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/ontology/FASTA_AA.py,v
retrieving revision 1.4
retrieving revision 1.5
diff -u -r1.4 -r1.5
--- /home/repository/moby/moby-live/Python/bioMoby/ontology/FASTA_AA.py	2005/02/01 08:52:15	1.4
+++ /home/repository/moby/moby-live/Python/bioMoby/ontology/FASTA_AA.py	2005/02/01 14:20:44	1.5
@@ -26,7 +26,9 @@
         """ Load the attributes from an XML string
         """
         from bioMoby.mobyMarshal import MobyUnmarshaller
-        doc=parseString(value).firstChild
+        doc=value
+        if isinstance(value, str):
+            doc=parseString(value).firstChild
         um=MobyUnmarshaller()
         self.content=""
         self.namespace=doc.getAttribute("moby:namespace")
@@ -46,4 +48,4 @@
             if elt.nodeName=="CrossReference" or elt.nodeName=="moby:CrossReference":
                 self.__cross__=[]
                 for ref in elt.childNodes:
-                    self.__cross__.append(ref.toxml())
\ No newline at end of file
+                    self.__cross__.append(um.loads(ref))
\ No newline at end of file

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/ontology/FASTA_NA.py,v
retrieving revision 1.4
retrieving revision 1.5
diff -u -r1.4 -r1.5
--- /home/repository/moby/moby-live/Python/bioMoby/ontology/FASTA_NA.py	2005/02/01 08:52:15	1.4
+++ /home/repository/moby/moby-live/Python/bioMoby/ontology/FASTA_NA.py	2005/02/01 14:20:44	1.5
@@ -26,7 +26,9 @@
         """ Load the attributes from an XML string
         """
         from bioMoby.mobyMarshal import MobyUnmarshaller
-        doc=parseString(value).firstChild
+        doc=value
+        if isinstance(value, str):
+            doc=parseString(value).firstChild
         um=MobyUnmarshaller()
         self.content=""
         self.namespace=doc.getAttribute("moby:namespace")
@@ -46,4 +48,4 @@
             if elt.nodeName=="CrossReference" or elt.nodeName=="moby:CrossReference":
                 self.__cross__=[]
                 for ref in elt.childNodes:
-                    self.__cross__.append(ref.toxml())
\ No newline at end of file
+                    self.__cross__.append(um.loads(ref))
\ No newline at end of file

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/ontology/FASTA_Text.py,v
retrieving revision 1.4
retrieving revision 1.5
diff -u -r1.4 -r1.5
--- /home/repository/moby/moby-live/Python/bioMoby/ontology/FASTA_Text.py	2005/02/01 08:52:15	1.4
+++ /home/repository/moby/moby-live/Python/bioMoby/ontology/FASTA_Text.py	2005/02/01 14:20:44	1.5
@@ -26,7 +26,9 @@
         """ Load the attributes from an XML string
         """
         from bioMoby.mobyMarshal import MobyUnmarshaller
-        doc=parseString(value).firstChild
+        doc=value
+        if isinstance(value, str):
+            doc=parseString(value).firstChild
         um=MobyUnmarshaller()
         self.content=""
         self.namespace=doc.getAttribute("moby:namespace")
@@ -46,4 +48,4 @@
             if elt.nodeName=="CrossReference" or elt.nodeName=="moby:CrossReference":
                 self.__cross__=[]
                 for ref in elt.childNodes:
-                    self.__cross__.append(ref.toxml())
\ No newline at end of file
+                    self.__cross__.append(um.loads(ref))
\ No newline at end of file

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/ontology/GFF.py,v
retrieving revision 1.4
retrieving revision 1.5
diff -u -r1.4 -r1.5
--- /home/repository/moby/moby-live/Python/bioMoby/ontology/GFF.py	2005/02/01 08:52:15	1.4
+++ /home/repository/moby/moby-live/Python/bioMoby/ontology/GFF.py	2005/02/01 14:20:44	1.5
@@ -26,7 +26,9 @@
         """ Load the attributes from an XML string
         """
         from bioMoby.mobyMarshal import MobyUnmarshaller
-        doc=parseString(value).firstChild
+        doc=value
+        if isinstance(value, str):
+            doc=parseString(value).firstChild
         um=MobyUnmarshaller()
         self.content=""
         self.namespace=doc.getAttribute("moby:namespace")
@@ -46,4 +48,4 @@
             if elt.nodeName=="CrossReference" or elt.nodeName=="moby:CrossReference":
                 self.__cross__=[]
                 for ref in elt.childNodes:
-                    self.__cross__.append(ref.toxml())
\ No newline at end of file
+                    self.__cross__.append(um.loads(ref))
\ No newline at end of file

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/ontology/GFF1.py,v
retrieving revision 1.4
retrieving revision 1.5
diff -u -r1.4 -r1.5
--- /home/repository/moby/moby-live/Python/bioMoby/ontology/GFF1.py	2005/02/01 08:52:15	1.4
+++ /home/repository/moby/moby-live/Python/bioMoby/ontology/GFF1.py	2005/02/01 14:20:44	1.5
@@ -26,7 +26,9 @@
         """ Load the attributes from an XML string
         """
         from bioMoby.mobyMarshal import MobyUnmarshaller
-        doc=parseString(value).firstChild
+        doc=value
+        if isinstance(value, str):
+            doc=parseString(value).firstChild
         um=MobyUnmarshaller()
         self.content=""
         self.namespace=doc.getAttribute("moby:namespace")
@@ -46,4 +48,4 @@
             if elt.nodeName=="CrossReference" or elt.nodeName=="moby:CrossReference":
                 self.__cross__=[]
                 for ref in elt.childNodes:
-                    self.__cross__.append(ref.toxml())
\ No newline at end of file
+                    self.__cross__.append(um.loads(ref))
\ No newline at end of file

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/ontology/GFF2.py,v
retrieving revision 1.4
retrieving revision 1.5
diff -u -r1.4 -r1.5
--- /home/repository/moby/moby-live/Python/bioMoby/ontology/GFF2.py	2005/02/01 08:52:15	1.4
+++ /home/repository/moby/moby-live/Python/bioMoby/ontology/GFF2.py	2005/02/01 14:20:44	1.5
@@ -26,7 +26,9 @@
         """ Load the attributes from an XML string
         """
         from bioMoby.mobyMarshal import MobyUnmarshaller
-        doc=parseString(value).firstChild
+        doc=value
+        if isinstance(value, str):
+            doc=parseString(value).firstChild
         um=MobyUnmarshaller()
         self.content=""
         self.namespace=doc.getAttribute("moby:namespace")
@@ -46,4 +48,4 @@
             if elt.nodeName=="CrossReference" or elt.nodeName=="moby:CrossReference":
                 self.__cross__=[]
                 for ref in elt.childNodes:
-                    self.__cross__.append(ref.toxml())
\ No newline at end of file
+                    self.__cross__.append(um.loads(ref))
\ No newline at end of file

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/ontology/GFF2_5.py,v
retrieving revision 1.4
retrieving revision 1.5
diff -u -r1.4 -r1.5
--- /home/repository/moby/moby-live/Python/bioMoby/ontology/GFF2_5.py	2005/02/01 08:52:15	1.4
+++ /home/repository/moby/moby-live/Python/bioMoby/ontology/GFF2_5.py	2005/02/01 14:20:44	1.5
@@ -26,7 +26,9 @@
         """ Load the attributes from an XML string
         """
         from bioMoby.mobyMarshal import MobyUnmarshaller
-        doc=parseString(value).firstChild
+        doc=value
+        if isinstance(value, str):
+            doc=parseString(value).firstChild
         um=MobyUnmarshaller()
         self.content=""
         self.namespace=doc.getAttribute("moby:namespace")
@@ -46,4 +48,4 @@
             if elt.nodeName=="CrossReference" or elt.nodeName=="moby:CrossReference":
                 self.__cross__=[]
                 for ref in elt.childNodes:
-                    self.__cross__.append(ref.toxml())
\ No newline at end of file
+                    self.__cross__.append(um.loads(ref))
\ No newline at end of file

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/ontology/GFF3.py,v
retrieving revision 1.4
retrieving revision 1.5
diff -u -r1.4 -r1.5
--- /home/repository/moby/moby-live/Python/bioMoby/ontology/GFF3.py	2005/02/01 08:52:15	1.4
+++ /home/repository/moby/moby-live/Python/bioMoby/ontology/GFF3.py	2005/02/01 14:20:44	1.5
@@ -26,7 +26,9 @@
         """ Load the attributes from an XML string
         """
         from bioMoby.mobyMarshal import MobyUnmarshaller
-        doc=parseString(value).firstChild
+        doc=value
+        if isinstance(value, str):
+            doc=parseString(value).firstChild
         um=MobyUnmarshaller()
         self.content=""
         self.namespace=doc.getAttribute("moby:namespace")
@@ -46,4 +48,4 @@
             if elt.nodeName=="CrossReference" or elt.nodeName=="moby:CrossReference":
                 self.__cross__=[]
                 for ref in elt.childNodes:
-                    self.__cross__.append(ref.toxml())
\ No newline at end of file
+                    self.__cross__.append(um.loads(ref))
\ No newline at end of file

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/ontology/GO_Term.py,v
retrieving revision 1.4
retrieving revision 1.5
diff -u -r1.4 -r1.5
--- /home/repository/moby/moby-live/Python/bioMoby/ontology/GO_Term.py	2005/02/01 08:52:15	1.4
+++ /home/repository/moby/moby-live/Python/bioMoby/ontology/GO_Term.py	2005/02/01 14:20:44	1.5
@@ -28,7 +28,9 @@
         """ Load the attributes from an XML string
         """
         from bioMoby.mobyMarshal import MobyUnmarshaller
-        doc=parseString(value).firstChild
+        doc=value
+        if isinstance(value, str):
+            doc=parseString(value).firstChild
         um=MobyUnmarshaller()
         self.content=""
         self.namespace=doc.getAttribute("moby:namespace")
@@ -48,12 +50,12 @@
             if elt.nodeName=="CrossReference" or elt.nodeName=="moby:CrossReference":
                 self.__cross__=[]
                 for ref in elt.childNodes:
-                    self.__cross__.append(ref.toxml())
+                    self.__cross__.append(um.loads(ref))
             if elt.nodeType==elt.ELEMENT_NODE and (elt.nodeName=="String" or elt.nodeName=="moby:String") and (elt.getAttribute("articleName")=="Term" or elt.getAttribute("moby:articleName")=="Term"):
                 t=MobyString()
-                t.fromMoby(elt.toxml())
+                t.fromMoby(elt)
                 self.Term=t.content
             if elt.nodeType==elt.ELEMENT_NODE and (elt.nodeName=="String" or elt.nodeName=="moby:String") and (elt.getAttribute("articleName")=="Definition" or elt.getAttribute("moby:articleName")=="Definition"):
                 t=MobyString()
-                t.fromMoby(elt.toxml())
+                t.fromMoby(elt)
                 self.Definition=t.content
\ No newline at end of file

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/ontology/GenbankFlatfile.py,v
retrieving revision 1.4
retrieving revision 1.5
diff -u -r1.4 -r1.5
--- /home/repository/moby/moby-live/Python/bioMoby/ontology/GenbankFlatfile.py	2005/02/01 08:52:15	1.4
+++ /home/repository/moby/moby-live/Python/bioMoby/ontology/GenbankFlatfile.py	2005/02/01 14:20:44	1.5
@@ -26,7 +26,9 @@
         """ Load the attributes from an XML string
         """
         from bioMoby.mobyMarshal import MobyUnmarshaller
-        doc=parseString(value).firstChild
+        doc=value
+        if isinstance(value, str):
+            doc=parseString(value).firstChild
         um=MobyUnmarshaller()
         self.content=""
         self.namespace=doc.getAttribute("moby:namespace")
@@ -46,4 +48,4 @@
             if elt.nodeName=="CrossReference" or elt.nodeName=="moby:CrossReference":
                 self.__cross__=[]
                 for ref in elt.childNodes:
-                    self.__cross__.append(ref.toxml())
\ No newline at end of file
+                    self.__cross__.append(um.loads(ref))
\ No newline at end of file

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/ontology/GenericSequence.py,v
retrieving revision 1.4
retrieving revision 1.5
diff -u -r1.4 -r1.5
--- /home/repository/moby/moby-live/Python/bioMoby/ontology/GenericSequence.py	2005/02/01 08:52:15	1.4
+++ /home/repository/moby/moby-live/Python/bioMoby/ontology/GenericSequence.py	2005/02/01 14:20:44	1.5
@@ -29,7 +29,9 @@
         """ Load the attributes from an XML string
         """
         from bioMoby.mobyMarshal import MobyUnmarshaller
-        doc=parseString(value).firstChild
+        doc=value
+        if isinstance(value, str):
+            doc=parseString(value).firstChild
         um=MobyUnmarshaller()
         self.content=""
         self.namespace=doc.getAttribute("moby:namespace")
@@ -49,12 +51,12 @@
             if elt.nodeName=="CrossReference" or elt.nodeName=="moby:CrossReference":
                 self.__cross__=[]
                 for ref in elt.childNodes:
-                    self.__cross__.append(ref.toxml())
+                    self.__cross__.append(um.loads(ref))
             if elt.nodeType==elt.ELEMENT_NODE and (elt.nodeName=="Integer" or elt.nodeName=="moby:Integer") and (elt.getAttribute("articleName")=="Length" or elt.getAttribute("moby:articleName")=="Length"):
                 t=MobyInteger()
-                t.fromMoby(elt.toxml())
+                t.fromMoby(elt)
                 self.Length=t.content
             if elt.nodeType==elt.ELEMENT_NODE and (elt.nodeName=="String" or elt.nodeName=="moby:String") and (elt.getAttribute("articleName")=="SequenceString" or elt.getAttribute("moby:articleName")=="SequenceString"):
                 t=MobyString()
-                t.fromMoby(elt.toxml())
+                t.fromMoby(elt)
                 self.SequenceString=t.content
\ No newline at end of file

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/ontology/GeneticElement.py,v
retrieving revision 1.4
retrieving revision 1.5
diff -u -r1.4 -r1.5
--- /home/repository/moby/moby-live/Python/bioMoby/ontology/GeneticElement.py	2005/02/01 08:52:15	1.4
+++ /home/repository/moby/moby-live/Python/bioMoby/ontology/GeneticElement.py	2005/02/01 14:20:44	1.5
@@ -27,7 +27,9 @@
         """ Load the attributes from an XML string
         """
         from bioMoby.mobyMarshal import MobyUnmarshaller
-        doc=parseString(value).firstChild
+        doc=value
+        if isinstance(value, str):
+            doc=parseString(value).firstChild
         um=MobyUnmarshaller()
         self.content=""
         self.namespace=doc.getAttribute("moby:namespace")
@@ -47,8 +49,8 @@
             if elt.nodeName=="CrossReference" or elt.nodeName=="moby:CrossReference":
                 self.__cross__=[]
                 for ref in elt.childNodes:
-                    self.__cross__.append(ref.toxml())
+                    self.__cross__.append(um.loads(ref))
             if elt.nodeType==elt.ELEMENT_NODE and (elt.nodeName=="String" or elt.nodeName=="moby:String") and (elt.getAttribute("articleName")=="GeneticElement" or elt.getAttribute("moby:articleName")=="GeneticElement"):
                 t=MobyString()
-                t.fromMoby(elt.toxml())
+                t.fromMoby(elt)
                 self.GeneticElement=t.content
\ No newline at end of file

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/ontology/Genotype.py,v
retrieving revision 1.4
retrieving revision 1.5
diff -u -r1.4 -r1.5
--- /home/repository/moby/moby-live/Python/bioMoby/ontology/Genotype.py	2005/02/01 08:52:15	1.4
+++ /home/repository/moby/moby-live/Python/bioMoby/ontology/Genotype.py	2005/02/01 14:20:44	1.5
@@ -29,7 +29,9 @@
         """ Load the attributes from an XML string
         """
         from bioMoby.mobyMarshal import MobyUnmarshaller
-        doc=parseString(value).firstChild
+        doc=value
+        if isinstance(value, str):
+            doc=parseString(value).firstChild
         um=MobyUnmarshaller()
         self.content=""
         self.namespace=doc.getAttribute("moby:namespace")
@@ -49,16 +51,16 @@
             if elt.nodeName=="CrossReference" or elt.nodeName=="moby:CrossReference":
                 self.__cross__=[]
                 for ref in elt.childNodes:
-                    self.__cross__.append(ref.toxml())
+                    self.__cross__.append(um.loads(ref))
             if elt.nodeType==elt.ELEMENT_NODE and (elt.nodeName=="String" or elt.nodeName=="moby:String") and (elt.getAttribute("articleName")=="snp" or elt.getAttribute("moby:articleName")=="snp"):
                 t=MobyString()
-                t.fromMoby(elt.toxml())
+                t.fromMoby(elt)
                 self.Snp=t.content
             if elt.nodeType==elt.ELEMENT_NODE and (elt.nodeName=="String" or elt.nodeName=="moby:String") and (elt.getAttribute("articleName")=="sample" or elt.getAttribute("moby:articleName")=="sample"):
                 t=MobyString()
-                t.fromMoby(elt.toxml())
+                t.fromMoby(elt)
                 self.Sample=t.content
             if elt.nodeType==elt.ELEMENT_NODE and (elt.nodeName=="String" or elt.nodeName=="moby:String") and (elt.getAttribute("articleName")=="result" or elt.getAttribute("moby:articleName")=="result"):
                 t=MobyString()
-                t.fromMoby(elt.toxml())
+                t.fromMoby(elt)
                 self.Result=t.content
\ No newline at end of file

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/ontology/Germplasm_Details.py,v
retrieving revision 1.4
retrieving revision 1.5
diff -u -r1.4 -r1.5
--- /home/repository/moby/moby-live/Python/bioMoby/ontology/Germplasm_Details.py	2005/02/01 08:52:15	1.4
+++ /home/repository/moby/moby-live/Python/bioMoby/ontology/Germplasm_Details.py	2005/02/01 14:20:44	1.5
@@ -35,7 +35,9 @@
         """ Load the attributes from an XML string
         """
         from bioMoby.mobyMarshal import MobyUnmarshaller
-        doc=parseString(value).firstChild
+        doc=value
+        if isinstance(value, str):
+            doc=parseString(value).firstChild
         um=MobyUnmarshaller()
         self.content=""
         self.namespace=doc.getAttribute("moby:namespace")
@@ -55,36 +57,36 @@
             if elt.nodeName=="CrossReference" or elt.nodeName=="moby:CrossReference":
                 self.__cross__=[]
                 for ref in elt.childNodes:
-                    self.__cross__.append(ref.toxml())
+                    self.__cross__.append(um.loads(ref))
             if elt.nodeType==elt.ELEMENT_NODE and (elt.nodeName=="Integer" or elt.nodeName=="moby:Integer") and (elt.getAttribute("articleName")=="date" or elt.getAttribute("moby:articleName")=="date"):
                 t=MobyInteger()
-                t.fromMoby(elt.toxml())
+                t.fromMoby(elt)
                 self.Date=t.content
             if elt.nodeType==elt.ELEMENT_NODE and (elt.nodeName=="String" or elt.nodeName=="moby:String") and (elt.getAttribute("articleName")=="country" or elt.getAttribute("moby:articleName")=="country"):
                 t=MobyString()
-                t.fromMoby(elt.toxml())
+                t.fromMoby(elt)
                 self.Country=t.content
             if elt.nodeType==elt.ELEMENT_NODE and (elt.nodeName=="String" or elt.nodeName=="moby:String") and (elt.getAttribute("articleName")=="prefered_name" or elt.getAttribute("moby:articleName")=="prefered_name"):
                 t=MobyString()
-                t.fromMoby(elt.toxml())
+                t.fromMoby(elt)
                 self.Prefered_name=t.content
             if elt.nodeType==elt.ELEMENT_NODE and (elt.nodeName=="String" or elt.nodeName=="moby:String") and (elt.getAttribute("articleName")=="alternative_names" or elt.getAttribute("moby:articleName")=="alternative_names"):
                 t=MobyString()
-                t.fromMoby(elt.toxml())
+                t.fromMoby(elt)
                 self.Alternative_names=t.content
             if elt.nodeType==elt.ELEMENT_NODE and (elt.nodeName=="String" or elt.nodeName=="moby:String") and (elt.getAttribute("articleName")=="name_type" or elt.getAttribute("moby:articleName")=="name_type"):
                 t=MobyString()
-                t.fromMoby(elt.toxml())
+                t.fromMoby(elt)
                 self.Name_type=t.content
             if elt.nodeType==elt.ELEMENT_NODE and (elt.nodeName=="String" or elt.nodeName=="moby:String") and (elt.getAttribute("articleName")=="method" or elt.getAttribute("moby:articleName")=="method"):
                 t=MobyString()
-                t.fromMoby(elt.toxml())
+                t.fromMoby(elt)
                 self.Method=t.content
             if elt.nodeType==elt.ELEMENT_NODE and (elt.nodeName=="String" or elt.nodeName=="moby:String") and (elt.getAttribute("articleName")=="location" or elt.getAttribute("moby:articleName")=="location"):
                 t=MobyString()
-                t.fromMoby(elt.toxml())
+                t.fromMoby(elt)
                 self.Location=t.content
             if elt.nodeType==elt.ELEMENT_NODE and (elt.nodeName=="Integer" or elt.nodeName=="moby:Integer") and (elt.getAttribute("articleName")=="germplasm_id" or elt.getAttribute("moby:articleName")=="germplasm_id"):
                 t=MobyInteger()
-                t.fromMoby(elt.toxml())
+                t.fromMoby(elt)
                 self.Germplasm_id=t.content
\ No newline at end of file

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/ontology/Germplasm_List.py,v
retrieving revision 1.4
retrieving revision 1.5
diff -u -r1.4 -r1.5
--- /home/repository/moby/moby-live/Python/bioMoby/ontology/Germplasm_List.py	2005/02/01 08:52:16	1.4
+++ /home/repository/moby/moby-live/Python/bioMoby/ontology/Germplasm_List.py	2005/02/01 14:20:44	1.5
@@ -35,7 +35,9 @@
         """ Load the attributes from an XML string
         """
         from bioMoby.mobyMarshal import MobyUnmarshaller
-        doc=parseString(value).firstChild
+        doc=value
+        if isinstance(value, str):
+            doc=parseString(value).firstChild
         um=MobyUnmarshaller()
         self.content=""
         self.namespace=doc.getAttribute("moby:namespace")
@@ -55,36 +57,36 @@
             if elt.nodeName=="CrossReference" or elt.nodeName=="moby:CrossReference":
                 self.__cross__=[]
                 for ref in elt.childNodes:
-                    self.__cross__.append(ref.toxml())
+                    self.__cross__.append(um.loads(ref))
             if elt.nodeType==elt.ELEMENT_NODE and (elt.nodeName=="Integer" or elt.nodeName=="moby:Integer") and (elt.getAttribute("articleName")=="germplasm_id" or elt.getAttribute("moby:articleName")=="germplasm_id"):
                 t=MobyInteger()
-                t.fromMoby(elt.toxml())
+                t.fromMoby(elt)
                 self.Germplasm_id=t.content
             if elt.nodeType==elt.ELEMENT_NODE and (elt.nodeName=="String" or elt.nodeName=="moby:String") and (elt.getAttribute("articleName")=="germplasm_name" or elt.getAttribute("moby:articleName")=="germplasm_name"):
                 t=MobyString()
-                t.fromMoby(elt.toxml())
+                t.fromMoby(elt)
                 self.Germplasm_name=t.content
             if elt.nodeType==elt.ELEMENT_NODE and (elt.nodeName=="String" or elt.nodeName=="moby:String") and (elt.getAttribute("articleName")=="trait_value" or elt.getAttribute("moby:articleName")=="trait_value"):
                 t=MobyString()
-                t.fromMoby(elt.toxml())
+                t.fromMoby(elt)
                 self.Trait_value=t.content
             if elt.nodeType==elt.ELEMENT_NODE and (elt.nodeName=="Integer" or elt.nodeName=="moby:Integer") and (elt.getAttribute("articleName")=="trait_id" or elt.getAttribute("moby:articleName")=="trait_id"):
                 t=MobyInteger()
-                t.fromMoby(elt.toxml())
+                t.fromMoby(elt)
                 self.Trait_id=t.content
             if elt.nodeType==elt.ELEMENT_NODE and (elt.nodeName=="String" or elt.nodeName=="moby:String") and (elt.getAttribute("articleName")=="scale" or elt.getAttribute("moby:articleName")=="scale"):
                 t=MobyString()
-                t.fromMoby(elt.toxml())
+                t.fromMoby(elt)
                 self.Scale=t.content
             if elt.nodeType==elt.ELEMENT_NODE and (elt.nodeName=="String" or elt.nodeName=="moby:String") and (elt.getAttribute("articleName")=="scale_desc" or elt.getAttribute("moby:articleName")=="scale_desc"):
                 t=MobyString()
-                t.fromMoby(elt.toxml())
+                t.fromMoby(elt)
                 self.Scale_desc=t.content
             if elt.nodeType==elt.ELEMENT_NODE and (elt.nodeName=="String" or elt.nodeName=="moby:String") and (elt.getAttribute("articleName")=="method" or elt.getAttribute("moby:articleName")=="method"):
                 t=MobyString()
-                t.fromMoby(elt.toxml())
+                t.fromMoby(elt)
                 self.Method=t.content
             if elt.nodeType==elt.ELEMENT_NODE and (elt.nodeName=="String" or elt.nodeName=="moby:String") and (elt.getAttribute("articleName")=="study_id" or elt.getAttribute("moby:articleName")=="study_id"):
                 t=MobyString()
-                t.fromMoby(elt.toxml())
+                t.fromMoby(elt)
                 self.Study_id=t.content
\ No newline at end of file

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/ontology/Global_Keyword.py,v
retrieving revision 1.4
retrieving revision 1.5
diff -u -r1.4 -r1.5
--- /home/repository/moby/moby-live/Python/bioMoby/ontology/Global_Keyword.py	2005/02/01 08:52:16	1.4
+++ /home/repository/moby/moby-live/Python/bioMoby/ontology/Global_Keyword.py	2005/02/01 14:20:44	1.5
@@ -25,7 +25,9 @@
         """ Load the attributes from an XML string
         """
         from bioMoby.mobyMarshal import MobyUnmarshaller
-        doc=parseString(value).firstChild
+        doc=value
+        if isinstance(value, str):
+            doc=parseString(value).firstChild
         um=MobyUnmarshaller()
         self.content=""
         self.namespace=doc.getAttribute("moby:namespace")
@@ -45,4 +47,4 @@
             if elt.nodeName=="CrossReference" or elt.nodeName=="moby:CrossReference":
                 self.__cross__=[]
                 for ref in elt.childNodes:
-                    self.__cross__.append(ref.toxml())
\ No newline at end of file
+                    self.__cross__.append(um.loads(ref))
\ No newline at end of file

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/ontology/HBond_Pair.py,v
retrieving revision 1.4
retrieving revision 1.5
diff -u -r1.4 -r1.5
--- /home/repository/moby/moby-live/Python/bioMoby/ontology/HBond_Pair.py	2005/02/01 08:52:16	1.4
+++ /home/repository/moby/moby-live/Python/bioMoby/ontology/HBond_Pair.py	2005/02/01 14:20:44	1.5
@@ -29,7 +29,9 @@
         """ Load the attributes from an XML string
         """
         from bioMoby.mobyMarshal import MobyUnmarshaller
-        doc=parseString(value).firstChild
+        doc=value
+        if isinstance(value, str):
+            doc=parseString(value).firstChild
         um=MobyUnmarshaller()
         self.content=""
         self.namespace=doc.getAttribute("moby:namespace")
@@ -49,16 +51,16 @@
             if elt.nodeName=="CrossReference" or elt.nodeName=="moby:CrossReference":
                 self.__cross__=[]
                 for ref in elt.childNodes:
-                    self.__cross__.append(ref.toxml())
+                    self.__cross__.append(um.loads(ref))
             if elt.nodeType==elt.ELEMENT_NODE and (elt.nodeName=="String" or elt.nodeName=="moby:String") and (elt.getAttribute("articleName")=="A" or elt.getAttribute("moby:articleName")=="A"):
                 t=MobyString()
-                t.fromMoby(elt.toxml())
+                t.fromMoby(elt)
                 self.A=t.content
             if elt.nodeType==elt.ELEMENT_NODE and (elt.nodeName=="String" or elt.nodeName=="moby:String") and (elt.getAttribute("articleName")=="H" or elt.getAttribute("moby:articleName")=="H"):
                 t=MobyString()
-                t.fromMoby(elt.toxml())
+                t.fromMoby(elt)
                 self.H=t.content
             if elt.nodeType==elt.ELEMENT_NODE and (elt.nodeName=="String" or elt.nodeName=="moby:String") and (elt.getAttribute("articleName")=="D" or elt.getAttribute("moby:articleName")=="D"):
                 t=MobyString()
-                t.fromMoby(elt.toxml())
+                t.fromMoby(elt)
                 self.D=t.content
\ No newline at end of file

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/ontology/HFormatText.py,v
retrieving revision 1.4
retrieving revision 1.5
diff -u -r1.4 -r1.5
--- /home/repository/moby/moby-live/Python/bioMoby/ontology/HFormatText.py	2005/02/01 08:52:16	1.4
+++ /home/repository/moby/moby-live/Python/bioMoby/ontology/HFormatText.py	2005/02/01 14:20:44	1.5
@@ -26,7 +26,9 @@
         """ Load the attributes from an XML string
         """
         from bioMoby.mobyMarshal import MobyUnmarshaller
-        doc=parseString(value).firstChild
+        doc=value
+        if isinstance(value, str):
+            doc=parseString(value).firstChild
         um=MobyUnmarshaller()
         self.content=""
         self.namespace=doc.getAttribute("moby:namespace")
@@ -46,4 +48,4 @@
             if elt.nodeName=="CrossReference" or elt.nodeName=="moby:CrossReference":
                 self.__cross__=[]
                 for ref in elt.childNodes:
-                    self.__cross__.append(ref.toxml())
\ No newline at end of file
+                    self.__cross__.append(um.loads(ref))
\ No newline at end of file

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/ontology/Haplotyping_Study_obj.py,v
retrieving revision 1.4
retrieving revision 1.5
diff -u -r1.4 -r1.5
--- /home/repository/moby/moby-live/Python/bioMoby/ontology/Haplotyping_Study_obj.py	2005/02/01 08:52:16	1.4
+++ /home/repository/moby/moby-live/Python/bioMoby/ontology/Haplotyping_Study_obj.py	2005/02/01 14:20:44	1.5
@@ -25,7 +25,9 @@
         """ Load the attributes from an XML string
         """
         from bioMoby.mobyMarshal import MobyUnmarshaller
-        doc=parseString(value).firstChild
+        doc=value
+        if isinstance(value, str):
+            doc=parseString(value).firstChild
         um=MobyUnmarshaller()
         self.content=""
         self.namespace=doc.getAttribute("moby:namespace")
@@ -45,4 +47,4 @@
             if elt.nodeName=="CrossReference" or elt.nodeName=="moby:CrossReference":
                 self.__cross__=[]
                 for ref in elt.childNodes:
-                    self.__cross__.append(ref.toxml())
\ No newline at end of file
+                    self.__cross__.append(um.loads(ref))
\ No newline at end of file

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/ontology/ICIS_Query.py,v
retrieving revision 1.4
retrieving revision 1.5
diff -u -r1.4 -r1.5
--- /home/repository/moby/moby-live/Python/bioMoby/ontology/ICIS_Query.py	2005/02/01 08:52:16	1.4
+++ /home/repository/moby/moby-live/Python/bioMoby/ontology/ICIS_Query.py	2005/02/01 14:20:44	1.5
@@ -30,7 +30,9 @@
         """ Load the attributes from an XML string
         """
         from bioMoby.mobyMarshal import MobyUnmarshaller
-        doc=parseString(value).firstChild
+        doc=value
+        if isinstance(value, str):
+            doc=parseString(value).firstChild
         um=MobyUnmarshaller()
         self.content=""
         self.namespace=doc.getAttribute("moby:namespace")
@@ -50,16 +52,16 @@
             if elt.nodeName=="CrossReference" or elt.nodeName=="moby:CrossReference":
                 self.__cross__=[]
                 for ref in elt.childNodes:
-                    self.__cross__.append(ref.toxml())
+                    self.__cross__.append(um.loads(ref))
             if elt.nodeType==elt.ELEMENT_NODE and (elt.nodeName=="Integer" or elt.nodeName=="moby:Integer") and (elt.getAttribute("articleName")=="end_row" or elt.getAttribute("moby:articleName")=="end_row"):
                 t=MobyInteger()
-                t.fromMoby(elt.toxml())
+                t.fromMoby(elt)
                 self.End_row=t.content
             if elt.nodeType==elt.ELEMENT_NODE and (elt.nodeName=="Integer" or elt.nodeName=="moby:Integer") and (elt.getAttribute("articleName")=="start_row" or elt.getAttribute("moby:articleName")=="start_row"):
                 t=MobyInteger()
-                t.fromMoby(elt.toxml())
+                t.fromMoby(elt)
                 self.Start_row=t.content
             if elt.nodeType==elt.ELEMENT_NODE and (elt.nodeName=="String" or elt.nodeName=="moby:String") and (elt.getAttribute("articleName")=="search_text" or elt.getAttribute("moby:articleName")=="search_text"):
                 t=MobyString()
-                t.fromMoby(elt.toxml())
+                t.fromMoby(elt)
                 self.Search_text=t.content
\ No newline at end of file

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/ontology/ICIS_Query2.py,v
retrieving revision 1.4
retrieving revision 1.5
diff -u -r1.4 -r1.5
--- /home/repository/moby/moby-live/Python/bioMoby/ontology/ICIS_Query2.py	2005/02/01 08:52:16	1.4
+++ /home/repository/moby/moby-live/Python/bioMoby/ontology/ICIS_Query2.py	2005/02/01 14:20:44	1.5
@@ -32,7 +32,9 @@
         """ Load the attributes from an XML string
         """
         from bioMoby.mobyMarshal import MobyUnmarshaller
-        doc=parseString(value).firstChild
+        doc=value
+        if isinstance(value, str):
+            doc=parseString(value).firstChild
         um=MobyUnmarshaller()
         self.content=""
         self.namespace=doc.getAttribute("moby:namespace")
@@ -52,24 +54,24 @@
             if elt.nodeName=="CrossReference" or elt.nodeName=="moby:CrossReference":
                 self.__cross__=[]
                 for ref in elt.childNodes:
-                    self.__cross__.append(ref.toxml())
+                    self.__cross__.append(um.loads(ref))
             if elt.nodeType==elt.ELEMENT_NODE and (elt.nodeName=="String" or elt.nodeName=="moby:String") and (elt.getAttribute("articleName")=="search_text1" or elt.getAttribute("moby:articleName")=="search_text1"):
                 t=MobyString()
-                t.fromMoby(elt.toxml())
+                t.fromMoby(elt)
                 self.Search_text1=t.content
             if elt.nodeType==elt.ELEMENT_NODE and (elt.nodeName=="String" or elt.nodeName=="moby:String") and (elt.getAttribute("articleName")=="search_text2" or elt.getAttribute("moby:articleName")=="search_text2"):
                 t=MobyString()
-                t.fromMoby(elt.toxml())
+                t.fromMoby(elt)
                 self.Search_text2=t.content
             if elt.nodeType==elt.ELEMENT_NODE and (elt.nodeName=="String" or elt.nodeName=="moby:String") and (elt.getAttribute("articleName")=="search_text3" or elt.getAttribute("moby:articleName")=="search_text3"):
                 t=MobyString()
-                t.fromMoby(elt.toxml())
+                t.fromMoby(elt)
                 self.Search_text3=t.content
             if elt.nodeType==elt.ELEMENT_NODE and (elt.nodeName=="Integer" or elt.nodeName=="moby:Integer") and (elt.getAttribute("articleName")=="start_row" or elt.getAttribute("moby:articleName")=="start_row"):
                 t=MobyInteger()
-                t.fromMoby(elt.toxml())
+                t.fromMoby(elt)
                 self.Start_row=t.content
             if elt.nodeType==elt.ELEMENT_NODE and (elt.nodeName=="Integer" or elt.nodeName=="moby:Integer") and (elt.getAttribute("articleName")=="end_row" or elt.getAttribute("moby:articleName")=="end_row"):
                 t=MobyInteger()
-                t.fromMoby(elt.toxml())
+                t.fromMoby(elt)
                 self.End_row=t.content
\ No newline at end of file

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/ontology/ICIS_Query3.py,v
retrieving revision 1.4
retrieving revision 1.5
diff -u -r1.4 -r1.5
--- /home/repository/moby/moby-live/Python/bioMoby/ontology/ICIS_Query3.py	2005/02/01 08:52:16	1.4
+++ /home/repository/moby/moby-live/Python/bioMoby/ontology/ICIS_Query3.py	2005/02/01 14:20:44	1.5
@@ -30,7 +30,9 @@
         """ Load the attributes from an XML string
         """
         from bioMoby.mobyMarshal import MobyUnmarshaller
-        doc=parseString(value).firstChild
+        doc=value
+        if isinstance(value, str):
+            doc=parseString(value).firstChild
         um=MobyUnmarshaller()
         self.content=""
         self.namespace=doc.getAttribute("moby:namespace")
@@ -50,20 +52,20 @@
             if elt.nodeName=="CrossReference" or elt.nodeName=="moby:CrossReference":
                 self.__cross__=[]
                 for ref in elt.childNodes:
-                    self.__cross__.append(ref.toxml())
+                    self.__cross__.append(um.loads(ref))
             if elt.nodeType==elt.ELEMENT_NODE and (elt.nodeName=="Integer" or elt.nodeName=="moby:Integer") and (elt.getAttribute("articleName")=="search_text1" or elt.getAttribute("moby:articleName")=="search_text1"):
                 t=MobyInteger()
-                t.fromMoby(elt.toxml())
+                t.fromMoby(elt)
                 self.Search_text1=t.content
             if elt.nodeType==elt.ELEMENT_NODE and (elt.nodeName=="Integer" or elt.nodeName=="moby:Integer") and (elt.getAttribute("articleName")=="search_text2" or elt.getAttribute("moby:articleName")=="search_text2"):
                 t=MobyInteger()
-                t.fromMoby(elt.toxml())
+                t.fromMoby(elt)
                 self.Search_text2=t.content
             if elt.nodeType==elt.ELEMENT_NODE and (elt.nodeName=="Integer" or elt.nodeName=="moby:Integer") and (elt.getAttribute("articleName")=="start_row" or elt.getAttribute("moby:articleName")=="start_row"):
                 t=MobyInteger()
-                t.fromMoby(elt.toxml())
+                t.fromMoby(elt)
                 self.Start_row=t.content
             if elt.nodeType==elt.ELEMENT_NODE and (elt.nodeName=="Integer" or elt.nodeName=="moby:Integer") and (elt.getAttribute("articleName")=="end_row" or elt.getAttribute("moby:articleName")=="end_row"):
                 t=MobyInteger()
-                t.fromMoby(elt.toxml())
+                t.fromMoby(elt)
                 self.End_row=t.content
\ No newline at end of file

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/ontology/IntAct_XML.py,v
retrieving revision 1.4
retrieving revision 1.5
diff -u -r1.4 -r1.5
--- /home/repository/moby/moby-live/Python/bioMoby/ontology/IntAct_XML.py	2005/02/01 08:52:16	1.4
+++ /home/repository/moby/moby-live/Python/bioMoby/ontology/IntAct_XML.py	2005/02/01 14:20:44	1.5
@@ -26,7 +26,9 @@
         """ Load the attributes from an XML string
         """
         from bioMoby.mobyMarshal import MobyUnmarshaller
-        doc=parseString(value).firstChild
+        doc=value
+        if isinstance(value, str):
+            doc=parseString(value).firstChild
         um=MobyUnmarshaller()
         self.content=""
         self.namespace=doc.getAttribute("moby:namespace")
@@ -46,4 +48,4 @@
             if elt.nodeName=="CrossReference" or elt.nodeName=="moby:CrossReference":
                 self.__cross__=[]
                 for ref in elt.childNodes:
-                    self.__cross__.append(ref.toxml())
\ No newline at end of file
+                    self.__cross__.append(um.loads(ref))
\ No newline at end of file

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/ontology/Interaction.py,v
retrieving revision 1.4
retrieving revision 1.5
diff -u -r1.4 -r1.5
--- /home/repository/moby/moby-live/Python/bioMoby/ontology/Interaction.py	2005/02/01 08:52:16	1.4
+++ /home/repository/moby/moby-live/Python/bioMoby/ontology/Interaction.py	2005/02/01 14:20:44	1.5
@@ -30,7 +30,9 @@
         """ Load the attributes from an XML string
         """
         from bioMoby.mobyMarshal import MobyUnmarshaller
-        doc=parseString(value).firstChild
+        doc=value
+        if isinstance(value, str):
+            doc=parseString(value).firstChild
         um=MobyUnmarshaller()
         self.content=""
         self.namespace=doc.getAttribute("moby:namespace")
@@ -51,15 +53,15 @@
             if elt.nodeName=="CrossReference" or elt.nodeName=="moby:CrossReference":
                 self.__cross__=[]
                 for ref in elt.childNodes:
-                    self.__cross__.append(ref.toxml())
+                    self.__cross__.append(um.loads(ref))
             if elt.nodeType==elt.ELEMENT_NODE and (elt.nodeName=="String" or elt.nodeName=="moby:String") and (elt.getAttribute("articleName")=="result" or elt.getAttribute("moby:articleName")=="result"):
                 t=MobyString()
-                t.fromMoby(elt.toxml())
+                t.fromMoby(elt)
                 self.Result=t.content
             if elt.nodeType==elt.ELEMENT_NODE and (elt.nodeName=="String" or elt.nodeName=="moby:String") and (elt.getAttribute("articleName")=="resultUnits" or elt.getAttribute("moby:articleName")=="resultUnits"):
                 t=MobyString()
-                t.fromMoby(elt.toxml())
+                t.fromMoby(elt)
                 self.ResultUnits=t.content
             if elt.nodeType==elt.ELEMENT_NODE and (elt.nodeName=="Interactor" or elt.nodeName=="moby:Interactor") and (elt.getAttribute("articleName")=="participant" or elt.getAttribute("moby:articleName")=="participant"):
                 self.Participant=MobyInteractor()
-                self.Participant.fromMoby(elt.toxml())
\ No newline at end of file
+                self.Participant.fromMoby(elt)
\ No newline at end of file

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/ontology/InteractionMethod.py,v
retrieving revision 1.4
retrieving revision 1.5
diff -u -r1.4 -r1.5
--- /home/repository/moby/moby-live/Python/bioMoby/ontology/InteractionMethod.py	2005/02/01 08:52:16	1.4
+++ /home/repository/moby/moby-live/Python/bioMoby/ontology/InteractionMethod.py	2005/02/01 14:20:44	1.5
@@ -29,7 +29,9 @@
         """ Load the attributes from an XML string
         """
         from bioMoby.mobyMarshal import MobyUnmarshaller
-        doc=parseString(value).firstChild
+        doc=value
+        if isinstance(value, str):
+            doc=parseString(value).firstChild
         um=MobyUnmarshaller()
         self.content=""
         self.namespace=doc.getAttribute("moby:namespace")
@@ -49,16 +51,16 @@
             if elt.nodeName=="CrossReference" or elt.nodeName=="moby:CrossReference":
                 self.__cross__=[]
                 for ref in elt.childNodes:
-                    self.__cross__.append(ref.toxml())
+                    self.__cross__.append(um.loads(ref))
             if elt.nodeType==elt.ELEMENT_NODE and (elt.nodeName=="String" or elt.nodeName=="moby:String") and (elt.getAttribute("articleName")=="shortlabel" or elt.getAttribute("moby:articleName")=="shortlabel"):
                 t=MobyString()
-                t.fromMoby(elt.toxml())
+                t.fromMoby(elt)
                 self.Shortlabel=t.content
             if elt.nodeType==elt.ELEMENT_NODE and (elt.nodeName=="String" or elt.nodeName=="moby:String") and (elt.getAttribute("articleName")=="term" or elt.getAttribute("moby:articleName")=="term"):
                 t=MobyString()
-                t.fromMoby(elt.toxml())
+                t.fromMoby(elt)
                 self.Term=t.content
             if elt.nodeType==elt.ELEMENT_NODE and (elt.nodeName=="String" or elt.nodeName=="moby:String") and (elt.getAttribute("articleName")=="definition" or elt.getAttribute("moby:articleName")=="definition"):
                 t=MobyString()
-                t.fromMoby(elt.toxml())
+                t.fromMoby(elt)
                 self.Definition=t.content
\ No newline at end of file

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/ontology/Interaction_partner.py,v
retrieving revision 1.4
retrieving revision 1.5
diff -u -r1.4 -r1.5
--- /home/repository/moby/moby-live/Python/bioMoby/ontology/Interaction_partner.py	2005/02/01 08:52:16	1.4
+++ /home/repository/moby/moby-live/Python/bioMoby/ontology/Interaction_partner.py	2005/02/01 14:20:44	1.5
@@ -29,7 +29,9 @@
         """ Load the attributes from an XML string
         """
         from bioMoby.mobyMarshal import MobyUnmarshaller
-        doc=parseString(value).firstChild
+        doc=value
+        if isinstance(value, str):
+            doc=parseString(value).firstChild
         um=MobyUnmarshaller()
         self.content=""
         self.namespace=doc.getAttribute("moby:namespace")
@@ -49,12 +51,12 @@
             if elt.nodeName=="CrossReference" or elt.nodeName=="moby:CrossReference":
                 self.__cross__=[]
                 for ref in elt.childNodes:
-                    self.__cross__.append(ref.toxml())
+                    self.__cross__.append(um.loads(ref))
             if elt.nodeType==elt.ELEMENT_NODE and (elt.nodeName=="Integer" or elt.nodeName=="moby:Integer") and (elt.getAttribute("articleName")=="direction" or elt.getAttribute("moby:articleName")=="direction"):
                 t=MobyInteger()
-                t.fromMoby(elt.toxml())
+                t.fromMoby(elt)
                 self.Direction=t.content
             if elt.nodeType==elt.ELEMENT_NODE and (elt.nodeName=="String" or elt.nodeName=="moby:String") and (elt.getAttribute("articleName")=="partner" or elt.getAttribute("moby:articleName")=="partner"):
                 t=MobyString()
-                t.fromMoby(elt.toxml())
+                t.fromMoby(elt)
                 self.Partner=t.content
\ No newline at end of file

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/ontology/Interactor.py,v
retrieving revision 1.4
retrieving revision 1.5
diff -u -r1.4 -r1.5
--- /home/repository/moby/moby-live/Python/bioMoby/ontology/Interactor.py	2005/02/01 08:52:16	1.4
+++ /home/repository/moby/moby-live/Python/bioMoby/ontology/Interactor.py	2005/02/01 14:20:44	1.5
@@ -27,7 +27,9 @@
         """ Load the attributes from an XML string
         """
         from bioMoby.mobyMarshal import MobyUnmarshaller
-        doc=parseString(value).firstChild
+        doc=value
+        if isinstance(value, str):
+            doc=parseString(value).firstChild
         um=MobyUnmarshaller()
         self.content=""
         self.namespace=doc.getAttribute("moby:namespace")
@@ -47,8 +49,8 @@
             if elt.nodeName=="CrossReference" or elt.nodeName=="moby:CrossReference":
                 self.__cross__=[]
                 for ref in elt.childNodes:
-                    self.__cross__.append(ref.toxml())
+                    self.__cross__.append(um.loads(ref))
             if elt.nodeType==elt.ELEMENT_NODE and (elt.nodeName=="String" or elt.nodeName=="moby:String") and (elt.getAttribute("articleName")=="role" or elt.getAttribute("moby:articleName")=="role"):
                 t=MobyString()
-                t.fromMoby(elt.toxml())
+                t.fromMoby(elt)
                 self.Role=t.content
\ No newline at end of file

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/ontology/MEME_Text.py,v
retrieving revision 1.4
retrieving revision 1.5
diff -u -r1.4 -r1.5
--- /home/repository/moby/moby-live/Python/bioMoby/ontology/MEME_Text.py	2005/02/01 08:52:16	1.4
+++ /home/repository/moby/moby-live/Python/bioMoby/ontology/MEME_Text.py	2005/02/01 14:20:44	1.5
@@ -26,7 +26,9 @@
         """ Load the attributes from an XML string
         """
         from bioMoby.mobyMarshal import MobyUnmarshaller
-        doc=parseString(value).firstChild
+        doc=value
+        if isinstance(value, str):
+            doc=parseString(value).firstChild
         um=MobyUnmarshaller()
         self.content=""
         self.namespace=doc.getAttribute("moby:namespace")
@@ -46,4 +48,4 @@
             if elt.nodeName=="CrossReference" or elt.nodeName=="moby:CrossReference":
                 self.__cross__=[]
                 for ref in elt.childNodes:
-                    self.__cross__.append(ref.toxml())
\ No newline at end of file
+                    self.__cross__.append(um.loads(ref))
\ No newline at end of file

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/ontology/MGIS_ACCESSION.py,v
retrieving revision 1.4
retrieving revision 1.5
diff -u -r1.4 -r1.5
--- /home/repository/moby/moby-live/Python/bioMoby/ontology/MGIS_ACCESSION.py	2005/02/01 08:52:16	1.4
+++ /home/repository/moby/moby-live/Python/bioMoby/ontology/MGIS_ACCESSION.py	2005/02/01 14:20:44	1.5
@@ -46,7 +46,9 @@
         """ Load the attributes from an XML string
         """
         from bioMoby.mobyMarshal import MobyUnmarshaller
-        doc=parseString(value).firstChild
+        doc=value
+        if isinstance(value, str):
+            doc=parseString(value).firstChild
         um=MobyUnmarshaller()
         self.content=""
         self.namespace=doc.getAttribute("moby:namespace")
@@ -66,84 +68,84 @@
             if elt.nodeName=="CrossReference" or elt.nodeName=="moby:CrossReference":
                 self.__cross__=[]
                 for ref in elt.childNodes:
-                    self.__cross__.append(ref.toxml())
+                    self.__cross__.append(um.loads(ref))
             if elt.nodeType==elt.ELEMENT_NODE and (elt.nodeName=="String" or elt.nodeName=="moby:String") and (elt.getAttribute("articleName")=="Biotic_stress_Yellowsig" or elt.getAttribute("moby:articleName")=="Biotic_stress_Yellowsig"):
                 t=MobyString()
-                t.fromMoby(elt.toxml())
+                t.fromMoby(elt)
                 self.Biotic_stress_Yellowsig=t.content
             if elt.nodeType==elt.ELEMENT_NODE and (elt.nodeName=="String" or elt.nodeName=="moby:String") and (elt.getAttribute("articleName")=="mcpd:ORIGCTY" or elt.getAttribute("moby:articleName")=="mcpd:ORIGCTY"):
                 t=MobyString()
-                t.fromMoby(elt.toxml())
+                t.fromMoby(elt)
                 self.McpdORIGCTY=t.content
             if elt.nodeType==elt.ELEMENT_NODE and (elt.nodeName=="String" or elt.nodeName=="moby:String") and (elt.getAttribute("articleName")=="mgis:SECTION" or elt.getAttribute("moby:articleName")=="mgis:SECTION"):
                 t=MobyString()
-                t.fromMoby(elt.toxml())
+                t.fromMoby(elt)
                 self.MgisSECTION=t.content
             if elt.nodeType==elt.ELEMENT_NODE and (elt.nodeName=="String" or elt.nodeName=="moby:String") and (elt.getAttribute("articleName")=="mcpd:SPECIES" or elt.getAttribute("moby:articleName")=="mcpd:SPECIES"):
                 t=MobyString()
-                t.fromMoby(elt.toxml())
+                t.fromMoby(elt)
                 self.McpdSPECIES=t.content
             if elt.nodeType==elt.ELEMENT_NODE and (elt.nodeName=="String" or elt.nodeName=="moby:String") and (elt.getAttribute("articleName")=="mcpd:COLLCODE" or elt.getAttribute("moby:articleName")=="mcpd:COLLCODE"):
                 t=MobyString()
-                t.fromMoby(elt.toxml())
+                t.fromMoby(elt)
                 self.McpdCOLLCODE=t.content
             if elt.nodeType==elt.ELEMENT_NODE and (elt.nodeName=="String" or elt.nodeName=="moby:String") and (elt.getAttribute("articleName")=="Biotic_stress_Blacksig" or elt.getAttribute("moby:articleName")=="Biotic_stress_Blacksig"):
                 t=MobyString()
-                t.fromMoby(elt.toxml())
+                t.fromMoby(elt)
                 self.Biotic_stress_Blacksig=t.content
             if elt.nodeType==elt.ELEMENT_NODE and (elt.nodeName=="String" or elt.nodeName=="moby:String") and (elt.getAttribute("articleName")=="Biotic_stress_Fusarium" or elt.getAttribute("moby:articleName")=="Biotic_stress_Fusarium"):
                 t=MobyString()
-                t.fromMoby(elt.toxml())
+                t.fromMoby(elt)
                 self.Biotic_stress_Fusarium=t.content
             if elt.nodeType==elt.ELEMENT_NODE and (elt.nodeName=="String" or elt.nodeName=="moby:String") and (elt.getAttribute("articleName")=="Biotic_stress_pseudomonas" or elt.getAttribute("moby:articleName")=="Biotic_stress_pseudomonas"):
                 t=MobyString()
-                t.fromMoby(elt.toxml())
+                t.fromMoby(elt)
                 self.Biotic_stress_pseudomonas=t.content
             if elt.nodeType==elt.ELEMENT_NODE and (elt.nodeName=="String" or elt.nodeName=="moby:String") and (elt.getAttribute("articleName")=="Biotic_stress_Radopholus" or elt.getAttribute("moby:articleName")=="Biotic_stress_Radopholus"):
                 t=MobyString()
-                t.fromMoby(elt.toxml())
+                t.fromMoby(elt)
                 self.Biotic_stress_Radopholus=t.content
             if elt.nodeType==elt.ELEMENT_NODE and (elt.nodeName=="String" or elt.nodeName=="moby:String") and (elt.getAttribute("articleName")=="Biotic_stress_Pratylenchuscof" or elt.getAttribute("moby:articleName")=="Biotic_stress_Pratylenchuscof"):
                 t=MobyString()
-                t.fromMoby(elt.toxml())
+                t.fromMoby(elt)
                 self.Biotic_stress_Pratylenchuscof=t.content
             if elt.nodeType==elt.ELEMENT_NODE and (elt.nodeName=="String" or elt.nodeName=="moby:String") and (elt.getAttribute("articleName")=="Biotic_stress_Pratylenchusgood" or elt.getAttribute("moby:articleName")=="Biotic_stress_Pratylenchusgood"):
                 t=MobyString()
-                t.fromMoby(elt.toxml())
+                t.fromMoby(elt)
                 self.Biotic_stress_Pratylenchusgood=t.content
             if elt.nodeType==elt.ELEMENT_NODE and (elt.nodeName=="String" or elt.nodeName=="moby:String") and (elt.getAttribute("articleName")=="Biotic_stress_cosmopolites" or elt.getAttribute("moby:articleName")=="Biotic_stress_cosmopolites"):
                 t=MobyString()
-                t.fromMoby(elt.toxml())
+                t.fromMoby(elt)
                 self.Biotic_stress_cosmopolites=t.content
             if elt.nodeType==elt.ELEMENT_NODE and (elt.nodeName=="String" or elt.nodeName=="moby:String") and (elt.getAttribute("articleName")=="Abiotic_stress_Lowtemp" or elt.getAttribute("moby:articleName")=="Abiotic_stress_Lowtemp"):
                 t=MobyString()
-                t.fromMoby(elt.toxml())
+                t.fromMoby(elt)
                 self.Abiotic_stress_Lowtemp=t.content
             if elt.nodeType==elt.ELEMENT_NODE and (elt.nodeName=="String" or elt.nodeName=="moby:String") and (elt.getAttribute("articleName")=="Abiotic_stress_Drought" or elt.getAttribute("moby:articleName")=="Abiotic_stress_Drought"):
                 t=MobyString()
-                t.fromMoby(elt.toxml())
+                t.fromMoby(elt)
                 self.Abiotic_stress_Drought=t.content
             if elt.nodeType==elt.ELEMENT_NODE and (elt.nodeName=="String" or elt.nodeName=="moby:String") and (elt.getAttribute("articleName")=="Abiotic_stress_Flooding" or elt.getAttribute("moby:articleName")=="Abiotic_stress_Flooding"):
                 t=MobyString()
-                t.fromMoby(elt.toxml())
+                t.fromMoby(elt)
                 self.Abiotic_stress_Flooding=t.content
             if elt.nodeType==elt.ELEMENT_NODE and (elt.nodeName=="String" or elt.nodeName=="moby:String") and (elt.getAttribute("articleName")=="Abiotic_stress_Mineraldef" or elt.getAttribute("moby:articleName")=="Abiotic_stress_Mineraldef"):
                 t=MobyString()
-                t.fromMoby(elt.toxml())
+                t.fromMoby(elt)
                 self.Abiotic_stress_Mineraldef=t.content
             if elt.nodeType==elt.ELEMENT_NODE and (elt.nodeName=="String" or elt.nodeName=="moby:String") and (elt.getAttribute("articleName")=="Abiotic_stress_Winds" or elt.getAttribute("moby:articleName")=="Abiotic_stress_Winds"):
                 t=MobyString()
-                t.fromMoby(elt.toxml())
+                t.fromMoby(elt)
                 self.Abiotic_stress_Winds=t.content
             if elt.nodeType==elt.ELEMENT_NODE and (elt.nodeName=="String" or elt.nodeName=="moby:String") and (elt.getAttribute("articleName")=="Abiotic_stress_Soilacidity" or elt.getAttribute("moby:articleName")=="Abiotic_stress_Soilacidity"):
                 t=MobyString()
-                t.fromMoby(elt.toxml())
+                t.fromMoby(elt)
                 self.Abiotic_stress_Soilacidity=t.content
             if elt.nodeType==elt.ELEMENT_NODE and (elt.nodeName=="String" or elt.nodeName=="moby:String") and (elt.getAttribute("articleName")=="Abiotic_stress_Manganesetox" or elt.getAttribute("moby:articleName")=="Abiotic_stress_Manganesetox"):
                 t=MobyString()
-                t.fromMoby(elt.toxml())
+                t.fromMoby(elt)
                 self.Abiotic_stress_Manganesetox=t.content
             if elt.nodeType==elt.ELEMENT_NODE and (elt.nodeName=="String" or elt.nodeName=="moby:String") and (elt.getAttribute("articleName")=="Abiotic_stress_Hightemp" or elt.getAttribute("moby:articleName")=="Abiotic_stress_Hightemp"):
                 t=MobyString()
-                t.fromMoby(elt.toxml())
+                t.fromMoby(elt)
                 self.Abiotic_stress_Hightemp=t.content
\ No newline at end of file

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/ontology/MMP_Locus.py,v
retrieving revision 1.4
retrieving revision 1.5
diff -u -r1.4 -r1.5
--- /home/repository/moby/moby-live/Python/bioMoby/ontology/MMP_Locus.py	2005/02/01 08:52:16	1.4
+++ /home/repository/moby/moby-live/Python/bioMoby/ontology/MMP_Locus.py	2005/02/01 14:20:44	1.5
@@ -25,7 +25,9 @@
         """ Load the attributes from an XML string
         """
         from bioMoby.mobyMarshal import MobyUnmarshaller
-        doc=parseString(value).firstChild
+        doc=value
+        if isinstance(value, str):
+            doc=parseString(value).firstChild
         um=MobyUnmarshaller()
         self.content=""
         self.namespace=doc.getAttribute("moby:namespace")
@@ -45,4 +47,4 @@
             if elt.nodeName=="CrossReference" or elt.nodeName=="moby:CrossReference":
                 self.__cross__=[]
                 for ref in elt.childNodes:
-                    self.__cross__.append(ref.toxml())
\ No newline at end of file
+                    self.__cross__.append(um.loads(ref))
\ No newline at end of file

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/ontology/MO_Term_Test.py,v
retrieving revision 1.4
retrieving revision 1.5
diff -u -r1.4 -r1.5
--- /home/repository/moby/moby-live/Python/bioMoby/ontology/MO_Term_Test.py	2005/02/01 08:52:16	1.4
+++ /home/repository/moby/moby-live/Python/bioMoby/ontology/MO_Term_Test.py	2005/02/01 14:20:44	1.5
@@ -30,7 +30,9 @@
         """ Load the attributes from an XML string
         """
         from bioMoby.mobyMarshal import MobyUnmarshaller
-        doc=parseString(value).firstChild
+        doc=value
+        if isinstance(value, str):
+            doc=parseString(value).firstChild
         um=MobyUnmarshaller()
         self.content=""
         self.namespace=doc.getAttribute("moby:namespace")
@@ -50,20 +52,20 @@
             if elt.nodeName=="CrossReference" or elt.nodeName=="moby:CrossReference":
                 self.__cross__=[]
                 for ref in elt.childNodes:
-                    self.__cross__.append(ref.toxml())
+                    self.__cross__.append(um.loads(ref))
             if elt.nodeType==elt.ELEMENT_NODE and (elt.nodeName=="String" or elt.nodeName=="moby:String") and (elt.getAttribute("articleName")=="class_name" or elt.getAttribute("moby:articleName")=="class_name"):
                 t=MobyString()
-                t.fromMoby(elt.toxml())
+                t.fromMoby(elt)
                 self.Class_name=t.content
             if elt.nodeType==elt.ELEMENT_NODE and (elt.nodeName=="String" or elt.nodeName=="moby:String") and (elt.getAttribute("articleName")=="individual_name" or elt.getAttribute("moby:articleName")=="individual_name"):
                 t=MobyString()
-                t.fromMoby(elt.toxml())
+                t.fromMoby(elt)
                 self.Individual_name=t.content
             if elt.nodeType==elt.ELEMENT_NODE and (elt.nodeName=="String" or elt.nodeName=="moby:String") and (elt.getAttribute("articleName")=="individual_desc" or elt.getAttribute("moby:articleName")=="individual_desc"):
                 t=MobyString()
-                t.fromMoby(elt.toxml())
+                t.fromMoby(elt)
                 self.Individual_desc=t.content
             if elt.nodeType==elt.ELEMENT_NODE and (elt.nodeName=="String" or elt.nodeName=="moby:String") and (elt.getAttribute("articleName")=="class_desc" or elt.getAttribute("moby:articleName")=="class_desc"):
                 t=MobyString()
-                t.fromMoby(elt.toxml())
+                t.fromMoby(elt)
                 self.Class_desc=t.content
\ No newline at end of file

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/ontology/MmCIFText.py,v
retrieving revision 1.4
retrieving revision 1.5
diff -u -r1.4 -r1.5
--- /home/repository/moby/moby-live/Python/bioMoby/ontology/MmCIFText.py	2005/02/01 08:52:16	1.4
+++ /home/repository/moby/moby-live/Python/bioMoby/ontology/MmCIFText.py	2005/02/01 14:20:44	1.5
@@ -26,7 +26,9 @@
         """ Load the attributes from an XML string
         """
         from bioMoby.mobyMarshal import MobyUnmarshaller
-        doc=parseString(value).firstChild
+        doc=value
+        if isinstance(value, str):
+            doc=parseString(value).firstChild
         um=MobyUnmarshaller()
         self.content=""
         self.namespace=doc.getAttribute("moby:namespace")
@@ -46,4 +48,4 @@
             if elt.nodeName=="CrossReference" or elt.nodeName=="moby:CrossReference":
                 self.__cross__=[]
                 for ref in elt.childNodes:
-                    self.__cross__.append(ref.toxml())
\ No newline at end of file
+                    self.__cross__.append(um.loads(ref))
\ No newline at end of file

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/ontology/Multi_key_value_pair.py,v
retrieving revision 1.4
retrieving revision 1.5
diff -u -r1.4 -r1.5
--- /home/repository/moby/moby-live/Python/bioMoby/ontology/Multi_key_value_pair.py	2005/02/01 08:52:16	1.4
+++ /home/repository/moby/moby-live/Python/bioMoby/ontology/Multi_key_value_pair.py	2005/02/01 14:20:44	1.5
@@ -28,7 +28,9 @@
         """ Load the attributes from an XML string
         """
         from bioMoby.mobyMarshal import MobyUnmarshaller
-        doc=parseString(value).firstChild
+        doc=value
+        if isinstance(value, str):
+            doc=parseString(value).firstChild
         um=MobyUnmarshaller()
         self.content=""
         self.namespace=doc.getAttribute("moby:namespace")
@@ -49,12 +51,12 @@
             if elt.nodeName=="CrossReference" or elt.nodeName=="moby:CrossReference":
                 self.__cross__=[]
                 for ref in elt.childNodes:
-                    self.__cross__.append(ref.toxml())
+                    self.__cross__.append(um.loads(ref))
             if elt.nodeType==elt.ELEMENT_NODE and (elt.nodeName=="String" or elt.nodeName=="moby:String") and (elt.getAttribute("articleName")=="key" or elt.getAttribute("moby:articleName")=="key"):
                 t=MobyString()
-                t.fromMoby(elt.toxml())
+                t.fromMoby(elt)
                 self.Key=t.content
             if elt.nodeType==elt.ELEMENT_NODE and (elt.nodeName=="String" or elt.nodeName=="moby:String") and (elt.getAttribute("articleName")=="value" or elt.getAttribute("moby:articleName")=="value"):
                 t=MobyString()
-                t.fromMoby(elt.toxml())
+                t.fromMoby(elt)
                 self.Value.append(t.content)
\ No newline at end of file

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/ontology/MyTestingDataType_11024145298313.py,v
retrieving revision 1.4
retrieving revision 1.5
diff -u -r1.4 -r1.5
--- /home/repository/moby/moby-live/Python/bioMoby/ontology/MyTestingDataType_11024145298313.py	2005/02/01 08:52:16	1.4
+++ /home/repository/moby/moby-live/Python/bioMoby/ontology/MyTestingDataType_11024145298313.py	2005/02/01 14:20:44	1.5
@@ -26,7 +26,9 @@
         """ Load the attributes from an XML string
         """
         from bioMoby.mobyMarshal import MobyUnmarshaller
-        doc=parseString(value).firstChild
+        doc=value
+        if isinstance(value, str):
+            doc=parseString(value).firstChild
         um=MobyUnmarshaller()
         self.content=""
         self.namespace=doc.getAttribute("moby:namespace")
@@ -46,4 +48,4 @@
             if elt.nodeName=="CrossReference" or elt.nodeName=="moby:CrossReference":
                 self.__cross__=[]
                 for ref in elt.childNodes:
-                    self.__cross__.append(ref.toxml())
\ No newline at end of file
+                    self.__cross__.append(um.loads(ref))
\ No newline at end of file

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/ontology/MyTree.py,v
retrieving revision 1.4
retrieving revision 1.5
diff -u -r1.4 -r1.5
--- /home/repository/moby/moby-live/Python/bioMoby/ontology/MyTree.py	2005/02/01 08:52:16	1.4
+++ /home/repository/moby/moby-live/Python/bioMoby/ontology/MyTree.py	2005/02/01 14:20:44	1.5
@@ -26,7 +26,9 @@
         """ Load the attributes from an XML string
         """
         from bioMoby.mobyMarshal import MobyUnmarshaller
-        doc=parseString(value).firstChild
+        doc=value
+        if isinstance(value, str):
+            doc=parseString(value).firstChild
         um=MobyUnmarshaller()
         self.content=""
         self.namespace=doc.getAttribute("moby:namespace")
@@ -46,4 +48,4 @@
             if elt.nodeName=="CrossReference" or elt.nodeName=="moby:CrossReference":
                 self.__cross__=[]
                 for ref in elt.childNodes:
-                    self.__cross__.append(ref.toxml())
\ No newline at end of file
+                    self.__cross__.append(um.loads(ref))
\ No newline at end of file

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/ontology/NCBI_BLAST_Text.py,v
retrieving revision 1.4
retrieving revision 1.5
diff -u -r1.4 -r1.5
--- /home/repository/moby/moby-live/Python/bioMoby/ontology/NCBI_BLAST_Text.py	2005/02/01 08:52:16	1.4
+++ /home/repository/moby/moby-live/Python/bioMoby/ontology/NCBI_BLAST_Text.py	2005/02/01 14:20:44	1.5
@@ -26,7 +26,9 @@
         """ Load the attributes from an XML string
         """
         from bioMoby.mobyMarshal import MobyUnmarshaller
-        doc=parseString(value).firstChild
+        doc=value
+        if isinstance(value, str):
+            doc=parseString(value).firstChild
         um=MobyUnmarshaller()
         self.content=""
         self.namespace=doc.getAttribute("moby:namespace")
@@ -46,4 +48,4 @@
             if elt.nodeName=="CrossReference" or elt.nodeName=="moby:CrossReference":
                 self.__cross__=[]
                 for ref in elt.childNodes:
-                    self.__cross__.append(ref.toxml())
\ No newline at end of file
+                    self.__cross__.append(um.loads(ref))
\ No newline at end of file

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/ontology/NCBI_Blast_XML.py,v
retrieving revision 1.4
retrieving revision 1.5
diff -u -r1.4 -r1.5
--- /home/repository/moby/moby-live/Python/bioMoby/ontology/NCBI_Blast_XML.py	2005/02/01 08:52:16	1.4
+++ /home/repository/moby/moby-live/Python/bioMoby/ontology/NCBI_Blast_XML.py	2005/02/01 14:20:44	1.5
@@ -26,7 +26,9 @@
         """ Load the attributes from an XML string
         """
         from bioMoby.mobyMarshal import MobyUnmarshaller
-        doc=parseString(value).firstChild
+        doc=value
+        if isinstance(value, str):
+            doc=parseString(value).firstChild
         um=MobyUnmarshaller()
         self.content=""
         self.namespace=doc.getAttribute("moby:namespace")
@@ -46,4 +48,4 @@
             if elt.nodeName=="CrossReference" or elt.nodeName=="moby:CrossReference":
                 self.__cross__=[]
                 for ref in elt.childNodes:
-                    self.__cross__.append(ref.toxml())
\ No newline at end of file
+                    self.__cross__.append(um.loads(ref))
\ No newline at end of file

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/ontology/NCBI_Blast_XML_Gif.py,v
retrieving revision 1.4
retrieving revision 1.5
diff -u -r1.4 -r1.5
--- /home/repository/moby/moby-live/Python/bioMoby/ontology/NCBI_Blast_XML_Gif.py	2005/02/01 08:52:16	1.4
+++ /home/repository/moby/moby-live/Python/bioMoby/ontology/NCBI_Blast_XML_Gif.py	2005/02/01 14:20:44	1.5
@@ -28,7 +28,9 @@
         """ Load the attributes from an XML string
         """
         from bioMoby.mobyMarshal import MobyUnmarshaller
-        doc=parseString(value).firstChild
+        doc=value
+        if isinstance(value, str):
+            doc=parseString(value).firstChild
         um=MobyUnmarshaller()
         self.content=""
         self.namespace=doc.getAttribute("moby:namespace")
@@ -48,7 +50,7 @@
             if elt.nodeName=="CrossReference" or elt.nodeName=="moby:CrossReference":
                 self.__cross__=[]
                 for ref in elt.childNodes:
-                    self.__cross__.append(ref.toxml())
+                    self.__cross__.append(um.loads(ref))
             if elt.nodeType==elt.ELEMENT_NODE and (elt.nodeName=="b64_encoded_gif" or elt.nodeName=="moby:b64_encoded_gif") and (elt.getAttribute("articleName")=="hitGraph" or elt.getAttribute("moby:articleName")=="hitGraph"):
                 self.HitGraph=MobyB64_encoded_gif()
-                self.HitGraph.fromMoby(elt.toxml())
\ No newline at end of file
+                self.HitGraph.fromMoby(elt)
\ No newline at end of file

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/ontology/NCBI_Blast_XML_Gif_Map.py,v
retrieving revision 1.4
retrieving revision 1.5
diff -u -r1.4 -r1.5
--- /home/repository/moby/moby-live/Python/bioMoby/ontology/NCBI_Blast_XML_Gif_Map.py	2005/02/01 08:52:16	1.4
+++ /home/repository/moby/moby-live/Python/bioMoby/ontology/NCBI_Blast_XML_Gif_Map.py	2005/02/01 14:20:44	1.5
@@ -30,7 +30,9 @@
         """ Load the attributes from an XML string
         """
         from bioMoby.mobyMarshal import MobyUnmarshaller
-        doc=parseString(value).firstChild
+        doc=value
+        if isinstance(value, str):
+            doc=parseString(value).firstChild
         um=MobyUnmarshaller()
         self.content=""
         self.namespace=doc.getAttribute("moby:namespace")
@@ -50,10 +52,10 @@
             if elt.nodeName=="CrossReference" or elt.nodeName=="moby:CrossReference":
                 self.__cross__=[]
                 for ref in elt.childNodes:
-                    self.__cross__.append(ref.toxml())
+                    self.__cross__.append(um.loads(ref))
             if elt.nodeType==elt.ELEMENT_NODE and (elt.nodeName=="b64_encoded_gif" or elt.nodeName=="moby:b64_encoded_gif") and (elt.getAttribute("articleName")=="hitGraph" or elt.getAttribute("moby:articleName")=="hitGraph"):
                 self.HitGraph=MobyB64_encoded_gif()
-                self.HitGraph.fromMoby(elt.toxml())
+                self.HitGraph.fromMoby(elt)
             if elt.nodeType==elt.ELEMENT_NODE and (elt.nodeName=="text-html" or elt.nodeName=="moby:text-html") and (elt.getAttribute("articleName")=="areaMap" or elt.getAttribute("moby:articleName")=="areaMap"):
                 self.AreaMap=MobyTextHtml()
-                self.AreaMap.fromMoby(elt.toxml())
\ No newline at end of file
+                self.AreaMap.fromMoby(elt)
\ No newline at end of file

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/ontology/NCBI_MEME_Text.py,v
retrieving revision 1.4
retrieving revision 1.5
diff -u -r1.4 -r1.5
--- /home/repository/moby/moby-live/Python/bioMoby/ontology/NCBI_MEME_Text.py	2005/02/01 08:52:16	1.4
+++ /home/repository/moby/moby-live/Python/bioMoby/ontology/NCBI_MEME_Text.py	2005/02/01 14:20:44	1.5
@@ -26,7 +26,9 @@
         """ Load the attributes from an XML string
         """
         from bioMoby.mobyMarshal import MobyUnmarshaller
-        doc=parseString(value).firstChild
+        doc=value
+        if isinstance(value, str):
+            doc=parseString(value).firstChild
         um=MobyUnmarshaller()
         self.content=""
         self.namespace=doc.getAttribute("moby:namespace")
@@ -46,4 +48,4 @@
             if elt.nodeName=="CrossReference" or elt.nodeName=="moby:CrossReference":
                 self.__cross__=[]
                 for ref in elt.childNodes:
-                    self.__cross__.append(ref.toxml())
\ No newline at end of file
+                    self.__cross__.append(um.loads(ref))
\ No newline at end of file

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/ontology/NucleotideSequence.py,v
retrieving revision 1.4
retrieving revision 1.5
diff -u -r1.4 -r1.5
--- /home/repository/moby/moby-live/Python/bioMoby/ontology/NucleotideSequence.py	2005/02/01 08:52:16	1.4
+++ /home/repository/moby/moby-live/Python/bioMoby/ontology/NucleotideSequence.py	2005/02/01 14:20:44	1.5
@@ -29,7 +29,9 @@
         """ Load the attributes from an XML string
         """
         from bioMoby.mobyMarshal import MobyUnmarshaller
-        doc=parseString(value).firstChild
+        doc=value
+        if isinstance(value, str):
+            doc=parseString(value).firstChild
         um=MobyUnmarshaller()
         self.content=""
         self.namespace=doc.getAttribute("moby:namespace")
@@ -49,12 +51,12 @@
             if elt.nodeName=="CrossReference" or elt.nodeName=="moby:CrossReference":
                 self.__cross__=[]
                 for ref in elt.childNodes:
-                    self.__cross__.append(ref.toxml())
+                    self.__cross__.append(um.loads(ref))
             if elt.nodeType==elt.ELEMENT_NODE and (elt.nodeName=="Integer" or elt.nodeName=="moby:Integer") and (elt.getAttribute("articleName")=="Length" or elt.getAttribute("moby:articleName")=="Length"):
                 t=MobyInteger()
-                t.fromMoby(elt.toxml())
+                t.fromMoby(elt)
                 self.Length=t.content
             if elt.nodeType==elt.ELEMENT_NODE and (elt.nodeName=="String" or elt.nodeName=="moby:String") and (elt.getAttribute("articleName")=="SequenceString" or elt.getAttribute("moby:articleName")=="SequenceString"):
                 t=MobyString()
-                t.fromMoby(elt.toxml())
+                t.fromMoby(elt)
                 self.SequenceString=t.content
\ No newline at end of file

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/ontology/PDBFormattedText.py,v
retrieving revision 1.4
retrieving revision 1.5
diff -u -r1.4 -r1.5
--- /home/repository/moby/moby-live/Python/bioMoby/ontology/PDBFormattedText.py	2005/02/01 08:52:16	1.4
+++ /home/repository/moby/moby-live/Python/bioMoby/ontology/PDBFormattedText.py	2005/02/01 14:20:44	1.5
@@ -26,7 +26,9 @@
         """ Load the attributes from an XML string
         """
         from bioMoby.mobyMarshal import MobyUnmarshaller
-        doc=parseString(value).firstChild
+        doc=value
+        if isinstance(value, str):
+            doc=parseString(value).firstChild
         um=MobyUnmarshaller()
         self.content=""
         self.namespace=doc.getAttribute("moby:namespace")
@@ -46,4 +48,4 @@
             if elt.nodeName=="CrossReference" or elt.nodeName=="moby:CrossReference":
                 self.__cross__=[]
                 for ref in elt.childNodes:
-                    self.__cross__.append(ref.toxml())
\ No newline at end of file
+                    self.__cross__.append(um.loads(ref))
\ No newline at end of file

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/ontology/PDBText.py,v
retrieving revision 1.4
retrieving revision 1.5
diff -u -r1.4 -r1.5
--- /home/repository/moby/moby-live/Python/bioMoby/ontology/PDBText.py	2005/02/01 08:52:16	1.4
+++ /home/repository/moby/moby-live/Python/bioMoby/ontology/PDBText.py	2005/02/01 14:20:44	1.5
@@ -26,7 +26,9 @@
         """ Load the attributes from an XML string
         """
         from bioMoby.mobyMarshal import MobyUnmarshaller
-        doc=parseString(value).firstChild
+        doc=value
+        if isinstance(value, str):
+            doc=parseString(value).firstChild
         um=MobyUnmarshaller()
         self.content=""
         self.namespace=doc.getAttribute("moby:namespace")
@@ -46,4 +48,4 @@
             if elt.nodeName=="CrossReference" or elt.nodeName=="moby:CrossReference":
                 self.__cross__=[]
                 for ref in elt.childNodes:
-                    self.__cross__.append(ref.toxml())
\ No newline at end of file
+                    self.__cross__.append(um.loads(ref))
\ No newline at end of file

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/ontology/PDGJOB.py,v
retrieving revision 1.4
retrieving revision 1.5
diff -u -r1.4 -r1.5
--- /home/repository/moby/moby-live/Python/bioMoby/ontology/PDGJOB.py	2005/02/01 08:52:16	1.4
+++ /home/repository/moby/moby-live/Python/bioMoby/ontology/PDGJOB.py	2005/02/01 14:20:44	1.5
@@ -32,7 +32,9 @@
         """ Load the attributes from an XML string
         """
         from bioMoby.mobyMarshal import MobyUnmarshaller
-        doc=parseString(value).firstChild
+        doc=value
+        if isinstance(value, str):
+            doc=parseString(value).firstChild
         um=MobyUnmarshaller()
         self.content=""
         self.namespace=doc.getAttribute("moby:namespace")
@@ -52,23 +54,23 @@
             if elt.nodeName=="CrossReference" or elt.nodeName=="moby:CrossReference":
                 self.__cross__=[]
                 for ref in elt.childNodes:
-                    self.__cross__.append(ref.toxml())
+                    self.__cross__.append(um.loads(ref))
             if elt.nodeType==elt.ELEMENT_NODE and (elt.nodeName=="String" or elt.nodeName=="moby:String") and (elt.getAttribute("articleName")=="answerService" or elt.getAttribute("moby:articleName")=="answerService"):
                 t=MobyString()
-                t.fromMoby(elt.toxml())
+                t.fromMoby(elt)
                 self.AnswerService=t.content
             if elt.nodeType==elt.ELEMENT_NODE and (elt.nodeName=="String" or elt.nodeName=="moby:String") and (elt.getAttribute("articleName")=="authURI" or elt.getAttribute("moby:articleName")=="authURI"):
                 t=MobyString()
-                t.fromMoby(elt.toxml())
+                t.fromMoby(elt)
                 self.AuthURI=t.content
             if elt.nodeType==elt.ELEMENT_NODE and (elt.nodeName=="DateTime" or elt.nodeName=="moby:DateTime") and (elt.getAttribute("articleName")=="timeout" or elt.getAttribute("moby:articleName")=="timeout"):
                 self.Timeout=MobyDateTime()
-                self.Timeout.fromMoby(elt.toxml())
+                self.Timeout.fromMoby(elt)
             if elt.nodeType==elt.ELEMENT_NODE and (elt.nodeName=="String" or elt.nodeName=="moby:String") and (elt.getAttribute("articleName")=="killcode" or elt.getAttribute("moby:articleName")=="killcode"):
                 t=MobyString()
-                t.fromMoby(elt.toxml())
+                t.fromMoby(elt)
                 self.Killcode=t.content
             if elt.nodeType==elt.ELEMENT_NODE and (elt.nodeName=="String" or elt.nodeName=="moby:String") and (elt.getAttribute("articleName")=="killService" or elt.getAttribute("moby:articleName")=="killService"):
                 t=MobyString()
-                t.fromMoby(elt.toxml())
+                t.fromMoby(elt)
                 self.KillService=t.content
\ No newline at end of file

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/ontology/PHDText.py,v
retrieving revision 1.4
retrieving revision 1.5
diff -u -r1.4 -r1.5
--- /home/repository/moby/moby-live/Python/bioMoby/ontology/PHDText.py	2005/02/01 08:52:16	1.4
+++ /home/repository/moby/moby-live/Python/bioMoby/ontology/PHDText.py	2005/02/01 14:20:44	1.5
@@ -26,7 +26,9 @@
         """ Load the attributes from an XML string
         """
         from bioMoby.mobyMarshal import MobyUnmarshaller
-        doc=parseString(value).firstChild
+        doc=value
+        if isinstance(value, str):
+            doc=parseString(value).firstChild
         um=MobyUnmarshaller()
         self.content=""
         self.namespace=doc.getAttribute("moby:namespace")
@@ -46,4 +48,4 @@
             if elt.nodeName=="CrossReference" or elt.nodeName=="moby:CrossReference":
                 self.__cross__=[]
                 for ref in elt.childNodes:
-                    self.__cross__.append(ref.toxml())
\ No newline at end of file
+                    self.__cross__.append(um.loads(ref))
\ No newline at end of file

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/ontology/PMUTText.py,v
retrieving revision 1.4
retrieving revision 1.5
diff -u -r1.4 -r1.5
--- /home/repository/moby/moby-live/Python/bioMoby/ontology/PMUTText.py	2005/02/01 08:52:16	1.4
+++ /home/repository/moby/moby-live/Python/bioMoby/ontology/PMUTText.py	2005/02/01 14:20:44	1.5
@@ -26,7 +26,9 @@
         """ Load the attributes from an XML string
         """
         from bioMoby.mobyMarshal import MobyUnmarshaller
-        doc=parseString(value).firstChild
+        doc=value
+        if isinstance(value, str):
+            doc=parseString(value).firstChild
         um=MobyUnmarshaller()
         self.content=""
         self.namespace=doc.getAttribute("moby:namespace")
@@ -46,4 +48,4 @@
             if elt.nodeName=="CrossReference" or elt.nodeName=="moby:CrossReference":
                 self.__cross__=[]
                 for ref in elt.childNodes:
-                    self.__cross__.append(ref.toxml())
\ No newline at end of file
+                    self.__cross__.append(um.loads(ref))
\ No newline at end of file

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/ontology/PSeaTextFormatted.py,v
retrieving revision 1.4
retrieving revision 1.5
diff -u -r1.4 -r1.5
--- /home/repository/moby/moby-live/Python/bioMoby/ontology/PSeaTextFormatted.py	2005/02/01 08:52:16	1.4
+++ /home/repository/moby/moby-live/Python/bioMoby/ontology/PSeaTextFormatted.py	2005/02/01 14:20:44	1.5
@@ -26,7 +26,9 @@
         """ Load the attributes from an XML string
         """
         from bioMoby.mobyMarshal import MobyUnmarshaller
-        doc=parseString(value).firstChild
+        doc=value
+        if isinstance(value, str):
+            doc=parseString(value).firstChild
         um=MobyUnmarshaller()
         self.content=""
         self.namespace=doc.getAttribute("moby:namespace")
@@ -46,4 +48,4 @@
             if elt.nodeName=="CrossReference" or elt.nodeName=="moby:CrossReference":
                 self.__cross__=[]
                 for ref in elt.childNodes:
-                    self.__cross__.append(ref.toxml())
\ No newline at end of file
+                    self.__cross__.append(um.loads(ref))
\ No newline at end of file

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/ontology/PhenotypeDescription.py,v
retrieving revision 1.4
retrieving revision 1.5
diff -u -r1.4 -r1.5
--- /home/repository/moby/moby-live/Python/bioMoby/ontology/PhenotypeDescription.py	2005/02/01 08:52:16	1.4
+++ /home/repository/moby/moby-live/Python/bioMoby/ontology/PhenotypeDescription.py	2005/02/01 14:20:44	1.5
@@ -27,7 +27,9 @@
         """ Load the attributes from an XML string
         """
         from bioMoby.mobyMarshal import MobyUnmarshaller
-        doc=parseString(value).firstChild
+        doc=value
+        if isinstance(value, str):
+            doc=parseString(value).firstChild
         um=MobyUnmarshaller()
         self.content=""
         self.namespace=doc.getAttribute("moby:namespace")
@@ -47,8 +49,8 @@
             if elt.nodeName=="CrossReference" or elt.nodeName=="moby:CrossReference":
                 self.__cross__=[]
                 for ref in elt.childNodes:
-                    self.__cross__.append(ref.toxml())
+                    self.__cross__.append(um.loads(ref))
             if elt.nodeType==elt.ELEMENT_NODE and (elt.nodeName=="String" or elt.nodeName=="moby:String") and (elt.getAttribute("articleName")=="Phenotype" or elt.getAttribute("moby:articleName")=="Phenotype"):
                 t=MobyString()
-                t.fromMoby(elt.toxml())
+                t.fromMoby(elt)
                 self.Phenotype=t.content
\ No newline at end of file

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/ontology/PubMedMEDLINE.py,v
retrieving revision 1.4
retrieving revision 1.5
diff -u -r1.4 -r1.5
--- /home/repository/moby/moby-live/Python/bioMoby/ontology/PubMedMEDLINE.py	2005/02/01 08:52:16	1.4
+++ /home/repository/moby/moby-live/Python/bioMoby/ontology/PubMedMEDLINE.py	2005/02/01 14:20:44	1.5
@@ -26,7 +26,9 @@
         """ Load the attributes from an XML string
         """
         from bioMoby.mobyMarshal import MobyUnmarshaller
-        doc=parseString(value).firstChild
+        doc=value
+        if isinstance(value, str):
+            doc=parseString(value).firstChild
         um=MobyUnmarshaller()
         self.content=""
         self.namespace=doc.getAttribute("moby:namespace")
@@ -46,4 +48,4 @@
             if elt.nodeName=="CrossReference" or elt.nodeName=="moby:CrossReference":
                 self.__cross__=[]
                 for ref in elt.childNodes:
-                    self.__cross__.append(ref.toxml())
\ No newline at end of file
+                    self.__cross__.append(um.loads(ref))
\ No newline at end of file

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/ontology/RNASequence.py,v
retrieving revision 1.4
retrieving revision 1.5
diff -u -r1.4 -r1.5
--- /home/repository/moby/moby-live/Python/bioMoby/ontology/RNASequence.py	2005/02/01 08:52:16	1.4
+++ /home/repository/moby/moby-live/Python/bioMoby/ontology/RNASequence.py	2005/02/01 14:20:44	1.5
@@ -29,7 +29,9 @@
         """ Load the attributes from an XML string
         """
         from bioMoby.mobyMarshal import MobyUnmarshaller
-        doc=parseString(value).firstChild
+        doc=value
+        if isinstance(value, str):
+            doc=parseString(value).firstChild
         um=MobyUnmarshaller()
         self.content=""
         self.namespace=doc.getAttribute("moby:namespace")
@@ -49,12 +51,12 @@
             if elt.nodeName=="CrossReference" or elt.nodeName=="moby:CrossReference":
                 self.__cross__=[]
                 for ref in elt.childNodes:
-                    self.__cross__.append(ref.toxml())
+                    self.__cross__.append(um.loads(ref))
             if elt.nodeType==elt.ELEMENT_NODE and (elt.nodeName=="Integer" or elt.nodeName=="moby:Integer") and (elt.getAttribute("articleName")=="Length" or elt.getAttribute("moby:articleName")=="Length"):
                 t=MobyInteger()
-                t.fromMoby(elt.toxml())
+                t.fromMoby(elt)
                 self.Length=t.content
             if elt.nodeType==elt.ELEMENT_NODE and (elt.nodeName=="String" or elt.nodeName=="moby:String") and (elt.getAttribute("articleName")=="SequenceString" or elt.getAttribute("moby:articleName")=="SequenceString"):
                 t=MobyString()
-                t.fromMoby(elt.toxml())
+                t.fromMoby(elt)
                 self.SequenceString=t.content
\ No newline at end of file

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/ontology/SINGER_ACCESSION.py,v
retrieving revision 1.4
retrieving revision 1.5
diff -u -r1.4 -r1.5
--- /home/repository/moby/moby-live/Python/bioMoby/ontology/SINGER_ACCESSION.py	2005/02/01 08:52:16	1.4
+++ /home/repository/moby/moby-live/Python/bioMoby/ontology/SINGER_ACCESSION.py	2005/02/01 14:20:44	1.5
@@ -30,7 +30,9 @@
         """ Load the attributes from an XML string
         """
         from bioMoby.mobyMarshal import MobyUnmarshaller
-        doc=parseString(value).firstChild
+        doc=value
+        if isinstance(value, str):
+            doc=parseString(value).firstChild
         um=MobyUnmarshaller()
         self.content=""
         self.namespace=doc.getAttribute("moby:namespace")
@@ -50,20 +52,20 @@
             if elt.nodeName=="CrossReference" or elt.nodeName=="moby:CrossReference":
                 self.__cross__=[]
                 for ref in elt.childNodes:
-                    self.__cross__.append(ref.toxml())
+                    self.__cross__.append(um.loads(ref))
             if elt.nodeType==elt.ELEMENT_NODE and (elt.nodeName=="String" or elt.nodeName=="moby:String") and (elt.getAttribute("articleName")=="ACCNO" or elt.getAttribute("moby:articleName")=="ACCNO"):
                 t=MobyString()
-                t.fromMoby(elt.toxml())
+                t.fromMoby(elt)
                 self.ACCNO=t.content
             if elt.nodeType==elt.ELEMENT_NODE and (elt.nodeName=="String" or elt.nodeName=="moby:String") and (elt.getAttribute("articleName")=="ORIGCTY" or elt.getAttribute("moby:articleName")=="ORIGCTY"):
                 t=MobyString()
-                t.fromMoby(elt.toxml())
+                t.fromMoby(elt)
                 self.ORIGCTY=t.content
             if elt.nodeType==elt.ELEMENT_NODE and (elt.nodeName=="String" or elt.nodeName=="moby:String") and (elt.getAttribute("articleName")=="GENUS" or elt.getAttribute("moby:articleName")=="GENUS"):
                 t=MobyString()
-                t.fromMoby(elt.toxml())
+                t.fromMoby(elt)
                 self.GENUS=t.content
             if elt.nodeType==elt.ELEMENT_NODE and (elt.nodeName=="String" or elt.nodeName=="moby:String") and (elt.getAttribute("articleName")=="SPECIES" or elt.getAttribute("moby:articleName")=="SPECIES"):
                 t=MobyString()
-                t.fromMoby(elt.toxml())
+                t.fromMoby(elt)
                 self.SPECIES=t.content
\ No newline at end of file

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/ontology/Sample.py,v
retrieving revision 1.4
retrieving revision 1.5
diff -u -r1.4 -r1.5
--- /home/repository/moby/moby-live/Python/bioMoby/ontology/Sample.py	2005/02/01 08:52:16	1.4
+++ /home/repository/moby/moby-live/Python/bioMoby/ontology/Sample.py	2005/02/01 14:20:44	1.5
@@ -29,7 +29,9 @@
         """ Load the attributes from an XML string
         """
         from bioMoby.mobyMarshal import MobyUnmarshaller
-        doc=parseString(value).firstChild
+        doc=value
+        if isinstance(value, str):
+            doc=parseString(value).firstChild
         um=MobyUnmarshaller()
         self.content=""
         self.namespace=doc.getAttribute("moby:namespace")
@@ -49,12 +51,12 @@
             if elt.nodeName=="CrossReference" or elt.nodeName=="moby:CrossReference":
                 self.__cross__=[]
                 for ref in elt.childNodes:
-                    self.__cross__.append(ref.toxml())
+                    self.__cross__.append(um.loads(ref))
             if elt.nodeType==elt.ELEMENT_NODE and (elt.nodeName=="String" or elt.nodeName=="moby:String") and (elt.getAttribute("articleName")=="code" or elt.getAttribute("moby:articleName")=="code"):
                 t=MobyString()
-                t.fromMoby(elt.toxml())
+                t.fromMoby(elt)
                 self.Code=t.content
             if elt.nodeType==elt.ELEMENT_NODE and (elt.nodeName=="Integer" or elt.nodeName=="moby:Integer") and (elt.getAttribute("articleName")=="affectation" or elt.getAttribute("moby:articleName")=="affectation"):
                 t=MobyInteger()
-                t.fromMoby(elt.toxml())
+                t.fromMoby(elt)
                 self.Affectation=t.content
\ No newline at end of file

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/ontology/SchematikonMotifID.py,v
retrieving revision 1.4
retrieving revision 1.5
diff -u -r1.4 -r1.5
--- /home/repository/moby/moby-live/Python/bioMoby/ontology/SchematikonMotifID.py	2005/02/01 08:52:16	1.4
+++ /home/repository/moby/moby-live/Python/bioMoby/ontology/SchematikonMotifID.py	2005/02/01 14:20:44	1.5
@@ -27,7 +27,9 @@
         """ Load the attributes from an XML string
         """
         from bioMoby.mobyMarshal import MobyUnmarshaller
-        doc=parseString(value).firstChild
+        doc=value
+        if isinstance(value, str):
+            doc=parseString(value).firstChild
         um=MobyUnmarshaller()
         self.content=""
         self.namespace=doc.getAttribute("moby:namespace")
@@ -47,8 +49,8 @@
             if elt.nodeName=="CrossReference" or elt.nodeName=="moby:CrossReference":
                 self.__cross__=[]
                 for ref in elt.childNodes:
-                    self.__cross__.append(ref.toxml())
+                    self.__cross__.append(um.loads(ref))
             if elt.nodeType==elt.ELEMENT_NODE and (elt.nodeName=="String" or elt.nodeName=="moby:String") and (elt.getAttribute("articleName")=="ID" or elt.getAttribute("moby:articleName")=="ID"):
                 t=MobyString()
-                t.fromMoby(elt.toxml())
+                t.fromMoby(elt)
                 self.ID=t.content
\ No newline at end of file

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/ontology/SchematikonMotifSupport.py,v
retrieving revision 1.4
retrieving revision 1.5
diff -u -r1.4 -r1.5
--- /home/repository/moby/moby-live/Python/bioMoby/ontology/SchematikonMotifSupport.py	2005/02/01 08:52:16	1.4
+++ /home/repository/moby/moby-live/Python/bioMoby/ontology/SchematikonMotifSupport.py	2005/02/01 14:20:44	1.5
@@ -28,7 +28,9 @@
         """ Load the attributes from an XML string
         """
         from bioMoby.mobyMarshal import MobyUnmarshaller
-        doc=parseString(value).firstChild
+        doc=value
+        if isinstance(value, str):
+            doc=parseString(value).firstChild
         um=MobyUnmarshaller()
         self.content=""
         self.namespace=doc.getAttribute("moby:namespace")
@@ -48,12 +50,12 @@
             if elt.nodeName=="CrossReference" or elt.nodeName=="moby:CrossReference":
                 self.__cross__=[]
                 for ref in elt.childNodes:
-                    self.__cross__.append(ref.toxml())
+                    self.__cross__.append(um.loads(ref))
             if elt.nodeType==elt.ELEMENT_NODE and (elt.nodeName=="Integer" or elt.nodeName=="moby:Integer") and (elt.getAttribute("articleName")=="UniqueSupport" or elt.getAttribute("moby:articleName")=="UniqueSupport"):
                 t=MobyInteger()
-                t.fromMoby(elt.toxml())
+                t.fromMoby(elt)
                 self.UniqueSupport=t.content
             if elt.nodeType==elt.ELEMENT_NODE and (elt.nodeName=="Integer" or elt.nodeName=="moby:Integer") and (elt.getAttribute("articleName")=="Support" or elt.getAttribute("moby:articleName")=="Support"):
                 t=MobyInteger()
-                t.fromMoby(elt.toxml())
+                t.fromMoby(elt)
                 self.Support=t.content
\ No newline at end of file

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/ontology/SchematikonSegmentAttributes.py,v
retrieving revision 1.4
retrieving revision 1.5
diff -u -r1.4 -r1.5
--- /home/repository/moby/moby-live/Python/bioMoby/ontology/SchematikonSegmentAttributes.py	2005/02/01 08:52:16	1.4
+++ /home/repository/moby/moby-live/Python/bioMoby/ontology/SchematikonSegmentAttributes.py	2005/02/01 14:20:44	1.5
@@ -32,7 +32,9 @@
         """ Load the attributes from an XML string
         """
         from bioMoby.mobyMarshal import MobyUnmarshaller
-        doc=parseString(value).firstChild
+        doc=value
+        if isinstance(value, str):
+            doc=parseString(value).firstChild
         um=MobyUnmarshaller()
         self.content=""
         self.namespace=doc.getAttribute("moby:namespace")
@@ -52,24 +54,24 @@
             if elt.nodeName=="CrossReference" or elt.nodeName=="moby:CrossReference":
                 self.__cross__=[]
                 for ref in elt.childNodes:
-                    self.__cross__.append(ref.toxml())
+                    self.__cross__.append(um.loads(ref))
             if elt.nodeType==elt.ELEMENT_NODE and (elt.nodeName=="Integer" or elt.nodeName=="moby:Integer") and (elt.getAttribute("articleName")=="Length" or elt.getAttribute("moby:articleName")=="Length"):
                 t=MobyInteger()
-                t.fromMoby(elt.toxml())
+                t.fromMoby(elt)
                 self.Length=t.content
             if elt.nodeType==elt.ELEMENT_NODE and (elt.nodeName=="String" or elt.nodeName=="moby:String") and (elt.getAttribute("articleName")=="Insert code" or elt.getAttribute("moby:articleName")=="Insert code"):
                 t=MobyString()
-                t.fromMoby(elt.toxml())
+                t.fromMoby(elt)
                 self.InsertCode=t.content
             if elt.nodeType==elt.ELEMENT_NODE and (elt.nodeName=="Integer" or elt.nodeName=="moby:Integer") and (elt.getAttribute("articleName")=="Starting amino acid position" or elt.getAttribute("moby:articleName")=="Starting amino acid position"):
                 t=MobyInteger()
-                t.fromMoby(elt.toxml())
+                t.fromMoby(elt)
                 self.StartingAminoAcidPosition=t.content
             if elt.nodeType==elt.ELEMENT_NODE and (elt.nodeName=="String" or elt.nodeName=="moby:String") and (elt.getAttribute("articleName")=="Chain ID" or elt.getAttribute("moby:articleName")=="Chain ID"):
                 t=MobyString()
-                t.fromMoby(elt.toxml())
+                t.fromMoby(elt)
                 self.ChainID=t.content
             if elt.nodeType==elt.ELEMENT_NODE and (elt.nodeName=="String" or elt.nodeName=="moby:String") and (elt.getAttribute("articleName")=="PDB ID" or elt.getAttribute("moby:articleName")=="PDB ID"):
                 t=MobyString()
-                t.fromMoby(elt.toxml())
+                t.fromMoby(elt)
                 self.PDBID=t.content
\ No newline at end of file

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/ontology/SchematikonSegmentID.py,v
retrieving revision 1.4
retrieving revision 1.5
diff -u -r1.4 -r1.5
--- /home/repository/moby/moby-live/Python/bioMoby/ontology/SchematikonSegmentID.py	2005/02/01 08:52:16	1.4
+++ /home/repository/moby/moby-live/Python/bioMoby/ontology/SchematikonSegmentID.py	2005/02/01 14:20:44	1.5
@@ -27,7 +27,9 @@
         """ Load the attributes from an XML string
         """
         from bioMoby.mobyMarshal import MobyUnmarshaller
-        doc=parseString(value).firstChild
+        doc=value
+        if isinstance(value, str):
+            doc=parseString(value).firstChild
         um=MobyUnmarshaller()
         self.content=""
         self.namespace=doc.getAttribute("moby:namespace")
@@ -47,8 +49,8 @@
             if elt.nodeName=="CrossReference" or elt.nodeName=="moby:CrossReference":
                 self.__cross__=[]
                 for ref in elt.childNodes:
-                    self.__cross__.append(ref.toxml())
+                    self.__cross__.append(um.loads(ref))
             if elt.nodeType==elt.ELEMENT_NODE and (elt.nodeName=="String" or elt.nodeName=="moby:String") and (elt.getAttribute("articleName")=="ID" or elt.getAttribute("moby:articleName")=="ID"):
                 t=MobyString()
-                t.fromMoby(elt.toxml())
+                t.fromMoby(elt)
                 self.ID=t.content
\ No newline at end of file

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/ontology/SchematikonStructureAnnotation.py,v
retrieving revision 1.4
retrieving revision 1.5
diff -u -r1.4 -r1.5
--- /home/repository/moby/moby-live/Python/bioMoby/ontology/SchematikonStructureAnnotation.py	2005/02/01 08:52:16	1.4
+++ /home/repository/moby/moby-live/Python/bioMoby/ontology/SchematikonStructureAnnotation.py	2005/02/01 14:20:44	1.5
@@ -30,7 +30,9 @@
         """ Load the attributes from an XML string
         """
         from bioMoby.mobyMarshal import MobyUnmarshaller
-        doc=parseString(value).firstChild
+        doc=value
+        if isinstance(value, str):
+            doc=parseString(value).firstChild
         um=MobyUnmarshaller()
         self.content=""
         self.namespace=doc.getAttribute("moby:namespace")
@@ -50,20 +52,20 @@
             if elt.nodeName=="CrossReference" or elt.nodeName=="moby:CrossReference":
                 self.__cross__=[]
                 for ref in elt.childNodes:
-                    self.__cross__.append(ref.toxml())
+                    self.__cross__.append(um.loads(ref))
             if elt.nodeType==elt.ELEMENT_NODE and (elt.nodeName=="String" or elt.nodeName=="moby:String") and (elt.getAttribute("articleName")=="PROMOTIF gamma-turn" or elt.getAttribute("moby:articleName")=="PROMOTIF gamma-turn"):
                 t=MobyString()
-                t.fromMoby(elt.toxml())
+                t.fromMoby(elt)
                 self.PROMOTIFGammaTurn=t.content
             if elt.nodeType==elt.ELEMENT_NODE and (elt.nodeName=="String" or elt.nodeName=="moby:String") and (elt.getAttribute("articleName")=="PROMOTIF beta-turn" or elt.getAttribute("moby:articleName")=="PROMOTIF beta-turn"):
                 t=MobyString()
-                t.fromMoby(elt.toxml())
+                t.fromMoby(elt)
                 self.PROMOTIFBetaTurn=t.content
             if elt.nodeType==elt.ELEMENT_NODE and (elt.nodeName=="String" or elt.nodeName=="moby:String") and (elt.getAttribute("articleName")=="DSSP" or elt.getAttribute("moby:articleName")=="DSSP"):
                 t=MobyString()
-                t.fromMoby(elt.toxml())
+                t.fromMoby(elt)
                 self.DSSP=t.content
             if elt.nodeType==elt.ELEMENT_NODE and (elt.nodeName=="String" or elt.nodeName=="moby:String") and (elt.getAttribute("articleName")=="STRIDE" or elt.getAttribute("moby:articleName")=="STRIDE"):
                 t=MobyString()
-                t.fromMoby(elt.toxml())
+                t.fromMoby(elt)
                 self.STRIDE=t.content
\ No newline at end of file

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/ontology/SchematikonVorocodeName.py,v
retrieving revision 1.4
retrieving revision 1.5
diff -u -r1.4 -r1.5
--- /home/repository/moby/moby-live/Python/bioMoby/ontology/SchematikonVorocodeName.py	2005/02/01 08:52:16	1.4
+++ /home/repository/moby/moby-live/Python/bioMoby/ontology/SchematikonVorocodeName.py	2005/02/01 14:20:44	1.5
@@ -27,7 +27,9 @@
         """ Load the attributes from an XML string
         """
         from bioMoby.mobyMarshal import MobyUnmarshaller
-        doc=parseString(value).firstChild
+        doc=value
+        if isinstance(value, str):
+            doc=parseString(value).firstChild
         um=MobyUnmarshaller()
         self.content=""
         self.namespace=doc.getAttribute("moby:namespace")
@@ -47,8 +49,8 @@
             if elt.nodeName=="CrossReference" or elt.nodeName=="moby:CrossReference":
                 self.__cross__=[]
                 for ref in elt.childNodes:
-                    self.__cross__.append(ref.toxml())
+                    self.__cross__.append(um.loads(ref))
             if elt.nodeType==elt.ELEMENT_NODE and (elt.nodeName=="String" or elt.nodeName=="moby:String") and (elt.getAttribute("articleName")=="VorocodeName" or elt.getAttribute("moby:articleName")=="VorocodeName"):
                 t=MobyString()
-                t.fromMoby(elt.toxml())
+                t.fromMoby(elt)
                 self.VorocodeName=t.content
\ No newline at end of file

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/ontology/Scored_acronym_string.py,v
retrieving revision 1.4
retrieving revision 1.5
diff -u -r1.4 -r1.5
--- /home/repository/moby/moby-live/Python/bioMoby/ontology/Scored_acronym_string.py	2005/02/01 08:52:16	1.4
+++ /home/repository/moby/moby-live/Python/bioMoby/ontology/Scored_acronym_string.py	2005/02/01 14:20:44	1.5
@@ -30,7 +30,9 @@
         """ Load the attributes from an XML string
         """
         from bioMoby.mobyMarshal import MobyUnmarshaller
-        doc=parseString(value).firstChild
+        doc=value
+        if isinstance(value, str):
+            doc=parseString(value).firstChild
         um=MobyUnmarshaller()
         self.content=""
         self.namespace=doc.getAttribute("moby:namespace")
@@ -50,15 +52,15 @@
             if elt.nodeName=="CrossReference" or elt.nodeName=="moby:CrossReference":
                 self.__cross__=[]
                 for ref in elt.childNodes:
-                    self.__cross__.append(ref.toxml())
+                    self.__cross__.append(um.loads(ref))
             if elt.nodeType==elt.ELEMENT_NODE and (elt.nodeName=="Float" or elt.nodeName=="moby:Float") and (elt.getAttribute("articleName")=="score" or elt.getAttribute("moby:articleName")=="score"):
                 t=MobyFloat()
-                t.fromMoby(elt.toxml())
+                t.fromMoby(elt)
                 self.Score=t.content
             if elt.nodeType==elt.ELEMENT_NODE and (elt.nodeName=="Object" or elt.nodeName=="moby:Object") and (elt.getAttribute("articleName")=="string_component" or elt.getAttribute("moby:articleName")=="string_component"):
                 self.String_component=MobyObject()
-                self.String_component.fromMoby(elt.toxml())
+                self.String_component.fromMoby(elt)
             if elt.nodeType==elt.ELEMENT_NODE and (elt.nodeName=="String" or elt.nodeName=="moby:String") and (elt.getAttribute("articleName")=="acronym" or elt.getAttribute("moby:articleName")=="acronym"):
                 t=MobyString()
-                t.fromMoby(elt.toxml())
+                t.fromMoby(elt)
                 self.Acronym=t.content
\ No newline at end of file

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/ontology/SimpleAnnotatedGIFImage.py,v
retrieving revision 1.4
retrieving revision 1.5
diff -u -r1.4 -r1.5
--- /home/repository/moby/moby-live/Python/bioMoby/ontology/SimpleAnnotatedGIFImage.py	2005/02/01 08:52:16	1.4
+++ /home/repository/moby/moby-live/Python/bioMoby/ontology/SimpleAnnotatedGIFImage.py	2005/02/01 14:20:44	1.5
@@ -28,7 +28,9 @@
         """ Load the attributes from an XML string
         """
         from bioMoby.mobyMarshal import MobyUnmarshaller
-        doc=parseString(value).firstChild
+        doc=value
+        if isinstance(value, str):
+            doc=parseString(value).firstChild
         um=MobyUnmarshaller()
         self.content=""
         self.namespace=doc.getAttribute("moby:namespace")
@@ -48,8 +50,8 @@
             if elt.nodeName=="CrossReference" or elt.nodeName=="moby:CrossReference":
                 self.__cross__=[]
                 for ref in elt.childNodes:
-                    self.__cross__.append(ref.toxml())
+                    self.__cross__.append(um.loads(ref))
             if elt.nodeType==elt.ELEMENT_NODE and (elt.nodeName=="String" or elt.nodeName=="moby:String") and (elt.getAttribute("articleName")=="Description" or elt.getAttribute("moby:articleName")=="Description"):
                 t=MobyString()
-                t.fromMoby(elt.toxml())
+                t.fromMoby(elt)
                 self.Description=t.content
\ No newline at end of file

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/ontology/SimpleAnnotatedJPEGImage.py,v
retrieving revision 1.4
retrieving revision 1.5
diff -u -r1.4 -r1.5
--- /home/repository/moby/moby-live/Python/bioMoby/ontology/SimpleAnnotatedJPEGImage.py	2005/02/01 08:52:16	1.4
+++ /home/repository/moby/moby-live/Python/bioMoby/ontology/SimpleAnnotatedJPEGImage.py	2005/02/01 14:20:44	1.5
@@ -28,7 +28,9 @@
         """ Load the attributes from an XML string
         """
         from bioMoby.mobyMarshal import MobyUnmarshaller
-        doc=parseString(value).firstChild
+        doc=value
+        if isinstance(value, str):
+            doc=parseString(value).firstChild
         um=MobyUnmarshaller()
         self.content=""
         self.namespace=doc.getAttribute("moby:namespace")
@@ -49,8 +51,8 @@
             if elt.nodeName=="CrossReference" or elt.nodeName=="moby:CrossReference":
                 self.__cross__=[]
                 for ref in elt.childNodes:
-                    self.__cross__.append(ref.toxml())
+                    self.__cross__.append(um.loads(ref))
             if elt.nodeType==elt.ELEMENT_NODE and (elt.nodeName=="String" or elt.nodeName=="moby:String") and (elt.getAttribute("articleName")=="Description" or elt.getAttribute("moby:articleName")=="Description"):
                 t=MobyString()
-                t.fromMoby(elt.toxml())
+                t.fromMoby(elt)
                 self.Description.append(t.content)
\ No newline at end of file

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/ontology/Simple_key_value_pair.py,v
retrieving revision 1.4
retrieving revision 1.5
diff -u -r1.4 -r1.5
--- /home/repository/moby/moby-live/Python/bioMoby/ontology/Simple_key_value_pair.py	2005/02/01 08:52:16	1.4
+++ /home/repository/moby/moby-live/Python/bioMoby/ontology/Simple_key_value_pair.py	2005/02/01 14:20:44	1.5
@@ -28,7 +28,9 @@
         """ Load the attributes from an XML string
         """
         from bioMoby.mobyMarshal import MobyUnmarshaller
-        doc=parseString(value).firstChild
+        doc=value
+        if isinstance(value, str):
+            doc=parseString(value).firstChild
         um=MobyUnmarshaller()
         self.content=""
         self.namespace=doc.getAttribute("moby:namespace")
@@ -48,12 +50,12 @@
             if elt.nodeName=="CrossReference" or elt.nodeName=="moby:CrossReference":
                 self.__cross__=[]
                 for ref in elt.childNodes:
-                    self.__cross__.append(ref.toxml())
+                    self.__cross__.append(um.loads(ref))
             if elt.nodeType==elt.ELEMENT_NODE and (elt.nodeName=="String" or elt.nodeName=="moby:String") and (elt.getAttribute("articleName")=="value" or elt.getAttribute("moby:articleName")=="value"):
                 t=MobyString()
-                t.fromMoby(elt.toxml())
+                t.fromMoby(elt)
                 self.Value=t.content
             if elt.nodeType==elt.ELEMENT_NODE and (elt.nodeName=="String" or elt.nodeName=="moby:String") and (elt.getAttribute("articleName")=="key" or elt.getAttribute("moby:articleName")=="key"):
                 t=MobyString()
-                t.fromMoby(elt.toxml())
+                t.fromMoby(elt)
                 self.Key=t.content
\ No newline at end of file

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/ontology/Snp_allele.py,v
retrieving revision 1.4
retrieving revision 1.5
diff -u -r1.4 -r1.5
--- /home/repository/moby/moby-live/Python/bioMoby/ontology/Snp_allele.py	2005/02/01 08:52:16	1.4
+++ /home/repository/moby/moby-live/Python/bioMoby/ontology/Snp_allele.py	2005/02/01 14:20:44	1.5
@@ -23,7 +23,9 @@
         """ Load the attributes from an XML string
         """
         from bioMoby.mobyMarshal import MobyUnmarshaller
-        doc=parseString(value).firstChild
+        doc=value
+        if isinstance(value, str):
+            doc=parseString(value).firstChild
         um=MobyUnmarshaller()
         self.content=""
 
@@ -37,7 +39,7 @@
             if elt.nodeName=="CrossReference" or elt.nodeName=="moby:CrossReference":
                 self.__cross__=[]
                 for ref in elt.childNodes:
-                    self.__cross__.append(ref.toxml())
+                    self.__cross__.append(um.loads(ref))
             if elt.nodeType==elt.ELEMENT_NODE and (elt.nodeName=="DNASequence" or elt.nodeName=="moby:DNASequence") and (elt.getAttribute("articleName")=="snp_allele" or elt.getAttribute("moby:articleName")=="snp_allele"):
                 self.Snp_allele=MobyDNASequence()
-                self.Snp_allele.fromMoby(elt.toxml())
\ No newline at end of file
+                self.Snp_allele.fromMoby(elt)
\ No newline at end of file

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/ontology/Snp_genotype.py,v
retrieving revision 1.4
retrieving revision 1.5
diff -u -r1.4 -r1.5
--- /home/repository/moby/moby-live/Python/bioMoby/ontology/Snp_genotype.py	2005/02/01 08:52:16	1.4
+++ /home/repository/moby/moby-live/Python/bioMoby/ontology/Snp_genotype.py	2005/02/01 14:20:44	1.5
@@ -24,7 +24,9 @@
         """ Load the attributes from an XML string
         """
         from bioMoby.mobyMarshal import MobyUnmarshaller
-        doc=parseString(value).firstChild
+        doc=value
+        if isinstance(value, str):
+            doc=parseString(value).firstChild
         um=MobyUnmarshaller()
         self.content=""
 
@@ -38,10 +40,10 @@
             if elt.nodeName=="CrossReference" or elt.nodeName=="moby:CrossReference":
                 self.__cross__=[]
                 for ref in elt.childNodes:
-                    self.__cross__.append(ref.toxml())
+                    self.__cross__.append(um.loads(ref))
             if elt.nodeType==elt.ELEMENT_NODE and (elt.nodeName=="snp_allele" or elt.nodeName=="moby:snp_allele") and (elt.getAttribute("articleName")=="allele1" or elt.getAttribute("moby:articleName")=="allele1"):
                 self.Allele1=MobySnp_allele()
-                self.Allele1.fromMoby(elt.toxml())
+                self.Allele1.fromMoby(elt)
             if elt.nodeType==elt.ELEMENT_NODE and (elt.nodeName=="snp_allele" or elt.nodeName=="moby:snp_allele") and (elt.getAttribute("articleName")=="allele2" or elt.getAttribute("moby:articleName")=="allele2"):
                 self.Allele2=MobySnp_allele()
-                self.Allele2.fromMoby(elt.toxml())
\ No newline at end of file
+                self.Allele2.fromMoby(elt)
\ No newline at end of file

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/ontology/Study.py,v
retrieving revision 1.4
retrieving revision 1.5
diff -u -r1.4 -r1.5
--- /home/repository/moby/moby-live/Python/bioMoby/ontology/Study.py	2005/02/01 08:52:16	1.4
+++ /home/repository/moby/moby-live/Python/bioMoby/ontology/Study.py	2005/02/01 14:20:44	1.5
@@ -30,7 +30,9 @@
         """ Load the attributes from an XML string
         """
         from bioMoby.mobyMarshal import MobyUnmarshaller
-        doc=parseString(value).firstChild
+        doc=value
+        if isinstance(value, str):
+            doc=parseString(value).firstChild
         um=MobyUnmarshaller()
         self.content=""
         self.namespace=doc.getAttribute("moby:namespace")
@@ -50,16 +52,16 @@
             if elt.nodeName=="CrossReference" or elt.nodeName=="moby:CrossReference":
                 self.__cross__=[]
                 for ref in elt.childNodes:
-                    self.__cross__.append(ref.toxml())
+                    self.__cross__.append(um.loads(ref))
             if elt.nodeType==elt.ELEMENT_NODE and (elt.nodeName=="String" or elt.nodeName=="moby:String") and (elt.getAttribute("articleName")=="study_name" or elt.getAttribute("moby:articleName")=="study_name"):
                 t=MobyString()
-                t.fromMoby(elt.toxml())
+                t.fromMoby(elt)
                 self.Study_name=t.content
             if elt.nodeType==elt.ELEMENT_NODE and (elt.nodeName=="Integer" or elt.nodeName=="moby:Integer") and (elt.getAttribute("articleName")=="study_id" or elt.getAttribute("moby:articleName")=="study_id"):
                 t=MobyInteger()
-                t.fromMoby(elt.toxml())
+                t.fromMoby(elt)
                 self.Study_id=t.content
             if elt.nodeType==elt.ELEMENT_NODE and (elt.nodeName=="String" or elt.nodeName=="moby:String") and (elt.getAttribute("articleName")=="study_desc" or elt.getAttribute("moby:articleName")=="study_desc"):
                 t=MobyString()
-                t.fromMoby(elt.toxml())
+                t.fromMoby(elt)
                 self.Study_desc=t.content
\ No newline at end of file

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/ontology/TEST.py,v
retrieving revision 1.4
retrieving revision 1.5
diff -u -r1.4 -r1.5
--- /home/repository/moby/moby-live/Python/bioMoby/ontology/TEST.py	2005/02/01 08:52:16	1.4
+++ /home/repository/moby/moby-live/Python/bioMoby/ontology/TEST.py	2005/02/01 14:20:44	1.5
@@ -26,7 +26,9 @@
         """ Load the attributes from an XML string
         """
         from bioMoby.mobyMarshal import MobyUnmarshaller
-        doc=parseString(value).firstChild
+        doc=value
+        if isinstance(value, str):
+            doc=parseString(value).firstChild
         um=MobyUnmarshaller()
         self.content=""
         self.namespace=doc.getAttribute("moby:namespace")
@@ -46,4 +48,4 @@
             if elt.nodeName=="CrossReference" or elt.nodeName=="moby:CrossReference":
                 self.__cross__=[]
                 for ref in elt.childNodes:
-                    self.__cross__.append(ref.toxml())
\ No newline at end of file
+                    self.__cross__.append(um.loads(ref))
\ No newline at end of file

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/ontology/TargetP_result.py,v
retrieving revision 1.4
retrieving revision 1.5
diff -u -r1.4 -r1.5
--- /home/repository/moby/moby-live/Python/bioMoby/ontology/TargetP_result.py	2005/02/01 08:52:16	1.4
+++ /home/repository/moby/moby-live/Python/bioMoby/ontology/TargetP_result.py	2005/02/01 14:20:44	1.5
@@ -32,7 +32,9 @@
         """ Load the attributes from an XML string
         """
         from bioMoby.mobyMarshal import MobyUnmarshaller
-        doc=parseString(value).firstChild
+        doc=value
+        if isinstance(value, str):
+            doc=parseString(value).firstChild
         um=MobyUnmarshaller()
         self.content=""
         self.namespace=doc.getAttribute("moby:namespace")
@@ -52,24 +54,24 @@
             if elt.nodeName=="CrossReference" or elt.nodeName=="moby:CrossReference":
                 self.__cross__=[]
                 for ref in elt.childNodes:
-                    self.__cross__.append(ref.toxml())
+                    self.__cross__.append(um.loads(ref))
             if elt.nodeType==elt.ELEMENT_NODE and (elt.nodeName=="Float" or elt.nodeName=="moby:Float") and (elt.getAttribute("articleName")=="o_score" or elt.getAttribute("moby:articleName")=="o_score"):
                 t=MobyFloat()
-                t.fromMoby(elt.toxml())
+                t.fromMoby(elt)
                 self.O_score=t.content
             if elt.nodeType==elt.ELEMENT_NODE and (elt.nodeName=="Float" or elt.nodeName=="moby:Float") and (elt.getAttribute("articleName")=="s_score" or elt.getAttribute("moby:articleName")=="s_score"):
                 t=MobyFloat()
-                t.fromMoby(elt.toxml())
+                t.fromMoby(elt)
                 self.S_score=t.content
             if elt.nodeType==elt.ELEMENT_NODE and (elt.nodeName=="Float" or elt.nodeName=="moby:Float") and (elt.getAttribute("articleName")=="m_score" or elt.getAttribute("moby:articleName")=="m_score"):
                 t=MobyFloat()
-                t.fromMoby(elt.toxml())
+                t.fromMoby(elt)
                 self.M_score=t.content
             if elt.nodeType==elt.ELEMENT_NODE and (elt.nodeName=="Float" or elt.nodeName=="moby:Float") and (elt.getAttribute("articleName")=="c_score" or elt.getAttribute("moby:articleName")=="c_score"):
                 t=MobyFloat()
-                t.fromMoby(elt.toxml())
+                t.fromMoby(elt)
                 self.C_score=t.content
             if elt.nodeType==elt.ELEMENT_NODE and (elt.nodeName=="String" or elt.nodeName=="moby:String") and (elt.getAttribute("articleName")=="compartment" or elt.getAttribute("moby:articleName")=="compartment"):
                 t=MobyString()
-                t.fromMoby(elt.toxml())
+                t.fromMoby(elt)
                 self.Compartment=t.content
\ No newline at end of file

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/ontology/Testout.py,v
retrieving revision 1.4
retrieving revision 1.5
diff -u -r1.4 -r1.5
--- /home/repository/moby/moby-live/Python/bioMoby/ontology/Testout.py	2005/02/01 08:52:16	1.4
+++ /home/repository/moby/moby-live/Python/bioMoby/ontology/Testout.py	2005/02/01 14:20:44	1.5
@@ -31,7 +31,9 @@
         """ Load the attributes from an XML string
         """
         from bioMoby.mobyMarshal import MobyUnmarshaller
-        doc=parseString(value).firstChild
+        doc=value
+        if isinstance(value, str):
+            doc=parseString(value).firstChild
         um=MobyUnmarshaller()
         self.content=""
         self.namespace=doc.getAttribute("moby:namespace")
@@ -51,20 +53,20 @@
             if elt.nodeName=="CrossReference" or elt.nodeName=="moby:CrossReference":
                 self.__cross__=[]
                 for ref in elt.childNodes:
-                    self.__cross__.append(ref.toxml())
+                    self.__cross__.append(um.loads(ref))
             if elt.nodeType==elt.ELEMENT_NODE and (elt.nodeName=="Integer" or elt.nodeName=="moby:Integer") and (elt.getAttribute("articleName")=="gid" or elt.getAttribute("moby:articleName")=="gid"):
                 t=MobyInteger()
-                t.fromMoby(elt.toxml())
+                t.fromMoby(elt)
                 self.Gid=t.content
             if elt.nodeType==elt.ELEMENT_NODE and (elt.nodeName=="String" or elt.nodeName=="moby:String") and (elt.getAttribute("articleName")=="dvalue" or elt.getAttribute("moby:articleName")=="dvalue"):
                 t=MobyString()
-                t.fromMoby(elt.toxml())
+                t.fromMoby(elt)
                 self.Dvalue=t.content
             if elt.nodeType==elt.ELEMENT_NODE and (elt.nodeName=="Integer" or elt.nodeName=="moby:Integer") and (elt.getAttribute("articleName")=="scaleid" or elt.getAttribute("moby:articleName")=="scaleid"):
                 t=MobyInteger()
-                t.fromMoby(elt.toxml())
+                t.fromMoby(elt)
                 self.Scaleid=t.content
             if elt.nodeType==elt.ELEMENT_NODE and (elt.nodeName=="Integer" or elt.nodeName=="moby:Integer") and (elt.getAttribute("articleName")=="tmethid" or elt.getAttribute("moby:articleName")=="tmethid"):
                 t=MobyInteger()
-                t.fromMoby(elt.toxml())
+                t.fromMoby(elt)
                 self.Tmethid=t.content
\ No newline at end of file

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/ontology/TextBase64.py,v
retrieving revision 1.4
retrieving revision 1.5
diff -u -r1.4 -r1.5
--- /home/repository/moby/moby-live/Python/bioMoby/ontology/TextBase64.py	2005/02/01 08:52:16	1.4
+++ /home/repository/moby/moby-live/Python/bioMoby/ontology/TextBase64.py	2005/02/01 14:20:44	1.5
@@ -26,7 +26,9 @@
         """ Load the attributes from an XML string
         """
         from bioMoby.mobyMarshal import MobyUnmarshaller
-        doc=parseString(value).firstChild
+        doc=value
+        if isinstance(value, str):
+            doc=parseString(value).firstChild
         um=MobyUnmarshaller()
         self.content=""
         self.namespace=doc.getAttribute("moby:namespace")
@@ -46,4 +48,4 @@
             if elt.nodeName=="CrossReference" or elt.nodeName=="moby:CrossReference":
                 self.__cross__=[]
                 for ref in elt.childNodes:
-                    self.__cross__.append(ref.toxml())
\ No newline at end of file
+                    self.__cross__.append(um.loads(ref))
\ No newline at end of file

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/ontology/TextFormatted.py,v
retrieving revision 1.4
retrieving revision 1.5
diff -u -r1.4 -r1.5
--- /home/repository/moby/moby-live/Python/bioMoby/ontology/TextFormatted.py	2005/02/01 08:52:16	1.4
+++ /home/repository/moby/moby-live/Python/bioMoby/ontology/TextFormatted.py	2005/02/01 14:20:44	1.5
@@ -26,7 +26,9 @@
         """ Load the attributes from an XML string
         """
         from bioMoby.mobyMarshal import MobyUnmarshaller
-        doc=parseString(value).firstChild
+        doc=value
+        if isinstance(value, str):
+            doc=parseString(value).firstChild
         um=MobyUnmarshaller()
         self.content=""
         self.namespace=doc.getAttribute("moby:namespace")
@@ -46,4 +48,4 @@
             if elt.nodeName=="CrossReference" or elt.nodeName=="moby:CrossReference":
                 self.__cross__=[]
                 for ref in elt.childNodes:
-                    self.__cross__.append(ref.toxml())
\ No newline at end of file
+                    self.__cross__.append(um.loads(ref))
\ No newline at end of file

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/ontology/TextHtml.py,v
retrieving revision 1.4
retrieving revision 1.5
diff -u -r1.4 -r1.5
--- /home/repository/moby/moby-live/Python/bioMoby/ontology/TextHtml.py	2005/02/01 08:52:16	1.4
+++ /home/repository/moby/moby-live/Python/bioMoby/ontology/TextHtml.py	2005/02/01 14:20:44	1.5
@@ -26,7 +26,9 @@
         """ Load the attributes from an XML string
         """
         from bioMoby.mobyMarshal import MobyUnmarshaller
-        doc=parseString(value).firstChild
+        doc=value
+        if isinstance(value, str):
+            doc=parseString(value).firstChild
         um=MobyUnmarshaller()
         self.content=""
         self.namespace=doc.getAttribute("moby:namespace")
@@ -46,4 +48,4 @@
             if elt.nodeName=="CrossReference" or elt.nodeName=="moby:CrossReference":
                 self.__cross__=[]
                 for ref in elt.childNodes:
-                    self.__cross__.append(ref.toxml())
\ No newline at end of file
+                    self.__cross__.append(um.loads(ref))
\ No newline at end of file

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/ontology/TextPlain.py,v
retrieving revision 1.4
retrieving revision 1.5
diff -u -r1.4 -r1.5
--- /home/repository/moby/moby-live/Python/bioMoby/ontology/TextPlain.py	2005/02/01 08:52:16	1.4
+++ /home/repository/moby/moby-live/Python/bioMoby/ontology/TextPlain.py	2005/02/01 14:20:44	1.5
@@ -26,7 +26,9 @@
         """ Load the attributes from an XML string
         """
         from bioMoby.mobyMarshal import MobyUnmarshaller
-        doc=parseString(value).firstChild
+        doc=value
+        if isinstance(value, str):
+            doc=parseString(value).firstChild
         um=MobyUnmarshaller()
         self.content=""
         self.namespace=doc.getAttribute("moby:namespace")
@@ -46,4 +48,4 @@
             if elt.nodeName=="CrossReference" or elt.nodeName=="moby:CrossReference":
                 self.__cross__=[]
                 for ref in elt.childNodes:
-                    self.__cross__.append(ref.toxml())
\ No newline at end of file
+                    self.__cross__.append(um.loads(ref))
\ No newline at end of file

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/ontology/TextUuencoded.py,v
retrieving revision 1.4
retrieving revision 1.5
diff -u -r1.4 -r1.5
--- /home/repository/moby/moby-live/Python/bioMoby/ontology/TextUuencoded.py	2005/02/01 08:52:16	1.4
+++ /home/repository/moby/moby-live/Python/bioMoby/ontology/TextUuencoded.py	2005/02/01 14:20:44	1.5
@@ -26,7 +26,9 @@
         """ Load the attributes from an XML string
         """
         from bioMoby.mobyMarshal import MobyUnmarshaller
-        doc=parseString(value).firstChild
+        doc=value
+        if isinstance(value, str):
+            doc=parseString(value).firstChild
         um=MobyUnmarshaller()
         self.content=""
         self.namespace=doc.getAttribute("moby:namespace")
@@ -46,4 +48,4 @@
             if elt.nodeName=="CrossReference" or elt.nodeName=="moby:CrossReference":
                 self.__cross__=[]
                 for ref in elt.childNodes:
-                    self.__cross__.append(ref.toxml())
\ No newline at end of file
+                    self.__cross__.append(um.loads(ref))
\ No newline at end of file

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/ontology/TextXml.py,v
retrieving revision 1.4
retrieving revision 1.5
diff -u -r1.4 -r1.5
--- /home/repository/moby/moby-live/Python/bioMoby/ontology/TextXml.py	2005/02/01 08:52:16	1.4
+++ /home/repository/moby/moby-live/Python/bioMoby/ontology/TextXml.py	2005/02/01 14:20:44	1.5
@@ -26,7 +26,9 @@
         """ Load the attributes from an XML string
         """
         from bioMoby.mobyMarshal import MobyUnmarshaller
-        doc=parseString(value).firstChild
+        doc=value
+        if isinstance(value, str):
+            doc=parseString(value).firstChild
         um=MobyUnmarshaller()
         self.content=""
         self.namespace=doc.getAttribute("moby:namespace")
@@ -46,4 +48,4 @@
             if elt.nodeName=="CrossReference" or elt.nodeName=="moby:CrossReference":
                 self.__cross__=[]
                 for ref in elt.childNodes:
-                    self.__cross__.append(ref.toxml())
\ No newline at end of file
+                    self.__cross__.append(um.loads(ref))
\ No newline at end of file

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/ontology/Text_plain.py,v
retrieving revision 1.4
retrieving revision 1.5
diff -u -r1.4 -r1.5
--- /home/repository/moby/moby-live/Python/bioMoby/ontology/Text_plain.py	2005/02/01 08:52:16	1.4
+++ /home/repository/moby/moby-live/Python/bioMoby/ontology/Text_plain.py	2005/02/01 14:20:44	1.5
@@ -26,7 +26,9 @@
         """ Load the attributes from an XML string
         """
         from bioMoby.mobyMarshal import MobyUnmarshaller
-        doc=parseString(value).firstChild
+        doc=value
+        if isinstance(value, str):
+            doc=parseString(value).firstChild
         um=MobyUnmarshaller()
         self.content=""
         self.namespace=doc.getAttribute("moby:namespace")
@@ -46,4 +48,4 @@
             if elt.nodeName=="CrossReference" or elt.nodeName=="moby:CrossReference":
                 self.__cross__=[]
                 for ref in elt.childNodes:
-                    self.__cross__.append(ref.toxml())
\ No newline at end of file
+                    self.__cross__.append(um.loads(ref))
\ No newline at end of file

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/ontology/Trait_Details.py,v
retrieving revision 1.4
retrieving revision 1.5
diff -u -r1.4 -r1.5
--- /home/repository/moby/moby-live/Python/bioMoby/ontology/Trait_Details.py	2005/02/01 08:52:16	1.4
+++ /home/repository/moby/moby-live/Python/bioMoby/ontology/Trait_Details.py	2005/02/01 14:20:44	1.5
@@ -32,7 +32,9 @@
         """ Load the attributes from an XML string
         """
         from bioMoby.mobyMarshal import MobyUnmarshaller
-        doc=parseString(value).firstChild
+        doc=value
+        if isinstance(value, str):
+            doc=parseString(value).firstChild
         um=MobyUnmarshaller()
         self.content=""
         self.namespace=doc.getAttribute("moby:namespace")
@@ -52,24 +54,24 @@
             if elt.nodeName=="CrossReference" or elt.nodeName=="moby:CrossReference":
                 self.__cross__=[]
                 for ref in elt.childNodes:
-                    self.__cross__.append(ref.toxml())
+                    self.__cross__.append(um.loads(ref))
             if elt.nodeType==elt.ELEMENT_NODE and (elt.nodeName=="String" or elt.nodeName=="moby:String") and (elt.getAttribute("articleName")=="trait_desc" or elt.getAttribute("moby:articleName")=="trait_desc"):
                 t=MobyString()
-                t.fromMoby(elt.toxml())
+                t.fromMoby(elt)
                 self.Trait_desc=t.content
             if elt.nodeType==elt.ELEMENT_NODE and (elt.nodeName=="Integer" or elt.nodeName=="moby:Integer") and (elt.getAttribute("articleName")=="num_studies" or elt.getAttribute("moby:articleName")=="num_studies"):
                 t=MobyInteger()
-                t.fromMoby(elt.toxml())
+                t.fromMoby(elt)
                 self.Num_studies=t.content
             if elt.nodeType==elt.ELEMENT_NODE and (elt.nodeName=="String" or elt.nodeName=="moby:String") and (elt.getAttribute("articleName")=="trait_abbr" or elt.getAttribute("moby:articleName")=="trait_abbr"):
                 t=MobyString()
-                t.fromMoby(elt.toxml())
+                t.fromMoby(elt)
                 self.Trait_abbr=t.content
             if elt.nodeType==elt.ELEMENT_NODE and (elt.nodeName=="Integer" or elt.nodeName=="moby:Integer") and (elt.getAttribute("articleName")=="trait_id" or elt.getAttribute("moby:articleName")=="trait_id"):
                 t=MobyInteger()
-                t.fromMoby(elt.toxml())
+                t.fromMoby(elt)
                 self.Trait_id=t.content
             if elt.nodeType==elt.ELEMENT_NODE and (elt.nodeName=="String" or elt.nodeName=="moby:String") and (elt.getAttribute("articleName")=="trait_name" or elt.getAttribute("moby:articleName")=="trait_name"):
                 t=MobyString()
-                t.fromMoby(elt.toxml())
+                t.fromMoby(elt)
                 self.Trait_name=t.content
\ No newline at end of file

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/ontology/Tree.py,v
retrieving revision 1.4
retrieving revision 1.5
diff -u -r1.4 -r1.5
--- /home/repository/moby/moby-live/Python/bioMoby/ontology/Tree.py	2005/02/01 08:52:16	1.4
+++ /home/repository/moby/moby-live/Python/bioMoby/ontology/Tree.py	2005/02/01 14:20:44	1.5
@@ -26,7 +26,9 @@
         """ Load the attributes from an XML string
         """
         from bioMoby.mobyMarshal import MobyUnmarshaller
-        doc=parseString(value).firstChild
+        doc=value
+        if isinstance(value, str):
+            doc=parseString(value).firstChild
         um=MobyUnmarshaller()
         self.content=""
         self.namespace=doc.getAttribute("moby:namespace")
@@ -46,4 +48,4 @@
             if elt.nodeName=="CrossReference" or elt.nodeName=="moby:CrossReference":
                 self.__cross__=[]
                 for ref in elt.childNodes:
-                    self.__cross__.append(ref.toxml())
\ No newline at end of file
+                    self.__cross__.append(um.loads(ref))
\ No newline at end of file

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/ontology/TropGENE_ACCESSION.py,v
retrieving revision 1.4
retrieving revision 1.5
diff -u -r1.4 -r1.5
--- /home/repository/moby/moby-live/Python/bioMoby/ontology/TropGENE_ACCESSION.py	2005/02/01 08:52:16	1.4
+++ /home/repository/moby/moby-live/Python/bioMoby/ontology/TropGENE_ACCESSION.py	2005/02/01 14:20:44	1.5
@@ -36,7 +36,9 @@
         """ Load the attributes from an XML string
         """
         from bioMoby.mobyMarshal import MobyUnmarshaller
-        doc=parseString(value).firstChild
+        doc=value
+        if isinstance(value, str):
+            doc=parseString(value).firstChild
         um=MobyUnmarshaller()
         self.content=""
         self.namespace=doc.getAttribute("moby:namespace")
@@ -66,34 +68,34 @@
             if elt.nodeName=="CrossReference" or elt.nodeName=="moby:CrossReference":
                 self.__cross__=[]
                 for ref in elt.childNodes:
-                    self.__cross__.append(ref.toxml())
+                    self.__cross__.append(um.loads(ref))
             if elt.nodeType==elt.ELEMENT_NODE and (elt.nodeName=="TropGENE_LOCUS" or elt.nodeName=="moby:TropGENE_LOCUS") and (elt.getAttribute("articleName")=="RFLP" or elt.getAttribute("moby:articleName")=="RFLP"):
                 self.RFLP=MobyTropGENE_LOCUS()
-                self.RFLP.fromMoby(elt.toxml())
+                self.RFLP.fromMoby(elt)
             if elt.nodeType==elt.ELEMENT_NODE and (elt.nodeName=="TropGENE_LOCUS" or elt.nodeName=="moby:TropGENE_LOCUS") and (elt.getAttribute("articleName")=="AFLP" or elt.getAttribute("moby:articleName")=="AFLP"):
                 self.AFLP=MobyTropGENE_LOCUS()
-                self.AFLP.fromMoby(elt.toxml())
+                self.AFLP.fromMoby(elt)
             if elt.nodeType==elt.ELEMENT_NODE and (elt.nodeName=="TropGENE_LOCUS" or elt.nodeName=="moby:TropGENE_LOCUS") and (elt.getAttribute("articleName")=="RAPD" or elt.getAttribute("moby:articleName")=="RAPD"):
                 self.RAPD=MobyTropGENE_LOCUS()
-                self.RAPD.fromMoby(elt.toxml())
+                self.RAPD.fromMoby(elt)
             if elt.nodeType==elt.ELEMENT_NODE and (elt.nodeName=="TropGENE_LOCUS" or elt.nodeName=="moby:TropGENE_LOCUS") and (elt.getAttribute("articleName")=="Isozyme" or elt.getAttribute("moby:articleName")=="Isozyme"):
                 self.Isozyme=MobyTropGENE_LOCUS()
-                self.Isozyme.fromMoby(elt.toxml())
+                self.Isozyme.fromMoby(elt)
             if elt.nodeType==elt.ELEMENT_NODE and (elt.nodeName=="TropGENE_LOCUS" or elt.nodeName=="moby:TropGENE_LOCUS") and (elt.getAttribute("articleName")=="Polyphenol" or elt.getAttribute("moby:articleName")=="Polyphenol"):
                 self.Polyphenol=MobyTropGENE_LOCUS()
-                self.Polyphenol.fromMoby(elt.toxml())
+                self.Polyphenol.fromMoby(elt)
             if elt.nodeType==elt.ELEMENT_NODE and (elt.nodeName=="TropGENE_LOCUS" or elt.nodeName=="moby:TropGENE_LOCUS") and (elt.getAttribute("articleName")=="Morphological" or elt.getAttribute("moby:articleName")=="Morphological"):
                 self.Morphological=MobyTropGENE_LOCUS()
-                self.Morphological.fromMoby(elt.toxml())
+                self.Morphological.fromMoby(elt)
             if elt.nodeType==elt.ELEMENT_NODE and (elt.nodeName=="TropGENE_LOCUS" or elt.nodeName=="moby:TropGENE_LOCUS") and (elt.getAttribute("articleName")=="Microsatellite" or elt.getAttribute("moby:articleName")=="Microsatellite"):
                 self.Microsatellite=MobyTropGENE_LOCUS()
-                self.Microsatellite.fromMoby(elt.toxml())
+                self.Microsatellite.fromMoby(elt)
             if elt.nodeType==elt.ELEMENT_NODE and (elt.nodeName=="TropGENE_LOCUS" or elt.nodeName=="moby:TropGENE_LOCUS") and (elt.getAttribute("articleName")=="SNP" or elt.getAttribute("moby:articleName")=="SNP"):
                 self.SNP=MobyTropGENE_LOCUS()
-                self.SNP.fromMoby(elt.toxml())
+                self.SNP.fromMoby(elt)
             if elt.nodeType==elt.ELEMENT_NODE and (elt.nodeName=="TropGENE_LOCUS" or elt.nodeName=="moby:TropGENE_LOCUS") and (elt.getAttribute("articleName")=="CAPS" or elt.getAttribute("moby:articleName")=="CAPS"):
                 self.CAPS=MobyTropGENE_LOCUS()
-                self.CAPS.fromMoby(elt.toxml())
+                self.CAPS.fromMoby(elt)
             if elt.nodeType==elt.ELEMENT_NODE and (elt.nodeName=="TropGENE_LOCUS" or elt.nodeName=="moby:TropGENE_LOCUS") and (elt.getAttribute("articleName")=="TAMPL" or elt.getAttribute("moby:articleName")=="TAMPL"):
                 self.TAMPL=MobyTropGENE_LOCUS()
-                self.TAMPL.fromMoby(elt.toxml())
\ No newline at end of file
+                self.TAMPL.fromMoby(elt)
\ No newline at end of file

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/ontology/TropGENE_Diversity_Matrix.py,v
retrieving revision 1.4
retrieving revision 1.5
diff -u -r1.4 -r1.5
--- /home/repository/moby/moby-live/Python/bioMoby/ontology/TropGENE_Diversity_Matrix.py	2005/02/01 08:52:16	1.4
+++ /home/repository/moby/moby-live/Python/bioMoby/ontology/TropGENE_Diversity_Matrix.py	2005/02/01 14:20:44	1.5
@@ -26,7 +26,9 @@
         """ Load the attributes from an XML string
         """
         from bioMoby.mobyMarshal import MobyUnmarshaller
-        doc=parseString(value).firstChild
+        doc=value
+        if isinstance(value, str):
+            doc=parseString(value).firstChild
         um=MobyUnmarshaller()
         self.content=""
         self.namespace=doc.getAttribute("moby:namespace")
@@ -46,4 +48,4 @@
             if elt.nodeName=="CrossReference" or elt.nodeName=="moby:CrossReference":
                 self.__cross__=[]
                 for ref in elt.childNodes:
-                    self.__cross__.append(ref.toxml())
\ No newline at end of file
+                    self.__cross__.append(um.loads(ref))
\ No newline at end of file

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/ontology/TropGENE_LOCUS.py,v
retrieving revision 1.4
retrieving revision 1.5
diff -u -r1.4 -r1.5
--- /home/repository/moby/moby-live/Python/bioMoby/ontology/TropGENE_LOCUS.py	2005/02/01 08:52:16	1.4
+++ /home/repository/moby/moby-live/Python/bioMoby/ontology/TropGENE_LOCUS.py	2005/02/01 14:20:44	1.5
@@ -25,7 +25,9 @@
         """ Load the attributes from an XML string
         """
         from bioMoby.mobyMarshal import MobyUnmarshaller
-        doc=parseString(value).firstChild
+        doc=value
+        if isinstance(value, str):
+            doc=parseString(value).firstChild
         um=MobyUnmarshaller()
         self.content=""
         self.namespace=doc.getAttribute("moby:namespace")
@@ -45,4 +47,4 @@
             if elt.nodeName=="CrossReference" or elt.nodeName=="moby:CrossReference":
                 self.__cross__=[]
                 for ref in elt.childNodes:
-                    self.__cross__.append(ref.toxml())
\ No newline at end of file
+                    self.__cross__.append(um.loads(ref))
\ No newline at end of file

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/ontology/VirtualSequence.py,v
retrieving revision 1.4
retrieving revision 1.5
diff -u -r1.4 -r1.5
--- /home/repository/moby/moby-live/Python/bioMoby/ontology/VirtualSequence.py	2005/02/01 08:52:16	1.4
+++ /home/repository/moby/moby-live/Python/bioMoby/ontology/VirtualSequence.py	2005/02/01 14:20:44	1.5
@@ -27,7 +27,9 @@
         """ Load the attributes from an XML string
         """
         from bioMoby.mobyMarshal import MobyUnmarshaller
-        doc=parseString(value).firstChild
+        doc=value
+        if isinstance(value, str):
+            doc=parseString(value).firstChild
         um=MobyUnmarshaller()
         self.content=""
         self.namespace=doc.getAttribute("moby:namespace")
@@ -47,8 +49,8 @@
             if elt.nodeName=="CrossReference" or elt.nodeName=="moby:CrossReference":
                 self.__cross__=[]
                 for ref in elt.childNodes:
-                    self.__cross__.append(ref.toxml())
+                    self.__cross__.append(um.loads(ref))
             if elt.nodeType==elt.ELEMENT_NODE and (elt.nodeName=="Integer" or elt.nodeName=="moby:Integer") and (elt.getAttribute("articleName")=="Length" or elt.getAttribute("moby:articleName")=="Length"):
                 t=MobyInteger()
-                t.fromMoby(elt.toxml())
+                t.fromMoby(elt)
                 self.Length=t.content
\ No newline at end of file

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/ontology/WU_BLAST_Text.py,v
retrieving revision 1.4
retrieving revision 1.5
diff -u -r1.4 -r1.5
--- /home/repository/moby/moby-live/Python/bioMoby/ontology/WU_BLAST_Text.py	2005/02/01 08:52:16	1.4
+++ /home/repository/moby/moby-live/Python/bioMoby/ontology/WU_BLAST_Text.py	2005/02/01 14:20:44	1.5
@@ -26,7 +26,9 @@
         """ Load the attributes from an XML string
         """
         from bioMoby.mobyMarshal import MobyUnmarshaller
-        doc=parseString(value).firstChild
+        doc=value
+        if isinstance(value, str):
+            doc=parseString(value).firstChild
         um=MobyUnmarshaller()
         self.content=""
         self.namespace=doc.getAttribute("moby:namespace")
@@ -46,4 +48,4 @@
             if elt.nodeName=="CrossReference" or elt.nodeName=="moby:CrossReference":
                 self.__cross__=[]
                 for ref in elt.childNodes:
-                    self.__cross__.append(ref.toxml())
\ No newline at end of file
+                    self.__cross__.append(um.loads(ref))
\ No newline at end of file

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/ontology/Wildcard_Query.py,v
retrieving revision 1.4
retrieving revision 1.5
diff -u -r1.4 -r1.5
--- /home/repository/moby/moby-live/Python/bioMoby/ontology/Wildcard_Query.py	2005/02/01 08:52:16	1.4
+++ /home/repository/moby/moby-live/Python/bioMoby/ontology/Wildcard_Query.py	2005/02/01 14:20:44	1.5
@@ -30,7 +30,9 @@
         """ Load the attributes from an XML string
         """
         from bioMoby.mobyMarshal import MobyUnmarshaller
-        doc=parseString(value).firstChild
+        doc=value
+        if isinstance(value, str):
+            doc=parseString(value).firstChild
         um=MobyUnmarshaller()
         self.content=""
         self.namespace=doc.getAttribute("moby:namespace")
@@ -50,16 +52,16 @@
             if elt.nodeName=="CrossReference" or elt.nodeName=="moby:CrossReference":
                 self.__cross__=[]
                 for ref in elt.childNodes:
-                    self.__cross__.append(ref.toxml())
+                    self.__cross__.append(um.loads(ref))
             if elt.nodeType==elt.ELEMENT_NODE and (elt.nodeName=="Integer" or elt.nodeName=="moby:Integer") and (elt.getAttribute("articleName")=="end_row" or elt.getAttribute("moby:articleName")=="end_row"):
                 t=MobyInteger()
-                t.fromMoby(elt.toxml())
+                t.fromMoby(elt)
                 self.End_row=t.content
             if elt.nodeType==elt.ELEMENT_NODE and (elt.nodeName=="Integer" or elt.nodeName=="moby:Integer") and (elt.getAttribute("articleName")=="start_row" or elt.getAttribute("moby:articleName")=="start_row"):
                 t=MobyInteger()
-                t.fromMoby(elt.toxml())
+                t.fromMoby(elt)
                 self.Start_row=t.content
             if elt.nodeType==elt.ELEMENT_NODE and (elt.nodeName=="String" or elt.nodeName=="moby:String") and (elt.getAttribute("articleName")=="germplasm_name" or elt.getAttribute("moby:articleName")=="germplasm_name"):
                 t=MobyString()
-                t.fromMoby(elt.toxml())
+                t.fromMoby(elt)
                 self.Germplasm_name=t.content
\ No newline at end of file

From yanwong at pub.open-bio.org  Mon Feb  7 09:12:35 2005
From: yanwong at pub.open-bio.org (Yan Wong)
Date: Thu Apr 14 12:22:58 2005
Subject: [MOBY-guts] biomoby commit
Message-ID: <200502071423.j17ENYJS018965@pub.open-bio.org>


yanwong
Mon Feb  7 09:23:33 EST 2005
Update of /home/repository/moby/moby-live/Python/bioMoby/ontology
In directory pub.open-bio.org:/tmp/cvs-serv18508

Modified Files:
	Alignment.py AlleleAssociation.py Allele_freq.py 
	AminoAcidSequence.py B64_Encoded_PNG.py 
	B64_Encoded_Postscript.py B64_encoded_PDB.py 
	B64_encoded_gif.py B64_encoded_jpeg.py BLASTText.py 
	BasicGFFSequenceFeature.py ClustalAlnFormattedText.py 
	ClustalMsfFormattedText.py CommentedAASequence.py 
	CommentedDNASequence.py CommentedRNASequence.py DNASequence.py 
	DNASequenceWithGFFFeatures.py DateTime.py Decypher_Text.py 
	Edge.py EmblFlatfile.py FASTA.py FASTA_AA.py FASTA_NA.py 
	FASTA_NA_multi.py FASTA_Text.py GFF.py GFF1.py GFF2.py 
	GFF2_5.py GFF3.py GO_Term.py GenbankFlatfile.py 
	Gene_Expression_data.py GenericSequence.py GeneticElement.py 
	Genotype.py Germplasm_Details.py Germplasm_List.py 
	Global_Keyword.py HBond_Pair.py HFormatText.py 
	Haplotyping_Study_obj.py ICIS_Query.py ICIS_Query2.py 
	ICIS_Query3.py IntAct_XML.py Interaction.py 
	InteractionMethod.py Interaction_partner.py Interactor.py 
	MEME_Text.py MGIS_ACCESSION.py MMP_Locus.py MO_Term_Test.py 
	MSF.py MmCIFText.py Multi_key_value_pair.py 
	MyTestingDataType_11024145298313.py MyTree.py 
	NCBI_BLAST_Text.py NCBI_Blast_XML.py NCBI_Blast_XML_Gif.py 
	NCBI_Blast_XML_Gif_Map.py NCBI_MEME_Text.py 
	NucleotideSequence.py PDBFormattedText.py PDBText.py PDGJOB.py 
	PHDText.py PMUTText.py PSeaTextFormatted.py 
	PhenotypeDescription.py PubMedMEDLINE.py RNASequence.py 
	SINGER_ACCESSION.py Sample.py SchematikonMotifID.py 
	SchematikonMotifSupport.py SchematikonSegmentAttributes.py 
	SchematikonSegmentID.py SchematikonStructureAnnotation.py 
	SchematikonVorocodeName.py Scored_acronym_string.py 
	SimpleAnnotatedGIFImage.py SimpleAnnotatedJPEGImage.py 
	Simple_key_value_pair.py Snp_allele.py Snp_genotype.py 
	Study.py TEST.py TargetP_result.py Testout.py TextBase64.py 
	TextFormatted.py TextHtml.py TextPlain.py TextUuencoded.py 
	TextXml.py Text_plain.py Trait_Details.py Tree.py 
	TropGENE_ACCESSION.py TropGENE_Diversity_Matrix.py 
	TropGENE_LOCUS.py VirtualSequence.py WU_BLAST_Text.py 
	Wildcard_Query.py 
Log Message:


moby-live/Python/bioMoby/ontology Alignment.py,1.1,1.2 AlleleAssociation.py,1.5,1.6 Allele_freq.py,1.5,1.6 AminoAcidSequence.py,1.5,1.6 B64_Encoded_PNG.py,1.5,1.6 B64_Encoded_Postscript.py,1.5,1.6 B64_encoded_PDB.py,1.5,1.6 B64_encoded_gif.py,1.5,1.6 B64_encoded_jpeg.py,1.5,1.6 BLASTText.py,1.5,1.6 BasicGFFSequenceFeature.py,1.5,1.6 ClustalAlnFormattedText.py,1.5,1.6 ClustalMsfFormattedText.py,1.5,1.6 CommentedAASequence.py,1.5,1.6 CommentedDNASequence.py,1.5,1.6 CommentedRNASequence.py,1.5,1.6 DNASequence.py,1.5,1.6 DNASequenceWithGFFFeatures.py,1.5,1.6 DateTime.py,1.5,1.6 Decypher_Text.py,1.5,1.6 Edge.py,1.5,1.6 EmblFlatfile.py,1.5,1.6 FASTA.py,1.5,1.6 FASTA_AA.py,1.5,1.6 FASTA_NA.py,1.5,1.6 FASTA_NA_multi.py,1.1,1.2 FASTA_Text.py,1.5,1.6 GFF.py,1.5,1.6 GFF1.py,1.5,1.6 GFF2.py,1.5,1.6 GFF2_5.py,1.5,1.6 GFF3.py,1.5,1.6 GO_Term.py,1.5,1.6 GenbankFlatfile.py,1.5,1.6 Gene_Expression_data.py,1.1,1.2 GenericSequence.py,1.5,1.6 GeneticElement.py,1.5,1.6 Genotype.py,1.5,1.6 Germpl!
asm_Details.py,1.5,1.6 Germplasm_List.py,1.5,1.6 Global_Keyword.py,1.5,1.6 HBond_Pair.py,1.5,1.6 HFormatText.py,1.5,1.6 Haplotyping_Study_obj.py,1.5,1.6 ICIS_Query.py,1.5,1.6 ICIS_Query2.py,1.5,1.6 ICIS_Query3.py,1.5,1.6 IntAct_XML.py,1.5,1.6 Interaction.py,1.5,1.6 InteractionMethod.py,1.5,1.6 Interaction_partner.py,1.5,1.6 Interactor.py,1.5,1.6 MEME_Text.py,1.5,1.6 MGIS_ACCESSION.py,1.5,1.6 MMP_Locus.py,1.5,1.6 MO_Term_Test.py,1.5,1.6 MSF.py,1.1,1.2 MmCIFText.py,1.5,1.6 Multi_key_value_pair.py,1.5,1.6 MyTestingDataType_11024145298313.py,1.5,1.6 MyTree.py,1.5,1.6 NCBI_BLAST_Text.py,1.5,1.6 NCBI_Blast_XML.py,1.5,1.6 NCBI_Blast_XML_Gif.py,1.5,1.6 NCBI_Blast_XML_Gif_Map.py,1.5,1.6 NCBI_MEME_Text.py,1.5,1.6 NucleotideSequence.py,1.5,1.6 PDBFormattedText.py,1.5,1.6 PDBText.py,1.5,1.6 PDGJOB.py,1.5,1.6 PHDText.py,1.5,1.6 PMUTText.py,1.5,1.6 PSeaTextFormatted.py,1.5,1.6 PhenotypeDescription.py,1.5,1.6 PubMedMEDLINE.py,1.5,1.6 RNASequence.py,1.5,1.6 SINGER_ACCESSION.py,1.5,1.6 Sampl!
e.py,1.5,1.6 SchematikonMotifID.py,1.5,1.6 SchematikonMotifSu!
pport.py,1.5,1.6 SchematikonSegmentAttributes.py,1.5,1.6 SchematikonSegmentID.py,1.5,1.6 SchematikonStructureAnnotation.py,1.5,1.6 SchematikonVorocodeName.py,1.5,1.6 Scored_acronym_string.py,1.5,1.6 SimpleAnnotatedGIFImage.py,1.5,1.6 SimpleAnnotatedJPEGImage.py,1.5,1.6 Simple_key_value_pair.py,1.5,1.6 Snp_allele.py,1.5,1.6 Snp_genotype.py,1.5,1.6 Study.py,1.5,1.6 TEST.py,1.5,1.6 TargetP_result.py,1.5,1.6 Testout.py,1.5,1.6 TextBase64.py,1.5,1.6 TextFormatted.py,1.5,1.6 TextHtml.py,1.5,1.6 TextPlain.py,1.5,1.6 TextUuencoded.py,1.5,1.6 TextXml.py,1.5,1.6 Text_plain.py,1.5,1.6 Trait_Details.py,1.5,1.6 Tree.py,1.5,1.6 TropGENE_ACCESSION.py,1.5,1.6 TropGENE_Diversity_Matrix.py,1.5,1.6 TropGENE_LOCUS.py,1.5,1.6 VirtualSequence.py,1.5,1.6 WU_BLAST_Text.py,1.5,1.6 Wildcard_Query.py,1.5,1.6
===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/ontology/Alignment.py,v
retrieving revision 1.1
retrieving revision 1.2
diff -u -r1.1 -r1.2
--- /home/repository/moby/moby-live/Python/bioMoby/ontology/Alignment.py	2005/02/02 15:18:06	1.1
+++ /home/repository/moby/moby-live/Python/bioMoby/ontology/Alignment.py	2005/02/07 14:23:32	1.2
@@ -48,4 +48,5 @@
             if elt.nodeName=="CrossReference" or elt.nodeName=="moby:CrossReference":
                 self.__cross__=[]
                 for ref in elt.childNodes:
-                    self.__cross__.append(um.loads(ref))
\ No newline at end of file
+                    if ref.nodeType==ref.ELEMENT_NODE:
+                        self.__cross__.append(um.loadn(ref))
\ No newline at end of file

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/ontology/AlleleAssociation.py,v
retrieving revision 1.5
retrieving revision 1.6
diff -u -r1.5 -r1.6
--- /home/repository/moby/moby-live/Python/bioMoby/ontology/AlleleAssociation.py	2005/02/01 14:20:44	1.5
+++ /home/repository/moby/moby-live/Python/bioMoby/ontology/AlleleAssociation.py	2005/02/07 14:23:32	1.6
@@ -52,7 +52,8 @@
             if elt.nodeName=="CrossReference" or elt.nodeName=="moby:CrossReference":
                 self.__cross__=[]
                 for ref in elt.childNodes:
-                    self.__cross__.append(um.loads(ref))
+                    if ref.nodeType==ref.ELEMENT_NODE:
+                        self.__cross__.append(um.loadn(ref))
             if elt.nodeType==elt.ELEMENT_NODE and (elt.nodeName=="String" or elt.nodeName=="moby:String") and (elt.getAttribute("articleName")=="snp" or elt.getAttribute("moby:articleName")=="snp"):
                 t=MobyString()
                 t.fromMoby(elt)

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/ontology/Allele_freq.py,v
retrieving revision 1.5
retrieving revision 1.6
diff -u -r1.5 -r1.6
--- /home/repository/moby/moby-live/Python/bioMoby/ontology/Allele_freq.py	2005/02/01 14:20:44	1.5
+++ /home/repository/moby/moby-live/Python/bioMoby/ontology/Allele_freq.py	2005/02/07 14:23:32	1.6
@@ -46,7 +46,8 @@
             if elt.nodeName=="CrossReference" or elt.nodeName=="moby:CrossReference":
                 self.__cross__=[]
                 for ref in elt.childNodes:
-                    self.__cross__.append(um.loads(ref))
+                    if ref.nodeType==ref.ELEMENT_NODE:
+                        self.__cross__.append(um.loadn(ref))
             if elt.nodeType==elt.ELEMENT_NODE and (elt.nodeName=="Object" or elt.nodeName=="moby:Object") and (elt.getAttribute("articleName")=="panel_lsid" or elt.getAttribute("moby:articleName")=="panel_lsid"):
                 self.Panel_lsid=MobyObject()
                 self.Panel_lsid.fromMoby(elt)

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/ontology/AminoAcidSequence.py,v
retrieving revision 1.5
retrieving revision 1.6
diff -u -r1.5 -r1.6
--- /home/repository/moby/moby-live/Python/bioMoby/ontology/AminoAcidSequence.py	2005/02/01 14:20:44	1.5
+++ /home/repository/moby/moby-live/Python/bioMoby/ontology/AminoAcidSequence.py	2005/02/07 14:23:32	1.6
@@ -51,7 +51,8 @@
             if elt.nodeName=="CrossReference" or elt.nodeName=="moby:CrossReference":
                 self.__cross__=[]
                 for ref in elt.childNodes:
-                    self.__cross__.append(um.loads(ref))
+                    if ref.nodeType==ref.ELEMENT_NODE:
+                        self.__cross__.append(um.loadn(ref))
             if elt.nodeType==elt.ELEMENT_NODE and (elt.nodeName=="Integer" or elt.nodeName=="moby:Integer") and (elt.getAttribute("articleName")=="Length" or elt.getAttribute("moby:articleName")=="Length"):
                 t=MobyInteger()
                 t.fromMoby(elt)

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/ontology/B64_Encoded_PNG.py,v
retrieving revision 1.5
retrieving revision 1.6
diff -u -r1.5 -r1.6
--- /home/repository/moby/moby-live/Python/bioMoby/ontology/B64_Encoded_PNG.py	2005/02/01 14:20:44	1.5
+++ /home/repository/moby/moby-live/Python/bioMoby/ontology/B64_Encoded_PNG.py	2005/02/07 14:23:32	1.6
@@ -48,4 +48,5 @@
             if elt.nodeName=="CrossReference" or elt.nodeName=="moby:CrossReference":
                 self.__cross__=[]
                 for ref in elt.childNodes:
-                    self.__cross__.append(um.loads(ref))
\ No newline at end of file
+                    if ref.nodeType==ref.ELEMENT_NODE:
+                        self.__cross__.append(um.loadn(ref))
\ No newline at end of file

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/ontology/B64_Encoded_Postscript.py,v
retrieving revision 1.5
retrieving revision 1.6
diff -u -r1.5 -r1.6
--- /home/repository/moby/moby-live/Python/bioMoby/ontology/B64_Encoded_Postscript.py	2005/02/01 14:20:44	1.5
+++ /home/repository/moby/moby-live/Python/bioMoby/ontology/B64_Encoded_Postscript.py	2005/02/07 14:23:32	1.6
@@ -48,4 +48,5 @@
             if elt.nodeName=="CrossReference" or elt.nodeName=="moby:CrossReference":
                 self.__cross__=[]
                 for ref in elt.childNodes:
-                    self.__cross__.append(um.loads(ref))
\ No newline at end of file
+                    if ref.nodeType==ref.ELEMENT_NODE:
+                        self.__cross__.append(um.loadn(ref))
\ No newline at end of file

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/ontology/B64_encoded_PDB.py,v
retrieving revision 1.5
retrieving revision 1.6
diff -u -r1.5 -r1.6
--- /home/repository/moby/moby-live/Python/bioMoby/ontology/B64_encoded_PDB.py	2005/02/01 14:20:44	1.5
+++ /home/repository/moby/moby-live/Python/bioMoby/ontology/B64_encoded_PDB.py	2005/02/07 14:23:32	1.6
@@ -48,4 +48,5 @@
             if elt.nodeName=="CrossReference" or elt.nodeName=="moby:CrossReference":
                 self.__cross__=[]
                 for ref in elt.childNodes:
-                    self.__cross__.append(um.loads(ref))
\ No newline at end of file
+                    if ref.nodeType==ref.ELEMENT_NODE:
+                        self.__cross__.append(um.loadn(ref))
\ No newline at end of file

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/ontology/B64_encoded_gif.py,v
retrieving revision 1.5
retrieving revision 1.6
diff -u -r1.5 -r1.6
--- /home/repository/moby/moby-live/Python/bioMoby/ontology/B64_encoded_gif.py	2005/02/01 14:20:44	1.5
+++ /home/repository/moby/moby-live/Python/bioMoby/ontology/B64_encoded_gif.py	2005/02/07 14:23:32	1.6
@@ -48,4 +48,5 @@
             if elt.nodeName=="CrossReference" or elt.nodeName=="moby:CrossReference":
                 self.__cross__=[]
                 for ref in elt.childNodes:
-                    self.__cross__.append(um.loads(ref))
\ No newline at end of file
+                    if ref.nodeType==ref.ELEMENT_NODE:
+                        self.__cross__.append(um.loadn(ref))
\ No newline at end of file

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/ontology/B64_encoded_jpeg.py,v
retrieving revision 1.5
retrieving revision 1.6
diff -u -r1.5 -r1.6
--- /home/repository/moby/moby-live/Python/bioMoby/ontology/B64_encoded_jpeg.py	2005/02/01 14:20:44	1.5
+++ /home/repository/moby/moby-live/Python/bioMoby/ontology/B64_encoded_jpeg.py	2005/02/07 14:23:32	1.6
@@ -48,4 +48,5 @@
             if elt.nodeName=="CrossReference" or elt.nodeName=="moby:CrossReference":
                 self.__cross__=[]
                 for ref in elt.childNodes:
-                    self.__cross__.append(um.loads(ref))
\ No newline at end of file
+                    if ref.nodeType==ref.ELEMENT_NODE:
+                        self.__cross__.append(um.loadn(ref))
\ No newline at end of file

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/ontology/BLASTText.py,v
retrieving revision 1.5
retrieving revision 1.6
diff -u -r1.5 -r1.6
--- /home/repository/moby/moby-live/Python/bioMoby/ontology/BLASTText.py	2005/02/01 14:20:44	1.5
+++ /home/repository/moby/moby-live/Python/bioMoby/ontology/BLASTText.py	2005/02/07 14:23:32	1.6
@@ -48,4 +48,5 @@
             if elt.nodeName=="CrossReference" or elt.nodeName=="moby:CrossReference":
                 self.__cross__=[]
                 for ref in elt.childNodes:
-                    self.__cross__.append(um.loads(ref))
\ No newline at end of file
+                    if ref.nodeType==ref.ELEMENT_NODE:
+                        self.__cross__.append(um.loadn(ref))
\ No newline at end of file

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/ontology/BasicGFFSequenceFeature.py,v
retrieving revision 1.5
retrieving revision 1.6
diff -u -r1.5 -r1.6
--- /home/repository/moby/moby-live/Python/bioMoby/ontology/BasicGFFSequenceFeature.py	2005/02/01 14:20:44	1.5
+++ /home/repository/moby/moby-live/Python/bioMoby/ontology/BasicGFFSequenceFeature.py	2005/02/07 14:23:32	1.6
@@ -62,7 +62,8 @@
             if elt.nodeName=="CrossReference" or elt.nodeName=="moby:CrossReference":
                 self.__cross__=[]
                 for ref in elt.childNodes:
-                    self.__cross__.append(um.loads(ref))
+                    if ref.nodeType==ref.ELEMENT_NODE:
+                        self.__cross__.append(um.loadn(ref))
             if elt.nodeType==elt.ELEMENT_NODE and (elt.nodeName=="String" or elt.nodeName=="moby:String") and (elt.getAttribute("articleName")=="reference" or elt.getAttribute("moby:articleName")=="reference"):
                 t=MobyString()
                 t.fromMoby(elt)

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/ontology/ClustalAlnFormattedText.py,v
retrieving revision 1.5
retrieving revision 1.6
diff -u -r1.5 -r1.6
--- /home/repository/moby/moby-live/Python/bioMoby/ontology/ClustalAlnFormattedText.py	2005/02/01 14:20:44	1.5
+++ /home/repository/moby/moby-live/Python/bioMoby/ontology/ClustalAlnFormattedText.py	2005/02/07 14:23:32	1.6
@@ -48,4 +48,5 @@
             if elt.nodeName=="CrossReference" or elt.nodeName=="moby:CrossReference":
                 self.__cross__=[]
                 for ref in elt.childNodes:
-                    self.__cross__.append(um.loads(ref))
\ No newline at end of file
+                    if ref.nodeType==ref.ELEMENT_NODE:
+                        self.__cross__.append(um.loadn(ref))
\ No newline at end of file

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/ontology/ClustalMsfFormattedText.py,v
retrieving revision 1.5
retrieving revision 1.6
diff -u -r1.5 -r1.6
--- /home/repository/moby/moby-live/Python/bioMoby/ontology/ClustalMsfFormattedText.py	2005/02/01 14:20:44	1.5
+++ /home/repository/moby/moby-live/Python/bioMoby/ontology/ClustalMsfFormattedText.py	2005/02/07 14:23:32	1.6
@@ -48,4 +48,5 @@
             if elt.nodeName=="CrossReference" or elt.nodeName=="moby:CrossReference":
                 self.__cross__=[]
                 for ref in elt.childNodes:
-                    self.__cross__.append(um.loads(ref))
\ No newline at end of file
+                    if ref.nodeType==ref.ELEMENT_NODE:
+                        self.__cross__.append(um.loadn(ref))
\ No newline at end of file

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/ontology/CommentedAASequence.py,v
retrieving revision 1.5
retrieving revision 1.6
diff -u -r1.5 -r1.6
--- /home/repository/moby/moby-live/Python/bioMoby/ontology/CommentedAASequence.py	2005/02/01 14:20:44	1.5
+++ /home/repository/moby/moby-live/Python/bioMoby/ontology/CommentedAASequence.py	2005/02/07 14:23:32	1.6
@@ -52,7 +52,8 @@
             if elt.nodeName=="CrossReference" or elt.nodeName=="moby:CrossReference":
                 self.__cross__=[]
                 for ref in elt.childNodes:
-                    self.__cross__.append(um.loads(ref))
+                    if ref.nodeType==ref.ELEMENT_NODE:
+                        self.__cross__.append(um.loadn(ref))
             if elt.nodeType==elt.ELEMENT_NODE and (elt.nodeName=="Integer" or elt.nodeName=="moby:Integer") and (elt.getAttribute("articleName")=="Length" or elt.getAttribute("moby:articleName")=="Length"):
                 t=MobyInteger()
                 t.fromMoby(elt)

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/ontology/CommentedDNASequence.py,v
retrieving revision 1.5
retrieving revision 1.6
diff -u -r1.5 -r1.6
--- /home/repository/moby/moby-live/Python/bioMoby/ontology/CommentedDNASequence.py	2005/02/01 14:20:44	1.5
+++ /home/repository/moby/moby-live/Python/bioMoby/ontology/CommentedDNASequence.py	2005/02/07 14:23:32	1.6
@@ -52,7 +52,8 @@
             if elt.nodeName=="CrossReference" or elt.nodeName=="moby:CrossReference":
                 self.__cross__=[]
                 for ref in elt.childNodes:
-                    self.__cross__.append(um.loads(ref))
+                    if ref.nodeType==ref.ELEMENT_NODE:
+                        self.__cross__.append(um.loadn(ref))
             if elt.nodeType==elt.ELEMENT_NODE and (elt.nodeName=="Integer" or elt.nodeName=="moby:Integer") and (elt.getAttribute("articleName")=="Length" or elt.getAttribute("moby:articleName")=="Length"):
                 t=MobyInteger()
                 t.fromMoby(elt)

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/ontology/CommentedRNASequence.py,v
retrieving revision 1.5
retrieving revision 1.6
diff -u -r1.5 -r1.6
--- /home/repository/moby/moby-live/Python/bioMoby/ontology/CommentedRNASequence.py	2005/02/01 14:20:44	1.5
+++ /home/repository/moby/moby-live/Python/bioMoby/ontology/CommentedRNASequence.py	2005/02/07 14:23:32	1.6
@@ -52,7 +52,8 @@
             if elt.nodeName=="CrossReference" or elt.nodeName=="moby:CrossReference":
                 self.__cross__=[]
                 for ref in elt.childNodes:
-                    self.__cross__.append(um.loads(ref))
+                    if ref.nodeType==ref.ELEMENT_NODE:
+                        self.__cross__.append(um.loadn(ref))
             if elt.nodeType==elt.ELEMENT_NODE and (elt.nodeName=="Integer" or elt.nodeName=="moby:Integer") and (elt.getAttribute("articleName")=="Length" or elt.getAttribute("moby:articleName")=="Length"):
                 t=MobyInteger()
                 t.fromMoby(elt)

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/ontology/DNASequence.py,v
retrieving revision 1.5
retrieving revision 1.6
diff -u -r1.5 -r1.6
--- /home/repository/moby/moby-live/Python/bioMoby/ontology/DNASequence.py	2005/02/01 14:20:44	1.5
+++ /home/repository/moby/moby-live/Python/bioMoby/ontology/DNASequence.py	2005/02/07 14:23:32	1.6
@@ -51,7 +51,8 @@
             if elt.nodeName=="CrossReference" or elt.nodeName=="moby:CrossReference":
                 self.__cross__=[]
                 for ref in elt.childNodes:
-                    self.__cross__.append(um.loads(ref))
+                    if ref.nodeType==ref.ELEMENT_NODE:
+                        self.__cross__.append(um.loadn(ref))
             if elt.nodeType==elt.ELEMENT_NODE and (elt.nodeName=="Integer" or elt.nodeName=="moby:Integer") and (elt.getAttribute("articleName")=="Length" or elt.getAttribute("moby:articleName")=="Length"):
                 t=MobyInteger()
                 t.fromMoby(elt)

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/ontology/DNASequenceWithGFFFeatures.py,v
retrieving revision 1.5
retrieving revision 1.6
diff -u -r1.5 -r1.6
--- /home/repository/moby/moby-live/Python/bioMoby/ontology/DNASequenceWithGFFFeatures.py	2005/02/01 14:20:44	1.5
+++ /home/repository/moby/moby-live/Python/bioMoby/ontology/DNASequenceWithGFFFeatures.py	2005/02/07 14:23:33	1.6
@@ -54,7 +54,8 @@
             if elt.nodeName=="CrossReference" or elt.nodeName=="moby:CrossReference":
                 self.__cross__=[]
                 for ref in elt.childNodes:
-                    self.__cross__.append(um.loads(ref))
+                    if ref.nodeType==ref.ELEMENT_NODE:
+                        self.__cross__.append(um.loadn(ref))
             if elt.nodeType==elt.ELEMENT_NODE and (elt.nodeName=="Integer" or elt.nodeName=="moby:Integer") and (elt.getAttribute("articleName")=="Length" or elt.getAttribute("moby:articleName")=="Length"):
                 t=MobyInteger()
                 t.fromMoby(elt)

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/ontology/DateTime.py,v
retrieving revision 1.5
retrieving revision 1.6
diff -u -r1.5 -r1.6
--- /home/repository/moby/moby-live/Python/bioMoby/ontology/DateTime.py	2005/02/01 14:20:44	1.5
+++ /home/repository/moby/moby-live/Python/bioMoby/ontology/DateTime.py	2005/02/07 14:23:33	1.6
@@ -48,4 +48,5 @@
             if elt.nodeName=="CrossReference" or elt.nodeName=="moby:CrossReference":
                 self.__cross__=[]
                 for ref in elt.childNodes:
-                    self.__cross__.append(um.loads(ref))
\ No newline at end of file
+                    if ref.nodeType==ref.ELEMENT_NODE:
+                        self.__cross__.append(um.loadn(ref))
\ No newline at end of file

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/ontology/Decypher_Text.py,v
retrieving revision 1.5
retrieving revision 1.6
diff -u -r1.5 -r1.6
--- /home/repository/moby/moby-live/Python/bioMoby/ontology/Decypher_Text.py	2005/02/01 14:20:44	1.5
+++ /home/repository/moby/moby-live/Python/bioMoby/ontology/Decypher_Text.py	2005/02/07 14:23:33	1.6
@@ -48,4 +48,5 @@
             if elt.nodeName=="CrossReference" or elt.nodeName=="moby:CrossReference":
                 self.__cross__=[]
                 for ref in elt.childNodes:
-                    self.__cross__.append(um.loads(ref))
\ No newline at end of file
+                    if ref.nodeType==ref.ELEMENT_NODE:
+                        self.__cross__.append(um.loadn(ref))
\ No newline at end of file

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/ontology/Edge.py,v
retrieving revision 1.5
retrieving revision 1.6
diff -u -r1.5 -r1.6
--- /home/repository/moby/moby-live/Python/bioMoby/ontology/Edge.py	2005/02/01 14:20:44	1.5
+++ /home/repository/moby/moby-live/Python/bioMoby/ontology/Edge.py	2005/02/07 14:23:33	1.6
@@ -51,7 +51,8 @@
             if elt.nodeName=="CrossReference" or elt.nodeName=="moby:CrossReference":
                 self.__cross__=[]
                 for ref in elt.childNodes:
-                    self.__cross__.append(um.loads(ref))
+                    if ref.nodeType==ref.ELEMENT_NODE:
+                        self.__cross__.append(um.loadn(ref))
             if elt.nodeType==elt.ELEMENT_NODE and (elt.nodeName=="String" or elt.nodeName=="moby:String") and (elt.getAttribute("articleName")=="partner" or elt.getAttribute("moby:articleName")=="partner"):
                 t=MobyString()
                 t.fromMoby(elt)

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/ontology/EmblFlatfile.py,v
retrieving revision 1.5
retrieving revision 1.6
diff -u -r1.5 -r1.6
--- /home/repository/moby/moby-live/Python/bioMoby/ontology/EmblFlatfile.py	2005/02/01 14:20:44	1.5
+++ /home/repository/moby/moby-live/Python/bioMoby/ontology/EmblFlatfile.py	2005/02/07 14:23:33	1.6
@@ -48,4 +48,5 @@
             if elt.nodeName=="CrossReference" or elt.nodeName=="moby:CrossReference":
                 self.__cross__=[]
                 for ref in elt.childNodes:
-                    self.__cross__.append(um.loads(ref))
\ No newline at end of file
+                    if ref.nodeType==ref.ELEMENT_NODE:
+                        self.__cross__.append(um.loadn(ref))
\ No newline at end of file

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/ontology/FASTA.py,v
retrieving revision 1.5
retrieving revision 1.6
diff -u -r1.5 -r1.6
--- /home/repository/moby/moby-live/Python/bioMoby/ontology/FASTA.py	2005/02/01 14:20:44	1.5
+++ /home/repository/moby/moby-live/Python/bioMoby/ontology/FASTA.py	2005/02/07 14:23:33	1.6
@@ -48,4 +48,5 @@
             if elt.nodeName=="CrossReference" or elt.nodeName=="moby:CrossReference":
                 self.__cross__=[]
                 for ref in elt.childNodes:
-                    self.__cross__.append(um.loads(ref))
\ No newline at end of file
+                    if ref.nodeType==ref.ELEMENT_NODE:
+                        self.__cross__.append(um.loadn(ref))
\ No newline at end of file

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/ontology/FASTA_AA.py,v
retrieving revision 1.5
retrieving revision 1.6
diff -u -r1.5 -r1.6
--- /home/repository/moby/moby-live/Python/bioMoby/ontology/FASTA_AA.py	2005/02/01 14:20:44	1.5
+++ /home/repository/moby/moby-live/Python/bioMoby/ontology/FASTA_AA.py	2005/02/07 14:23:33	1.6
@@ -48,4 +48,5 @@
             if elt.nodeName=="CrossReference" or elt.nodeName=="moby:CrossReference":
                 self.__cross__=[]
                 for ref in elt.childNodes:
-                    self.__cross__.append(um.loads(ref))
\ No newline at end of file
+                    if ref.nodeType==ref.ELEMENT_NODE:
+                        self.__cross__.append(um.loadn(ref))
\ No newline at end of file

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/ontology/FASTA_NA.py,v
retrieving revision 1.5
retrieving revision 1.6
diff -u -r1.5 -r1.6
--- /home/repository/moby/moby-live/Python/bioMoby/ontology/FASTA_NA.py	2005/02/01 14:20:44	1.5
+++ /home/repository/moby/moby-live/Python/bioMoby/ontology/FASTA_NA.py	2005/02/07 14:23:33	1.6
@@ -48,4 +48,5 @@
             if elt.nodeName=="CrossReference" or elt.nodeName=="moby:CrossReference":
                 self.__cross__=[]
                 for ref in elt.childNodes:
-                    self.__cross__.append(um.loads(ref))
\ No newline at end of file
+                    if ref.nodeType==ref.ELEMENT_NODE:
+                        self.__cross__.append(um.loadn(ref))
\ No newline at end of file

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/ontology/FASTA_NA_multi.py,v
retrieving revision 1.1
retrieving revision 1.2
diff -u -r1.1 -r1.2
--- /home/repository/moby/moby-live/Python/bioMoby/ontology/FASTA_NA_multi.py	2005/02/02 15:20:55	1.1
+++ /home/repository/moby/moby-live/Python/bioMoby/ontology/FASTA_NA_multi.py	2005/02/07 14:23:33	1.2
@@ -48,4 +48,5 @@
             if elt.nodeName=="CrossReference" or elt.nodeName=="moby:CrossReference":
                 self.__cross__=[]
                 for ref in elt.childNodes:
-                    self.__cross__.append(um.loads(ref))
\ No newline at end of file
+                    if ref.nodeType==ref.ELEMENT_NODE:
+                        self.__cross__.append(um.loadn(ref))
\ No newline at end of file

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/ontology/FASTA_Text.py,v
retrieving revision 1.5
retrieving revision 1.6
diff -u -r1.5 -r1.6
--- /home/repository/moby/moby-live/Python/bioMoby/ontology/FASTA_Text.py	2005/02/01 14:20:44	1.5
+++ /home/repository/moby/moby-live/Python/bioMoby/ontology/FASTA_Text.py	2005/02/07 14:23:33	1.6
@@ -48,4 +48,5 @@
             if elt.nodeName=="CrossReference" or elt.nodeName=="moby:CrossReference":
                 self.__cross__=[]
                 for ref in elt.childNodes:
-                    self.__cross__.append(um.loads(ref))
\ No newline at end of file
+                    if ref.nodeType==ref.ELEMENT_NODE:
+                        self.__cross__.append(um.loadn(ref))
\ No newline at end of file

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/ontology/GFF.py,v
retrieving revision 1.5
retrieving revision 1.6
diff -u -r1.5 -r1.6
--- /home/repository/moby/moby-live/Python/bioMoby/ontology/GFF.py	2005/02/01 14:20:44	1.5
+++ /home/repository/moby/moby-live/Python/bioMoby/ontology/GFF.py	2005/02/07 14:23:33	1.6
@@ -48,4 +48,5 @@
             if elt.nodeName=="CrossReference" or elt.nodeName=="moby:CrossReference":
                 self.__cross__=[]
                 for ref in elt.childNodes:
-                    self.__cross__.append(um.loads(ref))
\ No newline at end of file
+                    if ref.nodeType==ref.ELEMENT_NODE:
+                        self.__cross__.append(um.loadn(ref))
\ No newline at end of file

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/ontology/GFF1.py,v
retrieving revision 1.5
retrieving revision 1.6
diff -u -r1.5 -r1.6
--- /home/repository/moby/moby-live/Python/bioMoby/ontology/GFF1.py	2005/02/01 14:20:44	1.5
+++ /home/repository/moby/moby-live/Python/bioMoby/ontology/GFF1.py	2005/02/07 14:23:33	1.6
@@ -48,4 +48,5 @@
             if elt.nodeName=="CrossReference" or elt.nodeName=="moby:CrossReference":
                 self.__cross__=[]
                 for ref in elt.childNodes:
-                    self.__cross__.append(um.loads(ref))
\ No newline at end of file
+                    if ref.nodeType==ref.ELEMENT_NODE:
+                        self.__cross__.append(um.loadn(ref))
\ No newline at end of file

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/ontology/GFF2.py,v
retrieving revision 1.5
retrieving revision 1.6
diff -u -r1.5 -r1.6
--- /home/repository/moby/moby-live/Python/bioMoby/ontology/GFF2.py	2005/02/01 14:20:44	1.5
+++ /home/repository/moby/moby-live/Python/bioMoby/ontology/GFF2.py	2005/02/07 14:23:33	1.6
@@ -48,4 +48,5 @@
             if elt.nodeName=="CrossReference" or elt.nodeName=="moby:CrossReference":
                 self.__cross__=[]
                 for ref in elt.childNodes:
-                    self.__cross__.append(um.loads(ref))
\ No newline at end of file
+                    if ref.nodeType==ref.ELEMENT_NODE:
+                        self.__cross__.append(um.loadn(ref))
\ No newline at end of file

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/ontology/GFF2_5.py,v
retrieving revision 1.5
retrieving revision 1.6
diff -u -r1.5 -r1.6
--- /home/repository/moby/moby-live/Python/bioMoby/ontology/GFF2_5.py	2005/02/01 14:20:44	1.5
+++ /home/repository/moby/moby-live/Python/bioMoby/ontology/GFF2_5.py	2005/02/07 14:23:33	1.6
@@ -48,4 +48,5 @@
             if elt.nodeName=="CrossReference" or elt.nodeName=="moby:CrossReference":
                 self.__cross__=[]
                 for ref in elt.childNodes:
-                    self.__cross__.append(um.loads(ref))
\ No newline at end of file
+                    if ref.nodeType==ref.ELEMENT_NODE:
+                        self.__cross__.append(um.loadn(ref))
\ No newline at end of file

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/ontology/GFF3.py,v
retrieving revision 1.5
retrieving revision 1.6
diff -u -r1.5 -r1.6
--- /home/repository/moby/moby-live/Python/bioMoby/ontology/GFF3.py	2005/02/01 14:20:44	1.5
+++ /home/repository/moby/moby-live/Python/bioMoby/ontology/GFF3.py	2005/02/07 14:23:33	1.6
@@ -48,4 +48,5 @@
             if elt.nodeName=="CrossReference" or elt.nodeName=="moby:CrossReference":
                 self.__cross__=[]
                 for ref in elt.childNodes:
-                    self.__cross__.append(um.loads(ref))
\ No newline at end of file
+                    if ref.nodeType==ref.ELEMENT_NODE:
+                        self.__cross__.append(um.loadn(ref))
\ No newline at end of file

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/ontology/GO_Term.py,v
retrieving revision 1.5
retrieving revision 1.6
diff -u -r1.5 -r1.6
--- /home/repository/moby/moby-live/Python/bioMoby/ontology/GO_Term.py	2005/02/01 14:20:44	1.5
+++ /home/repository/moby/moby-live/Python/bioMoby/ontology/GO_Term.py	2005/02/07 14:23:33	1.6
@@ -50,7 +50,8 @@
             if elt.nodeName=="CrossReference" or elt.nodeName=="moby:CrossReference":
                 self.__cross__=[]
                 for ref in elt.childNodes:
-                    self.__cross__.append(um.loads(ref))
+                    if ref.nodeType==ref.ELEMENT_NODE:
+                        self.__cross__.append(um.loadn(ref))
             if elt.nodeType==elt.ELEMENT_NODE and (elt.nodeName=="String" or elt.nodeName=="moby:String") and (elt.getAttribute("articleName")=="Term" or elt.getAttribute("moby:articleName")=="Term"):
                 t=MobyString()
                 t.fromMoby(elt)

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/ontology/GenbankFlatfile.py,v
retrieving revision 1.5
retrieving revision 1.6
diff -u -r1.5 -r1.6
--- /home/repository/moby/moby-live/Python/bioMoby/ontology/GenbankFlatfile.py	2005/02/01 14:20:44	1.5
+++ /home/repository/moby/moby-live/Python/bioMoby/ontology/GenbankFlatfile.py	2005/02/07 14:23:33	1.6
@@ -48,4 +48,5 @@
             if elt.nodeName=="CrossReference" or elt.nodeName=="moby:CrossReference":
                 self.__cross__=[]
                 for ref in elt.childNodes:
-                    self.__cross__.append(um.loads(ref))
\ No newline at end of file
+                    if ref.nodeType==ref.ELEMENT_NODE:
+                        self.__cross__.append(um.loadn(ref))
\ No newline at end of file

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/ontology/Gene_Expression_data.py,v
retrieving revision 1.1
retrieving revision 1.2
diff -u -r1.1 -r1.2
--- /home/repository/moby/moby-live/Python/bioMoby/ontology/Gene_Expression_data.py	2005/02/02 15:20:55	1.1
+++ /home/repository/moby/moby-live/Python/bioMoby/ontology/Gene_Expression_data.py	2005/02/07 14:23:33	1.2
@@ -49,7 +49,8 @@
             if elt.nodeName=="CrossReference" or elt.nodeName=="moby:CrossReference":
                 self.__cross__=[]
                 for ref in elt.childNodes:
-                    self.__cross__.append(um.loads(ref))
+                    if ref.nodeType==ref.ELEMENT_NODE:
+                        self.__cross__.append(um.loadn(ref))
             if elt.nodeType==elt.ELEMENT_NODE and (elt.nodeName=="String" or elt.nodeName=="moby:String") and (elt.getAttribute("articleName")=="Expression data" or elt.getAttribute("moby:articleName")=="Expression data"):
                 t=MobyString()
                 t.fromMoby(elt)

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/ontology/GenericSequence.py,v
retrieving revision 1.5
retrieving revision 1.6
diff -u -r1.5 -r1.6
--- /home/repository/moby/moby-live/Python/bioMoby/ontology/GenericSequence.py	2005/02/01 14:20:44	1.5
+++ /home/repository/moby/moby-live/Python/bioMoby/ontology/GenericSequence.py	2005/02/07 14:23:33	1.6
@@ -51,7 +51,8 @@
             if elt.nodeName=="CrossReference" or elt.nodeName=="moby:CrossReference":
                 self.__cross__=[]
                 for ref in elt.childNodes:
-                    self.__cross__.append(um.loads(ref))
+                    if ref.nodeType==ref.ELEMENT_NODE:
+                        self.__cross__.append(um.loadn(ref))
             if elt.nodeType==elt.ELEMENT_NODE and (elt.nodeName=="Integer" or elt.nodeName=="moby:Integer") and (elt.getAttribute("articleName")=="Length" or elt.getAttribute("moby:articleName")=="Length"):
                 t=MobyInteger()
                 t.fromMoby(elt)

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/ontology/GeneticElement.py,v
retrieving revision 1.5
retrieving revision 1.6
diff -u -r1.5 -r1.6
--- /home/repository/moby/moby-live/Python/bioMoby/ontology/GeneticElement.py	2005/02/01 14:20:44	1.5
+++ /home/repository/moby/moby-live/Python/bioMoby/ontology/GeneticElement.py	2005/02/07 14:23:33	1.6
@@ -49,7 +49,8 @@
             if elt.nodeName=="CrossReference" or elt.nodeName=="moby:CrossReference":
                 self.__cross__=[]
                 for ref in elt.childNodes:
-                    self.__cross__.append(um.loads(ref))
+                    if ref.nodeType==ref.ELEMENT_NODE:
+                        self.__cross__.append(um.loadn(ref))
             if elt.nodeType==elt.ELEMENT_NODE and (elt.nodeName=="String" or elt.nodeName=="moby:String") and (elt.getAttribute("articleName")=="GeneticElement" or elt.getAttribute("moby:articleName")=="GeneticElement"):
                 t=MobyString()
                 t.fromMoby(elt)

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/ontology/Genotype.py,v
retrieving revision 1.5
retrieving revision 1.6
diff -u -r1.5 -r1.6
--- /home/repository/moby/moby-live/Python/bioMoby/ontology/Genotype.py	2005/02/01 14:20:44	1.5
+++ /home/repository/moby/moby-live/Python/bioMoby/ontology/Genotype.py	2005/02/07 14:23:33	1.6
@@ -51,7 +51,8 @@
             if elt.nodeName=="CrossReference" or elt.nodeName=="moby:CrossReference":
                 self.__cross__=[]
                 for ref in elt.childNodes:
-                    self.__cross__.append(um.loads(ref))
+                    if ref.nodeType==ref.ELEMENT_NODE:
+                        self.__cross__.append(um.loadn(ref))
             if elt.nodeType==elt.ELEMENT_NODE and (elt.nodeName=="String" or elt.nodeName=="moby:String") and (elt.getAttribute("articleName")=="snp" or elt.getAttribute("moby:articleName")=="snp"):
                 t=MobyString()
                 t.fromMoby(elt)

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/ontology/Germplasm_Details.py,v
retrieving revision 1.5
retrieving revision 1.6
diff -u -r1.5 -r1.6
--- /home/repository/moby/moby-live/Python/bioMoby/ontology/Germplasm_Details.py	2005/02/01 14:20:44	1.5
+++ /home/repository/moby/moby-live/Python/bioMoby/ontology/Germplasm_Details.py	2005/02/07 14:23:33	1.6
@@ -57,7 +57,8 @@
             if elt.nodeName=="CrossReference" or elt.nodeName=="moby:CrossReference":
                 self.__cross__=[]
                 for ref in elt.childNodes:
-                    self.__cross__.append(um.loads(ref))
+                    if ref.nodeType==ref.ELEMENT_NODE:
+                        self.__cross__.append(um.loadn(ref))
             if elt.nodeType==elt.ELEMENT_NODE and (elt.nodeName=="Integer" or elt.nodeName=="moby:Integer") and (elt.getAttribute("articleName")=="date" or elt.getAttribute("moby:articleName")=="date"):
                 t=MobyInteger()
                 t.fromMoby(elt)

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/ontology/Germplasm_List.py,v
retrieving revision 1.5
retrieving revision 1.6
diff -u -r1.5 -r1.6
--- /home/repository/moby/moby-live/Python/bioMoby/ontology/Germplasm_List.py	2005/02/01 14:20:44	1.5
+++ /home/repository/moby/moby-live/Python/bioMoby/ontology/Germplasm_List.py	2005/02/07 14:23:33	1.6
@@ -57,7 +57,8 @@
             if elt.nodeName=="CrossReference" or elt.nodeName=="moby:CrossReference":
                 self.__cross__=[]
                 for ref in elt.childNodes:
-                    self.__cross__.append(um.loads(ref))
+                    if ref.nodeType==ref.ELEMENT_NODE:
+                        self.__cross__.append(um.loadn(ref))
             if elt.nodeType==elt.ELEMENT_NODE and (elt.nodeName=="Integer" or elt.nodeName=="moby:Integer") and (elt.getAttribute("articleName")=="germplasm_id" or elt.getAttribute("moby:articleName")=="germplasm_id"):
                 t=MobyInteger()
                 t.fromMoby(elt)

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/ontology/Global_Keyword.py,v
retrieving revision 1.5
retrieving revision 1.6
diff -u -r1.5 -r1.6
--- /home/repository/moby/moby-live/Python/bioMoby/ontology/Global_Keyword.py	2005/02/01 14:20:44	1.5
+++ /home/repository/moby/moby-live/Python/bioMoby/ontology/Global_Keyword.py	2005/02/07 14:23:33	1.6
@@ -47,4 +47,5 @@
             if elt.nodeName=="CrossReference" or elt.nodeName=="moby:CrossReference":
                 self.__cross__=[]
                 for ref in elt.childNodes:
-                    self.__cross__.append(um.loads(ref))
\ No newline at end of file
+                    if ref.nodeType==ref.ELEMENT_NODE:
+                        self.__cross__.append(um.loadn(ref))
\ No newline at end of file

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/ontology/HBond_Pair.py,v
retrieving revision 1.5
retrieving revision 1.6
diff -u -r1.5 -r1.6
--- /home/repository/moby/moby-live/Python/bioMoby/ontology/HBond_Pair.py	2005/02/01 14:20:44	1.5
+++ /home/repository/moby/moby-live/Python/bioMoby/ontology/HBond_Pair.py	2005/02/07 14:23:33	1.6
@@ -51,7 +51,8 @@
             if elt.nodeName=="CrossReference" or elt.nodeName=="moby:CrossReference":
                 self.__cross__=[]
                 for ref in elt.childNodes:
-                    self.__cross__.append(um.loads(ref))
+                    if ref.nodeType==ref.ELEMENT_NODE:
+                        self.__cross__.append(um.loadn(ref))
             if elt.nodeType==elt.ELEMENT_NODE and (elt.nodeName=="String" or elt.nodeName=="moby:String") and (elt.getAttribute("articleName")=="A" or elt.getAttribute("moby:articleName")=="A"):
                 t=MobyString()
                 t.fromMoby(elt)

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/ontology/HFormatText.py,v
retrieving revision 1.5
retrieving revision 1.6
diff -u -r1.5 -r1.6
--- /home/repository/moby/moby-live/Python/bioMoby/ontology/HFormatText.py	2005/02/01 14:20:44	1.5
+++ /home/repository/moby/moby-live/Python/bioMoby/ontology/HFormatText.py	2005/02/07 14:23:33	1.6
@@ -48,4 +48,5 @@
             if elt.nodeName=="CrossReference" or elt.nodeName=="moby:CrossReference":
                 self.__cross__=[]
                 for ref in elt.childNodes:
-                    self.__cross__.append(um.loads(ref))
\ No newline at end of file
+                    if ref.nodeType==ref.ELEMENT_NODE:
+                        self.__cross__.append(um.loadn(ref))
\ No newline at end of file

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/ontology/Haplotyping_Study_obj.py,v
retrieving revision 1.5
retrieving revision 1.6
diff -u -r1.5 -r1.6
--- /home/repository/moby/moby-live/Python/bioMoby/ontology/Haplotyping_Study_obj.py	2005/02/01 14:20:44	1.5
+++ /home/repository/moby/moby-live/Python/bioMoby/ontology/Haplotyping_Study_obj.py	2005/02/07 14:23:33	1.6
@@ -47,4 +47,5 @@
             if elt.nodeName=="CrossReference" or elt.nodeName=="moby:CrossReference":
                 self.__cross__=[]
                 for ref in elt.childNodes:
-                    self.__cross__.append(um.loads(ref))
\ No newline at end of file
+                    if ref.nodeType==ref.ELEMENT_NODE:
+                        self.__cross__.append(um.loadn(ref))
\ No newline at end of file

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/ontology/ICIS_Query.py,v
retrieving revision 1.5
retrieving revision 1.6
diff -u -r1.5 -r1.6
--- /home/repository/moby/moby-live/Python/bioMoby/ontology/ICIS_Query.py	2005/02/01 14:20:44	1.5
+++ /home/repository/moby/moby-live/Python/bioMoby/ontology/ICIS_Query.py	2005/02/07 14:23:33	1.6
@@ -52,7 +52,8 @@
             if elt.nodeName=="CrossReference" or elt.nodeName=="moby:CrossReference":
                 self.__cross__=[]
                 for ref in elt.childNodes:
-                    self.__cross__.append(um.loads(ref))
+                    if ref.nodeType==ref.ELEMENT_NODE:
+                        self.__cross__.append(um.loadn(ref))
             if elt.nodeType==elt.ELEMENT_NODE and (elt.nodeName=="Integer" or elt.nodeName=="moby:Integer") and (elt.getAttribute("articleName")=="end_row" or elt.getAttribute("moby:articleName")=="end_row"):
                 t=MobyInteger()
                 t.fromMoby(elt)

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/ontology/ICIS_Query2.py,v
retrieving revision 1.5
retrieving revision 1.6
diff -u -r1.5 -r1.6
--- /home/repository/moby/moby-live/Python/bioMoby/ontology/ICIS_Query2.py	2005/02/01 14:20:44	1.5
+++ /home/repository/moby/moby-live/Python/bioMoby/ontology/ICIS_Query2.py	2005/02/07 14:23:33	1.6
@@ -54,7 +54,8 @@
             if elt.nodeName=="CrossReference" or elt.nodeName=="moby:CrossReference":
                 self.__cross__=[]
                 for ref in elt.childNodes:
-                    self.__cross__.append(um.loads(ref))
+                    if ref.nodeType==ref.ELEMENT_NODE:
+                        self.__cross__.append(um.loadn(ref))
             if elt.nodeType==elt.ELEMENT_NODE and (elt.nodeName=="String" or elt.nodeName=="moby:String") and (elt.getAttribute("articleName")=="search_text1" or elt.getAttribute("moby:articleName")=="search_text1"):
                 t=MobyString()
                 t.fromMoby(elt)

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/ontology/ICIS_Query3.py,v
retrieving revision 1.5
retrieving revision 1.6
diff -u -r1.5 -r1.6
--- /home/repository/moby/moby-live/Python/bioMoby/ontology/ICIS_Query3.py	2005/02/01 14:20:44	1.5
+++ /home/repository/moby/moby-live/Python/bioMoby/ontology/ICIS_Query3.py	2005/02/07 14:23:33	1.6
@@ -52,7 +52,8 @@
             if elt.nodeName=="CrossReference" or elt.nodeName=="moby:CrossReference":
                 self.__cross__=[]
                 for ref in elt.childNodes:
-                    self.__cross__.append(um.loads(ref))
+                    if ref.nodeType==ref.ELEMENT_NODE:
+                        self.__cross__.append(um.loadn(ref))
             if elt.nodeType==elt.ELEMENT_NODE and (elt.nodeName=="Integer" or elt.nodeName=="moby:Integer") and (elt.getAttribute("articleName")=="search_text1" or elt.getAttribute("moby:articleName")=="search_text1"):
                 t=MobyInteger()
                 t.fromMoby(elt)

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/ontology/IntAct_XML.py,v
retrieving revision 1.5
retrieving revision 1.6
diff -u -r1.5 -r1.6
--- /home/repository/moby/moby-live/Python/bioMoby/ontology/IntAct_XML.py	2005/02/01 14:20:44	1.5
+++ /home/repository/moby/moby-live/Python/bioMoby/ontology/IntAct_XML.py	2005/02/07 14:23:33	1.6
@@ -48,4 +48,5 @@
             if elt.nodeName=="CrossReference" or elt.nodeName=="moby:CrossReference":
                 self.__cross__=[]
                 for ref in elt.childNodes:
-                    self.__cross__.append(um.loads(ref))
\ No newline at end of file
+                    if ref.nodeType==ref.ELEMENT_NODE:
+                        self.__cross__.append(um.loadn(ref))
\ No newline at end of file

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/ontology/Interaction.py,v
retrieving revision 1.5
retrieving revision 1.6
diff -u -r1.5 -r1.6
--- /home/repository/moby/moby-live/Python/bioMoby/ontology/Interaction.py	2005/02/01 14:20:44	1.5
+++ /home/repository/moby/moby-live/Python/bioMoby/ontology/Interaction.py	2005/02/07 14:23:33	1.6
@@ -53,7 +53,8 @@
             if elt.nodeName=="CrossReference" or elt.nodeName=="moby:CrossReference":
                 self.__cross__=[]
                 for ref in elt.childNodes:
-                    self.__cross__.append(um.loads(ref))
+                    if ref.nodeType==ref.ELEMENT_NODE:
+                        self.__cross__.append(um.loadn(ref))
             if elt.nodeType==elt.ELEMENT_NODE and (elt.nodeName=="String" or elt.nodeName=="moby:String") and (elt.getAttribute("articleName")=="result" or elt.getAttribute("moby:articleName")=="result"):
                 t=MobyString()
                 t.fromMoby(elt)

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/ontology/InteractionMethod.py,v
retrieving revision 1.5
retrieving revision 1.6
diff -u -r1.5 -r1.6
--- /home/repository/moby/moby-live/Python/bioMoby/ontology/InteractionMethod.py	2005/02/01 14:20:44	1.5
+++ /home/repository/moby/moby-live/Python/bioMoby/ontology/InteractionMethod.py	2005/02/07 14:23:33	1.6
@@ -51,7 +51,8 @@
             if elt.nodeName=="CrossReference" or elt.nodeName=="moby:CrossReference":
                 self.__cross__=[]
                 for ref in elt.childNodes:
-                    self.__cross__.append(um.loads(ref))
+                    if ref.nodeType==ref.ELEMENT_NODE:
+                        self.__cross__.append(um.loadn(ref))
             if elt.nodeType==elt.ELEMENT_NODE and (elt.nodeName=="String" or elt.nodeName=="moby:String") and (elt.getAttribute("articleName")=="shortlabel" or elt.getAttribute("moby:articleName")=="shortlabel"):
                 t=MobyString()
                 t.fromMoby(elt)

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/ontology/Interaction_partner.py,v
retrieving revision 1.5
retrieving revision 1.6
diff -u -r1.5 -r1.6
--- /home/repository/moby/moby-live/Python/bioMoby/ontology/Interaction_partner.py	2005/02/01 14:20:44	1.5
+++ /home/repository/moby/moby-live/Python/bioMoby/ontology/Interaction_partner.py	2005/02/07 14:23:33	1.6
@@ -51,7 +51,8 @@
             if elt.nodeName=="CrossReference" or elt.nodeName=="moby:CrossReference":
                 self.__cross__=[]
                 for ref in elt.childNodes:
-                    self.__cross__.append(um.loads(ref))
+                    if ref.nodeType==ref.ELEMENT_NODE:
+                        self.__cross__.append(um.loadn(ref))
             if elt.nodeType==elt.ELEMENT_NODE and (elt.nodeName=="Integer" or elt.nodeName=="moby:Integer") and (elt.getAttribute("articleName")=="direction" or elt.getAttribute("moby:articleName")=="direction"):
                 t=MobyInteger()
                 t.fromMoby(elt)

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/ontology/Interactor.py,v
retrieving revision 1.5
retrieving revision 1.6
diff -u -r1.5 -r1.6
--- /home/repository/moby/moby-live/Python/bioMoby/ontology/Interactor.py	2005/02/01 14:20:44	1.5
+++ /home/repository/moby/moby-live/Python/bioMoby/ontology/Interactor.py	2005/02/07 14:23:33	1.6
@@ -49,7 +49,8 @@
             if elt.nodeName=="CrossReference" or elt.nodeName=="moby:CrossReference":
                 self.__cross__=[]
                 for ref in elt.childNodes:
-                    self.__cross__.append(um.loads(ref))
+                    if ref.nodeType==ref.ELEMENT_NODE:
+                        self.__cross__.append(um.loadn(ref))
             if elt.nodeType==elt.ELEMENT_NODE and (elt.nodeName=="String" or elt.nodeName=="moby:String") and (elt.getAttribute("articleName")=="role" or elt.getAttribute("moby:articleName")=="role"):
                 t=MobyString()
                 t.fromMoby(elt)

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/ontology/MEME_Text.py,v
retrieving revision 1.5
retrieving revision 1.6
diff -u -r1.5 -r1.6
--- /home/repository/moby/moby-live/Python/bioMoby/ontology/MEME_Text.py	2005/02/01 14:20:44	1.5
+++ /home/repository/moby/moby-live/Python/bioMoby/ontology/MEME_Text.py	2005/02/07 14:23:33	1.6
@@ -48,4 +48,5 @@
             if elt.nodeName=="CrossReference" or elt.nodeName=="moby:CrossReference":
                 self.__cross__=[]
                 for ref in elt.childNodes:
-                    self.__cross__.append(um.loads(ref))
\ No newline at end of file
+                    if ref.nodeType==ref.ELEMENT_NODE:
+                        self.__cross__.append(um.loadn(ref))
\ No newline at end of file

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/ontology/MGIS_ACCESSION.py,v
retrieving revision 1.5
retrieving revision 1.6
diff -u -r1.5 -r1.6
--- /home/repository/moby/moby-live/Python/bioMoby/ontology/MGIS_ACCESSION.py	2005/02/01 14:20:44	1.5
+++ /home/repository/moby/moby-live/Python/bioMoby/ontology/MGIS_ACCESSION.py	2005/02/07 14:23:33	1.6
@@ -68,7 +68,8 @@
             if elt.nodeName=="CrossReference" or elt.nodeName=="moby:CrossReference":
                 self.__cross__=[]
                 for ref in elt.childNodes:
-                    self.__cross__.append(um.loads(ref))
+                    if ref.nodeType==ref.ELEMENT_NODE:
+                        self.__cross__.append(um.loadn(ref))
             if elt.nodeType==elt.ELEMENT_NODE and (elt.nodeName=="String" or elt.nodeName=="moby:String") and (elt.getAttribute("articleName")=="Biotic_stress_Yellowsig" or elt.getAttribute("moby:articleName")=="Biotic_stress_Yellowsig"):
                 t=MobyString()
                 t.fromMoby(elt)

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/ontology/MMP_Locus.py,v
retrieving revision 1.5
retrieving revision 1.6
diff -u -r1.5 -r1.6
--- /home/repository/moby/moby-live/Python/bioMoby/ontology/MMP_Locus.py	2005/02/01 14:20:44	1.5
+++ /home/repository/moby/moby-live/Python/bioMoby/ontology/MMP_Locus.py	2005/02/07 14:23:33	1.6
@@ -47,4 +47,5 @@
             if elt.nodeName=="CrossReference" or elt.nodeName=="moby:CrossReference":
                 self.__cross__=[]
                 for ref in elt.childNodes:
-                    self.__cross__.append(um.loads(ref))
\ No newline at end of file
+                    if ref.nodeType==ref.ELEMENT_NODE:
+                        self.__cross__.append(um.loadn(ref))
\ No newline at end of file

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/ontology/MO_Term_Test.py,v
retrieving revision 1.5
retrieving revision 1.6
diff -u -r1.5 -r1.6
--- /home/repository/moby/moby-live/Python/bioMoby/ontology/MO_Term_Test.py	2005/02/01 14:20:44	1.5
+++ /home/repository/moby/moby-live/Python/bioMoby/ontology/MO_Term_Test.py	2005/02/07 14:23:33	1.6
@@ -52,7 +52,8 @@
             if elt.nodeName=="CrossReference" or elt.nodeName=="moby:CrossReference":
                 self.__cross__=[]
                 for ref in elt.childNodes:
-                    self.__cross__.append(um.loads(ref))
+                    if ref.nodeType==ref.ELEMENT_NODE:
+                        self.__cross__.append(um.loadn(ref))
             if elt.nodeType==elt.ELEMENT_NODE and (elt.nodeName=="String" or elt.nodeName=="moby:String") and (elt.getAttribute("articleName")=="class_name" or elt.getAttribute("moby:articleName")=="class_name"):
                 t=MobyString()
                 t.fromMoby(elt)

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/ontology/MSF.py,v
retrieving revision 1.1
retrieving revision 1.2
diff -u -r1.1 -r1.2
--- /home/repository/moby/moby-live/Python/bioMoby/ontology/MSF.py	2005/02/02 15:08:34	1.1
+++ /home/repository/moby/moby-live/Python/bioMoby/ontology/MSF.py	2005/02/07 14:23:33	1.2
@@ -48,4 +48,5 @@
             if elt.nodeName=="CrossReference" or elt.nodeName=="moby:CrossReference":
                 self.__cross__=[]
                 for ref in elt.childNodes:
-                    self.__cross__.append(um.loads(ref))
\ No newline at end of file
+                    if ref.nodeType==ref.ELEMENT_NODE:
+                        self.__cross__.append(um.loadn(ref))
\ No newline at end of file

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/ontology/MmCIFText.py,v
retrieving revision 1.5
retrieving revision 1.6
diff -u -r1.5 -r1.6
--- /home/repository/moby/moby-live/Python/bioMoby/ontology/MmCIFText.py	2005/02/01 14:20:44	1.5
+++ /home/repository/moby/moby-live/Python/bioMoby/ontology/MmCIFText.py	2005/02/07 14:23:33	1.6
@@ -48,4 +48,5 @@
             if elt.nodeName=="CrossReference" or elt.nodeName=="moby:CrossReference":
                 self.__cross__=[]
                 for ref in elt.childNodes:
-                    self.__cross__.append(um.loads(ref))
\ No newline at end of file
+                    if ref.nodeType==ref.ELEMENT_NODE:
+                        self.__cross__.append(um.loadn(ref))
\ No newline at end of file

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/ontology/Multi_key_value_pair.py,v
retrieving revision 1.5
retrieving revision 1.6
diff -u -r1.5 -r1.6
--- /home/repository/moby/moby-live/Python/bioMoby/ontology/Multi_key_value_pair.py	2005/02/01 14:20:44	1.5
+++ /home/repository/moby/moby-live/Python/bioMoby/ontology/Multi_key_value_pair.py	2005/02/07 14:23:33	1.6
@@ -51,7 +51,8 @@
             if elt.nodeName=="CrossReference" or elt.nodeName=="moby:CrossReference":
                 self.__cross__=[]
                 for ref in elt.childNodes:
-                    self.__cross__.append(um.loads(ref))
+                    if ref.nodeType==ref.ELEMENT_NODE:
+                        self.__cross__.append(um.loadn(ref))
             if elt.nodeType==elt.ELEMENT_NODE and (elt.nodeName=="String" or elt.nodeName=="moby:String") and (elt.getAttribute("articleName")=="key" or elt.getAttribute("moby:articleName")=="key"):
                 t=MobyString()
                 t.fromMoby(elt)

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/ontology/MyTestingDataType_11024145298313.py,v
retrieving revision 1.5
retrieving revision 1.6
diff -u -r1.5 -r1.6
--- /home/repository/moby/moby-live/Python/bioMoby/ontology/MyTestingDataType_11024145298313.py	2005/02/01 14:20:44	1.5
+++ /home/repository/moby/moby-live/Python/bioMoby/ontology/MyTestingDataType_11024145298313.py	2005/02/07 14:23:33	1.6
@@ -48,4 +48,5 @@
             if elt.nodeName=="CrossReference" or elt.nodeName=="moby:CrossReference":
                 self.__cross__=[]
                 for ref in elt.childNodes:
-                    self.__cross__.append(um.loads(ref))
\ No newline at end of file
+                    if ref.nodeType==ref.ELEMENT_NODE:
+                        self.__cross__.append(um.loadn(ref))
\ No newline at end of file

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/ontology/MyTree.py,v
retrieving revision 1.5
retrieving revision 1.6
diff -u -r1.5 -r1.6
--- /home/repository/moby/moby-live/Python/bioMoby/ontology/MyTree.py	2005/02/01 14:20:44	1.5
+++ /home/repository/moby/moby-live/Python/bioMoby/ontology/MyTree.py	2005/02/07 14:23:33	1.6
@@ -48,4 +48,5 @@
             if elt.nodeName=="CrossReference" or elt.nodeName=="moby:CrossReference":
                 self.__cross__=[]
                 for ref in elt.childNodes:
-                    self.__cross__.append(um.loads(ref))
\ No newline at end of file
+                    if ref.nodeType==ref.ELEMENT_NODE:
+                        self.__cross__.append(um.loadn(ref))
\ No newline at end of file

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/ontology/NCBI_BLAST_Text.py,v
retrieving revision 1.5
retrieving revision 1.6
diff -u -r1.5 -r1.6
--- /home/repository/moby/moby-live/Python/bioMoby/ontology/NCBI_BLAST_Text.py	2005/02/01 14:20:44	1.5
+++ /home/repository/moby/moby-live/Python/bioMoby/ontology/NCBI_BLAST_Text.py	2005/02/07 14:23:33	1.6
@@ -48,4 +48,5 @@
             if elt.nodeName=="CrossReference" or elt.nodeName=="moby:CrossReference":
                 self.__cross__=[]
                 for ref in elt.childNodes:
-                    self.__cross__.append(um.loads(ref))
\ No newline at end of file
+                    if ref.nodeType==ref.ELEMENT_NODE:
+                        self.__cross__.append(um.loadn(ref))
\ No newline at end of file

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/ontology/NCBI_Blast_XML.py,v
retrieving revision 1.5
retrieving revision 1.6
diff -u -r1.5 -r1.6
--- /home/repository/moby/moby-live/Python/bioMoby/ontology/NCBI_Blast_XML.py	2005/02/01 14:20:44	1.5
+++ /home/repository/moby/moby-live/Python/bioMoby/ontology/NCBI_Blast_XML.py	2005/02/07 14:23:33	1.6
@@ -48,4 +48,5 @@
             if elt.nodeName=="CrossReference" or elt.nodeName=="moby:CrossReference":
                 self.__cross__=[]
                 for ref in elt.childNodes:
-                    self.__cross__.append(um.loads(ref))
\ No newline at end of file
+                    if ref.nodeType==ref.ELEMENT_NODE:
+                        self.__cross__.append(um.loadn(ref))
\ No newline at end of file

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/ontology/NCBI_Blast_XML_Gif.py,v
retrieving revision 1.5
retrieving revision 1.6
diff -u -r1.5 -r1.6
--- /home/repository/moby/moby-live/Python/bioMoby/ontology/NCBI_Blast_XML_Gif.py	2005/02/01 14:20:44	1.5
+++ /home/repository/moby/moby-live/Python/bioMoby/ontology/NCBI_Blast_XML_Gif.py	2005/02/07 14:23:33	1.6
@@ -50,7 +50,8 @@
             if elt.nodeName=="CrossReference" or elt.nodeName=="moby:CrossReference":
                 self.__cross__=[]
                 for ref in elt.childNodes:
-                    self.__cross__.append(um.loads(ref))
+                    if ref.nodeType==ref.ELEMENT_NODE:
+                        self.__cross__.append(um.loadn(ref))
             if elt.nodeType==elt.ELEMENT_NODE and (elt.nodeName=="b64_encoded_gif" or elt.nodeName=="moby:b64_encoded_gif") and (elt.getAttribute("articleName")=="hitGraph" or elt.getAttribute("moby:articleName")=="hitGraph"):
                 self.HitGraph=MobyB64_encoded_gif()
                 self.HitGraph.fromMoby(elt)
\ No newline at end of file

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/ontology/NCBI_Blast_XML_Gif_Map.py,v
retrieving revision 1.5
retrieving revision 1.6
diff -u -r1.5 -r1.6
--- /home/repository/moby/moby-live/Python/bioMoby/ontology/NCBI_Blast_XML_Gif_Map.py	2005/02/01 14:20:44	1.5
+++ /home/repository/moby/moby-live/Python/bioMoby/ontology/NCBI_Blast_XML_Gif_Map.py	2005/02/07 14:23:33	1.6
@@ -52,7 +52,8 @@
             if elt.nodeName=="CrossReference" or elt.nodeName=="moby:CrossReference":
                 self.__cross__=[]
                 for ref in elt.childNodes:
-                    self.__cross__.append(um.loads(ref))
+                    if ref.nodeType==ref.ELEMENT_NODE:
+                        self.__cross__.append(um.loadn(ref))
             if elt.nodeType==elt.ELEMENT_NODE and (elt.nodeName=="b64_encoded_gif" or elt.nodeName=="moby:b64_encoded_gif") and (elt.getAttribute("articleName")=="hitGraph" or elt.getAttribute("moby:articleName")=="hitGraph"):
                 self.HitGraph=MobyB64_encoded_gif()
                 self.HitGraph.fromMoby(elt)

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/ontology/NCBI_MEME_Text.py,v
retrieving revision 1.5
retrieving revision 1.6
diff -u -r1.5 -r1.6
--- /home/repository/moby/moby-live/Python/bioMoby/ontology/NCBI_MEME_Text.py	2005/02/01 14:20:44	1.5
+++ /home/repository/moby/moby-live/Python/bioMoby/ontology/NCBI_MEME_Text.py	2005/02/07 14:23:33	1.6
@@ -48,4 +48,5 @@
             if elt.nodeName=="CrossReference" or elt.nodeName=="moby:CrossReference":
                 self.__cross__=[]
                 for ref in elt.childNodes:
-                    self.__cross__.append(um.loads(ref))
\ No newline at end of file
+                    if ref.nodeType==ref.ELEMENT_NODE:
+                        self.__cross__.append(um.loadn(ref))
\ No newline at end of file

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/ontology/NucleotideSequence.py,v
retrieving revision 1.5
retrieving revision 1.6
diff -u -r1.5 -r1.6
--- /home/repository/moby/moby-live/Python/bioMoby/ontology/NucleotideSequence.py	2005/02/01 14:20:44	1.5
+++ /home/repository/moby/moby-live/Python/bioMoby/ontology/NucleotideSequence.py	2005/02/07 14:23:33	1.6
@@ -51,7 +51,8 @@
             if elt.nodeName=="CrossReference" or elt.nodeName=="moby:CrossReference":
                 self.__cross__=[]
                 for ref in elt.childNodes:
-                    self.__cross__.append(um.loads(ref))
+                    if ref.nodeType==ref.ELEMENT_NODE:
+                        self.__cross__.append(um.loadn(ref))
             if elt.nodeType==elt.ELEMENT_NODE and (elt.nodeName=="Integer" or elt.nodeName=="moby:Integer") and (elt.getAttribute("articleName")=="Length" or elt.getAttribute("moby:articleName")=="Length"):
                 t=MobyInteger()
                 t.fromMoby(elt)

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/ontology/PDBFormattedText.py,v
retrieving revision 1.5
retrieving revision 1.6
diff -u -r1.5 -r1.6
--- /home/repository/moby/moby-live/Python/bioMoby/ontology/PDBFormattedText.py	2005/02/01 14:20:44	1.5
+++ /home/repository/moby/moby-live/Python/bioMoby/ontology/PDBFormattedText.py	2005/02/07 14:23:33	1.6
@@ -48,4 +48,5 @@
             if elt.nodeName=="CrossReference" or elt.nodeName=="moby:CrossReference":
                 self.__cross__=[]
                 for ref in elt.childNodes:
-                    self.__cross__.append(um.loads(ref))
\ No newline at end of file
+                    if ref.nodeType==ref.ELEMENT_NODE:
+                        self.__cross__.append(um.loadn(ref))
\ No newline at end of file

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/ontology/PDBText.py,v
retrieving revision 1.5
retrieving revision 1.6
diff -u -r1.5 -r1.6
--- /home/repository/moby/moby-live/Python/bioMoby/ontology/PDBText.py	2005/02/01 14:20:44	1.5
+++ /home/repository/moby/moby-live/Python/bioMoby/ontology/PDBText.py	2005/02/07 14:23:33	1.6
@@ -48,4 +48,5 @@
             if elt.nodeName=="CrossReference" or elt.nodeName=="moby:CrossReference":
                 self.__cross__=[]
                 for ref in elt.childNodes:
-                    self.__cross__.append(um.loads(ref))
\ No newline at end of file
+                    if ref.nodeType==ref.ELEMENT_NODE:
+                        self.__cross__.append(um.loadn(ref))
\ No newline at end of file

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/ontology/PDGJOB.py,v
retrieving revision 1.5
retrieving revision 1.6
diff -u -r1.5 -r1.6
--- /home/repository/moby/moby-live/Python/bioMoby/ontology/PDGJOB.py	2005/02/01 14:20:44	1.5
+++ /home/repository/moby/moby-live/Python/bioMoby/ontology/PDGJOB.py	2005/02/07 14:23:33	1.6
@@ -54,7 +54,8 @@
             if elt.nodeName=="CrossReference" or elt.nodeName=="moby:CrossReference":
                 self.__cross__=[]
                 for ref in elt.childNodes:
-                    self.__cross__.append(um.loads(ref))
+                    if ref.nodeType==ref.ELEMENT_NODE:
+                        self.__cross__.append(um.loadn(ref))
             if elt.nodeType==elt.ELEMENT_NODE and (elt.nodeName=="String" or elt.nodeName=="moby:String") and (elt.getAttribute("articleName")=="answerService" or elt.getAttribute("moby:articleName")=="answerService"):
                 t=MobyString()
                 t.fromMoby(elt)

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/ontology/PHDText.py,v
retrieving revision 1.5
retrieving revision 1.6
diff -u -r1.5 -r1.6
--- /home/repository/moby/moby-live/Python/bioMoby/ontology/PHDText.py	2005/02/01 14:20:44	1.5
+++ /home/repository/moby/moby-live/Python/bioMoby/ontology/PHDText.py	2005/02/07 14:23:33	1.6
@@ -48,4 +48,5 @@
             if elt.nodeName=="CrossReference" or elt.nodeName=="moby:CrossReference":
                 self.__cross__=[]
                 for ref in elt.childNodes:
-                    self.__cross__.append(um.loads(ref))
\ No newline at end of file
+                    if ref.nodeType==ref.ELEMENT_NODE:
+                        self.__cross__.append(um.loadn(ref))
\ No newline at end of file

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/ontology/PMUTText.py,v
retrieving revision 1.5
retrieving revision 1.6
diff -u -r1.5 -r1.6
--- /home/repository/moby/moby-live/Python/bioMoby/ontology/PMUTText.py	2005/02/01 14:20:44	1.5
+++ /home/repository/moby/moby-live/Python/bioMoby/ontology/PMUTText.py	2005/02/07 14:23:33	1.6
@@ -48,4 +48,5 @@
             if elt.nodeName=="CrossReference" or elt.nodeName=="moby:CrossReference":
                 self.__cross__=[]
                 for ref in elt.childNodes:
-                    self.__cross__.append(um.loads(ref))
\ No newline at end of file
+                    if ref.nodeType==ref.ELEMENT_NODE:
+                        self.__cross__.append(um.loadn(ref))
\ No newline at end of file

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/ontology/PSeaTextFormatted.py,v
retrieving revision 1.5
retrieving revision 1.6
diff -u -r1.5 -r1.6
--- /home/repository/moby/moby-live/Python/bioMoby/ontology/PSeaTextFormatted.py	2005/02/01 14:20:44	1.5
+++ /home/repository/moby/moby-live/Python/bioMoby/ontology/PSeaTextFormatted.py	2005/02/07 14:23:33	1.6
@@ -48,4 +48,5 @@
             if elt.nodeName=="CrossReference" or elt.nodeName=="moby:CrossReference":
                 self.__cross__=[]
                 for ref in elt.childNodes:
-                    self.__cross__.append(um.loads(ref))
\ No newline at end of file
+                    if ref.nodeType==ref.ELEMENT_NODE:
+                        self.__cross__.append(um.loadn(ref))
\ No newline at end of file

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/ontology/PhenotypeDescription.py,v
retrieving revision 1.5
retrieving revision 1.6
diff -u -r1.5 -r1.6
--- /home/repository/moby/moby-live/Python/bioMoby/ontology/PhenotypeDescription.py	2005/02/01 14:20:44	1.5
+++ /home/repository/moby/moby-live/Python/bioMoby/ontology/PhenotypeDescription.py	2005/02/07 14:23:33	1.6
@@ -49,7 +49,8 @@
             if elt.nodeName=="CrossReference" or elt.nodeName=="moby:CrossReference":
                 self.__cross__=[]
                 for ref in elt.childNodes:
-                    self.__cross__.append(um.loads(ref))
+                    if ref.nodeType==ref.ELEMENT_NODE:
+                        self.__cross__.append(um.loadn(ref))
             if elt.nodeType==elt.ELEMENT_NODE and (elt.nodeName=="String" or elt.nodeName=="moby:String") and (elt.getAttribute("articleName")=="Phenotype" or elt.getAttribute("moby:articleName")=="Phenotype"):
                 t=MobyString()
                 t.fromMoby(elt)

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/ontology/PubMedMEDLINE.py,v
retrieving revision 1.5
retrieving revision 1.6
diff -u -r1.5 -r1.6
--- /home/repository/moby/moby-live/Python/bioMoby/ontology/PubMedMEDLINE.py	2005/02/01 14:20:44	1.5
+++ /home/repository/moby/moby-live/Python/bioMoby/ontology/PubMedMEDLINE.py	2005/02/07 14:23:33	1.6
@@ -48,4 +48,5 @@
             if elt.nodeName=="CrossReference" or elt.nodeName=="moby:CrossReference":
                 self.__cross__=[]
                 for ref in elt.childNodes:
-                    self.__cross__.append(um.loads(ref))
\ No newline at end of file
+                    if ref.nodeType==ref.ELEMENT_NODE:
+                        self.__cross__.append(um.loadn(ref))
\ No newline at end of file

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/ontology/RNASequence.py,v
retrieving revision 1.5
retrieving revision 1.6
diff -u -r1.5 -r1.6
--- /home/repository/moby/moby-live/Python/bioMoby/ontology/RNASequence.py	2005/02/01 14:20:44	1.5
+++ /home/repository/moby/moby-live/Python/bioMoby/ontology/RNASequence.py	2005/02/07 14:23:33	1.6
@@ -51,7 +51,8 @@
             if elt.nodeName=="CrossReference" or elt.nodeName=="moby:CrossReference":
                 self.__cross__=[]
                 for ref in elt.childNodes:
-                    self.__cross__.append(um.loads(ref))
+                    if ref.nodeType==ref.ELEMENT_NODE:
+                        self.__cross__.append(um.loadn(ref))
             if elt.nodeType==elt.ELEMENT_NODE and (elt.nodeName=="Integer" or elt.nodeName=="moby:Integer") and (elt.getAttribute("articleName")=="Length" or elt.getAttribute("moby:articleName")=="Length"):
                 t=MobyInteger()
                 t.fromMoby(elt)

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/ontology/SINGER_ACCESSION.py,v
retrieving revision 1.5
retrieving revision 1.6
diff -u -r1.5 -r1.6
--- /home/repository/moby/moby-live/Python/bioMoby/ontology/SINGER_ACCESSION.py	2005/02/01 14:20:44	1.5
+++ /home/repository/moby/moby-live/Python/bioMoby/ontology/SINGER_ACCESSION.py	2005/02/07 14:23:33	1.6
@@ -52,7 +52,8 @@
             if elt.nodeName=="CrossReference" or elt.nodeName=="moby:CrossReference":
                 self.__cross__=[]
                 for ref in elt.childNodes:
-                    self.__cross__.append(um.loads(ref))
+                    if ref.nodeType==ref.ELEMENT_NODE:
+                        self.__cross__.append(um.loadn(ref))
             if elt.nodeType==elt.ELEMENT_NODE and (elt.nodeName=="String" or elt.nodeName=="moby:String") and (elt.getAttribute("articleName")=="ACCNO" or elt.getAttribute("moby:articleName")=="ACCNO"):
                 t=MobyString()
                 t.fromMoby(elt)

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/ontology/Sample.py,v
retrieving revision 1.5
retrieving revision 1.6
diff -u -r1.5 -r1.6
--- /home/repository/moby/moby-live/Python/bioMoby/ontology/Sample.py	2005/02/01 14:20:44	1.5
+++ /home/repository/moby/moby-live/Python/bioMoby/ontology/Sample.py	2005/02/07 14:23:33	1.6
@@ -51,7 +51,8 @@
             if elt.nodeName=="CrossReference" or elt.nodeName=="moby:CrossReference":
                 self.__cross__=[]
                 for ref in elt.childNodes:
-                    self.__cross__.append(um.loads(ref))
+                    if ref.nodeType==ref.ELEMENT_NODE:
+                        self.__cross__.append(um.loadn(ref))
             if elt.nodeType==elt.ELEMENT_NODE and (elt.nodeName=="String" or elt.nodeName=="moby:String") and (elt.getAttribute("articleName")=="code" or elt.getAttribute("moby:articleName")=="code"):
                 t=MobyString()
                 t.fromMoby(elt)

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/ontology/SchematikonMotifID.py,v
retrieving revision 1.5
retrieving revision 1.6
diff -u -r1.5 -r1.6
--- /home/repository/moby/moby-live/Python/bioMoby/ontology/SchematikonMotifID.py	2005/02/01 14:20:44	1.5
+++ /home/repository/moby/moby-live/Python/bioMoby/ontology/SchematikonMotifID.py	2005/02/07 14:23:33	1.6
@@ -49,7 +49,8 @@
             if elt.nodeName=="CrossReference" or elt.nodeName=="moby:CrossReference":
                 self.__cross__=[]
                 for ref in elt.childNodes:
-                    self.__cross__.append(um.loads(ref))
+                    if ref.nodeType==ref.ELEMENT_NODE:
+                        self.__cross__.append(um.loadn(ref))
             if elt.nodeType==elt.ELEMENT_NODE and (elt.nodeName=="String" or elt.nodeName=="moby:String") and (elt.getAttribute("articleName")=="ID" or elt.getAttribute("moby:articleName")=="ID"):
                 t=MobyString()
                 t.fromMoby(elt)

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/ontology/SchematikonMotifSupport.py,v
retrieving revision 1.5
retrieving revision 1.6
diff -u -r1.5 -r1.6
--- /home/repository/moby/moby-live/Python/bioMoby/ontology/SchematikonMotifSupport.py	2005/02/01 14:20:44	1.5
+++ /home/repository/moby/moby-live/Python/bioMoby/ontology/SchematikonMotifSupport.py	2005/02/07 14:23:33	1.6
@@ -50,7 +50,8 @@
             if elt.nodeName=="CrossReference" or elt.nodeName=="moby:CrossReference":
                 self.__cross__=[]
                 for ref in elt.childNodes:
-                    self.__cross__.append(um.loads(ref))
+                    if ref.nodeType==ref.ELEMENT_NODE:
+                        self.__cross__.append(um.loadn(ref))
             if elt.nodeType==elt.ELEMENT_NODE and (elt.nodeName=="Integer" or elt.nodeName=="moby:Integer") and (elt.getAttribute("articleName")=="UniqueSupport" or elt.getAttribute("moby:articleName")=="UniqueSupport"):
                 t=MobyInteger()
                 t.fromMoby(elt)

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/ontology/SchematikonSegmentAttributes.py,v
retrieving revision 1.5
retrieving revision 1.6
diff -u -r1.5 -r1.6
--- /home/repository/moby/moby-live/Python/bioMoby/ontology/SchematikonSegmentAttributes.py	2005/02/01 14:20:44	1.5
+++ /home/repository/moby/moby-live/Python/bioMoby/ontology/SchematikonSegmentAttributes.py	2005/02/07 14:23:33	1.6
@@ -54,7 +54,8 @@
             if elt.nodeName=="CrossReference" or elt.nodeName=="moby:CrossReference":
                 self.__cross__=[]
                 for ref in elt.childNodes:
-                    self.__cross__.append(um.loads(ref))
+                    if ref.nodeType==ref.ELEMENT_NODE:
+                        self.__cross__.append(um.loadn(ref))
             if elt.nodeType==elt.ELEMENT_NODE and (elt.nodeName=="Integer" or elt.nodeName=="moby:Integer") and (elt.getAttribute("articleName")=="Length" or elt.getAttribute("moby:articleName")=="Length"):
                 t=MobyInteger()
                 t.fromMoby(elt)

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/ontology/SchematikonSegmentID.py,v
retrieving revision 1.5
retrieving revision 1.6
diff -u -r1.5 -r1.6
--- /home/repository/moby/moby-live/Python/bioMoby/ontology/SchematikonSegmentID.py	2005/02/01 14:20:44	1.5
+++ /home/repository/moby/moby-live/Python/bioMoby/ontology/SchematikonSegmentID.py	2005/02/07 14:23:33	1.6
@@ -49,7 +49,8 @@
             if elt.nodeName=="CrossReference" or elt.nodeName=="moby:CrossReference":
                 self.__cross__=[]
                 for ref in elt.childNodes:
-                    self.__cross__.append(um.loads(ref))
+                    if ref.nodeType==ref.ELEMENT_NODE:
+                        self.__cross__.append(um.loadn(ref))
             if elt.nodeType==elt.ELEMENT_NODE and (elt.nodeName=="String" or elt.nodeName=="moby:String") and (elt.getAttribute("articleName")=="ID" or elt.getAttribute("moby:articleName")=="ID"):
                 t=MobyString()
                 t.fromMoby(elt)

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/ontology/SchematikonStructureAnnotation.py,v
retrieving revision 1.5
retrieving revision 1.6
diff -u -r1.5 -r1.6
--- /home/repository/moby/moby-live/Python/bioMoby/ontology/SchematikonStructureAnnotation.py	2005/02/01 14:20:44	1.5
+++ /home/repository/moby/moby-live/Python/bioMoby/ontology/SchematikonStructureAnnotation.py	2005/02/07 14:23:33	1.6
@@ -52,7 +52,8 @@
             if elt.nodeName=="CrossReference" or elt.nodeName=="moby:CrossReference":
                 self.__cross__=[]
                 for ref in elt.childNodes:
-                    self.__cross__.append(um.loads(ref))
+                    if ref.nodeType==ref.ELEMENT_NODE:
+                        self.__cross__.append(um.loadn(ref))
             if elt.nodeType==elt.ELEMENT_NODE and (elt.nodeName=="String" or elt.nodeName=="moby:String") and (elt.getAttribute("articleName")=="PROMOTIF gamma-turn" or elt.getAttribute("moby:articleName")=="PROMOTIF gamma-turn"):
                 t=MobyString()
                 t.fromMoby(elt)

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/ontology/SchematikonVorocodeName.py,v
retrieving revision 1.5
retrieving revision 1.6
diff -u -r1.5 -r1.6
--- /home/repository/moby/moby-live/Python/bioMoby/ontology/SchematikonVorocodeName.py	2005/02/01 14:20:44	1.5
+++ /home/repository/moby/moby-live/Python/bioMoby/ontology/SchematikonVorocodeName.py	2005/02/07 14:23:33	1.6
@@ -49,7 +49,8 @@
             if elt.nodeName=="CrossReference" or elt.nodeName=="moby:CrossReference":
                 self.__cross__=[]
                 for ref in elt.childNodes:
-                    self.__cross__.append(um.loads(ref))
+                    if ref.nodeType==ref.ELEMENT_NODE:
+                        self.__cross__.append(um.loadn(ref))
             if elt.nodeType==elt.ELEMENT_NODE and (elt.nodeName=="String" or elt.nodeName=="moby:String") and (elt.getAttribute("articleName")=="VorocodeName" or elt.getAttribute("moby:articleName")=="VorocodeName"):
                 t=MobyString()
                 t.fromMoby(elt)

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/ontology/Scored_acronym_string.py,v
retrieving revision 1.5
retrieving revision 1.6
diff -u -r1.5 -r1.6
--- /home/repository/moby/moby-live/Python/bioMoby/ontology/Scored_acronym_string.py	2005/02/01 14:20:44	1.5
+++ /home/repository/moby/moby-live/Python/bioMoby/ontology/Scored_acronym_string.py	2005/02/07 14:23:33	1.6
@@ -52,7 +52,8 @@
             if elt.nodeName=="CrossReference" or elt.nodeName=="moby:CrossReference":
                 self.__cross__=[]
                 for ref in elt.childNodes:
-                    self.__cross__.append(um.loads(ref))
+                    if ref.nodeType==ref.ELEMENT_NODE:
+                        self.__cross__.append(um.loadn(ref))
             if elt.nodeType==elt.ELEMENT_NODE and (elt.nodeName=="Float" or elt.nodeName=="moby:Float") and (elt.getAttribute("articleName")=="score" or elt.getAttribute("moby:articleName")=="score"):
                 t=MobyFloat()
                 t.fromMoby(elt)

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/ontology/SimpleAnnotatedGIFImage.py,v
retrieving revision 1.5
retrieving revision 1.6
diff -u -r1.5 -r1.6
--- /home/repository/moby/moby-live/Python/bioMoby/ontology/SimpleAnnotatedGIFImage.py	2005/02/01 14:20:44	1.5
+++ /home/repository/moby/moby-live/Python/bioMoby/ontology/SimpleAnnotatedGIFImage.py	2005/02/07 14:23:33	1.6
@@ -50,7 +50,8 @@
             if elt.nodeName=="CrossReference" or elt.nodeName=="moby:CrossReference":
                 self.__cross__=[]
                 for ref in elt.childNodes:
-                    self.__cross__.append(um.loads(ref))
+                    if ref.nodeType==ref.ELEMENT_NODE:
+                        self.__cross__.append(um.loadn(ref))
             if elt.nodeType==elt.ELEMENT_NODE and (elt.nodeName=="String" or elt.nodeName=="moby:String") and (elt.getAttribute("articleName")=="Description" or elt.getAttribute("moby:articleName")=="Description"):
                 t=MobyString()
                 t.fromMoby(elt)

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/ontology/SimpleAnnotatedJPEGImage.py,v
retrieving revision 1.5
retrieving revision 1.6
diff -u -r1.5 -r1.6
--- /home/repository/moby/moby-live/Python/bioMoby/ontology/SimpleAnnotatedJPEGImage.py	2005/02/01 14:20:44	1.5
+++ /home/repository/moby/moby-live/Python/bioMoby/ontology/SimpleAnnotatedJPEGImage.py	2005/02/07 14:23:33	1.6
@@ -51,7 +51,8 @@
             if elt.nodeName=="CrossReference" or elt.nodeName=="moby:CrossReference":
                 self.__cross__=[]
                 for ref in elt.childNodes:
-                    self.__cross__.append(um.loads(ref))
+                    if ref.nodeType==ref.ELEMENT_NODE:
+                        self.__cross__.append(um.loadn(ref))
             if elt.nodeType==elt.ELEMENT_NODE and (elt.nodeName=="String" or elt.nodeName=="moby:String") and (elt.getAttribute("articleName")=="Description" or elt.getAttribute("moby:articleName")=="Description"):
                 t=MobyString()
                 t.fromMoby(elt)

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/ontology/Simple_key_value_pair.py,v
retrieving revision 1.5
retrieving revision 1.6
diff -u -r1.5 -r1.6
--- /home/repository/moby/moby-live/Python/bioMoby/ontology/Simple_key_value_pair.py	2005/02/01 14:20:44	1.5
+++ /home/repository/moby/moby-live/Python/bioMoby/ontology/Simple_key_value_pair.py	2005/02/07 14:23:33	1.6
@@ -50,7 +50,8 @@
             if elt.nodeName=="CrossReference" or elt.nodeName=="moby:CrossReference":
                 self.__cross__=[]
                 for ref in elt.childNodes:
-                    self.__cross__.append(um.loads(ref))
+                    if ref.nodeType==ref.ELEMENT_NODE:
+                        self.__cross__.append(um.loadn(ref))
             if elt.nodeType==elt.ELEMENT_NODE and (elt.nodeName=="String" or elt.nodeName=="moby:String") and (elt.getAttribute("articleName")=="value" or elt.getAttribute("moby:articleName")=="value"):
                 t=MobyString()
                 t.fromMoby(elt)

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/ontology/Snp_allele.py,v
retrieving revision 1.5
retrieving revision 1.6
diff -u -r1.5 -r1.6
--- /home/repository/moby/moby-live/Python/bioMoby/ontology/Snp_allele.py	2005/02/01 14:20:44	1.5
+++ /home/repository/moby/moby-live/Python/bioMoby/ontology/Snp_allele.py	2005/02/07 14:23:33	1.6
@@ -39,7 +39,8 @@
             if elt.nodeName=="CrossReference" or elt.nodeName=="moby:CrossReference":
                 self.__cross__=[]
                 for ref in elt.childNodes:
-                    self.__cross__.append(um.loads(ref))
+                    if ref.nodeType==ref.ELEMENT_NODE:
+                        self.__cross__.append(um.loadn(ref))
             if elt.nodeType==elt.ELEMENT_NODE and (elt.nodeName=="DNASequence" or elt.nodeName=="moby:DNASequence") and (elt.getAttribute("articleName")=="snp_allele" or elt.getAttribute("moby:articleName")=="snp_allele"):
                 self.Snp_allele=MobyDNASequence()
                 self.Snp_allele.fromMoby(elt)
\ No newline at end of file

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/ontology/Snp_genotype.py,v
retrieving revision 1.5
retrieving revision 1.6
diff -u -r1.5 -r1.6
--- /home/repository/moby/moby-live/Python/bioMoby/ontology/Snp_genotype.py	2005/02/01 14:20:44	1.5
+++ /home/repository/moby/moby-live/Python/bioMoby/ontology/Snp_genotype.py	2005/02/07 14:23:33	1.6
@@ -40,7 +40,8 @@
             if elt.nodeName=="CrossReference" or elt.nodeName=="moby:CrossReference":
                 self.__cross__=[]
                 for ref in elt.childNodes:
-                    self.__cross__.append(um.loads(ref))
+                    if ref.nodeType==ref.ELEMENT_NODE:
+                        self.__cross__.append(um.loadn(ref))
             if elt.nodeType==elt.ELEMENT_NODE and (elt.nodeName=="snp_allele" or elt.nodeName=="moby:snp_allele") and (elt.getAttribute("articleName")=="allele1" or elt.getAttribute("moby:articleName")=="allele1"):
                 self.Allele1=MobySnp_allele()
                 self.Allele1.fromMoby(elt)

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/ontology/Study.py,v
retrieving revision 1.5
retrieving revision 1.6
diff -u -r1.5 -r1.6
--- /home/repository/moby/moby-live/Python/bioMoby/ontology/Study.py	2005/02/01 14:20:44	1.5
+++ /home/repository/moby/moby-live/Python/bioMoby/ontology/Study.py	2005/02/07 14:23:33	1.6
@@ -52,7 +52,8 @@
             if elt.nodeName=="CrossReference" or elt.nodeName=="moby:CrossReference":
                 self.__cross__=[]
                 for ref in elt.childNodes:
-                    self.__cross__.append(um.loads(ref))
+                    if ref.nodeType==ref.ELEMENT_NODE:
+                        self.__cross__.append(um.loadn(ref))
             if elt.nodeType==elt.ELEMENT_NODE and (elt.nodeName=="String" or elt.nodeName=="moby:String") and (elt.getAttribute("articleName")=="study_name" or elt.getAttribute("moby:articleName")=="study_name"):
                 t=MobyString()
                 t.fromMoby(elt)

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/ontology/TEST.py,v
retrieving revision 1.5
retrieving revision 1.6
diff -u -r1.5 -r1.6
--- /home/repository/moby/moby-live/Python/bioMoby/ontology/TEST.py	2005/02/01 14:20:44	1.5
+++ /home/repository/moby/moby-live/Python/bioMoby/ontology/TEST.py	2005/02/07 14:23:33	1.6
@@ -48,4 +48,5 @@
             if elt.nodeName=="CrossReference" or elt.nodeName=="moby:CrossReference":
                 self.__cross__=[]
                 for ref in elt.childNodes:
-                    self.__cross__.append(um.loads(ref))
\ No newline at end of file
+                    if ref.nodeType==ref.ELEMENT_NODE:
+                        self.__cross__.append(um.loadn(ref))
\ No newline at end of file

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/ontology/TargetP_result.py,v
retrieving revision 1.5
retrieving revision 1.6
diff -u -r1.5 -r1.6
--- /home/repository/moby/moby-live/Python/bioMoby/ontology/TargetP_result.py	2005/02/01 14:20:44	1.5
+++ /home/repository/moby/moby-live/Python/bioMoby/ontology/TargetP_result.py	2005/02/07 14:23:33	1.6
@@ -54,7 +54,8 @@
             if elt.nodeName=="CrossReference" or elt.nodeName=="moby:CrossReference":
                 self.__cross__=[]
                 for ref in elt.childNodes:
-                    self.__cross__.append(um.loads(ref))
+                    if ref.nodeType==ref.ELEMENT_NODE:
+                        self.__cross__.append(um.loadn(ref))
             if elt.nodeType==elt.ELEMENT_NODE and (elt.nodeName=="Float" or elt.nodeName=="moby:Float") and (elt.getAttribute("articleName")=="o_score" or elt.getAttribute("moby:articleName")=="o_score"):
                 t=MobyFloat()
                 t.fromMoby(elt)

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/ontology/Testout.py,v
retrieving revision 1.5
retrieving revision 1.6
diff -u -r1.5 -r1.6
--- /home/repository/moby/moby-live/Python/bioMoby/ontology/Testout.py	2005/02/01 14:20:44	1.5
+++ /home/repository/moby/moby-live/Python/bioMoby/ontology/Testout.py	2005/02/07 14:23:33	1.6
@@ -53,7 +53,8 @@
             if elt.nodeName=="CrossReference" or elt.nodeName=="moby:CrossReference":
                 self.__cross__=[]
                 for ref in elt.childNodes:
-                    self.__cross__.append(um.loads(ref))
+                    if ref.nodeType==ref.ELEMENT_NODE:
+                        self.__cross__.append(um.loadn(ref))
             if elt.nodeType==elt.ELEMENT_NODE and (elt.nodeName=="Integer" or elt.nodeName=="moby:Integer") and (elt.getAttribute("articleName")=="gid" or elt.getAttribute("moby:articleName")=="gid"):
                 t=MobyInteger()
                 t.fromMoby(elt)

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/ontology/TextBase64.py,v
retrieving revision 1.5
retrieving revision 1.6
diff -u -r1.5 -r1.6
--- /home/repository/moby/moby-live/Python/bioMoby/ontology/TextBase64.py	2005/02/01 14:20:44	1.5
+++ /home/repository/moby/moby-live/Python/bioMoby/ontology/TextBase64.py	2005/02/07 14:23:33	1.6
@@ -48,4 +48,5 @@
             if elt.nodeName=="CrossReference" or elt.nodeName=="moby:CrossReference":
                 self.__cross__=[]
                 for ref in elt.childNodes:
-                    self.__cross__.append(um.loads(ref))
\ No newline at end of file
+                    if ref.nodeType==ref.ELEMENT_NODE:
+                        self.__cross__.append(um.loadn(ref))
\ No newline at end of file

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/ontology/TextFormatted.py,v
retrieving revision 1.5
retrieving revision 1.6
diff -u -r1.5 -r1.6
--- /home/repository/moby/moby-live/Python/bioMoby/ontology/TextFormatted.py	2005/02/01 14:20:44	1.5
+++ /home/repository/moby/moby-live/Python/bioMoby/ontology/TextFormatted.py	2005/02/07 14:23:33	1.6
@@ -48,4 +48,5 @@
             if elt.nodeName=="CrossReference" or elt.nodeName=="moby:CrossReference":
                 self.__cross__=[]
                 for ref in elt.childNodes:
-                    self.__cross__.append(um.loads(ref))
\ No newline at end of file
+                    if ref.nodeType==ref.ELEMENT_NODE:
+                        self.__cross__.append(um.loadn(ref))
\ No newline at end of file

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/ontology/TextHtml.py,v
retrieving revision 1.5
retrieving revision 1.6
diff -u -r1.5 -r1.6
--- /home/repository/moby/moby-live/Python/bioMoby/ontology/TextHtml.py	2005/02/01 14:20:44	1.5
+++ /home/repository/moby/moby-live/Python/bioMoby/ontology/TextHtml.py	2005/02/07 14:23:33	1.6
@@ -48,4 +48,5 @@
             if elt.nodeName=="CrossReference" or elt.nodeName=="moby:CrossReference":
                 self.__cross__=[]
                 for ref in elt.childNodes:
-                    self.__cross__.append(um.loads(ref))
\ No newline at end of file
+                    if ref.nodeType==ref.ELEMENT_NODE:
+                        self.__cross__.append(um.loadn(ref))
\ No newline at end of file

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/ontology/TextPlain.py,v
retrieving revision 1.5
retrieving revision 1.6
diff -u -r1.5 -r1.6
--- /home/repository/moby/moby-live/Python/bioMoby/ontology/TextPlain.py	2005/02/01 14:20:44	1.5
+++ /home/repository/moby/moby-live/Python/bioMoby/ontology/TextPlain.py	2005/02/07 14:23:33	1.6
@@ -48,4 +48,5 @@
             if elt.nodeName=="CrossReference" or elt.nodeName=="moby:CrossReference":
                 self.__cross__=[]
                 for ref in elt.childNodes:
-                    self.__cross__.append(um.loads(ref))
\ No newline at end of file
+                    if ref.nodeType==ref.ELEMENT_NODE:
+                        self.__cross__.append(um.loadn(ref))
\ No newline at end of file

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/ontology/TextUuencoded.py,v
retrieving revision 1.5
retrieving revision 1.6
diff -u -r1.5 -r1.6
--- /home/repository/moby/moby-live/Python/bioMoby/ontology/TextUuencoded.py	2005/02/01 14:20:44	1.5
+++ /home/repository/moby/moby-live/Python/bioMoby/ontology/TextUuencoded.py	2005/02/07 14:23:33	1.6
@@ -48,4 +48,5 @@
             if elt.nodeName=="CrossReference" or elt.nodeName=="moby:CrossReference":
                 self.__cross__=[]
                 for ref in elt.childNodes:
-                    self.__cross__.append(um.loads(ref))
\ No newline at end of file
+                    if ref.nodeType==ref.ELEMENT_NODE:
+                        self.__cross__.append(um.loadn(ref))
\ No newline at end of file

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/ontology/TextXml.py,v
retrieving revision 1.5
retrieving revision 1.6
diff -u -r1.5 -r1.6
--- /home/repository/moby/moby-live/Python/bioMoby/ontology/TextXml.py	2005/02/01 14:20:44	1.5
+++ /home/repository/moby/moby-live/Python/bioMoby/ontology/TextXml.py	2005/02/07 14:23:33	1.6
@@ -48,4 +48,5 @@
             if elt.nodeName=="CrossReference" or elt.nodeName=="moby:CrossReference":
                 self.__cross__=[]
                 for ref in elt.childNodes:
-                    self.__cross__.append(um.loads(ref))
\ No newline at end of file
+                    if ref.nodeType==ref.ELEMENT_NODE:
+                        self.__cross__.append(um.loadn(ref))
\ No newline at end of file

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/ontology/Text_plain.py,v
retrieving revision 1.5
retrieving revision 1.6
diff -u -r1.5 -r1.6
--- /home/repository/moby/moby-live/Python/bioMoby/ontology/Text_plain.py	2005/02/01 14:20:44	1.5
+++ /home/repository/moby/moby-live/Python/bioMoby/ontology/Text_plain.py	2005/02/07 14:23:33	1.6
@@ -48,4 +48,5 @@
             if elt.nodeName=="CrossReference" or elt.nodeName=="moby:CrossReference":
                 self.__cross__=[]
                 for ref in elt.childNodes:
-                    self.__cross__.append(um.loads(ref))
\ No newline at end of file
+                    if ref.nodeType==ref.ELEMENT_NODE:
+                        self.__cross__.append(um.loadn(ref))
\ No newline at end of file

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/ontology/Trait_Details.py,v
retrieving revision 1.5
retrieving revision 1.6
diff -u -r1.5 -r1.6
--- /home/repository/moby/moby-live/Python/bioMoby/ontology/Trait_Details.py	2005/02/01 14:20:44	1.5
+++ /home/repository/moby/moby-live/Python/bioMoby/ontology/Trait_Details.py	2005/02/07 14:23:33	1.6
@@ -54,7 +54,8 @@
             if elt.nodeName=="CrossReference" or elt.nodeName=="moby:CrossReference":
                 self.__cross__=[]
                 for ref in elt.childNodes:
-                    self.__cross__.append(um.loads(ref))
+                    if ref.nodeType==ref.ELEMENT_NODE:
+                        self.__cross__.append(um.loadn(ref))
             if elt.nodeType==elt.ELEMENT_NODE and (elt.nodeName=="String" or elt.nodeName=="moby:String") and (elt.getAttribute("articleName")=="trait_desc" or elt.getAttribute("moby:articleName")=="trait_desc"):
                 t=MobyString()
                 t.fromMoby(elt)

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/ontology/Tree.py,v
retrieving revision 1.5
retrieving revision 1.6
diff -u -r1.5 -r1.6
--- /home/repository/moby/moby-live/Python/bioMoby/ontology/Tree.py	2005/02/01 14:20:44	1.5
+++ /home/repository/moby/moby-live/Python/bioMoby/ontology/Tree.py	2005/02/07 14:23:33	1.6
@@ -48,4 +48,5 @@
             if elt.nodeName=="CrossReference" or elt.nodeName=="moby:CrossReference":
                 self.__cross__=[]
                 for ref in elt.childNodes:
-                    self.__cross__.append(um.loads(ref))
\ No newline at end of file
+                    if ref.nodeType==ref.ELEMENT_NODE:
+                        self.__cross__.append(um.loadn(ref))
\ No newline at end of file

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/ontology/TropGENE_ACCESSION.py,v
retrieving revision 1.5
retrieving revision 1.6
diff -u -r1.5 -r1.6
--- /home/repository/moby/moby-live/Python/bioMoby/ontology/TropGENE_ACCESSION.py	2005/02/01 14:20:44	1.5
+++ /home/repository/moby/moby-live/Python/bioMoby/ontology/TropGENE_ACCESSION.py	2005/02/07 14:23:33	1.6
@@ -68,7 +68,8 @@
             if elt.nodeName=="CrossReference" or elt.nodeName=="moby:CrossReference":
                 self.__cross__=[]
                 for ref in elt.childNodes:
-                    self.__cross__.append(um.loads(ref))
+                    if ref.nodeType==ref.ELEMENT_NODE:
+                        self.__cross__.append(um.loadn(ref))
             if elt.nodeType==elt.ELEMENT_NODE and (elt.nodeName=="TropGENE_LOCUS" or elt.nodeName=="moby:TropGENE_LOCUS") and (elt.getAttribute("articleName")=="RFLP" or elt.getAttribute("moby:articleName")=="RFLP"):
                 self.RFLP=MobyTropGENE_LOCUS()
                 self.RFLP.fromMoby(elt)

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/ontology/TropGENE_Diversity_Matrix.py,v
retrieving revision 1.5
retrieving revision 1.6
diff -u -r1.5 -r1.6
--- /home/repository/moby/moby-live/Python/bioMoby/ontology/TropGENE_Diversity_Matrix.py	2005/02/01 14:20:44	1.5
+++ /home/repository/moby/moby-live/Python/bioMoby/ontology/TropGENE_Diversity_Matrix.py	2005/02/07 14:23:33	1.6
@@ -48,4 +48,5 @@
             if elt.nodeName=="CrossReference" or elt.nodeName=="moby:CrossReference":
                 self.__cross__=[]
                 for ref in elt.childNodes:
-                    self.__cross__.append(um.loads(ref))
\ No newline at end of file
+                    if ref.nodeType==ref.ELEMENT_NODE:
+                        self.__cross__.append(um.loadn(ref))
\ No newline at end of file

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/ontology/TropGENE_LOCUS.py,v
retrieving revision 1.5
retrieving revision 1.6
diff -u -r1.5 -r1.6
--- /home/repository/moby/moby-live/Python/bioMoby/ontology/TropGENE_LOCUS.py	2005/02/01 14:20:44	1.5
+++ /home/repository/moby/moby-live/Python/bioMoby/ontology/TropGENE_LOCUS.py	2005/02/07 14:23:33	1.6
@@ -47,4 +47,5 @@
             if elt.nodeName=="CrossReference" or elt.nodeName=="moby:CrossReference":
                 self.__cross__=[]
                 for ref in elt.childNodes:
-                    self.__cross__.append(um.loads(ref))
\ No newline at end of file
+                    if ref.nodeType==ref.ELEMENT_NODE:
+                        self.__cross__.append(um.loadn(ref))
\ No newline at end of file

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/ontology/VirtualSequence.py,v
retrieving revision 1.5
retrieving revision 1.6
diff -u -r1.5 -r1.6
--- /home/repository/moby/moby-live/Python/bioMoby/ontology/VirtualSequence.py	2005/02/01 14:20:44	1.5
+++ /home/repository/moby/moby-live/Python/bioMoby/ontology/VirtualSequence.py	2005/02/07 14:23:33	1.6
@@ -49,7 +49,8 @@
             if elt.nodeName=="CrossReference" or elt.nodeName=="moby:CrossReference":
                 self.__cross__=[]
                 for ref in elt.childNodes:
-                    self.__cross__.append(um.loads(ref))
+                    if ref.nodeType==ref.ELEMENT_NODE:
+                        self.__cross__.append(um.loadn(ref))
             if elt.nodeType==elt.ELEMENT_NODE and (elt.nodeName=="Integer" or elt.nodeName=="moby:Integer") and (elt.getAttribute("articleName")=="Length" or elt.getAttribute("moby:articleName")=="Length"):
                 t=MobyInteger()
                 t.fromMoby(elt)

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/ontology/WU_BLAST_Text.py,v
retrieving revision 1.5
retrieving revision 1.6
diff -u -r1.5 -r1.6
--- /home/repository/moby/moby-live/Python/bioMoby/ontology/WU_BLAST_Text.py	2005/02/01 14:20:44	1.5
+++ /home/repository/moby/moby-live/Python/bioMoby/ontology/WU_BLAST_Text.py	2005/02/07 14:23:33	1.6
@@ -48,4 +48,5 @@
             if elt.nodeName=="CrossReference" or elt.nodeName=="moby:CrossReference":
                 self.__cross__=[]
                 for ref in elt.childNodes:
-                    self.__cross__.append(um.loads(ref))
\ No newline at end of file
+                    if ref.nodeType==ref.ELEMENT_NODE:
+                        self.__cross__.append(um.loadn(ref))
\ No newline at end of file

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/ontology/Wildcard_Query.py,v
retrieving revision 1.5
retrieving revision 1.6
diff -u -r1.5 -r1.6
--- /home/repository/moby/moby-live/Python/bioMoby/ontology/Wildcard_Query.py	2005/02/01 14:20:44	1.5
+++ /home/repository/moby/moby-live/Python/bioMoby/ontology/Wildcard_Query.py	2005/02/07 14:23:33	1.6
@@ -52,7 +52,8 @@
             if elt.nodeName=="CrossReference" or elt.nodeName=="moby:CrossReference":
                 self.__cross__=[]
                 for ref in elt.childNodes:
-                    self.__cross__.append(um.loads(ref))
+                    if ref.nodeType==ref.ELEMENT_NODE:
+                        self.__cross__.append(um.loadn(ref))
             if elt.nodeType==elt.ELEMENT_NODE and (elt.nodeName=="Integer" or elt.nodeName=="moby:Integer") and (elt.getAttribute("articleName")=="end_row" or elt.getAttribute("moby:articleName")=="end_row"):
                 t=MobyInteger()
                 t.fromMoby(elt)

From yanwong at pub.open-bio.org  Tue Feb  1 03:52:17 2005
From: yanwong at pub.open-bio.org (Yan Wong)
Date: Tue, 1 Feb 2005 03:52:17 -0500
Subject: [MOBY-guts] biomoby commit
Message-ID: <200502010852.j118qHHl013127@pub.open-bio.org>


yanwong
Tue Feb  1 03:52:17 EST 2005
Update of /home/repository/moby/moby-live/Python/bioMoby/webservice
In directory pub.open-bio.org:/tmp/cvs-serv12609/webservice

Modified Files:
	Dispatcher.py Invocators.py TCBioMoby.py __init__.py 
Log Message:


moby-live/Python/bioMoby/webservice Dispatcher.py,1.2,1.3 Invocators.py,1.2,1.3 TCBioMoby.py,1.2,1.3 __init__.py,1.2,1.3
===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/webservice/Dispatcher.py,v
retrieving revision 1.2
retrieving revision 1.3
diff -u -r1.2 -r1.3
--- /home/repository/moby/moby-live/Python/bioMoby/webservice/Dispatcher.py	2005/01/18 13:46:24	1.2
+++ /home/repository/moby/moby-live/Python/bioMoby/webservice/Dispatcher.py	2005/02/01 08:52:17	1.3
@@ -76,7 +76,7 @@
     def __str__(self):
         return "An error occurs during the Dispatcher process: "
 
-	
+        
 class AbstractDispatcher:
     """ Subclass this one to create your own dispatcher class
         a Dispatcher class must have a execute method
@@ -91,16 +91,16 @@
 
         from bioMoby import MobyUnmarshaller
 
-	self._isbase64=False
-	self._workdir=workdir
-	self.answers={}
-	
-	#First see if we have a MobyContent Object or a string
-	mc=mobyContentXML
-	self._isString=False
-	
-	if not hasattr(mobyContentXML, 'queryData'):
-	    self._isString=True
+        self._isbase64=False
+        self._workdir=workdir
+        self.answers={}
+        
+        #First see if we have a MobyContent Object or a string
+        mc=mobyContentXML
+        self._isString=False
+        
+        if not hasattr(mobyContentXML, 'queryData'):
+            self._isString=True
             try:
                 #Do some cleaning on the XML Document before proceeding...
                 #Remove all \t|\n from the <a>\n\t</a>
@@ -110,117 +110,117 @@
                 mc=um.loads("><".join(r.split(mobyContentXML)))
             except:
                 try:
-		    mc=um.loads(base64.decodestring(mobyContentXML))
-	            self._isbase64=True
-	        except binascii.Error:
-	            raise  EDispatchError, "Invalid types in the moby Content object"
+                    mc=um.loads(base64.decodestring(mobyContentXML))
+                    self._isbase64=True
+                except binascii.Error:
+                    raise  EDispatchError, "Invalid types in the moby Content object"
 
         self.queryData=mc.queryData
         self.invocator=Invocator
-	self._invocatorParameters=invocatorParameters
+        self._invocatorParameters=invocatorParameters
         self.commandBuilder=CommandBuilder
         self.formatter=formatter
-	
-	del MobyUnmarshaller
+        
+        del MobyUnmarshaller
 
     def execute(self):
-	""" Override this method
-	"""
-	pass
+        """ Override this method
+        """
+        pass
 
     def _toMoby(self):
-	"""Return the results as a MobyContent Object
-	"""
-	from bioMoby import MobyContent
-	
-	if self._isbase64:
-	    return base64.encodestring(str(MobyContent(self.answers)))
-	
+        """Return the results as a MobyContent Object
+        """
+        from bioMoby import MobyContent
+        
+        if self._isbase64:
+            return base64.encodestring(str(MobyContent(self.answers)))
+        
         return str(MobyContent(self.answers))
 
-	
+        
 class SimpleDispatcher(AbstractDispatcher):
     """ A simple dispatcher execute sequentially the treatments
     """
     def __init__(self, mobyContentXML, Invocator, InvocatorParameters, CommandBuilder, formatter=None, workdir="/tmp"):
-	AbstractDispatcher.__init__(self, mobyContentXML, Invocator, InvocatorParameters, CommandBuilder, formatter, workdir)
-	
-	from bioMoby import MobyObject
-	
-	if 'JOBSESSION' in self.queryData.keys():
-	    self._sessionid=self.queryData['JOBSESSION'][0].id
-	else:
-	    self._sessionid=`random.randint(0,sys.maxint-1)`
-	    
-	    while "session"+self._sessionid in os.listdir(self._workdir):
-		self._sessionid=`random.randint(0,sys.maxint-1)`
-		
+        AbstractDispatcher.__init__(self, mobyContentXML, Invocator, InvocatorParameters, CommandBuilder, formatter, workdir)
+        
+        from bioMoby import MobyObject
+        
+        if 'JOBSESSION' in self.queryData.keys():
+            self._sessionid=self.queryData['JOBSESSION'][0].id
+        else:
+            self._sessionid=`random.randint(0,sys.maxint-1)`
+            
+            while "session"+self._sessionid in os.listdir(self._workdir):
+                self._sessionid=`random.randint(0,sys.maxint-1)`
+                
             os.mkdir(self._workdir+"/session"+self._sessionid)
-	
-	os.chdir(self._workdir+"/session"+self._sessionid)
-	
+        
+        os.chdir(self._workdir+"/session"+self._sessionid)
+        
         self.answers={'JOBSESSION':[MobyObject(namespace="SESSIONID", id=self._sessionid)]}
 
     def _clean(self):
-	"""Clean the session directory
-	"""
+        """Clean the session directory
+        """
         #Clean the session directory
         os.chdir(self._workdir)
         shutil.rmtree(self._workdir+"/session"+self._sessionid)
-	    
+            
     def _fetchAnswers(self):
-	""" Fetch the answers and clean the session directory
-	"""
-	from bioMoby import GeneralInvocator
-	
-	answers={}
+        """ Fetch the answers and clean the session directory
+        """
+        from bioMoby import GeneralInvocator
+        
+        answers={}
 
-	ruserdir="session"+self._sessionid
+        ruserdir="session"+self._sessionid
         try:
-	    l=os.listdir(self._workdir+"/"+ruserdir)
-	except:
-	    l=[]
-	
-	if len(l)>0:
-	    #There is a session directory
+            l=os.listdir(self._workdir+"/"+ruserdir)
+        except:
+            l=[]
+        
+        if len(l)>0:
+            #There is a session directory
             for querykey in l:
-		if querykey[:8]=="results-":
-		    aQueryName=querykey[8:]
-	            gi=GeneralInvocator(aQueryName ,userdir=self._workdir+"/"+ruserdir)
-	            answers[aQueryName]=[gi.getResults()]
+                if querykey[:8]=="results-":
+                    aQueryName=querykey[8:]
+                    gi=GeneralInvocator(aQueryName ,userdir=self._workdir+"/"+ruserdir)
+                    answers[aQueryName]=[gi.getResults()]
 
                     if self.formatter != None:
                         answers[aQueryName]=self.formatter(answers[aQueryName][0])
-			
+                        
             if len(answers.keys())>0:
-	        self.answers=answers
-		
-                self._clean()	
+                self.answers=answers
+                
+                self._clean()        
 
-	del GeneralInvocator
-		
+        del GeneralInvocator
+                
     def execute(self):
-	"""Execute the queries sequentially
-	"""
+        """Execute the queries sequentially
+        """
 
-	try:
+        try:
             for key in self.queryData.keys():
-	        query=self.queryData[key]
-	        r=self.invocator(key, self.commandBuilder(query), userdir=self._workdir+"/session"+self._sessionid)
-	        r.execute()
-	    
-	    self._fetchAnswers()
-	except:
-	    import traceback
-	    import StringIO
-	    from bioMoby import MobyString
-	    sio=StringIO.StringIO()
-	    traceback.print_exc(file=sio)
-	    
-	    self.answers['JOBSESSION']=[MobyString(content=sio.getvalue())]
-	    self._clean()
-	
-	return self._toMoby()
+                query=self.queryData[key]
+                r=self.invocator(key, self.commandBuilder(query), userdir=self._workdir+"/session"+self._sessionid)
+                r.execute()
+            
+            self._fetchAnswers()
+        except:
+            import traceback
+            import StringIO
+            from bioMoby import MobyString
+            sio=StringIO.StringIO()
+            traceback.print_exc(file=sio)
+            
+            self.answers['JOBSESSION']=[MobyString(content=sio.getvalue())]
+            self._clean()
+        
+        return self._toMoby()
 
 class MultiThreadDispatcher(SimpleDispatcher):
     """ Use a MultiThread to execute a query
@@ -231,114 +231,114 @@
         from bioMoby import MobyString
 
         query=self.queryData[queryKey]
-	
-	#Execute the query
+        
+        #Execute the query
         try:
             r=self.invocator(queryKey, self.commandBuilder(query), userdir=self._workdir+"/session"+self._sessionid)
-	    r.execute()
+            r.execute()
             time.sleep(0)
-	    
+            
         except:
-	    #If there is a problem, we return the generated exception
-	    import traceback
-	    import StringIO
-	    sio=StringIO.StringIO()
-	    traceback.print_exc(file=sio)
-	    
-	    self.answers['JOBSESSION']=[MobyString(content=sio.getvalue())]
-	    self._clean()
+            #If there is a problem, we return the generated exception
+            import traceback
+            import StringIO
+            sio=StringIO.StringIO()
+            traceback.print_exc(file=sio)
+            
+            self.answers['JOBSESSION']=[MobyString(content=sio.getvalue())]
+            self._clean()
 
 
         del MobyString
 
     
     def execute(self):
-	""" Execute the queries with threads
-	"""
-	
-	try:
+        """ Execute the queries with threads
+        """
+        
+        try:
             os.chdir(self._workdir+"/session"+self._sessionid)
             mt=MultiThread(self._execute, self.queryData.keys())
             mt.start()
             mt.join()
 
-	    self._fetchAnswers()
+            self._fetchAnswers()
         except:
-	    self._clean()
-	    
-	return self._toMoby()
+            self._clean()
+            
+        return self._toMoby()
 
-	
+        
 class PBSDispatcher(SimpleDispatcher):
     """Dispatcher for PBS jobs
     """
 
     def __init__(self, mobyContentXML, InvocatorParameters, CommandBuilder, formatter=None, workdir="/tmp"):
-	""" PBS Dispatcher work with PBSInvocator
-	    it uses a session directory, a session file (where the queries IDs are stored)
-	    when the execute method is call with an session id, it reads all entries from the session file and
-	    make a qstat on each ids.
-	"""
-	from bioMoby.webservice import PBSInvocator
-	
-	SimpleDispatcher.__init__(self, mobyContentXML, PBSInvocator, InvocatorParameters, CommandBuilder, formatter, workdir)
+        """ PBS Dispatcher work with PBSInvocator
+            it uses a session directory, a session file (where the queries IDs are stored)
+            when the execute method is call with an session id, it reads all entries from the session file and
+            make a qstat on each ids.
+        """
+        from bioMoby.webservice import PBSInvocator
+        
+        SimpleDispatcher.__init__(self, mobyContentXML, PBSInvocator, InvocatorParameters, CommandBuilder, formatter, workdir)
     
     def _getResults(self):
-	""" Do a qstat and check availability of results
-	"""
-	from bioMoby import GeneralInvocator
-	
-	answers={}
-	outputfiles={}
-	queryKeys=[]
-	
-	#Read the sessions file, in which there are all queries identifiers
-	
-	fp=file("sessions","r")
-	for queryInformation in fp.readlines():
-	    #for each queries, retrieve the qsub ids, and associated output files.
-	    #delete the CR at the end of the line before proceding
-	    queryInformation=queryInformation[:-1] 
-	    #Get the IDs
-	    qsubId=queryInformation.split(";")[1].split(".")[0]
-	    qk=queryInformation.split(";")[0]
-	    #Get the query key
-	    queryKeys.append(qk)
+        """ Do a qstat and check availability of results
+        """
+        from bioMoby import GeneralInvocator
+        
+        answers={}
+        outputfiles={}
+        queryKeys=[]
+        
+        #Read the sessions file, in which there are all queries identifiers
+        
+        fp=file("sessions","r")
+        for queryInformation in fp.readlines():
+            #for each queries, retrieve the qsub ids, and associated output files.
+            #delete the CR at the end of the line before proceding
+            queryInformation=queryInformation[:-1] 
+            #Get the IDs
+            qsubId=queryInformation.split(";")[1].split(".")[0]
+            qk=queryInformation.split(";")[0]
+            #Get the query key
+            queryKeys.append(qk)
             #get the associated Outputfiles
-	    outputfiles[qk]=queryInformation.split(";")[2].split("::")
+            outputfiles[qk]=queryInformation.split(";")[2].split("::")
 
-	    #Do a qstat and check if the job is still running or on queue
-	    i, o, e = os.popen3("qstat %s"%qsubId)
+            #Do a qstat and check if the job is still running or on queue
+            i, o, e = os.popen3("qstat %s"%qsubId)
 
-	    orl=o.readlines()
-	    erl=e.readlines()
-	    
-	    if len(orl)>0:
-		#if one job is not finished, exit the _getResults function
-		#The dispatcher will give all the results or none 
-		return None
-	
-	fp.close()
-	
-	# At this step, all jobs are done
-	tdir=self._workdir+"/session"+self._sessionid
-	
-	
-	for querykey in queryKeys:
-	    #check the results-query.out:
-	    if "results-"+querykey+".out" in os.listdir(tdir):
+            orl=o.readlines()
+            erl=e.readlines()
+            
+            if len(orl)>0:
+                #if one job is not finished, exit the _getResults function
+                #The dispatcher will give all the results or none 
+                return None
+        
+        fp.close()
+        
+        # At this step, all jobs are done
+        tdir=self._workdir+"/session"+self._sessionid
+        
+        
+        for querykey in queryKeys:
+            #check the results-query.out:
+            if "results-"+querykey+".out" in os.listdir(tdir):
                 fp=file(tdir+"/results-"+querykey+".out")
-	        s=fp.readlines()
-	        fp.close()
+                s=fp.readlines()
+                fp.close()
 
                 if len(s)==0:
-	            os.remove(tdir+"/results-"+querykey+".out")
-	        else:
-		    if len(outputfiles.keys())>0:
-		        shutil.copy(tdir+"/results-"+querykey+".out", tdir+"/results-"+querykey+"/results.out")
+                    os.remove(tdir+"/results-"+querykey+".out")
+                else:
+                    if len(outputfiles.keys())>0:
+                        shutil.copy(tdir+"/results-"+querykey+".out", tdir+"/results-"+querykey+"/results.out")
 
             for f in outputfiles[querykey]:
-	        ruserdir=tdir+"/results-"+querykey
+                ruserdir=tdir+"/results-"+querykey
                 # if it is a file then retrieve the file
                 if os.path.isfile(f):
                     aTemp=f.split('/')
@@ -351,48 +351,48 @@
                         os.remove(f+"/"+fs)
                     os.removedirs(f)
 
-	#retrieve all the results
+        #retrieve all the results
         try:
-	    l=os.listdir(tdir)
-	except:
-	    l=[]
-	
-	if len(l)>0:
+            l=os.listdir(tdir)
+        except:
+            l=[]
+        
+        if len(l)>0:
             for querykey in l:
-		if querykey[:8]=="results-":
-		    aQueryName=querykey[8:]
-	            gi=GeneralInvocator(aQueryName, userdir=tdir)
-	            answers[aQueryName]=[gi.getResults()]
+                if querykey[:8]=="results-":
+                    aQueryName=querykey[8:]
+                    gi=GeneralInvocator(aQueryName, userdir=tdir)
+                    answers[aQueryName]=[gi.getResults()]
 
                     if self.formatter != None:
                         answers[aQueryName]=self.formatter(answers[aQueryName][0])
-			
+                        
             if len(answers.keys())>0:
-	        self.answers=answers
-		
+                self.answers=answers
+                
                 self._clean()
-	
-	del GeneralInvocator
+        
+        del GeneralInvocator
 
-	
+        
     def execute(self):
-	"""Execute the command in a PBS script using the PBSInvocator
-	"""
+        """Execute the command in a PBS script using the PBSInvocator
+        """
 
         if 'JOBSESSION' in self.queryData.keys():
-	    self.answers=self.queryData
+            self.answers=self.queryData
 
-	    self._getResults()
-	else:
-	    #we need to store informations in a file
-	    #query id, qsubid, outputfiles
-	    fp=file("sessions","w")
-	    for queryKey in self.queryData.keys():
-		query=self.queryData[queryKey]
-	        r=self.invocator(queryKey, self.commandBuilder(query), fp, userdir=self._workdir+"/session"+self._sessionid)
-		r.setParameters(self._invocatorParameters)
-		r.execute()
-	    fp.close()
+            self._getResults()
+        else:
+            #we need to store informations in a file
+            #query id, qsubid, outputfiles
+            fp=file("sessions","w")
+            for queryKey in self.queryData.keys():
+                query=self.queryData[queryKey]
+                r=self.invocator(queryKey, self.commandBuilder(query), fp, userdir=self._workdir+"/session"+self._sessionid)
+                r.setParameters(self._invocatorParameters)
+                r.execute()
+            fp.close()
 
         return self._toMoby()
 
@@ -405,18 +405,18 @@
             The commandBuilder function shall return  a command, arguments, and a set of temporary files
             [queryData]-->("commandName","commandArgs", ["tempfiles"])
         """
-	SimpleDispatcher.__init__(self, mobyContentXML, Invocator, None, CommandBuilder, formatter, workdir)
-	
-	import pyipc
-	
-	#Create a Jobsession ID, a semaphore and a session directory
-	if 'JOBSESSION' in self.queryData.keys():
-	    self._sem=pyipc.SemaphoreGroup(int(self._sessionid))
-	else:
+        SimpleDispatcher.__init__(self, mobyContentXML, Invocator, None, CommandBuilder, formatter, workdir)
+        
+        import pyipc
+        
+        #Create a Jobsession ID, a semaphore and a session directory
+        if 'JOBSESSION' in self.queryData.keys():
+            self._sem=pyipc.SemaphoreGroup(int(self._sessionid))
+        else:
             self._sem=pyipc.SemaphoreGroup(int(self._sessionid))
             self._sem.wait()
-	
-	del pyipc
+        
+        del pyipc
 
     def _execute(self, queryKey):
         """ Execute a single query, store the result in the answers attribute
@@ -424,99 +424,99 @@
         from bioMoby import MobyString
 
         query=self.queryData[queryKey]
-	
-	#Execute the query
+        
+        #Execute the query
         try:
             r=self.invocator(queryKey, self.commandBuilder(query), userdir=self._workdir+"/session"+self._sessionid)
-	    r.execute()
+            r.execute()
             time.sleep(0)
         except:
-	    #If there is a problem, we return the generated exception
-	    import traceback
-	    fp=file(self._workdir+"/session"+self._sessionid+"/results-"+queryKey,"w")
-	    fp.write("The query: "+queryKey+" has not been processed")
-	    traceback.print_exc(file=fp)
-	    fp.close()
+            #If there is a problem, we return the generated exception
+            import traceback
+            fp=file(self._workdir+"/session"+self._sessionid+"/results-"+queryKey,"w")
+            fp.write("The query: "+queryKey+" has not been processed")
+            traceback.print_exc(file=fp)
+            fp.close()
 
         del MobyString
 
     def _getSem(self):
-	try:
-	    #Wait for answers of all queries
-	    self._sem.wait()
-	    self._fetchAnswers()
+        try:
+            #Wait for answers of all queries
+            self._sem.wait()
+            self._fetchAnswers()
 
-	    #Remove the IPC
+            #Remove the IPC
             import pyipc
-	    pyipc.removeIPC(self._sem)
-	    del pyipc
+            pyipc.removeIPC(self._sem)
+            del pyipc
         except:
-	    pass
-	
+            pass
+        
     def execute(self, timeout=120):
         """Execute the queries with a pool of threads, store the results in a mobyContent Object
         """
-	import signal
-	
-	#Do a fetchAnswers if the user has a sessionid
-	if 'JOBSESSION' in self.queryData.keys():
-	    self.answers=self.queryData
-
-	    t=threading.Thread(target=self._getSem)
-	    t.start()
-	    t.join(timeout)
+        import signal
+        
+        #Do a fetchAnswers if the user has a sessionid
+        if 'JOBSESSION' in self.queryData.keys():
+            self.answers=self.queryData
+
+            t=threading.Thread(target=self._getSem)
+            t.start()
+            t.join(timeout)
 
             return self._toMoby()
         else:
-	    #A MobyContent without jobsession id has been received
-	    try:
-		#make a fork
-	        pid=os.fork()
-	    except:
-		raise Exception, "Cannot treat any further request, please retry"
-
-	    if pid>0:
-		#try to get the results
-#		os.wait()
-	        t=threading.Thread(target=self._getSem)
-	        t.start()
-	        t.join(timeout)
+            #A MobyContent without jobsession id has been received
+            try:
+                #make a fork
+                pid=os.fork()
+            except:
+                raise Exception, "Cannot treat any further request, please retry"
+
+            if pid>0:
+                #try to get the results
+#                os.wait()
+                t=threading.Thread(target=self._getSem)
+                t.start()
+                t.join(timeout)
 
                 return self._toMoby()
-	    else:
+            else:
                 #do second fork
                 try: 
                     pid = os.fork()
-		except:
-		    raise Exception, "Cannot treat any further request, please retry"
-		    
+                except:
+                    raise Exception, "Cannot treat any further request, please retry"
+                    
                 if pid>0:
-		    #it it is too long, kill the process
-		    time.sleep(1.05*timeout)
+                    #it it is too long, kill the process
+                    time.sleep(1.05*timeout)
                     os.kill(os.getppid(), signal.SIGKILL)
-		    os._exit(0)
-		else:
-		    #execute the treatment
+                    os._exit(0)
+                else:
+                    #execute the treatment
                     os.setpgrp()
-		    
-		    try:
-		        os.chdir(self._workdir+"/session"+self._sessionid)
-	                mt=MultiThread(self._execute, self.queryData.keys())
+                    
+                    try:
+                        os.chdir(self._workdir+"/session"+self._sessionid)
+                        mt=MultiThread(self._execute, self.queryData.keys())
                         mt.start()
                         mt.join()
-		    except:
-			self._clean()
+                    except:
+                        self._clean()
 
-		    try:
-	                self._sem.signal()
+                    try:
+                        self._sem.signal()
                     finally:
-			if os.getppid()>1:
-                  	    try:
-			        os.kill(os.getppid(), signal.SIGKILL)
-		            except:
-			        pass
-			    
-		        os._exit(0)
+                        if os.getppid()>1:
+                              try:
+                                  os.kill(os.getppid(), signal.SIGKILL)
+                              except:
+                                  pass
+                            
+                        os._exit(0)
 
-	#if nothing works return nothing
-	return {}
+        #if nothing works return nothing
+        return {}

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/webservice/Invocators.py,v
retrieving revision 1.2
retrieving revision 1.3
diff -u -r1.2 -r1.3
--- /home/repository/moby/moby-live/Python/bioMoby/webservice/Invocators.py	2005/01/18 13:46:24	1.2
+++ /home/repository/moby/moby-live/Python/bioMoby/webservice/Invocators.py	2005/02/01 08:52:17	1.3
@@ -18,34 +18,34 @@
     """
     
     def __init__(self, queryid, userdir="/tmp", timeout=None):
-	"""queryid is the identifier of a query, userdir is the session directory, timeout the limit time of execution of the query
-	"""
+        """queryid is the identifier of a query, userdir is the session directory, timeout the limit time of execution of the query
+        """
         self.command=""
         from bioMoby import MobyObject
 
         self.results=[]
         self.queryid=queryid
-	
+        
         del MobyObject
         self.errors=""
         self.userdir=userdir
         
 
     def getResults(self):
-	"""retrieve the results if available
-	"""
+        """retrieve the results if available
+        """
         import os
             
         fname=self.userdir+"/results-"+self.queryid
 
         if os.path.isfile(fname):
-	    #if it is a single file
+            #if it is a single file
             fp=file(fname,"r")
             self.results=[fp.read()]
             fp.close()
 #            os.remove(fname)
         else:
-	    #or a directory
+            #or a directory
             self.results=[]
             for fs in os.listdir(fname):
                 if os.path.isfile(fname+"/"+fs):
@@ -87,32 +87,32 @@
 
         results=[]
 
-	ruserdir=self.userdir+"/results-"+self.queryid
-	
+        ruserdir=self.userdir+"/results-"+self.queryid
+        
         #if there are some output files then retrieve them as results
         if len(self.outputfiles) !=0:
             i,o,e=os.popen3(self.command)
 
-	    #read error first and then standard output
-	    
+            #read error first and then standard output
+            
             try:
                 et=e.read()
-		fp=file(self.userdir+"/"+self.queryid+".err")
-		fp.write(et)
-		fp.close()
+                fp=file(self.userdir+"/"+self.queryid+".err")
+                fp.write(et)
+                fp.close()
             except:
-		pass
-	    
-	    try:
+                pass
+            
+            try:
                 ot=o.read()
-		fp=file(self.userdir+"/"+self.queryid+".out")
-		fp.write(ot)
-		fp.close()
-	    except:
-		pass
+                fp=file(self.userdir+"/"+self.queryid+".out")
+                fp.write(ot)
+                fp.close()
+            except:
+                pass
 
-	    #wait unfinished sub process
-		
+            #wait unfinished sub process
+                
             try:
                 os.wait()
             except:
@@ -123,7 +123,7 @@
             for f in self.outputfiles:
                 # if it is a file then retrieve the file
                 if os.path.isfile(f):
-		    aTemp=f.split('/')
+                    aTemp=f.split('/')
                     shutil.copy(f, ruserdir+"/"+aTemp[len(aTemp)-1])
                     os.remove(f)
                 elif os.path.isdir(f):
@@ -135,20 +135,20 @@
         else:
             stdin, stdout, stderr=os.popen3(self.command)
             results=stdout.read()
-	    
-	    fp=file(self.userdir+"/results-"+self.queryid,"w")
-	    fp.write(results)
-	    fp.close()
-	    
-#	    t=stderr.read()
+            
+            fp=file(self.userdir+"/results-"+self.queryid,"w")
+            fp.write(results)
+            fp.close()
+            
+#            t=stderr.read()
 
             stdin.close()
             stdout.close()
             stderr.close()
             os.wait()    
 
-	#Make all the cleaning wipe the session directory
-	    
+        #Make all the cleaning wipe the session directory
+            
         for tmpfile in self.tempfiles:
             try:
                 if os.path.isfile(tmpfile):
@@ -163,71 +163,71 @@
     """Parameters for the qsub command
     """
     def __init__(self, queueName, qsubParameters):
-	""" queueName: name of the PBS queue
-	    qsubParameters: a list of parameters for the -l option: ['ncpus=4', 'walltime=01:00:00']
-	"""
-	self.queueName=queueName
-	self.qsubParameters=qsubParameters
-	
-	
+        """ queueName: name of the PBS queue
+            qsubParameters: a list of parameters for the -l option: ['ncpus=4', 'walltime=01:00:00']
+        """
+        self.queueName=queueName
+        self.qsubParameters=qsubParameters
+        
+        
 class PBSInvocator(LocalInvocator):
     """Invokes a command in a qsub
     """
     
     def __init__(self, queryKey, command, aFile, userdir="/tmp"):
-	"""The file is needed here to keep the generated outputfiles
-	"""
-	LocalInvocator.__init__(self, queryKey, command, userdir)
-	self._queueName=""
-	self._PBSparameters=[]
-	self._aFile=aFile
+        """The file is needed here to keep the generated outputfiles
+        """
+        LocalInvocator.__init__(self, queryKey, command, userdir)
+        self._queueName=""
+        self._PBSparameters=[]
+        self._aFile=aFile
 
     def setParameters(self, invocatorParameters):
-	"""Set parameters of qsub
-	"""
-	self._queueName=invocatorParameters.queueName
-	self._PBSparameters=invocatorParameters.qsubParameters
-	
+        """Set parameters of qsub
+        """
+        self._queueName=invocatorParameters.queueName
+        self._PBSparameters=invocatorParameters.qsubParameters
+        
     def execute(self):
-	"""execute the command in a qsub script
-	"""
-	
-	#we write in the session directory a small script
-	fp=file(self.userdir+"/"+self.queryid+".sh","w")
-	fp.write("#!/bin/bash\n")
-	fp.write("#PBS -S /bin/bash\n")
-	fp.write("#PBS -o "+self.userdir+"/results-"+self.queryid+".out\n")
-	fp.write("#PBS -e "+self.userdir+"/"+self.queryid+".err\n")
-	fp.write("#PBS -q %s\n"%self._queueName)
-	fp.write("#PBS -l %s\n"%":".join(self._PBSparameters))
-	
-	#we add to the script the cd command in order to be in the session directory
-	fp.write("cd %s\n"%self.userdir)
-	fp.write("%s\n"%self.command)
-	fp.close()
-	
-	import os
-	
-	#execute the qsub command
-	i, o, e=os.popen3("qsub "+self.userdir+"/"+self.queryid+".sh")
-	
-	#see if there are mistakes
-	erl=e.read()
-	
-	if erl!="":
-	    raise Exception, "".join(erl)
+        """execute the command in a qsub script
+        """
+        
+        #we write in the session directory a small script
+        fp=file(self.userdir+"/"+self.queryid+".sh","w")
+        fp.write("#!/bin/bash\n")
+        fp.write("#PBS -S /bin/bash\n")
+        fp.write("#PBS -o "+self.userdir+"/results-"+self.queryid+".out\n")
+        fp.write("#PBS -e "+self.userdir+"/"+self.queryid+".err\n")
+        fp.write("#PBS -q %s\n"%self._queueName)
+        fp.write("#PBS -l %s\n"%":".join(self._PBSparameters))
+        
+        #we add to the script the cd command in order to be in the session directory
+        fp.write("cd %s\n"%self.userdir)
+        fp.write("%s\n"%self.command)
+        fp.close()
+        
+        import os
+        
+        #execute the qsub command
+        i, o, e=os.popen3("qsub "+self.userdir+"/"+self.queryid+".sh")
+        
+        #see if there are mistakes
+        erl=e.read()
+        
+        if erl!="":
+            raise Exception, "".join(erl)
 
-	#write in the session file the queries, qsub identifiers and the output files
-	orl=o.readlines()
+        #write in the session file the queries, qsub identifiers and the output files
+        orl=o.readlines()
         anId=orl[0].split('\n')[0]
 
-	if len(self.outputfiles) !=0:
-	    self._aFile.write(self.queryid+";"+anId+";"+"::".join(self.outputfiles)+"\n")
-	    os.mkdir(self.userdir+"/results-"+self.queryid)
-	    
-	del os
-	#return the qsub identifier
-	return anId
+        if len(self.outputfiles) !=0:
+            self._aFile.write(self.queryid+";"+anId+";"+"::".join(self.outputfiles)+"\n")
+            os.mkdir(self.userdir+"/results-"+self.queryid)
+            
+        del os
+        #return the qsub identifier
+        return anId
 
 class CGIPostMInvocator(GeneralInvocator):
     """Functions for multipart post
@@ -241,9 +241,9 @@
         files is a sequence of (name, filename, value) elements for data to be uploaded as files
         Return the server's response page.
         """
-	    
+            
         import httplib    
-	
+        
         content_type, body = self.encode_multipart_formdata()
         print content_type, body
         h = httplib.HTTP(host)
@@ -253,9 +253,9 @@
         h.endheaders()
         h.send(body)
         errcode, errmsg, headers = h.getreply()
-	    
+            
         del httplib
-	
+        
         return h.file.readlines()
 
     def encode_multipart_formdata(self):

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/webservice/TCBioMoby.py,v
retrieving revision 1.2
retrieving revision 1.3
diff -u -r1.2 -r1.3
--- /home/repository/moby/moby-live/Python/bioMoby/webservice/TCBioMoby.py	2005/01/18 13:46:24	1.2
+++ /home/repository/moby/moby-live/Python/bioMoby/webservice/TCBioMoby.py	2005/02/01 08:52:17	1.3
@@ -53,4 +53,4 @@
         from xml.dom.minidom import parseString
      
         print >>sw, '''<%s><![CDATA[%s]]></%s>''' % (self.tag, parseString(toReturn).toprettyxml(), self.tag)
-	
+        

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/webservice/__init__.py,v
retrieving revision 1.2
retrieving revision 1.3
diff -u -r1.2 -r1.3
--- /home/repository/moby/moby-live/Python/bioMoby/webservice/__init__.py	2005/01/18 13:46:24	1.2
+++ /home/repository/moby/moby-live/Python/bioMoby/webservice/__init__.py	2005/02/01 08:52:17	1.3
@@ -35,7 +35,7 @@
     l=filter(filterfunc, setOfParameters)
     
     if l:
-	return l[0]
+        return l[0]
 
     return 
     
@@ -56,6 +56,6 @@
     l=filter(filterfunc, setOfParameters)
     
     if l:
-	return l[0]
-	
+        return l[0]
+        
     return
\ No newline at end of file



From yanwong at pub.open-bio.org  Tue Feb  1 03:59:44 2005
From: yanwong at pub.open-bio.org (Yan Wong)
Date: Tue, 1 Feb 2005 03:59:44 -0500
Subject: [MOBY-guts] biomoby commit
Message-ID: <200502010859.j118xiLU013177@pub.open-bio.org>


yanwong
Tue Feb  1 03:59:44 EST 2005
Update of /home/repository/moby/moby-live/Python/utils/wx
In directory pub.open-bio.org:/tmp/cvs-serv13152

Modified Files:
	objectBrowser.py 
Log Message:


moby-live/Python/utils/wx objectBrowser.py,1.5,1.6
===================================================================
RCS file: /home/repository/moby/moby-live/Python/utils/wx/objectBrowser.py,v
retrieving revision 1.5
retrieving revision 1.6
diff -u -r1.5 -r1.6
--- /home/repository/moby/moby-live/Python/utils/wx/objectBrowser.py	2005/01/27 08:44:06	1.5
+++ /home/repository/moby/moby-live/Python/utils/wx/objectBrowser.py	2005/02/01 08:59:44	1.6
@@ -65,7 +65,7 @@
                 obj=obj[len(obj)-1]
             else:
                 obj="None"
-	    
+        
             if obj in self._ISARelations:
                 self._ISARelations[obj].append(objectName)
             else:
@@ -102,7 +102,7 @@
 
         self.staticText1 = wxStaticText(id=wxID_WXFRAME1STATICTEXT1,
               label='Description', name='staticText1', parent=self.panel1,
-              pos=wxPoint(16, 0), size=wxSize(64, 16), style=0)
+              pos=wxPoint(16, 0), size=wxSize(70, 16), style=0)
 
         self.textCtrl1 = wxTextCtrl(id=wxID_WXFRAME1TEXTCTRL1, name='textCtrl1',
               parent=self.panel1, pos=wxPoint(16, 16), size=wxSize(400, 56),
@@ -110,7 +110,7 @@
 
         self.staticText2 = wxStaticText(id=wxID_WXFRAME1STATICTEXT2,
               label='Contact Email', name='staticText2', parent=self.panel1,
-              pos=wxPoint(16, 80), size=wxSize(80, 16), style=0)
+              pos=wxPoint(16, 80), size=wxSize(90, 16), style=0)
 
         self.textCtrl2 = wxTextCtrl(id=wxID_WXFRAME1TEXTCTRL2, name='textCtrl2',
               parent=self.panel1, pos=wxPoint(16, 96), size=wxSize(400, 22),
@@ -118,7 +118,7 @@
 
         self.staticText3 = wxStaticText(id=wxID_WXFRAME1STATICTEXT3,
               label='Authority URI', name='staticText3', parent=self.panel1,
-              pos=wxPoint(16, 128), size=wxSize(80, 16), style=0)
+              pos=wxPoint(16, 128), size=wxSize(90, 16), style=0)
 
         self.textCtrl3 = wxTextCtrl(id=wxID_WXFRAME1TEXTCTRL3, name='textCtrl3',
               parent=self.panel1, pos=wxPoint(16, 144), size=wxSize(400, 24),
@@ -126,7 +126,7 @@
 
         self.staticText4 = wxStaticText(id=wxID_WXFRAME1STATICTEXT4,
               label='HAS', name='staticText4', parent=self.panel1,
-              pos=wxPoint(16, 184), size=wxSize(32, 16), style=0)
+              pos=wxPoint(16, 184), size=wxSize(40, 16), style=0)
 
         self.listBox1 = wxListBox(choices=[], id=wxID_WXFRAME1LISTBOX1,
               name='listBox1', parent=self.panel1, pos=wxPoint(16, 200),
@@ -134,7 +134,7 @@
 
         self.staticText5 = wxStaticText(id=wxID_WXFRAME1STATICTEXT5,
               label='HASA', name='staticText5', parent=self.panel1,
-              pos=wxPoint(16, 264), size=wxSize(56, 16), style=0)
+              pos=wxPoint(16, 264), size=wxSize(60, 16), style=0)
 
         self.listBox2 = wxListBox(choices=[], id=wxID_WXFRAME1LISTBOX2,
               name='listBox2', parent=self.panel1, pos=wxPoint(16, 280),
@@ -143,7 +143,7 @@
         self.staticText6 = wxStaticText(id=wxID_WXFRAME1STATICTEXT6,
               label='Services that take this data type as input:',
               name='staticText6', parent=self.panel1, pos=wxPoint(16, 352),
-              size=wxSize(230, 16), style=0)
+              size=wxSize(250, 16), style=0)
 
         self.listBox3 = wxListBox(choices=[], id=wxID_WXFRAME1LISTBOX3,
               name='listBox3', parent=self.panel1, pos=wxPoint(16, 368),
@@ -156,15 +156,15 @@
 
         self.staticText7 = wxStaticText(id=wxID_WXFRAME1STATICTEXT7,
               label='URL', name='staticText7', parent=self, pos=wxPoint(8, 16),
-              size=wxSize(24, 16), style=0)
+              size=wxSize(30, 16), style=0)
 
         self.staticText8 = wxStaticText(id=wxID_WXFRAME1STATICTEXT8, label='NS',
               name='staticText8', parent=self, pos=wxPoint(8, 56),
-              size=wxSize(16, 16), style=0)
+              size=wxSize(20, 16), style=0)
 
         self.button2 = wxButton(id=wxID_WXFRAME1BUTTON2,
               label='Retrieve objects', name='button2', parent=self,
-              pos=wxPoint(8, 136), size=wxSize(120, 22), style=0)
+              pos=wxPoint(8, 136), size=wxSize(120, 24), style=0)
         EVT_BUTTON(self.button2, wxID_WXFRAME1BUTTON2, self.OnButton2Button)
 
         self.gauge1 = wxGauge(id=wxID_WXFRAME1GAUGE1, name='gauge1',
@@ -174,7 +174,7 @@
         self.staticText9 = wxStaticText(id=wxID_WXFRAME1STATICTEXT9,
               label='Services that take this data type as output:',
               name='staticText9', parent=self.panel1, pos=wxPoint(16, 440),
-              size=wxSize(237, 16), style=0)
+              size=wxSize(260, 16), style=0)
 
         self.listBox4 = wxListBox(choices=[], id=wxID_WXFRAME1LISTBOX4,
               name='listBox4', parent=self.panel1, pos=wxPoint(16, 456),
@@ -194,7 +194,7 @@
 
         self.checkBox1 = wxCheckBox(id=wxID_WXFRAME1CHECKBOX1,
               label='Fetch data from cache (if there is any)', name='checkBox1',
-              parent=self, pos=wxPoint(8, 104), size=wxSize(248, 24), style=0)
+              parent=self, pos=wxPoint(8, 104), size=wxSize(260, 24), style=0)
         self.checkBox1.SetValue(False)
 
     def __init__(self, parent):



From yanwong at pub.open-bio.org  Tue Feb  1 06:25:53 2005
From: yanwong at pub.open-bio.org (Yan Wong)
Date: Tue, 1 Feb 2005 06:25:53 -0500
Subject: [MOBY-guts] biomoby commit
Message-ID: <200502011125.j11BPrpK013895@pub.open-bio.org>


yanwong
Tue Feb  1 06:25:53 EST 2005
Update of /home/repository/moby/moby-live/Python/bioMoby
In directory pub.open-bio.org:/tmp/cvs-serv13870

Modified Files:
	mobyDataTypes.py 
Log Message:


moby-live/Python/bioMoby mobyDataTypes.py,1.6,1.7
===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/mobyDataTypes.py,v
retrieving revision 1.6
retrieving revision 1.7
diff -u -r1.6 -r1.7
--- /home/repository/moby/moby-live/Python/bioMoby/mobyDataTypes.py	2005/02/01 08:52:15	1.6
+++ /home/repository/moby/moby-live/Python/bioMoby/mobyDataTypes.py	2005/02/01 11:25:53	1.7
@@ -149,7 +149,7 @@
         #Put the raw content of the object
         #If you want to put your special object, then then you should write 
         #a __str__ method
-        if hasattr(self, "content") and self.content:
+        if hasattr(self, "content") and self.content!=none and self.content!="":
             result.append("%s"%(self.content))
         
         result.append("</%s:%s>"%(self.__prefix__, self.__tag__))



From yanwong at pub.open-bio.org  Tue Feb  1 06:31:22 2005
From: yanwong at pub.open-bio.org (Yan Wong)
Date: Tue, 1 Feb 2005 06:31:22 -0500
Subject: [MOBY-guts] biomoby commit
Message-ID: <200502011131.j11BVMog013947@pub.open-bio.org>


yanwong
Tue Feb  1 06:31:22 EST 2005
Update of /home/repository/moby/moby-live/Python/bioMoby
In directory pub.open-bio.org:/tmp/cvs-serv13922

Modified Files:
	mobyDataTypes.py 
Log Message:


moby-live/Python/bioMoby mobyDataTypes.py,1.7,1.8
===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/mobyDataTypes.py,v
retrieving revision 1.7
retrieving revision 1.8
diff -u -r1.7 -r1.8
--- /home/repository/moby/moby-live/Python/bioMoby/mobyDataTypes.py	2005/02/01 11:25:53	1.7
+++ /home/repository/moby/moby-live/Python/bioMoby/mobyDataTypes.py	2005/02/01 11:31:22	1.8
@@ -149,7 +149,7 @@
         #Put the raw content of the object
         #If you want to put your special object, then then you should write 
         #a __str__ method
-        if hasattr(self, "content") and self.content!=none and self.content!="":
+        if hasattr(self, "content") and self.content!=None and self.content!="":
             result.append("%s"%(self.content))
         
         result.append("</%s:%s>"%(self.__prefix__, self.__tag__))



From yanwong at pub.open-bio.org  Tue Feb  1 09:20:46 2005
From: yanwong at pub.open-bio.org (Yan Wong)
Date: Tue, 1 Feb 2005 09:20:46 -0500
Subject: [MOBY-guts] biomoby commit
Message-ID: <200502011420.j11EKkG9014847@pub.open-bio.org>


yanwong
Tue Feb  1 09:20:46 EST 2005
Update of /home/repository/moby/moby-live/Python/utils
In directory pub.open-bio.org:/tmp/cvs-serv14364/utils

Modified Files:
	moby2python.py 
Log Message:


moby-live/Python/utils moby2python.py,1.4,1.5
===================================================================
RCS file: /home/repository/moby/moby-live/Python/utils/moby2python.py,v
retrieving revision 1.4
retrieving revision 1.5
diff -u -r1.4 -r1.5
--- /home/repository/moby/moby-live/Python/utils/moby2python.py	2005/01/18 13:44:04	1.4
+++ /home/repository/moby/moby-live/Python/utils/moby2python.py	2005/02/01 14:20:46	1.5
@@ -53,7 +53,9 @@
     res=["    def fromMoby(self, value):\n"]
     res.append("        \"\"\" Load the attributes from an XML string\n        \"\"\"")
     res.append("        from bioMoby.mobyMarshal import MobyUnmarshaller")
-    res.append("        doc=parseString(value).firstChild")
+    res.append("        doc=value")
+    res.append("        if isinstance(value, str):")
+    res.append("            doc=parseString(value).firstChild")
     res.append("        um=MobyUnmarshaller()")
     res.append("        self.content=\"\"")
     
@@ -83,7 +85,7 @@
     res.append("            if elt.nodeName==\"CrossReference\" or elt.nodeName==\"moby:CrossReference\":")
     res.append("                self.__cross__=[]")
     res.append("                for ref in elt.childNodes:")
-    res.append("                    self.__cross__.append(ref.toxml())")        
+    res.append("                    self.__cross__.append(um.loads(ref))")        
 
 
     for parameter in parameters:
@@ -92,7 +94,7 @@
             
             if parameter[2]=='Integer' or parameter[2]=='Float' or parameter[2]=='String':
                 res.append("                t="+makeMobyName(parameter[2])+"()")
-                res.append("                t.fromMoby(elt.toxml())")
+                res.append("                t.fromMoby(elt)")
                 if parameter[1]!="[]":
                     res.append("                self."+cleanName(parameter[0])+"=t.content")
                 else:
@@ -100,7 +102,7 @@
                     
             elif parameter[0]!='content':
                 res.append("                self."+cleanName(parameter[0])+"="+makeMobyName(parameter[2])+"()")
-                res.append("                self."+cleanName(parameter[0])+".fromMoby(elt.toxml())")
+                res.append("                self."+cleanName(parameter[0])+".fromMoby(elt)")
                     
     return "\n".join(res)
 
@@ -133,7 +135,7 @@
 
         if ancestor not in paramDict.keys():
             makeInterface(ancestor, path)
-	
+    
         for aProp in getPropertiesFromAncestor(ancestor):
             properties.append(aProp)
    
@@ -150,7 +152,7 @@
                 
             properties.append((articleName,"None",articleType))
 
-	    
+        
     if "HAS" in objectDefinition["Relationship"].keys():
         for hasRelationship in objectDefinition["Relationship"]["HAS"]:
             articleName=hasRelationship[0]
@@ -197,9 +199,9 @@
         pyResult.append("class "+mObjectName+":\n")
 
     if "Description" in objectDefinition:
-	description=objectDefinition["Description"]
+        description=objectDefinition["Description"]
     if "authURI" in objectDefinition:
-	author=objectDefinition["authURI"]
+        author=objectDefinition["authURI"]
     if "contactEmail" in objectDefinition:
         contact=objectDefinition["contactEmail"]
     



From yanwong at pub.open-bio.org  Tue Feb  1 09:20:44 2005
From: yanwong at pub.open-bio.org (Yan Wong)
Date: Tue, 1 Feb 2005 09:20:44 -0500
Subject: [MOBY-guts] biomoby commit
Message-ID: <200502011420.j11EKi83014390@pub.open-bio.org>


yanwong
Tue Feb  1 09:20:44 EST 2005
Update of /home/repository/moby/moby-live/Python/bioMoby
In directory pub.open-bio.org:/tmp/cvs-serv14364/bioMoby

Modified Files:
	mobyDataTypes.py 
Log Message:


moby-live/Python/bioMoby mobyDataTypes.py,1.8,1.9
===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/mobyDataTypes.py,v
retrieving revision 1.8
retrieving revision 1.9
diff -u -r1.8 -r1.9
--- /home/repository/moby/moby-live/Python/bioMoby/mobyDataTypes.py	2005/02/01 11:31:22	1.8
+++ /home/repository/moby/moby-live/Python/bioMoby/mobyDataTypes.py	2005/02/01 14:20:44	1.9
@@ -209,10 +209,10 @@
                     #if there is already an object, then store it inside a list and 
                     #append the other objects in the list 
                     if hasattr(self, associatedObjectName):
-                        if type(getattr(self, associatedObjectName)) is list:
+                        if isinstance(getattr(self, associatedObjectName), list):
                             getattr(self, associatedObjectName).append(o)
                         else:
-                            setattr(self, associatedObjectName, [o])
+                            setattr(self, associatedObjectName, o)
                     else:
                         setattr(self, associatedObjectName, o)
             else:



From yanwong at pub.open-bio.org  Tue Feb  1 09:33:49 2005
From: yanwong at pub.open-bio.org (Yan Wong)
Date: Tue, 1 Feb 2005 09:33:49 -0500
Subject: [MOBY-guts] biomoby commit
Message-ID: <200502011433.j11EXn74014904@pub.open-bio.org>


yanwong
Tue Feb  1 09:33:49 EST 2005
Update of /home/repository/moby/moby-live/Python/bioMoby
In directory pub.open-bio.org:/tmp/cvs-serv14879/bioMoby

Modified Files:
	mobyDataTypes.py 
Log Message:


moby-live/Python/bioMoby mobyDataTypes.py,1.9,1.10
===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/mobyDataTypes.py,v
retrieving revision 1.9
retrieving revision 1.10
diff -u -r1.9 -r1.10
--- /home/repository/moby/moby-live/Python/bioMoby/mobyDataTypes.py	2005/02/01 14:20:44	1.9
+++ /home/repository/moby/moby-live/Python/bioMoby/mobyDataTypes.py	2005/02/01 14:33:49	1.10
@@ -107,7 +107,7 @@
         mobyObjects=filter(filterFunc, dir(self))
         
         #If none, return the tag closed
-        if len(mobyObjects)==0 and (not hasattr(self, "__cross__") or len(self.__cross__)==0) and (not hasattr(self, "__PIB__") or len(self.__PIB__)==0) and (not hasattr(self, "content") or not self.content):
+        if len(mobyObjects)==0 and (not hasattr(self, "__cross__") or len(self.__cross__)==0) and (not hasattr(self, "__PIB__") or len(self.__PIB__)==0) and (not hasattr(self, "content") or self.content==None or self.content==""):
             beginTag.append("/>")
             return " ".join(beginTag)
 



From yanwong at pub.open-bio.org  Wed Feb  2 10:08:34 2005
From: yanwong at pub.open-bio.org (Yan Wong)
Date: Wed, 2 Feb 2005 10:08:34 -0500
Subject: [MOBY-guts] biomoby commit
Message-ID: <200502021508.j12F8YLi020349@pub.open-bio.org>


yanwong
Wed Feb  2 10:08:34 EST 2005
Update of /home/repository/moby/moby-live/Python/bioMoby/ontology
In directory pub.open-bio.org:/tmp/cvs-serv20328

Added Files:
	MSF.py 
Log Message:


moby-live/Python/bioMoby/ontology MSF.py,NONE,1.1


From yanwong at pub.open-bio.org  Wed Feb  2 10:18:06 2005
From: yanwong at pub.open-bio.org (Yan Wong)
Date: Wed, 2 Feb 2005 10:18:06 -0500
Subject: [MOBY-guts] biomoby commit
Message-ID: <200502021518.j12FI6DL020441@pub.open-bio.org>


yanwong
Wed Feb  2 10:18:06 EST 2005
Update of /home/repository/moby/moby-live/Python/bioMoby/ontology
In directory pub.open-bio.org:/tmp/cvs-serv20420

Added Files:
	Alignment.py 
Log Message:


moby-live/Python/bioMoby/ontology Alignment.py,NONE,1.1


From yanwong at pub.open-bio.org  Wed Feb  2 10:20:55 2005
From: yanwong at pub.open-bio.org (Yan Wong)
Date: Wed, 2 Feb 2005 10:20:55 -0500
Subject: [MOBY-guts] biomoby commit
Message-ID: <200502021520.j12FKtBS020499@pub.open-bio.org>


yanwong
Wed Feb  2 10:20:55 EST 2005
Update of /home/repository/moby/moby-live/Python/bioMoby/ontology
In directory pub.open-bio.org:/tmp/cvs-serv20478

Added Files:
	FASTA_NA_multi.py Gene_Expression_data.py 
Log Message:


moby-live/Python/bioMoby/ontology FASTA_NA_multi.py,NONE,1.1 Gene_Expression_data.py,NONE,1.1


From kawas at pub.open-bio.org  Wed Feb  2 11:49:18 2005
From: kawas at pub.open-bio.org (Eddie Kawas)
Date: Wed, 2 Feb 2005 11:49:18 -0500
Subject: [MOBY-guts] biomoby commit
Message-ID: <200502021649.j12GnHCr020760@pub.open-bio.org>


kawas
Wed Feb  2 11:49:17 EST 2005
Update of /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/gui/objectCreationTool
In directory pub.open-bio.org:/tmp/cvs-serv20735/org/biomoby/client/gui/objectCreationTool

Modified Files:
	Construct.java 
Log Message:
Changed the declaration that creates an empty rdf model. Hopefully helps get rid of the logging issues.

moby-live/Java/src/main/org/biomoby/client/gui/objectCreationTool Construct.java,1.1,1.2
===================================================================
RCS file: /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/gui/objectCreationTool/Construct.java,v
retrieving revision 1.1
retrieving revision 1.2
diff -u -r1.1 -r1.2
--- /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/gui/objectCreationTool/Construct.java	2004/09/27 22:15:13	1.1
+++ /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/gui/objectCreationTool/Construct.java	2005/02/02 16:49:17	1.2
@@ -8,6 +8,7 @@
 
 import com.hp.hpl.jena.mem.ModelMem;
 import com.hp.hpl.jena.rdf.model.Model;
+import com.hp.hpl.jena.rdf.model.ModelFactory;
 import com.hp.hpl.jena.rdf.model.Statement;
 import com.hp.hpl.jena.rdf.model.StmtIterator;
 
@@ -52,7 +53,7 @@
 		HashMap homes = new HashMap(); // (key=parent,val=household)
 		try {
 			// create an empty model
-			Model model = new ModelMem();
+			Model model = ModelFactory.createDefaultModel();
 
 			InputStream in =
 				new URL(url)



From yanwong at pub.open-bio.org  Wed Feb  2 11:52:31 2005
From: yanwong at pub.open-bio.org (Yan Wong)
Date: Wed, 2 Feb 2005 11:52:31 -0500
Subject: [MOBY-guts] biomoby commit
Message-ID: <200502021652.j12GqVgK020799@pub.open-bio.org>


yanwong
Wed Feb  2 11:52:31 EST 2005
Update of /home/repository/moby/moby-live/Python/bioMoby
In directory pub.open-bio.org:/tmp/cvs-serv20774

Modified Files:
	mobyDataTypes.py 
Log Message:


moby-live/Python/bioMoby mobyDataTypes.py,1.10,1.11
===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/mobyDataTypes.py,v
retrieving revision 1.10
retrieving revision 1.11
diff -u -r1.10 -r1.11
--- /home/repository/moby/moby-live/Python/bioMoby/mobyDataTypes.py	2005/02/01 14:33:49	1.10
+++ /home/repository/moby/moby-live/Python/bioMoby/mobyDataTypes.py	2005/02/02 16:52:31	1.11
@@ -87,7 +87,7 @@
         
         self.content=content
         
-                
+    
     def toMoby(self):
         """Deserializes the content in XML api
         """
@@ -98,7 +98,7 @@
         for attribute in __ATTRIBUTES__:
             if hasattr(self, attribute) and getattr(self, attribute):
                 beginTag.append("%s:%s=\"%s\""%(self.__prefix__, attribute, getattr(self,attribute)))
-
+            
         #Retrieve only object's attributes that are public.
         filterFunc=lambda x: x[0] != "_" and not callable(getattr(self, x)) and x !="content" and x not in __ATTRIBUTES__
         
@@ -107,13 +107,13 @@
         mobyObjects=filter(filterFunc, dir(self))
         
         #If none, return the tag closed
-        if len(mobyObjects)==0 and (not hasattr(self, "__cross__") or len(self.__cross__)==0) and (not hasattr(self, "__PIB__") or len(self.__PIB__)==0) and (not hasattr(self, "content") or self.content==None or self.content==""):
+        if len(mobyObjects)==0 and (not hasattr(self, "__cross__") or len(self.__cross__)==0) and (not hasattr(self, "__PIB__") or len(self.__PIB__)==0) and (not hasattr(self, "content") or self.content is None or self.content==""):
             beginTag.append("/>")
             return " ".join(beginTag)
-
+        
         #Else, end begin tag and serialize the associated objects
         beginTag.append(">")
-
+        
         result=[" ".join(beginTag)]
         
         #Serialize Cross references
@@ -162,8 +162,8 @@
         elem=xml
         
         if isinstance(xml, str):
-            doc=parseString(xmlstring)
-        
+            doc=parseString(xml)
+            
             elem=doc.firstChild
         
         self.__tag__=elem.localName
@@ -195,10 +195,10 @@
                 else:
                     #Do the same for the other objects
                     associatedObjectName=child.getAttribute("moby:articleName")
-                
+                    
                     if not associatedObjectName:
                         associatedObjectName=child.getAttribute("articleName")
-                
+                        
                     if not associatedObjectName:
                         associatedObjectName="associated"
                     
@@ -252,7 +252,7 @@
         doc=xml
         
         uri=doc.namespaceURI
-    
+        
         MobyObject.fromMoby(self, doc)
         
         self.authURI=doc.getAttributeNS(uri, "authURI")
@@ -260,7 +260,6 @@
         self.evidenceCode=doc.getAttributeNS(uri, "evidenceCode")
         self.xrefType=doc.getAttributeNS(uri, "xrefType")
 
-        
 class MobyInteger(MobyObject):
     """Use this object to serialize/deserialize integers
     """
@@ -311,30 +310,30 @@
         """
         from mobyMarshal import MobyMarshaller
         m=MobyMarshaller()        
-
+        
         result=['<?xml version="1.0" encoding="UTF-8"?><moby:MOBY xmlns:moby="http://www.biomoby.org/moby"><moby:mobyContent']
-                
+        
         if self.authority !="":
             result.append(' moby:authority="'+self.authority+'"')
-                    
+        
         result.append('>')
-                    
+        
         if self.servicenotes !="":
             result.append('<moby:serviceNotes>'+self.servicenotes+'</moby:serviceNotes>')
-
+        
         for queryKey in self.queryData:
             result.append("<moby:mobyData moby:queryID='"+queryKey+"'>")
-
+            
             #For serialization, use the MobyMarshaller object
             
             for queryObject in self.queryData[queryKey]:
                 #if the Collection ('CollectionName',[MobyObjects])
                 if queryObject.__class__ is tuple:
                     result.append("<moby:Collection moby:articleName='"+queryObject[0]+"'>")
-
+                    
                     for aSimple in queryObject[1]:
                         result.append('<moby:Simple>'+m.dumps(aSimple)+'</moby:Simple>')
-                    
+                        
                     result.append("</moby:Collection>")
                 #If it is a parameter
                 elif queryObject.__class__ is Parameter:
@@ -342,13 +341,13 @@
                 #Or a simple object
                 else: 
                     result.append("<moby:Simple>"+m.dumps(queryObject)+"</moby:Simple>")
-
+                
             result.append("</moby:mobyData>")
-
+            
         result.append('</moby:mobyContent></moby:MOBY>')
-
+        
         del MobyMarshaller
-
+        
         return "".join(result)
 
     def fromMoby(self, xmlObject):
@@ -357,7 +356,7 @@
         from bioMoby import MobyUnmarshaller
         
         um=MobyUnmarshaller()
-
+        
         self.queryData={}
         
         doc=xmlObject
@@ -366,35 +365,35 @@
             doc=parseString(xmlObject)
         
         mdl=doc.getElementsByTagName('mobyData')
-
+        
         if not mdl:
             mdl=doc.getElementsByTagName('moby:mobyData')
-
+        
         #For each query            
         for elt in mdl:
             #Get the ID
             queryID=str(elt.getAttribute('queryID'))
-
+            
             if not queryID:
                 queryID=str(elt.getAttribute('moby:queryID'))
-
+            
             #Collect the data
             data=[]
-
+            
             #for each datum translate it in MobyObject, and put it in the list
             for datum in elt.childNodes:
                 #If it is a collection
                 if datum.nodeType==datum.ELEMENT_NODE and datum.localName=="Collection":
                     articleName=datum.getAttribute('moby:articleName')
-        
+                    
                     articles=[]
-        
+                    
                     for article in datum.childNodes:
                         if article.nodeType==article.ELEMENT_NODE and article.localName=="Simple":
                             for child in article.childNodes:
                                 if child.nodeType==child.ELEMENT_NODE:
                                     articles.append(um.loadn(child))
-
+                                    
                     data.append((articleName, articles))
                 #if it is a Simple object
                 elif datum.nodeType==datum.ELEMENT_NODE and datum.localName=="Simple":
@@ -442,7 +441,6 @@
             queries["%s-%s"%(queryName, queryID)]=aSimple
             
         return queries
-                
         
     def getObject(self, queryName, objectName):
         """Get an object from a query with its name
@@ -451,8 +449,7 @@
         
         for obj in filter(filterfunc, self.queryData[queryName]):
             return obj
-
-                
+            
     def getObjects(self, queryName):
         """Retrieve objects from a query
         """
@@ -470,7 +467,7 @@
             result[param.articleName]=param.value
                 
         return result
-
+        
     def getParameter(self, queryName, parameterName):
         """Retrieve a parameter from a query and his name
         """
@@ -484,4 +481,4 @@
     def __repr__(self):
         """put the xml of the Content
         """
-        return self.__str__()
+        return self.__str__()
\ No newline at end of file



From gordonp at pub.open-bio.org  Thu Feb  3 17:37:31 2005
From: gordonp at pub.open-bio.org (Paul Gordon)
Date: Thu, 3 Feb 2005 17:37:31 -0500
Subject: [MOBY-guts] biomoby commit
Message-ID: <200502032237.j13MbV1o027017@pub.open-bio.org>


gordonp
Thu Feb  3 17:37:30 EST 2005
Update of /home/repository/moby/moby-live/Java/src/main/org/biomoby/client
In directory pub.open-bio.org:/tmp/cvs-serv26992

Modified Files:
	MobyRequest.java 
Log Message:
Updated response Vector creation to fix spurious Java array run-time type safety check issues

moby-live/Java/src/main/org/biomoby/client MobyRequest.java,1.5,1.6
===================================================================
RCS file: /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/MobyRequest.java,v
retrieving revision 1.5
retrieving revision 1.6
diff -u -r1.5 -r1.6
--- /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/MobyRequest.java	2004/09/03 20:28:16	1.5
+++ /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/MobyRequest.java	2005/02/03 22:37:30	1.6
@@ -206,6 +206,8 @@
     }
 
     /**
+     * @return a vector of MobyDataInstance[], each element of the vector is the collection of response objects for the correspondingly indexed input request.
+     *
      * @throws MobyException if you try to get the results before calling InvokeService
      */
     public Vector getOutput() throws MobyException{
@@ -679,7 +681,8 @@
 
 	    // What we're building is a Vector, where each element represents
 	    // a Response's DataInstance Output (i.e. Simple and Collection return values)
-	    responsesOutput.add(out.toArray());
+            MobyDataInstance[] mdis = new MobyDataInstance[out.size()];
+	    responsesOutput.add(out.toArray(mdis));
 
 	    releaseXPath(response);
 	}



From yanwong at pub.open-bio.org  Fri Feb  4 07:58:25 2005
From: yanwong at pub.open-bio.org (Yan Wong)
Date: Fri, 4 Feb 2005 07:58:25 -0500
Subject: [MOBY-guts] biomoby commit
Message-ID: <200502041258.j14CwPFg029623@pub.open-bio.org>


yanwong
Fri Feb  4 07:58:24 EST 2005
Update of /home/repository/moby/moby-live/Python/bioMoby/webservice
In directory pub.open-bio.org:/tmp/cvs-serv29563/webservice

Modified Files:
	Dispatcher.py 
Log Message:


moby-live/Python/bioMoby/webservice Dispatcher.py,1.3,1.4
===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/webservice/Dispatcher.py,v
retrieving revision 1.3
retrieving revision 1.4
diff -u -r1.3 -r1.4
--- /home/repository/moby/moby-live/Python/bioMoby/webservice/Dispatcher.py	2005/02/01 08:52:17	1.3
+++ /home/repository/moby/moby-live/Python/bioMoby/webservice/Dispatcher.py	2005/02/04 12:58:24	1.4
@@ -88,9 +88,9 @@
             formatter: a function that transforms raw results from the Invocator into Moby Objects
             workdir: the session directory
         """
-
+        
         from bioMoby import MobyUnmarshaller
-
+        
         self._isbase64=False
         self._workdir=workdir
         self.answers={}
@@ -105,7 +105,7 @@
                 #Do some cleaning on the XML Document before proceeding...
                 #Remove all \t|\n from the <a>\n\t</a>
                 um=MobyUnmarshaller()
-
+                
                 r=re.compile("\>[\n|\t]+\<")
                 mc=um.loads("><".join(r.split(mobyContentXML)))
             except:
@@ -114,7 +114,7 @@
                     self._isbase64=True
                 except binascii.Error:
                     raise  EDispatchError, "Invalid types in the moby Content object"
-
+        
         self.queryData=mc.queryData
         self.invocator=Invocator
         self._invocatorParameters=invocatorParameters
@@ -137,7 +137,7 @@
             return base64.encodestring(str(MobyContent(self.answers)))
         
         return str(MobyContent(self.answers))
-
+        
         
 class SimpleDispatcher(AbstractDispatcher):
     """ A simple dispatcher execute sequentially the treatments
@@ -167,14 +167,14 @@
         #Clean the session directory
         os.chdir(self._workdir)
         shutil.rmtree(self._workdir+"/session"+self._sessionid)
-            
+    
     def _fetchAnswers(self):
         """ Fetch the answers and clean the session directory
         """
         from bioMoby import GeneralInvocator
         
         answers={}
-
+        
         ruserdir="session"+self._sessionid
         try:
             l=os.listdir(self._workdir+"/"+ruserdir)
@@ -188,7 +188,7 @@
                     aQueryName=querykey[8:]
                     gi=GeneralInvocator(aQueryName ,userdir=self._workdir+"/"+ruserdir)
                     answers[aQueryName]=[gi.getResults()]
-
+                    
                     if self.formatter != None:
                         answers[aQueryName]=self.formatter(answers[aQueryName][0])
                         
@@ -196,13 +196,13 @@
                 self.answers=answers
                 
                 self._clean()        
-
+        
         del GeneralInvocator
-                
+    
     def execute(self):
         """Execute the queries sequentially
         """
-
+        
         try:
             for key in self.queryData.keys():
                 query=self.queryData[key]
@@ -229,7 +229,7 @@
         """ Execute a single query, store the result in the answers attribute
         """
         from bioMoby import MobyString
-
+        
         query=self.queryData[queryKey]
         
         #Execute the query
@@ -247,8 +247,7 @@
             
             self.answers['JOBSESSION']=[MobyString(content=sio.getvalue())]
             self._clean()
-
-
+        
         del MobyString
 
     
@@ -261,14 +260,13 @@
             mt=MultiThread(self._execute, self.queryData.keys())
             mt.start()
             mt.join()
-
+            
             self._fetchAnswers()
         except:
             self._clean()
-            
+        
         return self._toMoby()
 
-        
 class PBSDispatcher(SimpleDispatcher):
     """Dispatcher for PBS jobs
     """
@@ -306,10 +304,10 @@
             queryKeys.append(qk)
             #get the associated Outputfiles
             outputfiles[qk]=queryInformation.split(";")[2].split("::")
-
+            
             #Do a qstat and check if the job is still running or on queue
             i, o, e = os.popen3("qstat %s"%qsubId)
-
+            
             orl=o.readlines()
             erl=e.readlines()
             
@@ -330,13 +328,13 @@
                 fp=file(tdir+"/results-"+querykey+".out")
                 s=fp.readlines()
                 fp.close()
-
+                
                 if len(s)==0:
                     os.remove(tdir+"/results-"+querykey+".out")
                 else:
                     if len(outputfiles.keys())>0:
                         shutil.copy(tdir+"/results-"+querykey+".out", tdir+"/results-"+querykey+"/results.out")
-
+            
             for f in outputfiles[querykey]:
                 ruserdir=tdir+"/results-"+querykey
                 # if it is a file then retrieve the file
@@ -350,7 +348,7 @@
                         shutil.copy(f+"/"+fs, ruserdir+"/"+fs)
                         os.remove(f+"/"+fs)
                     os.removedirs(f)
-
+        
         #retrieve all the results
         try:
             l=os.listdir(tdir)
@@ -363,7 +361,7 @@
                     aQueryName=querykey[8:]
                     gi=GeneralInvocator(aQueryName, userdir=tdir)
                     answers[aQueryName]=[gi.getResults()]
-
+                    
                     if self.formatter != None:
                         answers[aQueryName]=self.formatter(answers[aQueryName][0])
                         
@@ -374,14 +372,13 @@
         
         del GeneralInvocator
 
-        
     def execute(self):
         """Execute the command in a PBS script using the PBSInvocator
         """
-
+        
         if 'JOBSESSION' in self.queryData.keys():
             self.answers=self.queryData
-
+            
             self._getResults()
         else:
             #we need to store informations in a file
@@ -393,7 +390,7 @@
                 r.setParameters(self._invocatorParameters)
                 r.execute()
             fp.close()
-
+        
         return self._toMoby()
 
 class Dispatcher(SimpleDispatcher):
@@ -422,7 +419,7 @@
         """ Execute a single query, store the result in the answers attribute
         """
         from bioMoby import MobyString
-
+        
         query=self.queryData[queryKey]
         
         #Execute the query
@@ -437,7 +434,7 @@
             fp.write("The query: "+queryKey+" has not been processed")
             traceback.print_exc(file=fp)
             fp.close()
-
+        
         del MobyString
 
     def _getSem(self):
@@ -445,14 +442,14 @@
             #Wait for answers of all queries
             self._sem.wait()
             self._fetchAnswers()
-
+            
             #Remove the IPC
             import pyipc
             pyipc.removeIPC(self._sem)
             del pyipc
         except:
             pass
-        
+    
     def execute(self, timeout=120):
         """Execute the queries with a pool of threads, store the results in a mobyContent Object
         """
@@ -461,11 +458,11 @@
         #Do a fetchAnswers if the user has a sessionid
         if 'JOBSESSION' in self.queryData.keys():
             self.answers=self.queryData
-
+            
             t=threading.Thread(target=self._getSem)
             t.start()
             t.join(timeout)
-
+            
             return self._toMoby()
         else:
             #A MobyContent without jobsession id has been received
@@ -474,14 +471,14 @@
                 pid=os.fork()
             except:
                 raise Exception, "Cannot treat any further request, please retry"
-
+            
             if pid>0:
                 #try to get the results
 #                os.wait()
                 t=threading.Thread(target=self._getSem)
                 t.start()
                 t.join(timeout)
-
+                
                 return self._toMoby()
             else:
                 #do second fork
@@ -506,7 +503,7 @@
                         mt.join()
                     except:
                         self._clean()
-
+                    
                     try:
                         self._sem.signal()
                     finally:



From yanwong at pub.open-bio.org  Fri Feb  4 07:58:25 2005
From: yanwong at pub.open-bio.org (Yan Wong)
Date: Fri, 4 Feb 2005 07:58:25 -0500
Subject: [MOBY-guts] biomoby commit
Message-ID: <200502041258.j14CwPk7029604@pub.open-bio.org>


yanwong
Fri Feb  4 07:58:24 EST 2005
Update of /home/repository/moby/moby-live/Python/bioMoby
In directory pub.open-bio.org:/tmp/cvs-serv29563

Modified Files:
	mobyClient.py mobyDataTypes.py mobyMarshal.py mobyRegister.py 
	mobyService.py 
Log Message:


moby-live/Python/bioMoby mobyClient.py,1.3,1.4 mobyDataTypes.py,1.11,1.12 mobyMarshal.py,1.4,1.5 mobyRegister.py,1.3,1.4 mobyService.py,1.3,1.4
===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/mobyClient.py,v
retrieving revision 1.3
retrieving revision 1.4
diff -u -r1.3 -r1.4
--- /home/repository/moby/moby-live/Python/bioMoby/mobyClient.py	2005/02/01 08:52:15	1.3
+++ /home/repository/moby/moby-live/Python/bioMoby/mobyClient.py	2005/02/04 12:58:24	1.4
@@ -32,7 +32,7 @@
     def call_method(self, method, arguments):
         """It invokes a remote method of the bioMoby server
         """
-
+        
         #soapaction is necessary, if not, remote calls don't work
         self.server.soapaction=self.ns+"#"+method
         
@@ -48,21 +48,21 @@
             it returns a dictionary {'name':descriptions', ...}
         """
         result={}
-
+        
         #Remote call of the method on the Moby server
         xmlt=self.call_method("retrieveObjectNames", None)
-
+        
         doc=parseString(xmlt)
         
         for node in doc.getElementsByTagName("Object"):
             objectName=node.getAttribute("name")
-
+            
             for subNode in node.childNodes:
                 if subNode.nodeType==subNode.ELEMENT_NODE:
                     for ssNode in subNode.childNodes:
                         if ssNode.nodeType==ssNode.CDATA_SECTION_NODE:
                             result[objectName]=ssNode.nodeValue
-
+        
         return result
 
     def retrieveObjectDefinition(self, objectName):
@@ -72,10 +72,10 @@
         "urn:lsid:biomoby.org:objectrelation:hasa":"HASA",
         "urn:lsid:biomoby.org:objectrelation:has":"HAS"
         }
-
+        
         definition={}
         definition["Relationship"]={}
-
+        
         xmlinput="<retrieveObjectDefinition><objectType>"+objectName+"</objectType></retrieveObjectDefinition>"
         doc=parseString(self.call_method("retrieveObjectDefinition", xmlinput))
         
@@ -85,7 +85,7 @@
                 for elem in child.childNodes:
                     if elem.nodeType==elem.ELEMENT_NODE and elem.nodeName=="objectType" and elem.firstChild:
                         definition["Relationship"][dc[child.getAttribute("relationshipType")]].append((elem.getAttribute("articleName"), elem.firstChild.nodeValue))
-
+            
             elif child.nodeType==child.ELEMENT_NODE:
                 if child.firstChild:
                         definition[str(child.nodeName)]=child.firstChild.nodeValue
@@ -104,23 +104,22 @@
         result=[]
         
         xmlt=self.call_method("retrieveServiceProviders", None)
-
+        
         doc=parseString(xmlt)
         
         for node in doc.getElementsByTagName("serviceProvider"):
             serviceProviderName= node.getAttribute("name")
             result.append(serviceProviderName)
-            
-        return result
-
         
+        return result
+    
     def retrieveNamespaces(self):
         """Retrieves a list of namespaces as a dictionary
         """
         result={}
         
         xmlt=self.call_method("retrieveNamespaces", None)
-
+        
         doc=parseString(xmlt)
         
         for node in doc.getElementsByTagName("Namespace"):
@@ -130,9 +129,8 @@
                     for ssNode in subNode.childNodes:
                         if ssNode.nodeType==ssNode.CDATA_SECTION_NODE:
                             result[ns]=ssNode.nodeValue
-
+        
         return result
-            
 
     def retrieveServiceNames(self):
         """Retrieves a list of service's names as a dictionary {'name':'URI'}
@@ -148,87 +146,84 @@
             authURI=node.getAttribute("authURI")
             
             result[serviceName]=authURI
-   
+        
         return result
 
-
     def retrieveServiceTypes(self):
         """Retrieves a list of service's types as a dictionary {'Name':'Description'}
         """        
         result={}
         
         xmlt=self.call_method("retrieveServiceTypes", None)
-
+        
         doc=parseString(xmlt)
         
         for node in doc.getElementsByTagName("serviceType"):
             st=node.getAttribute("name")      
-
+            
             for subNode in node.childNodes:
                 if subNode.nodeType==subNode.ELEMENT_NODE:
                     for ssNode in subNode.childNodes:
                         if ssNode.nodeType==ssNode.CDATA_SECTION_NODE:
                             result[st]=ssNode.nodeValue
-    
+        
         return result
-
-
+        
     def retrieveServiceWSDLByAuthority(self, serviceName, authority):
         """Retrieves a WSDL from moby from a service name and a URI
         """
         xmlinput="<retrieveService><Service authURI=\"" + authority + "\" serviceName=\"" + serviceName + "\"/></retrieveService>"
         
         xmlt=self.call_method("retrieveService", xmlinput)
-
+        
         doc=parseString(xmlt)
         
         service=doc.firstChild
         wsdl=service.firstChild.nodeValue
-
+        
         return wsdl
-
-
+        
     def retrieveServiceWSDL(self, serviceName):
         """Retrieves a WSDL from the name of a service
         """
         m=self.retrieveServiceNames()
         return self.retrieveServiceWSDLByAuthority(serviceName, m[serviceName])
-
+        
     def retrieveServiceTypesRelationships(self, serviceType, expand):
         """Retrieves the list of service's type's relationships
         """
         result=[]
         
-
+        
         xmlinput="<Relationship><serviceType>" + serviceType + "</serviceType><relationshipType>ISA</relationshipType><expandRelationship>" + `expand` + "</expandRelationship></Relationship>"
         
         xmlt=self.call_method("Relationships", xmlinput)
-
+        
         doc=parseString(xmlt)
         
         for node in doc.getElementsByTagName("Relationship"):
             for serviceType in node.childNodes:
                 if serviceType.nodeType==serviceType.ELEMENT_NODE:
                     result.append(serviceType.firstChild.nodeValue)
-                    
+        
         return result
-    
+        
     def retrieveDataTypesRelationships(self, dataTypeName):
         """Retrieves only ISA relationships
         """
-
+        
         return self.retrieveDataTypesRelationsByType(dataTypeName, 'ISA')
-
+        
     def retrieveDataTypesRelationsByType(self, dataTypeName, relationType):
         """Retrieves data types relationships
         """
-
+        
         result={}
         
         xmlinput="<Relationship><objectType>" + dataTypeName + "</objectType><relationshipType>"+relationType+"</relationshipType><relationshipType>HASA</relationshipType><relationshipType>HAS</relationshipType><expandRelationship>1</expandRelationship></Relationship>"
-
+        
         xmlt=self.call_method("Relationships", xmlinput)
-
+        
         doc=parseString(xmlt)
         
         for node in doc.getElementsByTagName("Relationship"):
@@ -239,15 +234,14 @@
                     relationTypeResults.append(ssNode.firstChild.nodeValue)
                     
             result[relationType]=relationTypeResults
-
-        return result
         
+        return result
         
     def findService(self, mobyQuery):
         """Finds a service from a set of queries
         """
         from mobyService import ServiceQuery ,ServiceList
-
+        
         if mobyQuery.__class__==ServiceQuery:
             xmlInput="<findService>"+str(mobyQuery)+"</findService>"
             
@@ -262,4 +256,4 @@
     def __init__(self, url="http://mobycentral.cbr.nrc.ca/cgi-bin/MOBY05/mobycentral.pl", ns="http://mobycentral.cbr.nrc.ca/MOBY/Central"):
         """Constructor for class Client
         """
-        Central.__init__(self, url, ns)
+        Central.__init__(self, url, ns)
\ No newline at end of file

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/mobyDataTypes.py,v
retrieving revision 1.11
retrieving revision 1.12
diff -u -r1.11 -r1.12
--- /home/repository/moby/moby-live/Python/bioMoby/mobyDataTypes.py	2005/02/02 16:52:31	1.11
+++ /home/repository/moby/moby-live/Python/bioMoby/mobyDataTypes.py	2005/02/04 12:58:24	1.12
@@ -27,12 +27,12 @@
         self.articleName=articleName
         self.value=value
         self.__isSecondary__=True
-        
+    
     def toMoby(self):
         """Returns the object as a XML
         """
         return "<moby:Parameter moby:articleName='"+self.articleName+"'><moby:value>"+str(self.value)+"</moby:value></moby:Parameter>"
-            
+    
     def __str__(self):
         """Return the Parameter in its XML form
         """
@@ -42,7 +42,7 @@
         """Print the XML on the python command line.
         """
         return self.toMoby()
-            
+    
     def fromMoby(self, xml):
         """Get the attributes from a XML string
         """
@@ -55,9 +55,9 @@
         l=xmlelt.getElementsByTagName("value")
         if len(l)==0:
             l=xmlelt.getElementsByTagName("moby:value")
-
+            
             self.value=l[0].firstChild.nodeValue
-        
+
 class MobyGeneric(object):
     """A Generic object (to use with the Marshaller)
     """
@@ -71,7 +71,7 @@
         
         for name, value in kw.items():
             setattr(self, name, value)
-        
+
 class MobyObject(MobyGeneric):
     """Define a Moby XML Object
        It has methods toMoby and fromMoby 
@@ -86,7 +86,7 @@
         self.__PIB__=[]
         
         self.content=content
-        
+
     
     def toMoby(self):
         """Deserializes the content in XML api
@@ -155,7 +155,7 @@
         result.append("</%s:%s>"%(self.__prefix__, self.__tag__))
         
         return "".join(result)
-        
+    
     def fromMoby(self, xml):
         """Deserialization method
         """
@@ -219,14 +219,14 @@
                 self.content.append(child.nodeValue)
                 
         self.content="".join(self.content)
-        
+    
 
     def __str__(self):
         return self.toMoby()
-        
+    
     def __repr__(self):
         return self.toMoby()
-        
+    
 
 class MobyXref(MobyObject):
     """Describes an Xref
@@ -237,7 +237,7 @@
         self.serviceName=serviceName
         self.evidenceCode=evidenceCode
         self.xrefType=xrefType
-        
+    
     def toMoby(self):
         """Serialize the Xref object
         """
@@ -269,7 +269,7 @@
     def fromMoby(self, xml):
         MobyObject.fromMoby(self, xml)
         self.content = int(self.content)
-        
+
 class MobyFloat(MobyObject):
     """Serialize/deserialize floating point numbers
     """
@@ -279,7 +279,7 @@
     def fromMoby(self, xml):
         MobyObject.fromMoby(self, xml)
         self.content=float(self.content)
-        
+
 
 class MobyString(MobyObject):
     """String Moby object
@@ -304,7 +304,7 @@
         """return the XML form of the Moby Content object
         """
         return self.toMoby()
-        
+    
     def toMoby(self):
         """The XML reprentation of the content
         """
@@ -408,12 +408,12 @@
                     data.append(p)
                     
             self.queryData[queryID]=data
-            
+    
     def __getitem__(self, key):
         """Get a query from his name
         """
         return self.queryData[key]
-        
+    
     def __setitem__(self, key, item):
         """Store a query in the dictionary
         """
@@ -423,12 +423,12 @@
         """Return the number of elements inside the dictionary
         """
         return len(self.queryData)
-        
+    
     def keys(self):
         """Return all queries's name
         """
         return self.queryData.keys()
-        
+    
     def collectionToQueries(self, aCollection):
         """Turn a collection of object into a set of queries
         """
@@ -441,7 +441,7 @@
             queries["%s-%s"%(queryName, queryID)]=aSimple
             
         return queries
-        
+    
     def getObject(self, queryName, objectName):
         """Get an object from a query with its name
         """
@@ -449,14 +449,14 @@
         
         for obj in filter(filterfunc, self.queryData[queryName]):
             return obj
-            
+    
     def getObjects(self, queryName):
         """Retrieve objects from a query
         """
         filterfunc=lambda obj: not hasattr(obj, "__isSecondary__")
         
         return filter(filterfunc, self.queryData[queryName])
-        
+    
     def getParameters(self, queryName):
         """Retrieve parameters from a query
         """
@@ -467,7 +467,7 @@
             result[param.articleName]=param.value
                 
         return result
-        
+    
     def getParameter(self, queryName, parameterName):
         """Retrieve a parameter from a query and his name
         """
@@ -477,7 +477,7 @@
         
         if l:
             return l[0]
-        
+    
     def __repr__(self):
         """put the xml of the Content
         """

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/mobyMarshal.py,v
retrieving revision 1.4
retrieving revision 1.5
diff -u -r1.4 -r1.5
--- /home/repository/moby/moby-live/Python/bioMoby/mobyMarshal.py	2005/02/01 08:52:15	1.4
+++ /home/repository/moby/moby-live/Python/bioMoby/mobyMarshal.py	2005/02/04 12:58:24	1.5
@@ -24,11 +24,11 @@
         """
         if type(value).__name__=='NoneType':
             return ""
-
+        
         tvalue=type(value).__name__
-
+        
         method="m_"+tvalue
-
+        
         if hasattr(value, "toMoby"):
             return value.toMoby()
         
@@ -36,15 +36,16 @@
             return getattr(self,method)(value,articleName=articleName)
         
         return self._compoundObject(value, articleName=articleName)
-            
-        
+    
+    
     def m_str(self, value, articleName=""):
         """Return a string as itself"""
         from bioMoby.mobyDataTypes  import MobyString
         m=MobyString(content=value, articleName=articleName)
         del MobyString
-        return str(m)
         
+        return str(m)
+    
     def m_unicode(self, value, articleName=""):
         """Turn a unicode string into a mobyString object
         """
@@ -54,7 +55,7 @@
         """Return a string object into a mobyString object
         """
         return self.m_str(value, articleName)
-        
+    
     def m_int(self, value, namespace="", id="", articleName=""):
         """Turn an integer into a Moby XML object
         """
@@ -62,7 +63,7 @@
         m=MobyInteger(value, namespace=namespace, id=id, articleName=articleName)
         
         return m.toMoby()
-        
+    
     def m_float(self, value, namespace="", id="", articleName=""):
         """Turn a float into a Moby XML object
         """
@@ -70,7 +71,7 @@
         m=MobyFloat(value, namespace=namespace, id=id, articleName=articleName)
         
         return m.toMoby()
-        
+    
     def m_list(self, value, articleName=""):
         """Turn a list into a Moby XML object
         """
@@ -96,8 +97,7 @@
         result.append('</moby:Dict>')
         
         return "".join(result)
-
-            
+    
     def m_tuple(self, value, namespace="", articleName=""):
         """Define a tuple as a Moby Object
         """
@@ -109,7 +109,7 @@
         result.append('</moby:Tuple>')
         
         return "".join(result)
-
+    
     def _compoundObject(self, value, articleName=""):
         """transforms an object and all properties into a XML
         """
@@ -140,7 +140,7 @@
             header.append(">")
             
         result.append(" ".join(header))
-
+        
         if properties:
             result.append("".join(properties))            
         
@@ -149,16 +149,14 @@
         
         if properties:
             result.append("</%s>"%tagName)
-
-
-        return r"".join(result)
-        
         
+        return r"".join(result)
+    
     def dumps(self, value, articleName=""):
         """Serialize the object into a Moby XML object
         """
         return self._marshal(value, articleName)
-        
+    
 
 class MobyUnmarshaller:
     """Transform an XML into a Moby Python Object
@@ -168,24 +166,24 @@
         """ Cleaning the name of the object
         """
         import re
-
+        
         aName=str(aName)
         
         if aName=="":
             return ""
-
+        
         if aName=="namespace" or aName=="id" or aName=='content':
             return aName
-
+        
         r=re.compile("\W")
-    
+        
         t=r.split(aName)
-    
+        
         for i in range(0,len(t)):
             t[i]=str.upper(t[i][0])+t[i][1:]
-
+        
         del re
-
+        
         return "".join(t)
 
     def loadn(self, xmlNode):
@@ -198,7 +196,7 @@
         
         #Try to see if this object got a deserializer
         object2build=self._cleanName(nn)
-
+        
         objectName=str.upper(object2build[0])+object2build[1:]
         
         if hasattr(bioMoby.mobyDataTypes, "Moby%s"%objectName):
@@ -224,14 +222,12 @@
 #            from bioMoby.mobyExceptions import EInvalidMobyXML    
             
 #            raise EInvalidMobyXML
-
-        
+    
     def loads(self, xmlString):
         """ Deserializes an xml string and return a bioMoby-Python object
         """
         if xmlString=="":
             return None    
-
 #        _typesmodule=["bioMoby.mobyDataTypes", "bioMoby.ontology"]
             
         doc=parseString(xmlString)
@@ -254,15 +250,16 @@
             return int(value.firstChild.nodeValue.replace("\n","").replace("\t","").replace(" ",""))
         else:
             return 0
-            
+    
     def m_Float(self, value):
         """Turn a Float XML element into a float number
         """
         value.normalize()
         if value.firstChild:
             return float(value.firstChild.nodeValue.replace("\n","").replace("\t","").replace(" ",""))
+        
         return 0.0
-            
+    
     def m_String(self, value):
         """Turn a Moby XML String element into a String object
         """
@@ -273,9 +270,8 @@
         for aChild in value.childNodes:
             if aChild.nodeType==aChild.TEXT_NODE or aChild.nodeType==aChild.CDATA_SECTION_NODE:
                 cnt.append(aChild.wholeText)
-                
-        return        r"".join(cnt)
         
+        return        r"".join(cnt)
 
     def m_Object(self, value):
         """Turn any XML into a generic object
@@ -283,7 +279,7 @@
         filterFunc= lambda x: x.nodeType==x.ELEMENT_NODE
         
         typeName="GMoby%s"%str(value.localName)
-
+        
         from bioMoby.mobyDataTypes import MobyGeneric
         
         NewType=type(typeName, (MobyGeneric,), {})
@@ -296,24 +292,24 @@
         for tupleAttribute in value.attributes.itemsNS():
             #First item, second field:
             setattr(anObject, str(tupleAttribute[0][1]), str(tupleAttribute[1]))
-
+        
         i=0    
         for elem in filter(filterFunc, value.childNodes):
             methodName="m_%s"%str(elem.localName)
-
+            
             articleName=elem.getAttribute("moby:articleName")
             
             if not articleName:
                 articleName=elem.getAttribute("articleName")
-                
+            
             if not articleName:
                 articleName="attribute_%s"%i
-                
+            
             if hasattr(self, methodName):
                 prop=getattr(self, methodName)(elem)
             else:
-                    prop=self.m_Object(elem)
-                
+                prop=self.m_Object(elem)
+            
             if hasattr(anObject, articleName):
                 t=prop
                 if not type(getattr(anObject, articleName)) is list:
@@ -323,17 +319,17 @@
             else:
                 setattr(anObject, articleName, prop)
             i+=1
-
+        
         content=[]
-
+        
         isContentNode= lambda x: x.nodeType==x.TEXT_NODE or x.nodeType==x.CDATA_SECTION_NODE
         
         for elem in filter(isContentNode, value.childNodes):
             content.append(str(elem.nodeValue))
-            
+        
         if content:
             anObject.content(r"".join(content))
-            
+        
         return anObject
 
     def m_MobyContent(self, value):
@@ -347,5 +343,4 @@
         
         del MobyContent
         
-        return mc
-        
+        return mc
\ No newline at end of file

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/mobyRegister.py,v
retrieving revision 1.3
retrieving revision 1.4
diff -u -r1.3 -r1.4
--- /home/repository/moby/moby-live/Python/bioMoby/mobyRegister.py	2005/02/01 08:52:15	1.3
+++ /home/repository/moby/moby-live/Python/bioMoby/mobyRegister.py	2005/02/04 12:58:24	1.4
@@ -20,10 +20,10 @@
         self.id=""
         self.message=""
         self.RDF=""
-
+        
         #Parse the document, retrieve the success, id, message and RDF fields
         doc=parseString(xmlInput)
-
+        
         if len(doc.getElementsByTagName("success")[0].childNodes)>0:
             self.success=int(doc.getElementsByTagName("success")[0].childNodes[0].nodeValue)
         if len(doc.getElementsByTagName("id")[0].childNodes)>0:
@@ -35,17 +35,17 @@
                 self.RDF=doc.getElementsByTagName("RDF")[0].firstChild.toprettyxml()
         except:
             pass
-
+    
     def __str__(self):
         """Return the moby xml of the instance
         """
         return "<MOBYRegistration><id>"+self.id+"</id><success>"+`self.success`+"</success><message><![CDATA["+self.message+"]]></message><RDF>"+self.RDF+"</RDF></MOBYRegistration>"
-        
+    
     def toTuple(self):
         """return the  tuple form of  the instance
         """
         return (self.id, self.success,  self.message, self.RDF)
-        
+    
     def isSuccess(self):
         """Indicate whether the registration was successful or not
         """
@@ -79,7 +79,7 @@
         GeneralInformations.__init__(self, contact=contactEmail, authURI=authURI, description=description)
         self.relationship=relationship
         self.serviceType=serviceType
-        
+    
     def __str__(self):
         """Return the instance as a Moby XML
         """
@@ -88,22 +88,21 @@
         result.append("<authURI>"+self.authURI+"</authURI>")
         result.append("<Description><![CDATA["+self.description+"]]></Description>")
         result.append('<Relationship relationshipType="'+self.relationship[0]+'">')
-    
+        
         for serviceType in self.relationship[1]:
             result.append('<serviceType>'+serviceType+'</serviceType>')
-
+        
         result.append("</Relationship>")
-            
-
-        return "".join(result)
-
         
+        
+        return "".join(result)
+    
     def register(self):
         """Register the service's type on the moby server
         """
         xmlinput="<registerServiceType>"+str(self)+"</registerServiceType>"
         return RegistrationObject(self.central.call_method("registerServiceType", xmlinput))
-        
+    
     def deregister(self):
         """Deregister the service's Type on moby
         """
@@ -126,7 +125,7 @@
         """
         result=["<objectType>"+self.objectType+"</objectType>"]
         result.append("<Description><![CDATA["+self.description+"]]></Description>")
-                
+        
         for relationship in self.relationships:
             result.append('<Relationship relationshipType="'+relationship[0]+'">')
             
@@ -134,12 +133,11 @@
                 result.append('<objectType articleName="'+objectTypeKey+'">'+relationship[1][objectTypeKey]+'</objectType>')
                 
             result.append("</Relationship>")
-
+        
         result.append("<authURI>"+self.authURI+"</authURI>")
         result.append("<contactEmail>"+self.contact+"</contactEmail>")
-
+        
         return "".join(result)
-
     
     def register(self):
         """Register the  object's class
@@ -160,12 +158,12 @@
     def __init__(self, namespaceType="", contact="", authURI="", description=""):
         GeneralInformations.__init__(self, contact=contact, authURI=authURI,description=description)
         self.namespaceType=namespaceType
-
+    
     def __str__(self):
         """return the XML of the name space
         """
         return "<namespaceType>"+self.namespaceType+"</namespaceType><contactEmail>"+self.contact+"</contactEmail><authURI>"+self.authURI+"</authURI><Description><![CDATA["+self.description+"]]></Description>"
-
+    
     def register(self):
         """Register the namespace on a Moby server
         """
@@ -176,4 +174,4 @@
         """Deregister the namespace
         """
         xmlinput="<deregisterNamespace>"+self.namespaceType+"</deregisterNamespace>"
-        return RegistrationObject(self.central.call_method("deregisterNamespace", xmlinput))
+        return RegistrationObject(self.central.call_method("deregisterNamespace", xmlinput))
\ No newline at end of file

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/mobyService.py,v
retrieving revision 1.3
retrieving revision 1.4
diff -u -r1.3 -r1.4
--- /home/repository/moby/moby-live/Python/bioMoby/mobyService.py	2005/02/01 08:52:15	1.3
+++ /home/repository/moby/moby-live/Python/bioMoby/mobyService.py	2005/02/04 12:58:24	1.4
@@ -33,16 +33,16 @@
         
         for namespace in self.namespaces:
             result.append('<Namespace>'+namespace+'</Namespace>')
-    
+        
         result.append('</Simple>')
         
         return "".join(result)
-
+    
     def fromXML(self, xml):
         """Return an article from a xml node
         """
         node=parseString(xml)
-
+        
         self.name=node.getAttribute("articleName")
         for otns in node.childNodes:
             if otns.nodeName=="objectType":
@@ -63,12 +63,11 @@
         
         self.enums=enums
 
-    
     def toTuple(self):
         """Return the object as a tuple
         """
         return (self.name, self.type, self.default, self.min, self.max, self.enums)
-            
+    
     def __str__(self):
         """Return the xml form of the object
         """
@@ -83,23 +82,23 @@
             
         if self.max !='':
             result.append('<max>'+self.max+'</max>')
-
+        
         for enum in self.enums:
             result.append('<enum>'+enum+'</enum>')
-
+        
         result.append('</Parameter>')
-
+        
         return "".join(result)
-
+    
     def fromXML(self, xml):
         """Return a parameter from a xml
         """
         
         node=parseString(xml)        
-
+        
         self.enums=[]
         self.name=node.getAttribute("articleName")
-
+        
         for childNode in node.childNodes:
             if childNode.nodeName=="datatype":
                 self.type=childNode.firstChild.nodeValue
@@ -129,11 +128,11 @@
         self.protocol="moby"
         self.authURI=""
         self.serviceName=""
-
+        
         self.expandObjects=0
         self.expandServices=1
         self.authoritative=0
-
+        
         if 'serviceName' in kw:
             self.serviceName=kw['serviceName']
         if 'serviceType' in kw:
@@ -148,15 +147,15 @@
             self.outputObjects=kw['outputObjects']
         if 'keywords' in kw:
             self.keywords=kw['keywords']
-            
+    
     def submits2XML(self, entries):
         """Tranforms inputs/outputs into xml
         """
-
+        
         import string
         result=[]
         for submit in entries:
-
+            
             #first look if it is an article or a collection
             #first case
             if submit[1].__class__ is string or submit[1].__class__ is str:
@@ -165,42 +164,41 @@
                 #otns[1] namespace
                 for namespace in submit[2]:
                     result.append("<Namespace>"+namespace+"</Namespace>")
-
+                
                 result.append("</Simple>")
                 #it is a collection
             else:
                 result.append('<Collection articleName="'+submit[0]+'">')
-
+                
                 for simpleArticle in submit[1]:
                     result.append('<Simple articleName="'+simpleArticle[0]+'"><objectType>'+simpleArticle[1]+'</objectType>')
                     for namespace in simpleArticle[2]:
                         result.append("<Namespace>"+namespace+"</namespace>")
-
+                    
                     result.append("</Simple>")
                         
                 result.append("</Collection>")
-
+        
         del string                    
         return "".join(result)
-
-
+    
     def keywords2XML(self, keywords):
         """Transform keywords into xml
         """
         result=[]
+        
         for keyword in keywords:
             result.append("<keyword>"+keyword+"</keyword>")
-            
-
+        
+        
         return "".join(result)
-
-
+    
     def __str__(self):
         """Give the xml form of the query
         """
         result=["<inputObjects><Input>"]
         result.append(self.submits2XML(self.inputObjects))
-
+        
         result.append("</Input></inputObjects><outputObjects><output>")
         result.append(self.submits2XML(self.outputObjects))
         result.append("</output></outputObjects>")
@@ -208,18 +206,18 @@
         result.append("<serviceType>"+self.serviceType+"</serviceType>")
         result.append("<Protocol>moby</Protocol>")
         result.append("<authURI>"+self.authURI+"</authURI>")
-
+        
         if self.serviceName != "" and self.serviceName !="dummy":
             result.append("<serviceName>"+self.serviceName+"</serviceName>")
-
+        
         result.append("<expandObjects>"+`self.expandObjects`+"</expandObjects>")
         result.append("<expandServices>"+`self.expandServices`+"</expandServices>")
         result.append("<authoritative>"+`self.authoritative`+"</authoritative>")
         result.append("<keywords>")
         result.append(self.keywords2XML(self.keywords))
         result.append("</keywords>")
-
-
+        
+        
         return "".join(result)
 
 
@@ -236,10 +234,10 @@
             
             -A WSDL
         """
-
+        
         GeneralInformations.__init__(self)
         self.namespace="http://biomoby.org/"
-
+        
         self.name=""
         self.type=""
         self.category=""
@@ -251,7 +249,7 @@
         self.secondaryArticles=[]
         self.methods=[]
         self.results=""
-
+        
         if len(arg)==1 and arg[0].__class__ is dict:
             arg=arg[0]
             for key in arg.keys():
@@ -291,11 +289,11 @@
         """
         self.methods=[]
         doc=parseString(wsdl)
-
+        
         for method in doc.getElementsByTagName("operation"):
             if method.getAttribute("name") not in self.methods:
                 self.methods.append(method.getAttribute("name"))
-
+        
         if self.url=="":
             for url in doc.getElementsByTagName("soap:address"):
                 self.url=url.getAttribute("location")
@@ -310,7 +308,7 @@
         """
         
         from SOAPpy import SOAPProxy
-
+        
         webservice=SOAPProxy(self.url,namespace=self.namespace)
         
         if method=="":
@@ -318,34 +316,34 @@
                 method=self.name
             else:
                 method=self.methods[0]
-
+        
         if method not in self.methods:
             from bioMoby.mobyExceptions import ENotAWSMethod
             raise ENotAWSMethod
-
+        
         webservice.soapaction=self.namespace+"#"+method
-
+        
         if debug:
             webservice.config.debug=1
         
         toQuery=str(query)
-
+        
         del  SOAPProxy
-
+        
         result=webservice.invoke(method, toQuery)
         
         if returnXml:
             return result
-            
+        
         #try to return a MobyContent Object instead
         from bioMoby.mobyDataTypes import MobyContent
         mc=MobyContent()
         mc.fromMoby(result)
         
         del MobyContent
-
+        
         return mc
-            
+    
     def __str__(self):
         """Returns The moby xml form of the web service
         """
@@ -358,7 +356,7 @@
         result.append("<contactEmail>"+self.contact+"</contactEmail>")
         result.append("<authoritativeService>"+`self.authoritative`+"</authoritativeService>")
         result.append("<Description><![CDATA["+self.description+"]]></Description>")
-
+        
         result.append("<Input>")
         
         for inputObject in self.inputObjects:
@@ -366,25 +364,25 @@
                 result.append(str(inputObject))
             elif inputObject.__class__ is dict:
                 result.append('<Collection articleName="'+inputObject.keys()[0]+'">')
-
+                
                 for aSimple in inputObject[inputObject.keys()[0]]:
                     result.append(str(aSimple))
-
+                
                 result.append("</Collection>")
             else:
                 from mobyExceptions import EInvalidArgument
                 raise EInvalidArgument, "Bad input object"
-            
+        
         result.append("</Input>")
-
+        
         result.append("<Output>")
-
+        
         for output in self.outputObjects:
             if output.__class__ is ServiceArticle:
                 result.append(str(output))
             elif output.__class__ is dict:
                 result.append('<Collection articleName="'+output.keys()[0]+'">')
-
+                
                 for aSimple in output[output.keys()[0]]:
                     result.append(str(aSimple))
                     
@@ -392,19 +390,18 @@
             else:
                 from mobyExceptions import EInvalidArgument
                 raise EInvalidArgument, "Bad output object"
-                    
-
+        
+        
         result.append("</Output>")
-
+        
         result.append("<secondaryArticles>")
         
         for secondaryArticle in self.secondaryArticles:
             result.append(str(secondaryArticle))
-
+        
         result.append("</secondaryArticles>")
-
+        
         return "".join(result)
-    
 
     def register(self):
         """Register the service on the Moby server    
@@ -435,8 +432,7 @@
         """
         
         self.results=self.execute(mobyContent, returnXml=(mobyContent.__class__ is str))
-                
-        
+    
     def start(self, mobycontent, timeout=-1):
         """Start the service as it was a thread
         """
@@ -447,16 +443,14 @@
             self._execThread=Thread(target=self._executeThread, args=(mobycontent,))
         else:
             self._execThread=Thread(target=self._executeThread, args=(mobycontent,), timeout=timeout)
-
-        self._execThread.start()
         
+        self._execThread.start()
+    
     def join(self):
         """Same as Thread.join
         """
         self._execThread.join()
-        
-        
-        
+    
 class ServiceList:
     """Class representing a service's list
     """
@@ -466,16 +460,16 @@
         """
         
         simpleArticle=ServiceArticle(name='',type='',namespaces=[])
-
+        
         simpleArticle.name=node.getAttribute("articleName")
         for otns in node.childNodes:
             if otns.nodeName=="objectType":
                 simpleArticle.type=otns.firstChild.nodeValue
             elif otns.nodeName=="Namespace":
                 simpleArticle.namespaces.append(otns.firstChild.nodeValue)
-                
+        
         return simpleArticle
-
+    
     def toCollection(self, node):
         """Return a collection of articles
         """
@@ -485,21 +479,20 @@
         for simpleArticle in node.childNodes:
             if simpleArticle.nodeName=="Simple":
                 collection.append(self.toSimpleArticle(simpleArticle))
-            
+        
         result[collectionName]=collection
         
         return result
     
-
     def toSecondary(self, node):
         """Return a parameter from a xml
         """
         secondary=ServiceSecondary(name="", type="", default="", min="", max="", enums=[])
-
+        
         secondary.enums=[]
-
+        
         secondary.name=node.getAttribute("articleName")
-
+        
         for childNode in node.childNodes:
             if childNode.nodeName=="datatype":
                 if childNode.firstChild:
@@ -516,18 +509,18 @@
             elif childNode.nodeName=="enum":
                 if childNode.firstChild:
                     secondary.enums.append(childNode.firstChild.nodeValue)
-
+        
         return secondary
 
     def __init__(self, xmlt):
         """Give the instance of an object from xml
         """
         self.list=[]
-
+        
         doc=parseString(xmlt)
         #for each service
         for node in doc.getElementsByTagName("Service"):
-
+            
             service=Service()
             service.name=node.getAttribute("serviceName")
             service.methods=[service.name]
@@ -565,7 +558,7 @@
                     for secondary in child.childNodes:
                         if secondary.nodeName=="Parameter":
                             service.secondaryArticles.append(self.toSecondary(secondary))
-                            
+            
             self.list.append(service)
 
     def getServiceByName(self, nameOfService):
@@ -574,7 +567,7 @@
         for service in self.list:
             if service.name==nameOfService:
                 return service
-                
+        
         return None
     
     def getServiceByAuthURI(self, authURI):
@@ -583,7 +576,7 @@
         for service in self.list:
             if service.authURI==authURI:
                 return service
-                
+        
         return None
 
     def __getitem__(self, key):



From yanwong at pub.open-bio.org  Fri Feb  4 10:58:37 2005
From: yanwong at pub.open-bio.org (Yan Wong)
Date: Fri, 4 Feb 2005 10:58:37 -0500
Subject: [MOBY-guts] biomoby commit
Message-ID: <200502041558.j14Fwbbt030084@pub.open-bio.org>


yanwong
Fri Feb  4 10:58:37 EST 2005
Update of /home/repository/moby/moby-live/Python/bioMoby
In directory pub.open-bio.org:/tmp/cvs-serv30059

Modified Files:
	mobyDataTypes.py 
Log Message:


moby-live/Python/bioMoby mobyDataTypes.py,1.12,1.13
===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/mobyDataTypes.py,v
retrieving revision 1.12
retrieving revision 1.13
diff -u -r1.12 -r1.13
--- /home/repository/moby/moby-live/Python/bioMoby/mobyDataTypes.py	2005/02/04 12:58:24	1.12
+++ /home/repository/moby/moby-live/Python/bioMoby/mobyDataTypes.py	2005/02/04 15:58:37	1.13
@@ -438,7 +438,7 @@
         queryID=1
         
         for aSimple in aCollection[1]:
-            queries["%s-%s"%(queryName, queryID)]=aSimple
+            queries["%s-%s"%(queryName, queryID)]=[aSimple]
             
         return queries
     



From yanwong at pub.open-bio.org  Fri Feb  4 11:03:40 2005
From: yanwong at pub.open-bio.org (Yan Wong)
Date: Fri, 4 Feb 2005 11:03:40 -0500
Subject: [MOBY-guts] biomoby commit
Message-ID: <200502041603.j14G3eqD030127@pub.open-bio.org>


yanwong
Fri Feb  4 11:03:40 EST 2005
Update of /home/repository/moby/moby-live/Python/bioMoby
In directory pub.open-bio.org:/tmp/cvs-serv30102

Modified Files:
	mobyDataTypes.py 
Log Message:


moby-live/Python/bioMoby mobyDataTypes.py,1.13,1.14
===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/mobyDataTypes.py,v
retrieving revision 1.13
retrieving revision 1.14
diff -u -r1.13 -r1.14
--- /home/repository/moby/moby-live/Python/bioMoby/mobyDataTypes.py	2005/02/04 15:58:37	1.13
+++ /home/repository/moby/moby-live/Python/bioMoby/mobyDataTypes.py	2005/02/04 16:03:40	1.14
@@ -439,6 +439,7 @@
         
         for aSimple in aCollection[1]:
             queries["%s-%s"%(queryName, queryID)]=[aSimple]
+            queryID+=1
             
         return queries
     



From mwilkinson at pub.open-bio.org  Sun Feb  6 16:58:36 2005
From: mwilkinson at pub.open-bio.org (Mark Wilkinson)
Date: Sun, 6 Feb 2005 16:58:36 -0500
Subject: [MOBY-guts] biomoby commit
Message-ID: <200502062158.j16LwaE7014950@pub.open-bio.org>


mwilkinson
Sun Feb  6 16:58:36 EST 2005
Update of /home/repository/moby/moby-live/Perl/MOBY
In directory pub.open-bio.org:/tmp/cvs-serv14931

Modified Files:
	Central.pm 
Log Message:
should fiux problem with servicd registration

moby-live/Perl/MOBY Central.pm,1.146,1.147
===================================================================
RCS file: /home/repository/moby/moby-live/Perl/MOBY/Central.pm,v
retrieving revision 1.146
retrieving revision 1.147
diff -u -r1.146 -r1.147
--- /home/repository/moby/moby-live/Perl/MOBY/Central.pm	2004/12/14 20:55:11	1.146
+++ /home/repository/moby/moby-live/Perl/MOBY/Central.pm	2005/02/06 21:58:35	1.147
@@ -3220,7 +3220,7 @@
 		  && &_LOG( $_->nodeType, "\t", $_->toString, "\n" );
 
 		#next unless $_->nodeType == TEXT_NODE;
-		$content .= $_->toString;
+		$content .= $_->textContent;
 	}
 	return $content;
 }
@@ -3243,7 +3243,7 @@
 		if ($_->toString =~ /<!\[CDATA\[((?>[^\]]+))\]\]>/) {
 			$content .= $1;
 		} else {
-			$content .= $_->toString;
+			$content .= $_->textContent;
 		}
 	}
 	return $content;



From mwilkinson at pub.open-bio.org  Sun Feb  6 17:24:48 2005
From: mwilkinson at pub.open-bio.org (Mark Wilkinson)
Date: Sun, 6 Feb 2005 17:24:48 -0500
Subject: [MOBY-guts] biomoby commit
Message-ID: <200502062224.j16MOmFc015075@pub.open-bio.org>


mwilkinson
Sun Feb  6 17:24:47 EST 2005
Update of /home/repository/moby/moby-live/Perl/MOBY/Client
In directory pub.open-bio.org:/tmp/cvs-serv15056/MOBY/Client

Modified Files:
	Central.pm 
Log Message:
fixing at teh client side as well

moby-live/Perl/MOBY/Client Central.pm,1.87,1.88
===================================================================
RCS file: /home/repository/moby/moby-live/Perl/MOBY/Client/Central.pm,v
retrieving revision 1.87
retrieving revision 1.88
diff -u -r1.87 -r1.88
--- /home/repository/moby/moby-live/Perl/MOBY/Client/Central.pm	2004/12/15 19:37:12	1.87
+++ /home/repository/moby/moby-live/Perl/MOBY/Client/Central.pm	2005/02/06 22:24:47	1.88
@@ -1863,7 +1863,7 @@
 
 		#print getNodeTypeName($_), "\t", $_->toString,"\n";
 		next unless $_->nodeType == TEXT_NODE;
-		$content = $_->toString;
+		$content = $_->textContent;
 	}
     $content ||="";
 	$content =~ s/<!\[CDATA\[((?>[^\]]+))\]\]>/$1/gs;
@@ -1883,14 +1883,14 @@
 
 		#print getNodeTypeName($_), "\t", $_->toString,"\n";
 		next unless $_->nodeType == TEXT_NODE;
-		$content = $_->toString;
+		$content = $_->textContent;
 	}
 	return $content;
 }
 
 sub _nodeRawContent {
 
-	# will get text of **all** child $node from the given $DOM
+	# will get XML of **all** child $node from the given $DOM
 	# regardless of their depth!!
 	my ( $DOM, $node ) = @_;
 	my $x = $DOM->getElementsByTagName( $node );
@@ -1923,7 +1923,7 @@
 
 			#print getNodeTypeName($_), "\t", $_->toString,"\n";
 			next unless $_->nodeType == TEXT_NODE;
-			push @result, $_->toString;
+			push @result, $_->textContent;
 		}
 	}
 	return @result;



From mwilkinson at pub.open-bio.org  Sun Feb  6 17:46:45 2005
From: mwilkinson at pub.open-bio.org (Mark Wilkinson)
Date: Sun, 6 Feb 2005 17:46:45 -0500
Subject: [MOBY-guts] biomoby commit
Message-ID: <200502062246.j16MkjAO015335@pub.open-bio.org>


mwilkinson
Sun Feb  6 17:46:45 EST 2005
Update of /home/repository/moby/moby-live/Perl/MOBY/Client
In directory pub.open-bio.org:/tmp/cvs-serv15316

Modified Files:
	Central.pm 
Log Message:
fixing the registration object output

moby-live/Perl/MOBY/Client Central.pm,1.88,1.89
===================================================================
RCS file: /home/repository/moby/moby-live/Perl/MOBY/Client/Central.pm,v
retrieving revision 1.88
retrieving revision 1.89
diff -u -r1.88 -r1.89
--- /home/repository/moby/moby-live/Perl/MOBY/Client/Central.pm	2005/02/06 22:24:47	1.88
+++ /home/repository/moby/moby-live/Perl/MOBY/Client/Central.pm	2005/02/06 22:46:45	1.89
@@ -1829,6 +1829,7 @@
 	my $id      = &_nodeTextContent( $Object,  'id' );
 	my $success = &_nodeTextContent( $Object,  'success' );
 	my $message = &_nodeCDATAContent( $Object, 'message' );
+print STDERR "******$message******\n";
 	my $RDF     = &_nodeRawContent( $Object,   'RDF' );
 	my $reg = MOBY::Client::Registration->new(
 											   success         => $success,
@@ -1862,7 +1863,7 @@
 	foreach ( @child ) {
 
 		#print getNodeTypeName($_), "\t", $_->toString,"\n";
-		next unless $_->nodeType == TEXT_NODE;
+		next unless (($_->nodeType == TEXT_NODE) || ($_->nodeType == CDATA_SECTION_NODE));
 		$content = $_->textContent;
 	}
     $content ||="";
@@ -1882,7 +1883,7 @@
 	foreach ( @child ) {
 
 		#print getNodeTypeName($_), "\t", $_->toString,"\n";
-		next unless $_->nodeType == TEXT_NODE;
+		next unless (($_->nodeType == TEXT_NODE) || ($_->nodeType == CDATA_SECTION_NODE));
 		$content = $_->textContent;
 	}
 	return $content;
@@ -1922,7 +1923,7 @@
 		foreach ( @child2 ) {
 
 			#print getNodeTypeName($_), "\t", $_->toString,"\n";
-			next unless $_->nodeType == TEXT_NODE;
+			next unless (($_->nodeType == TEXT_NODE) || ($_->nodeType == CDATA_SECTION_NODE));
 			push @result, $_->textContent;
 		}
 	}



From yanwong at pub.open-bio.org  Mon Feb  7 09:23:13 2005
From: yanwong at pub.open-bio.org (Yan Wong)
Date: Mon, 7 Feb 2005 09:23:13 -0500
Subject: [MOBY-guts] biomoby commit
Message-ID: <200502071423.j17ENDn9018500@pub.open-bio.org>


yanwong
Mon Feb  7 09:23:13 EST 2005
Update of /home/repository/moby/moby-live/Python/utils
In directory pub.open-bio.org:/tmp/cvs-serv18475

Modified Files:
	moby2python.py 
Log Message:


moby-live/Python/utils moby2python.py,1.5,1.6
===================================================================
RCS file: /home/repository/moby/moby-live/Python/utils/moby2python.py,v
retrieving revision 1.5
retrieving revision 1.6
diff -u -r1.5 -r1.6
--- /home/repository/moby/moby-live/Python/utils/moby2python.py	2005/02/01 14:20:46	1.5
+++ /home/repository/moby/moby-live/Python/utils/moby2python.py	2005/02/07 14:23:13	1.6
@@ -85,7 +85,8 @@
     res.append("            if elt.nodeName==\"CrossReference\" or elt.nodeName==\"moby:CrossReference\":")
     res.append("                self.__cross__=[]")
     res.append("                for ref in elt.childNodes:")
-    res.append("                    self.__cross__.append(um.loads(ref))")        
+    res.append("                    if ref.nodeType==ref.ELEMENT_NODE:")    
+    res.append("                        self.__cross__.append(um.loadn(ref))")        
 
 
     for parameter in parameters:



From kawas at pub.open-bio.org  Mon Feb  7 20:50:32 2005
From: kawas at pub.open-bio.org (Eddie Kawas)
Date: Mon, 7 Feb 2005 20:50:32 -0500
Subject: [MOBY-guts] biomoby commit
Message-ID: <200502080150.j181oWm1020725@pub.open-bio.org>


kawas
Mon Feb  7 20:50:31 EST 2005
Update of /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/gui/serviceInstanceCreationTool
In directory pub.open-bio.org:/tmp/cvs-serv20700/org/biomoby/client/gui/serviceInstanceCreationTool

Modified Files:
	MobyUtilities.java 
Log Message:
Fixed GetRelations so that the name argument can be an LSID - Eddie

moby-live/Java/src/main/org/biomoby/client/gui/serviceInstanceCreationTool MobyUtilities.java,1.1,1.2
===================================================================
RCS file: /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/gui/serviceInstanceCreationTool/MobyUtilities.java,v
retrieving revision 1.1
retrieving revision 1.2
diff -u -r1.1 -r1.2
--- /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/gui/serviceInstanceCreationTool/MobyUtilities.java	2004/09/27 21:29:14	1.1
+++ /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/gui/serviceInstanceCreationTool/MobyUtilities.java	2005/02/08 01:50:31	1.2
@@ -7,6 +7,8 @@
 import java.util.Iterator;
 import java.util.LinkedList;
 import java.util.StringTokenizer;
+import java.util.regex.Matcher;
+import java.util.regex.Pattern;
 
 import javax.swing.tree.TreePath;
 
@@ -19,147 +21,160 @@
  */
 
 public class MobyUtilities {
-	// strings that when concatenated return the attributes, articlename, etc of an object
-	final private static String MURL = new String("http://mobycentral.cbr.nrc.ca/cgi-bin/types/Objects?name=");
-	final private static String MURL2 = new String("&lsid_name");
-
-	/**
-	 * PRE: None.<p>
-	 * POST: a linked list of all the relations is returned, such that:<p>
-	 * => The first item in the list is a string representation of the parent<p>
-	 * => The second item is a linked list of all the 'HAS' container relationships<p>
-	 * => The third item is a linked list of all the 'HASA' container relationships
-	 * @param name, the name of the object to query for.
-	 * @return returns a linked list {String, LinkedList, LinkedList} of relationships
-	 */
-	public static LinkedList GetRelations(String name) throws IOException {
-		URL url = null;
-		url = new URL(MURL + name + MURL2);
-		BufferedReader in = new BufferedReader(new InputStreamReader(url.openStream()));
-		String input;
-		String parent = "";
-		LinkedList llHas = new LinkedList();
-		LinkedList llHasa = new LinkedList();
-
-		while ((input = in.readLine()) != null) {
-			StringTokenizer st = new StringTokenizer(input, "\t");
-			if (st.countTokens() > 2) {
-				st.nextToken(); // object name that was queried
-				StringTokenizer lsid = new StringTokenizer(st.nextToken(), ":");
-				String relation = "";
-				while (lsid.hasMoreTokens())
-					relation = lsid.nextToken(); // isa, hasa, etc
-				if (relation.equalsIgnoreCase("isa"))
-					parent = st.nextToken();
-				else if (relation.equalsIgnoreCase("has"))
-					llHas.add(st.nextToken());
-				else if (relation.equalsIgnoreCase("hasa"))
-					llHasa.add(st.nextToken());
-			}
-		}
-		if (parent.equals("")) {
-			return null;
-		}
-		LinkedList listToReturn = new LinkedList();
-		listToReturn.addFirst(parent);
-		listToReturn.add(llHas);
-		listToReturn.add(llHasa);
-		return listToReturn;
-	}
-
-	/**
-	 * 
-	 * PRE: None.<p>
-	 * POST: a Pair object is returned if the String could be parsed, otherwise, null is returned.
-	 * @param rel - the string representation of the relation in the form Attribute(articleName), i.e. Integer(Count).
-	 * @return returns a fully constructed Pair object if the relation was valid, otherwise, null is returned. 
-	 */
-	public static Pair ParseRelation(String rel) {
-		// integer(length) == attribute(articlename)
-		Pair p = null;
-		int x = -1;
-		String attribute, articleName;
-		if ((x = rel.indexOf("(")) >= 0) {
-			attribute = rel.substring(0, x);
-			articleName = rel.substring(x + 1, rel.length() - 1);
-			p = new Pair(articleName, attribute);
-		}
-
-		return p;
-	}
-
-	/**
-	 * 
-	 * PRE: None.<p>
-	 * POST: Returns the leaf object in a TreePath if path is not null, otherwise, null is returned.
-	 * @param path - a TreePath containing the object of interest.
-	 * @return returns the name of the leaf object contained in the path.
-	 */
-	public static String GetObject(TreePath path) {
-		if (path == null)
-			return null;
-		String s = path.toString();
-		int start = s.lastIndexOf(", ");
-		int end = s.indexOf("]");
-		if (start < 0) {
-			start = 0;
-		}
-		int space = -1;
-		if ((space = s.lastIndexOf(" ")) >= 0) {
-			s = s.substring(space + 1, end);
-		} else
-			s = s.substring(start + 1, end);
-		return s;
-	}
-
-	/**
-	 * 
-	 * PRE: ll is a valid linkedlist, panelDetails is a valid MobyUserPanel.<p>
-	 * POST: All the relations of child are outputted to the MobyUserPanel panelDetails.
-	 * @param ll - a linked list created via GetRelations()
-	 * @param panelDetails - the MobyUserPanel to output the relationships
-	 * @param child - the object that GetRelations() was called with.
-	 */
-	public static String WriteToPanel(LinkedList ll, String child) {
-		//System.out.println(ll);
-		StringBuffer sb = new StringBuffer("");
-		sb.append(child + System.getProperty("line.separator") + "ISA: " + System.getProperty("line.separator") + "\t");
-		String parent = (String) ll.removeFirst();
-		sb.append(parent + System.getProperty("line.separator"));
-		LinkedList llhas = (LinkedList) ll.removeFirst();
-		if (llhas != null) {
-			sb.append("Has: ");
-			Iterator i = llhas.iterator();
-			while (i.hasNext()) {
-				Pair p = MobyUtilities.ParseRelation((String) i.next());
-				if (p != null)
-					sb.append(
-						System.getProperty("line.separator")
-							+ "\t"
-							+ p.getAttribute()
-							+ " - "
-							+ p.getArticlename()
-							+ " ");
-			}
-			sb.append(System.getProperty("line.separator"));
-		}
-		LinkedList llhasa = (LinkedList) ll.removeFirst();
-		if (llhasa != null) {
-			sb.append("Hasa: ");
-			Iterator i = llhasa.iterator();
-			while (i.hasNext()) {
-				Pair p = MobyUtilities.ParseRelation((String) i.next());
-				if (p != null)
-					sb.append(
-						System.getProperty("line.separator")
-							+ "\t"
-							+ p.getAttribute()
-							+ "->"
-							+ p.getArticlename()
-							+ " ");
-			}
-		}
-		return sb.toString();
-	}
-
-}
+    // strings that when concatenated return the attributes, articlename, etc of an object
+    final private static String URL_OBJECT = new String(
+            "http://mobycentral.cbr.nrc.ca/cgi-bin/types/Objects?name=");
+
+    final private static String URL_LSID = new String(
+            "http://mobycentral.cbr.nrc.ca/cgi-bin/types/Objects?lsid_name=");
+
+    /**
+     * PRE: None.<p>
+     * POST: a linked list of all the relations is returned, such that:<p>
+     * => The first item in the list is a string representation of the parent<p>
+     * => The second item is a linked list of all the 'HAS' container relationships<p>
+     * => The third item is a linked list of all the 'HASA' container relationships
+     * @param name, the name of the object to query for - can be an Moby Object LSID.
+     * @return returns a linked list {String, LinkedList, LinkedList} of relationships
+     */
+    public static LinkedList GetRelations(String name) throws IOException {
+        URL url = null;
+        boolean isLSID = false;
+        // TODO check if name == lsid
+        Pattern p = Pattern.compile("(^urn:lsid:biomoby.org:objectclass:\\S+)",
+                Pattern.CASE_INSENSITIVE);
+        Matcher m = p.matcher(name);
+        isLSID = m.matches();
+
+        if (!isLSID)
+            url = new URL(URL_OBJECT + name);
+        else
+            url = new URL(URL_LSID + name);
+        BufferedReader in = new BufferedReader(new InputStreamReader(url
+                .openStream()));
+        String input;
+        String parent = "Object";
+        LinkedList llHas = new LinkedList();
+        LinkedList llHasa = new LinkedList();
+
+        while ((input = in.readLine()) != null) {
+            StringTokenizer st = new StringTokenizer(input, "\t");
+            if (st.countTokens() > 2) {
+                st.nextToken(); // object name that was queried
+                StringTokenizer lsid = new StringTokenizer(st.nextToken(), ":");
+                String relation = "";
+                while (lsid.hasMoreTokens())
+                    relation = lsid.nextToken(); // isa, hasa, etc
+                if (relation.equalsIgnoreCase("isa"))
+                    parent = st.nextToken();
+                else if (relation.equalsIgnoreCase("has"))
+                    llHas.add(st.nextToken());
+                else if (relation.equalsIgnoreCase("hasa"))
+                    llHasa.add(st.nextToken());
+            }
+        }
+        if (parent.equals("")) {
+            return null;
+        }
+        LinkedList listToReturn = new LinkedList();
+        listToReturn.addFirst(parent);
+        listToReturn.add(llHas);
+        listToReturn.add(llHasa);
+        return listToReturn;
+    }
+
+    /**
+     * 
+     * PRE: None.<p>
+     * POST: a Pair object is returned if the String could be parsed, otherwise, null is returned.
+     * @param rel - the string representation of the relation in the form Attribute(articleName), i.e. Integer(Count).
+     * @return returns a fully constructed Pair object if the relation was valid, otherwise, null is returned. 
+     */
+    public static Pair ParseRelation(String rel) {
+        // integer(length) == attribute(articlename)
+        Pair p = null;
+        int x = -1;
+        String attribute, articleName;
+        if ((x = rel.indexOf("(")) >= 0) {
+            attribute = rel.substring(0, x);
+            articleName = rel.substring(x + 1, rel.length() - 1);
+            p = new Pair(articleName, attribute);
+        }
+
+        return p;
+    }
+
+    /**
+     * 
+     * PRE: None.<p>
+     * POST: Returns the leaf object in a TreePath if path is not null, otherwise, null is returned.
+     * @param path - a TreePath containing the object of interest.
+     * @return returns the name of the leaf object contained in the path.
+     */
+    public static String GetObject(TreePath path) {
+        if (path == null)
+            return null;
+        String s = path.toString();
+        int start = s.lastIndexOf(", ");
+        int end = s.indexOf("]");
+        if (start < 0) {
+            start = 0;
+        }
+        int space = -1;
+        if ((space = s.lastIndexOf(" ")) >= 0) {
+            s = s.substring(space + 1, end);
+        } else
+            s = s.substring(start + 1, end);
+        return s;
+    }
+
+    /**
+     * 
+     * PRE: ll is a valid linkedlist, panelDetails is a valid MobyUserPanel.<p>
+     * POST: All the relations of child are outputted to the MobyUserPanel panelDetails.
+     * @param ll - a linked list created via GetRelations()
+     * @param panelDetails - the MobyUserPanel to output the relationships
+     * @param child - the object that GetRelations() was called with.
+     */
+    public static String WriteToPanel(LinkedList ll, String child) {
+        //System.out.println(ll);
+        StringBuffer sb = new StringBuffer("");
+        sb.append(child + System.getProperty("line.separator") + "ISA: "
+                + System.getProperty("line.separator") + "\t");
+        String parent = (String) ll.removeFirst();
+        sb.append(parent + System.getProperty("line.separator"));
+        LinkedList llhas = (LinkedList) ll.removeFirst();
+        if (llhas != null) {
+            sb.append("Has: ");
+            Iterator i = llhas.iterator();
+            while (i.hasNext()) {
+                Pair p = MobyUtilities.ParseRelation((String) i.next());
+                if (p != null)
+                    sb.append(System.getProperty("line.separator") + "\t"
+                            + p.getAttribute() + " - " + p.getArticlename()
+                            + " ");
+            }
+            sb.append(System.getProperty("line.separator"));
+        }
+        LinkedList llhasa = (LinkedList) ll.removeFirst();
+        if (llhasa != null) {
+            sb.append("Hasa: ");
+            Iterator i = llhasa.iterator();
+            while (i.hasNext()) {
+                Pair p = MobyUtilities.ParseRelation((String) i.next());
+                if (p != null)
+                    sb.append(System.getProperty("line.separator") + "\t"
+                            + p.getAttribute() + "->" + p.getArticlename()
+                            + " ");
+            }
+        }
+        return sb.toString();
+    }
+
+    public static void main(String[] args) throws IOException {
+        LinkedList ll = MobyUtilities.GetRelations("genbank-flatfile");
+        System.out.println(ll.toString());
+        ll = MobyUtilities.GetRelations("urn:lsid:biomoby.org:objectclass:Object");
+        System.out.println(ll.toString());
+    }
+}
\ No newline at end of file



From mwilkinson at pub.open-bio.org  Tue Feb  8 11:49:16 2005
From: mwilkinson at pub.open-bio.org (Mark Wilkinson)
Date: Tue, 8 Feb 2005 11:49:16 -0500
Subject: [MOBY-guts] biomoby commit
Message-ID: <200502081649.j18GnGgD024562@pub.open-bio.org>


mwilkinson
Tue Feb  8 11:49:16 EST 2005
Update of /home/repository/moby/moby-live/Perl/MOBY
In directory pub.open-bio.org:/tmp/cvs-serv24543/MOBY

Modified Files:
	CommonSubs.pm 
Log Message:
thanks to Sophie for squashing this bug.  Crossreferences were not being detected if prefixed by moby: 

moby-live/Perl/MOBY CommonSubs.pm,1.58,1.59
===================================================================
RCS file: /home/repository/moby/moby-live/Perl/MOBY/CommonSubs.pm,v
retrieving revision 1.58
retrieving revision 1.59
diff -u -r1.58 -r1.59
--- /home/repository/moby/moby-live/Perl/MOBY/CommonSubs.pm	2004/12/15 17:49:44	1.58
+++ /home/repository/moby/moby-live/Perl/MOBY/CommonSubs.pm	2005/02/08 16:49:15	1.59
@@ -1617,7 +1617,7 @@
 	$ns = $xref->getAttributeNode( 'moby:namespace' ) unless $ns;
 	return undef unless $ns;
 	my $id = $xref->getAttributeNode( 'id' );
-	$id = $xref->getAttributeNode( 'moby:id' ) unless $ns;
+	$id = $xref->getAttributeNode( 'moby:id' ) unless $id;
 	return undef unless $id;
 	my $XREF = MOBY::CrossReference->new(
 										  type      => "object",



From nopushneva at pub.open-bio.org  Tue Feb  8 18:32:15 2005
From: nopushneva at pub.open-bio.org (Nina Opushneva)
Date: Tue, 8 Feb 2005 18:32:15 -0500
Subject: [MOBY-guts] biomoby commit
Message-ID: <200502082332.j18NWFpI026780@pub.open-bio.org>


nopushneva
Tue Feb  8 18:32:14 EST 2005
Update of /home/repository/moby/moby-live/Perl/MOBY
In directory pub.open-bio.org:/tmp/cvs-serv26754

Modified Files:
	Central.pm 
Log Message:
add the RDFagent call

moby-live/Perl/MOBY Central.pm,1.147,1.148
===================================================================
RCS file: /home/repository/moby/moby-live/Perl/MOBY/Central.pm,v
retrieving revision 1.147
retrieving revision 1.148
diff -u -r1.147 -r1.148
--- /home/repository/moby/moby-live/Perl/MOBY/Central.pm	2005/02/06 21:58:35	1.147
+++ /home/repository/moby/moby-live/Perl/MOBY/Central.pm	2005/02/08 23:32:14	1.148
@@ -1234,6 +1234,26 @@
 		 $OUTPUTS,      $SECONDARY,   $signatureURL
 	  )
 	  = &_registerServicePayload( $payload );
+
+#--------RDFagent call----------------------------------------
+
+if (defined $signatureURL){
+  my $ch = 0;
+  my $i;
+  foreach $i ($serviceName, $serviceType, $AuthURI, $contactEmail, $URL, $desc, $Category){
+       if (defined $i){
+          $ch = 1;
+        }        
+  }
+
+  if ($ch == 0){
+    my $rez = system("/export/home/nina/rdfagent/run-RDFagent ".$signatureURL);
+
+    return &_error("The RDFagent call was successful.  Report will send to you by E-mail","") if ($rez == 0);
+    return &_error("Some problem with a connection or RDF model building","") if ($rez != 0);
+  }
+}
+#---------------------------------------------------------------
 	$authoritativeService = defined( $authoritativeService ) ? 1 : 0;
 	my $error;
 	$error .= "missing serviceName \n" unless defined $serviceName;
@@ -1368,15 +1388,16 @@
 			""
 		);
 	}
-	use MOBY::Client::Central;
-	my $services         = MOBY::Client::Central::_parseServices( '', '', $si );
-	my $service_instance = shift @{$services};
-	my $storage          = new RDF::Core::Storage::Memory;
-	my $model            = new RDF::Core::Model( Storage => $storage );
-	my $RDF_MODEL = MOBY::RDF::ServiceInstanceRDF->new(
-										   model            => $model,
-										   service_instance => $service_instance );
-	my $RDF_XML = $RDF_MODEL->serialize;
+#	use MOBY::Client::Central;
+#	my $services         = MOBY::Client::Central::_parseServices( '', '', $si );
+#	my $service_instance = shift @{$services};
+#	my $storage          = new RDF::Core::Storage::Memory;
+#	my $model            = new RDF::Core::Model( Storage => $storage );
+#	my $RDF_MODEL = MOBY::RDF::ServiceInstanceRDF->new(
+										   #model            => $model,
+										   #service_instance => $service_instance );
+#	my $RDF_XML = $RDF_MODEL->serialize;
+        my $RDF_XML = "";
 	return &_success( "Registration successful",
 					  $SVC->service_instance_id, $RDF_XML );
 }
@@ -3757,4 +3778,39 @@
 	my $XSD;
 	return $XSD;
 }
+
+#=head2 runRDFagent
+
+#Title     :	runRDFagent
+#Usage     :	$MOBY->runRDFagent($inputXML)
+#Function  :	run RDFagent for signatureURL
+#Returns   :	
+#Args      :	
+      
+#inputXML  :
+#<runRDFagent>
+# <RDFfileURL>rdfFileURL</RDFfileURL>
+#</runRDFagent>
+			      
+#=cut
+		
+#sub _runRDFagent{
+		   
+# my ($self)=@_; 
+# my $Parser = new XML::DOM::Parser;
+# my $doc = $Parser->parse($payload);
+# my $Object      = $doc->getDocumentElement();
+# my $obj         = $Object->nodeName;
+# return undef unless ( $obj eq 'runRDFagent' );
+# my $url = &_nodeTextContent( $Object, "RDFfileURL" );
+# my $l = $url->getLength;
+# if ($l == 0){
+#   print "The RDFagent can't run without a parameter";
+# }else{
+#   system("/home/rdfagent/run-RDFagent"+ $url);
+#   print "The RDFagent run saccessfully. A result will sent to you by E-mail";
+# }
+										
+}
 1;
+`



From nopushneva at pub.open-bio.org  Tue Feb  8 18:43:06 2005
From: nopushneva at pub.open-bio.org (Nina Opushneva)
Date: Tue, 8 Feb 2005 18:43:06 -0500
Subject: [MOBY-guts] biomoby commit
Message-ID: <200502082343.j18Nh6I8026858@pub.open-bio.org>


nopushneva
Tue Feb  8 18:43:06 EST 2005
Update of /home/repository/moby/moby-live/Perl/MOBY/Client
In directory pub.open-bio.org:/tmp/cvs-serv26832

Modified Files:
	Central.pm 
Log Message:
added a check for RDFagent call, and call a new RDFbuilder

moby-live/Perl/MOBY/Client Central.pm,1.89,1.90
===================================================================
RCS file: /home/repository/moby/moby-live/Perl/MOBY/Client/Central.pm,v
retrieving revision 1.89
retrieving revision 1.90
diff -u -r1.89 -r1.90
--- /home/repository/moby/moby-live/Perl/MOBY/Client/Central.pm	2005/02/06 22:46:45	1.89
+++ /home/repository/moby/moby-live/Perl/MOBY/Client/Central.pm	2005/02/08 23:43:06	1.90
@@ -778,6 +778,36 @@
 	my $Category = lc( $a{category} );
 	chomp $Category;
 	$Category ||= "";
+
+#____________call RDFagent__________________________________________________
+if (defined $signatureURL){
+  my $ch = 0;
+  my $sign_req;
+    foreach $sign_req ($name, $type, $authURI, $email, $URL, $desc, $Category){
+      if ($sign_req ne ""){
+        $ch = 1;
+
+        }        
+    }  
+     if ($ch == 0){
+ print "call Agent\n";
+	     my $message = "
+		<registerService>
+			<Category></Category>
+			<serviceName></serviceName>
+			<serviceType></serviceType>
+			<Description></Description>
+                        <signatureURL>$signatureURL</signatureURL>
+			<URL></URL>
+			<authURI></authURI>
+			<contactEmail></contactEmail>
+	       </registerService>";		
+         my   ( $return ) = $self->_call( 'default', 'registerService', $message );
+	    return ( $self->parseRegXML( $return ) );
+
+    }
+}
+#____________________________________________________________________________________________
 	return $self->errorRegXML(
 "Only 'moby' and 'wsdl' Service Categories are currently allowed - you gave me $Category"
 	  )
@@ -798,7 +828,7 @@
 			<serviceName>$name</serviceName>
 			<serviceType>$type</serviceType>
 			<Description><![CDATA[$desc]]></Description>
-            <signatureURL>$signatureURL</signatureURL>
+                        <signatureURL>$signatureURL</signatureURL>
 			<URL>$URL</URL>
 			<authURI>$authURI</authURI>
 			<contactEmail>$email</contactEmail>";
@@ -950,7 +980,22 @@
 
 #	my $return = $self->SOAP_connection->call(registerService => ($message))->paramsall;
 	my ( $return ) = $self->_call( 'default', 'registerService', $message );
-	return ( $self->parseRegXML( $return ) );
+#	return ( $self->parseRegXML( $return ) );
+#_______call a new version RDFbuilder (by Eddie Kawas) _________________________________________
+  my $reg = $self->parseRegXML( $return );
+  if ($reg->success == 1){
+  require LWP::UserAgent;
+     
+     my $ua = LWP::UserAgent->new;
+         my $url='http://mobycentral.cbr.nrc.ca:8090/DemoServlet/forms/getSignatureResponse?domain='.$authURI.'&serviceName='.$name;
+	 
+	 my $response = $ua->get($url);
+	 my $rdf = $response->content;
+	 print "$rdf\n"; 
+}	 
+   return $reg;
+#_______________________________________________________________________________________________
+
 }
 
 =head2 registerServiceWSDL
@@ -970,6 +1015,7 @@
 
 #	my $return = $self->SOAP_connection->call(registerServiceWSDL => ($message))->paramsall;
 	my ( $return ) = $self->_call( 'default', 'registerServiceWSDL', $message );
+
 	return ( $self->parseRegXML( $return ) );
 }
 



From gordonp at pub.open-bio.org  Wed Feb  9 12:17:25 2005
From: gordonp at pub.open-bio.org (Paul Gordon)
Date: Wed, 9 Feb 2005 12:17:25 -0500
Subject: [MOBY-guts] biomoby commit
Message-ID: <200502091717.j19HHPY1030820@pub.open-bio.org>


gordonp
Wed Feb  9 12:17:25 EST 2005
Update of /home/repository/moby/moby-live/Java/src/main/org/biomoby/shared
In directory pub.open-bio.org:/tmp/cvs-serv30799/org/biomoby/shared

Added Files:
	MobyDataDateTime.java 
Log Message:
Utility class to deal with painful parsing and creation of ISO 8601 dates (as used by MOBY's DateTime objects)

moby-live/Java/src/main/org/biomoby/shared MobyDataDateTime.java,NONE,1.1


From gordonp at pub.open-bio.org  Wed Feb  9 12:20:38 2005
From: gordonp at pub.open-bio.org (Paul Gordon)
Date: Wed, 9 Feb 2005 12:20:38 -0500
Subject: [MOBY-guts] biomoby commit
Message-ID: <200502091720.j19HKcQQ030874@pub.open-bio.org>


gordonp
Wed Feb  9 12:20:38 EST 2005
Update of /home/repository/moby/moby-live/Java/src/main/org/biomoby/shared
In directory pub.open-bio.org:/tmp/cvs-serv30837/org/biomoby/shared

Modified Files:
	MobyDataFloat.java MobyDataInt.java 
	MobyDataSimpleInstance.java MobyDataString.java 
Log Message:
Updates to correct javadoc errors, plus addition of underlying object accessibility for MOBY Data Instances

moby-live/Java/src/main/org/biomoby/shared MobyDataFloat.java,1.1,1.2 MobyDataInt.java,1.1,1.2 MobyDataSimpleInstance.java,1.3,1.4 MobyDataString.java,1.1,1.2
===================================================================
RCS file: /home/repository/moby/moby-live/Java/src/main/org/biomoby/shared/MobyDataFloat.java,v
retrieving revision 1.1
retrieving revision 1.2
diff -u -r1.1 -r1.2
--- /home/repository/moby/moby-live/Java/src/main/org/biomoby/shared/MobyDataFloat.java	2004/09/03 20:28:16	1.1
+++ /home/repository/moby/moby-live/Java/src/main/org/biomoby/shared/MobyDataFloat.java	2005/02/09 17:20:38	1.2
@@ -61,6 +61,13 @@
 	return copy;
     }
 
+    /**
+     * @return a BigDecimal 
+     */
+    public Object getObject(){
+	return value;
+    }
+
     public String getValue(){
 	return ""+value;
     }

===================================================================
RCS file: /home/repository/moby/moby-live/Java/src/main/org/biomoby/shared/MobyDataInt.java,v
retrieving revision 1.1
retrieving revision 1.2
diff -u -r1.1 -r1.2
--- /home/repository/moby/moby-live/Java/src/main/org/biomoby/shared/MobyDataInt.java	2004/09/03 20:28:16	1.1
+++ /home/repository/moby/moby-live/Java/src/main/org/biomoby/shared/MobyDataInt.java	2005/02/09 17:20:38	1.2
@@ -3,10 +3,10 @@
 import java.math.*;
 
 /**
- * A class representing a MOBY Float primitive.  Note that the 
- * Float notion in MOBY does not define a specific bit precision.
- * All values in this class are stored as Java BigDecimal, which is 
- * arbitary precision to avoid loss of data integrity.
+ * A class representing a MOBY Integer primitive.  Note that the 
+ * Integer notion in MOBY does not define a specific bit precision.
+ * All values in this class are stored as Java BigInteger, which has no 
+ * minmum or maximum value, to avoid loss of data integrity.
  */
 
 public class MobyDataInt extends MobyDataSimpleInstance{
@@ -15,7 +15,8 @@
     
     /**
      * Constructor to use if the incoming value is a number object such as 
-     * Float, Double, Integer, BigDecimal, etc.
+     * Float, Double, Integer, BigInteger, BigDecimal, etc.
+     * Real numbers will be converted to their integer equivalents. 
      */
     public MobyDataInt(String articleName, Number n){
 	super(articleName);
@@ -33,7 +34,7 @@
 
     /**
      * Constructor to use if the incoming value is a primitive.
-     * If you want to pass in a float or int, cast it to a double.
+     * If you want to pass in a float or double, cast it to an int.
      */
     public MobyDataInt(String articleName, int i){
 	super(articleName);
@@ -42,10 +43,10 @@
     }
 
     /**
-     * Constructor to use if the incoming value is a string representing a number 
-     * (including mantissa/exponent format).
+     * Constructor to use if the incoming value is a string representing an integer number. 
+     * 
      *
-     * @throws NumberFormatException if the string does not represent a number
+     * @throws NumberFormatException if the string does not represent an integer number
      */
     public MobyDataInt(String articleName, String stringNumber) throws NumberFormatException{
 	super(articleName);
@@ -61,6 +62,13 @@
 	return copy;
     }
 
+    /**
+     * @return a BigInteger
+     */
+    public Object getObject(){
+	return value;
+    }
+
     public String getValue(){
 	return ""+value;
     }

===================================================================
RCS file: /home/repository/moby/moby-live/Java/src/main/org/biomoby/shared/MobyDataSimpleInstance.java,v
retrieving revision 1.3
retrieving revision 1.4
diff -u -r1.3 -r1.4
--- /home/repository/moby/moby-live/Java/src/main/org/biomoby/shared/MobyDataSimpleInstance.java	2004/09/23 10:20:29	1.3
+++ /home/repository/moby/moby-live/Java/src/main/org/biomoby/shared/MobyDataSimpleInstance.java	2005/02/09 17:20:38	1.4
@@ -132,6 +132,16 @@
     }
 
     /**
+     * Gives access to the Java object instance underlying the MobyData instance.  
+     * For example, to increment a MOBY integer object, call ((BigInteger) (data.getObject()).add(BigInteger.ONE)
+     *
+     * Not yet fully implemented for base objects whose setValue() method has been called.
+     */
+    public Object getObject(){
+	return dataValue;
+    }
+
+    /**
      * Convenience method to get the basic XML representation
      * @return the raw XML representation of the object
      */

===================================================================
RCS file: /home/repository/moby/moby-live/Java/src/main/org/biomoby/shared/MobyDataString.java,v
retrieving revision 1.1
retrieving revision 1.2
diff -u -r1.1 -r1.2
--- /home/repository/moby/moby-live/Java/src/main/org/biomoby/shared/MobyDataString.java	2004/09/03 20:28:16	1.1
+++ /home/repository/moby/moby-live/Java/src/main/org/biomoby/shared/MobyDataString.java	2005/02/09 17:20:38	1.2
@@ -3,10 +3,7 @@
 import java.math.*;
 
 /**
- * A class representing a MOBY Float primitive.  Note that the 
- * Float notion in MOBY does not define a specific bit precision.
- * All values in this class are stored as Java BigDecimal, which is 
- * arbitary precision to avoid loss of data integrity.
+ * A class representing a MOBY String primitive. 
  */
 
 public class MobyDataString extends MobyDataSimpleInstance{
@@ -44,17 +41,33 @@
 	return copy;
     }
 
+    /**
+     * @return a String
+     */
+    public Object getObject(){
+	return value;
+    }
+
     public String getValue(){
 	return value;
     }
 
+    /**
+     * This class sanitizes strings of XML escape characters such as the ampersand (&amp;) and the 
+     * less-than sign (&lt;).  WARNING: this method will not escape ampersand in the string "&amp;amp;", 
+     * or '&amp;#x26;' style character references.  We will assume that is this case you've probably 
+     * already written the string as XML. 
+     *
+     * WARNING: As of yet, we do not deal with the false escaping of strings containg already-escaped 
+     * CDATA sections!
+     */
     public String toXML(){
 	MobyNamespace[] ns = getNamespaces();
 	if(xmlMode == SERVICE_XML_MODE){
 	    String tmpValue = value;
 	    if(tmpValue != null){
 		tmpValue = tmpValue.replaceAll("<", "&lt;");
-		tmpValue = tmpValue.replaceAll("&", "&amp;");
+		tmpValue = tmpValue.replaceAll("&(?!(amp|#x\\d+);)", "&amp;");
 	    }
 	    
 	    return "<moby:String moby:namespace=\""+ 



From gordonp at pub.open-bio.org  Wed Feb  9 12:39:17 2005
From: gordonp at pub.open-bio.org (Paul Gordon)
Date: Wed, 9 Feb 2005 12:39:17 -0500
Subject: [MOBY-guts] biomoby commit
Message-ID: <200502091739.j19HdHEF030977@pub.open-bio.org>


gordonp
Wed Feb  9 12:39:17 EST 2005
Update of /home/repository/moby/moby-live/Java/src/main/org/biomoby/shared
In directory pub.open-bio.org:/tmp/cvs-serv30952/org/biomoby/shared

Modified Files:
	MobyPrefixResolver.java 
Log Message:
Changed attribute namespace conditional to check for both empty string and null, as different parsers can use one or the other to represent the fact that an attribute is not bound to a namespace

moby-live/Java/src/main/org/biomoby/shared MobyPrefixResolver.java,1.2,1.3
===================================================================
RCS file: /home/repository/moby/moby-live/Java/src/main/org/biomoby/shared/MobyPrefixResolver.java,v
retrieving revision 1.2
retrieving revision 1.3
diff -u -r1.2 -r1.3
--- /home/repository/moby/moby-live/Java/src/main/org/biomoby/shared/MobyPrefixResolver.java	2004/07/07 16:02:47	1.2
+++ /home/repository/moby/moby-live/Java/src/main/org/biomoby/shared/MobyPrefixResolver.java	2005/02/09 17:39:17	1.3
@@ -45,7 +45,7 @@
      */
     public static String getAttr(org.w3c.dom.Element e, String attrName){
 	String value = e.getAttributeNS(MOBY_XML_NAMESPACE, attrName);
-	if(value == null){
+	if(value == null || "".equals(value)){
 	    value = e.getAttributeNS(null, attrName);
 	}
 	return value;



From kawas at pub.open-bio.org  Wed Feb  9 13:26:41 2005
From: kawas at pub.open-bio.org (Eddie Kawas)
Date: Wed, 9 Feb 2005 13:26:41 -0500
Subject: [MOBY-guts] biomoby commit
Message-ID: <200502091826.j19IQfEA031153@pub.open-bio.org>


kawas
Wed Feb  9 13:26:41 EST 2005
Update of /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/gui/serviceInstanceCreationTool
In directory pub.open-bio.org:/tmp/cvs-serv31128/org/biomoby/client/gui/serviceInstanceCreationTool

Modified Files:
	MobyUtilities.java 
Log Message:
Fixed GetRelations so that it executes quickly and doesnt spin off
into infinite loops with bad input - Eddie

moby-live/Java/src/main/org/biomoby/client/gui/serviceInstanceCreationTool MobyUtilities.java,1.2,1.3
===================================================================
RCS file: /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/gui/serviceInstanceCreationTool/MobyUtilities.java,v
retrieving revision 1.2
retrieving revision 1.3
diff -u -r1.2 -r1.3
--- /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/gui/serviceInstanceCreationTool/MobyUtilities.java	2005/02/08 01:50:31	1.2
+++ /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/gui/serviceInstanceCreationTool/MobyUtilities.java	2005/02/09 18:26:41	1.3
@@ -4,6 +4,7 @@
 import java.io.IOException;
 import java.io.InputStreamReader;
 import java.net.URL;
+import java.util.ArrayList;
 import java.util.Iterator;
 import java.util.LinkedList;
 import java.util.StringTokenizer;
@@ -12,6 +13,9 @@
 
 import javax.swing.tree.TreePath;
 
+import org.biomoby.client.gui.util.MobyObjectPrimitiveExtractor;
+import org.biomoby.client.gui.util.Triples;
+
 /**
  * Utilities that are useful for retrieving information about certain objects, parsing objects, etc.
  * @author Eddie Kawas
@@ -21,12 +25,6 @@
  */
 
 public class MobyUtilities {
-    // strings that when concatenated return the attributes, articlename, etc of an object
-    final private static String URL_OBJECT = new String(
-            "http://mobycentral.cbr.nrc.ca/cgi-bin/types/Objects?name=");
-
-    final private static String URL_LSID = new String(
-            "http://mobycentral.cbr.nrc.ca/cgi-bin/types/Objects?lsid_name=");
 
     /**
      * PRE: None.<p>
@@ -40,44 +38,31 @@
     public static LinkedList GetRelations(String name) throws IOException {
         URL url = null;
         boolean isLSID = false;
-        // TODO check if name == lsid
-        Pattern p = Pattern.compile("(^urn:lsid:biomoby.org:objectclass:\\S+)",
+        Pattern p = Pattern.compile("(^urn:lsid:biomoby.org:objectclass:\\S+$)",
                 Pattern.CASE_INSENSITIVE);
         Matcher m = p.matcher(name);
         isLSID = m.matches();
+        if (isLSID) {
+            int x = name.lastIndexOf(":")+1;
+            name = name.substring(x);
+        }
 
-        if (!isLSID)
-            url = new URL(URL_OBJECT + name);
-        else
-            url = new URL(URL_LSID + name);
-        BufferedReader in = new BufferedReader(new InputStreamReader(url
-                .openStream()));
-        String input;
-        String parent = "Object";
         LinkedList llHas = new LinkedList();
         LinkedList llHasa = new LinkedList();
-
-        while ((input = in.readLine()) != null) {
-            StringTokenizer st = new StringTokenizer(input, "\t");
-            if (st.countTokens() > 2) {
-                st.nextToken(); // object name that was queried
-                StringTokenizer lsid = new StringTokenizer(st.nextToken(), ":");
-                String relation = "";
-                while (lsid.hasMoreTokens())
-                    relation = lsid.nextToken(); // isa, hasa, etc
-                if (relation.equalsIgnoreCase("isa"))
-                    parent = st.nextToken();
-                else if (relation.equalsIgnoreCase("has"))
-                    llHas.add(st.nextToken());
-                else if (relation.equalsIgnoreCase("hasa"))
-                    llHasa.add(st.nextToken());
+        MobyObjectPrimitiveExtractor mope = new MobyObjectPrimitiveExtractor();
+        ArrayList al = mope.getPrimitives(name);
+        for (Iterator x = al.iterator(); x.hasNext();) {
+            Triples t = (Triples)x.next();
+            if (t.getType() == Triples.HAS) {
+                llHas.add(t.getPrimitive());
+            }
+            if (t.getType() == Triples.HASA) {
+                llHasa.add(t.getPrimitive());
             }
         }
-        if (parent.equals("")) {
-            return null;
-        }
+        // set up the return list
         LinkedList listToReturn = new LinkedList();
-        listToReturn.addFirst(parent);
+        listToReturn.addFirst("Object");
         listToReturn.add(llHas);
         listToReturn.add(llHasa);
         return listToReturn;
@@ -172,9 +157,9 @@
     }
 
     public static void main(String[] args) throws IOException {
-        LinkedList ll = MobyUtilities.GetRelations("genbank-flatfile");
+        LinkedList ll = MobyUtilities.GetRelations("DNASequence");
         System.out.println(ll.toString());
-        ll = MobyUtilities.GetRelations("urn:lsid:biomoby.org:objectclass:Object");
+        ll = MobyUtilities.GetRelations("urn:lsid:biomoby.org:objectclass:DNASequence");
         System.out.println(ll.toString());
     }
 }
\ No newline at end of file



From nopushneva at pub.open-bio.org  Wed Feb  9 19:17:45 2005
From: nopushneva at pub.open-bio.org (Nina Opushneva)
Date: Wed, 9 Feb 2005 19:17:45 -0500
Subject: [MOBY-guts] biomoby commit
Message-ID: <200502100017.j1A0HjbZ032063@pub.open-bio.org>


nopushneva
Wed Feb  9 19:17:45 EST 2005
Update of /home/repository/moby/moby-live/Perl/MOBY
In directory pub.open-bio.org:/tmp/cvs-serv32037

Modified Files:
	Central.pm 
Log Message:
delete some typo

moby-live/Perl/MOBY Central.pm,1.148,1.149
===================================================================
RCS file: /home/repository/moby/moby-live/Perl/MOBY/Central.pm,v
retrieving revision 1.148
retrieving revision 1.149
diff -u -r1.148 -r1.149
--- /home/repository/moby/moby-live/Perl/MOBY/Central.pm	2005/02/08 23:32:14	1.148
+++ /home/repository/moby/moby-live/Perl/MOBY/Central.pm	2005/02/10 00:17:45	1.149
@@ -3779,38 +3779,6 @@
 	return $XSD;
 }
 
-#=head2 runRDFagent
 
-#Title     :	runRDFagent
-#Usage     :	$MOBY->runRDFagent($inputXML)
-#Function  :	run RDFagent for signatureURL
-#Returns   :	
-#Args      :	
-      
-#inputXML  :
-#<runRDFagent>
-# <RDFfileURL>rdfFileURL</RDFfileURL>
-#</runRDFagent>
-			      
-#=cut
-		
-#sub _runRDFagent{
-		   
-# my ($self)=@_; 
-# my $Parser = new XML::DOM::Parser;
-# my $doc = $Parser->parse($payload);
-# my $Object      = $doc->getDocumentElement();
-# my $obj         = $Object->nodeName;
-# return undef unless ( $obj eq 'runRDFagent' );
-# my $url = &_nodeTextContent( $Object, "RDFfileURL" );
-# my $l = $url->getLength;
-# if ($l == 0){
-#   print "The RDFagent can't run without a parameter";
-# }else{
-#   system("/home/rdfagent/run-RDFagent"+ $url);
-#   print "The RDFagent run saccessfully. A result will sent to you by E-mail";
-# }
-										
-}
 1;
-`
+



From gordonp at pub.open-bio.org  Tue Feb 15 12:47:40 2005
From: gordonp at pub.open-bio.org (Paul Gordon)
Date: Tue, 15 Feb 2005 12:47:40 -0500
Subject: [MOBY-guts] biomoby commit
Message-ID: <200502151747.j1FHlevD006970@pub.open-bio.org>


gordonp
Tue Feb 15 12:47:40 EST 2005
Update of /home/repository/moby/moby-live/Java/src/main/org/biomoby/client
In directory pub.open-bio.org:/tmp/cvs-serv6945

Modified Files:
	MobyRequest.java 
Log Message:
Added conveinece method to create XML envelope when you only have one input request to process

moby-live/Java/src/main/org/biomoby/client MobyRequest.java,1.6,1.7
===================================================================
RCS file: /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/MobyRequest.java,v
retrieving revision 1.6
retrieving revision 1.7
diff -u -r1.6 -r1.7
--- /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/MobyRequest.java	2005/02/03 22:37:30	1.6
+++ /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/MobyRequest.java	2005/02/15 17:47:39	1.7
@@ -543,6 +543,11 @@
 	return domDoc.getDocumentElement();
     }
 
+    public String convertMOBYDataToMOBYRequest(MobyDataInstance data, MobyDataSecondaryInstance[] secondary) throws MobyException{
+        MobyDataInstance[] mdsis = new MobyDataInstance[1];
+        mdsis[0] = data;
+        return convertMOBYDataToMOBYRequest(mdsis, secondary);
+    }
 
     /**
      * @param data the array of input parameters to put in a MOBY XML request



From kawas at pub.open-bio.org  Wed Feb 16 10:38:28 2005
From: kawas at pub.open-bio.org (Eddie Kawas)
Date: Wed, 16 Feb 2005 10:38:28 -0500
Subject: [MOBY-guts] biomoby commit
Message-ID: <200502161538.j1GFcSic011487@pub.open-bio.org>


kawas
Wed Feb 16 10:38:28 EST 2005
Update of /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/gui/util
In directory pub.open-bio.org:/tmp/cvs-serv11466/org/biomoby/client/gui/util

Added Files:
	MobyObjectPrimitiveExtractor.java Triples.java 
Log Message:
Adding MobyObjectPrimitiveExtractor and Triples. May be duplicating code, but are necessary to ensure that other classes compile.

moby-live/Java/src/main/org/biomoby/client/gui/util MobyObjectPrimitiveExtractor.java,NONE,1.1 Triples.java,NONE,1.1


From yanwong at pub.open-bio.org  Wed Feb 16 10:38:46 2005
From: yanwong at pub.open-bio.org (Yan Wong)
Date: Wed, 16 Feb 2005 10:38:46 -0500
Subject: [MOBY-guts] biomoby commit
Message-ID: <200502161538.j1GFck0o011539@pub.open-bio.org>


yanwong
Wed Feb 16 10:38:46 EST 2005
Update of /home/repository/moby/moby-live/Python/bioMoby
In directory pub.open-bio.org:/tmp/cvs-serv11495/bioMoby

Modified Files:
	mobyDataTypes.py 
Log Message:


moby-live/Python/bioMoby mobyDataTypes.py,1.14,1.15
===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/mobyDataTypes.py,v
retrieving revision 1.14
retrieving revision 1.15
diff -u -r1.14 -r1.15
--- /home/repository/moby/moby-live/Python/bioMoby/mobyDataTypes.py	2005/02/04 16:03:40	1.14
+++ /home/repository/moby/moby-live/Python/bioMoby/mobyDataTypes.py	2005/02/16 15:38:46	1.15
@@ -172,7 +172,7 @@
         
         self.content=[]
         
-        if elem.nodeName.split(":")>1:
+        if elem.nodeName.split(":")==2:
             self.__prefix__=elem.nodeName.split(":")[0]
         
         #Set the object's attributes
@@ -406,8 +406,11 @@
                     p=Parameter()
                     p.fromMoby(datum)
                     data.append(p)
-                    
-            self.queryData[queryID]=data
+            
+            if not queryID in self.queryData.keys():
+                self.queryData[queryID]=data
+            else:
+                self.queryData[str(len(self.queryData.keys())+1)]=data
     
     def __getitem__(self, key):
         """Get a query from his name



From yanwong at pub.open-bio.org  Wed Feb 16 10:38:46 2005
From: yanwong at pub.open-bio.org (Yan Wong)
Date: Wed, 16 Feb 2005 10:38:46 -0500
Subject: [MOBY-guts] biomoby commit
Message-ID: <200502161538.j1GFckEr011520@pub.open-bio.org>


yanwong
Wed Feb 16 10:38:46 EST 2005
Update of /home/repository/moby/moby-live/Python
In directory pub.open-bio.org:/tmp/cvs-serv11495

Modified Files:
	changelog 
Log Message:


moby-live/Python changelog,1.5,1.6
===================================================================
RCS file: /home/repository/moby/moby-live/Python/changelog,v
retrieving revision 1.5
retrieving revision 1.6
diff -u -r1.5 -r1.6
--- /home/repository/moby/moby-live/Python/changelog	2005/01/27 08:44:04	1.5
+++ /home/repository/moby/moby-live/Python/changelog	2005/02/16 15:38:46	1.6
@@ -63,3 +63,4 @@
      The objectBrowser serializes the results in a file in order to save time of retrieval :p 
 
      Some cosmetic changes on the code.
+0.8p1: Changed some code about serialization/deserialization



From yanwong at pub.open-bio.org  Thu Feb 17 08:20:38 2005
From: yanwong at pub.open-bio.org (Yan Wong)
Date: Thu, 17 Feb 2005 08:20:38 -0500
Subject: [MOBY-guts] biomoby commit
Message-ID: <200502171320.j1HDKcGc017174@pub.open-bio.org>


yanwong
Thu Feb 17 08:20:37 EST 2005
Update of /home/repository/moby/moby-live/Python/bioMoby
In directory pub.open-bio.org:/tmp/cvs-serv17142/bioMoby

Modified Files:
	mobyDataTypes.py 
Log Message:

Corrected a bug in Mobycontent that prevent it to fill the properties servicenotes and authority

moby-live/Python/bioMoby mobyDataTypes.py,1.15,1.16
===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/mobyDataTypes.py,v
retrieving revision 1.15
retrieving revision 1.16
diff -u -r1.15 -r1.16
--- /home/repository/moby/moby-live/Python/bioMoby/mobyDataTypes.py	2005/02/16 15:38:46	1.15
+++ /home/repository/moby/moby-live/Python/bioMoby/mobyDataTypes.py	2005/02/17 13:20:37	1.16
@@ -364,6 +364,27 @@
         if isinstance(xmlObject, str):
             doc=parseString(xmlObject)
         
+        #Get the authority
+        authnode=doc.getElementsByTagName("mobyContent")
+        
+        if not authnode:
+            authnode=doc.getElementsByTagName("moby:mobyContent")
+            
+        if authnode:
+            self.authority=authnode[0].getAttribute("authority")
+        
+        if self.authority=="":
+            self.authority=authnode[0].getAttribute("moby:authority")
+        
+        #Get the service notes
+        servicenodes=doc.getElementsByTagName("serviceNotes")
+        
+        if not servicenodes:
+            servicenodes=doc.getElementsByTagName("moby:serviceNotes")
+        
+        if servicenodes and servicenodes[0].firstChild:
+            self.servicenotes=servicenodes[0].firstChild.nodeValue
+        
         mdl=doc.getElementsByTagName('mobyData')
         
         if not mdl:



From mwilkinson at pub.open-bio.org  Fri Feb 18 10:21:03 2005
From: mwilkinson at pub.open-bio.org (Mark Wilkinson)
Date: Fri, 18 Feb 2005 10:21:03 -0500
Subject: [MOBY-guts] biomoby commit
Message-ID: <200502181521.j1IFL3cd026610@pub.open-bio.org>


mwilkinson
Fri Feb 18 10:21:03 EST 2005
Update of /home/repository/moby/moby-live/Perl
In directory pub.open-bio.org:/tmp/cvs-serv26591

Modified Files:
	Makefile.PL 
Log Message:
switching from XML DOM to XML LibXML in the Makefile depedencies

moby-live/Perl Makefile.PL,1.6,1.7
===================================================================
RCS file: /home/repository/moby/moby-live/Perl/Makefile.PL,v
retrieving revision 1.6
retrieving revision 1.7
diff -u -r1.6 -r1.7
--- /home/repository/moby/moby-live/Perl/Makefile.PL	2003/11/12 22:33:09	1.6
+++ /home/repository/moby/moby-live/Perl/Makefile.PL	2005/02/18 15:21:03	1.7
@@ -76,7 +76,7 @@
 	      'VERSION'	      => $VERSION, 
 	      'PREREQ_PM'     => {
               'SOAP::Lite' => 0.55,
-              'XML::DOM' => 1.42,
+              'XML::LibXML' => 1.58,
 	      }, # e.g., Module::Name => 1.1
 	      #'PM_FILTER'     => "", 
 	      ($] >= 5.005 ?    ## Add these new keywords supported since 5.005



From yanwong at pub.open-bio.org  Fri Feb 18 10:54:10 2005
From: yanwong at pub.open-bio.org (Yan Wong)
Date: Fri, 18 Feb 2005 10:54:10 -0500
Subject: [MOBY-guts] biomoby commit
Message-ID: <200502181554.j1IFsAvZ026720@pub.open-bio.org>


yanwong
Fri Feb 18 10:54:10 EST 2005
Update of /home/repository/moby/moby-live/Python/bioMoby
In directory pub.open-bio.org:/tmp/cvs-serv26689

Modified Files:
	mobyDataTypes.py mobyMarshal.py 
Log Message:
The code has been modified in order to implement Provision Information Block
Actually, PIB is only a set of string :

  o.__PIB__=["<Remarks author= \"an Author\">this small remark will appear in the PIB</Remarks>"]

moby-live/Python/bioMoby mobyDataTypes.py,1.16,1.17 mobyMarshal.py,1.5,1.6
===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/mobyDataTypes.py,v
retrieving revision 1.16
retrieving revision 1.17
diff -u -r1.16 -r1.17
--- /home/repository/moby/moby-live/Python/bioMoby/mobyDataTypes.py	2005/02/17 13:20:37	1.16
+++ /home/repository/moby/moby-live/Python/bioMoby/mobyDataTypes.py	2005/02/18 15:54:10	1.17
@@ -130,7 +130,9 @@
             result.append("<ProvisionInformation>")
             
             for aPIB in self.__PIB__:
-                result.append(aPIB.toMoby())
+                #Decide that a PIB will be a string where people can put its
+                #own stuff
+                result.append(str(aPIB))
                 
             result.append("</ProvisionInformation>")
         
@@ -192,6 +194,9 @@
                             anObj=MobyObject()
                             anObj.fromMoby(aCross)
                             self.__cross__.append(anObj)
+                elif child.localName=="ProvisionInformation":
+                    for aPIB in child.childNodes:
+                        self.__PIB__.append(aPIB.toxml())
                 else:
                     #Do the same for the other objects
                     associatedObjectName=child.getAttribute("moby:articleName")

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/mobyMarshal.py,v
retrieving revision 1.5
retrieving revision 1.6
diff -u -r1.5 -r1.6
--- /home/repository/moby/moby-live/Python/bioMoby/mobyMarshal.py	2005/02/04 12:58:24	1.5
+++ /home/repository/moby/moby-live/Python/bioMoby/mobyMarshal.py	2005/02/18 15:54:10	1.6
@@ -280,55 +280,13 @@
         
         typeName="GMoby%s"%str(value.localName)
         
-        from bioMoby.mobyDataTypes import MobyGeneric
+        from bioMoby.mobyDataTypes import MobyObject
         
-        NewType=type(typeName, (MobyGeneric,), {})
+        NewType=type(typeName, (MobyObject,), {})
         
         anObject=NewType()
         
-        anObject.__prefix__="moby"
-        anObject.__tag__=str(value.localName)
-        
-        for tupleAttribute in value.attributes.itemsNS():
-            #First item, second field:
-            setattr(anObject, str(tupleAttribute[0][1]), str(tupleAttribute[1]))
-        
-        i=0    
-        for elem in filter(filterFunc, value.childNodes):
-            methodName="m_%s"%str(elem.localName)
-            
-            articleName=elem.getAttribute("moby:articleName")
-            
-            if not articleName:
-                articleName=elem.getAttribute("articleName")
-            
-            if not articleName:
-                articleName="attribute_%s"%i
-            
-            if hasattr(self, methodName):
-                prop=getattr(self, methodName)(elem)
-            else:
-                prop=self.m_Object(elem)
-            
-            if hasattr(anObject, articleName):
-                t=prop
-                if not type(getattr(anObject, articleName)) is list:
-                    t=getattr(anObject, articleName)
-                    setattr(anObject, articleName, [])
-                getattr(anObject, articleName).append(t)
-            else:
-                setattr(anObject, articleName, prop)
-            i+=1
-        
-        content=[]
-        
-        isContentNode= lambda x: x.nodeType==x.TEXT_NODE or x.nodeType==x.CDATA_SECTION_NODE
-        
-        for elem in filter(isContentNode, value.childNodes):
-            content.append(str(elem.nodeValue))
-        
-        if content:
-            anObject.content(r"".join(content))
+        anObject.fromMoby(value)
         
         return anObject
 



From yanwong at pub.open-bio.org  Fri Feb 18 10:58:21 2005
From: yanwong at pub.open-bio.org (Yan Wong)
Date: Fri, 18 Feb 2005 10:58:21 -0500
Subject: [MOBY-guts] biomoby commit
Message-ID: <200502181558.j1IFwL3R026773@pub.open-bio.org>


yanwong
Fri Feb 18 10:58:21 EST 2005
Update of /home/repository/moby/moby-live/Python
In directory pub.open-bio.org:/tmp/cvs-serv26740

Modified Files:
	PKG-INFO README changelog 
Log Message:
Implementation of the PIB

moby-live/Python PKG-INFO,1.5,1.6 README,1.4,1.5 changelog,1.6,1.7
===================================================================
RCS file: /home/repository/moby/moby-live/Python/PKG-INFO,v
retrieving revision 1.5
retrieving revision 1.6
diff -u -r1.5 -r1.6
--- /home/repository/moby/moby-live/Python/PKG-INFO	2005/01/27 08:44:04	1.5
+++ /home/repository/moby/moby-live/Python/PKG-INFO	2005/02/18 15:58:21	1.6
@@ -1,6 +1,6 @@
 Metadata-Version: 1.0
 Name: bioMoby
-Version: 0.8
+Version: 0.9
 Summary: Python interface for bioMoby
 Home-page: http://bioserv.rpbs.jussieu.fr
 Author: Yan Wong

===================================================================
RCS file: /home/repository/moby/moby-live/Python/README,v
retrieving revision 1.4
retrieving revision 1.5
diff -u -r1.4 -r1.5
--- /home/repository/moby/moby-live/Python/README	2004/12/08 14:57:28	1.4
+++ /home/repository/moby/moby-live/Python/README	2005/02/18 15:58:21	1.5
@@ -49,5 +49,5 @@
 +tutorials: Some scripts in order to show some of the functions
 +webservice: Example of webservice in Python using bioMoby-python's API
 +utils: moby2python is a program that convert mobyObject definitions into Python files (all derived from MobyObject and has a personalized fromMoby method)
-+ZSI-1.5.0-patched: the patched version of ZSI 1.5.0 
++ZSI-1.6.0 
 Suggestions welcome!

===================================================================
RCS file: /home/repository/moby/moby-live/Python/changelog,v
retrieving revision 1.6
retrieving revision 1.7
diff -u -r1.6 -r1.7
--- /home/repository/moby/moby-live/Python/changelog	2005/02/16 15:38:46	1.6
+++ /home/repository/moby/moby-live/Python/changelog	2005/02/18 15:58:21	1.7
@@ -63,4 +63,7 @@
      The objectBrowser serializes the results in a file in order to save time of retrieval :p 
 
      Some cosmetic changes on the code.
+
 0.8p1: Changed some code about serialization/deserialization
+
+0.9: PIB implemented as a set of string in the __PIB__ field



From kawas at pub.open-bio.org  Wed Feb 23 10:39:07 2005
From: kawas at pub.open-bio.org (Eddie Kawas)
Date: Wed, 23 Feb 2005 10:39:07 -0500
Subject: [MOBY-guts] biomoby commit
Message-ID: <200502231539.j1NFd7HO027915@pub.open-bio.org>


kawas
Wed Feb 23 10:39:06 EST 2005
Update of /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/gui/serviceInstanceCreationTool
In directory pub.open-bio.org:/tmp/cvs-serv27890/org/biomoby/client/gui/serviceInstanceCreationTool

Modified Files:
	MobyUtilities.java 
Log Message:
Fixed imports and removed getRelations() - see getPrimitives(...)
in MobyObjectPrimitiveExtractor instead.
Eddie

moby-live/Java/src/main/org/biomoby/client/gui/serviceInstanceCreationTool MobyUtilities.java,1.3,1.4
===================================================================
RCS file: /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/gui/serviceInstanceCreationTool/MobyUtilities.java,v
retrieving revision 1.3
retrieving revision 1.4
diff -u -r1.3 -r1.4
--- /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/gui/serviceInstanceCreationTool/MobyUtilities.java	2005/02/09 18:26:41	1.3
+++ /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/gui/serviceInstanceCreationTool/MobyUtilities.java	2005/02/23 15:39:06	1.4
@@ -1,21 +1,11 @@
 package org.biomoby.client.gui.serviceInstanceCreationTool;
 
-import java.io.BufferedReader;
 import java.io.IOException;
-import java.io.InputStreamReader;
-import java.net.URL;
-import java.util.ArrayList;
 import java.util.Iterator;
 import java.util.LinkedList;
-import java.util.StringTokenizer;
-import java.util.regex.Matcher;
-import java.util.regex.Pattern;
 
 import javax.swing.tree.TreePath;
 
-import org.biomoby.client.gui.util.MobyObjectPrimitiveExtractor;
-import org.biomoby.client.gui.util.Triples;
-
 /**
  * Utilities that are useful for retrieving information about certain objects, parsing objects, etc.
  * @author Eddie Kawas
@@ -27,45 +17,11 @@
 public class MobyUtilities {
 
     /**
-     * PRE: None.<p>
-     * POST: a linked list of all the relations is returned, such that:<p>
-     * => The first item in the list is a string representation of the parent<p>
-     * => The second item is a linked list of all the 'HAS' container relationships<p>
-     * => The third item is a linked list of all the 'HASA' container relationships
-     * @param name, the name of the object to query for - can be an Moby Object LSID.
-     * @return returns a linked list {String, LinkedList, LinkedList} of relationships
+     * @deprecated please see MobyObjectPrimitiveExtractor.java
      */
     public static LinkedList GetRelations(String name) throws IOException {
-        URL url = null;
-        boolean isLSID = false;
-        Pattern p = Pattern.compile("(^urn:lsid:biomoby.org:objectclass:\\S+$)",
-                Pattern.CASE_INSENSITIVE);
-        Matcher m = p.matcher(name);
-        isLSID = m.matches();
-        if (isLSID) {
-            int x = name.lastIndexOf(":")+1;
-            name = name.substring(x);
-        }
-
-        LinkedList llHas = new LinkedList();
-        LinkedList llHasa = new LinkedList();
-        MobyObjectPrimitiveExtractor mope = new MobyObjectPrimitiveExtractor();
-        ArrayList al = mope.getPrimitives(name);
-        for (Iterator x = al.iterator(); x.hasNext();) {
-            Triples t = (Triples)x.next();
-            if (t.getType() == Triples.HAS) {
-                llHas.add(t.getPrimitive());
-            }
-            if (t.getType() == Triples.HASA) {
-                llHasa.add(t.getPrimitive());
-            }
-        }
-        // set up the return list
-        LinkedList listToReturn = new LinkedList();
-        listToReturn.addFirst("Object");
-        listToReturn.add(llHas);
-        listToReturn.add(llHasa);
-        return listToReturn;
+        
+        return new LinkedList();
     }
 
     /**



From kawas at pub.open-bio.org  Wed Feb 23 10:41:03 2005
From: kawas at pub.open-bio.org (Eddie Kawas)
Date: Wed, 23 Feb 2005 10:41:03 -0500
Subject: [MOBY-guts] biomoby commit
Message-ID: <200502231541.j1NFf3iM028054@pub.open-bio.org>


kawas
Wed Feb 23 10:41:03 EST 2005
Update of /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/gui/util
In directory pub.open-bio.org:/tmp/cvs-serv28029/org/biomoby/client/gui/util

Modified Files:
	MobyObjectPrimitiveExtractor.java 
Log Message:
Corrected the use of Dom from JDOM to w3c DOM to make class compatible
with other jMoby classes.
Eddie

moby-live/Java/src/main/org/biomoby/client/gui/util MobyObjectPrimitiveExtractor.java,1.1,1.2
===================================================================
RCS file: /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/gui/util/MobyObjectPrimitiveExtractor.java,v
retrieving revision 1.1
retrieving revision 1.2
diff -u -r1.1 -r1.2
--- /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/gui/util/MobyObjectPrimitiveExtractor.java	2005/02/16 15:38:28	1.1
+++ /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/gui/util/MobyObjectPrimitiveExtractor.java	2005/02/23 15:41:03	1.2
@@ -5,60 +5,91 @@
 package org.biomoby.client.gui.util;
 
 import java.io.BufferedReader;
-import java.io.ByteArrayInputStream;
 import java.io.ByteArrayOutputStream;
 import java.io.IOException;
 import java.io.InputStreamReader;
+import java.io.OutputStream;
+import java.io.StringReader;
 import java.net.MalformedURLException;
 import java.net.URL;
 import java.util.ArrayList;
 import java.util.Iterator;
-import java.util.List;
 
+import javax.xml.parsers.DocumentBuilder;
+import javax.xml.parsers.DocumentBuilderFactory;
 import javax.xml.parsers.ParserConfigurationException;
+import javax.xml.transform.Transformer;
+import javax.xml.transform.TransformerConfigurationException;
+import javax.xml.transform.TransformerException;
+import javax.xml.transform.TransformerFactory;
+import javax.xml.transform.dom.DOMSource;
+import javax.xml.transform.stream.StreamResult;
 
-import org.jdom.Attribute;
-import org.jdom.Document;
-import org.jdom.Element;
-import org.jdom.JDOMException;
-import org.jdom.Namespace;
-import org.jdom.input.SAXBuilder;
+import org.biomoby.shared.MobyDataFloat;
+import org.biomoby.shared.MobyDataInt;
+import org.biomoby.shared.MobyDataSimpleInstance;
+import org.biomoby.shared.MobyDataString;
+import org.biomoby.shared.MobyDataType;
+import org.jdom.input.DOMBuilder;
 import org.jdom.output.Format;
 import org.jdom.output.XMLOutputter;
+import org.w3c.dom.Document;
+import org.w3c.dom.Element;
+import org.w3c.dom.Node;
+import org.w3c.dom.NodeList;
+import org.xml.sax.InputSource;
 import org.xml.sax.SAXException;
 
-import com.hp.hpl.jena.vocabulary.RDF;
-import com.hp.hpl.jena.vocabulary.RDFS;
-
 /**
  * @author Eddie Kawas
- * <p>Created for
  * <p>This class was created to ...
  * <p>For questions, comments, or bugs
  * <p>email me at edward.kawas at gmail.com
  */
 public class MobyObjectPrimitiveExtractor {
     final private static String URL_OBJECT = new String(
-    	"http://mobycentral.cbr.nrc.ca:8090/authority/metadata?lsid=");
-    final static Namespace HAS = Namespace.getNamespace("has","http://biomoby.org/RESOURCES/MOBY-S/Predicates#");
-    final static Namespace HASA = Namespace.getNamespace("hasa","http://biomoby.org/RESOURCES/MOBY-S/Predicates#");
-    final static Namespace ARTICLE = Namespace.getNamespace("articleName","http://biomoby.org/RESOURCES/MOBY-S/Predicates#");
-    final static String[] PRIMITIVES = {"String", "Float", "Integer", "Object", "DateTime"};
+            "http://mobycentral.cbr.nrc.ca:8090/authority/metadata?lsid=");
+
+    final static String[] PRIMITIVES = {
+            "String",
+            "Float",
+            "Integer",
+            "Object",
+            "DateTime" };
+
+    final static String MOBY = "http://www.biomoby.org/moby";
+
+    /**
+     *  
+     * <b>PRE:</b><p>
+     * <b>POST:</b><p>
+     * @param MobyElement - The Element containing the MOBY Object to find primitives for
+     * @return an array of MobyDataSimpleInstances that are the primitives for MobyElement.
+     */
+    public MobyDataSimpleInstance[] getPrimitives(Element MobyElement) {
+        return getPrimitivesHelper(MobyElement.getTagName());
+    }
+
     /**
      *  
      * <b>PRE:</b><p>
      * <b>POST:</b><p>
-     * @param name - name of the Moby Object to decompose
-     * @return Triples[] - an array of Triples or null if an error occured
-     * @throws ParserConfigurationException
-     * @throws IOException
-     * @throws SAXException
+     * @param Object - The object to find primitives for
+     * @return an array of MobyDataSimpleInstances that are the primitives for Object.
+     */
+    public MobyDataSimpleInstance[] getPrimitives(String object) {
+        return getPrimitivesHelper(object);
+    }
+
+    /*
+     * getPrimitives helper.
      */
-    public ArrayList getPrimitives(String name) {
+    private MobyDataSimpleInstance[] getPrimitivesHelper(String name) {
         ArrayList list = new ArrayList();
         if (isPrimitive(name)) {
-            list.add(new Triples(name, name, Triples.HASA));
-            return list;
+            MobyDataSimpleInstance mdsi = new MobyDataSimpleInstance("");
+            mdsi.setDataType(new MobyDataType(name));
+            return new MobyDataSimpleInstance[] { mdsi };
         }
         String lsid = "urn:lsid:biomoby.org:objectclass:" + name;
         String rdf = getObjectRDF(lsid);
@@ -69,121 +100,130 @@
         // create a DOM document
         Document doc = getDOMDocument(rdf);
         // start parsing
-        List rdfsClassList = doc.getRootElement().getContent();
-        Iterator it = rdfsClassList.iterator();
-        while (it.hasNext()) {
-            Object obj = it.next();
-            Element hasa = null, has = null;
-            if (obj instanceof Element) {
-                Element classElement = (Element) obj;
-                // set up appropriate iterators
-                Iterator hasIterator = classElement.getChildren("has", HAS).iterator();
-                Iterator hasaIterator = classElement.getChildren("hasa",HASA).iterator();
-                Iterator subClassIterator = classElement.getChildren("subClassOf", Namespace.getNamespace(RDFS.getURI())).iterator();
-                // iterate through the lists
-                while (hasIterator.hasNext()) {
-                    Element hasElement = (Element) hasIterator.next();
-                    List hasInnerElementList = hasElement.getChildren();
-                    if (!hasInnerElementList.isEmpty()) {
-                        Element mobyObject = (Element) hasInnerElementList.get(0);
-                        String primitive = mobyObject.getName();
-                        int type = Triples.HAS;
-                        String articleName = mobyObject.getChildText("articleName", ARTICLE);
-                        // check if primitive is a primitive
-                        if (isPrimitive(primitive)) {
-                            Triples t =  new Triples(articleName, primitive, type);
-                            list.add(t);
-                        } else {
-                            // recurse
-                            ArrayList recurse = getPrimitives(primitive);
-                            if (recurse == null) {
-                                return null;
-                            }
-                            processRecursionList(list, recurse);
+        Element root = doc.getDocumentElement();
+        NodeList rdfsClassList = root.getElementsByTagName("rdfs:Class");
+        for (int x = 0; x < rdfsClassList.getLength(); x++) {
+            // process each class:
+            Element _class = ((Element) rdfsClassList.item(x));
+            NodeList has = _class.getElementsByTagName("mobyPred:has");
+            NodeList hasa = _class.getElementsByTagName("mobyPred:hasa");
+            // subClassOf can contain attributes or just an element
+            NodeList subClassOf = _class
+                    .getElementsByTagName("rdfs:subClassOf");
+            for (int i = 0; i < has.getLength(); i++) {
+                NodeList children = ((Element) has.item(i)).getChildNodes();
+                for (int j = 0; j < children.getLength(); j++) {
+                    if (!(children.item(j) instanceof Element))
+                        continue;
+                    Element child = (Element) children.item(j);
+                    Node articleNode = child.getElementsByTagName(
+                            "mobyPred:articleName").item(0);
+                    String localName = child.getLocalName();
+                    String articleName = (articleNode == null) ? ""
+                            : articleNode.getTextContent();
+                    //                  TODO - recurse if object is not a primitive
+                    if (isPrimitive(localName)) {
+                        MobyDataSimpleInstance mdsi = createPrimitiveType(localName, articleName);
+                        list.add(mdsi);
+                    } else {
+                        MobyDataSimpleInstance[] recurseArray = getPrimitives(localName);
+                        for (int k = 0; k < recurseArray.length; k++) {
+                            list.add(recurseArray[k]);
                         }
                     }
                 }
-                hasIterator = null;
-                while (hasaIterator.hasNext()) {
-                    Element hasaElement = (Element) hasaIterator.next();
-                    List hasaInnerElementList = hasaElement.getChildren();
-                    if (!hasaInnerElementList.isEmpty()) {
-                        Element mobyObject = (Element) hasaInnerElementList.get(0);
-                        String primitive = mobyObject.getName();
-                        int type = Triples.HASA;
-                        String articleName = mobyObject.getChildText("articleName", ARTICLE);
-                        // check if primitive is a primitive
-                        if (isPrimitive(primitive)) {
-                            Triples t =  new Triples(articleName, primitive, type);
-                            list.add(t);
+            }
+            for (int i = 0; i < hasa.getLength(); i++) {
+                NodeList children = ((Element) hasa.item(i)).getChildNodes();
+                for (int j = 0; j < children.getLength(); j++) {
+                    if (children.item(j) instanceof Element) {
+                        Element child = (Element) children.item(j);
+                        Node articleNode = child.getElementsByTagName(
+                                "mobyPred:articleName").item(0);
+                        String localName = child.getLocalName();
+                        String articleName = (articleNode == null) ? ""
+                                : articleNode.getTextContent();
+                        //                      TODO - recurse if object is not a primitive
+                        if (isPrimitive(localName)) {
+                            MobyDataSimpleInstance mdsi = createPrimitiveType(localName, articleName);
+                            list.add(mdsi);
                         } else {
-                            // recurse
-                            ArrayList recurse = getPrimitives(primitive);
-                            if (recurse == null) {
-                                return null;
+                            MobyDataSimpleInstance[] recurseArray = getPrimitives(localName);
+                            for (int k = 0; k < recurseArray.length; k++) {
+                                list.add(recurseArray[k]);
                             }
-                            processRecursionList(list, recurse);
                         }
                     }
                 }
-                hasaIterator = null;
-                /*
-                 * iterate through subClassOf
-                 * checking to see if the object is
-                 * a subclass of a primitive
-                 */
-                while (subClassIterator.hasNext()) {
-                    Element sub = (Element)subClassIterator.next();
-                    
-                    // check if we have an element called Class
-                    Element rdfsClass = sub.getChild("Class", Namespace.getNamespace(RDFS.getURI()));
-                    if (rdfsClass != null) {
-                        // get the rdf:about attribute
-                        String attr = rdfsClass.getAttributeValue("about", Namespace.getNamespace(RDF.getURI()));
-                        if (attr != null) {
-                            // i.e. http://biomoby.org/RESOURCES/MOBY-S/Objects#text-plain
-                            if (attr.indexOf("#") > 0) {
-                                attr = attr.substring(attr.indexOf("#")+1);
-                            }
-                            if (isPrimitive(attr)&& !attr.equals("Object")) {
-                                // assume if you are something, it means you have it (singular)
-                                Triples t =  new Triples(name, attr, Triples.HASA);
-                                list.add(t);
-                            }
-                        }
+            }
+
+            for (int i = 0; i < subClassOf.getLength(); i++) {
+                Element subClass = (Element) subClassOf.item(i);
+                // check for attributes
+                if (subClass.hasAttributes()) {
+                    String object = subClass.getAttribute("rdf:resource");
+                    if (object.indexOf("#") > 0) {
+                        object = object.substring(object.indexOf("#") + 1);
                     }
-                    /* process <rdfs:subClassOf rdf:resource="..."/> */
-                    String attr = sub.getAttributeValue("resource", Namespace.getNamespace(RDF.getURI()));
-                    if (attr != null) {
-                        if (attr.indexOf("#") > 0) {
-                            attr = attr.substring(attr.indexOf("#") + 1);
-                        }
-                        if (isPrimitive(attr) && !attr.equals("Object")) {
-                            // assume if you are something, it means you have it (singular)
-                            Triples t = new Triples(name, attr, Triples.HASA);
-                            list.add(t);
-                        }
+                    if (isPrimitive(object) && !object.equals("Object")) {
+                        MobyDataSimpleInstance mdsi = new MobyDataSimpleInstance(
+                                object);
+                        mdsi.setDataType(new MobyDataType(object));
+                        list.add(mdsi);
+                    }
+                } else {
+                    String object = ((Element) ((Element) subClass)
+                            .getElementsByTagName("rdfs:Class").item(0))
+                            .getAttribute("rdf:about");
+                    if (object.indexOf("#") > 0) {
+                        object = object.substring(object.indexOf("#") + 1);
+                    }
+                    if (isPrimitive(object) && !object.equals("Object")) {
+                        MobyDataSimpleInstance mdsi = new MobyDataSimpleInstance(
+                                object);
+                        mdsi.setDataType(new MobyDataType(object));
+                        list.add(mdsi);
                     }
                 }
+
             }
         }
-        
-        return list;
+
+        return convertArrayList(list);
     }
-    
-    private void processRecursionList(ArrayList list, ArrayList recurse) {
-        for (Iterator x = recurse.iterator(); x.hasNext();) {
-            Triples t = (Triples) x.next();
-            list.add(t);
+
+
+    /*
+     * method to create default DataTypes.
+     */
+    private MobyDataSimpleInstance createPrimitiveType(String localName, String articleName) {
+        if (localName.equalsIgnoreCase("Float")) {
+            return new MobyDataFloat(articleName, 0.0);
+        } else if (localName.equalsIgnoreCase("String")) {
+            return new MobyDataString(articleName, "");
+        } else if (localName.equalsIgnoreCase("Integer")) {
+            return new MobyDataInt(articleName, 0);
+        } else if(localName.equalsIgnoreCase("DateTime")) {
+            MobyDataSimpleInstance mdsi = new MobyDataSimpleInstance(articleName);
+            mdsi.setDataType(new MobyDataType(localName));
+            return mdsi;
         }
+        // error
+        return null;
     }
 
-    /**
-     *  
-     * <b>PRE:</b><p>
-     * <b>POST:</b><p>
-     * @param test - the test Moby object name to test with
-     * @return true if test is a primitive, false otherwise
+    private MobyDataSimpleInstance[] convertArrayList(ArrayList list) {
+        int size = list.size();
+        MobyDataSimpleInstance[] mdsi = new MobyDataSimpleInstance[size];
+        size = 0;
+        for (Iterator x = list.iterator(); x.hasNext(); size++) {
+            mdsi[size] = (MobyDataSimpleInstance) x.next();
+        }
+        return mdsi;
+    }
+
+    /*
+     * simply tests whether a string is a primitive
      */
     private boolean isPrimitive(String test) {
         for (int x = 0; x < PRIMITIVES.length; x++) {
@@ -192,94 +232,106 @@
         }
         return false;
     }
+
     /*
      * given an xml string, create a DOM document
      */
     private Document getDOMDocument(String rdfXML) {
-        // start creating the triples
-        SAXBuilder builder = new SAXBuilder();
-        Document doc = null;
         try {
-            // Create the document
-            doc = builder.build(new ByteArrayInputStream(rdfXML.getBytes()));
-        } catch (JDOMException e) {
-            System.err.println("Error in getPrimitives:1 - JDOMException.\n" + e.getMessage());
-            return null;
-        } catch (IOException e) {
-            System.err.println("Error in getPrimitives:2 - IOException.\n"+ e.getMessage());
-            return null;
-        }
-        return doc;
+            // Create a builder factory
+            DocumentBuilderFactory factory = DocumentBuilderFactory
+                    .newInstance();
+            factory.setNamespaceAware(true);
+            // Create the builder and parse the file
+            Document doc = factory.newDocumentBuilder().parse(
+                    new InputSource(new StringReader(rdfXML)));
+            return doc;
+        } catch (SAXException e) {
+            // A parsing error occurred; the xml input is not valid
+        } catch (ParserConfigurationException e) {} catch (IOException e) {}
+        return null;
     }
-    
+
     /*
      * given an lsdi, get the moby object rdf document
      */
     private String getObjectRDF(String lsid) {
         URL url;
         try {
-            url = new URL(URL_OBJECT+lsid);
+            url = new URL(URL_OBJECT + lsid);
         } catch (MalformedURLException e) {
-            System.err.println("Error in getObjectRDF:1 - MalformedURLException.");
+            System.err
+                    .println("Error in getObjectRDF:1 - MalformedURLException.");
             return null;
         }
         BufferedReader in = null;
         try {
             in = new BufferedReader(new InputStreamReader(url.openStream()));
         } catch (IOException e1) {
-            System.err.println("Error in getObjectRDF:2 - IOException. \n- Can't read from URL");
+            System.err
+                    .println("Error in getObjectRDF:2 - IOException. \n- Can't read from URL");
             return null;
         }
         String input;
         StringBuffer sb = new StringBuffer();
         try {
             while ((input = in.readLine()) != null) {
-                sb.append(input+System.getProperty("line.separator"));
+                sb.append(input + System.getProperty("line.separator"));
             }
         } catch (IOException e2) {
-            System.err.println("Error in getObjectRDF:3 - IOException.\n-Problems reading from URL");
+            System.err
+                    .println("Error in getObjectRDF:3 - IOException.\n-Problems reading from URL");
             return null;
         }
 
         return sb.toString();
     }
-    
+
     /**
      *  
      * <b>PRE:</b> Object is a valid Moby Object<p>
      * <b>POST:</b> An element representing the moby class structure is created.</br>>
      * @link http://www.biomoby.org/twiki/bin//view/Moby/MobySAPI#ObjectStructure
      * @param object - the Moby object to create a structure for
-     * @param triples - the primitives in Triples format to add to this structure 
-     * @return an Element representing the Moby Class Structure
+     * @param mdsi - an array of MobyDataSimpleInstances to add to the element 
+     * @return an Element representing the Moby Class Structure containing the MobyDataSimpleInstances
      */
-    public Element getElementContainingTriples(String object, ArrayList triples) {
+    public Element getElementContainingPrimitives(String object,
+            MobyDataSimpleInstance[] mdsi) {
         /*
-<moby:GenericSequence namespace='AGI_LocusCode' id='At2g42410'>   
-	<CrossReference>    
-		<Object namespace='Global_Keyword' id='superman'/> 
-	</CrossReference>
-	<moby:Integer namespace='' id='' articleName='Length'>214</moby:Integer> 
-	<moby:String namespace='' id=''articleName='SequenceString'>MKRTHLASFSNRDKTRLGYL</moby:String>
-</moby:GenericSequence>
+         <moby:GenericSequence namespace='AGI_LocusCode' id='At2g42410'>   
+         <CrossReference>    
+         <Object namespace='Global_Keyword' id='superman'/> 
+         </CrossReference>
+         <moby:Integer namespace='' id='' articleName='Length'>214</moby:Integer> 
+         <moby:String namespace='' id=''articleName='SequenceString'>MKRTHLASFSNRDKTRLGYL</moby:String>
+         </moby:GenericSequence>
          */
         /*root element*/
         Element root = null;
-        Namespace ns = Namespace.getNamespace("moby", "http://www.biomoby.org/moby");
-        root = new Element(object);
-        root.setNamespace(ns);
-        
+        Document doc = createDomDocument();
+        root = doc.createElementNS(MOBY, object);
         /*iterate through triples, create elements and add to root*/
-        Iterator it = triples.iterator();
-        while (it.hasNext()) {
-            Triples t = (Triples)it.next();
-            Element e = new Element(t.getPrimitive(), ns);
-            e.setAttribute(new Attribute("id", ""));
-            e.setAttribute(new Attribute("articleName", t.getArticleName()));
-            root.addContent(e);
+        for (int x = 0; x < mdsi.length; x++) {
+            MobyDataSimpleInstance mds = mdsi[x];
+            Element e = doc.createElementNS(MOBY, mds.getDataType().getName());
+            e.setAttribute("id", "");
+            e.setAttribute("articleName", mds.getName());
+            root.appendChild(e);
         }
         return root;
     }
+
+    private Document createDomDocument() {
+        try {
+            DocumentBuilder builder = DocumentBuilderFactory.newInstance()
+                    .newDocumentBuilder();
+            Document doc = builder.newDocument();
+            return doc;
+        } catch (ParserConfigurationException e) {}
+        return null;
+    }
+
     /**
      *  
      * <b>PRE:</b>Element e exists and Class, namespace, and id are valid.<p>
@@ -290,30 +342,33 @@
      * @param id - the identifier within that namespace that specifies the precise resource represented in the object
      * @return Element - the root element containing the CRIB just added.
      */
-    public Element addCrossReferenceToElement(Element e, String Class, String namespace, String id) {
+    public Element addCrossReferenceToElement(Element e, String Class,
+            String namespace, String id) {
         /* first make sure that the element doesnt already contain
          * the CrossReference child
          */
-        Iterator it = e.getChildren("CrossReference").iterator();
+        NodeList it = e.getElementsByTagName("CrossReference");
         Element cross = null;
-        if (it.hasNext()) {
+        if (it.getLength() > 0) {
             /*There is a pre-existing tag*/
-            cross = (Element)it.next();
-            Element object = new Element(Class);
-            object.setAttribute(new Attribute("namespace", namespace));
-            object.setAttribute(new Attribute("id", id));
-            cross.addContent(object);
+            cross = (Element) it.item(0);
+            Document doc = createDomDocument();
+            Element object = doc.createElement(Class);
+            object.setAttribute("namespace", namespace);
+            object.setAttribute("id", id);
+            cross.appendChild(object);
         } else {
-            cross = new Element ("CrossReference");
-            Element object = new Element(Class);
-            object.setAttribute(new Attribute("namespace", namespace));
-            object.setAttribute(new Attribute("id", id));
-            cross.addContent(object);
-            e.addContent(cross);
+            Document doc = e.getOwnerDocument();
+            Element object = doc.createElement(Class);
+            cross = doc.createElement("CrossReference");
+            object.setAttribute("namespace", namespace);
+            object.setAttribute("id", id);
+            cross.appendChild(object);
+            e.appendChild(cross);
         }
         return e;
     }
-    
+
     /**
      *  
      * <b>PRE:</b><p>
@@ -328,49 +383,55 @@
      * @param description - this is the textual content of the XML element, and contains a human-readable description of the intended interpretation of this cross-reference.
      * @return - the root object Element with the Xref cross reference added to it.
      */
-    public Element addXrefCrossReferenceToElement(Element e, String id, String namespace, String authURI, String serviceName, String evidenceCode, String XrefType, String description) {
+
+    public Element addXrefCrossReferenceToElement(Element e, String id,
+            String namespace, String authURI, String serviceName,
+            String evidenceCode, String XrefType, String description) {
         /*
          * everything is required other than description
          */
-        if (namespace == null || id == null || authURI == null || serviceName == null || evidenceCode == null || XrefType == null)
+        if (namespace == null || id == null || authURI == null
+                || serviceName == null || evidenceCode == null
+                || XrefType == null)
             return e;
         /* 
          * make sure that the element doesnt already contain
          * the CrossReference child
          */
-        Iterator it = e.getChildren("CrossReference").iterator();
+        NodeList it = e.getElementsByTagName("CrossReference");
         Element cross = null;
-        if (it.hasNext()) {
+        if (it.getLength() > 0) {
+            Document doc = e.getOwnerDocument();
             /*There is a pre-existing tag*/
-            cross = (Element)it.next();
-            Element object = new Element("Xref");
-            object.setAttribute(new Attribute("namespace", namespace));
-            object.setAttribute(new Attribute("id", id));
-            object.setAttribute(new Attribute("authURI", authURI));
-            object.setAttribute(new Attribute("serviceName", serviceName));
-            object.setAttribute(new Attribute("evidenceCode", evidenceCode));
-            object.setAttribute(new Attribute("XrefType", XrefType));
+            cross = (Element) it.item(0);
+            Element object = doc.createElement("Xref");
+            object.setAttribute("namespace", namespace);
+            object.setAttribute("id", id);
+            object.setAttribute("authURI", authURI);
+            object.setAttribute("serviceName", serviceName);
+            object.setAttribute("evidenceCode", evidenceCode);
+            object.setAttribute("XrefType", XrefType);
             if (description != null)
-                object.setText(description);
-            cross.addContent(object);
+                object.setNodeValue(description);
+            cross.appendChild(object);
         } else {
-            cross = new Element ("CrossReference");
-            Element object = new Element("Xref");
-            object.setAttribute(new Attribute("namespace", namespace));
-            object.setAttribute(new Attribute("id", id));
-            object.setAttribute(new Attribute("authURI", authURI));
-            object.setAttribute(new Attribute("serviceName", serviceName));
-            object.setAttribute(new Attribute("evidenceCode", evidenceCode));
-            object.setAttribute(new Attribute("XrefType", XrefType));
+            Document doc = e.getOwnerDocument();
+            cross = doc.createElement("CrossReference");
+            Element object = doc.createElement("Xref");
+            object.setAttribute("namespace", namespace);
+            object.setAttribute("id", id);
+            object.setAttribute("authURI", authURI);
+            object.setAttribute("serviceName", serviceName);
+            object.setAttribute("evidenceCode", evidenceCode);
+            object.setAttribute("XrefType", XrefType);
             if (description != null)
-                object.setText(description);
-            cross.addContent(object);
-            e.addContent(cross);
+                object.setNodeValue(description);
+            cross.appendChild(object);
+            e.appendChild(cross);
         }
         return e;
     }
-    
-    
+
     /**
      *  
      * <b>PRE:</b><p>
@@ -381,27 +442,30 @@
      */
     /*
      * <ProvisionInformation>
-              ... one or more of the provision elements (below) ...
-       </ProvisionInformation>
-       
-       <serviceSoftware software_name="" software_version="" software_comment=""/>
-       <serviceDatabase database_name="" database_version="" database_comment=""/>
-       <serviceComment>comment here</serviceComment>
+     ... one or more of the provision elements (below) ...
+     </ProvisionInformation>
+     
+     <serviceSoftware software_name="" software_version="" software_comment=""/>
+     <serviceDatabase database_name="" database_version="" database_comment=""/>
+     <serviceComment>comment here</serviceComment>
      */
-    public Element addProvisionInformationBlock(Element root, Element[] elements){
+    public Element addProvisionInformationBlock(Element root, Element[] elements) {
         if (elements == null || root == null || elements.length < 1)
             return root;
         /* only add PIB to a root element with no PIB child*/
-        if (!root.getChildren("ProvisionInformation").isEmpty()) {
+        if (root.getElementsByTagName("ProvisionInformation").item(0) != null) {
             return root;
         }
-        Element pib = new Element("ProvisionInformation");
-        for (int x=0; x < elements.length; x++)
-            pib.addContent(elements[x]);
-        root.addContent(pib);
+        Document doc = root.getOwnerDocument();
+        Element pib = doc.createElement("ProvisionInformation");
+        for (int x = 0; x < elements.length; x++) {
+            doc.adoptNode(elements[x]);
+            pib.appendChild(elements[x]);
+        }
+        root.appendChild(pib);
         return root;
     }
-    
+
     /**
      *  
      * <b>PRE:</b><p>
@@ -411,15 +475,18 @@
      * @param comment - any applicable comments
      * @return - a serviceSoftware Element with its attributes appropriately set.
      */
-    public Element createPIBServiceSoftwareElement(String name, String version, String comment) {
+    public Element createPIBServiceSoftwareElement(String name, String version,
+            String comment) {
         if (name == null || version == null || comment == null)
             return null;
-        Element e = new Element("serviceSoftware");
-        e.setAttribute(new Attribute("software_name", name));
-        e.setAttribute(new Attribute("software_version", version));
-        e.setAttribute(new Attribute("software_comment", comment));
+        Document doc = createDomDocument();
+        Element e = doc.createElement("serviceSoftware");
+        e.setAttribute("software_name", name);
+        e.setAttribute("software_version", version);
+        e.setAttribute("software_comment", comment);
         return e;
     }
+
     /**
      *  
      * <b>PRE:</b><p>
@@ -429,16 +496,18 @@
      * @param comment - any applicable comments
      * @return - a serviceDatabase Element with its attributes appropriately set.
      */
-    public Element createPIBServiceDatabaseElement(String name, String version, String comment) {
+    public Element createPIBServiceDatabaseElement(String name, String version,
+            String comment) {
         if (name == null || version == null || comment == null)
             return null;
-        Element e = new Element("serviceDatabase");
-        e.setAttribute(new Attribute("database_name", name));
-        e.setAttribute(new Attribute("database_version", version));
-        e.setAttribute(new Attribute("database_comment", comment));
+        Document doc = createDomDocument();
+        Element e = doc.createElement("serviceDatabase");
+        e.setAttribute("database_name", name);
+        e.setAttribute("database_version", version);
+        e.setAttribute("database_comment", comment);
         return e;
     }
-    
+
     /**
      *  
      * <b>PRE:</b><p>
@@ -449,24 +518,12 @@
     public Element createPIBServiceCommentElement(String comment) {
         if (comment == null)
             return null;
-        Element e = new Element("serviceComment");
-        e.setText(comment);
+
+        Element e = createDomDocument().createElement("serviceComment");
+        e.setTextContent(comment);
         return e;
     }
-    
-    public static void main(String[] args) {
-        MobyObjectPrimitiveExtractor g = new MobyObjectPrimitiveExtractor();
-        ArrayList l = g.getPrimitives("GenericSequence");
-        Element e = g.getElementContainingTriples("GenericSequence", l);
-        System.out.println(output(e));
-        e = g.addCrossReferenceToElement(e, "Object","NCBI_gi", "bob");
-        System.out.println(output(e));
-        e = g.addXrefCrossReferenceToElement(e, "myNamespace", "545454", "www.illuminae.com", "myServiceName", "myCode", "myXtype", "bob is your description");
-        System.out.println(output(e));
-        //g.getPrimitives("DNASequence");
-        //g.getPrimitives("CommentedRNASequence");
-    }
-    
+
     /**
      *  
      * <b>PRE:</b><p>
@@ -474,7 +531,7 @@
      * @param e - the dom element to stringify.
      * @return - a string representation of the element
      */
-    public static String output(Element e) {
+    public String createStringFromElement(Element e) {
         ByteArrayOutputStream buf = new ByteArrayOutputStream();
         // Create the document
         XMLOutputter fmt = new XMLOutputter();
@@ -483,10 +540,36 @@
         format.setIndent("     ");
         fmt.setFormat(format);
         try {
-            fmt.output(e, buf);
+            fmt.output(convert(e), buf);
         } catch (IOException ex) {
             System.out.println("Error: " + ex.getLocalizedMessage());
         }
-        return "Document: \n" + buf.toString();
+        return buf.toString();
     }
-}
+
+    private void outputDocumentToStream(Document doc, OutputStream s) {
+        // Use a Transformer for output
+        TransformerFactory tFactory = TransformerFactory.newInstance();
+        Transformer transformer;
+        try {
+            transformer = tFactory.newTransformer();
+            DOMSource source = new DOMSource(doc);
+            StreamResult result = new StreamResult(s);
+            transformer.transform(source, result);
+        } catch (TransformerConfigurationException e1) {
+            System.err.println("Couldnt print out DOM Doc.1 "
+                    + e1.getLocalizedMessage());
+        } catch (TransformerException e) {
+            System.err.println("Couldnt print out DOM Doc.2 "
+                    + e.getLocalizedMessage());
+        }
+    }
+
+    private static org.jdom.Element convert(Element domDoc) throws IOException {
+        // Create new DOMBuilder, using default parser
+        DOMBuilder builder = new DOMBuilder();
+        org.jdom.Element jdomDoc = builder.build(domDoc);
+        return jdomDoc;
+    }
+    
+}
\ No newline at end of file



From kawas at pub.open-bio.org  Thu Feb 24 18:55:59 2005
From: kawas at pub.open-bio.org (Eddie Kawas)
Date: Thu, 24 Feb 2005 18:55:59 -0500
Subject: [MOBY-guts] biomoby commit
Message-ID: <200502242355.j1ONtxKU002191@pub.open-bio.org>


kawas
Thu Feb 24 18:55:59 EST 2005
Update of /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/gui/util
In directory pub.open-bio.org:/tmp/cvs-serv2169

Removed Files:
	MobyObjectPrimitiveExtractor.java 
Log Message:
removed this class because it required 'extra' work to get it to compile properly.
once everyone is using java 1.5.0 or has extra time on their hands, i will put it back.
Sorry.

moby-live/Java/src/main/org/biomoby/client/gui/util MobyObjectPrimitiveExtractor.java,1.2,NONE
rcsdiff: /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/gui/util/RCS/MobyObjectPrimitiveExtractor.java,v: No such file or directory



From kawas at pub.open-bio.org  Thu Feb 24 18:56:15 2005
From: kawas at pub.open-bio.org (Eddie Kawas)
Date: Thu, 24 Feb 2005 18:56:15 -0500
Subject: [MOBY-guts] biomoby commit
Message-ID: <200502242356.j1ONuFpp002222@pub.open-bio.org>


kawas
Thu Feb 24 18:56:15 EST 2005
Update of /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/gui/util
In directory pub.open-bio.org:/tmp/cvs-serv2200

Removed Files:
	Triples.java 
Log Message:
removed this class because it required 'extra' work to get it to compile properly.
once everyone is using java 1.5.0 or has extra time on their hands, i will put it back.
Sorry.

moby-live/Java/src/main/org/biomoby/client/gui/util Triples.java,1.1,NONE
rcsdiff: /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/gui/util/RCS/Triples.java,v: No such file or directory



From yanwong at pub.open-bio.org  Tue Feb  1 03:41:38 2005
From: yanwong at pub.open-bio.org (Yan Wong)
Date: Tue, 01 Feb 2005 08:41:38 -0000
Subject: [MOBY-guts] biomoby commit
Message-ID: <200502010852.j118qGxG012654@pub.open-bio.org>


yanwong
Tue Feb  1 03:52:15 EST 2005
Update of /home/repository/moby/moby-live/Python/bioMoby
In directory pub.open-bio.org:/tmp/cvs-serv12609

Modified Files:
	mobyClient.py mobyDataTypes.py mobyExceptions.py 
	mobyMarshal.py mobyRegister.py mobyService.py 
Log Message:


moby-live/Python/bioMoby mobyClient.py,1.2,1.3 mobyDataTypes.py,1.5,1.6 mobyExceptions.py,1.2,1.3 mobyMarshal.py,1.3,1.4 mobyRegister.py,1.2,1.3 mobyService.py,1.2,1.3
===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/mobyClient.py,v
retrieving revision 1.2
retrieving revision 1.3
diff -u -r1.2 -r1.3
--- /home/repository/moby/moby-live/Python/bioMoby/mobyClient.py	2005/01/18 13:46:22	1.2
+++ /home/repository/moby/moby-live/Python/bioMoby/mobyClient.py	2005/02/01 08:52:15	1.3
@@ -22,10 +22,10 @@
         
         from SOAPpy import SOAPProxy        
         self.server=SOAPProxy(self.url, namespace=self.ns)
-	
-	if debug:
-	    self.server.config.debug=1
-	    
+        
+        if debug:
+            self.server.config.debug=1
+            
         del SOAPProxy
 
 
@@ -68,28 +68,28 @@
     def retrieveObjectDefinition(self, objectName):
         """Retrieves a list of object's definitions
         """
-	dc={"urn:lsid:biomoby.org:objectrelation:isa":"ISA",
-	"urn:lsid:biomoby.org:objectrelation:hasa":"HASA",
-	"urn:lsid:biomoby.org:objectrelation:has":"HAS"
-	}
+        dc={"urn:lsid:biomoby.org:objectrelation:isa":"ISA",
+        "urn:lsid:biomoby.org:objectrelation:hasa":"HASA",
+        "urn:lsid:biomoby.org:objectrelation:has":"HAS"
+        }
 
-	definition={}
-	definition["Relationship"]={}
+        definition={}
+        definition["Relationship"]={}
 
         xmlinput="<retrieveObjectDefinition><objectType>"+objectName+"</objectType></retrieveObjectDefinition>"
         doc=parseString(self.call_method("retrieveObjectDefinition", xmlinput))
-	
-	for child in doc.firstChild.childNodes:
-	    if child.nodeType==child.ELEMENT_NODE and child.nodeName=="Relationship":
-		definition["Relationship"][dc[child.getAttribute("relationshipType")]]=[]
-		for elem in child.childNodes:
-	            if elem.nodeType==elem.ELEMENT_NODE and elem.nodeName=="objectType" and elem.firstChild:
-			definition["Relationship"][dc[child.getAttribute("relationshipType")]].append((elem.getAttribute("articleName"), elem.firstChild.nodeValue))
-
-	    elif child.nodeType==child.ELEMENT_NODE:
-		if child.firstChild:
-			definition[str(child.nodeName)]=child.firstChild.nodeValue
-	
+        
+        for child in doc.firstChild.childNodes:
+            if child.nodeType==child.ELEMENT_NODE and child.nodeName=="Relationship":
+                definition["Relationship"][dc[child.getAttribute("relationshipType")]]=[]
+                for elem in child.childNodes:
+                    if elem.nodeType==elem.ELEMENT_NODE and elem.nodeName=="objectType" and elem.firstChild:
+                        definition["Relationship"][dc[child.getAttribute("relationshipType")]].append((elem.getAttribute("articleName"), elem.firstChild.nodeValue))
+
+            elif child.nodeType==child.ELEMENT_NODE:
+                if child.firstChild:
+                        definition[str(child.nodeName)]=child.firstChild.nodeValue
+        
         return definition
 
     def retrieveObjectSchema(self, objectName):
@@ -260,6 +260,6 @@
             raise ETypeMismatch
             
     def __init__(self, url="http://mobycentral.cbr.nrc.ca/cgi-bin/MOBY05/mobycentral.pl", ns="http://mobycentral.cbr.nrc.ca/MOBY/Central"):
-	"""Constructor for class Client
-	"""
+        """Constructor for class Client
+        """
         Central.__init__(self, url, ns)

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/mobyDataTypes.py,v
retrieving revision 1.5
retrieving revision 1.6
diff -u -r1.5 -r1.6
--- /home/repository/moby/moby-live/Python/bioMoby/mobyDataTypes.py	2005/01/27 13:46:57	1.5
+++ /home/repository/moby/moby-live/Python/bioMoby/mobyDataTypes.py	2005/02/01 08:52:15	1.6
@@ -26,7 +26,7 @@
     def __init__(self, articleName="", value=""):
         self.articleName=articleName
         self.value=value
-	self.__isSecondary__=True
+        self.__isSecondary__=True
         
     def toMoby(self):
         """Returns the object as a XML
@@ -34,199 +34,199 @@
         return "<moby:Parameter moby:articleName='"+self.articleName+"'><moby:value>"+str(self.value)+"</moby:value></moby:Parameter>"
             
     def __str__(self):
-	"""Return the Parameter in its XML form
-	"""
+        """Return the Parameter in its XML form
+        """
         return self.toMoby()
 
     def __repr__(self):
-	"""Print the XML on the python command line.
-	"""
+        """Print the XML on the python command line.
+        """
         return self.toMoby()
             
     def fromMoby(self, xml):
         """Get the attributes from a XML string
         """
-	xmlelt=xml
-	
-	if isinstance(xml, str):
-	    xmlelt=parseString(xml).firstChild
-	    
+        xmlelt=xml
+        
+        if isinstance(xml, str):
+            xmlelt=parseString(xml).firstChild
+            
         self.articleName=xmlelt.getAttribute('moby:articleName')
-	l=xmlelt.getElementsByTagName("value")
-	if len(l)==0:
-	    l=xmlelt.getElementsByTagName("moby:value")
+        l=xmlelt.getElementsByTagName("value")
+        if len(l)==0:
+            l=xmlelt.getElementsByTagName("moby:value")
 
-       	self.value=l[0].firstChild.nodeValue
-	
+            self.value=l[0].firstChild.nodeValue
+        
 class MobyGeneric(object):
     """A Generic object (to use with the Marshaller)
     """
     def __init__(self, namespace="", id="", articleName="", *args, **kw):
-	"""Class constructor, basic attributes are namespace, 
-	   identifier and the article's name
-	"""
-	self.namespace=namespace
-	self.id=id
-	self.articleName=articleName
-	
-	for name, value in kw.items():
+        """Class constructor, basic attributes are namespace, 
+           identifier and the article's name
+        """
+        self.namespace=namespace
+        self.id=id
+        self.articleName=articleName
+        
+        for name, value in kw.items():
             setattr(self, name, value)
-	
+        
 class MobyObject(MobyGeneric):
     """Define a Moby XML Object
        It has methods toMoby and fromMoby 
     """
     def __init__(self, prefix="moby", tag="Object", content="", *args, **kw):
-	"""Class constructor for a bioMoby Object
-	"""
-	MobyGeneric.__init__(self, *args, **kw)
-	self.__prefix__=prefix
-	self.__tag__=tag
-	self.__cross__=[]
-	self.__PIB__=[]
-	
-	self.content=content
-	
-		
+        """Class constructor for a bioMoby Object
+        """
+        MobyGeneric.__init__(self, *args, **kw)
+        self.__prefix__=prefix
+        self.__tag__=tag
+        self.__cross__=[]
+        self.__PIB__=[]
+        
+        self.content=content
+        
+                
     def toMoby(self):
-	"""Deserializes the content in XML api
-	"""
-	
-	beginTag=["<%s:%s"%(self.__prefix__,self.__tag__)]
-	
-	#First see if the object has an  identifier, a namepsace and a name
-	for attribute in __ATTRIBUTES__:
-	    if hasattr(self, attribute) and getattr(self, attribute):
-		beginTag.append("%s:%s=\"%s\""%(self.__prefix__, attribute, getattr(self,attribute)))
-
-	#Retrieve only object's attributes that are public.
-	filterFunc=lambda x: x[0] != "_" and not callable(getattr(self, x)) and x !="content" and x not in __ATTRIBUTES__
-	
-	#Retrieve the associated objects
-	#In MobyObject, associated objects are object's attributes
-	mobyObjects=filter(filterFunc, dir(self))
-	
-	#If none, return the tag closed
-	if len(mobyObjects)==0 and (not hasattr(self, "__cross__") or len(self.__cross__)==0) and (not hasattr(self, "__PIB__") or len(self.__PIB__)==0) and (not hasattr(self, "content") or not self.content):
-	    beginTag.append("/>")
-	    return " ".join(beginTag)
+        """Deserializes the content in XML api
+        """
+        
+        beginTag=["<%s:%s"%(self.__prefix__,self.__tag__)]
+        
+        #First see if the object has an  identifier, a namepsace and a name
+        for attribute in __ATTRIBUTES__:
+            if hasattr(self, attribute) and getattr(self, attribute):
+                beginTag.append("%s:%s=\"%s\""%(self.__prefix__, attribute, getattr(self,attribute)))
 
-	#Else, end begin tag and serialize the associated objects
+        #Retrieve only object's attributes that are public.
+        filterFunc=lambda x: x[0] != "_" and not callable(getattr(self, x)) and x !="content" and x not in __ATTRIBUTES__
+        
+        #Retrieve the associated objects
+        #In MobyObject, associated objects are object's attributes
+        mobyObjects=filter(filterFunc, dir(self))
+        
+        #If none, return the tag closed
+        if len(mobyObjects)==0 and (not hasattr(self, "__cross__") or len(self.__cross__)==0) and (not hasattr(self, "__PIB__") or len(self.__PIB__)==0) and (not hasattr(self, "content") or not self.content):
+            beginTag.append("/>")
+            return " ".join(beginTag)
+
+        #Else, end begin tag and serialize the associated objects
         beginTag.append(">")
 
-	result=[" ".join(beginTag)]
-	
-	#Serialize Cross references
-	if hasattr(self, "__cross__") and self.__cross__:
-	    result.append("<CrossReference>")
-	    
-	    for aCross in self.__cross__:
-		result.append(aCross.toMoby())
-		
-	    result.append("</CrossReference>")
-	
+        result=[" ".join(beginTag)]
+        
+        #Serialize Cross references
+        if hasattr(self, "__cross__") and self.__cross__:
+            result.append("<CrossReference>")
+            
+            for aCross in self.__cross__:
+                result.append(aCross.toMoby())
+                
+            result.append("</CrossReference>")
+        
         #Serialize PIB
-	if hasattr(self, "__PIB__") and self.__PIB__:
-	    result.append("<ProvisionInformation>")
-	    
-	    for aPIB in self.__PIB__:
-		result.append(aPIB.toMoby())
-		
-	    result.append("</ProvisionInformation>")
-	
-	#Serialize the other attibutes
-	#If the attributes has a toMoby method, then use it
-	#Else, use a MobyMarshaller object to serialize
-	for mobyObject in mobyObjects:
-	    if hasattr(getattr(self,mobyObject), "toMoby"):
+        if hasattr(self, "__PIB__") and self.__PIB__:
+            result.append("<ProvisionInformation>")
+            
+            for aPIB in self.__PIB__:
+                result.append(aPIB.toMoby())
+                
+            result.append("</ProvisionInformation>")
+        
+        #Serialize the other attibutes
+        #If the attributes has a toMoby method, then use it
+        #Else, use a MobyMarshaller object to serialize
+        for mobyObject in mobyObjects:
+            if hasattr(getattr(self,mobyObject), "toMoby"):
                 getattr(self, mobyObject).__articleName__=mobyObject
                 result.append(getattr(self, mobyObject).toMoby())
-	    else:
-		from bioMoby import MobyMarshaller
-		m=MobyMarshaller()
-		result.append(m.dumps(getattr(self, mobyObject), articleName=mobyObject))
-	
-	#Put the raw content of the object
-	#If you want to put your special object, then then you should write 
-	#a __str__ method
-	if hasattr(self, "content") and self.content:
-	    result.append("%s"%(self.content))
-	
-	result.append("</%s:%s>"%(self.__prefix__, self.__tag__))
-	
-	return "".join(result)
-	
+            else:
+                from bioMoby import MobyMarshaller
+                m=MobyMarshaller()
+                result.append(m.dumps(getattr(self, mobyObject), articleName=mobyObject))
+        
+        #Put the raw content of the object
+        #If you want to put your special object, then then you should write 
+        #a __str__ method
+        if hasattr(self, "content") and self.content:
+            result.append("%s"%(self.content))
+        
+        result.append("</%s:%s>"%(self.__prefix__, self.__tag__))
+        
+        return "".join(result)
+        
     def fromMoby(self, xml):
-	"""Deserialization method
-	"""
-	elem=xml
-	
-	if isinstance(xml, str):
-	    doc=parseString(xmlstring)
-	
-	    elem=doc.firstChild
-	
-	self.__tag__=elem.localName
-	
-	self.__prefix__="moby"
-	
-	self.content=[]
-	
-	if elem.nodeName.split(":")>1:
-	    self.__prefix__=elem.nodeName.split(":")[0]
-	
-	#Set the object's attributes
-	for attribute in elem.attributes.values():
-	    setattr(self, attribute.localName, str(attribute.nodeValue))
-
-	for child in elem.childNodes:
-	    if child.nodeType==child.ELEMENT_NODE:
-		#deserializes the cross references
-		if child.localName=="CrossReference":
-		    for aCross in child.childNodes:
-			if aCross.localName=="Xref":
-			    aXref=MobyXref()
-			    aXref.fromMoby(aCross)
-			    self.__cross__.append(aXref)
-			if aCross.localName=="Object":
-			    anObj=MobyObject()
-			    anObj.fromMoby(aCross)
-			    self.__cross__.append(anObj)
-		else:
-		    #Do the same for the other objects
-		    associatedObjectName=child.getAttribute("moby:articleName")
-		
-		    if not associatedObjectName:
-		        associatedObjectName=child.getAttribute("articleName")
-		
-		    if not associatedObjectName:
-		        associatedObjectName="associated"
-		    
-		    #Create an object
-		    o=MobyObject()
-		    o.fromMoby(child)
-		    
-		    #if there is already an object, then store it inside a list and 
-		    #append the other objects in the list 
-		    if hasattr(self, associatedObjectName):
-		        if type(getattr(self, associatedObjectName)) is list:
-			    getattr(self, associatedObjectName).append(o)
-		        else:
-			    setattr(self, associatedObjectName, [o])
-		    else:
+        """Deserialization method
+        """
+        elem=xml
+        
+        if isinstance(xml, str):
+            doc=parseString(xmlstring)
+        
+            elem=doc.firstChild
+        
+        self.__tag__=elem.localName
+        
+        self.__prefix__="moby"
+        
+        self.content=[]
+        
+        if elem.nodeName.split(":")>1:
+            self.__prefix__=elem.nodeName.split(":")[0]
+        
+        #Set the object's attributes
+        for attribute in elem.attributes.values():
+            setattr(self, attribute.localName, str(attribute.nodeValue))
+
+        for child in elem.childNodes:
+            if child.nodeType==child.ELEMENT_NODE:
+                #deserializes the cross references
+                if child.localName=="CrossReference":
+                    for aCross in child.childNodes:
+                        if aCross.localName=="Xref":
+                            aXref=MobyXref()
+                            aXref.fromMoby(aCross)
+                            self.__cross__.append(aXref)
+                        if aCross.localName=="Object":
+                            anObj=MobyObject()
+                            anObj.fromMoby(aCross)
+                            self.__cross__.append(anObj)
+                else:
+                    #Do the same for the other objects
+                    associatedObjectName=child.getAttribute("moby:articleName")
+                
+                    if not associatedObjectName:
+                        associatedObjectName=child.getAttribute("articleName")
+                
+                    if not associatedObjectName:
+                        associatedObjectName="associated"
+                    
+                    #Create an object
+                    o=MobyObject()
+                    o.fromMoby(child)
+                    
+                    #if there is already an object, then store it inside a list and 
+                    #append the other objects in the list 
+                    if hasattr(self, associatedObjectName):
+                        if type(getattr(self, associatedObjectName)) is list:
+                            getattr(self, associatedObjectName).append(o)
+                        else:
+                            setattr(self, associatedObjectName, [o])
+                    else:
                         setattr(self, associatedObjectName, o)
             else:
-		self.content.append(child.nodeValue)
-		
-	self.content="".join(self.content)
-	
+                self.content.append(child.nodeValue)
+                
+        self.content="".join(self.content)
+        
 
     def __str__(self):
-	return self.toMoby()
-	
+        return self.toMoby()
+        
     def __repr__(self):
-	return self.toMoby()
-	
+        return self.toMoby()
+        
 
 class MobyXref(MobyObject):
     """Describes an Xref
@@ -246,48 +246,48 @@
     def fromMoby(self, xml):
         """Deserialize the Xref Object
         """
-	if isinstance(xml, str):
-	    doc=parseString(xml).firstChild
-	
-	doc=xml
-	
+        if isinstance(xml, str):
+            doc=parseString(xml).firstChild
+        
+        doc=xml
+        
         uri=doc.namespaceURI
     
-	MobyObject.fromMoby(self, doc)
+        MobyObject.fromMoby(self, doc)
         
         self.authURI=doc.getAttributeNS(uri, "authURI")
         self.serviceName=doc.getAttributeNS(uri, "serviceName")
         self.evidenceCode=doc.getAttributeNS(uri, "evidenceCode")
         self.xrefType=doc.getAttributeNS(uri, "xrefType")
 
-	
+        
 class MobyInteger(MobyObject):
     """Use this object to serialize/deserialize integers
     """
     def __init__(self, value=0, *args, **kw):
-	MobyObject.__init__(self, content=value, tag="Integer", *args, **kw)
+        MobyObject.__init__(self, content=value, tag="Integer", *args, **kw)
 
     def fromMoby(self, xml):
-	MobyObject.fromMoby(self, xml)
-	self.content = int(self.content)
-	
+        MobyObject.fromMoby(self, xml)
+        self.content = int(self.content)
+        
 class MobyFloat(MobyObject):
     """Serialize/deserialize floating point numbers
     """
     def __init__(self, value=0, *args, **kw):
-	MobyObject.__init__(self, content=value, tag="Float", *args, **kw)
-	
+        MobyObject.__init__(self, content=value, tag="Float", *args, **kw)
+        
     def fromMoby(self, xml):
-	MobyObject.fromMoby(self, xml)
-	self.content=float(self.content)
-	
+        MobyObject.fromMoby(self, xml)
+        self.content=float(self.content)
+        
 
 class MobyString(MobyObject):
     """String Moby object
     """
     def __init__(self, content="", *args, **kw):
-	MobyObject.__init__(self, content=content, *args, **kw)
-	self.__tag__="String"
+        MobyObject.__init__(self, content=content, *args, **kw)
+        self.__tag__="String"
 
 class MobyContent:
     """The class describes a Moby Content (for queries or answers)
@@ -302,10 +302,10 @@
         self.queryData=queryData
 
     def __str__(self):
-	"""return the XML form of the Moby Content object
-	"""
-	return self.toMoby()
-	
+        """return the XML form of the Moby Content object
+        """
+        return self.toMoby()
+        
     def toMoby(self):
         """The XML reprentation of the content
         """
@@ -325,8 +325,8 @@
         for queryKey in self.queryData:
             result.append("<moby:mobyData moby:queryID='"+queryKey+"'>")
 
-	    #For serialization, use the MobyMarshaller object
-	    
+            #For serialization, use the MobyMarshaller object
+            
             for queryObject in self.queryData[queryKey]:
                 #if the Collection ('CollectionName',[MobyObjects])
                 if queryObject.__class__ is tuple:
@@ -352,19 +352,19 @@
         return "".join(result)
 
     def fromMoby(self, xmlObject):
-	"""fill the properties from an XML
+        """fill the properties from an XML
         """
         from bioMoby import MobyUnmarshaller
-	
-	um=MobyUnmarshaller()
+        
+        um=MobyUnmarshaller()
 
         self.queryData={}
-	
-	doc=xmlObject
-	
-	if isinstance(xmlObject, str):
-	    doc=parseString(xmlObject)
-	
+        
+        doc=xmlObject
+        
+        if isinstance(xmlObject, str):
+            doc=parseString(xmlObject)
+        
         mdl=doc.getElementsByTagName('mobyData')
 
         if not mdl:
@@ -373,115 +373,115 @@
         #For each query            
         for elt in mdl:
             #Get the ID
-	    queryID=str(elt.getAttribute('queryID'))
+            queryID=str(elt.getAttribute('queryID'))
 
             if not queryID:
                 queryID=str(elt.getAttribute('moby:queryID'))
 
-	    #Collect the data
+            #Collect the data
             data=[]
 
-	    #for each datum translate it in MobyObject, and put it in the list
+            #for each datum translate it in MobyObject, and put it in the list
             for datum in elt.childNodes:
-		#If it is a collection
+                #If it is a collection
                 if datum.nodeType==datum.ELEMENT_NODE and datum.localName=="Collection":
-		    articleName=datum.getAttribute('moby:articleName')
+                    articleName=datum.getAttribute('moby:articleName')
         
                     articles=[]
         
                     for article in datum.childNodes:
                         if article.nodeType==article.ELEMENT_NODE and article.localName=="Simple":
-			    for child in article.childNodes:
-				if child.nodeType==child.ELEMENT_NODE:
+                            for child in article.childNodes:
+                                if child.nodeType==child.ELEMENT_NODE:
                                     articles.append(um.loadn(child))
 
                     data.append((articleName, articles))
-		#if it is a Simple object
+                #if it is a Simple object
                 elif datum.nodeType==datum.ELEMENT_NODE and datum.localName=="Simple":
-		    for elt in datum.childNodes:
+                    for elt in datum.childNodes:
                         if elt.nodeType==elt.ELEMENT_NODE:
-		            o=um.loadn(elt)
-		            data.append(o)
-	        elif datum.nodeType==datum.ELEMENT_NODE and datum.localName=="Parameter":
-		    #It is a Parameter
-		    p=Parameter()
-		    p.fromMoby(datum)
-		    data.append(p)
+                            o=um.loadn(elt)
+                            data.append(o)
+                elif datum.nodeType==datum.ELEMENT_NODE and datum.localName=="Parameter":
+                    #It is a Parameter
+                    p=Parameter()
+                    p.fromMoby(datum)
+                    data.append(p)
                     
             self.queryData[queryID]=data
-	    
+            
     def __getitem__(self, key):
-	"""Get a query from his name
+        """Get a query from his name
         """
         return self.queryData[key]
         
     def __setitem__(self, key, item):
-	"""Store a query in the dictionary
-	"""
+        """Store a query in the dictionary
+        """
         self.queryData[key]=item
 
     def __len__(self):
-	"""Return the number of elements inside the dictionary
-	"""
+        """Return the number of elements inside the dictionary
+        """
         return len(self.queryData)
         
     def keys(self):
-	"""Return all queries's name
-	"""
+        """Return all queries's name
+        """
         return self.queryData.keys()
-	
+        
     def collectionToQueries(self, aCollection):
-	"""Turn a collection of object into a set of queries
-	"""
-	queries={}
-	queryName=aCollection[0]
-	
-	queryID=1
-	
-	for aSimple in aCollection[1]:
-	    queries["%s-%s"%(queryName, queryID)]=aSimple
-	    
-	return queries
-		
-	
+        """Turn a collection of object into a set of queries
+        """
+        queries={}
+        queryName=aCollection[0]
+        
+        queryID=1
+        
+        for aSimple in aCollection[1]:
+            queries["%s-%s"%(queryName, queryID)]=aSimple
+            
+        return queries
+                
+        
     def getObject(self, queryName, objectName):
-	"""Get an object from a query with its name
-	"""
-	filterfunc=lambda obj: not hasattr(obj,'__isSecondary__') and hasattr(obj, "articleName") and obj.articleName==objectName
-	
-	for obj in filter(filterfunc, self.queryData[queryName]):
+        """Get an object from a query with its name
+        """
+        filterfunc=lambda obj: not hasattr(obj,'__isSecondary__') and hasattr(obj, "articleName") and obj.articleName==objectName
+        
+        for obj in filter(filterfunc, self.queryData[queryName]):
             return obj
 
-		
+                
     def getObjects(self, queryName):
-	"""Retrieve objects from a query
-	"""
-	filterfunc=lambda obj: not hasattr(obj, "__isSecondary__")
-	
-	return filter(filterfunc, self.queryData[queryName])
-	
+        """Retrieve objects from a query
+        """
+        filterfunc=lambda obj: not hasattr(obj, "__isSecondary__")
+        
+        return filter(filterfunc, self.queryData[queryName])
+        
     def getParameters(self, queryName):
-	"""Retrieve parameters from a query
-	"""
-	filterfunc=lambda param: hasattr(param, "__isSecondary__")
-	
-	result={}
-	for param in filter(filterfunc, self.queryData[queryName]):
-	    result[param.articleName]=param.value
-		
-	return result
+        """Retrieve parameters from a query
+        """
+        filterfunc=lambda param: hasattr(param, "__isSecondary__")
+        
+        result={}
+        for param in filter(filterfunc, self.queryData[queryName]):
+            result[param.articleName]=param.value
+                
+        return result
 
     def getParameter(self, queryName, parameterName):
-	"""Retrieve a parameter from a query and his name
-	"""
-	filterfunc=lambda param: hasattr(param, "__isSecondary__") and hasattr(param, "articleName") and param.articleName==parameterName
-	
-	l=filter(filterfunc, self.queryData[queryName])
-	
-	if l:
-	    return l[0]
-	
+        """Retrieve a parameter from a query and his name
+        """
+        filterfunc=lambda param: hasattr(param, "__isSecondary__") and hasattr(param, "articleName") and param.articleName==parameterName
+        
+        l=filter(filterfunc, self.queryData[queryName])
+        
+        if l:
+            return l[0]
+        
     def __repr__(self):
-	"""put the xml of the Content
-	"""
-	return self.__str__()
+        """put the xml of the Content
+        """
+        return self.__str__()

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/mobyExceptions.py,v
retrieving revision 1.2
retrieving revision 1.3
diff -u -r1.2 -r1.3
--- /home/repository/moby/moby-live/Python/bioMoby/mobyExceptions.py	2005/01/18 13:46:22	1.2
+++ /home/repository/moby/moby-live/Python/bioMoby/mobyExceptions.py	2005/02/01 08:52:15	1.3
@@ -41,4 +41,4 @@
     """A XML input is not a Moby XML Object.
     """
     def __str__(self):
-	return "The bioMoby XML object couldn't be parsed"
\ No newline at end of file
+        return "The bioMoby XML object couldn't be parsed"
\ No newline at end of file

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/mobyMarshal.py,v
retrieving revision 1.3
retrieving revision 1.4
diff -u -r1.3 -r1.4
--- /home/repository/moby/moby-live/Python/bioMoby/mobyMarshal.py	2005/01/27 08:44:05	1.3
+++ /home/repository/moby/moby-live/Python/bioMoby/mobyMarshal.py	2005/02/01 08:52:15	1.4
@@ -10,7 +10,7 @@
     
     01/17/2005: MobyMarshaller and MobyUnmarshaller can operate on all objects
                 serialisation and deserialisation are done only on public (no _ prefix) non callable attributes
-		The serialisation and deserialisation is recursive.
+                The serialisation and deserialisation is recursive.
 """
 
 from xml.dom.minidom import parseString
@@ -20,8 +20,8 @@
     """
     
     def _marshal(self, value, articleName=""):
-	"""this method do the serialization of the object
-	"""
+        """this method do the serialization of the object
+        """
         if type(value).__name__=='NoneType':
             return ""
 
@@ -29,9 +29,9 @@
 
         method="m_"+tvalue
 
-	if hasattr(value, "toMoby"):
-	    return value.toMoby()
-	
+        if hasattr(value, "toMoby"):
+            return value.toMoby()
+        
         if hasattr(self, method):
             return getattr(self,method)(value,articleName=articleName)
         
@@ -46,8 +46,8 @@
         return str(m)
         
     def m_unicode(self, value, articleName=""):
-	"""Turn a unicode string into a mobyString object
-	"""
+        """Turn a unicode string into a mobyString object
+        """
         return self.m_str(str(value), articleName)
 
     def m_string(self, value, articleName=""):
@@ -59,18 +59,18 @@
         """Turn an integer into a Moby XML object
         """
         from bioMoby.mobyDataTypes import MobyInteger
-	m=MobyInteger(value, namespace=namespace, id=id, articleName=articleName)
-	
-	return m.toMoby()
-	
+        m=MobyInteger(value, namespace=namespace, id=id, articleName=articleName)
+        
+        return m.toMoby()
+        
     def m_float(self, value, namespace="", id="", articleName=""):
         """Turn a float into a Moby XML object
         """
         from bioMoby.mobyDataTypes import MobyFloat
-	m=MobyFloat(value, namespace=namespace, id=id, articleName=articleName)
-	
-	return m.toMoby()
-	
+        m=MobyFloat(value, namespace=namespace, id=id, articleName=articleName)
+        
+        return m.toMoby()
+        
     def m_list(self, value, articleName=""):
         """Turn a list into a Moby XML object
         """
@@ -113,50 +113,50 @@
     def _compoundObject(self, value, articleName=""):
         """transforms an object and all properties into a XML
         """
-	
-	result=[]
-	
-	properties=[]
-	
-	filterfunc=lambda x: x[0] != "_" and not callable(getattr(value, x)) and x !="content" and x not in ["id", "namespace", "articleName", "content"]
-	attribfunc= lambda x: hasattr(value, x)
-	
-	tagName="moby:%s"%type(value).__name__
-	
-	if hasattr(value, "__tag__") and value.__tag__:
-	    tagName="moby:%s"%value.__tag__
-	
-	header=["<%s"%tagName]
-	
-	for attribute in filter(attribfunc, ["id", "namespace", "articleName"]):
-	    header.append("moby:%s=\"%s\""%(attribute,getattr(value,attribute)))
-	
-	for prop in filter(filterfunc, dir(value)):
-	    properties.append(self._marshal(getattr(value, prop), articleName=prop))
-	    
-	if not properties and not (hasattr(value, "content") and value.content):
-	    header.append("/>")
-	else:
-	    header.append(">")
-	    
-	result.append(" ".join(header))
-
-	if properties:
-	    result.append("".join(properties))	    
-	
-	if hasattr(value, "content") and value.content:
-	    result.append("<![CDATA[%s]]>"%value.content)
-	
-	if properties:
-	    result.append("</%s>"%tagName)
-
-
-	return r"".join(result)
-	
-	
+        
+        result=[]
+        
+        properties=[]
+        
+        filterfunc=lambda x: x[0] != "_" and not callable(getattr(value, x)) and x !="content" and x not in ["id", "namespace", "articleName", "content"]
+        attribfunc= lambda x: hasattr(value, x)
+        
+        tagName="moby:%s"%type(value).__name__
+        
+        if hasattr(value, "__tag__") and value.__tag__:
+            tagName="moby:%s"%value.__tag__
+        
+        header=["<%s"%tagName]
+        
+        for attribute in filter(attribfunc, ["id", "namespace", "articleName"]):
+            header.append("moby:%s=\"%s\""%(attribute,getattr(value,attribute)))
+        
+        for prop in filter(filterfunc, dir(value)):
+            properties.append(self._marshal(getattr(value, prop), articleName=prop))
+            
+        if not properties and not (hasattr(value, "content") and value.content):
+            header.append("/>")
+        else:
+            header.append(">")
+            
+        result.append(" ".join(header))
+
+        if properties:
+            result.append("".join(properties))            
+        
+        if hasattr(value, "content") and value.content:
+            result.append("<![CDATA[%s]]>"%value.content)
+        
+        if properties:
+            result.append("</%s>"%tagName)
+
+
+        return r"".join(result)
+        
+        
     def dumps(self, value, articleName=""):
-	"""Serialize the object into a Moby XML object
-	"""
+        """Serialize the object into a Moby XML object
+        """
         return self._marshal(value, articleName)
         
 
@@ -169,8 +169,8 @@
         """
         import re
 
-	aName=str(aName)
-	
+        aName=str(aName)
+        
         if aName=="":
             return ""
 
@@ -189,51 +189,51 @@
         return "".join(t)
 
     def loadn(self, xmlNode):
-	"""Deserializes an XML node and return a Python Object
-	"""
-	import bioMoby.mobyDataTypes
-	import bioMoby.ontology
-	
-	nn=xmlNode.localName
-	
+        """Deserializes an XML node and return a Python Object
+        """
+        import bioMoby.mobyDataTypes
+        import bioMoby.ontology
+        
+        nn=xmlNode.localName
+        
         #Try to see if this object got a deserializer
         object2build=self._cleanName(nn)
 
         objectName=str.upper(object2build[0])+object2build[1:]
-	
-	if hasattr(bioMoby.mobyDataTypes, "Moby%s"%objectName):
-	    o=getattr(bioMoby.mobyDataTypes, "Moby%s"%objectName)()
-	    if hasattr(o, "fromMoby"):
-		o.fromMoby(xmlNode)
-	    return o
-	elif hasattr(bioMoby.ontology, "Moby%s"%objectName):
-	    o=getattr(bioMoby.ontology, "Moby%s"%objectName)()
-	    if hasattr(o, "fromMoby"):
-		o.fromMoby(xmlNode)
-	    return o
-	    
+        
+        if hasattr(bioMoby.mobyDataTypes, "Moby%s"%objectName):
+            o=getattr(bioMoby.mobyDataTypes, "Moby%s"%objectName)()
+            if hasattr(o, "fromMoby"):
+                o.fromMoby(xmlNode)
+            return o
+        elif hasattr(bioMoby.ontology, "Moby%s"%objectName):
+            o=getattr(bioMoby.ontology, "Moby%s"%objectName)()
+            if hasattr(o, "fromMoby"):
+                o.fromMoby(xmlNode)
+            return o
+            
         methodName=str('m_'+nn)
-	    
-	if not hasattr(self, methodName):
+            
+        if not hasattr(self, methodName):
             methodName="m_Object"
-		
-#	try:
+                
+#        try:
         return getattr(self,methodName)(xmlNode)
 #        except:
-#	    #if not, Raise an invalid moby XML :-(
-#	    from bioMoby.mobyExceptions import EInvalidMobyXML    
-	    
+#            #if not, Raise an invalid moby XML :-(
+#            from bioMoby.mobyExceptions import EInvalidMobyXML    
+            
 #            raise EInvalidMobyXML
 
-	
+        
     def loads(self, xmlString):
-	""" Deserializes an xml string and return a bioMoby-Python object
-	"""
+        """ Deserializes an xml string and return a bioMoby-Python object
+        """
         if xmlString=="":
             return None    
 
-#	_typesmodule=["bioMoby.mobyDataTypes", "bioMoby.ontology"]
-	    
+#        _typesmodule=["bioMoby.mobyDataTypes", "bioMoby.ontology"]
+            
         doc=parseString(xmlString)
         
         mcl=doc.getElementsByTagNameNS('http://www.biomoby.org/moby','mobyContent')
@@ -243,109 +243,109 @@
             
         element=doc.firstChild
         
-	self.loadn(element)
+        self.loadn(element)
 
     def m_Integer(self, value):
-	"""Turn a Integer XML element into an integer
-	"""
-	value.normalize()
-	
-	if value.firstChild:
-	    return int(value.firstChild.nodeValue.replace("\n","").replace("\t","").replace(" ",""))
-	else:
-	    return 0
-	    
+        """Turn a Integer XML element into an integer
+        """
+        value.normalize()
+        
+        if value.firstChild:
+            return int(value.firstChild.nodeValue.replace("\n","").replace("\t","").replace(" ",""))
+        else:
+            return 0
+            
     def m_Float(self, value):
-	"""Turn a Float XML element into a float number
-	"""
-	value.normalize()
-	if value.firstChild:
-	    return float(value.firstChild.nodeValue.replace("\n","").replace("\t","").replace(" ",""))
+        """Turn a Float XML element into a float number
+        """
+        value.normalize()
+        if value.firstChild:
+            return float(value.firstChild.nodeValue.replace("\n","").replace("\t","").replace(" ",""))
         return 0.0
-	    
+            
     def m_String(self, value):
-	"""Turn a Moby XML String element into a String object
-	"""
-	
-	cnt=[]
-	value.normalize()
-	
-	for aChild in value.childNodes:
-	    if aChild.nodeType==aChild.TEXT_NODE or aChild.nodeType==aChild.CDATA_SECTION_NODE:
-		cnt.append(aChild.wholeText)
-		
-	return	r"".join(cnt)
-	
+        """Turn a Moby XML String element into a String object
+        """
+        
+        cnt=[]
+        value.normalize()
+        
+        for aChild in value.childNodes:
+            if aChild.nodeType==aChild.TEXT_NODE or aChild.nodeType==aChild.CDATA_SECTION_NODE:
+                cnt.append(aChild.wholeText)
+                
+        return        r"".join(cnt)
+        
 
     def m_Object(self, value):
-	"""Turn any XML into a generic object
-	"""
-	filterFunc= lambda x: x.nodeType==x.ELEMENT_NODE
-	
-	typeName="GMoby%s"%str(value.localName)
-
-	from bioMoby.mobyDataTypes import MobyGeneric
-	
-	NewType=type(typeName, (MobyGeneric,), {})
-	
-	anObject=NewType()
-	
-	anObject.__prefix__="moby"
-	anObject.__tag__=str(value.localName)
-	
-	for tupleAttribute in value.attributes.itemsNS():
-	    #First item, second field:
-	    setattr(anObject, str(tupleAttribute[0][1]), str(tupleAttribute[1]))
-
-	i=0    
-	for elem in filter(filterFunc, value.childNodes):
-	    methodName="m_%s"%str(elem.localName)
-
-	    articleName=elem.getAttribute("moby:articleName")
-	    
-	    if not articleName:
-		articleName=elem.getAttribute("articleName")
-		
-	    if not articleName:
-		articleName="attribute_%s"%i
-		
-	    if hasattr(self, methodName):
-		prop=getattr(self, methodName)(elem)
-	    else:
-	    	prop=self.m_Object(elem)
-		
-	    if hasattr(anObject, articleName):
-	        t=prop
-	        if not type(getattr(anObject, articleName)) is list:
-		    t=getattr(anObject, articleName)
-		    setattr(anObject, articleName, [])
-		getattr(anObject, articleName).append(t)
-	    else:
-	        setattr(anObject, articleName, prop)
-	    i+=1
-
-	content=[]
-
-	isContentNode= lambda x: x.nodeType==x.TEXT_NODE or x.nodeType==x.CDATA_SECTION_NODE
-	
-	for elem in filter(isContentNode, value.childNodes):
-	    content.append(str(elem.nodeValue))
-	    
-	if content:
-	    anObject.content(r"".join(content))
-	    
-	return anObject
+        """Turn any XML into a generic object
+        """
+        filterFunc= lambda x: x.nodeType==x.ELEMENT_NODE
+        
+        typeName="GMoby%s"%str(value.localName)
+
+        from bioMoby.mobyDataTypes import MobyGeneric
+        
+        NewType=type(typeName, (MobyGeneric,), {})
+        
+        anObject=NewType()
+        
+        anObject.__prefix__="moby"
+        anObject.__tag__=str(value.localName)
+        
+        for tupleAttribute in value.attributes.itemsNS():
+            #First item, second field:
+            setattr(anObject, str(tupleAttribute[0][1]), str(tupleAttribute[1]))
+
+        i=0    
+        for elem in filter(filterFunc, value.childNodes):
+            methodName="m_%s"%str(elem.localName)
+
+            articleName=elem.getAttribute("moby:articleName")
+            
+            if not articleName:
+                articleName=elem.getAttribute("articleName")
+                
+            if not articleName:
+                articleName="attribute_%s"%i
+                
+            if hasattr(self, methodName):
+                prop=getattr(self, methodName)(elem)
+            else:
+                    prop=self.m_Object(elem)
+                
+            if hasattr(anObject, articleName):
+                t=prop
+                if not type(getattr(anObject, articleName)) is list:
+                    t=getattr(anObject, articleName)
+                    setattr(anObject, articleName, [])
+                getattr(anObject, articleName).append(t)
+            else:
+                setattr(anObject, articleName, prop)
+            i+=1
+
+        content=[]
+
+        isContentNode= lambda x: x.nodeType==x.TEXT_NODE or x.nodeType==x.CDATA_SECTION_NODE
+        
+        for elem in filter(isContentNode, value.childNodes):
+            content.append(str(elem.nodeValue))
+            
+        if content:
+            anObject.content(r"".join(content))
+            
+        return anObject
 
     def m_MobyContent(self, value):
-	"""Turn an MobyContentXML into a MobyContent object
-	"""
-	from bioMoby.mobyDataTypes import MobyContent
-	
-	mc=MobyContent({})
-	
-	mc.fromMoby(value)
-	
-	del MobyContent
-	
-	return mc
-	
+        """Turn an MobyContentXML into a MobyContent object
+        """
+        from bioMoby.mobyDataTypes import MobyContent
+        
+        mc=MobyContent({})
+        
+        mc.fromMoby(value)
+        
+        del MobyContent
+        
+        return mc
+        

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/mobyRegister.py,v
retrieving revision 1.2
retrieving revision 1.3
diff -u -r1.2 -r1.3
--- /home/repository/moby/moby-live/Python/bioMoby/mobyRegister.py	2005/01/18 13:46:22	1.2
+++ /home/repository/moby/moby-live/Python/bioMoby/mobyRegister.py	2005/02/01 08:52:15	1.3
@@ -19,9 +19,9 @@
         self.success=0
         self.id=""
         self.message=""
-	self.RDF=""
+        self.RDF=""
 
-	#Parse the document, retrieve the success, id, message and RDF fields
+        #Parse the document, retrieve the success, id, message and RDF fields
         doc=parseString(xmlInput)
 
         if len(doc.getElementsByTagName("success")[0].childNodes)>0:
@@ -32,9 +32,9 @@
             self.message=doc.getElementsByTagName("message")[0].childNodes[0].nodeValue
         try:
             if len(doc.getElementsByTagName("RDF"))>0:
-	        self.RDF=doc.getElementsByTagName("RDF")[0].firstChild.toprettyxml()
-	except:
-	    pass
+                self.RDF=doc.getElementsByTagName("RDF")[0].firstChild.toprettyxml()
+        except:
+            pass
 
     def __str__(self):
         """Return the moby xml of the instance
@@ -63,7 +63,7 @@
         self.authURI=authURI
         self.description=description
         #it uses a central object for registration
-    	from mobyClient import Central
+        from mobyClient import Central
         self.central=Central()
         del Central
 
@@ -78,8 +78,8 @@
         self.serviceType=serviceType
         GeneralInformations.__init__(self, contact=contactEmail, authURI=authURI, description=description)
         self.relationship=relationship
-	self.serviceType=serviceType
-	
+        self.serviceType=serviceType
+        
     def __str__(self):
         """Return the instance as a Moby XML
         """

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/mobyService.py,v
retrieving revision 1.2
retrieving revision 1.3
diff -u -r1.2 -r1.3
--- /home/repository/moby/moby-live/Python/bioMoby/mobyService.py	2005/01/18 13:46:22	1.2
+++ /home/repository/moby/moby-live/Python/bioMoby/mobyService.py	2005/02/01 08:52:15	1.3
@@ -6,7 +6,7 @@
     Author: Wong Yan
     
     01/17/2004: Service can be executed as a Thread, thus several queries can be made
-    		in the same time.
+                    in the same time.
 """
 
 from mobyRegister import GeneralInformations
@@ -244,7 +244,7 @@
         self.type=""
         self.category=""
         self.url=""
-	self.signatureURL=""
+        self.signatureURL=""
         self.authoritative=0
         self.inputObjects=[]
         self.outputObjects=[]
@@ -264,8 +264,8 @@
                     self.type=arg[key]
                 elif key=='url':
                     self.url=arg['url']
-		elif key=='signatureURL':
-		    self.signatureURL=arg['signatureURL']
+                elif key=='signatureURL':
+                    self.signatureURL=arg['signatureURL']
                 elif key=='authoritative':
                     self.authoritative=arg[key]
                 elif key=='contactEmail':
@@ -311,7 +311,7 @@
         
         from SOAPpy import SOAPProxy
 
-	webservice=SOAPProxy(self.url,namespace=self.namespace)
+        webservice=SOAPProxy(self.url,namespace=self.namespace)
         
         if method=="":
             if len(self.methods)==0:
@@ -325,9 +325,9 @@
 
         webservice.soapaction=self.namespace+"#"+method
 
-	if debug:
-	    webservice.config.debug=1
-	
+        if debug:
+            webservice.config.debug=1
+        
         toQuery=str(query)
 
         del  SOAPProxy
@@ -339,13 +339,13 @@
             
         #try to return a MobyContent Object instead
         from bioMoby.mobyDataTypes import MobyContent
-	mc=MobyContent()
-	mc.fromMoby(result)
+        mc=MobyContent()
+        mc.fromMoby(result)
         
         del MobyContent
 
         return mc
-    	
+            
     def __str__(self):
         """Returns The moby xml form of the web service
         """
@@ -354,7 +354,7 @@
         result.append("<serviceType>"+self.type+"</serviceType>")
         result.append("<authURI>"+self.authURI+"</authURI>")
         result.append("<URL>"+self.url+"</URL>")
-	result.append("<signatureURL>"+self.signatureURL+"</signatureURL>")
+        result.append("<signatureURL>"+self.signatureURL+"</signatureURL>")
         result.append("<contactEmail>"+self.contact+"</contactEmail>")
         result.append("<authoritativeService>"+`self.authoritative`+"</authoritativeService>")
         result.append("<Description><![CDATA["+self.description+"]]></Description>")
@@ -367,10 +367,10 @@
             elif inputObject.__class__ is dict:
                 result.append('<Collection articleName="'+inputObject.keys()[0]+'">')
 
-		for aSimple in inputObject[inputObject.keys()[0]]:
+                for aSimple in inputObject[inputObject.keys()[0]]:
                     result.append(str(aSimple))
 
-		result.append("</Collection>")
+                result.append("</Collection>")
             else:
                 from mobyExceptions import EInvalidArgument
                 raise EInvalidArgument, "Bad input object"
@@ -385,10 +385,10 @@
             elif output.__class__ is dict:
                 result.append('<Collection articleName="'+output.keys()[0]+'">')
 
-		for aSimple in output[output.keys()[0]]:
+                for aSimple in output[output.keys()[0]]:
                     result.append(str(aSimple))
-		    
-		result.append("</Collection>")
+                    
+                result.append("</Collection>")
             else:
                 from mobyExceptions import EInvalidArgument
                 raise EInvalidArgument, "Bad output object"
@@ -410,10 +410,10 @@
         """Register the service on the Moby server    
            has been added  here a code to verify that signatureURL is not empty :)
         """
-	if self.signatureURL=="":
-	    from mobyExceptions import EInvalidArgument
-	    raise EInvalidArgument, "field signatureURL cannot be empty"
-	
+        if self.signatureURL=="":
+            from mobyExceptions import EInvalidArgument
+            raise EInvalidArgument, "field signatureURL cannot be empty"
+        
         xmlinput="<registerService>"+str(self)+"</registerService>"
         
         from mobyRegister import RegistrationObject
@@ -431,32 +431,32 @@
         return result
 
     def _executeThread(self, mobyContent):
-	"""Execute the service, store the result in a field
-	"""
-	
-	self.results=self.execute(mobyContent, returnXml=(mobyContent.__class__ is str))
-		
-	
+        """Execute the service, store the result in a field
+        """
+        
+        self.results=self.execute(mobyContent, returnXml=(mobyContent.__class__ is str))
+                
+        
     def start(self, mobycontent, timeout=-1):
-	"""Start the service as it was a thread
-	"""
-	from threading import Thread
-	
-	
-	if timeout != -1:
-	    self._execThread=Thread(target=self._executeThread, args=(mobycontent,))
-	else:
-	    self._execThread=Thread(target=self._executeThread, args=(mobycontent,), timeout=timeout)
+        """Start the service as it was a thread
+        """
+        from threading import Thread
+        
+        
+        if timeout != -1:
+            self._execThread=Thread(target=self._executeThread, args=(mobycontent,))
+        else:
+            self._execThread=Thread(target=self._executeThread, args=(mobycontent,), timeout=timeout)
 
-	self._execThread.start()
-	
+        self._execThread.start()
+        
     def join(self):
-	"""Same as Thread.join
-	"""
-	self._execThread.join()
-	
-	
-	
+        """Same as Thread.join
+        """
+        self._execThread.join()
+        
+        
+        
 class ServiceList:
     """Class representing a service's list
     """
@@ -502,17 +502,17 @@
 
         for childNode in node.childNodes:
             if childNode.nodeName=="datatype":
-		if childNode.firstChild:
+                if childNode.firstChild:
                     secondary.type=childNode.firstChild.nodeValue
             elif childNode.nodeName=="default":
                 if childNode.firstChild:
-		    secondary.default=childNode.firstChild.nodeValue
+                    secondary.default=childNode.firstChild.nodeValue
             elif childNode.nodeName=="min":
                 if childNode.firstChild:
-		    secondary.min=childNode.firstChild.nodeValue
+                    secondary.min=childNode.firstChild.nodeValue
             elif childNode.nodeName=="max":
                 if childNode.firstChild:
-		    secondary.max=childNode.firstChild.nodeValue
+                    secondary.max=childNode.firstChild.nodeValue
             elif childNode.nodeName=="enum":
                 if childNode.firstChild:
                     secondary.enums.append(childNode.firstChild.nodeValue)
@@ -547,7 +547,7 @@
                     service.contact=child.firstChild.nodeValue
                 elif child.nodeName=="URL" and child.firstChild:
                     service.url=child.firstChild.nodeValue
-		elif child.nodeName=="signatureURL" and child.firstChild:
+                elif child.nodeName=="signatureURL" and child.firstChild:
                     service.signatureURL=child.firstChild.nodeValue
                 elif child.nodeName=="Input":
                     for article in child.childNodes:



From yanwong at pub.open-bio.org  Tue Feb  1 03:42:57 2005
From: yanwong at pub.open-bio.org (Yan Wong)
Date: Tue, 01 Feb 2005 08:42:57 -0000
Subject: [MOBY-guts] biomoby commit
Message-ID: <200502010852.j118qHRx013096@pub.open-bio.org>


yanwong
Tue Feb  1 03:52:16 EST 2005
Update of /home/repository/moby/moby-live/Python/bioMoby/ontology
In directory pub.open-bio.org:/tmp/cvs-serv12609/ontology

Modified Files:
	AlleleAssociation.py Allele_freq.py AminoAcidSequence.py 
	B64_Encoded_PNG.py B64_Encoded_Postscript.py 
	B64_encoded_PDB.py B64_encoded_gif.py B64_encoded_jpeg.py 
	BLASTText.py BasicGFFSequenceFeature.py 
	ClustalAlnFormattedText.py ClustalMsfFormattedText.py 
	CommentedAASequence.py CommentedDNASequence.py 
	CommentedRNASequence.py DNASequence.py 
	DNASequenceWithGFFFeatures.py DateTime.py Decypher_Text.py 
	Edge.py EmblFlatfile.py FASTA.py FASTA_AA.py FASTA_NA.py 
	FASTA_Text.py GFF.py GFF1.py GFF2.py GFF2_5.py GFF3.py 
	GO_Term.py GenbankFlatfile.py GenericSequence.py 
	GeneticElement.py Genotype.py Germplasm_Details.py 
	Germplasm_List.py Global_Keyword.py HBond_Pair.py 
	HFormatText.py Haplotyping_Study_obj.py ICIS_Query.py 
	ICIS_Query2.py ICIS_Query3.py IntAct_XML.py Interaction.py 
	InteractionMethod.py Interaction_partner.py Interactor.py 
	MEME_Text.py MGIS_ACCESSION.py MMP_Locus.py MO_Term_Test.py 
	MmCIFText.py Multi_key_value_pair.py 
	MyTestingDataType_11024145298313.py MyTree.py 
	NCBI_BLAST_Text.py NCBI_Blast_XML.py NCBI_Blast_XML_Gif.py 
	NCBI_Blast_XML_Gif_Map.py NCBI_MEME_Text.py 
	NucleotideSequence.py PDBFormattedText.py PDBText.py PDGJOB.py 
	PHDText.py PMUTText.py PSeaTextFormatted.py 
	PhenotypeDescription.py PubMedMEDLINE.py RNASequence.py 
	SINGER_ACCESSION.py Sample.py SchematikonMotifID.py 
	SchematikonMotifSupport.py SchematikonSegmentAttributes.py 
	SchematikonSegmentID.py SchematikonStructureAnnotation.py 
	SchematikonVorocodeName.py Scored_acronym_string.py 
	SimpleAnnotatedGIFImage.py SimpleAnnotatedJPEGImage.py 
	Simple_key_value_pair.py Snp_allele.py Snp_genotype.py 
	Study.py TEST.py TargetP_result.py Testout.py TextBase64.py 
	TextFormatted.py TextHtml.py TextPlain.py TextUuencoded.py 
	TextXml.py Text_plain.py Trait_Details.py Tree.py 
	TropGENE_ACCESSION.py TropGENE_Diversity_Matrix.py 
	TropGENE_LOCUS.py VirtualSequence.py WU_BLAST_Text.py 
	Wildcard_Query.py __init__.py 
Log Message:


moby-live/Python/bioMoby/ontology AlleleAssociation.py,1.3,1.4 Allele_freq.py,1.3,1.4 AminoAcidSequence.py,1.3,1.4 B64_Encoded_PNG.py,1.3,1.4 B64_Encoded_Postscript.py,1.3,1.4 B64_encoded_PDB.py,1.3,1.4 B64_encoded_gif.py,1.3,1.4 B64_encoded_jpeg.py,1.3,1.4 BLASTText.py,1.3,1.4 BasicGFFSequenceFeature.py,1.3,1.4 ClustalAlnFormattedText.py,1.3,1.4 ClustalMsfFormattedText.py,1.3,1.4 CommentedAASequence.py,1.3,1.4 CommentedDNASequence.py,1.3,1.4 CommentedRNASequence.py,1.3,1.4 DNASequence.py,1.3,1.4 DNASequenceWithGFFFeatures.py,1.3,1.4 DateTime.py,1.3,1.4 Decypher_Text.py,1.3,1.4 Edge.py,1.3,1.4 EmblFlatfile.py,1.3,1.4 FASTA.py,1.3,1.4 FASTA_AA.py,1.3,1.4 FASTA_NA.py,1.3,1.4 FASTA_Text.py,1.3,1.4 GFF.py,1.3,1.4 GFF1.py,1.3,1.4 GFF2.py,1.3,1.4 GFF2_5.py,1.3,1.4 GFF3.py,1.3,1.4 GO_Term.py,1.3,1.4 GenbankFlatfile.py,1.3,1.4 GenericSequence.py,1.3,1.4 GeneticElement.py,1.3,1.4 Genotype.py,1.3,1.4 Germplasm_Details.py,1.3,1.4 Germplasm_List.py,1.3,1.4 Global_Keyword.py,1.3,1.4 HBon!
d_Pair.py,1.3,1.4 HFormatText.py,1.3,1.4 Haplotyping_Study_obj.py,1.3,1.4 ICIS_Query.py,1.3,1.4 ICIS_Query2.py,1.3,1.4 ICIS_Query3.py,1.3,1.4 IntAct_XML.py,1.3,1.4 Interaction.py,1.3,1.4 InteractionMethod.py,1.3,1.4 Interaction_partner.py,1.3,1.4 Interactor.py,1.3,1.4 MEME_Text.py,1.3,1.4 MGIS_ACCESSION.py,1.3,1.4 MMP_Locus.py,1.3,1.4 MO_Term_Test.py,1.3,1.4 MmCIFText.py,1.3,1.4 Multi_key_value_pair.py,1.3,1.4 MyTestingDataType_11024145298313.py,1.3,1.4 MyTree.py,1.3,1.4 NCBI_BLAST_Text.py,1.3,1.4 NCBI_Blast_XML.py,1.3,1.4 NCBI_Blast_XML_Gif.py,1.3,1.4 NCBI_Blast_XML_Gif_Map.py,1.3,1.4 NCBI_MEME_Text.py,1.3,1.4 NucleotideSequence.py,1.3,1.4 PDBFormattedText.py,1.3,1.4 PDBText.py,1.3,1.4 PDGJOB.py,1.3,1.4 PHDText.py,1.3,1.4 PMUTText.py,1.3,1.4 PSeaTextFormatted.py,1.3,1.4 PhenotypeDescription.py,1.3,1.4 PubMedMEDLINE.py,1.3,1.4 RNASequence.py,1.3,1.4 SINGER_ACCESSION.py,1.3,1.4 Sample.py,1.3,1.4 SchematikonMotifID.py,1.3,1.4 SchematikonMotifSupport.py,1.3,1.4 SchematikonSegme!
ntAttributes.py,1.3,1.4 SchematikonSegmentID.py,1.3,1.4 Schem!
atikonStructureAnnotation.py,1.3,1.4 SchematikonVorocodeName.py,1.3,1.4 Scored_acronym_string.py,1.3,1.4 SimpleAnnotatedGIFImage.py,1.3,1.4 SimpleAnnotatedJPEGImage.py,1.3,1.4 Simple_key_value_pair.py,1.3,1.4 Snp_allele.py,1.3,1.4 Snp_genotype.py,1.3,1.4 Study.py,1.3,1.4 TEST.py,1.3,1.4 TargetP_result.py,1.3,1.4 Testout.py,1.3,1.4 TextBase64.py,1.3,1.4 TextFormatted.py,1.3,1.4 TextHtml.py,1.3,1.4 TextPlain.py,1.3,1.4 TextUuencoded.py,1.3,1.4 TextXml.py,1.3,1.4 Text_plain.py,1.3,1.4 Trait_Details.py,1.3,1.4 Tree.py,1.3,1.4 TropGENE_ACCESSION.py,1.3,1.4 TropGENE_Diversity_Matrix.py,1.3,1.4 TropGENE_LOCUS.py,1.3,1.4 VirtualSequence.py,1.3,1.4 WU_BLAST_Text.py,1.3,1.4 Wildcard_Query.py,1.3,1.4 __init__.py,1.2,1.3
===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/ontology/AlleleAssociation.py,v
retrieving revision 1.3
retrieving revision 1.4
diff -u -r1.3 -r1.4
--- /home/repository/moby/moby-live/Python/bioMoby/ontology/AlleleAssociation.py	2005/01/27 08:44:05	1.3
+++ /home/repository/moby/moby-live/Python/bioMoby/ontology/AlleleAssociation.py	2005/02/01 08:52:15	1.4
@@ -50,8 +50,7 @@
             if elt.nodeName=="CrossReference" or elt.nodeName=="moby:CrossReference":
                 self.__cross__=[]
                 for ref in elt.childNodes:
-                    if ref.nodeType==ref.ELEMENT_NODE:
-                        self.__cross__.append(um.loads(ref.toxml()))
+                    self.__cross__.append(ref.toxml())
             if elt.nodeType==elt.ELEMENT_NODE and (elt.nodeName=="String" or elt.nodeName=="moby:String") and (elt.getAttribute("articleName")=="snp" or elt.getAttribute("moby:articleName")=="snp"):
                 t=MobyString()
                 t.fromMoby(elt.toxml())

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/ontology/Allele_freq.py,v
retrieving revision 1.3
retrieving revision 1.4
diff -u -r1.3 -r1.4
--- /home/repository/moby/moby-live/Python/bioMoby/ontology/Allele_freq.py	2005/01/27 08:44:05	1.3
+++ /home/repository/moby/moby-live/Python/bioMoby/ontology/Allele_freq.py	2005/02/01 08:52:15	1.4
@@ -44,8 +44,7 @@
             if elt.nodeName=="CrossReference" or elt.nodeName=="moby:CrossReference":
                 self.__cross__=[]
                 for ref in elt.childNodes:
-                    if ref.nodeType==ref.ELEMENT_NODE:
-                        self.__cross__.append(um.loads(ref.toxml()))
+                    self.__cross__.append(ref.toxml())
             if elt.nodeType==elt.ELEMENT_NODE and (elt.nodeName=="Object" or elt.nodeName=="moby:Object") and (elt.getAttribute("articleName")=="panel_lsid" or elt.getAttribute("moby:articleName")=="panel_lsid"):
                 self.Panel_lsid=MobyObject()
                 self.Panel_lsid.fromMoby(elt.toxml())

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/ontology/AminoAcidSequence.py,v
retrieving revision 1.3
retrieving revision 1.4
diff -u -r1.3 -r1.4
--- /home/repository/moby/moby-live/Python/bioMoby/ontology/AminoAcidSequence.py	2005/01/27 08:44:05	1.3
+++ /home/repository/moby/moby-live/Python/bioMoby/ontology/AminoAcidSequence.py	2005/02/01 08:52:15	1.4
@@ -49,8 +49,7 @@
             if elt.nodeName=="CrossReference" or elt.nodeName=="moby:CrossReference":
                 self.__cross__=[]
                 for ref in elt.childNodes:
-                    if ref.nodeType==ref.ELEMENT_NODE:
-                        self.__cross__.append(um.loads(ref.toxml()))
+                    self.__cross__.append(ref.toxml())
             if elt.nodeType==elt.ELEMENT_NODE and (elt.nodeName=="Integer" or elt.nodeName=="moby:Integer") and (elt.getAttribute("articleName")=="Length" or elt.getAttribute("moby:articleName")=="Length"):
                 t=MobyInteger()
                 t.fromMoby(elt.toxml())

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/ontology/B64_Encoded_PNG.py,v
retrieving revision 1.3
retrieving revision 1.4
diff -u -r1.3 -r1.4
--- /home/repository/moby/moby-live/Python/bioMoby/ontology/B64_Encoded_PNG.py	2005/01/27 08:44:05	1.3
+++ /home/repository/moby/moby-live/Python/bioMoby/ontology/B64_Encoded_PNG.py	2005/02/01 08:52:15	1.4
@@ -46,5 +46,4 @@
             if elt.nodeName=="CrossReference" or elt.nodeName=="moby:CrossReference":
                 self.__cross__=[]
                 for ref in elt.childNodes:
-                    if ref.nodeType==ref.ELEMENT_NODE:
-                        self.__cross__.append(um.loads(ref.toxml()))
\ No newline at end of file
+                    self.__cross__.append(ref.toxml())
\ No newline at end of file

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/ontology/B64_Encoded_Postscript.py,v
retrieving revision 1.3
retrieving revision 1.4
diff -u -r1.3 -r1.4
--- /home/repository/moby/moby-live/Python/bioMoby/ontology/B64_Encoded_Postscript.py	2005/01/27 08:44:05	1.3
+++ /home/repository/moby/moby-live/Python/bioMoby/ontology/B64_Encoded_Postscript.py	2005/02/01 08:52:15	1.4
@@ -46,5 +46,4 @@
             if elt.nodeName=="CrossReference" or elt.nodeName=="moby:CrossReference":
                 self.__cross__=[]
                 for ref in elt.childNodes:
-                    if ref.nodeType==ref.ELEMENT_NODE:
-                        self.__cross__.append(um.loads(ref.toxml()))
\ No newline at end of file
+                    self.__cross__.append(ref.toxml())
\ No newline at end of file

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/ontology/B64_encoded_PDB.py,v
retrieving revision 1.3
retrieving revision 1.4
diff -u -r1.3 -r1.4
--- /home/repository/moby/moby-live/Python/bioMoby/ontology/B64_encoded_PDB.py	2005/01/27 08:44:05	1.3
+++ /home/repository/moby/moby-live/Python/bioMoby/ontology/B64_encoded_PDB.py	2005/02/01 08:52:15	1.4
@@ -46,5 +46,4 @@
             if elt.nodeName=="CrossReference" or elt.nodeName=="moby:CrossReference":
                 self.__cross__=[]
                 for ref in elt.childNodes:
-                    if ref.nodeType==ref.ELEMENT_NODE:
-                        self.__cross__.append(um.loads(ref.toxml()))
\ No newline at end of file
+                    self.__cross__.append(ref.toxml())
\ No newline at end of file

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/ontology/B64_encoded_gif.py,v
retrieving revision 1.3
retrieving revision 1.4
diff -u -r1.3 -r1.4
--- /home/repository/moby/moby-live/Python/bioMoby/ontology/B64_encoded_gif.py	2005/01/27 08:44:05	1.3
+++ /home/repository/moby/moby-live/Python/bioMoby/ontology/B64_encoded_gif.py	2005/02/01 08:52:15	1.4
@@ -46,5 +46,4 @@
             if elt.nodeName=="CrossReference" or elt.nodeName=="moby:CrossReference":
                 self.__cross__=[]
                 for ref in elt.childNodes:
-                    if ref.nodeType==ref.ELEMENT_NODE:
-                        self.__cross__.append(um.loads(ref.toxml()))
\ No newline at end of file
+                    self.__cross__.append(ref.toxml())
\ No newline at end of file

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/ontology/B64_encoded_jpeg.py,v
retrieving revision 1.3
retrieving revision 1.4
diff -u -r1.3 -r1.4
--- /home/repository/moby/moby-live/Python/bioMoby/ontology/B64_encoded_jpeg.py	2005/01/27 08:44:05	1.3
+++ /home/repository/moby/moby-live/Python/bioMoby/ontology/B64_encoded_jpeg.py	2005/02/01 08:52:15	1.4
@@ -46,5 +46,4 @@
             if elt.nodeName=="CrossReference" or elt.nodeName=="moby:CrossReference":
                 self.__cross__=[]
                 for ref in elt.childNodes:
-                    if ref.nodeType==ref.ELEMENT_NODE:
-                        self.__cross__.append(um.loads(ref.toxml()))
\ No newline at end of file
+                    self.__cross__.append(ref.toxml())
\ No newline at end of file

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/ontology/BLASTText.py,v
retrieving revision 1.3
retrieving revision 1.4
diff -u -r1.3 -r1.4
--- /home/repository/moby/moby-live/Python/bioMoby/ontology/BLASTText.py	2005/01/27 08:44:05	1.3
+++ /home/repository/moby/moby-live/Python/bioMoby/ontology/BLASTText.py	2005/02/01 08:52:15	1.4
@@ -46,5 +46,4 @@
             if elt.nodeName=="CrossReference" or elt.nodeName=="moby:CrossReference":
                 self.__cross__=[]
                 for ref in elt.childNodes:
-                    if ref.nodeType==ref.ELEMENT_NODE:
-                        self.__cross__.append(um.loads(ref.toxml()))
\ No newline at end of file
+                    self.__cross__.append(ref.toxml())
\ No newline at end of file

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/ontology/BasicGFFSequenceFeature.py,v
retrieving revision 1.3
retrieving revision 1.4
diff -u -r1.3 -r1.4
--- /home/repository/moby/moby-live/Python/bioMoby/ontology/BasicGFFSequenceFeature.py	2005/01/27 08:44:05	1.3
+++ /home/repository/moby/moby-live/Python/bioMoby/ontology/BasicGFFSequenceFeature.py	2005/02/01 08:52:15	1.4
@@ -60,8 +60,7 @@
             if elt.nodeName=="CrossReference" or elt.nodeName=="moby:CrossReference":
                 self.__cross__=[]
                 for ref in elt.childNodes:
-                    if ref.nodeType==ref.ELEMENT_NODE:
-                        self.__cross__.append(um.loads(ref.toxml()))
+                    self.__cross__.append(ref.toxml())
             if elt.nodeType==elt.ELEMENT_NODE and (elt.nodeName=="String" or elt.nodeName=="moby:String") and (elt.getAttribute("articleName")=="reference" or elt.getAttribute("moby:articleName")=="reference"):
                 t=MobyString()
                 t.fromMoby(elt.toxml())

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/ontology/ClustalAlnFormattedText.py,v
retrieving revision 1.3
retrieving revision 1.4
diff -u -r1.3 -r1.4
--- /home/repository/moby/moby-live/Python/bioMoby/ontology/ClustalAlnFormattedText.py	2005/01/27 08:44:05	1.3
+++ /home/repository/moby/moby-live/Python/bioMoby/ontology/ClustalAlnFormattedText.py	2005/02/01 08:52:15	1.4
@@ -46,5 +46,4 @@
             if elt.nodeName=="CrossReference" or elt.nodeName=="moby:CrossReference":
                 self.__cross__=[]
                 for ref in elt.childNodes:
-                    if ref.nodeType==ref.ELEMENT_NODE:
-                        self.__cross__.append(um.loads(ref.toxml()))
\ No newline at end of file
+                    self.__cross__.append(ref.toxml())
\ No newline at end of file

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/ontology/ClustalMsfFormattedText.py,v
retrieving revision 1.3
retrieving revision 1.4
diff -u -r1.3 -r1.4
--- /home/repository/moby/moby-live/Python/bioMoby/ontology/ClustalMsfFormattedText.py	2005/01/27 08:44:05	1.3
+++ /home/repository/moby/moby-live/Python/bioMoby/ontology/ClustalMsfFormattedText.py	2005/02/01 08:52:15	1.4
@@ -46,5 +46,4 @@
             if elt.nodeName=="CrossReference" or elt.nodeName=="moby:CrossReference":
                 self.__cross__=[]
                 for ref in elt.childNodes:
-                    if ref.nodeType==ref.ELEMENT_NODE:
-                        self.__cross__.append(um.loads(ref.toxml()))
\ No newline at end of file
+                    self.__cross__.append(ref.toxml())
\ No newline at end of file

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/ontology/CommentedAASequence.py,v
retrieving revision 1.3
retrieving revision 1.4
diff -u -r1.3 -r1.4
--- /home/repository/moby/moby-live/Python/bioMoby/ontology/CommentedAASequence.py	2005/01/27 08:44:05	1.3
+++ /home/repository/moby/moby-live/Python/bioMoby/ontology/CommentedAASequence.py	2005/02/01 08:52:15	1.4
@@ -50,8 +50,7 @@
             if elt.nodeName=="CrossReference" or elt.nodeName=="moby:CrossReference":
                 self.__cross__=[]
                 for ref in elt.childNodes:
-                    if ref.nodeType==ref.ELEMENT_NODE:
-                        self.__cross__.append(um.loads(ref.toxml()))
+                    self.__cross__.append(ref.toxml())
             if elt.nodeType==elt.ELEMENT_NODE and (elt.nodeName=="Integer" or elt.nodeName=="moby:Integer") and (elt.getAttribute("articleName")=="Length" or elt.getAttribute("moby:articleName")=="Length"):
                 t=MobyInteger()
                 t.fromMoby(elt.toxml())

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/ontology/CommentedDNASequence.py,v
retrieving revision 1.3
retrieving revision 1.4
diff -u -r1.3 -r1.4
--- /home/repository/moby/moby-live/Python/bioMoby/ontology/CommentedDNASequence.py	2005/01/27 08:44:05	1.3
+++ /home/repository/moby/moby-live/Python/bioMoby/ontology/CommentedDNASequence.py	2005/02/01 08:52:15	1.4
@@ -50,8 +50,7 @@
             if elt.nodeName=="CrossReference" or elt.nodeName=="moby:CrossReference":
                 self.__cross__=[]
                 for ref in elt.childNodes:
-                    if ref.nodeType==ref.ELEMENT_NODE:
-                        self.__cross__.append(um.loads(ref.toxml()))
+                    self.__cross__.append(ref.toxml())
             if elt.nodeType==elt.ELEMENT_NODE and (elt.nodeName=="Integer" or elt.nodeName=="moby:Integer") and (elt.getAttribute("articleName")=="Length" or elt.getAttribute("moby:articleName")=="Length"):
                 t=MobyInteger()
                 t.fromMoby(elt.toxml())

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/ontology/CommentedRNASequence.py,v
retrieving revision 1.3
retrieving revision 1.4
diff -u -r1.3 -r1.4
--- /home/repository/moby/moby-live/Python/bioMoby/ontology/CommentedRNASequence.py	2005/01/27 08:44:05	1.3
+++ /home/repository/moby/moby-live/Python/bioMoby/ontology/CommentedRNASequence.py	2005/02/01 08:52:15	1.4
@@ -50,8 +50,7 @@
             if elt.nodeName=="CrossReference" or elt.nodeName=="moby:CrossReference":
                 self.__cross__=[]
                 for ref in elt.childNodes:
-                    if ref.nodeType==ref.ELEMENT_NODE:
-                        self.__cross__.append(um.loads(ref.toxml()))
+                    self.__cross__.append(ref.toxml())
             if elt.nodeType==elt.ELEMENT_NODE and (elt.nodeName=="Integer" or elt.nodeName=="moby:Integer") and (elt.getAttribute("articleName")=="Length" or elt.getAttribute("moby:articleName")=="Length"):
                 t=MobyInteger()
                 t.fromMoby(elt.toxml())

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/ontology/DNASequence.py,v
retrieving revision 1.3
retrieving revision 1.4
diff -u -r1.3 -r1.4
--- /home/repository/moby/moby-live/Python/bioMoby/ontology/DNASequence.py	2005/01/27 08:44:05	1.3
+++ /home/repository/moby/moby-live/Python/bioMoby/ontology/DNASequence.py	2005/02/01 08:52:15	1.4
@@ -49,8 +49,7 @@
             if elt.nodeName=="CrossReference" or elt.nodeName=="moby:CrossReference":
                 self.__cross__=[]
                 for ref in elt.childNodes:
-                    if ref.nodeType==ref.ELEMENT_NODE:
-                        self.__cross__.append(um.loads(ref.toxml()))
+                    self.__cross__.append(ref.toxml())
             if elt.nodeType==elt.ELEMENT_NODE and (elt.nodeName=="Integer" or elt.nodeName=="moby:Integer") and (elt.getAttribute("articleName")=="Length" or elt.getAttribute("moby:articleName")=="Length"):
                 t=MobyInteger()
                 t.fromMoby(elt.toxml())

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/ontology/DNASequenceWithGFFFeatures.py,v
retrieving revision 1.3
retrieving revision 1.4
diff -u -r1.3 -r1.4
--- /home/repository/moby/moby-live/Python/bioMoby/ontology/DNASequenceWithGFFFeatures.py	2005/01/27 08:44:05	1.3
+++ /home/repository/moby/moby-live/Python/bioMoby/ontology/DNASequenceWithGFFFeatures.py	2005/02/01 08:52:15	1.4
@@ -52,8 +52,7 @@
             if elt.nodeName=="CrossReference" or elt.nodeName=="moby:CrossReference":
                 self.__cross__=[]
                 for ref in elt.childNodes:
-                    if ref.nodeType==ref.ELEMENT_NODE:
-                        self.__cross__.append(um.loads(ref.toxml()))
+                    self.__cross__.append(ref.toxml())
             if elt.nodeType==elt.ELEMENT_NODE and (elt.nodeName=="Integer" or elt.nodeName=="moby:Integer") and (elt.getAttribute("articleName")=="Length" or elt.getAttribute("moby:articleName")=="Length"):
                 t=MobyInteger()
                 t.fromMoby(elt.toxml())

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/ontology/DateTime.py,v
retrieving revision 1.3
retrieving revision 1.4
diff -u -r1.3 -r1.4
--- /home/repository/moby/moby-live/Python/bioMoby/ontology/DateTime.py	2005/01/27 08:44:05	1.3
+++ /home/repository/moby/moby-live/Python/bioMoby/ontology/DateTime.py	2005/02/01 08:52:15	1.4
@@ -46,5 +46,4 @@
             if elt.nodeName=="CrossReference" or elt.nodeName=="moby:CrossReference":
                 self.__cross__=[]
                 for ref in elt.childNodes:
-                    if ref.nodeType==ref.ELEMENT_NODE:
-                        self.__cross__.append(um.loads(ref.toxml()))
\ No newline at end of file
+                    self.__cross__.append(ref.toxml())
\ No newline at end of file

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/ontology/Decypher_Text.py,v
retrieving revision 1.3
retrieving revision 1.4
diff -u -r1.3 -r1.4
--- /home/repository/moby/moby-live/Python/bioMoby/ontology/Decypher_Text.py	2005/01/27 08:44:05	1.3
+++ /home/repository/moby/moby-live/Python/bioMoby/ontology/Decypher_Text.py	2005/02/01 08:52:15	1.4
@@ -46,5 +46,4 @@
             if elt.nodeName=="CrossReference" or elt.nodeName=="moby:CrossReference":
                 self.__cross__=[]
                 for ref in elt.childNodes:
-                    if ref.nodeType==ref.ELEMENT_NODE:
-                        self.__cross__.append(um.loads(ref.toxml()))
\ No newline at end of file
+                    self.__cross__.append(ref.toxml())
\ No newline at end of file

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/ontology/Edge.py,v
retrieving revision 1.3
retrieving revision 1.4
diff -u -r1.3 -r1.4
--- /home/repository/moby/moby-live/Python/bioMoby/ontology/Edge.py	2005/01/27 08:44:05	1.3
+++ /home/repository/moby/moby-live/Python/bioMoby/ontology/Edge.py	2005/02/01 08:52:15	1.4
@@ -49,8 +49,7 @@
             if elt.nodeName=="CrossReference" or elt.nodeName=="moby:CrossReference":
                 self.__cross__=[]
                 for ref in elt.childNodes:
-                    if ref.nodeType==ref.ELEMENT_NODE:
-                        self.__cross__.append(um.loads(ref.toxml()))
+                    self.__cross__.append(ref.toxml())
             if elt.nodeType==elt.ELEMENT_NODE and (elt.nodeName=="String" or elt.nodeName=="moby:String") and (elt.getAttribute("articleName")=="partner" or elt.getAttribute("moby:articleName")=="partner"):
                 t=MobyString()
                 t.fromMoby(elt.toxml())

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/ontology/EmblFlatfile.py,v
retrieving revision 1.3
retrieving revision 1.4
diff -u -r1.3 -r1.4
--- /home/repository/moby/moby-live/Python/bioMoby/ontology/EmblFlatfile.py	2005/01/27 08:44:05	1.3
+++ /home/repository/moby/moby-live/Python/bioMoby/ontology/EmblFlatfile.py	2005/02/01 08:52:15	1.4
@@ -46,5 +46,4 @@
             if elt.nodeName=="CrossReference" or elt.nodeName=="moby:CrossReference":
                 self.__cross__=[]
                 for ref in elt.childNodes:
-                    if ref.nodeType==ref.ELEMENT_NODE:
-                        self.__cross__.append(um.loads(ref.toxml()))
\ No newline at end of file
+                    self.__cross__.append(ref.toxml())
\ No newline at end of file

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/ontology/FASTA.py,v
retrieving revision 1.3
retrieving revision 1.4
diff -u -r1.3 -r1.4
--- /home/repository/moby/moby-live/Python/bioMoby/ontology/FASTA.py	2005/01/27 08:44:05	1.3
+++ /home/repository/moby/moby-live/Python/bioMoby/ontology/FASTA.py	2005/02/01 08:52:15	1.4
@@ -46,5 +46,4 @@
             if elt.nodeName=="CrossReference" or elt.nodeName=="moby:CrossReference":
                 self.__cross__=[]
                 for ref in elt.childNodes:
-                    if ref.nodeType==ref.ELEMENT_NODE:
-                        self.__cross__.append(um.loads(ref.toxml()))
\ No newline at end of file
+                    self.__cross__.append(ref.toxml())
\ No newline at end of file

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/ontology/FASTA_AA.py,v
retrieving revision 1.3
retrieving revision 1.4
diff -u -r1.3 -r1.4
--- /home/repository/moby/moby-live/Python/bioMoby/ontology/FASTA_AA.py	2005/01/27 08:44:05	1.3
+++ /home/repository/moby/moby-live/Python/bioMoby/ontology/FASTA_AA.py	2005/02/01 08:52:15	1.4
@@ -46,5 +46,4 @@
             if elt.nodeName=="CrossReference" or elt.nodeName=="moby:CrossReference":
                 self.__cross__=[]
                 for ref in elt.childNodes:
-                    if ref.nodeType==ref.ELEMENT_NODE:
-                        self.__cross__.append(um.loads(ref.toxml()))
\ No newline at end of file
+                    self.__cross__.append(ref.toxml())
\ No newline at end of file

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/ontology/FASTA_NA.py,v
retrieving revision 1.3
retrieving revision 1.4
diff -u -r1.3 -r1.4
--- /home/repository/moby/moby-live/Python/bioMoby/ontology/FASTA_NA.py	2005/01/27 08:44:05	1.3
+++ /home/repository/moby/moby-live/Python/bioMoby/ontology/FASTA_NA.py	2005/02/01 08:52:15	1.4
@@ -46,5 +46,4 @@
             if elt.nodeName=="CrossReference" or elt.nodeName=="moby:CrossReference":
                 self.__cross__=[]
                 for ref in elt.childNodes:
-                    if ref.nodeType==ref.ELEMENT_NODE:
-                        self.__cross__.append(um.loads(ref.toxml()))
\ No newline at end of file
+                    self.__cross__.append(ref.toxml())
\ No newline at end of file

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/ontology/FASTA_Text.py,v
retrieving revision 1.3
retrieving revision 1.4
diff -u -r1.3 -r1.4
--- /home/repository/moby/moby-live/Python/bioMoby/ontology/FASTA_Text.py	2005/01/27 08:44:05	1.3
+++ /home/repository/moby/moby-live/Python/bioMoby/ontology/FASTA_Text.py	2005/02/01 08:52:15	1.4
@@ -46,5 +46,4 @@
             if elt.nodeName=="CrossReference" or elt.nodeName=="moby:CrossReference":
                 self.__cross__=[]
                 for ref in elt.childNodes:
-                    if ref.nodeType==ref.ELEMENT_NODE:
-                        self.__cross__.append(um.loads(ref.toxml()))
\ No newline at end of file
+                    self.__cross__.append(ref.toxml())
\ No newline at end of file

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/ontology/GFF.py,v
retrieving revision 1.3
retrieving revision 1.4
diff -u -r1.3 -r1.4
--- /home/repository/moby/moby-live/Python/bioMoby/ontology/GFF.py	2005/01/27 08:44:05	1.3
+++ /home/repository/moby/moby-live/Python/bioMoby/ontology/GFF.py	2005/02/01 08:52:15	1.4
@@ -46,5 +46,4 @@
             if elt.nodeName=="CrossReference" or elt.nodeName=="moby:CrossReference":
                 self.__cross__=[]
                 for ref in elt.childNodes:
-                    if ref.nodeType==ref.ELEMENT_NODE:
-                        self.__cross__.append(um.loads(ref.toxml()))
\ No newline at end of file
+                    self.__cross__.append(ref.toxml())
\ No newline at end of file

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/ontology/GFF1.py,v
retrieving revision 1.3
retrieving revision 1.4
diff -u -r1.3 -r1.4
--- /home/repository/moby/moby-live/Python/bioMoby/ontology/GFF1.py	2005/01/27 08:44:05	1.3
+++ /home/repository/moby/moby-live/Python/bioMoby/ontology/GFF1.py	2005/02/01 08:52:15	1.4
@@ -46,5 +46,4 @@
             if elt.nodeName=="CrossReference" or elt.nodeName=="moby:CrossReference":
                 self.__cross__=[]
                 for ref in elt.childNodes:
-                    if ref.nodeType==ref.ELEMENT_NODE:
-                        self.__cross__.append(um.loads(ref.toxml()))
\ No newline at end of file
+                    self.__cross__.append(ref.toxml())
\ No newline at end of file

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/ontology/GFF2.py,v
retrieving revision 1.3
retrieving revision 1.4
diff -u -r1.3 -r1.4
--- /home/repository/moby/moby-live/Python/bioMoby/ontology/GFF2.py	2005/01/27 08:44:05	1.3
+++ /home/repository/moby/moby-live/Python/bioMoby/ontology/GFF2.py	2005/02/01 08:52:15	1.4
@@ -46,5 +46,4 @@
             if elt.nodeName=="CrossReference" or elt.nodeName=="moby:CrossReference":
                 self.__cross__=[]
                 for ref in elt.childNodes:
-                    if ref.nodeType==ref.ELEMENT_NODE:
-                        self.__cross__.append(um.loads(ref.toxml()))
\ No newline at end of file
+                    self.__cross__.append(ref.toxml())
\ No newline at end of file

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/ontology/GFF2_5.py,v
retrieving revision 1.3
retrieving revision 1.4
diff -u -r1.3 -r1.4
--- /home/repository/moby/moby-live/Python/bioMoby/ontology/GFF2_5.py	2005/01/27 08:44:05	1.3
+++ /home/repository/moby/moby-live/Python/bioMoby/ontology/GFF2_5.py	2005/02/01 08:52:15	1.4
@@ -46,5 +46,4 @@
             if elt.nodeName=="CrossReference" or elt.nodeName=="moby:CrossReference":
                 self.__cross__=[]
                 for ref in elt.childNodes:
-                    if ref.nodeType==ref.ELEMENT_NODE:
-                        self.__cross__.append(um.loads(ref.toxml()))
\ No newline at end of file
+                    self.__cross__.append(ref.toxml())
\ No newline at end of file

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/ontology/GFF3.py,v
retrieving revision 1.3
retrieving revision 1.4
diff -u -r1.3 -r1.4
--- /home/repository/moby/moby-live/Python/bioMoby/ontology/GFF3.py	2005/01/27 08:44:05	1.3
+++ /home/repository/moby/moby-live/Python/bioMoby/ontology/GFF3.py	2005/02/01 08:52:15	1.4
@@ -46,5 +46,4 @@
             if elt.nodeName=="CrossReference" or elt.nodeName=="moby:CrossReference":
                 self.__cross__=[]
                 for ref in elt.childNodes:
-                    if ref.nodeType==ref.ELEMENT_NODE:
-                        self.__cross__.append(um.loads(ref.toxml()))
\ No newline at end of file
+                    self.__cross__.append(ref.toxml())
\ No newline at end of file

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/ontology/GO_Term.py,v
retrieving revision 1.3
retrieving revision 1.4
diff -u -r1.3 -r1.4
--- /home/repository/moby/moby-live/Python/bioMoby/ontology/GO_Term.py	2005/01/27 08:44:05	1.3
+++ /home/repository/moby/moby-live/Python/bioMoby/ontology/GO_Term.py	2005/02/01 08:52:15	1.4
@@ -48,8 +48,7 @@
             if elt.nodeName=="CrossReference" or elt.nodeName=="moby:CrossReference":
                 self.__cross__=[]
                 for ref in elt.childNodes:
-                    if ref.nodeType==ref.ELEMENT_NODE:
-                        self.__cross__.append(um.loads(ref.toxml()))
+                    self.__cross__.append(ref.toxml())
             if elt.nodeType==elt.ELEMENT_NODE and (elt.nodeName=="String" or elt.nodeName=="moby:String") and (elt.getAttribute("articleName")=="Term" or elt.getAttribute("moby:articleName")=="Term"):
                 t=MobyString()
                 t.fromMoby(elt.toxml())

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/ontology/GenbankFlatfile.py,v
retrieving revision 1.3
retrieving revision 1.4
diff -u -r1.3 -r1.4
--- /home/repository/moby/moby-live/Python/bioMoby/ontology/GenbankFlatfile.py	2005/01/27 08:44:05	1.3
+++ /home/repository/moby/moby-live/Python/bioMoby/ontology/GenbankFlatfile.py	2005/02/01 08:52:15	1.4
@@ -46,5 +46,4 @@
             if elt.nodeName=="CrossReference" or elt.nodeName=="moby:CrossReference":
                 self.__cross__=[]
                 for ref in elt.childNodes:
-                    if ref.nodeType==ref.ELEMENT_NODE:
-                        self.__cross__.append(um.loads(ref.toxml()))
\ No newline at end of file
+                    self.__cross__.append(ref.toxml())
\ No newline at end of file

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/ontology/GenericSequence.py,v
retrieving revision 1.3
retrieving revision 1.4
diff -u -r1.3 -r1.4
--- /home/repository/moby/moby-live/Python/bioMoby/ontology/GenericSequence.py	2005/01/27 08:44:05	1.3
+++ /home/repository/moby/moby-live/Python/bioMoby/ontology/GenericSequence.py	2005/02/01 08:52:15	1.4
@@ -49,8 +49,7 @@
             if elt.nodeName=="CrossReference" or elt.nodeName=="moby:CrossReference":
                 self.__cross__=[]
                 for ref in elt.childNodes:
-                    if ref.nodeType==ref.ELEMENT_NODE:
-                        self.__cross__.append(um.loads(ref.toxml()))
+                    self.__cross__.append(ref.toxml())
             if elt.nodeType==elt.ELEMENT_NODE and (elt.nodeName=="Integer" or elt.nodeName=="moby:Integer") and (elt.getAttribute("articleName")=="Length" or elt.getAttribute("moby:articleName")=="Length"):
                 t=MobyInteger()
                 t.fromMoby(elt.toxml())

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/ontology/GeneticElement.py,v
retrieving revision 1.3
retrieving revision 1.4
diff -u -r1.3 -r1.4
--- /home/repository/moby/moby-live/Python/bioMoby/ontology/GeneticElement.py	2005/01/27 08:44:05	1.3
+++ /home/repository/moby/moby-live/Python/bioMoby/ontology/GeneticElement.py	2005/02/01 08:52:15	1.4
@@ -47,8 +47,7 @@
             if elt.nodeName=="CrossReference" or elt.nodeName=="moby:CrossReference":
                 self.__cross__=[]
                 for ref in elt.childNodes:
-                    if ref.nodeType==ref.ELEMENT_NODE:
-                        self.__cross__.append(um.loads(ref.toxml()))
+                    self.__cross__.append(ref.toxml())
             if elt.nodeType==elt.ELEMENT_NODE and (elt.nodeName=="String" or elt.nodeName=="moby:String") and (elt.getAttribute("articleName")=="GeneticElement" or elt.getAttribute("moby:articleName")=="GeneticElement"):
                 t=MobyString()
                 t.fromMoby(elt.toxml())

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/ontology/Genotype.py,v
retrieving revision 1.3
retrieving revision 1.4
diff -u -r1.3 -r1.4
--- /home/repository/moby/moby-live/Python/bioMoby/ontology/Genotype.py	2005/01/27 08:44:05	1.3
+++ /home/repository/moby/moby-live/Python/bioMoby/ontology/Genotype.py	2005/02/01 08:52:15	1.4
@@ -49,8 +49,7 @@
             if elt.nodeName=="CrossReference" or elt.nodeName=="moby:CrossReference":
                 self.__cross__=[]
                 for ref in elt.childNodes:
-                    if ref.nodeType==ref.ELEMENT_NODE:
-                        self.__cross__.append(um.loads(ref.toxml()))
+                    self.__cross__.append(ref.toxml())
             if elt.nodeType==elt.ELEMENT_NODE and (elt.nodeName=="String" or elt.nodeName=="moby:String") and (elt.getAttribute("articleName")=="snp" or elt.getAttribute("moby:articleName")=="snp"):
                 t=MobyString()
                 t.fromMoby(elt.toxml())

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/ontology/Germplasm_Details.py,v
retrieving revision 1.3
retrieving revision 1.4
diff -u -r1.3 -r1.4
--- /home/repository/moby/moby-live/Python/bioMoby/ontology/Germplasm_Details.py	2005/01/27 08:44:05	1.3
+++ /home/repository/moby/moby-live/Python/bioMoby/ontology/Germplasm_Details.py	2005/02/01 08:52:15	1.4
@@ -55,8 +55,7 @@
             if elt.nodeName=="CrossReference" or elt.nodeName=="moby:CrossReference":
                 self.__cross__=[]
                 for ref in elt.childNodes:
-                    if ref.nodeType==ref.ELEMENT_NODE:
-                        self.__cross__.append(um.loads(ref.toxml()))
+                    self.__cross__.append(ref.toxml())
             if elt.nodeType==elt.ELEMENT_NODE and (elt.nodeName=="Integer" or elt.nodeName=="moby:Integer") and (elt.getAttribute("articleName")=="date" or elt.getAttribute("moby:articleName")=="date"):
                 t=MobyInteger()
                 t.fromMoby(elt.toxml())

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/ontology/Germplasm_List.py,v
retrieving revision 1.3
retrieving revision 1.4
diff -u -r1.3 -r1.4
--- /home/repository/moby/moby-live/Python/bioMoby/ontology/Germplasm_List.py	2005/01/27 08:44:05	1.3
+++ /home/repository/moby/moby-live/Python/bioMoby/ontology/Germplasm_List.py	2005/02/01 08:52:16	1.4
@@ -55,8 +55,7 @@
             if elt.nodeName=="CrossReference" or elt.nodeName=="moby:CrossReference":
                 self.__cross__=[]
                 for ref in elt.childNodes:
-                    if ref.nodeType==ref.ELEMENT_NODE:
-                        self.__cross__.append(um.loads(ref.toxml()))
+                    self.__cross__.append(ref.toxml())
             if elt.nodeType==elt.ELEMENT_NODE and (elt.nodeName=="Integer" or elt.nodeName=="moby:Integer") and (elt.getAttribute("articleName")=="germplasm_id" or elt.getAttribute("moby:articleName")=="germplasm_id"):
                 t=MobyInteger()
                 t.fromMoby(elt.toxml())

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/ontology/Global_Keyword.py,v
retrieving revision 1.3
retrieving revision 1.4
diff -u -r1.3 -r1.4
--- /home/repository/moby/moby-live/Python/bioMoby/ontology/Global_Keyword.py	2005/01/27 08:44:05	1.3
+++ /home/repository/moby/moby-live/Python/bioMoby/ontology/Global_Keyword.py	2005/02/01 08:52:16	1.4
@@ -45,5 +45,4 @@
             if elt.nodeName=="CrossReference" or elt.nodeName=="moby:CrossReference":
                 self.__cross__=[]
                 for ref in elt.childNodes:
-                    if ref.nodeType==ref.ELEMENT_NODE:
-                        self.__cross__.append(um.loads(ref.toxml()))
\ No newline at end of file
+                    self.__cross__.append(ref.toxml())
\ No newline at end of file

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/ontology/HBond_Pair.py,v
retrieving revision 1.3
retrieving revision 1.4
diff -u -r1.3 -r1.4
--- /home/repository/moby/moby-live/Python/bioMoby/ontology/HBond_Pair.py	2005/01/27 08:44:05	1.3
+++ /home/repository/moby/moby-live/Python/bioMoby/ontology/HBond_Pair.py	2005/02/01 08:52:16	1.4
@@ -49,8 +49,7 @@
             if elt.nodeName=="CrossReference" or elt.nodeName=="moby:CrossReference":
                 self.__cross__=[]
                 for ref in elt.childNodes:
-                    if ref.nodeType==ref.ELEMENT_NODE:
-                        self.__cross__.append(um.loads(ref.toxml()))
+                    self.__cross__.append(ref.toxml())
             if elt.nodeType==elt.ELEMENT_NODE and (elt.nodeName=="String" or elt.nodeName=="moby:String") and (elt.getAttribute("articleName")=="A" or elt.getAttribute("moby:articleName")=="A"):
                 t=MobyString()
                 t.fromMoby(elt.toxml())

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/ontology/HFormatText.py,v
retrieving revision 1.3
retrieving revision 1.4
diff -u -r1.3 -r1.4
--- /home/repository/moby/moby-live/Python/bioMoby/ontology/HFormatText.py	2005/01/27 08:44:05	1.3
+++ /home/repository/moby/moby-live/Python/bioMoby/ontology/HFormatText.py	2005/02/01 08:52:16	1.4
@@ -46,5 +46,4 @@
             if elt.nodeName=="CrossReference" or elt.nodeName=="moby:CrossReference":
                 self.__cross__=[]
                 for ref in elt.childNodes:
-                    if ref.nodeType==ref.ELEMENT_NODE:
-                        self.__cross__.append(um.loads(ref.toxml()))
\ No newline at end of file
+                    self.__cross__.append(ref.toxml())
\ No newline at end of file

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/ontology/Haplotyping_Study_obj.py,v
retrieving revision 1.3
retrieving revision 1.4
diff -u -r1.3 -r1.4
--- /home/repository/moby/moby-live/Python/bioMoby/ontology/Haplotyping_Study_obj.py	2005/01/27 08:44:05	1.3
+++ /home/repository/moby/moby-live/Python/bioMoby/ontology/Haplotyping_Study_obj.py	2005/02/01 08:52:16	1.4
@@ -45,5 +45,4 @@
             if elt.nodeName=="CrossReference" or elt.nodeName=="moby:CrossReference":
                 self.__cross__=[]
                 for ref in elt.childNodes:
-                    if ref.nodeType==ref.ELEMENT_NODE:
-                        self.__cross__.append(um.loads(ref.toxml()))
\ No newline at end of file
+                    self.__cross__.append(ref.toxml())
\ No newline at end of file

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/ontology/ICIS_Query.py,v
retrieving revision 1.3
retrieving revision 1.4
diff -u -r1.3 -r1.4
--- /home/repository/moby/moby-live/Python/bioMoby/ontology/ICIS_Query.py	2005/01/27 08:44:05	1.3
+++ /home/repository/moby/moby-live/Python/bioMoby/ontology/ICIS_Query.py	2005/02/01 08:52:16	1.4
@@ -50,8 +50,7 @@
             if elt.nodeName=="CrossReference" or elt.nodeName=="moby:CrossReference":
                 self.__cross__=[]
                 for ref in elt.childNodes:
-                    if ref.nodeType==ref.ELEMENT_NODE:
-                        self.__cross__.append(um.loads(ref.toxml()))
+                    self.__cross__.append(ref.toxml())
             if elt.nodeType==elt.ELEMENT_NODE and (elt.nodeName=="Integer" or elt.nodeName=="moby:Integer") and (elt.getAttribute("articleName")=="end_row" or elt.getAttribute("moby:articleName")=="end_row"):
                 t=MobyInteger()
                 t.fromMoby(elt.toxml())

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/ontology/ICIS_Query2.py,v
retrieving revision 1.3
retrieving revision 1.4
diff -u -r1.3 -r1.4
--- /home/repository/moby/moby-live/Python/bioMoby/ontology/ICIS_Query2.py	2005/01/27 08:44:05	1.3
+++ /home/repository/moby/moby-live/Python/bioMoby/ontology/ICIS_Query2.py	2005/02/01 08:52:16	1.4
@@ -52,8 +52,7 @@
             if elt.nodeName=="CrossReference" or elt.nodeName=="moby:CrossReference":
                 self.__cross__=[]
                 for ref in elt.childNodes:
-                    if ref.nodeType==ref.ELEMENT_NODE:
-                        self.__cross__.append(um.loads(ref.toxml()))
+                    self.__cross__.append(ref.toxml())
             if elt.nodeType==elt.ELEMENT_NODE and (elt.nodeName=="String" or elt.nodeName=="moby:String") and (elt.getAttribute("articleName")=="search_text1" or elt.getAttribute("moby:articleName")=="search_text1"):
                 t=MobyString()
                 t.fromMoby(elt.toxml())

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/ontology/ICIS_Query3.py,v
retrieving revision 1.3
retrieving revision 1.4
diff -u -r1.3 -r1.4
--- /home/repository/moby/moby-live/Python/bioMoby/ontology/ICIS_Query3.py	2005/01/27 08:44:05	1.3
+++ /home/repository/moby/moby-live/Python/bioMoby/ontology/ICIS_Query3.py	2005/02/01 08:52:16	1.4
@@ -50,8 +50,7 @@
             if elt.nodeName=="CrossReference" or elt.nodeName=="moby:CrossReference":
                 self.__cross__=[]
                 for ref in elt.childNodes:
-                    if ref.nodeType==ref.ELEMENT_NODE:
-                        self.__cross__.append(um.loads(ref.toxml()))
+                    self.__cross__.append(ref.toxml())
             if elt.nodeType==elt.ELEMENT_NODE and (elt.nodeName=="Integer" or elt.nodeName=="moby:Integer") and (elt.getAttribute("articleName")=="search_text1" or elt.getAttribute("moby:articleName")=="search_text1"):
                 t=MobyInteger()
                 t.fromMoby(elt.toxml())

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/ontology/IntAct_XML.py,v
retrieving revision 1.3
retrieving revision 1.4
diff -u -r1.3 -r1.4
--- /home/repository/moby/moby-live/Python/bioMoby/ontology/IntAct_XML.py	2005/01/27 08:44:05	1.3
+++ /home/repository/moby/moby-live/Python/bioMoby/ontology/IntAct_XML.py	2005/02/01 08:52:16	1.4
@@ -46,5 +46,4 @@
             if elt.nodeName=="CrossReference" or elt.nodeName=="moby:CrossReference":
                 self.__cross__=[]
                 for ref in elt.childNodes:
-                    if ref.nodeType==ref.ELEMENT_NODE:
-                        self.__cross__.append(um.loads(ref.toxml()))
\ No newline at end of file
+                    self.__cross__.append(ref.toxml())
\ No newline at end of file

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/ontology/Interaction.py,v
retrieving revision 1.3
retrieving revision 1.4
diff -u -r1.3 -r1.4
--- /home/repository/moby/moby-live/Python/bioMoby/ontology/Interaction.py	2005/01/27 08:44:05	1.3
+++ /home/repository/moby/moby-live/Python/bioMoby/ontology/Interaction.py	2005/02/01 08:52:16	1.4
@@ -51,8 +51,7 @@
             if elt.nodeName=="CrossReference" or elt.nodeName=="moby:CrossReference":
                 self.__cross__=[]
                 for ref in elt.childNodes:
-                    if ref.nodeType==ref.ELEMENT_NODE:
-                        self.__cross__.append(um.loads(ref.toxml()))
+                    self.__cross__.append(ref.toxml())
             if elt.nodeType==elt.ELEMENT_NODE and (elt.nodeName=="String" or elt.nodeName=="moby:String") and (elt.getAttribute("articleName")=="result" or elt.getAttribute("moby:articleName")=="result"):
                 t=MobyString()
                 t.fromMoby(elt.toxml())

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/ontology/InteractionMethod.py,v
retrieving revision 1.3
retrieving revision 1.4
diff -u -r1.3 -r1.4
--- /home/repository/moby/moby-live/Python/bioMoby/ontology/InteractionMethod.py	2005/01/27 08:44:05	1.3
+++ /home/repository/moby/moby-live/Python/bioMoby/ontology/InteractionMethod.py	2005/02/01 08:52:16	1.4
@@ -49,8 +49,7 @@
             if elt.nodeName=="CrossReference" or elt.nodeName=="moby:CrossReference":
                 self.__cross__=[]
                 for ref in elt.childNodes:
-                    if ref.nodeType==ref.ELEMENT_NODE:
-                        self.__cross__.append(um.loads(ref.toxml()))
+                    self.__cross__.append(ref.toxml())
             if elt.nodeType==elt.ELEMENT_NODE and (elt.nodeName=="String" or elt.nodeName=="moby:String") and (elt.getAttribute("articleName")=="shortlabel" or elt.getAttribute("moby:articleName")=="shortlabel"):
                 t=MobyString()
                 t.fromMoby(elt.toxml())

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/ontology/Interaction_partner.py,v
retrieving revision 1.3
retrieving revision 1.4
diff -u -r1.3 -r1.4
--- /home/repository/moby/moby-live/Python/bioMoby/ontology/Interaction_partner.py	2005/01/27 08:44:05	1.3
+++ /home/repository/moby/moby-live/Python/bioMoby/ontology/Interaction_partner.py	2005/02/01 08:52:16	1.4
@@ -49,8 +49,7 @@
             if elt.nodeName=="CrossReference" or elt.nodeName=="moby:CrossReference":
                 self.__cross__=[]
                 for ref in elt.childNodes:
-                    if ref.nodeType==ref.ELEMENT_NODE:
-                        self.__cross__.append(um.loads(ref.toxml()))
+                    self.__cross__.append(ref.toxml())
             if elt.nodeType==elt.ELEMENT_NODE and (elt.nodeName=="Integer" or elt.nodeName=="moby:Integer") and (elt.getAttribute("articleName")=="direction" or elt.getAttribute("moby:articleName")=="direction"):
                 t=MobyInteger()
                 t.fromMoby(elt.toxml())

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/ontology/Interactor.py,v
retrieving revision 1.3
retrieving revision 1.4
diff -u -r1.3 -r1.4
--- /home/repository/moby/moby-live/Python/bioMoby/ontology/Interactor.py	2005/01/27 08:44:05	1.3
+++ /home/repository/moby/moby-live/Python/bioMoby/ontology/Interactor.py	2005/02/01 08:52:16	1.4
@@ -47,8 +47,7 @@
             if elt.nodeName=="CrossReference" or elt.nodeName=="moby:CrossReference":
                 self.__cross__=[]
                 for ref in elt.childNodes:
-                    if ref.nodeType==ref.ELEMENT_NODE:
-                        self.__cross__.append(um.loads(ref.toxml()))
+                    self.__cross__.append(ref.toxml())
             if elt.nodeType==elt.ELEMENT_NODE and (elt.nodeName=="String" or elt.nodeName=="moby:String") and (elt.getAttribute("articleName")=="role" or elt.getAttribute("moby:articleName")=="role"):
                 t=MobyString()
                 t.fromMoby(elt.toxml())

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/ontology/MEME_Text.py,v
retrieving revision 1.3
retrieving revision 1.4
diff -u -r1.3 -r1.4
--- /home/repository/moby/moby-live/Python/bioMoby/ontology/MEME_Text.py	2005/01/27 08:44:05	1.3
+++ /home/repository/moby/moby-live/Python/bioMoby/ontology/MEME_Text.py	2005/02/01 08:52:16	1.4
@@ -46,5 +46,4 @@
             if elt.nodeName=="CrossReference" or elt.nodeName=="moby:CrossReference":
                 self.__cross__=[]
                 for ref in elt.childNodes:
-                    if ref.nodeType==ref.ELEMENT_NODE:
-                        self.__cross__.append(um.loads(ref.toxml()))
\ No newline at end of file
+                    self.__cross__.append(ref.toxml())
\ No newline at end of file

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/ontology/MGIS_ACCESSION.py,v
retrieving revision 1.3
retrieving revision 1.4
diff -u -r1.3 -r1.4
--- /home/repository/moby/moby-live/Python/bioMoby/ontology/MGIS_ACCESSION.py	2005/01/27 08:44:05	1.3
+++ /home/repository/moby/moby-live/Python/bioMoby/ontology/MGIS_ACCESSION.py	2005/02/01 08:52:16	1.4
@@ -66,8 +66,7 @@
             if elt.nodeName=="CrossReference" or elt.nodeName=="moby:CrossReference":
                 self.__cross__=[]
                 for ref in elt.childNodes:
-                    if ref.nodeType==ref.ELEMENT_NODE:
-                        self.__cross__.append(um.loads(ref.toxml()))
+                    self.__cross__.append(ref.toxml())
             if elt.nodeType==elt.ELEMENT_NODE and (elt.nodeName=="String" or elt.nodeName=="moby:String") and (elt.getAttribute("articleName")=="Biotic_stress_Yellowsig" or elt.getAttribute("moby:articleName")=="Biotic_stress_Yellowsig"):
                 t=MobyString()
                 t.fromMoby(elt.toxml())

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/ontology/MMP_Locus.py,v
retrieving revision 1.3
retrieving revision 1.4
diff -u -r1.3 -r1.4
--- /home/repository/moby/moby-live/Python/bioMoby/ontology/MMP_Locus.py	2005/01/27 08:44:05	1.3
+++ /home/repository/moby/moby-live/Python/bioMoby/ontology/MMP_Locus.py	2005/02/01 08:52:16	1.4
@@ -45,5 +45,4 @@
             if elt.nodeName=="CrossReference" or elt.nodeName=="moby:CrossReference":
                 self.__cross__=[]
                 for ref in elt.childNodes:
-                    if ref.nodeType==ref.ELEMENT_NODE:
-                        self.__cross__.append(um.loads(ref.toxml()))
\ No newline at end of file
+                    self.__cross__.append(ref.toxml())
\ No newline at end of file

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/ontology/MO_Term_Test.py,v
retrieving revision 1.3
retrieving revision 1.4
diff -u -r1.3 -r1.4
--- /home/repository/moby/moby-live/Python/bioMoby/ontology/MO_Term_Test.py	2005/01/27 08:44:05	1.3
+++ /home/repository/moby/moby-live/Python/bioMoby/ontology/MO_Term_Test.py	2005/02/01 08:52:16	1.4
@@ -50,8 +50,7 @@
             if elt.nodeName=="CrossReference" or elt.nodeName=="moby:CrossReference":
                 self.__cross__=[]
                 for ref in elt.childNodes:
-                    if ref.nodeType==ref.ELEMENT_NODE:
-                        self.__cross__.append(um.loads(ref.toxml()))
+                    self.__cross__.append(ref.toxml())
             if elt.nodeType==elt.ELEMENT_NODE and (elt.nodeName=="String" or elt.nodeName=="moby:String") and (elt.getAttribute("articleName")=="class_name" or elt.getAttribute("moby:articleName")=="class_name"):
                 t=MobyString()
                 t.fromMoby(elt.toxml())

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/ontology/MmCIFText.py,v
retrieving revision 1.3
retrieving revision 1.4
diff -u -r1.3 -r1.4
--- /home/repository/moby/moby-live/Python/bioMoby/ontology/MmCIFText.py	2005/01/27 08:44:05	1.3
+++ /home/repository/moby/moby-live/Python/bioMoby/ontology/MmCIFText.py	2005/02/01 08:52:16	1.4
@@ -46,5 +46,4 @@
             if elt.nodeName=="CrossReference" or elt.nodeName=="moby:CrossReference":
                 self.__cross__=[]
                 for ref in elt.childNodes:
-                    if ref.nodeType==ref.ELEMENT_NODE:
-                        self.__cross__.append(um.loads(ref.toxml()))
\ No newline at end of file
+                    self.__cross__.append(ref.toxml())
\ No newline at end of file

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/ontology/Multi_key_value_pair.py,v
retrieving revision 1.3
retrieving revision 1.4
diff -u -r1.3 -r1.4
--- /home/repository/moby/moby-live/Python/bioMoby/ontology/Multi_key_value_pair.py	2005/01/27 08:44:05	1.3
+++ /home/repository/moby/moby-live/Python/bioMoby/ontology/Multi_key_value_pair.py	2005/02/01 08:52:16	1.4
@@ -49,8 +49,7 @@
             if elt.nodeName=="CrossReference" or elt.nodeName=="moby:CrossReference":
                 self.__cross__=[]
                 for ref in elt.childNodes:
-                    if ref.nodeType==ref.ELEMENT_NODE:
-                        self.__cross__.append(um.loads(ref.toxml()))
+                    self.__cross__.append(ref.toxml())
             if elt.nodeType==elt.ELEMENT_NODE and (elt.nodeName=="String" or elt.nodeName=="moby:String") and (elt.getAttribute("articleName")=="key" or elt.getAttribute("moby:articleName")=="key"):
                 t=MobyString()
                 t.fromMoby(elt.toxml())

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/ontology/MyTestingDataType_11024145298313.py,v
retrieving revision 1.3
retrieving revision 1.4
diff -u -r1.3 -r1.4
--- /home/repository/moby/moby-live/Python/bioMoby/ontology/MyTestingDataType_11024145298313.py	2005/01/27 08:44:05	1.3
+++ /home/repository/moby/moby-live/Python/bioMoby/ontology/MyTestingDataType_11024145298313.py	2005/02/01 08:52:16	1.4
@@ -46,5 +46,4 @@
             if elt.nodeName=="CrossReference" or elt.nodeName=="moby:CrossReference":
                 self.__cross__=[]
                 for ref in elt.childNodes:
-                    if ref.nodeType==ref.ELEMENT_NODE:
-                        self.__cross__.append(um.loads(ref.toxml()))
\ No newline at end of file
+                    self.__cross__.append(ref.toxml())
\ No newline at end of file

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/ontology/MyTree.py,v
retrieving revision 1.3
retrieving revision 1.4
diff -u -r1.3 -r1.4
--- /home/repository/moby/moby-live/Python/bioMoby/ontology/MyTree.py	2005/01/27 08:44:05	1.3
+++ /home/repository/moby/moby-live/Python/bioMoby/ontology/MyTree.py	2005/02/01 08:52:16	1.4
@@ -46,5 +46,4 @@
             if elt.nodeName=="CrossReference" or elt.nodeName=="moby:CrossReference":
                 self.__cross__=[]
                 for ref in elt.childNodes:
-                    if ref.nodeType==ref.ELEMENT_NODE:
-                        self.__cross__.append(um.loads(ref.toxml()))
\ No newline at end of file
+                    self.__cross__.append(ref.toxml())
\ No newline at end of file

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/ontology/NCBI_BLAST_Text.py,v
retrieving revision 1.3
retrieving revision 1.4
diff -u -r1.3 -r1.4
--- /home/repository/moby/moby-live/Python/bioMoby/ontology/NCBI_BLAST_Text.py	2005/01/27 08:44:05	1.3
+++ /home/repository/moby/moby-live/Python/bioMoby/ontology/NCBI_BLAST_Text.py	2005/02/01 08:52:16	1.4
@@ -46,5 +46,4 @@
             if elt.nodeName=="CrossReference" or elt.nodeName=="moby:CrossReference":
                 self.__cross__=[]
                 for ref in elt.childNodes:
-                    if ref.nodeType==ref.ELEMENT_NODE:
-                        self.__cross__.append(um.loads(ref.toxml()))
\ No newline at end of file
+                    self.__cross__.append(ref.toxml())
\ No newline at end of file

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/ontology/NCBI_Blast_XML.py,v
retrieving revision 1.3
retrieving revision 1.4
diff -u -r1.3 -r1.4
--- /home/repository/moby/moby-live/Python/bioMoby/ontology/NCBI_Blast_XML.py	2005/01/27 08:44:05	1.3
+++ /home/repository/moby/moby-live/Python/bioMoby/ontology/NCBI_Blast_XML.py	2005/02/01 08:52:16	1.4
@@ -46,5 +46,4 @@
             if elt.nodeName=="CrossReference" or elt.nodeName=="moby:CrossReference":
                 self.__cross__=[]
                 for ref in elt.childNodes:
-                    if ref.nodeType==ref.ELEMENT_NODE:
-                        self.__cross__.append(um.loads(ref.toxml()))
\ No newline at end of file
+                    self.__cross__.append(ref.toxml())
\ No newline at end of file

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/ontology/NCBI_Blast_XML_Gif.py,v
retrieving revision 1.3
retrieving revision 1.4
diff -u -r1.3 -r1.4
--- /home/repository/moby/moby-live/Python/bioMoby/ontology/NCBI_Blast_XML_Gif.py	2005/01/27 08:44:05	1.3
+++ /home/repository/moby/moby-live/Python/bioMoby/ontology/NCBI_Blast_XML_Gif.py	2005/02/01 08:52:16	1.4
@@ -48,8 +48,7 @@
             if elt.nodeName=="CrossReference" or elt.nodeName=="moby:CrossReference":
                 self.__cross__=[]
                 for ref in elt.childNodes:
-                    if ref.nodeType==ref.ELEMENT_NODE:
-                        self.__cross__.append(um.loads(ref.toxml()))
+                    self.__cross__.append(ref.toxml())
             if elt.nodeType==elt.ELEMENT_NODE and (elt.nodeName=="b64_encoded_gif" or elt.nodeName=="moby:b64_encoded_gif") and (elt.getAttribute("articleName")=="hitGraph" or elt.getAttribute("moby:articleName")=="hitGraph"):
                 self.HitGraph=MobyB64_encoded_gif()
                 self.HitGraph.fromMoby(elt.toxml())
\ No newline at end of file

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/ontology/NCBI_Blast_XML_Gif_Map.py,v
retrieving revision 1.3
retrieving revision 1.4
diff -u -r1.3 -r1.4
--- /home/repository/moby/moby-live/Python/bioMoby/ontology/NCBI_Blast_XML_Gif_Map.py	2005/01/27 08:44:05	1.3
+++ /home/repository/moby/moby-live/Python/bioMoby/ontology/NCBI_Blast_XML_Gif_Map.py	2005/02/01 08:52:16	1.4
@@ -50,8 +50,7 @@
             if elt.nodeName=="CrossReference" or elt.nodeName=="moby:CrossReference":
                 self.__cross__=[]
                 for ref in elt.childNodes:
-                    if ref.nodeType==ref.ELEMENT_NODE:
-                        self.__cross__.append(um.loads(ref.toxml()))
+                    self.__cross__.append(ref.toxml())
             if elt.nodeType==elt.ELEMENT_NODE and (elt.nodeName=="b64_encoded_gif" or elt.nodeName=="moby:b64_encoded_gif") and (elt.getAttribute("articleName")=="hitGraph" or elt.getAttribute("moby:articleName")=="hitGraph"):
                 self.HitGraph=MobyB64_encoded_gif()
                 self.HitGraph.fromMoby(elt.toxml())

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/ontology/NCBI_MEME_Text.py,v
retrieving revision 1.3
retrieving revision 1.4
diff -u -r1.3 -r1.4
--- /home/repository/moby/moby-live/Python/bioMoby/ontology/NCBI_MEME_Text.py	2005/01/27 08:44:05	1.3
+++ /home/repository/moby/moby-live/Python/bioMoby/ontology/NCBI_MEME_Text.py	2005/02/01 08:52:16	1.4
@@ -46,5 +46,4 @@
             if elt.nodeName=="CrossReference" or elt.nodeName=="moby:CrossReference":
                 self.__cross__=[]
                 for ref in elt.childNodes:
-                    if ref.nodeType==ref.ELEMENT_NODE:
-                        self.__cross__.append(um.loads(ref.toxml()))
\ No newline at end of file
+                    self.__cross__.append(ref.toxml())
\ No newline at end of file

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/ontology/NucleotideSequence.py,v
retrieving revision 1.3
retrieving revision 1.4
diff -u -r1.3 -r1.4
--- /home/repository/moby/moby-live/Python/bioMoby/ontology/NucleotideSequence.py	2005/01/27 08:44:05	1.3
+++ /home/repository/moby/moby-live/Python/bioMoby/ontology/NucleotideSequence.py	2005/02/01 08:52:16	1.4
@@ -49,8 +49,7 @@
             if elt.nodeName=="CrossReference" or elt.nodeName=="moby:CrossReference":
                 self.__cross__=[]
                 for ref in elt.childNodes:
-                    if ref.nodeType==ref.ELEMENT_NODE:
-                        self.__cross__.append(um.loads(ref.toxml()))
+                    self.__cross__.append(ref.toxml())
             if elt.nodeType==elt.ELEMENT_NODE and (elt.nodeName=="Integer" or elt.nodeName=="moby:Integer") and (elt.getAttribute("articleName")=="Length" or elt.getAttribute("moby:articleName")=="Length"):
                 t=MobyInteger()
                 t.fromMoby(elt.toxml())

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/ontology/PDBFormattedText.py,v
retrieving revision 1.3
retrieving revision 1.4
diff -u -r1.3 -r1.4
--- /home/repository/moby/moby-live/Python/bioMoby/ontology/PDBFormattedText.py	2005/01/27 08:44:05	1.3
+++ /home/repository/moby/moby-live/Python/bioMoby/ontology/PDBFormattedText.py	2005/02/01 08:52:16	1.4
@@ -46,5 +46,4 @@
             if elt.nodeName=="CrossReference" or elt.nodeName=="moby:CrossReference":
                 self.__cross__=[]
                 for ref in elt.childNodes:
-                    if ref.nodeType==ref.ELEMENT_NODE:
-                        self.__cross__.append(um.loads(ref.toxml()))
\ No newline at end of file
+                    self.__cross__.append(ref.toxml())
\ No newline at end of file

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/ontology/PDBText.py,v
retrieving revision 1.3
retrieving revision 1.4
diff -u -r1.3 -r1.4
--- /home/repository/moby/moby-live/Python/bioMoby/ontology/PDBText.py	2005/01/27 08:44:05	1.3
+++ /home/repository/moby/moby-live/Python/bioMoby/ontology/PDBText.py	2005/02/01 08:52:16	1.4
@@ -46,5 +46,4 @@
             if elt.nodeName=="CrossReference" or elt.nodeName=="moby:CrossReference":
                 self.__cross__=[]
                 for ref in elt.childNodes:
-                    if ref.nodeType==ref.ELEMENT_NODE:
-                        self.__cross__.append(um.loads(ref.toxml()))
\ No newline at end of file
+                    self.__cross__.append(ref.toxml())
\ No newline at end of file

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/ontology/PDGJOB.py,v
retrieving revision 1.3
retrieving revision 1.4
diff -u -r1.3 -r1.4
--- /home/repository/moby/moby-live/Python/bioMoby/ontology/PDGJOB.py	2005/01/27 08:44:05	1.3
+++ /home/repository/moby/moby-live/Python/bioMoby/ontology/PDGJOB.py	2005/02/01 08:52:16	1.4
@@ -52,8 +52,7 @@
             if elt.nodeName=="CrossReference" or elt.nodeName=="moby:CrossReference":
                 self.__cross__=[]
                 for ref in elt.childNodes:
-                    if ref.nodeType==ref.ELEMENT_NODE:
-                        self.__cross__.append(um.loads(ref.toxml()))
+                    self.__cross__.append(ref.toxml())
             if elt.nodeType==elt.ELEMENT_NODE and (elt.nodeName=="String" or elt.nodeName=="moby:String") and (elt.getAttribute("articleName")=="answerService" or elt.getAttribute("moby:articleName")=="answerService"):
                 t=MobyString()
                 t.fromMoby(elt.toxml())

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/ontology/PHDText.py,v
retrieving revision 1.3
retrieving revision 1.4
diff -u -r1.3 -r1.4
--- /home/repository/moby/moby-live/Python/bioMoby/ontology/PHDText.py	2005/01/27 08:44:05	1.3
+++ /home/repository/moby/moby-live/Python/bioMoby/ontology/PHDText.py	2005/02/01 08:52:16	1.4
@@ -46,5 +46,4 @@
             if elt.nodeName=="CrossReference" or elt.nodeName=="moby:CrossReference":
                 self.__cross__=[]
                 for ref in elt.childNodes:
-                    if ref.nodeType==ref.ELEMENT_NODE:
-                        self.__cross__.append(um.loads(ref.toxml()))
\ No newline at end of file
+                    self.__cross__.append(ref.toxml())
\ No newline at end of file

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/ontology/PMUTText.py,v
retrieving revision 1.3
retrieving revision 1.4
diff -u -r1.3 -r1.4
--- /home/repository/moby/moby-live/Python/bioMoby/ontology/PMUTText.py	2005/01/27 08:44:05	1.3
+++ /home/repository/moby/moby-live/Python/bioMoby/ontology/PMUTText.py	2005/02/01 08:52:16	1.4
@@ -46,5 +46,4 @@
             if elt.nodeName=="CrossReference" or elt.nodeName=="moby:CrossReference":
                 self.__cross__=[]
                 for ref in elt.childNodes:
-                    if ref.nodeType==ref.ELEMENT_NODE:
-                        self.__cross__.append(um.loads(ref.toxml()))
\ No newline at end of file
+                    self.__cross__.append(ref.toxml())
\ No newline at end of file

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/ontology/PSeaTextFormatted.py,v
retrieving revision 1.3
retrieving revision 1.4
diff -u -r1.3 -r1.4
--- /home/repository/moby/moby-live/Python/bioMoby/ontology/PSeaTextFormatted.py	2005/01/27 08:44:05	1.3
+++ /home/repository/moby/moby-live/Python/bioMoby/ontology/PSeaTextFormatted.py	2005/02/01 08:52:16	1.4
@@ -46,5 +46,4 @@
             if elt.nodeName=="CrossReference" or elt.nodeName=="moby:CrossReference":
                 self.__cross__=[]
                 for ref in elt.childNodes:
-                    if ref.nodeType==ref.ELEMENT_NODE:
-                        self.__cross__.append(um.loads(ref.toxml()))
\ No newline at end of file
+                    self.__cross__.append(ref.toxml())
\ No newline at end of file

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/ontology/PhenotypeDescription.py,v
retrieving revision 1.3
retrieving revision 1.4
diff -u -r1.3 -r1.4
--- /home/repository/moby/moby-live/Python/bioMoby/ontology/PhenotypeDescription.py	2005/01/27 08:44:05	1.3
+++ /home/repository/moby/moby-live/Python/bioMoby/ontology/PhenotypeDescription.py	2005/02/01 08:52:16	1.4
@@ -47,8 +47,7 @@
             if elt.nodeName=="CrossReference" or elt.nodeName=="moby:CrossReference":
                 self.__cross__=[]
                 for ref in elt.childNodes:
-                    if ref.nodeType==ref.ELEMENT_NODE:
-                        self.__cross__.append(um.loads(ref.toxml()))
+                    self.__cross__.append(ref.toxml())
             if elt.nodeType==elt.ELEMENT_NODE and (elt.nodeName=="String" or elt.nodeName=="moby:String") and (elt.getAttribute("articleName")=="Phenotype" or elt.getAttribute("moby:articleName")=="Phenotype"):
                 t=MobyString()
                 t.fromMoby(elt.toxml())

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/ontology/PubMedMEDLINE.py,v
retrieving revision 1.3
retrieving revision 1.4
diff -u -r1.3 -r1.4
--- /home/repository/moby/moby-live/Python/bioMoby/ontology/PubMedMEDLINE.py	2005/01/27 08:44:05	1.3
+++ /home/repository/moby/moby-live/Python/bioMoby/ontology/PubMedMEDLINE.py	2005/02/01 08:52:16	1.4
@@ -46,5 +46,4 @@
             if elt.nodeName=="CrossReference" or elt.nodeName=="moby:CrossReference":
                 self.__cross__=[]
                 for ref in elt.childNodes:
-                    if ref.nodeType==ref.ELEMENT_NODE:
-                        self.__cross__.append(um.loads(ref.toxml()))
\ No newline at end of file
+                    self.__cross__.append(ref.toxml())
\ No newline at end of file

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/ontology/RNASequence.py,v
retrieving revision 1.3
retrieving revision 1.4
diff -u -r1.3 -r1.4
--- /home/repository/moby/moby-live/Python/bioMoby/ontology/RNASequence.py	2005/01/27 08:44:05	1.3
+++ /home/repository/moby/moby-live/Python/bioMoby/ontology/RNASequence.py	2005/02/01 08:52:16	1.4
@@ -49,8 +49,7 @@
             if elt.nodeName=="CrossReference" or elt.nodeName=="moby:CrossReference":
                 self.__cross__=[]
                 for ref in elt.childNodes:
-                    if ref.nodeType==ref.ELEMENT_NODE:
-                        self.__cross__.append(um.loads(ref.toxml()))
+                    self.__cross__.append(ref.toxml())
             if elt.nodeType==elt.ELEMENT_NODE and (elt.nodeName=="Integer" or elt.nodeName=="moby:Integer") and (elt.getAttribute("articleName")=="Length" or elt.getAttribute("moby:articleName")=="Length"):
                 t=MobyInteger()
                 t.fromMoby(elt.toxml())

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/ontology/SINGER_ACCESSION.py,v
retrieving revision 1.3
retrieving revision 1.4
diff -u -r1.3 -r1.4
--- /home/repository/moby/moby-live/Python/bioMoby/ontology/SINGER_ACCESSION.py	2005/01/27 08:44:05	1.3
+++ /home/repository/moby/moby-live/Python/bioMoby/ontology/SINGER_ACCESSION.py	2005/02/01 08:52:16	1.4
@@ -50,8 +50,7 @@
             if elt.nodeName=="CrossReference" or elt.nodeName=="moby:CrossReference":
                 self.__cross__=[]
                 for ref in elt.childNodes:
-                    if ref.nodeType==ref.ELEMENT_NODE:
-                        self.__cross__.append(um.loads(ref.toxml()))
+                    self.__cross__.append(ref.toxml())
             if elt.nodeType==elt.ELEMENT_NODE and (elt.nodeName=="String" or elt.nodeName=="moby:String") and (elt.getAttribute("articleName")=="ACCNO" or elt.getAttribute("moby:articleName")=="ACCNO"):
                 t=MobyString()
                 t.fromMoby(elt.toxml())

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/ontology/Sample.py,v
retrieving revision 1.3
retrieving revision 1.4
diff -u -r1.3 -r1.4
--- /home/repository/moby/moby-live/Python/bioMoby/ontology/Sample.py	2005/01/27 08:44:05	1.3
+++ /home/repository/moby/moby-live/Python/bioMoby/ontology/Sample.py	2005/02/01 08:52:16	1.4
@@ -49,8 +49,7 @@
             if elt.nodeName=="CrossReference" or elt.nodeName=="moby:CrossReference":
                 self.__cross__=[]
                 for ref in elt.childNodes:
-                    if ref.nodeType==ref.ELEMENT_NODE:
-                        self.__cross__.append(um.loads(ref.toxml()))
+                    self.__cross__.append(ref.toxml())
             if elt.nodeType==elt.ELEMENT_NODE and (elt.nodeName=="String" or elt.nodeName=="moby:String") and (elt.getAttribute("articleName")=="code" or elt.getAttribute("moby:articleName")=="code"):
                 t=MobyString()
                 t.fromMoby(elt.toxml())

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/ontology/SchematikonMotifID.py,v
retrieving revision 1.3
retrieving revision 1.4
diff -u -r1.3 -r1.4
--- /home/repository/moby/moby-live/Python/bioMoby/ontology/SchematikonMotifID.py	2005/01/27 08:44:05	1.3
+++ /home/repository/moby/moby-live/Python/bioMoby/ontology/SchematikonMotifID.py	2005/02/01 08:52:16	1.4
@@ -47,8 +47,7 @@
             if elt.nodeName=="CrossReference" or elt.nodeName=="moby:CrossReference":
                 self.__cross__=[]
                 for ref in elt.childNodes:
-                    if ref.nodeType==ref.ELEMENT_NODE:
-                        self.__cross__.append(um.loads(ref.toxml()))
+                    self.__cross__.append(ref.toxml())
             if elt.nodeType==elt.ELEMENT_NODE and (elt.nodeName=="String" or elt.nodeName=="moby:String") and (elt.getAttribute("articleName")=="ID" or elt.getAttribute("moby:articleName")=="ID"):
                 t=MobyString()
                 t.fromMoby(elt.toxml())

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/ontology/SchematikonMotifSupport.py,v
retrieving revision 1.3
retrieving revision 1.4
diff -u -r1.3 -r1.4
--- /home/repository/moby/moby-live/Python/bioMoby/ontology/SchematikonMotifSupport.py	2005/01/27 08:44:05	1.3
+++ /home/repository/moby/moby-live/Python/bioMoby/ontology/SchematikonMotifSupport.py	2005/02/01 08:52:16	1.4
@@ -48,8 +48,7 @@
             if elt.nodeName=="CrossReference" or elt.nodeName=="moby:CrossReference":
                 self.__cross__=[]
                 for ref in elt.childNodes:
-                    if ref.nodeType==ref.ELEMENT_NODE:
-                        self.__cross__.append(um.loads(ref.toxml()))
+                    self.__cross__.append(ref.toxml())
             if elt.nodeType==elt.ELEMENT_NODE and (elt.nodeName=="Integer" or elt.nodeName=="moby:Integer") and (elt.getAttribute("articleName")=="UniqueSupport" or elt.getAttribute("moby:articleName")=="UniqueSupport"):
                 t=MobyInteger()
                 t.fromMoby(elt.toxml())

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/ontology/SchematikonSegmentAttributes.py,v
retrieving revision 1.3
retrieving revision 1.4
diff -u -r1.3 -r1.4
--- /home/repository/moby/moby-live/Python/bioMoby/ontology/SchematikonSegmentAttributes.py	2005/01/27 08:44:05	1.3
+++ /home/repository/moby/moby-live/Python/bioMoby/ontology/SchematikonSegmentAttributes.py	2005/02/01 08:52:16	1.4
@@ -52,8 +52,7 @@
             if elt.nodeName=="CrossReference" or elt.nodeName=="moby:CrossReference":
                 self.__cross__=[]
                 for ref in elt.childNodes:
-                    if ref.nodeType==ref.ELEMENT_NODE:
-                        self.__cross__.append(um.loads(ref.toxml()))
+                    self.__cross__.append(ref.toxml())
             if elt.nodeType==elt.ELEMENT_NODE and (elt.nodeName=="Integer" or elt.nodeName=="moby:Integer") and (elt.getAttribute("articleName")=="Length" or elt.getAttribute("moby:articleName")=="Length"):
                 t=MobyInteger()
                 t.fromMoby(elt.toxml())

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/ontology/SchematikonSegmentID.py,v
retrieving revision 1.3
retrieving revision 1.4
diff -u -r1.3 -r1.4
--- /home/repository/moby/moby-live/Python/bioMoby/ontology/SchematikonSegmentID.py	2005/01/27 08:44:05	1.3
+++ /home/repository/moby/moby-live/Python/bioMoby/ontology/SchematikonSegmentID.py	2005/02/01 08:52:16	1.4
@@ -47,8 +47,7 @@
             if elt.nodeName=="CrossReference" or elt.nodeName=="moby:CrossReference":
                 self.__cross__=[]
                 for ref in elt.childNodes:
-                    if ref.nodeType==ref.ELEMENT_NODE:
-                        self.__cross__.append(um.loads(ref.toxml()))
+                    self.__cross__.append(ref.toxml())
             if elt.nodeType==elt.ELEMENT_NODE and (elt.nodeName=="String" or elt.nodeName=="moby:String") and (elt.getAttribute("articleName")=="ID" or elt.getAttribute("moby:articleName")=="ID"):
                 t=MobyString()
                 t.fromMoby(elt.toxml())

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/ontology/SchematikonStructureAnnotation.py,v
retrieving revision 1.3
retrieving revision 1.4
diff -u -r1.3 -r1.4
--- /home/repository/moby/moby-live/Python/bioMoby/ontology/SchematikonStructureAnnotation.py	2005/01/27 08:44:05	1.3
+++ /home/repository/moby/moby-live/Python/bioMoby/ontology/SchematikonStructureAnnotation.py	2005/02/01 08:52:16	1.4
@@ -50,8 +50,7 @@
             if elt.nodeName=="CrossReference" or elt.nodeName=="moby:CrossReference":
                 self.__cross__=[]
                 for ref in elt.childNodes:
-                    if ref.nodeType==ref.ELEMENT_NODE:
-                        self.__cross__.append(um.loads(ref.toxml()))
+                    self.__cross__.append(ref.toxml())
             if elt.nodeType==elt.ELEMENT_NODE and (elt.nodeName=="String" or elt.nodeName=="moby:String") and (elt.getAttribute("articleName")=="PROMOTIF gamma-turn" or elt.getAttribute("moby:articleName")=="PROMOTIF gamma-turn"):
                 t=MobyString()
                 t.fromMoby(elt.toxml())

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/ontology/SchematikonVorocodeName.py,v
retrieving revision 1.3
retrieving revision 1.4
diff -u -r1.3 -r1.4
--- /home/repository/moby/moby-live/Python/bioMoby/ontology/SchematikonVorocodeName.py	2005/01/27 08:44:05	1.3
+++ /home/repository/moby/moby-live/Python/bioMoby/ontology/SchematikonVorocodeName.py	2005/02/01 08:52:16	1.4
@@ -47,8 +47,7 @@
             if elt.nodeName=="CrossReference" or elt.nodeName=="moby:CrossReference":
                 self.__cross__=[]
                 for ref in elt.childNodes:
-                    if ref.nodeType==ref.ELEMENT_NODE:
-                        self.__cross__.append(um.loads(ref.toxml()))
+                    self.__cross__.append(ref.toxml())
             if elt.nodeType==elt.ELEMENT_NODE and (elt.nodeName=="String" or elt.nodeName=="moby:String") and (elt.getAttribute("articleName")=="VorocodeName" or elt.getAttribute("moby:articleName")=="VorocodeName"):
                 t=MobyString()
                 t.fromMoby(elt.toxml())

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/ontology/Scored_acronym_string.py,v
retrieving revision 1.3
retrieving revision 1.4
diff -u -r1.3 -r1.4
--- /home/repository/moby/moby-live/Python/bioMoby/ontology/Scored_acronym_string.py	2005/01/27 08:44:05	1.3
+++ /home/repository/moby/moby-live/Python/bioMoby/ontology/Scored_acronym_string.py	2005/02/01 08:52:16	1.4
@@ -50,8 +50,7 @@
             if elt.nodeName=="CrossReference" or elt.nodeName=="moby:CrossReference":
                 self.__cross__=[]
                 for ref in elt.childNodes:
-                    if ref.nodeType==ref.ELEMENT_NODE:
-                        self.__cross__.append(um.loads(ref.toxml()))
+                    self.__cross__.append(ref.toxml())
             if elt.nodeType==elt.ELEMENT_NODE and (elt.nodeName=="Float" or elt.nodeName=="moby:Float") and (elt.getAttribute("articleName")=="score" or elt.getAttribute("moby:articleName")=="score"):
                 t=MobyFloat()
                 t.fromMoby(elt.toxml())

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/ontology/SimpleAnnotatedGIFImage.py,v
retrieving revision 1.3
retrieving revision 1.4
diff -u -r1.3 -r1.4
--- /home/repository/moby/moby-live/Python/bioMoby/ontology/SimpleAnnotatedGIFImage.py	2005/01/27 08:44:05	1.3
+++ /home/repository/moby/moby-live/Python/bioMoby/ontology/SimpleAnnotatedGIFImage.py	2005/02/01 08:52:16	1.4
@@ -48,8 +48,7 @@
             if elt.nodeName=="CrossReference" or elt.nodeName=="moby:CrossReference":
                 self.__cross__=[]
                 for ref in elt.childNodes:
-                    if ref.nodeType==ref.ELEMENT_NODE:
-                        self.__cross__.append(um.loads(ref.toxml()))
+                    self.__cross__.append(ref.toxml())
             if elt.nodeType==elt.ELEMENT_NODE and (elt.nodeName=="String" or elt.nodeName=="moby:String") and (elt.getAttribute("articleName")=="Description" or elt.getAttribute("moby:articleName")=="Description"):
                 t=MobyString()
                 t.fromMoby(elt.toxml())

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/ontology/SimpleAnnotatedJPEGImage.py,v
retrieving revision 1.3
retrieving revision 1.4
diff -u -r1.3 -r1.4
--- /home/repository/moby/moby-live/Python/bioMoby/ontology/SimpleAnnotatedJPEGImage.py	2005/01/27 08:44:05	1.3
+++ /home/repository/moby/moby-live/Python/bioMoby/ontology/SimpleAnnotatedJPEGImage.py	2005/02/01 08:52:16	1.4
@@ -49,8 +49,7 @@
             if elt.nodeName=="CrossReference" or elt.nodeName=="moby:CrossReference":
                 self.__cross__=[]
                 for ref in elt.childNodes:
-                    if ref.nodeType==ref.ELEMENT_NODE:
-                        self.__cross__.append(um.loads(ref.toxml()))
+                    self.__cross__.append(ref.toxml())
             if elt.nodeType==elt.ELEMENT_NODE and (elt.nodeName=="String" or elt.nodeName=="moby:String") and (elt.getAttribute("articleName")=="Description" or elt.getAttribute("moby:articleName")=="Description"):
                 t=MobyString()
                 t.fromMoby(elt.toxml())

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/ontology/Simple_key_value_pair.py,v
retrieving revision 1.3
retrieving revision 1.4
diff -u -r1.3 -r1.4
--- /home/repository/moby/moby-live/Python/bioMoby/ontology/Simple_key_value_pair.py	2005/01/27 08:44:05	1.3
+++ /home/repository/moby/moby-live/Python/bioMoby/ontology/Simple_key_value_pair.py	2005/02/01 08:52:16	1.4
@@ -48,8 +48,7 @@
             if elt.nodeName=="CrossReference" or elt.nodeName=="moby:CrossReference":
                 self.__cross__=[]
                 for ref in elt.childNodes:
-                    if ref.nodeType==ref.ELEMENT_NODE:
-                        self.__cross__.append(um.loads(ref.toxml()))
+                    self.__cross__.append(ref.toxml())
             if elt.nodeType==elt.ELEMENT_NODE and (elt.nodeName=="String" or elt.nodeName=="moby:String") and (elt.getAttribute("articleName")=="value" or elt.getAttribute("moby:articleName")=="value"):
                 t=MobyString()
                 t.fromMoby(elt.toxml())

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/ontology/Snp_allele.py,v
retrieving revision 1.3
retrieving revision 1.4
diff -u -r1.3 -r1.4
--- /home/repository/moby/moby-live/Python/bioMoby/ontology/Snp_allele.py	2005/01/27 08:44:05	1.3
+++ /home/repository/moby/moby-live/Python/bioMoby/ontology/Snp_allele.py	2005/02/01 08:52:16	1.4
@@ -37,8 +37,7 @@
             if elt.nodeName=="CrossReference" or elt.nodeName=="moby:CrossReference":
                 self.__cross__=[]
                 for ref in elt.childNodes:
-                    if ref.nodeType==ref.ELEMENT_NODE:
-                        self.__cross__.append(um.loads(ref.toxml()))
+                    self.__cross__.append(ref.toxml())
             if elt.nodeType==elt.ELEMENT_NODE and (elt.nodeName=="DNASequence" or elt.nodeName=="moby:DNASequence") and (elt.getAttribute("articleName")=="snp_allele" or elt.getAttribute("moby:articleName")=="snp_allele"):
                 self.Snp_allele=MobyDNASequence()
                 self.Snp_allele.fromMoby(elt.toxml())
\ No newline at end of file

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/ontology/Snp_genotype.py,v
retrieving revision 1.3
retrieving revision 1.4
diff -u -r1.3 -r1.4
--- /home/repository/moby/moby-live/Python/bioMoby/ontology/Snp_genotype.py	2005/01/27 08:44:05	1.3
+++ /home/repository/moby/moby-live/Python/bioMoby/ontology/Snp_genotype.py	2005/02/01 08:52:16	1.4
@@ -38,8 +38,7 @@
             if elt.nodeName=="CrossReference" or elt.nodeName=="moby:CrossReference":
                 self.__cross__=[]
                 for ref in elt.childNodes:
-                    if ref.nodeType==ref.ELEMENT_NODE:
-                        self.__cross__.append(um.loads(ref.toxml()))
+                    self.__cross__.append(ref.toxml())
             if elt.nodeType==elt.ELEMENT_NODE and (elt.nodeName=="snp_allele" or elt.nodeName=="moby:snp_allele") and (elt.getAttribute("articleName")=="allele1" or elt.getAttribute("moby:articleName")=="allele1"):
                 self.Allele1=MobySnp_allele()
                 self.Allele1.fromMoby(elt.toxml())

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/ontology/Study.py,v
retrieving revision 1.3
retrieving revision 1.4
diff -u -r1.3 -r1.4
--- /home/repository/moby/moby-live/Python/bioMoby/ontology/Study.py	2005/01/27 08:44:05	1.3
+++ /home/repository/moby/moby-live/Python/bioMoby/ontology/Study.py	2005/02/01 08:52:16	1.4
@@ -50,8 +50,7 @@
             if elt.nodeName=="CrossReference" or elt.nodeName=="moby:CrossReference":
                 self.__cross__=[]
                 for ref in elt.childNodes:
-                    if ref.nodeType==ref.ELEMENT_NODE:
-                        self.__cross__.append(um.loads(ref.toxml()))
+                    self.__cross__.append(ref.toxml())
             if elt.nodeType==elt.ELEMENT_NODE and (elt.nodeName=="String" or elt.nodeName=="moby:String") and (elt.getAttribute("articleName")=="study_name" or elt.getAttribute("moby:articleName")=="study_name"):
                 t=MobyString()
                 t.fromMoby(elt.toxml())

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/ontology/TEST.py,v
retrieving revision 1.3
retrieving revision 1.4
diff -u -r1.3 -r1.4
--- /home/repository/moby/moby-live/Python/bioMoby/ontology/TEST.py	2005/01/27 08:44:05	1.3
+++ /home/repository/moby/moby-live/Python/bioMoby/ontology/TEST.py	2005/02/01 08:52:16	1.4
@@ -46,5 +46,4 @@
             if elt.nodeName=="CrossReference" or elt.nodeName=="moby:CrossReference":
                 self.__cross__=[]
                 for ref in elt.childNodes:
-                    if ref.nodeType==ref.ELEMENT_NODE:
-                        self.__cross__.append(um.loads(ref.toxml()))
\ No newline at end of file
+                    self.__cross__.append(ref.toxml())
\ No newline at end of file

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/ontology/TargetP_result.py,v
retrieving revision 1.3
retrieving revision 1.4
diff -u -r1.3 -r1.4
--- /home/repository/moby/moby-live/Python/bioMoby/ontology/TargetP_result.py	2005/01/27 08:44:05	1.3
+++ /home/repository/moby/moby-live/Python/bioMoby/ontology/TargetP_result.py	2005/02/01 08:52:16	1.4
@@ -52,8 +52,7 @@
             if elt.nodeName=="CrossReference" or elt.nodeName=="moby:CrossReference":
                 self.__cross__=[]
                 for ref in elt.childNodes:
-                    if ref.nodeType==ref.ELEMENT_NODE:
-                        self.__cross__.append(um.loads(ref.toxml()))
+                    self.__cross__.append(ref.toxml())
             if elt.nodeType==elt.ELEMENT_NODE and (elt.nodeName=="Float" or elt.nodeName=="moby:Float") and (elt.getAttribute("articleName")=="o_score" or elt.getAttribute("moby:articleName")=="o_score"):
                 t=MobyFloat()
                 t.fromMoby(elt.toxml())

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/ontology/Testout.py,v
retrieving revision 1.3
retrieving revision 1.4
diff -u -r1.3 -r1.4
--- /home/repository/moby/moby-live/Python/bioMoby/ontology/Testout.py	2005/01/27 08:44:05	1.3
+++ /home/repository/moby/moby-live/Python/bioMoby/ontology/Testout.py	2005/02/01 08:52:16	1.4
@@ -51,8 +51,7 @@
             if elt.nodeName=="CrossReference" or elt.nodeName=="moby:CrossReference":
                 self.__cross__=[]
                 for ref in elt.childNodes:
-                    if ref.nodeType==ref.ELEMENT_NODE:
-                        self.__cross__.append(um.loads(ref.toxml()))
+                    self.__cross__.append(ref.toxml())
             if elt.nodeType==elt.ELEMENT_NODE and (elt.nodeName=="Integer" or elt.nodeName=="moby:Integer") and (elt.getAttribute("articleName")=="gid" or elt.getAttribute("moby:articleName")=="gid"):
                 t=MobyInteger()
                 t.fromMoby(elt.toxml())

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/ontology/TextBase64.py,v
retrieving revision 1.3
retrieving revision 1.4
diff -u -r1.3 -r1.4
--- /home/repository/moby/moby-live/Python/bioMoby/ontology/TextBase64.py	2005/01/27 08:44:05	1.3
+++ /home/repository/moby/moby-live/Python/bioMoby/ontology/TextBase64.py	2005/02/01 08:52:16	1.4
@@ -46,5 +46,4 @@
             if elt.nodeName=="CrossReference" or elt.nodeName=="moby:CrossReference":
                 self.__cross__=[]
                 for ref in elt.childNodes:
-                    if ref.nodeType==ref.ELEMENT_NODE:
-                        self.__cross__.append(um.loads(ref.toxml()))
\ No newline at end of file
+                    self.__cross__.append(ref.toxml())
\ No newline at end of file

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/ontology/TextFormatted.py,v
retrieving revision 1.3
retrieving revision 1.4
diff -u -r1.3 -r1.4
--- /home/repository/moby/moby-live/Python/bioMoby/ontology/TextFormatted.py	2005/01/27 08:44:05	1.3
+++ /home/repository/moby/moby-live/Python/bioMoby/ontology/TextFormatted.py	2005/02/01 08:52:16	1.4
@@ -46,5 +46,4 @@
             if elt.nodeName=="CrossReference" or elt.nodeName=="moby:CrossReference":
                 self.__cross__=[]
                 for ref in elt.childNodes:
-                    if ref.nodeType==ref.ELEMENT_NODE:
-                        self.__cross__.append(um.loads(ref.toxml()))
\ No newline at end of file
+                    self.__cross__.append(ref.toxml())
\ No newline at end of file

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/ontology/TextHtml.py,v
retrieving revision 1.3
retrieving revision 1.4
diff -u -r1.3 -r1.4
--- /home/repository/moby/moby-live/Python/bioMoby/ontology/TextHtml.py	2005/01/27 08:44:05	1.3
+++ /home/repository/moby/moby-live/Python/bioMoby/ontology/TextHtml.py	2005/02/01 08:52:16	1.4
@@ -46,5 +46,4 @@
             if elt.nodeName=="CrossReference" or elt.nodeName=="moby:CrossReference":
                 self.__cross__=[]
                 for ref in elt.childNodes:
-                    if ref.nodeType==ref.ELEMENT_NODE:
-                        self.__cross__.append(um.loads(ref.toxml()))
\ No newline at end of file
+                    self.__cross__.append(ref.toxml())
\ No newline at end of file

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/ontology/TextPlain.py,v
retrieving revision 1.3
retrieving revision 1.4
diff -u -r1.3 -r1.4
--- /home/repository/moby/moby-live/Python/bioMoby/ontology/TextPlain.py	2005/01/27 08:44:05	1.3
+++ /home/repository/moby/moby-live/Python/bioMoby/ontology/TextPlain.py	2005/02/01 08:52:16	1.4
@@ -46,5 +46,4 @@
             if elt.nodeName=="CrossReference" or elt.nodeName=="moby:CrossReference":
                 self.__cross__=[]
                 for ref in elt.childNodes:
-                    if ref.nodeType==ref.ELEMENT_NODE:
-                        self.__cross__.append(um.loads(ref.toxml()))
\ No newline at end of file
+                    self.__cross__.append(ref.toxml())
\ No newline at end of file

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/ontology/TextUuencoded.py,v
retrieving revision 1.3
retrieving revision 1.4
diff -u -r1.3 -r1.4
--- /home/repository/moby/moby-live/Python/bioMoby/ontology/TextUuencoded.py	2005/01/27 08:44:05	1.3
+++ /home/repository/moby/moby-live/Python/bioMoby/ontology/TextUuencoded.py	2005/02/01 08:52:16	1.4
@@ -46,5 +46,4 @@
             if elt.nodeName=="CrossReference" or elt.nodeName=="moby:CrossReference":
                 self.__cross__=[]
                 for ref in elt.childNodes:
-                    if ref.nodeType==ref.ELEMENT_NODE:
-                        self.__cross__.append(um.loads(ref.toxml()))
\ No newline at end of file
+                    self.__cross__.append(ref.toxml())
\ No newline at end of file

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/ontology/TextXml.py,v
retrieving revision 1.3
retrieving revision 1.4
diff -u -r1.3 -r1.4
--- /home/repository/moby/moby-live/Python/bioMoby/ontology/TextXml.py	2005/01/27 08:44:05	1.3
+++ /home/repository/moby/moby-live/Python/bioMoby/ontology/TextXml.py	2005/02/01 08:52:16	1.4
@@ -46,5 +46,4 @@
             if elt.nodeName=="CrossReference" or elt.nodeName=="moby:CrossReference":
                 self.__cross__=[]
                 for ref in elt.childNodes:
-                    if ref.nodeType==ref.ELEMENT_NODE:
-                        self.__cross__.append(um.loads(ref.toxml()))
\ No newline at end of file
+                    self.__cross__.append(ref.toxml())
\ No newline at end of file

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/ontology/Text_plain.py,v
retrieving revision 1.3
retrieving revision 1.4
diff -u -r1.3 -r1.4
--- /home/repository/moby/moby-live/Python/bioMoby/ontology/Text_plain.py	2005/01/27 08:44:05	1.3
+++ /home/repository/moby/moby-live/Python/bioMoby/ontology/Text_plain.py	2005/02/01 08:52:16	1.4
@@ -46,5 +46,4 @@
             if elt.nodeName=="CrossReference" or elt.nodeName=="moby:CrossReference":
                 self.__cross__=[]
                 for ref in elt.childNodes:
-                    if ref.nodeType==ref.ELEMENT_NODE:
-                        self.__cross__.append(um.loads(ref.toxml()))
\ No newline at end of file
+                    self.__cross__.append(ref.toxml())
\ No newline at end of file

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/ontology/Trait_Details.py,v
retrieving revision 1.3
retrieving revision 1.4
diff -u -r1.3 -r1.4
--- /home/repository/moby/moby-live/Python/bioMoby/ontology/Trait_Details.py	2005/01/27 08:44:05	1.3
+++ /home/repository/moby/moby-live/Python/bioMoby/ontology/Trait_Details.py	2005/02/01 08:52:16	1.4
@@ -52,8 +52,7 @@
             if elt.nodeName=="CrossReference" or elt.nodeName=="moby:CrossReference":
                 self.__cross__=[]
                 for ref in elt.childNodes:
-                    if ref.nodeType==ref.ELEMENT_NODE:
-                        self.__cross__.append(um.loads(ref.toxml()))
+                    self.__cross__.append(ref.toxml())
             if elt.nodeType==elt.ELEMENT_NODE and (elt.nodeName=="String" or elt.nodeName=="moby:String") and (elt.getAttribute("articleName")=="trait_desc" or elt.getAttribute("moby:articleName")=="trait_desc"):
                 t=MobyString()
                 t.fromMoby(elt.toxml())

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/ontology/Tree.py,v
retrieving revision 1.3
retrieving revision 1.4
diff -u -r1.3 -r1.4
--- /home/repository/moby/moby-live/Python/bioMoby/ontology/Tree.py	2005/01/27 08:44:05	1.3
+++ /home/repository/moby/moby-live/Python/bioMoby/ontology/Tree.py	2005/02/01 08:52:16	1.4
@@ -46,5 +46,4 @@
             if elt.nodeName=="CrossReference" or elt.nodeName=="moby:CrossReference":
                 self.__cross__=[]
                 for ref in elt.childNodes:
-                    if ref.nodeType==ref.ELEMENT_NODE:
-                        self.__cross__.append(um.loads(ref.toxml()))
\ No newline at end of file
+                    self.__cross__.append(ref.toxml())
\ No newline at end of file

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/ontology/TropGENE_ACCESSION.py,v
retrieving revision 1.3
retrieving revision 1.4
diff -u -r1.3 -r1.4
--- /home/repository/moby/moby-live/Python/bioMoby/ontology/TropGENE_ACCESSION.py	2005/01/27 08:44:05	1.3
+++ /home/repository/moby/moby-live/Python/bioMoby/ontology/TropGENE_ACCESSION.py	2005/02/01 08:52:16	1.4
@@ -66,8 +66,7 @@
             if elt.nodeName=="CrossReference" or elt.nodeName=="moby:CrossReference":
                 self.__cross__=[]
                 for ref in elt.childNodes:
-                    if ref.nodeType==ref.ELEMENT_NODE:
-                        self.__cross__.append(um.loads(ref.toxml()))
+                    self.__cross__.append(ref.toxml())
             if elt.nodeType==elt.ELEMENT_NODE and (elt.nodeName=="TropGENE_LOCUS" or elt.nodeName=="moby:TropGENE_LOCUS") and (elt.getAttribute("articleName")=="RFLP" or elt.getAttribute("moby:articleName")=="RFLP"):
                 self.RFLP=MobyTropGENE_LOCUS()
                 self.RFLP.fromMoby(elt.toxml())

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/ontology/TropGENE_Diversity_Matrix.py,v
retrieving revision 1.3
retrieving revision 1.4
diff -u -r1.3 -r1.4
--- /home/repository/moby/moby-live/Python/bioMoby/ontology/TropGENE_Diversity_Matrix.py	2005/01/27 08:44:05	1.3
+++ /home/repository/moby/moby-live/Python/bioMoby/ontology/TropGENE_Diversity_Matrix.py	2005/02/01 08:52:16	1.4
@@ -46,5 +46,4 @@
             if elt.nodeName=="CrossReference" or elt.nodeName=="moby:CrossReference":
                 self.__cross__=[]
                 for ref in elt.childNodes:
-                    if ref.nodeType==ref.ELEMENT_NODE:
-                        self.__cross__.append(um.loads(ref.toxml()))
\ No newline at end of file
+                    self.__cross__.append(ref.toxml())
\ No newline at end of file

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/ontology/TropGENE_LOCUS.py,v
retrieving revision 1.3
retrieving revision 1.4
diff -u -r1.3 -r1.4
--- /home/repository/moby/moby-live/Python/bioMoby/ontology/TropGENE_LOCUS.py	2005/01/27 08:44:05	1.3
+++ /home/repository/moby/moby-live/Python/bioMoby/ontology/TropGENE_LOCUS.py	2005/02/01 08:52:16	1.4
@@ -45,5 +45,4 @@
             if elt.nodeName=="CrossReference" or elt.nodeName=="moby:CrossReference":
                 self.__cross__=[]
                 for ref in elt.childNodes:
-                    if ref.nodeType==ref.ELEMENT_NODE:
-                        self.__cross__.append(um.loads(ref.toxml()))
\ No newline at end of file
+                    self.__cross__.append(ref.toxml())
\ No newline at end of file

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/ontology/VirtualSequence.py,v
retrieving revision 1.3
retrieving revision 1.4
diff -u -r1.3 -r1.4
--- /home/repository/moby/moby-live/Python/bioMoby/ontology/VirtualSequence.py	2005/01/27 08:44:05	1.3
+++ /home/repository/moby/moby-live/Python/bioMoby/ontology/VirtualSequence.py	2005/02/01 08:52:16	1.4
@@ -47,8 +47,7 @@
             if elt.nodeName=="CrossReference" or elt.nodeName=="moby:CrossReference":
                 self.__cross__=[]
                 for ref in elt.childNodes:
-                    if ref.nodeType==ref.ELEMENT_NODE:
-                        self.__cross__.append(um.loads(ref.toxml()))
+                    self.__cross__.append(ref.toxml())
             if elt.nodeType==elt.ELEMENT_NODE and (elt.nodeName=="Integer" or elt.nodeName=="moby:Integer") and (elt.getAttribute("articleName")=="Length" or elt.getAttribute("moby:articleName")=="Length"):
                 t=MobyInteger()
                 t.fromMoby(elt.toxml())

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/ontology/WU_BLAST_Text.py,v
retrieving revision 1.3
retrieving revision 1.4
diff -u -r1.3 -r1.4
--- /home/repository/moby/moby-live/Python/bioMoby/ontology/WU_BLAST_Text.py	2005/01/27 08:44:05	1.3
+++ /home/repository/moby/moby-live/Python/bioMoby/ontology/WU_BLAST_Text.py	2005/02/01 08:52:16	1.4
@@ -46,5 +46,4 @@
             if elt.nodeName=="CrossReference" or elt.nodeName=="moby:CrossReference":
                 self.__cross__=[]
                 for ref in elt.childNodes:
-                    if ref.nodeType==ref.ELEMENT_NODE:
-                        self.__cross__.append(um.loads(ref.toxml()))
\ No newline at end of file
+                    self.__cross__.append(ref.toxml())
\ No newline at end of file

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/ontology/Wildcard_Query.py,v
retrieving revision 1.3
retrieving revision 1.4
diff -u -r1.3 -r1.4
--- /home/repository/moby/moby-live/Python/bioMoby/ontology/Wildcard_Query.py	2005/01/27 08:44:05	1.3
+++ /home/repository/moby/moby-live/Python/bioMoby/ontology/Wildcard_Query.py	2005/02/01 08:52:16	1.4
@@ -50,8 +50,7 @@
             if elt.nodeName=="CrossReference" or elt.nodeName=="moby:CrossReference":
                 self.__cross__=[]
                 for ref in elt.childNodes:
-                    if ref.nodeType==ref.ELEMENT_NODE:
-                        self.__cross__.append(um.loads(ref.toxml()))
+                    self.__cross__.append(ref.toxml())
             if elt.nodeType==elt.ELEMENT_NODE and (elt.nodeName=="Integer" or elt.nodeName=="moby:Integer") and (elt.getAttribute("articleName")=="end_row" or elt.getAttribute("moby:articleName")=="end_row"):
                 t=MobyInteger()
                 t.fromMoby(elt.toxml())

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/ontology/__init__.py,v
retrieving revision 1.2
retrieving revision 1.3
diff -u -r1.2 -r1.3
--- /home/repository/moby/moby-live/Python/bioMoby/ontology/__init__.py	2005/01/18 13:46:22	1.2
+++ /home/repository/moby/moby-live/Python/bioMoby/ontology/__init__.py	2005/02/01 08:52:16	1.3
@@ -6,6 +6,7 @@
 from MO_Term_Test import MobyMO_Term_Test
 from CommentedDNASequence import MobyCommentedDNASequence
 from BasicGFFSequenceFeature import MobyBasicGFFSequenceFeature
+from MSF import MobyMSF
 from MyTestingDataType_11024145298313 import MobyMyTestingDataType_11024145298313
 from PDBFormattedText import MobyPDBFormattedText
 from Testout import MobyTestout
@@ -24,6 +25,7 @@
 from BLASTText import MobyBLASTText
 from Allele_freq import MobyAllele_freq
 from GenericSequence import MobyGenericSequence
+from Alignment import MobyAlignment
 from ICIS_Query import MobyICIS_Query
 from PHDText import MobyPHDText
 from WU_BLAST_Text import MobyWU_BLAST_Text
@@ -33,6 +35,7 @@
 from GFF3 import MobyGFF3
 from PDGJOB import MobyPDGJOB
 from CommentedAASequence import MobyCommentedAASequence
+from FASTA_NA_multi import MobyFASTA_NA_multi
 from ClustalMsfFormattedText import MobyClustalMsfFormattedText
 from Multi_key_value_pair import MobyMulti_key_value_pair
 from AlleleAssociation import MobyAlleleAssociation



From yanwong at pub.open-bio.org  Tue Feb  1 09:11:12 2005
From: yanwong at pub.open-bio.org (Yan Wong)
Date: Tue, 01 Feb 2005 14:11:12 -0000
Subject: [MOBY-guts] biomoby commit
Message-ID: <200502011420.j11EKksT014828@pub.open-bio.org>


yanwong
Tue Feb  1 09:20:44 EST 2005
Update of /home/repository/moby/moby-live/Python/bioMoby/ontology
In directory pub.open-bio.org:/tmp/cvs-serv14364/bioMoby/ontology

Modified Files:
	AlleleAssociation.py Allele_freq.py AminoAcidSequence.py 
	B64_Encoded_PNG.py B64_Encoded_Postscript.py 
	B64_encoded_PDB.py B64_encoded_gif.py B64_encoded_jpeg.py 
	BLASTText.py BasicGFFSequenceFeature.py 
	ClustalAlnFormattedText.py ClustalMsfFormattedText.py 
	CommentedAASequence.py CommentedDNASequence.py 
	CommentedRNASequence.py DNASequence.py 
	DNASequenceWithGFFFeatures.py DateTime.py Decypher_Text.py 
	Edge.py EmblFlatfile.py FASTA.py FASTA_AA.py FASTA_NA.py 
	FASTA_Text.py GFF.py GFF1.py GFF2.py GFF2_5.py GFF3.py 
	GO_Term.py GenbankFlatfile.py GenericSequence.py 
	GeneticElement.py Genotype.py Germplasm_Details.py 
	Germplasm_List.py Global_Keyword.py HBond_Pair.py 
	HFormatText.py Haplotyping_Study_obj.py ICIS_Query.py 
	ICIS_Query2.py ICIS_Query3.py IntAct_XML.py Interaction.py 
	InteractionMethod.py Interaction_partner.py Interactor.py 
	MEME_Text.py MGIS_ACCESSION.py MMP_Locus.py MO_Term_Test.py 
	MmCIFText.py Multi_key_value_pair.py 
	MyTestingDataType_11024145298313.py MyTree.py 
	NCBI_BLAST_Text.py NCBI_Blast_XML.py NCBI_Blast_XML_Gif.py 
	NCBI_Blast_XML_Gif_Map.py NCBI_MEME_Text.py 
	NucleotideSequence.py PDBFormattedText.py PDBText.py PDGJOB.py 
	PHDText.py PMUTText.py PSeaTextFormatted.py 
	PhenotypeDescription.py PubMedMEDLINE.py RNASequence.py 
	SINGER_ACCESSION.py Sample.py SchematikonMotifID.py 
	SchematikonMotifSupport.py SchematikonSegmentAttributes.py 
	SchematikonSegmentID.py SchematikonStructureAnnotation.py 
	SchematikonVorocodeName.py Scored_acronym_string.py 
	SimpleAnnotatedGIFImage.py SimpleAnnotatedJPEGImage.py 
	Simple_key_value_pair.py Snp_allele.py Snp_genotype.py 
	Study.py TEST.py TargetP_result.py Testout.py TextBase64.py 
	TextFormatted.py TextHtml.py TextPlain.py TextUuencoded.py 
	TextXml.py Text_plain.py Trait_Details.py Tree.py 
	TropGENE_ACCESSION.py TropGENE_Diversity_Matrix.py 
	TropGENE_LOCUS.py VirtualSequence.py WU_BLAST_Text.py 
	Wildcard_Query.py 
Log Message:


moby-live/Python/bioMoby/ontology AlleleAssociation.py,1.4,1.5 Allele_freq.py,1.4,1.5 AminoAcidSequence.py,1.4,1.5 B64_Encoded_PNG.py,1.4,1.5 B64_Encoded_Postscript.py,1.4,1.5 B64_encoded_PDB.py,1.4,1.5 B64_encoded_gif.py,1.4,1.5 B64_encoded_jpeg.py,1.4,1.5 BLASTText.py,1.4,1.5 BasicGFFSequenceFeature.py,1.4,1.5 ClustalAlnFormattedText.py,1.4,1.5 ClustalMsfFormattedText.py,1.4,1.5 CommentedAASequence.py,1.4,1.5 CommentedDNASequence.py,1.4,1.5 CommentedRNASequence.py,1.4,1.5 DNASequence.py,1.4,1.5 DNASequenceWithGFFFeatures.py,1.4,1.5 DateTime.py,1.4,1.5 Decypher_Text.py,1.4,1.5 Edge.py,1.4,1.5 EmblFlatfile.py,1.4,1.5 FASTA.py,1.4,1.5 FASTA_AA.py,1.4,1.5 FASTA_NA.py,1.4,1.5 FASTA_Text.py,1.4,1.5 GFF.py,1.4,1.5 GFF1.py,1.4,1.5 GFF2.py,1.4,1.5 GFF2_5.py,1.4,1.5 GFF3.py,1.4,1.5 GO_Term.py,1.4,1.5 GenbankFlatfile.py,1.4,1.5 GenericSequence.py,1.4,1.5 GeneticElement.py,1.4,1.5 Genotype.py,1.4,1.5 Germplasm_Details.py,1.4,1.5 Germplasm_List.py,1.4,1.5 Global_Keyword.py,1.4,1.5 HBon!
d_Pair.py,1.4,1.5 HFormatText.py,1.4,1.5 Haplotyping_Study_obj.py,1.4,1.5 ICIS_Query.py,1.4,1.5 ICIS_Query2.py,1.4,1.5 ICIS_Query3.py,1.4,1.5 IntAct_XML.py,1.4,1.5 Interaction.py,1.4,1.5 InteractionMethod.py,1.4,1.5 Interaction_partner.py,1.4,1.5 Interactor.py,1.4,1.5 MEME_Text.py,1.4,1.5 MGIS_ACCESSION.py,1.4,1.5 MMP_Locus.py,1.4,1.5 MO_Term_Test.py,1.4,1.5 MmCIFText.py,1.4,1.5 Multi_key_value_pair.py,1.4,1.5 MyTestingDataType_11024145298313.py,1.4,1.5 MyTree.py,1.4,1.5 NCBI_BLAST_Text.py,1.4,1.5 NCBI_Blast_XML.py,1.4,1.5 NCBI_Blast_XML_Gif.py,1.4,1.5 NCBI_Blast_XML_Gif_Map.py,1.4,1.5 NCBI_MEME_Text.py,1.4,1.5 NucleotideSequence.py,1.4,1.5 PDBFormattedText.py,1.4,1.5 PDBText.py,1.4,1.5 PDGJOB.py,1.4,1.5 PHDText.py,1.4,1.5 PMUTText.py,1.4,1.5 PSeaTextFormatted.py,1.4,1.5 PhenotypeDescription.py,1.4,1.5 PubMedMEDLINE.py,1.4,1.5 RNASequence.py,1.4,1.5 SINGER_ACCESSION.py,1.4,1.5 Sample.py,1.4,1.5 SchematikonMotifID.py,1.4,1.5 SchematikonMotifSupport.py,1.4,1.5 SchematikonSegme!
ntAttributes.py,1.4,1.5 SchematikonSegmentID.py,1.4,1.5 Schem!
atikonStructureAnnotation.py,1.4,1.5 SchematikonVorocodeName.py,1.4,1.5 Scored_acronym_string.py,1.4,1.5 SimpleAnnotatedGIFImage.py,1.4,1.5 SimpleAnnotatedJPEGImage.py,1.4,1.5 Simple_key_value_pair.py,1.4,1.5 Snp_allele.py,1.4,1.5 Snp_genotype.py,1.4,1.5 Study.py,1.4,1.5 TEST.py,1.4,1.5 TargetP_result.py,1.4,1.5 Testout.py,1.4,1.5 TextBase64.py,1.4,1.5 TextFormatted.py,1.4,1.5 TextHtml.py,1.4,1.5 TextPlain.py,1.4,1.5 TextUuencoded.py,1.4,1.5 TextXml.py,1.4,1.5 Text_plain.py,1.4,1.5 Trait_Details.py,1.4,1.5 Tree.py,1.4,1.5 TropGENE_ACCESSION.py,1.4,1.5 TropGENE_Diversity_Matrix.py,1.4,1.5 TropGENE_LOCUS.py,1.4,1.5 VirtualSequence.py,1.4,1.5 WU_BLAST_Text.py,1.4,1.5 Wildcard_Query.py,1.4,1.5
===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/ontology/AlleleAssociation.py,v
retrieving revision 1.4
retrieving revision 1.5
diff -u -r1.4 -r1.5
--- /home/repository/moby/moby-live/Python/bioMoby/ontology/AlleleAssociation.py	2005/02/01 08:52:15	1.4
+++ /home/repository/moby/moby-live/Python/bioMoby/ontology/AlleleAssociation.py	2005/02/01 14:20:44	1.5
@@ -30,7 +30,9 @@
         """ Load the attributes from an XML string
         """
         from bioMoby.mobyMarshal import MobyUnmarshaller
-        doc=parseString(value).firstChild
+        doc=value
+        if isinstance(value, str):
+            doc=parseString(value).firstChild
         um=MobyUnmarshaller()
         self.content=""
         self.namespace=doc.getAttribute("moby:namespace")
@@ -50,16 +52,16 @@
             if elt.nodeName=="CrossReference" or elt.nodeName=="moby:CrossReference":
                 self.__cross__=[]
                 for ref in elt.childNodes:
-                    self.__cross__.append(ref.toxml())
+                    self.__cross__.append(um.loads(ref))
             if elt.nodeType==elt.ELEMENT_NODE and (elt.nodeName=="String" or elt.nodeName=="moby:String") and (elt.getAttribute("articleName")=="snp" or elt.getAttribute("moby:articleName")=="snp"):
                 t=MobyString()
-                t.fromMoby(elt.toxml())
+                t.fromMoby(elt)
                 self.Snp=t.content
             if elt.nodeType==elt.ELEMENT_NODE and (elt.nodeName=="Float" or elt.nodeName=="moby:Float") and (elt.getAttribute("articleName")=="pValue" or elt.getAttribute("moby:articleName")=="pValue"):
                 t=MobyFloat()
-                t.fromMoby(elt.toxml())
+                t.fromMoby(elt)
                 self.PValue=t.content
             if elt.nodeType==elt.ELEMENT_NODE and (elt.nodeName=="String" or elt.nodeName=="moby:String") and (elt.getAttribute("articleName")=="validity" or elt.getAttribute("moby:articleName")=="validity"):
                 t=MobyString()
-                t.fromMoby(elt.toxml())
+                t.fromMoby(elt)
                 self.Validity=t.content
\ No newline at end of file

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/ontology/Allele_freq.py,v
retrieving revision 1.4
retrieving revision 1.5
diff -u -r1.4 -r1.5
--- /home/repository/moby/moby-live/Python/bioMoby/ontology/Allele_freq.py	2005/02/01 08:52:15	1.4
+++ /home/repository/moby/moby-live/Python/bioMoby/ontology/Allele_freq.py	2005/02/01 14:20:44	1.5
@@ -28,7 +28,9 @@
         """ Load the attributes from an XML string
         """
         from bioMoby.mobyMarshal import MobyUnmarshaller
-        doc=parseString(value).firstChild
+        doc=value
+        if isinstance(value, str):
+            doc=parseString(value).firstChild
         um=MobyUnmarshaller()
         self.content=""
 
@@ -44,17 +46,17 @@
             if elt.nodeName=="CrossReference" or elt.nodeName=="moby:CrossReference":
                 self.__cross__=[]
                 for ref in elt.childNodes:
-                    self.__cross__.append(ref.toxml())
+                    self.__cross__.append(um.loads(ref))
             if elt.nodeType==elt.ELEMENT_NODE and (elt.nodeName=="Object" or elt.nodeName=="moby:Object") and (elt.getAttribute("articleName")=="panel_lsid" or elt.getAttribute("moby:articleName")=="panel_lsid"):
                 self.Panel_lsid=MobyObject()
-                self.Panel_lsid.fromMoby(elt.toxml())
+                self.Panel_lsid.fromMoby(elt)
             if elt.nodeType==elt.ELEMENT_NODE and (elt.nodeName=="Object" or elt.nodeName=="moby:Object") and (elt.getAttribute("articleName")=="snp_lsid" or elt.getAttribute("moby:articleName")=="snp_lsid"):
                 self.Snp_lsid=MobyObject()
-                self.Snp_lsid.fromMoby(elt.toxml())
+                self.Snp_lsid.fromMoby(elt)
             if elt.nodeType==elt.ELEMENT_NODE and (elt.nodeName=="snp_allele" or elt.nodeName=="moby:snp_allele") and (elt.getAttribute("articleName")=="allele_freq" or elt.getAttribute("moby:articleName")=="allele_freq"):
                 self.Allele_freq=MobySnp_allele()
-                self.Allele_freq.fromMoby(elt.toxml())
+                self.Allele_freq.fromMoby(elt)
             if elt.nodeType==elt.ELEMENT_NODE and (elt.nodeName=="Integer" or elt.nodeName=="moby:Integer") and (elt.getAttribute("articleName")=="frequency" or elt.getAttribute("moby:articleName")=="frequency"):
                 t=MobyInteger()
-                t.fromMoby(elt.toxml())
+                t.fromMoby(elt)
                 self.Frequency.append(t.content)
\ No newline at end of file

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/ontology/AminoAcidSequence.py,v
retrieving revision 1.4
retrieving revision 1.5
diff -u -r1.4 -r1.5
--- /home/repository/moby/moby-live/Python/bioMoby/ontology/AminoAcidSequence.py	2005/02/01 08:52:15	1.4
+++ /home/repository/moby/moby-live/Python/bioMoby/ontology/AminoAcidSequence.py	2005/02/01 14:20:44	1.5
@@ -29,7 +29,9 @@
         """ Load the attributes from an XML string
         """
         from bioMoby.mobyMarshal import MobyUnmarshaller
-        doc=parseString(value).firstChild
+        doc=value
+        if isinstance(value, str):
+            doc=parseString(value).firstChild
         um=MobyUnmarshaller()
         self.content=""
         self.namespace=doc.getAttribute("moby:namespace")
@@ -49,12 +51,12 @@
             if elt.nodeName=="CrossReference" or elt.nodeName=="moby:CrossReference":
                 self.__cross__=[]
                 for ref in elt.childNodes:
-                    self.__cross__.append(ref.toxml())
+                    self.__cross__.append(um.loads(ref))
             if elt.nodeType==elt.ELEMENT_NODE and (elt.nodeName=="Integer" or elt.nodeName=="moby:Integer") and (elt.getAttribute("articleName")=="Length" or elt.getAttribute("moby:articleName")=="Length"):
                 t=MobyInteger()
-                t.fromMoby(elt.toxml())
+                t.fromMoby(elt)
                 self.Length=t.content
             if elt.nodeType==elt.ELEMENT_NODE and (elt.nodeName=="String" or elt.nodeName=="moby:String") and (elt.getAttribute("articleName")=="SequenceString" or elt.getAttribute("moby:articleName")=="SequenceString"):
                 t=MobyString()
-                t.fromMoby(elt.toxml())
+                t.fromMoby(elt)
                 self.SequenceString=t.content
\ No newline at end of file

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/ontology/B64_Encoded_PNG.py,v
retrieving revision 1.4
retrieving revision 1.5
diff -u -r1.4 -r1.5
--- /home/repository/moby/moby-live/Python/bioMoby/ontology/B64_Encoded_PNG.py	2005/02/01 08:52:15	1.4
+++ /home/repository/moby/moby-live/Python/bioMoby/ontology/B64_Encoded_PNG.py	2005/02/01 14:20:44	1.5
@@ -26,7 +26,9 @@
         """ Load the attributes from an XML string
         """
         from bioMoby.mobyMarshal import MobyUnmarshaller
-        doc=parseString(value).firstChild
+        doc=value
+        if isinstance(value, str):
+            doc=parseString(value).firstChild
         um=MobyUnmarshaller()
         self.content=""
         self.namespace=doc.getAttribute("moby:namespace")
@@ -46,4 +48,4 @@
             if elt.nodeName=="CrossReference" or elt.nodeName=="moby:CrossReference":
                 self.__cross__=[]
                 for ref in elt.childNodes:
-                    self.__cross__.append(ref.toxml())
\ No newline at end of file
+                    self.__cross__.append(um.loads(ref))
\ No newline at end of file

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/ontology/B64_Encoded_Postscript.py,v
retrieving revision 1.4
retrieving revision 1.5
diff -u -r1.4 -r1.5
--- /home/repository/moby/moby-live/Python/bioMoby/ontology/B64_Encoded_Postscript.py	2005/02/01 08:52:15	1.4
+++ /home/repository/moby/moby-live/Python/bioMoby/ontology/B64_Encoded_Postscript.py	2005/02/01 14:20:44	1.5
@@ -26,7 +26,9 @@
         """ Load the attributes from an XML string
         """
         from bioMoby.mobyMarshal import MobyUnmarshaller
-        doc=parseString(value).firstChild
+        doc=value
+        if isinstance(value, str):
+            doc=parseString(value).firstChild
         um=MobyUnmarshaller()
         self.content=""
         self.namespace=doc.getAttribute("moby:namespace")
@@ -46,4 +48,4 @@
             if elt.nodeName=="CrossReference" or elt.nodeName=="moby:CrossReference":
                 self.__cross__=[]
                 for ref in elt.childNodes:
-                    self.__cross__.append(ref.toxml())
\ No newline at end of file
+                    self.__cross__.append(um.loads(ref))
\ No newline at end of file

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/ontology/B64_encoded_PDB.py,v
retrieving revision 1.4
retrieving revision 1.5
diff -u -r1.4 -r1.5
--- /home/repository/moby/moby-live/Python/bioMoby/ontology/B64_encoded_PDB.py	2005/02/01 08:52:15	1.4
+++ /home/repository/moby/moby-live/Python/bioMoby/ontology/B64_encoded_PDB.py	2005/02/01 14:20:44	1.5
@@ -26,7 +26,9 @@
         """ Load the attributes from an XML string
         """
         from bioMoby.mobyMarshal import MobyUnmarshaller
-        doc=parseString(value).firstChild
+        doc=value
+        if isinstance(value, str):
+            doc=parseString(value).firstChild
         um=MobyUnmarshaller()
         self.content=""
         self.namespace=doc.getAttribute("moby:namespace")
@@ -46,4 +48,4 @@
             if elt.nodeName=="CrossReference" or elt.nodeName=="moby:CrossReference":
                 self.__cross__=[]
                 for ref in elt.childNodes:
-                    self.__cross__.append(ref.toxml())
\ No newline at end of file
+                    self.__cross__.append(um.loads(ref))
\ No newline at end of file

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/ontology/B64_encoded_gif.py,v
retrieving revision 1.4
retrieving revision 1.5
diff -u -r1.4 -r1.5
--- /home/repository/moby/moby-live/Python/bioMoby/ontology/B64_encoded_gif.py	2005/02/01 08:52:15	1.4
+++ /home/repository/moby/moby-live/Python/bioMoby/ontology/B64_encoded_gif.py	2005/02/01 14:20:44	1.5
@@ -26,7 +26,9 @@
         """ Load the attributes from an XML string
         """
         from bioMoby.mobyMarshal import MobyUnmarshaller
-        doc=parseString(value).firstChild
+        doc=value
+        if isinstance(value, str):
+            doc=parseString(value).firstChild
         um=MobyUnmarshaller()
         self.content=""
         self.namespace=doc.getAttribute("moby:namespace")
@@ -46,4 +48,4 @@
             if elt.nodeName=="CrossReference" or elt.nodeName=="moby:CrossReference":
                 self.__cross__=[]
                 for ref in elt.childNodes:
-                    self.__cross__.append(ref.toxml())
\ No newline at end of file
+                    self.__cross__.append(um.loads(ref))
\ No newline at end of file

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/ontology/B64_encoded_jpeg.py,v
retrieving revision 1.4
retrieving revision 1.5
diff -u -r1.4 -r1.5
--- /home/repository/moby/moby-live/Python/bioMoby/ontology/B64_encoded_jpeg.py	2005/02/01 08:52:15	1.4
+++ /home/repository/moby/moby-live/Python/bioMoby/ontology/B64_encoded_jpeg.py	2005/02/01 14:20:44	1.5
@@ -26,7 +26,9 @@
         """ Load the attributes from an XML string
         """
         from bioMoby.mobyMarshal import MobyUnmarshaller
-        doc=parseString(value).firstChild
+        doc=value
+        if isinstance(value, str):
+            doc=parseString(value).firstChild
         um=MobyUnmarshaller()
         self.content=""
         self.namespace=doc.getAttribute("moby:namespace")
@@ -46,4 +48,4 @@
             if elt.nodeName=="CrossReference" or elt.nodeName=="moby:CrossReference":
                 self.__cross__=[]
                 for ref in elt.childNodes:
-                    self.__cross__.append(ref.toxml())
\ No newline at end of file
+                    self.__cross__.append(um.loads(ref))
\ No newline at end of file

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/ontology/BLASTText.py,v
retrieving revision 1.4
retrieving revision 1.5
diff -u -r1.4 -r1.5
--- /home/repository/moby/moby-live/Python/bioMoby/ontology/BLASTText.py	2005/02/01 08:52:15	1.4
+++ /home/repository/moby/moby-live/Python/bioMoby/ontology/BLASTText.py	2005/02/01 14:20:44	1.5
@@ -26,7 +26,9 @@
         """ Load the attributes from an XML string
         """
         from bioMoby.mobyMarshal import MobyUnmarshaller
-        doc=parseString(value).firstChild
+        doc=value
+        if isinstance(value, str):
+            doc=parseString(value).firstChild
         um=MobyUnmarshaller()
         self.content=""
         self.namespace=doc.getAttribute("moby:namespace")
@@ -46,4 +48,4 @@
             if elt.nodeName=="CrossReference" or elt.nodeName=="moby:CrossReference":
                 self.__cross__=[]
                 for ref in elt.childNodes:
-                    self.__cross__.append(ref.toxml())
\ No newline at end of file
+                    self.__cross__.append(um.loads(ref))
\ No newline at end of file

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/ontology/BasicGFFSequenceFeature.py,v
retrieving revision 1.4
retrieving revision 1.5
diff -u -r1.4 -r1.5
--- /home/repository/moby/moby-live/Python/bioMoby/ontology/BasicGFFSequenceFeature.py	2005/02/01 08:52:15	1.4
+++ /home/repository/moby/moby-live/Python/bioMoby/ontology/BasicGFFSequenceFeature.py	2005/02/01 14:20:44	1.5
@@ -39,7 +39,9 @@
         """ Load the attributes from an XML string
         """
         from bioMoby.mobyMarshal import MobyUnmarshaller
-        doc=parseString(value).firstChild
+        doc=value
+        if isinstance(value, str):
+            doc=parseString(value).firstChild
         um=MobyUnmarshaller()
         self.content=""
         self.namespace=doc.getAttribute("moby:namespace")
@@ -60,43 +62,43 @@
             if elt.nodeName=="CrossReference" or elt.nodeName=="moby:CrossReference":
                 self.__cross__=[]
                 for ref in elt.childNodes:
-                    self.__cross__.append(ref.toxml())
+                    self.__cross__.append(um.loads(ref))
             if elt.nodeType==elt.ELEMENT_NODE and (elt.nodeName=="String" or elt.nodeName=="moby:String") and (elt.getAttribute("articleName")=="reference" or elt.getAttribute("moby:articleName")=="reference"):
                 t=MobyString()
-                t.fromMoby(elt.toxml())
+                t.fromMoby(elt)
                 self.Reference=t.content
             if elt.nodeType==elt.ELEMENT_NODE and (elt.nodeName=="String" or elt.nodeName=="moby:String") and (elt.getAttribute("articleName")=="source" or elt.getAttribute("moby:articleName")=="source"):
                 t=MobyString()
-                t.fromMoby(elt.toxml())
+                t.fromMoby(elt)
                 self.Source=t.content
             if elt.nodeType==elt.ELEMENT_NODE and (elt.nodeName=="String" or elt.nodeName=="moby:String") and (elt.getAttribute("articleName")=="method" or elt.getAttribute("moby:articleName")=="method"):
                 t=MobyString()
-                t.fromMoby(elt.toxml())
+                t.fromMoby(elt)
                 self.Method=t.content
             if elt.nodeType==elt.ELEMENT_NODE and (elt.nodeName=="Integer" or elt.nodeName=="moby:Integer") and (elt.getAttribute("articleName")=="start" or elt.getAttribute("moby:articleName")=="start"):
                 t=MobyInteger()
-                t.fromMoby(elt.toxml())
+                t.fromMoby(elt)
                 self.Start=t.content
             if elt.nodeType==elt.ELEMENT_NODE and (elt.nodeName=="Integer" or elt.nodeName=="moby:Integer") and (elt.getAttribute("articleName")=="stop" or elt.getAttribute("moby:articleName")=="stop"):
                 t=MobyInteger()
-                t.fromMoby(elt.toxml())
+                t.fromMoby(elt)
                 self.Stop=t.content
             if elt.nodeType==elt.ELEMENT_NODE and (elt.nodeName=="Float" or elt.nodeName=="moby:Float") and (elt.getAttribute("articleName")=="score" or elt.getAttribute("moby:articleName")=="score"):
                 t=MobyFloat()
-                t.fromMoby(elt.toxml())
+                t.fromMoby(elt)
                 self.Score=t.content
             if elt.nodeType==elt.ELEMENT_NODE and (elt.nodeName=="String" or elt.nodeName=="moby:String") and (elt.getAttribute("articleName")=="strand" or elt.getAttribute("moby:articleName")=="strand"):
                 t=MobyString()
-                t.fromMoby(elt.toxml())
+                t.fromMoby(elt)
                 self.Strand=t.content
             if elt.nodeType==elt.ELEMENT_NODE and (elt.nodeName=="String" or elt.nodeName=="moby:String") and (elt.getAttribute("articleName")=="frame" or elt.getAttribute("moby:articleName")=="frame"):
                 t=MobyString()
-                t.fromMoby(elt.toxml())
+                t.fromMoby(elt)
                 self.Frame=t.content
             if elt.nodeType==elt.ELEMENT_NODE and (elt.nodeName=="String" or elt.nodeName=="moby:String") and (elt.getAttribute("articleName")=="phase" or elt.getAttribute("moby:articleName")=="phase"):
                 t=MobyString()
-                t.fromMoby(elt.toxml())
+                t.fromMoby(elt)
                 self.Phase=t.content
             if elt.nodeType==elt.ELEMENT_NODE and (elt.nodeName=="multi_key_value_pair" or elt.nodeName=="moby:multi_key_value_pair") and (elt.getAttribute("articleName")=="column9_tag_value" or elt.getAttribute("moby:articleName")=="column9_tag_value"):
                 self.Column9_tag_value=MobyMulti_key_value_pair()
-                self.Column9_tag_value.fromMoby(elt.toxml())
\ No newline at end of file
+                self.Column9_tag_value.fromMoby(elt)
\ No newline at end of file

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/ontology/ClustalAlnFormattedText.py,v
retrieving revision 1.4
retrieving revision 1.5
diff -u -r1.4 -r1.5
--- /home/repository/moby/moby-live/Python/bioMoby/ontology/ClustalAlnFormattedText.py	2005/02/01 08:52:15	1.4
+++ /home/repository/moby/moby-live/Python/bioMoby/ontology/ClustalAlnFormattedText.py	2005/02/01 14:20:44	1.5
@@ -26,7 +26,9 @@
         """ Load the attributes from an XML string
         """
         from bioMoby.mobyMarshal import MobyUnmarshaller
-        doc=parseString(value).firstChild
+        doc=value
+        if isinstance(value, str):
+            doc=parseString(value).firstChild
         um=MobyUnmarshaller()
         self.content=""
         self.namespace=doc.getAttribute("moby:namespace")
@@ -46,4 +48,4 @@
             if elt.nodeName=="CrossReference" or elt.nodeName=="moby:CrossReference":
                 self.__cross__=[]
                 for ref in elt.childNodes:
-                    self.__cross__.append(ref.toxml())
\ No newline at end of file
+                    self.__cross__.append(um.loads(ref))
\ No newline at end of file

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/ontology/ClustalMsfFormattedText.py,v
retrieving revision 1.4
retrieving revision 1.5
diff -u -r1.4 -r1.5
--- /home/repository/moby/moby-live/Python/bioMoby/ontology/ClustalMsfFormattedText.py	2005/02/01 08:52:15	1.4
+++ /home/repository/moby/moby-live/Python/bioMoby/ontology/ClustalMsfFormattedText.py	2005/02/01 14:20:44	1.5
@@ -26,7 +26,9 @@
         """ Load the attributes from an XML string
         """
         from bioMoby.mobyMarshal import MobyUnmarshaller
-        doc=parseString(value).firstChild
+        doc=value
+        if isinstance(value, str):
+            doc=parseString(value).firstChild
         um=MobyUnmarshaller()
         self.content=""
         self.namespace=doc.getAttribute("moby:namespace")
@@ -46,4 +48,4 @@
             if elt.nodeName=="CrossReference" or elt.nodeName=="moby:CrossReference":
                 self.__cross__=[]
                 for ref in elt.childNodes:
-                    self.__cross__.append(ref.toxml())
\ No newline at end of file
+                    self.__cross__.append(um.loads(ref))
\ No newline at end of file

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/ontology/CommentedAASequence.py,v
retrieving revision 1.4
retrieving revision 1.5
diff -u -r1.4 -r1.5
--- /home/repository/moby/moby-live/Python/bioMoby/ontology/CommentedAASequence.py	2005/02/01 08:52:15	1.4
+++ /home/repository/moby/moby-live/Python/bioMoby/ontology/CommentedAASequence.py	2005/02/01 14:20:44	1.5
@@ -30,7 +30,9 @@
         """ Load the attributes from an XML string
         """
         from bioMoby.mobyMarshal import MobyUnmarshaller
-        doc=parseString(value).firstChild
+        doc=value
+        if isinstance(value, str):
+            doc=parseString(value).firstChild
         um=MobyUnmarshaller()
         self.content=""
         self.namespace=doc.getAttribute("moby:namespace")
@@ -50,16 +52,16 @@
             if elt.nodeName=="CrossReference" or elt.nodeName=="moby:CrossReference":
                 self.__cross__=[]
                 for ref in elt.childNodes:
-                    self.__cross__.append(ref.toxml())
+                    self.__cross__.append(um.loads(ref))
             if elt.nodeType==elt.ELEMENT_NODE and (elt.nodeName=="Integer" or elt.nodeName=="moby:Integer") and (elt.getAttribute("articleName")=="Length" or elt.getAttribute("moby:articleName")=="Length"):
                 t=MobyInteger()
-                t.fromMoby(elt.toxml())
+                t.fromMoby(elt)
                 self.Length=t.content
             if elt.nodeType==elt.ELEMENT_NODE and (elt.nodeName=="String" or elt.nodeName=="moby:String") and (elt.getAttribute("articleName")=="SequenceString" or elt.getAttribute("moby:articleName")=="SequenceString"):
                 t=MobyString()
-                t.fromMoby(elt.toxml())
+                t.fromMoby(elt)
                 self.SequenceString=t.content
             if elt.nodeType==elt.ELEMENT_NODE and (elt.nodeName=="String" or elt.nodeName=="moby:String") and (elt.getAttribute("articleName")=="Description" or elt.getAttribute("moby:articleName")=="Description"):
                 t=MobyString()
-                t.fromMoby(elt.toxml())
+                t.fromMoby(elt)
                 self.Description=t.content
\ No newline at end of file

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/ontology/CommentedDNASequence.py,v
retrieving revision 1.4
retrieving revision 1.5
diff -u -r1.4 -r1.5
--- /home/repository/moby/moby-live/Python/bioMoby/ontology/CommentedDNASequence.py	2005/02/01 08:52:15	1.4
+++ /home/repository/moby/moby-live/Python/bioMoby/ontology/CommentedDNASequence.py	2005/02/01 14:20:44	1.5
@@ -30,7 +30,9 @@
         """ Load the attributes from an XML string
         """
         from bioMoby.mobyMarshal import MobyUnmarshaller
-        doc=parseString(value).firstChild
+        doc=value
+        if isinstance(value, str):
+            doc=parseString(value).firstChild
         um=MobyUnmarshaller()
         self.content=""
         self.namespace=doc.getAttribute("moby:namespace")
@@ -50,16 +52,16 @@
             if elt.nodeName=="CrossReference" or elt.nodeName=="moby:CrossReference":
                 self.__cross__=[]
                 for ref in elt.childNodes:
-                    self.__cross__.append(ref.toxml())
+                    self.__cross__.append(um.loads(ref))
             if elt.nodeType==elt.ELEMENT_NODE and (elt.nodeName=="Integer" or elt.nodeName=="moby:Integer") and (elt.getAttribute("articleName")=="Length" or elt.getAttribute("moby:articleName")=="Length"):
                 t=MobyInteger()
-                t.fromMoby(elt.toxml())
+                t.fromMoby(elt)
                 self.Length=t.content
             if elt.nodeType==elt.ELEMENT_NODE and (elt.nodeName=="String" or elt.nodeName=="moby:String") and (elt.getAttribute("articleName")=="SequenceString" or elt.getAttribute("moby:articleName")=="SequenceString"):
                 t=MobyString()
-                t.fromMoby(elt.toxml())
+                t.fromMoby(elt)
                 self.SequenceString=t.content
             if elt.nodeType==elt.ELEMENT_NODE and (elt.nodeName=="String" or elt.nodeName=="moby:String") and (elt.getAttribute("articleName")=="Description" or elt.getAttribute("moby:articleName")=="Description"):
                 t=MobyString()
-                t.fromMoby(elt.toxml())
+                t.fromMoby(elt)
                 self.Description=t.content
\ No newline at end of file

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/ontology/CommentedRNASequence.py,v
retrieving revision 1.4
retrieving revision 1.5
diff -u -r1.4 -r1.5
--- /home/repository/moby/moby-live/Python/bioMoby/ontology/CommentedRNASequence.py	2005/02/01 08:52:15	1.4
+++ /home/repository/moby/moby-live/Python/bioMoby/ontology/CommentedRNASequence.py	2005/02/01 14:20:44	1.5
@@ -30,7 +30,9 @@
         """ Load the attributes from an XML string
         """
         from bioMoby.mobyMarshal import MobyUnmarshaller
-        doc=parseString(value).firstChild
+        doc=value
+        if isinstance(value, str):
+            doc=parseString(value).firstChild
         um=MobyUnmarshaller()
         self.content=""
         self.namespace=doc.getAttribute("moby:namespace")
@@ -50,16 +52,16 @@
             if elt.nodeName=="CrossReference" or elt.nodeName=="moby:CrossReference":
                 self.__cross__=[]
                 for ref in elt.childNodes:
-                    self.__cross__.append(ref.toxml())
+                    self.__cross__.append(um.loads(ref))
             if elt.nodeType==elt.ELEMENT_NODE and (elt.nodeName=="Integer" or elt.nodeName=="moby:Integer") and (elt.getAttribute("articleName")=="Length" or elt.getAttribute("moby:articleName")=="Length"):
                 t=MobyInteger()
-                t.fromMoby(elt.toxml())
+                t.fromMoby(elt)
                 self.Length=t.content
             if elt.nodeType==elt.ELEMENT_NODE and (elt.nodeName=="String" or elt.nodeName=="moby:String") and (elt.getAttribute("articleName")=="SequenceString" or elt.getAttribute("moby:articleName")=="SequenceString"):
                 t=MobyString()
-                t.fromMoby(elt.toxml())
+                t.fromMoby(elt)
                 self.SequenceString=t.content
             if elt.nodeType==elt.ELEMENT_NODE and (elt.nodeName=="String" or elt.nodeName=="moby:String") and (elt.getAttribute("articleName")=="Description" or elt.getAttribute("moby:articleName")=="Description"):
                 t=MobyString()
-                t.fromMoby(elt.toxml())
+                t.fromMoby(elt)
                 self.Description=t.content
\ No newline at end of file

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/ontology/DNASequence.py,v
retrieving revision 1.4
retrieving revision 1.5
diff -u -r1.4 -r1.5
--- /home/repository/moby/moby-live/Python/bioMoby/ontology/DNASequence.py	2005/02/01 08:52:15	1.4
+++ /home/repository/moby/moby-live/Python/bioMoby/ontology/DNASequence.py	2005/02/01 14:20:44	1.5
@@ -29,7 +29,9 @@
         """ Load the attributes from an XML string
         """
         from bioMoby.mobyMarshal import MobyUnmarshaller
-        doc=parseString(value).firstChild
+        doc=value
+        if isinstance(value, str):
+            doc=parseString(value).firstChild
         um=MobyUnmarshaller()
         self.content=""
         self.namespace=doc.getAttribute("moby:namespace")
@@ -49,12 +51,12 @@
             if elt.nodeName=="CrossReference" or elt.nodeName=="moby:CrossReference":
                 self.__cross__=[]
                 for ref in elt.childNodes:
-                    self.__cross__.append(ref.toxml())
+                    self.__cross__.append(um.loads(ref))
             if elt.nodeType==elt.ELEMENT_NODE and (elt.nodeName=="Integer" or elt.nodeName=="moby:Integer") and (elt.getAttribute("articleName")=="Length" or elt.getAttribute("moby:articleName")=="Length"):
                 t=MobyInteger()
-                t.fromMoby(elt.toxml())
+                t.fromMoby(elt)
                 self.Length=t.content
             if elt.nodeType==elt.ELEMENT_NODE and (elt.nodeName=="String" or elt.nodeName=="moby:String") and (elt.getAttribute("articleName")=="SequenceString" or elt.getAttribute("moby:articleName")=="SequenceString"):
                 t=MobyString()
-                t.fromMoby(elt.toxml())
+                t.fromMoby(elt)
                 self.SequenceString=t.content
\ No newline at end of file

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/ontology/DNASequenceWithGFFFeatures.py,v
retrieving revision 1.4
retrieving revision 1.5
diff -u -r1.4 -r1.5
--- /home/repository/moby/moby-live/Python/bioMoby/ontology/DNASequenceWithGFFFeatures.py	2005/02/01 08:52:15	1.4
+++ /home/repository/moby/moby-live/Python/bioMoby/ontology/DNASequenceWithGFFFeatures.py	2005/02/01 14:20:44	1.5
@@ -31,7 +31,9 @@
         """ Load the attributes from an XML string
         """
         from bioMoby.mobyMarshal import MobyUnmarshaller
-        doc=parseString(value).firstChild
+        doc=value
+        if isinstance(value, str):
+            doc=parseString(value).firstChild
         um=MobyUnmarshaller()
         self.content=""
         self.namespace=doc.getAttribute("moby:namespace")
@@ -52,15 +54,15 @@
             if elt.nodeName=="CrossReference" or elt.nodeName=="moby:CrossReference":
                 self.__cross__=[]
                 for ref in elt.childNodes:
-                    self.__cross__.append(ref.toxml())
+                    self.__cross__.append(um.loads(ref))
             if elt.nodeType==elt.ELEMENT_NODE and (elt.nodeName=="Integer" or elt.nodeName=="moby:Integer") and (elt.getAttribute("articleName")=="Length" or elt.getAttribute("moby:articleName")=="Length"):
                 t=MobyInteger()
-                t.fromMoby(elt.toxml())
+                t.fromMoby(elt)
                 self.Length=t.content
             if elt.nodeType==elt.ELEMENT_NODE and (elt.nodeName=="String" or elt.nodeName=="moby:String") and (elt.getAttribute("articleName")=="SequenceString" or elt.getAttribute("moby:articleName")=="SequenceString"):
                 t=MobyString()
-                t.fromMoby(elt.toxml())
+                t.fromMoby(elt)
                 self.SequenceString=t.content
             if elt.nodeType==elt.ELEMENT_NODE and (elt.nodeName=="BasicGFFSequenceFeature" or elt.nodeName=="moby:BasicGFFSequenceFeature") and (elt.getAttribute("articleName")=="DNASequenceWithGFFFeatures" or elt.getAttribute("moby:articleName")=="DNASequenceWithGFFFeatures"):
                 self.DNASequenceWithGFFFeatures=MobyBasicGFFSequenceFeature()
-                self.DNASequenceWithGFFFeatures.fromMoby(elt.toxml())
\ No newline at end of file
+                self.DNASequenceWithGFFFeatures.fromMoby(elt)
\ No newline at end of file

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/ontology/DateTime.py,v
retrieving revision 1.4
retrieving revision 1.5
diff -u -r1.4 -r1.5
--- /home/repository/moby/moby-live/Python/bioMoby/ontology/DateTime.py	2005/02/01 08:52:15	1.4
+++ /home/repository/moby/moby-live/Python/bioMoby/ontology/DateTime.py	2005/02/01 14:20:44	1.5
@@ -26,7 +26,9 @@
         """ Load the attributes from an XML string
         """
         from bioMoby.mobyMarshal import MobyUnmarshaller
-        doc=parseString(value).firstChild
+        doc=value
+        if isinstance(value, str):
+            doc=parseString(value).firstChild
         um=MobyUnmarshaller()
         self.content=""
         self.namespace=doc.getAttribute("moby:namespace")
@@ -46,4 +48,4 @@
             if elt.nodeName=="CrossReference" or elt.nodeName=="moby:CrossReference":
                 self.__cross__=[]
                 for ref in elt.childNodes:
-                    self.__cross__.append(ref.toxml())
\ No newline at end of file
+                    self.__cross__.append(um.loads(ref))
\ No newline at end of file

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/ontology/Decypher_Text.py,v
retrieving revision 1.4
retrieving revision 1.5
diff -u -r1.4 -r1.5
--- /home/repository/moby/moby-live/Python/bioMoby/ontology/Decypher_Text.py	2005/02/01 08:52:15	1.4
+++ /home/repository/moby/moby-live/Python/bioMoby/ontology/Decypher_Text.py	2005/02/01 14:20:44	1.5
@@ -26,7 +26,9 @@
         """ Load the attributes from an XML string
         """
         from bioMoby.mobyMarshal import MobyUnmarshaller
-        doc=parseString(value).firstChild
+        doc=value
+        if isinstance(value, str):
+            doc=parseString(value).firstChild
         um=MobyUnmarshaller()
         self.content=""
         self.namespace=doc.getAttribute("moby:namespace")
@@ -46,4 +48,4 @@
             if elt.nodeName=="CrossReference" or elt.nodeName=="moby:CrossReference":
                 self.__cross__=[]
                 for ref in elt.childNodes:
-                    self.__cross__.append(ref.toxml())
\ No newline at end of file
+                    self.__cross__.append(um.loads(ref))
\ No newline at end of file

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/ontology/Edge.py,v
retrieving revision 1.4
retrieving revision 1.5
diff -u -r1.4 -r1.5
--- /home/repository/moby/moby-live/Python/bioMoby/ontology/Edge.py	2005/02/01 08:52:15	1.4
+++ /home/repository/moby/moby-live/Python/bioMoby/ontology/Edge.py	2005/02/01 14:20:44	1.5
@@ -29,7 +29,9 @@
         """ Load the attributes from an XML string
         """
         from bioMoby.mobyMarshal import MobyUnmarshaller
-        doc=parseString(value).firstChild
+        doc=value
+        if isinstance(value, str):
+            doc=parseString(value).firstChild
         um=MobyUnmarshaller()
         self.content=""
         self.namespace=doc.getAttribute("moby:namespace")
@@ -49,12 +51,12 @@
             if elt.nodeName=="CrossReference" or elt.nodeName=="moby:CrossReference":
                 self.__cross__=[]
                 for ref in elt.childNodes:
-                    self.__cross__.append(ref.toxml())
+                    self.__cross__.append(um.loads(ref))
             if elt.nodeType==elt.ELEMENT_NODE and (elt.nodeName=="String" or elt.nodeName=="moby:String") and (elt.getAttribute("articleName")=="partner" or elt.getAttribute("moby:articleName")=="partner"):
                 t=MobyString()
-                t.fromMoby(elt.toxml())
+                t.fromMoby(elt)
                 self.Partner=t.content
             if elt.nodeType==elt.ELEMENT_NODE and (elt.nodeName=="Integer" or elt.nodeName=="moby:Integer") and (elt.getAttribute("articleName")=="direction" or elt.getAttribute("moby:articleName")=="direction"):
                 t=MobyInteger()
-                t.fromMoby(elt.toxml())
+                t.fromMoby(elt)
                 self.Direction=t.content
\ No newline at end of file

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/ontology/EmblFlatfile.py,v
retrieving revision 1.4
retrieving revision 1.5
diff -u -r1.4 -r1.5
--- /home/repository/moby/moby-live/Python/bioMoby/ontology/EmblFlatfile.py	2005/02/01 08:52:15	1.4
+++ /home/repository/moby/moby-live/Python/bioMoby/ontology/EmblFlatfile.py	2005/02/01 14:20:44	1.5
@@ -26,7 +26,9 @@
         """ Load the attributes from an XML string
         """
         from bioMoby.mobyMarshal import MobyUnmarshaller
-        doc=parseString(value).firstChild
+        doc=value
+        if isinstance(value, str):
+            doc=parseString(value).firstChild
         um=MobyUnmarshaller()
         self.content=""
         self.namespace=doc.getAttribute("moby:namespace")
@@ -46,4 +48,4 @@
             if elt.nodeName=="CrossReference" or elt.nodeName=="moby:CrossReference":
                 self.__cross__=[]
                 for ref in elt.childNodes:
-                    self.__cross__.append(ref.toxml())
\ No newline at end of file
+                    self.__cross__.append(um.loads(ref))
\ No newline at end of file

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/ontology/FASTA.py,v
retrieving revision 1.4
retrieving revision 1.5
diff -u -r1.4 -r1.5
--- /home/repository/moby/moby-live/Python/bioMoby/ontology/FASTA.py	2005/02/01 08:52:15	1.4
+++ /home/repository/moby/moby-live/Python/bioMoby/ontology/FASTA.py	2005/02/01 14:20:44	1.5
@@ -26,7 +26,9 @@
         """ Load the attributes from an XML string
         """
         from bioMoby.mobyMarshal import MobyUnmarshaller
-        doc=parseString(value).firstChild
+        doc=value
+        if isinstance(value, str):
+            doc=parseString(value).firstChild
         um=MobyUnmarshaller()
         self.content=""
         self.namespace=doc.getAttribute("moby:namespace")
@@ -46,4 +48,4 @@
             if elt.nodeName=="CrossReference" or elt.nodeName=="moby:CrossReference":
                 self.__cross__=[]
                 for ref in elt.childNodes:
-                    self.__cross__.append(ref.toxml())
\ No newline at end of file
+                    self.__cross__.append(um.loads(ref))
\ No newline at end of file

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/ontology/FASTA_AA.py,v
retrieving revision 1.4
retrieving revision 1.5
diff -u -r1.4 -r1.5
--- /home/repository/moby/moby-live/Python/bioMoby/ontology/FASTA_AA.py	2005/02/01 08:52:15	1.4
+++ /home/repository/moby/moby-live/Python/bioMoby/ontology/FASTA_AA.py	2005/02/01 14:20:44	1.5
@@ -26,7 +26,9 @@
         """ Load the attributes from an XML string
         """
         from bioMoby.mobyMarshal import MobyUnmarshaller
-        doc=parseString(value).firstChild
+        doc=value
+        if isinstance(value, str):
+            doc=parseString(value).firstChild
         um=MobyUnmarshaller()
         self.content=""
         self.namespace=doc.getAttribute("moby:namespace")
@@ -46,4 +48,4 @@
             if elt.nodeName=="CrossReference" or elt.nodeName=="moby:CrossReference":
                 self.__cross__=[]
                 for ref in elt.childNodes:
-                    self.__cross__.append(ref.toxml())
\ No newline at end of file
+                    self.__cross__.append(um.loads(ref))
\ No newline at end of file

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/ontology/FASTA_NA.py,v
retrieving revision 1.4
retrieving revision 1.5
diff -u -r1.4 -r1.5
--- /home/repository/moby/moby-live/Python/bioMoby/ontology/FASTA_NA.py	2005/02/01 08:52:15	1.4
+++ /home/repository/moby/moby-live/Python/bioMoby/ontology/FASTA_NA.py	2005/02/01 14:20:44	1.5
@@ -26,7 +26,9 @@
         """ Load the attributes from an XML string
         """
         from bioMoby.mobyMarshal import MobyUnmarshaller
-        doc=parseString(value).firstChild
+        doc=value
+        if isinstance(value, str):
+            doc=parseString(value).firstChild
         um=MobyUnmarshaller()
         self.content=""
         self.namespace=doc.getAttribute("moby:namespace")
@@ -46,4 +48,4 @@
             if elt.nodeName=="CrossReference" or elt.nodeName=="moby:CrossReference":
                 self.__cross__=[]
                 for ref in elt.childNodes:
-                    self.__cross__.append(ref.toxml())
\ No newline at end of file
+                    self.__cross__.append(um.loads(ref))
\ No newline at end of file

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/ontology/FASTA_Text.py,v
retrieving revision 1.4
retrieving revision 1.5
diff -u -r1.4 -r1.5
--- /home/repository/moby/moby-live/Python/bioMoby/ontology/FASTA_Text.py	2005/02/01 08:52:15	1.4
+++ /home/repository/moby/moby-live/Python/bioMoby/ontology/FASTA_Text.py	2005/02/01 14:20:44	1.5
@@ -26,7 +26,9 @@
         """ Load the attributes from an XML string
         """
         from bioMoby.mobyMarshal import MobyUnmarshaller
-        doc=parseString(value).firstChild
+        doc=value
+        if isinstance(value, str):
+            doc=parseString(value).firstChild
         um=MobyUnmarshaller()
         self.content=""
         self.namespace=doc.getAttribute("moby:namespace")
@@ -46,4 +48,4 @@
             if elt.nodeName=="CrossReference" or elt.nodeName=="moby:CrossReference":
                 self.__cross__=[]
                 for ref in elt.childNodes:
-                    self.__cross__.append(ref.toxml())
\ No newline at end of file
+                    self.__cross__.append(um.loads(ref))
\ No newline at end of file

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/ontology/GFF.py,v
retrieving revision 1.4
retrieving revision 1.5
diff -u -r1.4 -r1.5
--- /home/repository/moby/moby-live/Python/bioMoby/ontology/GFF.py	2005/02/01 08:52:15	1.4
+++ /home/repository/moby/moby-live/Python/bioMoby/ontology/GFF.py	2005/02/01 14:20:44	1.5
@@ -26,7 +26,9 @@
         """ Load the attributes from an XML string
         """
         from bioMoby.mobyMarshal import MobyUnmarshaller
-        doc=parseString(value).firstChild
+        doc=value
+        if isinstance(value, str):
+            doc=parseString(value).firstChild
         um=MobyUnmarshaller()
         self.content=""
         self.namespace=doc.getAttribute("moby:namespace")
@@ -46,4 +48,4 @@
             if elt.nodeName=="CrossReference" or elt.nodeName=="moby:CrossReference":
                 self.__cross__=[]
                 for ref in elt.childNodes:
-                    self.__cross__.append(ref.toxml())
\ No newline at end of file
+                    self.__cross__.append(um.loads(ref))
\ No newline at end of file

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/ontology/GFF1.py,v
retrieving revision 1.4
retrieving revision 1.5
diff -u -r1.4 -r1.5
--- /home/repository/moby/moby-live/Python/bioMoby/ontology/GFF1.py	2005/02/01 08:52:15	1.4
+++ /home/repository/moby/moby-live/Python/bioMoby/ontology/GFF1.py	2005/02/01 14:20:44	1.5
@@ -26,7 +26,9 @@
         """ Load the attributes from an XML string
         """
         from bioMoby.mobyMarshal import MobyUnmarshaller
-        doc=parseString(value).firstChild
+        doc=value
+        if isinstance(value, str):
+            doc=parseString(value).firstChild
         um=MobyUnmarshaller()
         self.content=""
         self.namespace=doc.getAttribute("moby:namespace")
@@ -46,4 +48,4 @@
             if elt.nodeName=="CrossReference" or elt.nodeName=="moby:CrossReference":
                 self.__cross__=[]
                 for ref in elt.childNodes:
-                    self.__cross__.append(ref.toxml())
\ No newline at end of file
+                    self.__cross__.append(um.loads(ref))
\ No newline at end of file

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/ontology/GFF2.py,v
retrieving revision 1.4
retrieving revision 1.5
diff -u -r1.4 -r1.5
--- /home/repository/moby/moby-live/Python/bioMoby/ontology/GFF2.py	2005/02/01 08:52:15	1.4
+++ /home/repository/moby/moby-live/Python/bioMoby/ontology/GFF2.py	2005/02/01 14:20:44	1.5
@@ -26,7 +26,9 @@
         """ Load the attributes from an XML string
         """
         from bioMoby.mobyMarshal import MobyUnmarshaller
-        doc=parseString(value).firstChild
+        doc=value
+        if isinstance(value, str):
+            doc=parseString(value).firstChild
         um=MobyUnmarshaller()
         self.content=""
         self.namespace=doc.getAttribute("moby:namespace")
@@ -46,4 +48,4 @@
             if elt.nodeName=="CrossReference" or elt.nodeName=="moby:CrossReference":
                 self.__cross__=[]
                 for ref in elt.childNodes:
-                    self.__cross__.append(ref.toxml())
\ No newline at end of file
+                    self.__cross__.append(um.loads(ref))
\ No newline at end of file

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/ontology/GFF2_5.py,v
retrieving revision 1.4
retrieving revision 1.5
diff -u -r1.4 -r1.5
--- /home/repository/moby/moby-live/Python/bioMoby/ontology/GFF2_5.py	2005/02/01 08:52:15	1.4
+++ /home/repository/moby/moby-live/Python/bioMoby/ontology/GFF2_5.py	2005/02/01 14:20:44	1.5
@@ -26,7 +26,9 @@
         """ Load the attributes from an XML string
         """
         from bioMoby.mobyMarshal import MobyUnmarshaller
-        doc=parseString(value).firstChild
+        doc=value
+        if isinstance(value, str):
+            doc=parseString(value).firstChild
         um=MobyUnmarshaller()
         self.content=""
         self.namespace=doc.getAttribute("moby:namespace")
@@ -46,4 +48,4 @@
             if elt.nodeName=="CrossReference" or elt.nodeName=="moby:CrossReference":
                 self.__cross__=[]
                 for ref in elt.childNodes:
-                    self.__cross__.append(ref.toxml())
\ No newline at end of file
+                    self.__cross__.append(um.loads(ref))
\ No newline at end of file

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/ontology/GFF3.py,v
retrieving revision 1.4
retrieving revision 1.5
diff -u -r1.4 -r1.5
--- /home/repository/moby/moby-live/Python/bioMoby/ontology/GFF3.py	2005/02/01 08:52:15	1.4
+++ /home/repository/moby/moby-live/Python/bioMoby/ontology/GFF3.py	2005/02/01 14:20:44	1.5
@@ -26,7 +26,9 @@
         """ Load the attributes from an XML string
         """
         from bioMoby.mobyMarshal import MobyUnmarshaller
-        doc=parseString(value).firstChild
+        doc=value
+        if isinstance(value, str):
+            doc=parseString(value).firstChild
         um=MobyUnmarshaller()
         self.content=""
         self.namespace=doc.getAttribute("moby:namespace")
@@ -46,4 +48,4 @@
             if elt.nodeName=="CrossReference" or elt.nodeName=="moby:CrossReference":
                 self.__cross__=[]
                 for ref in elt.childNodes:
-                    self.__cross__.append(ref.toxml())
\ No newline at end of file
+                    self.__cross__.append(um.loads(ref))
\ No newline at end of file

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/ontology/GO_Term.py,v
retrieving revision 1.4
retrieving revision 1.5
diff -u -r1.4 -r1.5
--- /home/repository/moby/moby-live/Python/bioMoby/ontology/GO_Term.py	2005/02/01 08:52:15	1.4
+++ /home/repository/moby/moby-live/Python/bioMoby/ontology/GO_Term.py	2005/02/01 14:20:44	1.5
@@ -28,7 +28,9 @@
         """ Load the attributes from an XML string
         """
         from bioMoby.mobyMarshal import MobyUnmarshaller
-        doc=parseString(value).firstChild
+        doc=value
+        if isinstance(value, str):
+            doc=parseString(value).firstChild
         um=MobyUnmarshaller()
         self.content=""
         self.namespace=doc.getAttribute("moby:namespace")
@@ -48,12 +50,12 @@
             if elt.nodeName=="CrossReference" or elt.nodeName=="moby:CrossReference":
                 self.__cross__=[]
                 for ref in elt.childNodes:
-                    self.__cross__.append(ref.toxml())
+                    self.__cross__.append(um.loads(ref))
             if elt.nodeType==elt.ELEMENT_NODE and (elt.nodeName=="String" or elt.nodeName=="moby:String") and (elt.getAttribute("articleName")=="Term" or elt.getAttribute("moby:articleName")=="Term"):
                 t=MobyString()
-                t.fromMoby(elt.toxml())
+                t.fromMoby(elt)
                 self.Term=t.content
             if elt.nodeType==elt.ELEMENT_NODE and (elt.nodeName=="String" or elt.nodeName=="moby:String") and (elt.getAttribute("articleName")=="Definition" or elt.getAttribute("moby:articleName")=="Definition"):
                 t=MobyString()
-                t.fromMoby(elt.toxml())
+                t.fromMoby(elt)
                 self.Definition=t.content
\ No newline at end of file

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/ontology/GenbankFlatfile.py,v
retrieving revision 1.4
retrieving revision 1.5
diff -u -r1.4 -r1.5
--- /home/repository/moby/moby-live/Python/bioMoby/ontology/GenbankFlatfile.py	2005/02/01 08:52:15	1.4
+++ /home/repository/moby/moby-live/Python/bioMoby/ontology/GenbankFlatfile.py	2005/02/01 14:20:44	1.5
@@ -26,7 +26,9 @@
         """ Load the attributes from an XML string
         """
         from bioMoby.mobyMarshal import MobyUnmarshaller
-        doc=parseString(value).firstChild
+        doc=value
+        if isinstance(value, str):
+            doc=parseString(value).firstChild
         um=MobyUnmarshaller()
         self.content=""
         self.namespace=doc.getAttribute("moby:namespace")
@@ -46,4 +48,4 @@
             if elt.nodeName=="CrossReference" or elt.nodeName=="moby:CrossReference":
                 self.__cross__=[]
                 for ref in elt.childNodes:
-                    self.__cross__.append(ref.toxml())
\ No newline at end of file
+                    self.__cross__.append(um.loads(ref))
\ No newline at end of file

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/ontology/GenericSequence.py,v
retrieving revision 1.4
retrieving revision 1.5
diff -u -r1.4 -r1.5
--- /home/repository/moby/moby-live/Python/bioMoby/ontology/GenericSequence.py	2005/02/01 08:52:15	1.4
+++ /home/repository/moby/moby-live/Python/bioMoby/ontology/GenericSequence.py	2005/02/01 14:20:44	1.5
@@ -29,7 +29,9 @@
         """ Load the attributes from an XML string
         """
         from bioMoby.mobyMarshal import MobyUnmarshaller
-        doc=parseString(value).firstChild
+        doc=value
+        if isinstance(value, str):
+            doc=parseString(value).firstChild
         um=MobyUnmarshaller()
         self.content=""
         self.namespace=doc.getAttribute("moby:namespace")
@@ -49,12 +51,12 @@
             if elt.nodeName=="CrossReference" or elt.nodeName=="moby:CrossReference":
                 self.__cross__=[]
                 for ref in elt.childNodes:
-                    self.__cross__.append(ref.toxml())
+                    self.__cross__.append(um.loads(ref))
             if elt.nodeType==elt.ELEMENT_NODE and (elt.nodeName=="Integer" or elt.nodeName=="moby:Integer") and (elt.getAttribute("articleName")=="Length" or elt.getAttribute("moby:articleName")=="Length"):
                 t=MobyInteger()
-                t.fromMoby(elt.toxml())
+                t.fromMoby(elt)
                 self.Length=t.content
             if elt.nodeType==elt.ELEMENT_NODE and (elt.nodeName=="String" or elt.nodeName=="moby:String") and (elt.getAttribute("articleName")=="SequenceString" or elt.getAttribute("moby:articleName")=="SequenceString"):
                 t=MobyString()
-                t.fromMoby(elt.toxml())
+                t.fromMoby(elt)
                 self.SequenceString=t.content
\ No newline at end of file

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/ontology/GeneticElement.py,v
retrieving revision 1.4
retrieving revision 1.5
diff -u -r1.4 -r1.5
--- /home/repository/moby/moby-live/Python/bioMoby/ontology/GeneticElement.py	2005/02/01 08:52:15	1.4
+++ /home/repository/moby/moby-live/Python/bioMoby/ontology/GeneticElement.py	2005/02/01 14:20:44	1.5
@@ -27,7 +27,9 @@
         """ Load the attributes from an XML string
         """
         from bioMoby.mobyMarshal import MobyUnmarshaller
-        doc=parseString(value).firstChild
+        doc=value
+        if isinstance(value, str):
+            doc=parseString(value).firstChild
         um=MobyUnmarshaller()
         self.content=""
         self.namespace=doc.getAttribute("moby:namespace")
@@ -47,8 +49,8 @@
             if elt.nodeName=="CrossReference" or elt.nodeName=="moby:CrossReference":
                 self.__cross__=[]
                 for ref in elt.childNodes:
-                    self.__cross__.append(ref.toxml())
+                    self.__cross__.append(um.loads(ref))
             if elt.nodeType==elt.ELEMENT_NODE and (elt.nodeName=="String" or elt.nodeName=="moby:String") and (elt.getAttribute("articleName")=="GeneticElement" or elt.getAttribute("moby:articleName")=="GeneticElement"):
                 t=MobyString()
-                t.fromMoby(elt.toxml())
+                t.fromMoby(elt)
                 self.GeneticElement=t.content
\ No newline at end of file

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/ontology/Genotype.py,v
retrieving revision 1.4
retrieving revision 1.5
diff -u -r1.4 -r1.5
--- /home/repository/moby/moby-live/Python/bioMoby/ontology/Genotype.py	2005/02/01 08:52:15	1.4
+++ /home/repository/moby/moby-live/Python/bioMoby/ontology/Genotype.py	2005/02/01 14:20:44	1.5
@@ -29,7 +29,9 @@
         """ Load the attributes from an XML string
         """
         from bioMoby.mobyMarshal import MobyUnmarshaller
-        doc=parseString(value).firstChild
+        doc=value
+        if isinstance(value, str):
+            doc=parseString(value).firstChild
         um=MobyUnmarshaller()
         self.content=""
         self.namespace=doc.getAttribute("moby:namespace")
@@ -49,16 +51,16 @@
             if elt.nodeName=="CrossReference" or elt.nodeName=="moby:CrossReference":
                 self.__cross__=[]
                 for ref in elt.childNodes:
-                    self.__cross__.append(ref.toxml())
+                    self.__cross__.append(um.loads(ref))
             if elt.nodeType==elt.ELEMENT_NODE and (elt.nodeName=="String" or elt.nodeName=="moby:String") and (elt.getAttribute("articleName")=="snp" or elt.getAttribute("moby:articleName")=="snp"):
                 t=MobyString()
-                t.fromMoby(elt.toxml())
+                t.fromMoby(elt)
                 self.Snp=t.content
             if elt.nodeType==elt.ELEMENT_NODE and (elt.nodeName=="String" or elt.nodeName=="moby:String") and (elt.getAttribute("articleName")=="sample" or elt.getAttribute("moby:articleName")=="sample"):
                 t=MobyString()
-                t.fromMoby(elt.toxml())
+                t.fromMoby(elt)
                 self.Sample=t.content
             if elt.nodeType==elt.ELEMENT_NODE and (elt.nodeName=="String" or elt.nodeName=="moby:String") and (elt.getAttribute("articleName")=="result" or elt.getAttribute("moby:articleName")=="result"):
                 t=MobyString()
-                t.fromMoby(elt.toxml())
+                t.fromMoby(elt)
                 self.Result=t.content
\ No newline at end of file

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/ontology/Germplasm_Details.py,v
retrieving revision 1.4
retrieving revision 1.5
diff -u -r1.4 -r1.5
--- /home/repository/moby/moby-live/Python/bioMoby/ontology/Germplasm_Details.py	2005/02/01 08:52:15	1.4
+++ /home/repository/moby/moby-live/Python/bioMoby/ontology/Germplasm_Details.py	2005/02/01 14:20:44	1.5
@@ -35,7 +35,9 @@
         """ Load the attributes from an XML string
         """
         from bioMoby.mobyMarshal import MobyUnmarshaller
-        doc=parseString(value).firstChild
+        doc=value
+        if isinstance(value, str):
+            doc=parseString(value).firstChild
         um=MobyUnmarshaller()
         self.content=""
         self.namespace=doc.getAttribute("moby:namespace")
@@ -55,36 +57,36 @@
             if elt.nodeName=="CrossReference" or elt.nodeName=="moby:CrossReference":
                 self.__cross__=[]
                 for ref in elt.childNodes:
-                    self.__cross__.append(ref.toxml())
+                    self.__cross__.append(um.loads(ref))
             if elt.nodeType==elt.ELEMENT_NODE and (elt.nodeName=="Integer" or elt.nodeName=="moby:Integer") and (elt.getAttribute("articleName")=="date" or elt.getAttribute("moby:articleName")=="date"):
                 t=MobyInteger()
-                t.fromMoby(elt.toxml())
+                t.fromMoby(elt)
                 self.Date=t.content
             if elt.nodeType==elt.ELEMENT_NODE and (elt.nodeName=="String" or elt.nodeName=="moby:String") and (elt.getAttribute("articleName")=="country" or elt.getAttribute("moby:articleName")=="country"):
                 t=MobyString()
-                t.fromMoby(elt.toxml())
+                t.fromMoby(elt)
                 self.Country=t.content
             if elt.nodeType==elt.ELEMENT_NODE and (elt.nodeName=="String" or elt.nodeName=="moby:String") and (elt.getAttribute("articleName")=="prefered_name" or elt.getAttribute("moby:articleName")=="prefered_name"):
                 t=MobyString()
-                t.fromMoby(elt.toxml())
+                t.fromMoby(elt)
                 self.Prefered_name=t.content
             if elt.nodeType==elt.ELEMENT_NODE and (elt.nodeName=="String" or elt.nodeName=="moby:String") and (elt.getAttribute("articleName")=="alternative_names" or elt.getAttribute("moby:articleName")=="alternative_names"):
                 t=MobyString()
-                t.fromMoby(elt.toxml())
+                t.fromMoby(elt)
                 self.Alternative_names=t.content
             if elt.nodeType==elt.ELEMENT_NODE and (elt.nodeName=="String" or elt.nodeName=="moby:String") and (elt.getAttribute("articleName")=="name_type" or elt.getAttribute("moby:articleName")=="name_type"):
                 t=MobyString()
-                t.fromMoby(elt.toxml())
+                t.fromMoby(elt)
                 self.Name_type=t.content
             if elt.nodeType==elt.ELEMENT_NODE and (elt.nodeName=="String" or elt.nodeName=="moby:String") and (elt.getAttribute("articleName")=="method" or elt.getAttribute("moby:articleName")=="method"):
                 t=MobyString()
-                t.fromMoby(elt.toxml())
+                t.fromMoby(elt)
                 self.Method=t.content
             if elt.nodeType==elt.ELEMENT_NODE and (elt.nodeName=="String" or elt.nodeName=="moby:String") and (elt.getAttribute("articleName")=="location" or elt.getAttribute("moby:articleName")=="location"):
                 t=MobyString()
-                t.fromMoby(elt.toxml())
+                t.fromMoby(elt)
                 self.Location=t.content
             if elt.nodeType==elt.ELEMENT_NODE and (elt.nodeName=="Integer" or elt.nodeName=="moby:Integer") and (elt.getAttribute("articleName")=="germplasm_id" or elt.getAttribute("moby:articleName")=="germplasm_id"):
                 t=MobyInteger()
-                t.fromMoby(elt.toxml())
+                t.fromMoby(elt)
                 self.Germplasm_id=t.content
\ No newline at end of file

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/ontology/Germplasm_List.py,v
retrieving revision 1.4
retrieving revision 1.5
diff -u -r1.4 -r1.5
--- /home/repository/moby/moby-live/Python/bioMoby/ontology/Germplasm_List.py	2005/02/01 08:52:16	1.4
+++ /home/repository/moby/moby-live/Python/bioMoby/ontology/Germplasm_List.py	2005/02/01 14:20:44	1.5
@@ -35,7 +35,9 @@
         """ Load the attributes from an XML string
         """
         from bioMoby.mobyMarshal import MobyUnmarshaller
-        doc=parseString(value).firstChild
+        doc=value
+        if isinstance(value, str):
+            doc=parseString(value).firstChild
         um=MobyUnmarshaller()
         self.content=""
         self.namespace=doc.getAttribute("moby:namespace")
@@ -55,36 +57,36 @@
             if elt.nodeName=="CrossReference" or elt.nodeName=="moby:CrossReference":
                 self.__cross__=[]
                 for ref in elt.childNodes:
-                    self.__cross__.append(ref.toxml())
+                    self.__cross__.append(um.loads(ref))
             if elt.nodeType==elt.ELEMENT_NODE and (elt.nodeName=="Integer" or elt.nodeName=="moby:Integer") and (elt.getAttribute("articleName")=="germplasm_id" or elt.getAttribute("moby:articleName")=="germplasm_id"):
                 t=MobyInteger()
-                t.fromMoby(elt.toxml())
+                t.fromMoby(elt)
                 self.Germplasm_id=t.content
             if elt.nodeType==elt.ELEMENT_NODE and (elt.nodeName=="String" or elt.nodeName=="moby:String") and (elt.getAttribute("articleName")=="germplasm_name" or elt.getAttribute("moby:articleName")=="germplasm_name"):
                 t=MobyString()
-                t.fromMoby(elt.toxml())
+                t.fromMoby(elt)
                 self.Germplasm_name=t.content
             if elt.nodeType==elt.ELEMENT_NODE and (elt.nodeName=="String" or elt.nodeName=="moby:String") and (elt.getAttribute("articleName")=="trait_value" or elt.getAttribute("moby:articleName")=="trait_value"):
                 t=MobyString()
-                t.fromMoby(elt.toxml())
+                t.fromMoby(elt)
                 self.Trait_value=t.content
             if elt.nodeType==elt.ELEMENT_NODE and (elt.nodeName=="Integer" or elt.nodeName=="moby:Integer") and (elt.getAttribute("articleName")=="trait_id" or elt.getAttribute("moby:articleName")=="trait_id"):
                 t=MobyInteger()
-                t.fromMoby(elt.toxml())
+                t.fromMoby(elt)
                 self.Trait_id=t.content
             if elt.nodeType==elt.ELEMENT_NODE and (elt.nodeName=="String" or elt.nodeName=="moby:String") and (elt.getAttribute("articleName")=="scale" or elt.getAttribute("moby:articleName")=="scale"):
                 t=MobyString()
-                t.fromMoby(elt.toxml())
+                t.fromMoby(elt)
                 self.Scale=t.content
             if elt.nodeType==elt.ELEMENT_NODE and (elt.nodeName=="String" or elt.nodeName=="moby:String") and (elt.getAttribute("articleName")=="scale_desc" or elt.getAttribute("moby:articleName")=="scale_desc"):
                 t=MobyString()
-                t.fromMoby(elt.toxml())
+                t.fromMoby(elt)
                 self.Scale_desc=t.content
             if elt.nodeType==elt.ELEMENT_NODE and (elt.nodeName=="String" or elt.nodeName=="moby:String") and (elt.getAttribute("articleName")=="method" or elt.getAttribute("moby:articleName")=="method"):
                 t=MobyString()
-                t.fromMoby(elt.toxml())
+                t.fromMoby(elt)
                 self.Method=t.content
             if elt.nodeType==elt.ELEMENT_NODE and (elt.nodeName=="String" or elt.nodeName=="moby:String") and (elt.getAttribute("articleName")=="study_id" or elt.getAttribute("moby:articleName")=="study_id"):
                 t=MobyString()
-                t.fromMoby(elt.toxml())
+                t.fromMoby(elt)
                 self.Study_id=t.content
\ No newline at end of file

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/ontology/Global_Keyword.py,v
retrieving revision 1.4
retrieving revision 1.5
diff -u -r1.4 -r1.5
--- /home/repository/moby/moby-live/Python/bioMoby/ontology/Global_Keyword.py	2005/02/01 08:52:16	1.4
+++ /home/repository/moby/moby-live/Python/bioMoby/ontology/Global_Keyword.py	2005/02/01 14:20:44	1.5
@@ -25,7 +25,9 @@
         """ Load the attributes from an XML string
         """
         from bioMoby.mobyMarshal import MobyUnmarshaller
-        doc=parseString(value).firstChild
+        doc=value
+        if isinstance(value, str):
+            doc=parseString(value).firstChild
         um=MobyUnmarshaller()
         self.content=""
         self.namespace=doc.getAttribute("moby:namespace")
@@ -45,4 +47,4 @@
             if elt.nodeName=="CrossReference" or elt.nodeName=="moby:CrossReference":
                 self.__cross__=[]
                 for ref in elt.childNodes:
-                    self.__cross__.append(ref.toxml())
\ No newline at end of file
+                    self.__cross__.append(um.loads(ref))
\ No newline at end of file

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/ontology/HBond_Pair.py,v
retrieving revision 1.4
retrieving revision 1.5
diff -u -r1.4 -r1.5
--- /home/repository/moby/moby-live/Python/bioMoby/ontology/HBond_Pair.py	2005/02/01 08:52:16	1.4
+++ /home/repository/moby/moby-live/Python/bioMoby/ontology/HBond_Pair.py	2005/02/01 14:20:44	1.5
@@ -29,7 +29,9 @@
         """ Load the attributes from an XML string
         """
         from bioMoby.mobyMarshal import MobyUnmarshaller
-        doc=parseString(value).firstChild
+        doc=value
+        if isinstance(value, str):
+            doc=parseString(value).firstChild
         um=MobyUnmarshaller()
         self.content=""
         self.namespace=doc.getAttribute("moby:namespace")
@@ -49,16 +51,16 @@
             if elt.nodeName=="CrossReference" or elt.nodeName=="moby:CrossReference":
                 self.__cross__=[]
                 for ref in elt.childNodes:
-                    self.__cross__.append(ref.toxml())
+                    self.__cross__.append(um.loads(ref))
             if elt.nodeType==elt.ELEMENT_NODE and (elt.nodeName=="String" or elt.nodeName=="moby:String") and (elt.getAttribute("articleName")=="A" or elt.getAttribute("moby:articleName")=="A"):
                 t=MobyString()
-                t.fromMoby(elt.toxml())
+                t.fromMoby(elt)
                 self.A=t.content
             if elt.nodeType==elt.ELEMENT_NODE and (elt.nodeName=="String" or elt.nodeName=="moby:String") and (elt.getAttribute("articleName")=="H" or elt.getAttribute("moby:articleName")=="H"):
                 t=MobyString()
-                t.fromMoby(elt.toxml())
+                t.fromMoby(elt)
                 self.H=t.content
             if elt.nodeType==elt.ELEMENT_NODE and (elt.nodeName=="String" or elt.nodeName=="moby:String") and (elt.getAttribute("articleName")=="D" or elt.getAttribute("moby:articleName")=="D"):
                 t=MobyString()
-                t.fromMoby(elt.toxml())
+                t.fromMoby(elt)
                 self.D=t.content
\ No newline at end of file

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/ontology/HFormatText.py,v
retrieving revision 1.4
retrieving revision 1.5
diff -u -r1.4 -r1.5
--- /home/repository/moby/moby-live/Python/bioMoby/ontology/HFormatText.py	2005/02/01 08:52:16	1.4
+++ /home/repository/moby/moby-live/Python/bioMoby/ontology/HFormatText.py	2005/02/01 14:20:44	1.5
@@ -26,7 +26,9 @@
         """ Load the attributes from an XML string
         """
         from bioMoby.mobyMarshal import MobyUnmarshaller
-        doc=parseString(value).firstChild
+        doc=value
+        if isinstance(value, str):
+            doc=parseString(value).firstChild
         um=MobyUnmarshaller()
         self.content=""
         self.namespace=doc.getAttribute("moby:namespace")
@@ -46,4 +48,4 @@
             if elt.nodeName=="CrossReference" or elt.nodeName=="moby:CrossReference":
                 self.__cross__=[]
                 for ref in elt.childNodes:
-                    self.__cross__.append(ref.toxml())
\ No newline at end of file
+                    self.__cross__.append(um.loads(ref))
\ No newline at end of file

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/ontology/Haplotyping_Study_obj.py,v
retrieving revision 1.4
retrieving revision 1.5
diff -u -r1.4 -r1.5
--- /home/repository/moby/moby-live/Python/bioMoby/ontology/Haplotyping_Study_obj.py	2005/02/01 08:52:16	1.4
+++ /home/repository/moby/moby-live/Python/bioMoby/ontology/Haplotyping_Study_obj.py	2005/02/01 14:20:44	1.5
@@ -25,7 +25,9 @@
         """ Load the attributes from an XML string
         """
         from bioMoby.mobyMarshal import MobyUnmarshaller
-        doc=parseString(value).firstChild
+        doc=value
+        if isinstance(value, str):
+            doc=parseString(value).firstChild
         um=MobyUnmarshaller()
         self.content=""
         self.namespace=doc.getAttribute("moby:namespace")
@@ -45,4 +47,4 @@
             if elt.nodeName=="CrossReference" or elt.nodeName=="moby:CrossReference":
                 self.__cross__=[]
                 for ref in elt.childNodes:
-                    self.__cross__.append(ref.toxml())
\ No newline at end of file
+                    self.__cross__.append(um.loads(ref))
\ No newline at end of file

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/ontology/ICIS_Query.py,v
retrieving revision 1.4
retrieving revision 1.5
diff -u -r1.4 -r1.5
--- /home/repository/moby/moby-live/Python/bioMoby/ontology/ICIS_Query.py	2005/02/01 08:52:16	1.4
+++ /home/repository/moby/moby-live/Python/bioMoby/ontology/ICIS_Query.py	2005/02/01 14:20:44	1.5
@@ -30,7 +30,9 @@
         """ Load the attributes from an XML string
         """
         from bioMoby.mobyMarshal import MobyUnmarshaller
-        doc=parseString(value).firstChild
+        doc=value
+        if isinstance(value, str):
+            doc=parseString(value).firstChild
         um=MobyUnmarshaller()
         self.content=""
         self.namespace=doc.getAttribute("moby:namespace")
@@ -50,16 +52,16 @@
             if elt.nodeName=="CrossReference" or elt.nodeName=="moby:CrossReference":
                 self.__cross__=[]
                 for ref in elt.childNodes:
-                    self.__cross__.append(ref.toxml())
+                    self.__cross__.append(um.loads(ref))
             if elt.nodeType==elt.ELEMENT_NODE and (elt.nodeName=="Integer" or elt.nodeName=="moby:Integer") and (elt.getAttribute("articleName")=="end_row" or elt.getAttribute("moby:articleName")=="end_row"):
                 t=MobyInteger()
-                t.fromMoby(elt.toxml())
+                t.fromMoby(elt)
                 self.End_row=t.content
             if elt.nodeType==elt.ELEMENT_NODE and (elt.nodeName=="Integer" or elt.nodeName=="moby:Integer") and (elt.getAttribute("articleName")=="start_row" or elt.getAttribute("moby:articleName")=="start_row"):
                 t=MobyInteger()
-                t.fromMoby(elt.toxml())
+                t.fromMoby(elt)
                 self.Start_row=t.content
             if elt.nodeType==elt.ELEMENT_NODE and (elt.nodeName=="String" or elt.nodeName=="moby:String") and (elt.getAttribute("articleName")=="search_text" or elt.getAttribute("moby:articleName")=="search_text"):
                 t=MobyString()
-                t.fromMoby(elt.toxml())
+                t.fromMoby(elt)
                 self.Search_text=t.content
\ No newline at end of file

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/ontology/ICIS_Query2.py,v
retrieving revision 1.4
retrieving revision 1.5
diff -u -r1.4 -r1.5
--- /home/repository/moby/moby-live/Python/bioMoby/ontology/ICIS_Query2.py	2005/02/01 08:52:16	1.4
+++ /home/repository/moby/moby-live/Python/bioMoby/ontology/ICIS_Query2.py	2005/02/01 14:20:44	1.5
@@ -32,7 +32,9 @@
         """ Load the attributes from an XML string
         """
         from bioMoby.mobyMarshal import MobyUnmarshaller
-        doc=parseString(value).firstChild
+        doc=value
+        if isinstance(value, str):
+            doc=parseString(value).firstChild
         um=MobyUnmarshaller()
         self.content=""
         self.namespace=doc.getAttribute("moby:namespace")
@@ -52,24 +54,24 @@
             if elt.nodeName=="CrossReference" or elt.nodeName=="moby:CrossReference":
                 self.__cross__=[]
                 for ref in elt.childNodes:
-                    self.__cross__.append(ref.toxml())
+                    self.__cross__.append(um.loads(ref))
             if elt.nodeType==elt.ELEMENT_NODE and (elt.nodeName=="String" or elt.nodeName=="moby:String") and (elt.getAttribute("articleName")=="search_text1" or elt.getAttribute("moby:articleName")=="search_text1"):
                 t=MobyString()
-                t.fromMoby(elt.toxml())
+                t.fromMoby(elt)
                 self.Search_text1=t.content
             if elt.nodeType==elt.ELEMENT_NODE and (elt.nodeName=="String" or elt.nodeName=="moby:String") and (elt.getAttribute("articleName")=="search_text2" or elt.getAttribute("moby:articleName")=="search_text2"):
                 t=MobyString()
-                t.fromMoby(elt.toxml())
+                t.fromMoby(elt)
                 self.Search_text2=t.content
             if elt.nodeType==elt.ELEMENT_NODE and (elt.nodeName=="String" or elt.nodeName=="moby:String") and (elt.getAttribute("articleName")=="search_text3" or elt.getAttribute("moby:articleName")=="search_text3"):
                 t=MobyString()
-                t.fromMoby(elt.toxml())
+                t.fromMoby(elt)
                 self.Search_text3=t.content
             if elt.nodeType==elt.ELEMENT_NODE and (elt.nodeName=="Integer" or elt.nodeName=="moby:Integer") and (elt.getAttribute("articleName")=="start_row" or elt.getAttribute("moby:articleName")=="start_row"):
                 t=MobyInteger()
-                t.fromMoby(elt.toxml())
+                t.fromMoby(elt)
                 self.Start_row=t.content
             if elt.nodeType==elt.ELEMENT_NODE and (elt.nodeName=="Integer" or elt.nodeName=="moby:Integer") and (elt.getAttribute("articleName")=="end_row" or elt.getAttribute("moby:articleName")=="end_row"):
                 t=MobyInteger()
-                t.fromMoby(elt.toxml())
+                t.fromMoby(elt)
                 self.End_row=t.content
\ No newline at end of file

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/ontology/ICIS_Query3.py,v
retrieving revision 1.4
retrieving revision 1.5
diff -u -r1.4 -r1.5
--- /home/repository/moby/moby-live/Python/bioMoby/ontology/ICIS_Query3.py	2005/02/01 08:52:16	1.4
+++ /home/repository/moby/moby-live/Python/bioMoby/ontology/ICIS_Query3.py	2005/02/01 14:20:44	1.5
@@ -30,7 +30,9 @@
         """ Load the attributes from an XML string
         """
         from bioMoby.mobyMarshal import MobyUnmarshaller
-        doc=parseString(value).firstChild
+        doc=value
+        if isinstance(value, str):
+            doc=parseString(value).firstChild
         um=MobyUnmarshaller()
         self.content=""
         self.namespace=doc.getAttribute("moby:namespace")
@@ -50,20 +52,20 @@
             if elt.nodeName=="CrossReference" or elt.nodeName=="moby:CrossReference":
                 self.__cross__=[]
                 for ref in elt.childNodes:
-                    self.__cross__.append(ref.toxml())
+                    self.__cross__.append(um.loads(ref))
             if elt.nodeType==elt.ELEMENT_NODE and (elt.nodeName=="Integer" or elt.nodeName=="moby:Integer") and (elt.getAttribute("articleName")=="search_text1" or elt.getAttribute("moby:articleName")=="search_text1"):
                 t=MobyInteger()
-                t.fromMoby(elt.toxml())
+                t.fromMoby(elt)
                 self.Search_text1=t.content
             if elt.nodeType==elt.ELEMENT_NODE and (elt.nodeName=="Integer" or elt.nodeName=="moby:Integer") and (elt.getAttribute("articleName")=="search_text2" or elt.getAttribute("moby:articleName")=="search_text2"):
                 t=MobyInteger()
-                t.fromMoby(elt.toxml())
+                t.fromMoby(elt)
                 self.Search_text2=t.content
             if elt.nodeType==elt.ELEMENT_NODE and (elt.nodeName=="Integer" or elt.nodeName=="moby:Integer") and (elt.getAttribute("articleName")=="start_row" or elt.getAttribute("moby:articleName")=="start_row"):
                 t=MobyInteger()
-                t.fromMoby(elt.toxml())
+                t.fromMoby(elt)
                 self.Start_row=t.content
             if elt.nodeType==elt.ELEMENT_NODE and (elt.nodeName=="Integer" or elt.nodeName=="moby:Integer") and (elt.getAttribute("articleName")=="end_row" or elt.getAttribute("moby:articleName")=="end_row"):
                 t=MobyInteger()
-                t.fromMoby(elt.toxml())
+                t.fromMoby(elt)
                 self.End_row=t.content
\ No newline at end of file

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/ontology/IntAct_XML.py,v
retrieving revision 1.4
retrieving revision 1.5
diff -u -r1.4 -r1.5
--- /home/repository/moby/moby-live/Python/bioMoby/ontology/IntAct_XML.py	2005/02/01 08:52:16	1.4
+++ /home/repository/moby/moby-live/Python/bioMoby/ontology/IntAct_XML.py	2005/02/01 14:20:44	1.5
@@ -26,7 +26,9 @@
         """ Load the attributes from an XML string
         """
         from bioMoby.mobyMarshal import MobyUnmarshaller
-        doc=parseString(value).firstChild
+        doc=value
+        if isinstance(value, str):
+            doc=parseString(value).firstChild
         um=MobyUnmarshaller()
         self.content=""
         self.namespace=doc.getAttribute("moby:namespace")
@@ -46,4 +48,4 @@
             if elt.nodeName=="CrossReference" or elt.nodeName=="moby:CrossReference":
                 self.__cross__=[]
                 for ref in elt.childNodes:
-                    self.__cross__.append(ref.toxml())
\ No newline at end of file
+                    self.__cross__.append(um.loads(ref))
\ No newline at end of file

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/ontology/Interaction.py,v
retrieving revision 1.4
retrieving revision 1.5
diff -u -r1.4 -r1.5
--- /home/repository/moby/moby-live/Python/bioMoby/ontology/Interaction.py	2005/02/01 08:52:16	1.4
+++ /home/repository/moby/moby-live/Python/bioMoby/ontology/Interaction.py	2005/02/01 14:20:44	1.5
@@ -30,7 +30,9 @@
         """ Load the attributes from an XML string
         """
         from bioMoby.mobyMarshal import MobyUnmarshaller
-        doc=parseString(value).firstChild
+        doc=value
+        if isinstance(value, str):
+            doc=parseString(value).firstChild
         um=MobyUnmarshaller()
         self.content=""
         self.namespace=doc.getAttribute("moby:namespace")
@@ -51,15 +53,15 @@
             if elt.nodeName=="CrossReference" or elt.nodeName=="moby:CrossReference":
                 self.__cross__=[]
                 for ref in elt.childNodes:
-                    self.__cross__.append(ref.toxml())
+                    self.__cross__.append(um.loads(ref))
             if elt.nodeType==elt.ELEMENT_NODE and (elt.nodeName=="String" or elt.nodeName=="moby:String") and (elt.getAttribute("articleName")=="result" or elt.getAttribute("moby:articleName")=="result"):
                 t=MobyString()
-                t.fromMoby(elt.toxml())
+                t.fromMoby(elt)
                 self.Result=t.content
             if elt.nodeType==elt.ELEMENT_NODE and (elt.nodeName=="String" or elt.nodeName=="moby:String") and (elt.getAttribute("articleName")=="resultUnits" or elt.getAttribute("moby:articleName")=="resultUnits"):
                 t=MobyString()
-                t.fromMoby(elt.toxml())
+                t.fromMoby(elt)
                 self.ResultUnits=t.content
             if elt.nodeType==elt.ELEMENT_NODE and (elt.nodeName=="Interactor" or elt.nodeName=="moby:Interactor") and (elt.getAttribute("articleName")=="participant" or elt.getAttribute("moby:articleName")=="participant"):
                 self.Participant=MobyInteractor()
-                self.Participant.fromMoby(elt.toxml())
\ No newline at end of file
+                self.Participant.fromMoby(elt)
\ No newline at end of file

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/ontology/InteractionMethod.py,v
retrieving revision 1.4
retrieving revision 1.5
diff -u -r1.4 -r1.5
--- /home/repository/moby/moby-live/Python/bioMoby/ontology/InteractionMethod.py	2005/02/01 08:52:16	1.4
+++ /home/repository/moby/moby-live/Python/bioMoby/ontology/InteractionMethod.py	2005/02/01 14:20:44	1.5
@@ -29,7 +29,9 @@
         """ Load the attributes from an XML string
         """
         from bioMoby.mobyMarshal import MobyUnmarshaller
-        doc=parseString(value).firstChild
+        doc=value
+        if isinstance(value, str):
+            doc=parseString(value).firstChild
         um=MobyUnmarshaller()
         self.content=""
         self.namespace=doc.getAttribute("moby:namespace")
@@ -49,16 +51,16 @@
             if elt.nodeName=="CrossReference" or elt.nodeName=="moby:CrossReference":
                 self.__cross__=[]
                 for ref in elt.childNodes:
-                    self.__cross__.append(ref.toxml())
+                    self.__cross__.append(um.loads(ref))
             if elt.nodeType==elt.ELEMENT_NODE and (elt.nodeName=="String" or elt.nodeName=="moby:String") and (elt.getAttribute("articleName")=="shortlabel" or elt.getAttribute("moby:articleName")=="shortlabel"):
                 t=MobyString()
-                t.fromMoby(elt.toxml())
+                t.fromMoby(elt)
                 self.Shortlabel=t.content
             if elt.nodeType==elt.ELEMENT_NODE and (elt.nodeName=="String" or elt.nodeName=="moby:String") and (elt.getAttribute("articleName")=="term" or elt.getAttribute("moby:articleName")=="term"):
                 t=MobyString()
-                t.fromMoby(elt.toxml())
+                t.fromMoby(elt)
                 self.Term=t.content
             if elt.nodeType==elt.ELEMENT_NODE and (elt.nodeName=="String" or elt.nodeName=="moby:String") and (elt.getAttribute("articleName")=="definition" or elt.getAttribute("moby:articleName")=="definition"):
                 t=MobyString()
-                t.fromMoby(elt.toxml())
+                t.fromMoby(elt)
                 self.Definition=t.content
\ No newline at end of file

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/ontology/Interaction_partner.py,v
retrieving revision 1.4
retrieving revision 1.5
diff -u -r1.4 -r1.5
--- /home/repository/moby/moby-live/Python/bioMoby/ontology/Interaction_partner.py	2005/02/01 08:52:16	1.4
+++ /home/repository/moby/moby-live/Python/bioMoby/ontology/Interaction_partner.py	2005/02/01 14:20:44	1.5
@@ -29,7 +29,9 @@
         """ Load the attributes from an XML string
         """
         from bioMoby.mobyMarshal import MobyUnmarshaller
-        doc=parseString(value).firstChild
+        doc=value
+        if isinstance(value, str):
+            doc=parseString(value).firstChild
         um=MobyUnmarshaller()
         self.content=""
         self.namespace=doc.getAttribute("moby:namespace")
@@ -49,12 +51,12 @@
             if elt.nodeName=="CrossReference" or elt.nodeName=="moby:CrossReference":
                 self.__cross__=[]
                 for ref in elt.childNodes:
-                    self.__cross__.append(ref.toxml())
+                    self.__cross__.append(um.loads(ref))
             if elt.nodeType==elt.ELEMENT_NODE and (elt.nodeName=="Integer" or elt.nodeName=="moby:Integer") and (elt.getAttribute("articleName")=="direction" or elt.getAttribute("moby:articleName")=="direction"):
                 t=MobyInteger()
-                t.fromMoby(elt.toxml())
+                t.fromMoby(elt)
                 self.Direction=t.content
             if elt.nodeType==elt.ELEMENT_NODE and (elt.nodeName=="String" or elt.nodeName=="moby:String") and (elt.getAttribute("articleName")=="partner" or elt.getAttribute("moby:articleName")=="partner"):
                 t=MobyString()
-                t.fromMoby(elt.toxml())
+                t.fromMoby(elt)
                 self.Partner=t.content
\ No newline at end of file

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/ontology/Interactor.py,v
retrieving revision 1.4
retrieving revision 1.5
diff -u -r1.4 -r1.5
--- /home/repository/moby/moby-live/Python/bioMoby/ontology/Interactor.py	2005/02/01 08:52:16	1.4
+++ /home/repository/moby/moby-live/Python/bioMoby/ontology/Interactor.py	2005/02/01 14:20:44	1.5
@@ -27,7 +27,9 @@
         """ Load the attributes from an XML string
         """
         from bioMoby.mobyMarshal import MobyUnmarshaller
-        doc=parseString(value).firstChild
+        doc=value
+        if isinstance(value, str):
+            doc=parseString(value).firstChild
         um=MobyUnmarshaller()
         self.content=""
         self.namespace=doc.getAttribute("moby:namespace")
@@ -47,8 +49,8 @@
             if elt.nodeName=="CrossReference" or elt.nodeName=="moby:CrossReference":
                 self.__cross__=[]
                 for ref in elt.childNodes:
-                    self.__cross__.append(ref.toxml())
+                    self.__cross__.append(um.loads(ref))
             if elt.nodeType==elt.ELEMENT_NODE and (elt.nodeName=="String" or elt.nodeName=="moby:String") and (elt.getAttribute("articleName")=="role" or elt.getAttribute("moby:articleName")=="role"):
                 t=MobyString()
-                t.fromMoby(elt.toxml())
+                t.fromMoby(elt)
                 self.Role=t.content
\ No newline at end of file

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/ontology/MEME_Text.py,v
retrieving revision 1.4
retrieving revision 1.5
diff -u -r1.4 -r1.5
--- /home/repository/moby/moby-live/Python/bioMoby/ontology/MEME_Text.py	2005/02/01 08:52:16	1.4
+++ /home/repository/moby/moby-live/Python/bioMoby/ontology/MEME_Text.py	2005/02/01 14:20:44	1.5
@@ -26,7 +26,9 @@
         """ Load the attributes from an XML string
         """
         from bioMoby.mobyMarshal import MobyUnmarshaller
-        doc=parseString(value).firstChild
+        doc=value
+        if isinstance(value, str):
+            doc=parseString(value).firstChild
         um=MobyUnmarshaller()
         self.content=""
         self.namespace=doc.getAttribute("moby:namespace")
@@ -46,4 +48,4 @@
             if elt.nodeName=="CrossReference" or elt.nodeName=="moby:CrossReference":
                 self.__cross__=[]
                 for ref in elt.childNodes:
-                    self.__cross__.append(ref.toxml())
\ No newline at end of file
+                    self.__cross__.append(um.loads(ref))
\ No newline at end of file

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/ontology/MGIS_ACCESSION.py,v
retrieving revision 1.4
retrieving revision 1.5
diff -u -r1.4 -r1.5
--- /home/repository/moby/moby-live/Python/bioMoby/ontology/MGIS_ACCESSION.py	2005/02/01 08:52:16	1.4
+++ /home/repository/moby/moby-live/Python/bioMoby/ontology/MGIS_ACCESSION.py	2005/02/01 14:20:44	1.5
@@ -46,7 +46,9 @@
         """ Load the attributes from an XML string
         """
         from bioMoby.mobyMarshal import MobyUnmarshaller
-        doc=parseString(value).firstChild
+        doc=value
+        if isinstance(value, str):
+            doc=parseString(value).firstChild
         um=MobyUnmarshaller()
         self.content=""
         self.namespace=doc.getAttribute("moby:namespace")
@@ -66,84 +68,84 @@
             if elt.nodeName=="CrossReference" or elt.nodeName=="moby:CrossReference":
                 self.__cross__=[]
                 for ref in elt.childNodes:
-                    self.__cross__.append(ref.toxml())
+                    self.__cross__.append(um.loads(ref))
             if elt.nodeType==elt.ELEMENT_NODE and (elt.nodeName=="String" or elt.nodeName=="moby:String") and (elt.getAttribute("articleName")=="Biotic_stress_Yellowsig" or elt.getAttribute("moby:articleName")=="Biotic_stress_Yellowsig"):
                 t=MobyString()
-                t.fromMoby(elt.toxml())
+                t.fromMoby(elt)
                 self.Biotic_stress_Yellowsig=t.content
             if elt.nodeType==elt.ELEMENT_NODE and (elt.nodeName=="String" or elt.nodeName=="moby:String") and (elt.getAttribute("articleName")=="mcpd:ORIGCTY" or elt.getAttribute("moby:articleName")=="mcpd:ORIGCTY"):
                 t=MobyString()
-                t.fromMoby(elt.toxml())
+                t.fromMoby(elt)
                 self.McpdORIGCTY=t.content
             if elt.nodeType==elt.ELEMENT_NODE and (elt.nodeName=="String" or elt.nodeName=="moby:String") and (elt.getAttribute("articleName")=="mgis:SECTION" or elt.getAttribute("moby:articleName")=="mgis:SECTION"):
                 t=MobyString()
-                t.fromMoby(elt.toxml())
+                t.fromMoby(elt)
                 self.MgisSECTION=t.content
             if elt.nodeType==elt.ELEMENT_NODE and (elt.nodeName=="String" or elt.nodeName=="moby:String") and (elt.getAttribute("articleName")=="mcpd:SPECIES" or elt.getAttribute("moby:articleName")=="mcpd:SPECIES"):
                 t=MobyString()
-                t.fromMoby(elt.toxml())
+                t.fromMoby(elt)
                 self.McpdSPECIES=t.content
             if elt.nodeType==elt.ELEMENT_NODE and (elt.nodeName=="String" or elt.nodeName=="moby:String") and (elt.getAttribute("articleName")=="mcpd:COLLCODE" or elt.getAttribute("moby:articleName")=="mcpd:COLLCODE"):
                 t=MobyString()
-                t.fromMoby(elt.toxml())
+                t.fromMoby(elt)
                 self.McpdCOLLCODE=t.content
             if elt.nodeType==elt.ELEMENT_NODE and (elt.nodeName=="String" or elt.nodeName=="moby:String") and (elt.getAttribute("articleName")=="Biotic_stress_Blacksig" or elt.getAttribute("moby:articleName")=="Biotic_stress_Blacksig"):
                 t=MobyString()
-                t.fromMoby(elt.toxml())
+                t.fromMoby(elt)
                 self.Biotic_stress_Blacksig=t.content
             if elt.nodeType==elt.ELEMENT_NODE and (elt.nodeName=="String" or elt.nodeName=="moby:String") and (elt.getAttribute("articleName")=="Biotic_stress_Fusarium" or elt.getAttribute("moby:articleName")=="Biotic_stress_Fusarium"):
                 t=MobyString()
-                t.fromMoby(elt.toxml())
+                t.fromMoby(elt)
                 self.Biotic_stress_Fusarium=t.content
             if elt.nodeType==elt.ELEMENT_NODE and (elt.nodeName=="String" or elt.nodeName=="moby:String") and (elt.getAttribute("articleName")=="Biotic_stress_pseudomonas" or elt.getAttribute("moby:articleName")=="Biotic_stress_pseudomonas"):
                 t=MobyString()
-                t.fromMoby(elt.toxml())
+                t.fromMoby(elt)
                 self.Biotic_stress_pseudomonas=t.content
             if elt.nodeType==elt.ELEMENT_NODE and (elt.nodeName=="String" or elt.nodeName=="moby:String") and (elt.getAttribute("articleName")=="Biotic_stress_Radopholus" or elt.getAttribute("moby:articleName")=="Biotic_stress_Radopholus"):
                 t=MobyString()
-                t.fromMoby(elt.toxml())
+                t.fromMoby(elt)
                 self.Biotic_stress_Radopholus=t.content
             if elt.nodeType==elt.ELEMENT_NODE and (elt.nodeName=="String" or elt.nodeName=="moby:String") and (elt.getAttribute("articleName")=="Biotic_stress_Pratylenchuscof" or elt.getAttribute("moby:articleName")=="Biotic_stress_Pratylenchuscof"):
                 t=MobyString()
-                t.fromMoby(elt.toxml())
+                t.fromMoby(elt)
                 self.Biotic_stress_Pratylenchuscof=t.content
             if elt.nodeType==elt.ELEMENT_NODE and (elt.nodeName=="String" or elt.nodeName=="moby:String") and (elt.getAttribute("articleName")=="Biotic_stress_Pratylenchusgood" or elt.getAttribute("moby:articleName")=="Biotic_stress_Pratylenchusgood"):
                 t=MobyString()
-                t.fromMoby(elt.toxml())
+                t.fromMoby(elt)
                 self.Biotic_stress_Pratylenchusgood=t.content
             if elt.nodeType==elt.ELEMENT_NODE and (elt.nodeName=="String" or elt.nodeName=="moby:String") and (elt.getAttribute("articleName")=="Biotic_stress_cosmopolites" or elt.getAttribute("moby:articleName")=="Biotic_stress_cosmopolites"):
                 t=MobyString()
-                t.fromMoby(elt.toxml())
+                t.fromMoby(elt)
                 self.Biotic_stress_cosmopolites=t.content
             if elt.nodeType==elt.ELEMENT_NODE and (elt.nodeName=="String" or elt.nodeName=="moby:String") and (elt.getAttribute("articleName")=="Abiotic_stress_Lowtemp" or elt.getAttribute("moby:articleName")=="Abiotic_stress_Lowtemp"):
                 t=MobyString()
-                t.fromMoby(elt.toxml())
+                t.fromMoby(elt)
                 self.Abiotic_stress_Lowtemp=t.content
             if elt.nodeType==elt.ELEMENT_NODE and (elt.nodeName=="String" or elt.nodeName=="moby:String") and (elt.getAttribute("articleName")=="Abiotic_stress_Drought" or elt.getAttribute("moby:articleName")=="Abiotic_stress_Drought"):
                 t=MobyString()
-                t.fromMoby(elt.toxml())
+                t.fromMoby(elt)
                 self.Abiotic_stress_Drought=t.content
             if elt.nodeType==elt.ELEMENT_NODE and (elt.nodeName=="String" or elt.nodeName=="moby:String") and (elt.getAttribute("articleName")=="Abiotic_stress_Flooding" or elt.getAttribute("moby:articleName")=="Abiotic_stress_Flooding"):
                 t=MobyString()
-                t.fromMoby(elt.toxml())
+                t.fromMoby(elt)
                 self.Abiotic_stress_Flooding=t.content
             if elt.nodeType==elt.ELEMENT_NODE and (elt.nodeName=="String" or elt.nodeName=="moby:String") and (elt.getAttribute("articleName")=="Abiotic_stress_Mineraldef" or elt.getAttribute("moby:articleName")=="Abiotic_stress_Mineraldef"):
                 t=MobyString()
-                t.fromMoby(elt.toxml())
+                t.fromMoby(elt)
                 self.Abiotic_stress_Mineraldef=t.content
             if elt.nodeType==elt.ELEMENT_NODE and (elt.nodeName=="String" or elt.nodeName=="moby:String") and (elt.getAttribute("articleName")=="Abiotic_stress_Winds" or elt.getAttribute("moby:articleName")=="Abiotic_stress_Winds"):
                 t=MobyString()
-                t.fromMoby(elt.toxml())
+                t.fromMoby(elt)
                 self.Abiotic_stress_Winds=t.content
             if elt.nodeType==elt.ELEMENT_NODE and (elt.nodeName=="String" or elt.nodeName=="moby:String") and (elt.getAttribute("articleName")=="Abiotic_stress_Soilacidity" or elt.getAttribute("moby:articleName")=="Abiotic_stress_Soilacidity"):
                 t=MobyString()
-                t.fromMoby(elt.toxml())
+                t.fromMoby(elt)
                 self.Abiotic_stress_Soilacidity=t.content
             if elt.nodeType==elt.ELEMENT_NODE and (elt.nodeName=="String" or elt.nodeName=="moby:String") and (elt.getAttribute("articleName")=="Abiotic_stress_Manganesetox" or elt.getAttribute("moby:articleName")=="Abiotic_stress_Manganesetox"):
                 t=MobyString()
-                t.fromMoby(elt.toxml())
+                t.fromMoby(elt)
                 self.Abiotic_stress_Manganesetox=t.content
             if elt.nodeType==elt.ELEMENT_NODE and (elt.nodeName=="String" or elt.nodeName=="moby:String") and (elt.getAttribute("articleName")=="Abiotic_stress_Hightemp" or elt.getAttribute("moby:articleName")=="Abiotic_stress_Hightemp"):
                 t=MobyString()
-                t.fromMoby(elt.toxml())
+                t.fromMoby(elt)
                 self.Abiotic_stress_Hightemp=t.content
\ No newline at end of file

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/ontology/MMP_Locus.py,v
retrieving revision 1.4
retrieving revision 1.5
diff -u -r1.4 -r1.5
--- /home/repository/moby/moby-live/Python/bioMoby/ontology/MMP_Locus.py	2005/02/01 08:52:16	1.4
+++ /home/repository/moby/moby-live/Python/bioMoby/ontology/MMP_Locus.py	2005/02/01 14:20:44	1.5
@@ -25,7 +25,9 @@
         """ Load the attributes from an XML string
         """
         from bioMoby.mobyMarshal import MobyUnmarshaller
-        doc=parseString(value).firstChild
+        doc=value
+        if isinstance(value, str):
+            doc=parseString(value).firstChild
         um=MobyUnmarshaller()
         self.content=""
         self.namespace=doc.getAttribute("moby:namespace")
@@ -45,4 +47,4 @@
             if elt.nodeName=="CrossReference" or elt.nodeName=="moby:CrossReference":
                 self.__cross__=[]
                 for ref in elt.childNodes:
-                    self.__cross__.append(ref.toxml())
\ No newline at end of file
+                    self.__cross__.append(um.loads(ref))
\ No newline at end of file

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/ontology/MO_Term_Test.py,v
retrieving revision 1.4
retrieving revision 1.5
diff -u -r1.4 -r1.5
--- /home/repository/moby/moby-live/Python/bioMoby/ontology/MO_Term_Test.py	2005/02/01 08:52:16	1.4
+++ /home/repository/moby/moby-live/Python/bioMoby/ontology/MO_Term_Test.py	2005/02/01 14:20:44	1.5
@@ -30,7 +30,9 @@
         """ Load the attributes from an XML string
         """
         from bioMoby.mobyMarshal import MobyUnmarshaller
-        doc=parseString(value).firstChild
+        doc=value
+        if isinstance(value, str):
+            doc=parseString(value).firstChild
         um=MobyUnmarshaller()
         self.content=""
         self.namespace=doc.getAttribute("moby:namespace")
@@ -50,20 +52,20 @@
             if elt.nodeName=="CrossReference" or elt.nodeName=="moby:CrossReference":
                 self.__cross__=[]
                 for ref in elt.childNodes:
-                    self.__cross__.append(ref.toxml())
+                    self.__cross__.append(um.loads(ref))
             if elt.nodeType==elt.ELEMENT_NODE and (elt.nodeName=="String" or elt.nodeName=="moby:String") and (elt.getAttribute("articleName")=="class_name" or elt.getAttribute("moby:articleName")=="class_name"):
                 t=MobyString()
-                t.fromMoby(elt.toxml())
+                t.fromMoby(elt)
                 self.Class_name=t.content
             if elt.nodeType==elt.ELEMENT_NODE and (elt.nodeName=="String" or elt.nodeName=="moby:String") and (elt.getAttribute("articleName")=="individual_name" or elt.getAttribute("moby:articleName")=="individual_name"):
                 t=MobyString()
-                t.fromMoby(elt.toxml())
+                t.fromMoby(elt)
                 self.Individual_name=t.content
             if elt.nodeType==elt.ELEMENT_NODE and (elt.nodeName=="String" or elt.nodeName=="moby:String") and (elt.getAttribute("articleName")=="individual_desc" or elt.getAttribute("moby:articleName")=="individual_desc"):
                 t=MobyString()
-                t.fromMoby(elt.toxml())
+                t.fromMoby(elt)
                 self.Individual_desc=t.content
             if elt.nodeType==elt.ELEMENT_NODE and (elt.nodeName=="String" or elt.nodeName=="moby:String") and (elt.getAttribute("articleName")=="class_desc" or elt.getAttribute("moby:articleName")=="class_desc"):
                 t=MobyString()
-                t.fromMoby(elt.toxml())
+                t.fromMoby(elt)
                 self.Class_desc=t.content
\ No newline at end of file

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/ontology/MmCIFText.py,v
retrieving revision 1.4
retrieving revision 1.5
diff -u -r1.4 -r1.5
--- /home/repository/moby/moby-live/Python/bioMoby/ontology/MmCIFText.py	2005/02/01 08:52:16	1.4
+++ /home/repository/moby/moby-live/Python/bioMoby/ontology/MmCIFText.py	2005/02/01 14:20:44	1.5
@@ -26,7 +26,9 @@
         """ Load the attributes from an XML string
         """
         from bioMoby.mobyMarshal import MobyUnmarshaller
-        doc=parseString(value).firstChild
+        doc=value
+        if isinstance(value, str):
+            doc=parseString(value).firstChild
         um=MobyUnmarshaller()
         self.content=""
         self.namespace=doc.getAttribute("moby:namespace")
@@ -46,4 +48,4 @@
             if elt.nodeName=="CrossReference" or elt.nodeName=="moby:CrossReference":
                 self.__cross__=[]
                 for ref in elt.childNodes:
-                    self.__cross__.append(ref.toxml())
\ No newline at end of file
+                    self.__cross__.append(um.loads(ref))
\ No newline at end of file

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/ontology/Multi_key_value_pair.py,v
retrieving revision 1.4
retrieving revision 1.5
diff -u -r1.4 -r1.5
--- /home/repository/moby/moby-live/Python/bioMoby/ontology/Multi_key_value_pair.py	2005/02/01 08:52:16	1.4
+++ /home/repository/moby/moby-live/Python/bioMoby/ontology/Multi_key_value_pair.py	2005/02/01 14:20:44	1.5
@@ -28,7 +28,9 @@
         """ Load the attributes from an XML string
         """
         from bioMoby.mobyMarshal import MobyUnmarshaller
-        doc=parseString(value).firstChild
+        doc=value
+        if isinstance(value, str):
+            doc=parseString(value).firstChild
         um=MobyUnmarshaller()
         self.content=""
         self.namespace=doc.getAttribute("moby:namespace")
@@ -49,12 +51,12 @@
             if elt.nodeName=="CrossReference" or elt.nodeName=="moby:CrossReference":
                 self.__cross__=[]
                 for ref in elt.childNodes:
-                    self.__cross__.append(ref.toxml())
+                    self.__cross__.append(um.loads(ref))
             if elt.nodeType==elt.ELEMENT_NODE and (elt.nodeName=="String" or elt.nodeName=="moby:String") and (elt.getAttribute("articleName")=="key" or elt.getAttribute("moby:articleName")=="key"):
                 t=MobyString()
-                t.fromMoby(elt.toxml())
+                t.fromMoby(elt)
                 self.Key=t.content
             if elt.nodeType==elt.ELEMENT_NODE and (elt.nodeName=="String" or elt.nodeName=="moby:String") and (elt.getAttribute("articleName")=="value" or elt.getAttribute("moby:articleName")=="value"):
                 t=MobyString()
-                t.fromMoby(elt.toxml())
+                t.fromMoby(elt)
                 self.Value.append(t.content)
\ No newline at end of file

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/ontology/MyTestingDataType_11024145298313.py,v
retrieving revision 1.4
retrieving revision 1.5
diff -u -r1.4 -r1.5
--- /home/repository/moby/moby-live/Python/bioMoby/ontology/MyTestingDataType_11024145298313.py	2005/02/01 08:52:16	1.4
+++ /home/repository/moby/moby-live/Python/bioMoby/ontology/MyTestingDataType_11024145298313.py	2005/02/01 14:20:44	1.5
@@ -26,7 +26,9 @@
         """ Load the attributes from an XML string
         """
         from bioMoby.mobyMarshal import MobyUnmarshaller
-        doc=parseString(value).firstChild
+        doc=value
+        if isinstance(value, str):
+            doc=parseString(value).firstChild
         um=MobyUnmarshaller()
         self.content=""
         self.namespace=doc.getAttribute("moby:namespace")
@@ -46,4 +48,4 @@
             if elt.nodeName=="CrossReference" or elt.nodeName=="moby:CrossReference":
                 self.__cross__=[]
                 for ref in elt.childNodes:
-                    self.__cross__.append(ref.toxml())
\ No newline at end of file
+                    self.__cross__.append(um.loads(ref))
\ No newline at end of file

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/ontology/MyTree.py,v
retrieving revision 1.4
retrieving revision 1.5
diff -u -r1.4 -r1.5
--- /home/repository/moby/moby-live/Python/bioMoby/ontology/MyTree.py	2005/02/01 08:52:16	1.4
+++ /home/repository/moby/moby-live/Python/bioMoby/ontology/MyTree.py	2005/02/01 14:20:44	1.5
@@ -26,7 +26,9 @@
         """ Load the attributes from an XML string
         """
         from bioMoby.mobyMarshal import MobyUnmarshaller
-        doc=parseString(value).firstChild
+        doc=value
+        if isinstance(value, str):
+            doc=parseString(value).firstChild
         um=MobyUnmarshaller()
         self.content=""
         self.namespace=doc.getAttribute("moby:namespace")
@@ -46,4 +48,4 @@
             if elt.nodeName=="CrossReference" or elt.nodeName=="moby:CrossReference":
                 self.__cross__=[]
                 for ref in elt.childNodes:
-                    self.__cross__.append(ref.toxml())
\ No newline at end of file
+                    self.__cross__.append(um.loads(ref))
\ No newline at end of file

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/ontology/NCBI_BLAST_Text.py,v
retrieving revision 1.4
retrieving revision 1.5
diff -u -r1.4 -r1.5
--- /home/repository/moby/moby-live/Python/bioMoby/ontology/NCBI_BLAST_Text.py	2005/02/01 08:52:16	1.4
+++ /home/repository/moby/moby-live/Python/bioMoby/ontology/NCBI_BLAST_Text.py	2005/02/01 14:20:44	1.5
@@ -26,7 +26,9 @@
         """ Load the attributes from an XML string
         """
         from bioMoby.mobyMarshal import MobyUnmarshaller
-        doc=parseString(value).firstChild
+        doc=value
+        if isinstance(value, str):
+            doc=parseString(value).firstChild
         um=MobyUnmarshaller()
         self.content=""
         self.namespace=doc.getAttribute("moby:namespace")
@@ -46,4 +48,4 @@
             if elt.nodeName=="CrossReference" or elt.nodeName=="moby:CrossReference":
                 self.__cross__=[]
                 for ref in elt.childNodes:
-                    self.__cross__.append(ref.toxml())
\ No newline at end of file
+                    self.__cross__.append(um.loads(ref))
\ No newline at end of file

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/ontology/NCBI_Blast_XML.py,v
retrieving revision 1.4
retrieving revision 1.5
diff -u -r1.4 -r1.5
--- /home/repository/moby/moby-live/Python/bioMoby/ontology/NCBI_Blast_XML.py	2005/02/01 08:52:16	1.4
+++ /home/repository/moby/moby-live/Python/bioMoby/ontology/NCBI_Blast_XML.py	2005/02/01 14:20:44	1.5
@@ -26,7 +26,9 @@
         """ Load the attributes from an XML string
         """
         from bioMoby.mobyMarshal import MobyUnmarshaller
-        doc=parseString(value).firstChild
+        doc=value
+        if isinstance(value, str):
+            doc=parseString(value).firstChild
         um=MobyUnmarshaller()
         self.content=""
         self.namespace=doc.getAttribute("moby:namespace")
@@ -46,4 +48,4 @@
             if elt.nodeName=="CrossReference" or elt.nodeName=="moby:CrossReference":
                 self.__cross__=[]
                 for ref in elt.childNodes:
-                    self.__cross__.append(ref.toxml())
\ No newline at end of file
+                    self.__cross__.append(um.loads(ref))
\ No newline at end of file

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/ontology/NCBI_Blast_XML_Gif.py,v
retrieving revision 1.4
retrieving revision 1.5
diff -u -r1.4 -r1.5
--- /home/repository/moby/moby-live/Python/bioMoby/ontology/NCBI_Blast_XML_Gif.py	2005/02/01 08:52:16	1.4
+++ /home/repository/moby/moby-live/Python/bioMoby/ontology/NCBI_Blast_XML_Gif.py	2005/02/01 14:20:44	1.5
@@ -28,7 +28,9 @@
         """ Load the attributes from an XML string
         """
         from bioMoby.mobyMarshal import MobyUnmarshaller
-        doc=parseString(value).firstChild
+        doc=value
+        if isinstance(value, str):
+            doc=parseString(value).firstChild
         um=MobyUnmarshaller()
         self.content=""
         self.namespace=doc.getAttribute("moby:namespace")
@@ -48,7 +50,7 @@
             if elt.nodeName=="CrossReference" or elt.nodeName=="moby:CrossReference":
                 self.__cross__=[]
                 for ref in elt.childNodes:
-                    self.__cross__.append(ref.toxml())
+                    self.__cross__.append(um.loads(ref))
             if elt.nodeType==elt.ELEMENT_NODE and (elt.nodeName=="b64_encoded_gif" or elt.nodeName=="moby:b64_encoded_gif") and (elt.getAttribute("articleName")=="hitGraph" or elt.getAttribute("moby:articleName")=="hitGraph"):
                 self.HitGraph=MobyB64_encoded_gif()
-                self.HitGraph.fromMoby(elt.toxml())
\ No newline at end of file
+                self.HitGraph.fromMoby(elt)
\ No newline at end of file

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/ontology/NCBI_Blast_XML_Gif_Map.py,v
retrieving revision 1.4
retrieving revision 1.5
diff -u -r1.4 -r1.5
--- /home/repository/moby/moby-live/Python/bioMoby/ontology/NCBI_Blast_XML_Gif_Map.py	2005/02/01 08:52:16	1.4
+++ /home/repository/moby/moby-live/Python/bioMoby/ontology/NCBI_Blast_XML_Gif_Map.py	2005/02/01 14:20:44	1.5
@@ -30,7 +30,9 @@
         """ Load the attributes from an XML string
         """
         from bioMoby.mobyMarshal import MobyUnmarshaller
-        doc=parseString(value).firstChild
+        doc=value
+        if isinstance(value, str):
+            doc=parseString(value).firstChild
         um=MobyUnmarshaller()
         self.content=""
         self.namespace=doc.getAttribute("moby:namespace")
@@ -50,10 +52,10 @@
             if elt.nodeName=="CrossReference" or elt.nodeName=="moby:CrossReference":
                 self.__cross__=[]
                 for ref in elt.childNodes:
-                    self.__cross__.append(ref.toxml())
+                    self.__cross__.append(um.loads(ref))
             if elt.nodeType==elt.ELEMENT_NODE and (elt.nodeName=="b64_encoded_gif" or elt.nodeName=="moby:b64_encoded_gif") and (elt.getAttribute("articleName")=="hitGraph" or elt.getAttribute("moby:articleName")=="hitGraph"):
                 self.HitGraph=MobyB64_encoded_gif()
-                self.HitGraph.fromMoby(elt.toxml())
+                self.HitGraph.fromMoby(elt)
             if elt.nodeType==elt.ELEMENT_NODE and (elt.nodeName=="text-html" or elt.nodeName=="moby:text-html") and (elt.getAttribute("articleName")=="areaMap" or elt.getAttribute("moby:articleName")=="areaMap"):
                 self.AreaMap=MobyTextHtml()
-                self.AreaMap.fromMoby(elt.toxml())
\ No newline at end of file
+                self.AreaMap.fromMoby(elt)
\ No newline at end of file

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/ontology/NCBI_MEME_Text.py,v
retrieving revision 1.4
retrieving revision 1.5
diff -u -r1.4 -r1.5
--- /home/repository/moby/moby-live/Python/bioMoby/ontology/NCBI_MEME_Text.py	2005/02/01 08:52:16	1.4
+++ /home/repository/moby/moby-live/Python/bioMoby/ontology/NCBI_MEME_Text.py	2005/02/01 14:20:44	1.5
@@ -26,7 +26,9 @@
         """ Load the attributes from an XML string
         """
         from bioMoby.mobyMarshal import MobyUnmarshaller
-        doc=parseString(value).firstChild
+        doc=value
+        if isinstance(value, str):
+            doc=parseString(value).firstChild
         um=MobyUnmarshaller()
         self.content=""
         self.namespace=doc.getAttribute("moby:namespace")
@@ -46,4 +48,4 @@
             if elt.nodeName=="CrossReference" or elt.nodeName=="moby:CrossReference":
                 self.__cross__=[]
                 for ref in elt.childNodes:
-                    self.__cross__.append(ref.toxml())
\ No newline at end of file
+                    self.__cross__.append(um.loads(ref))
\ No newline at end of file

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/ontology/NucleotideSequence.py,v
retrieving revision 1.4
retrieving revision 1.5
diff -u -r1.4 -r1.5
--- /home/repository/moby/moby-live/Python/bioMoby/ontology/NucleotideSequence.py	2005/02/01 08:52:16	1.4
+++ /home/repository/moby/moby-live/Python/bioMoby/ontology/NucleotideSequence.py	2005/02/01 14:20:44	1.5
@@ -29,7 +29,9 @@
         """ Load the attributes from an XML string
         """
         from bioMoby.mobyMarshal import MobyUnmarshaller
-        doc=parseString(value).firstChild
+        doc=value
+        if isinstance(value, str):
+            doc=parseString(value).firstChild
         um=MobyUnmarshaller()
         self.content=""
         self.namespace=doc.getAttribute("moby:namespace")
@@ -49,12 +51,12 @@
             if elt.nodeName=="CrossReference" or elt.nodeName=="moby:CrossReference":
                 self.__cross__=[]
                 for ref in elt.childNodes:
-                    self.__cross__.append(ref.toxml())
+                    self.__cross__.append(um.loads(ref))
             if elt.nodeType==elt.ELEMENT_NODE and (elt.nodeName=="Integer" or elt.nodeName=="moby:Integer") and (elt.getAttribute("articleName")=="Length" or elt.getAttribute("moby:articleName")=="Length"):
                 t=MobyInteger()
-                t.fromMoby(elt.toxml())
+                t.fromMoby(elt)
                 self.Length=t.content
             if elt.nodeType==elt.ELEMENT_NODE and (elt.nodeName=="String" or elt.nodeName=="moby:String") and (elt.getAttribute("articleName")=="SequenceString" or elt.getAttribute("moby:articleName")=="SequenceString"):
                 t=MobyString()
-                t.fromMoby(elt.toxml())
+                t.fromMoby(elt)
                 self.SequenceString=t.content
\ No newline at end of file

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/ontology/PDBFormattedText.py,v
retrieving revision 1.4
retrieving revision 1.5
diff -u -r1.4 -r1.5
--- /home/repository/moby/moby-live/Python/bioMoby/ontology/PDBFormattedText.py	2005/02/01 08:52:16	1.4
+++ /home/repository/moby/moby-live/Python/bioMoby/ontology/PDBFormattedText.py	2005/02/01 14:20:44	1.5
@@ -26,7 +26,9 @@
         """ Load the attributes from an XML string
         """
         from bioMoby.mobyMarshal import MobyUnmarshaller
-        doc=parseString(value).firstChild
+        doc=value
+        if isinstance(value, str):
+            doc=parseString(value).firstChild
         um=MobyUnmarshaller()
         self.content=""
         self.namespace=doc.getAttribute("moby:namespace")
@@ -46,4 +48,4 @@
             if elt.nodeName=="CrossReference" or elt.nodeName=="moby:CrossReference":
                 self.__cross__=[]
                 for ref in elt.childNodes:
-                    self.__cross__.append(ref.toxml())
\ No newline at end of file
+                    self.__cross__.append(um.loads(ref))
\ No newline at end of file

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/ontology/PDBText.py,v
retrieving revision 1.4
retrieving revision 1.5
diff -u -r1.4 -r1.5
--- /home/repository/moby/moby-live/Python/bioMoby/ontology/PDBText.py	2005/02/01 08:52:16	1.4
+++ /home/repository/moby/moby-live/Python/bioMoby/ontology/PDBText.py	2005/02/01 14:20:44	1.5
@@ -26,7 +26,9 @@
         """ Load the attributes from an XML string
         """
         from bioMoby.mobyMarshal import MobyUnmarshaller
-        doc=parseString(value).firstChild
+        doc=value
+        if isinstance(value, str):
+            doc=parseString(value).firstChild
         um=MobyUnmarshaller()
         self.content=""
         self.namespace=doc.getAttribute("moby:namespace")
@@ -46,4 +48,4 @@
             if elt.nodeName=="CrossReference" or elt.nodeName=="moby:CrossReference":
                 self.__cross__=[]
                 for ref in elt.childNodes:
-                    self.__cross__.append(ref.toxml())
\ No newline at end of file
+                    self.__cross__.append(um.loads(ref))
\ No newline at end of file

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/ontology/PDGJOB.py,v
retrieving revision 1.4
retrieving revision 1.5
diff -u -r1.4 -r1.5
--- /home/repository/moby/moby-live/Python/bioMoby/ontology/PDGJOB.py	2005/02/01 08:52:16	1.4
+++ /home/repository/moby/moby-live/Python/bioMoby/ontology/PDGJOB.py	2005/02/01 14:20:44	1.5
@@ -32,7 +32,9 @@
         """ Load the attributes from an XML string
         """
         from bioMoby.mobyMarshal import MobyUnmarshaller
-        doc=parseString(value).firstChild
+        doc=value
+        if isinstance(value, str):
+            doc=parseString(value).firstChild
         um=MobyUnmarshaller()
         self.content=""
         self.namespace=doc.getAttribute("moby:namespace")
@@ -52,23 +54,23 @@
             if elt.nodeName=="CrossReference" or elt.nodeName=="moby:CrossReference":
                 self.__cross__=[]
                 for ref in elt.childNodes:
-                    self.__cross__.append(ref.toxml())
+                    self.__cross__.append(um.loads(ref))
             if elt.nodeType==elt.ELEMENT_NODE and (elt.nodeName=="String" or elt.nodeName=="moby:String") and (elt.getAttribute("articleName")=="answerService" or elt.getAttribute("moby:articleName")=="answerService"):
                 t=MobyString()
-                t.fromMoby(elt.toxml())
+                t.fromMoby(elt)
                 self.AnswerService=t.content
             if elt.nodeType==elt.ELEMENT_NODE and (elt.nodeName=="String" or elt.nodeName=="moby:String") and (elt.getAttribute("articleName")=="authURI" or elt.getAttribute("moby:articleName")=="authURI"):
                 t=MobyString()
-                t.fromMoby(elt.toxml())
+                t.fromMoby(elt)
                 self.AuthURI=t.content
             if elt.nodeType==elt.ELEMENT_NODE and (elt.nodeName=="DateTime" or elt.nodeName=="moby:DateTime") and (elt.getAttribute("articleName")=="timeout" or elt.getAttribute("moby:articleName")=="timeout"):
                 self.Timeout=MobyDateTime()
-                self.Timeout.fromMoby(elt.toxml())
+                self.Timeout.fromMoby(elt)
             if elt.nodeType==elt.ELEMENT_NODE and (elt.nodeName=="String" or elt.nodeName=="moby:String") and (elt.getAttribute("articleName")=="killcode" or elt.getAttribute("moby:articleName")=="killcode"):
                 t=MobyString()
-                t.fromMoby(elt.toxml())
+                t.fromMoby(elt)
                 self.Killcode=t.content
             if elt.nodeType==elt.ELEMENT_NODE and (elt.nodeName=="String" or elt.nodeName=="moby:String") and (elt.getAttribute("articleName")=="killService" or elt.getAttribute("moby:articleName")=="killService"):
                 t=MobyString()
-                t.fromMoby(elt.toxml())
+                t.fromMoby(elt)
                 self.KillService=t.content
\ No newline at end of file

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/ontology/PHDText.py,v
retrieving revision 1.4
retrieving revision 1.5
diff -u -r1.4 -r1.5
--- /home/repository/moby/moby-live/Python/bioMoby/ontology/PHDText.py	2005/02/01 08:52:16	1.4
+++ /home/repository/moby/moby-live/Python/bioMoby/ontology/PHDText.py	2005/02/01 14:20:44	1.5
@@ -26,7 +26,9 @@
         """ Load the attributes from an XML string
         """
         from bioMoby.mobyMarshal import MobyUnmarshaller
-        doc=parseString(value).firstChild
+        doc=value
+        if isinstance(value, str):
+            doc=parseString(value).firstChild
         um=MobyUnmarshaller()
         self.content=""
         self.namespace=doc.getAttribute("moby:namespace")
@@ -46,4 +48,4 @@
             if elt.nodeName=="CrossReference" or elt.nodeName=="moby:CrossReference":
                 self.__cross__=[]
                 for ref in elt.childNodes:
-                    self.__cross__.append(ref.toxml())
\ No newline at end of file
+                    self.__cross__.append(um.loads(ref))
\ No newline at end of file

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/ontology/PMUTText.py,v
retrieving revision 1.4
retrieving revision 1.5
diff -u -r1.4 -r1.5
--- /home/repository/moby/moby-live/Python/bioMoby/ontology/PMUTText.py	2005/02/01 08:52:16	1.4
+++ /home/repository/moby/moby-live/Python/bioMoby/ontology/PMUTText.py	2005/02/01 14:20:44	1.5
@@ -26,7 +26,9 @@
         """ Load the attributes from an XML string
         """
         from bioMoby.mobyMarshal import MobyUnmarshaller
-        doc=parseString(value).firstChild
+        doc=value
+        if isinstance(value, str):
+            doc=parseString(value).firstChild
         um=MobyUnmarshaller()
         self.content=""
         self.namespace=doc.getAttribute("moby:namespace")
@@ -46,4 +48,4 @@
             if elt.nodeName=="CrossReference" or elt.nodeName=="moby:CrossReference":
                 self.__cross__=[]
                 for ref in elt.childNodes:
-                    self.__cross__.append(ref.toxml())
\ No newline at end of file
+                    self.__cross__.append(um.loads(ref))
\ No newline at end of file

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/ontology/PSeaTextFormatted.py,v
retrieving revision 1.4
retrieving revision 1.5
diff -u -r1.4 -r1.5
--- /home/repository/moby/moby-live/Python/bioMoby/ontology/PSeaTextFormatted.py	2005/02/01 08:52:16	1.4
+++ /home/repository/moby/moby-live/Python/bioMoby/ontology/PSeaTextFormatted.py	2005/02/01 14:20:44	1.5
@@ -26,7 +26,9 @@
         """ Load the attributes from an XML string
         """
         from bioMoby.mobyMarshal import MobyUnmarshaller
-        doc=parseString(value).firstChild
+        doc=value
+        if isinstance(value, str):
+            doc=parseString(value).firstChild
         um=MobyUnmarshaller()
         self.content=""
         self.namespace=doc.getAttribute("moby:namespace")
@@ -46,4 +48,4 @@
             if elt.nodeName=="CrossReference" or elt.nodeName=="moby:CrossReference":
                 self.__cross__=[]
                 for ref in elt.childNodes:
-                    self.__cross__.append(ref.toxml())
\ No newline at end of file
+                    self.__cross__.append(um.loads(ref))
\ No newline at end of file

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/ontology/PhenotypeDescription.py,v
retrieving revision 1.4
retrieving revision 1.5
diff -u -r1.4 -r1.5
--- /home/repository/moby/moby-live/Python/bioMoby/ontology/PhenotypeDescription.py	2005/02/01 08:52:16	1.4
+++ /home/repository/moby/moby-live/Python/bioMoby/ontology/PhenotypeDescription.py	2005/02/01 14:20:44	1.5
@@ -27,7 +27,9 @@
         """ Load the attributes from an XML string
         """
         from bioMoby.mobyMarshal import MobyUnmarshaller
-        doc=parseString(value).firstChild
+        doc=value
+        if isinstance(value, str):
+            doc=parseString(value).firstChild
         um=MobyUnmarshaller()
         self.content=""
         self.namespace=doc.getAttribute("moby:namespace")
@@ -47,8 +49,8 @@
             if elt.nodeName=="CrossReference" or elt.nodeName=="moby:CrossReference":
                 self.__cross__=[]
                 for ref in elt.childNodes:
-                    self.__cross__.append(ref.toxml())
+                    self.__cross__.append(um.loads(ref))
             if elt.nodeType==elt.ELEMENT_NODE and (elt.nodeName=="String" or elt.nodeName=="moby:String") and (elt.getAttribute("articleName")=="Phenotype" or elt.getAttribute("moby:articleName")=="Phenotype"):
                 t=MobyString()
-                t.fromMoby(elt.toxml())
+                t.fromMoby(elt)
                 self.Phenotype=t.content
\ No newline at end of file

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/ontology/PubMedMEDLINE.py,v
retrieving revision 1.4
retrieving revision 1.5
diff -u -r1.4 -r1.5
--- /home/repository/moby/moby-live/Python/bioMoby/ontology/PubMedMEDLINE.py	2005/02/01 08:52:16	1.4
+++ /home/repository/moby/moby-live/Python/bioMoby/ontology/PubMedMEDLINE.py	2005/02/01 14:20:44	1.5
@@ -26,7 +26,9 @@
         """ Load the attributes from an XML string
         """
         from bioMoby.mobyMarshal import MobyUnmarshaller
-        doc=parseString(value).firstChild
+        doc=value
+        if isinstance(value, str):
+            doc=parseString(value).firstChild
         um=MobyUnmarshaller()
         self.content=""
         self.namespace=doc.getAttribute("moby:namespace")
@@ -46,4 +48,4 @@
             if elt.nodeName=="CrossReference" or elt.nodeName=="moby:CrossReference":
                 self.__cross__=[]
                 for ref in elt.childNodes:
-                    self.__cross__.append(ref.toxml())
\ No newline at end of file
+                    self.__cross__.append(um.loads(ref))
\ No newline at end of file

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/ontology/RNASequence.py,v
retrieving revision 1.4
retrieving revision 1.5
diff -u -r1.4 -r1.5
--- /home/repository/moby/moby-live/Python/bioMoby/ontology/RNASequence.py	2005/02/01 08:52:16	1.4
+++ /home/repository/moby/moby-live/Python/bioMoby/ontology/RNASequence.py	2005/02/01 14:20:44	1.5
@@ -29,7 +29,9 @@
         """ Load the attributes from an XML string
         """
         from bioMoby.mobyMarshal import MobyUnmarshaller
-        doc=parseString(value).firstChild
+        doc=value
+        if isinstance(value, str):
+            doc=parseString(value).firstChild
         um=MobyUnmarshaller()
         self.content=""
         self.namespace=doc.getAttribute("moby:namespace")
@@ -49,12 +51,12 @@
             if elt.nodeName=="CrossReference" or elt.nodeName=="moby:CrossReference":
                 self.__cross__=[]
                 for ref in elt.childNodes:
-                    self.__cross__.append(ref.toxml())
+                    self.__cross__.append(um.loads(ref))
             if elt.nodeType==elt.ELEMENT_NODE and (elt.nodeName=="Integer" or elt.nodeName=="moby:Integer") and (elt.getAttribute("articleName")=="Length" or elt.getAttribute("moby:articleName")=="Length"):
                 t=MobyInteger()
-                t.fromMoby(elt.toxml())
+                t.fromMoby(elt)
                 self.Length=t.content
             if elt.nodeType==elt.ELEMENT_NODE and (elt.nodeName=="String" or elt.nodeName=="moby:String") and (elt.getAttribute("articleName")=="SequenceString" or elt.getAttribute("moby:articleName")=="SequenceString"):
                 t=MobyString()
-                t.fromMoby(elt.toxml())
+                t.fromMoby(elt)
                 self.SequenceString=t.content
\ No newline at end of file

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/ontology/SINGER_ACCESSION.py,v
retrieving revision 1.4
retrieving revision 1.5
diff -u -r1.4 -r1.5
--- /home/repository/moby/moby-live/Python/bioMoby/ontology/SINGER_ACCESSION.py	2005/02/01 08:52:16	1.4
+++ /home/repository/moby/moby-live/Python/bioMoby/ontology/SINGER_ACCESSION.py	2005/02/01 14:20:44	1.5
@@ -30,7 +30,9 @@
         """ Load the attributes from an XML string
         """
         from bioMoby.mobyMarshal import MobyUnmarshaller
-        doc=parseString(value).firstChild
+        doc=value
+        if isinstance(value, str):
+            doc=parseString(value).firstChild
         um=MobyUnmarshaller()
         self.content=""
         self.namespace=doc.getAttribute("moby:namespace")
@@ -50,20 +52,20 @@
             if elt.nodeName=="CrossReference" or elt.nodeName=="moby:CrossReference":
                 self.__cross__=[]
                 for ref in elt.childNodes:
-                    self.__cross__.append(ref.toxml())
+                    self.__cross__.append(um.loads(ref))
             if elt.nodeType==elt.ELEMENT_NODE and (elt.nodeName=="String" or elt.nodeName=="moby:String") and (elt.getAttribute("articleName")=="ACCNO" or elt.getAttribute("moby:articleName")=="ACCNO"):
                 t=MobyString()
-                t.fromMoby(elt.toxml())
+                t.fromMoby(elt)
                 self.ACCNO=t.content
             if elt.nodeType==elt.ELEMENT_NODE and (elt.nodeName=="String" or elt.nodeName=="moby:String") and (elt.getAttribute("articleName")=="ORIGCTY" or elt.getAttribute("moby:articleName")=="ORIGCTY"):
                 t=MobyString()
-                t.fromMoby(elt.toxml())
+                t.fromMoby(elt)
                 self.ORIGCTY=t.content
             if elt.nodeType==elt.ELEMENT_NODE and (elt.nodeName=="String" or elt.nodeName=="moby:String") and (elt.getAttribute("articleName")=="GENUS" or elt.getAttribute("moby:articleName")=="GENUS"):
                 t=MobyString()
-                t.fromMoby(elt.toxml())
+                t.fromMoby(elt)
                 self.GENUS=t.content
             if elt.nodeType==elt.ELEMENT_NODE and (elt.nodeName=="String" or elt.nodeName=="moby:String") and (elt.getAttribute("articleName")=="SPECIES" or elt.getAttribute("moby:articleName")=="SPECIES"):
                 t=MobyString()
-                t.fromMoby(elt.toxml())
+                t.fromMoby(elt)
                 self.SPECIES=t.content
\ No newline at end of file

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/ontology/Sample.py,v
retrieving revision 1.4
retrieving revision 1.5
diff -u -r1.4 -r1.5
--- /home/repository/moby/moby-live/Python/bioMoby/ontology/Sample.py	2005/02/01 08:52:16	1.4
+++ /home/repository/moby/moby-live/Python/bioMoby/ontology/Sample.py	2005/02/01 14:20:44	1.5
@@ -29,7 +29,9 @@
         """ Load the attributes from an XML string
         """
         from bioMoby.mobyMarshal import MobyUnmarshaller
-        doc=parseString(value).firstChild
+        doc=value
+        if isinstance(value, str):
+            doc=parseString(value).firstChild
         um=MobyUnmarshaller()
         self.content=""
         self.namespace=doc.getAttribute("moby:namespace")
@@ -49,12 +51,12 @@
             if elt.nodeName=="CrossReference" or elt.nodeName=="moby:CrossReference":
                 self.__cross__=[]
                 for ref in elt.childNodes:
-                    self.__cross__.append(ref.toxml())
+                    self.__cross__.append(um.loads(ref))
             if elt.nodeType==elt.ELEMENT_NODE and (elt.nodeName=="String" or elt.nodeName=="moby:String") and (elt.getAttribute("articleName")=="code" or elt.getAttribute("moby:articleName")=="code"):
                 t=MobyString()
-                t.fromMoby(elt.toxml())
+                t.fromMoby(elt)
                 self.Code=t.content
             if elt.nodeType==elt.ELEMENT_NODE and (elt.nodeName=="Integer" or elt.nodeName=="moby:Integer") and (elt.getAttribute("articleName")=="affectation" or elt.getAttribute("moby:articleName")=="affectation"):
                 t=MobyInteger()
-                t.fromMoby(elt.toxml())
+                t.fromMoby(elt)
                 self.Affectation=t.content
\ No newline at end of file

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/ontology/SchematikonMotifID.py,v
retrieving revision 1.4
retrieving revision 1.5
diff -u -r1.4 -r1.5
--- /home/repository/moby/moby-live/Python/bioMoby/ontology/SchematikonMotifID.py	2005/02/01 08:52:16	1.4
+++ /home/repository/moby/moby-live/Python/bioMoby/ontology/SchematikonMotifID.py	2005/02/01 14:20:44	1.5
@@ -27,7 +27,9 @@
         """ Load the attributes from an XML string
         """
         from bioMoby.mobyMarshal import MobyUnmarshaller
-        doc=parseString(value).firstChild
+        doc=value
+        if isinstance(value, str):
+            doc=parseString(value).firstChild
         um=MobyUnmarshaller()
         self.content=""
         self.namespace=doc.getAttribute("moby:namespace")
@@ -47,8 +49,8 @@
             if elt.nodeName=="CrossReference" or elt.nodeName=="moby:CrossReference":
                 self.__cross__=[]
                 for ref in elt.childNodes:
-                    self.__cross__.append(ref.toxml())
+                    self.__cross__.append(um.loads(ref))
             if elt.nodeType==elt.ELEMENT_NODE and (elt.nodeName=="String" or elt.nodeName=="moby:String") and (elt.getAttribute("articleName")=="ID" or elt.getAttribute("moby:articleName")=="ID"):
                 t=MobyString()
-                t.fromMoby(elt.toxml())
+                t.fromMoby(elt)
                 self.ID=t.content
\ No newline at end of file

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/ontology/SchematikonMotifSupport.py,v
retrieving revision 1.4
retrieving revision 1.5
diff -u -r1.4 -r1.5
--- /home/repository/moby/moby-live/Python/bioMoby/ontology/SchematikonMotifSupport.py	2005/02/01 08:52:16	1.4
+++ /home/repository/moby/moby-live/Python/bioMoby/ontology/SchematikonMotifSupport.py	2005/02/01 14:20:44	1.5
@@ -28,7 +28,9 @@
         """ Load the attributes from an XML string
         """
         from bioMoby.mobyMarshal import MobyUnmarshaller
-        doc=parseString(value).firstChild
+        doc=value
+        if isinstance(value, str):
+            doc=parseString(value).firstChild
         um=MobyUnmarshaller()
         self.content=""
         self.namespace=doc.getAttribute("moby:namespace")
@@ -48,12 +50,12 @@
             if elt.nodeName=="CrossReference" or elt.nodeName=="moby:CrossReference":
                 self.__cross__=[]
                 for ref in elt.childNodes:
-                    self.__cross__.append(ref.toxml())
+                    self.__cross__.append(um.loads(ref))
             if elt.nodeType==elt.ELEMENT_NODE and (elt.nodeName=="Integer" or elt.nodeName=="moby:Integer") and (elt.getAttribute("articleName")=="UniqueSupport" or elt.getAttribute("moby:articleName")=="UniqueSupport"):
                 t=MobyInteger()
-                t.fromMoby(elt.toxml())
+                t.fromMoby(elt)
                 self.UniqueSupport=t.content
             if elt.nodeType==elt.ELEMENT_NODE and (elt.nodeName=="Integer" or elt.nodeName=="moby:Integer") and (elt.getAttribute("articleName")=="Support" or elt.getAttribute("moby:articleName")=="Support"):
                 t=MobyInteger()
-                t.fromMoby(elt.toxml())
+                t.fromMoby(elt)
                 self.Support=t.content
\ No newline at end of file

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/ontology/SchematikonSegmentAttributes.py,v
retrieving revision 1.4
retrieving revision 1.5
diff -u -r1.4 -r1.5
--- /home/repository/moby/moby-live/Python/bioMoby/ontology/SchematikonSegmentAttributes.py	2005/02/01 08:52:16	1.4
+++ /home/repository/moby/moby-live/Python/bioMoby/ontology/SchematikonSegmentAttributes.py	2005/02/01 14:20:44	1.5
@@ -32,7 +32,9 @@
         """ Load the attributes from an XML string
         """
         from bioMoby.mobyMarshal import MobyUnmarshaller
-        doc=parseString(value).firstChild
+        doc=value
+        if isinstance(value, str):
+            doc=parseString(value).firstChild
         um=MobyUnmarshaller()
         self.content=""
         self.namespace=doc.getAttribute("moby:namespace")
@@ -52,24 +54,24 @@
             if elt.nodeName=="CrossReference" or elt.nodeName=="moby:CrossReference":
                 self.__cross__=[]
                 for ref in elt.childNodes:
-                    self.__cross__.append(ref.toxml())
+                    self.__cross__.append(um.loads(ref))
             if elt.nodeType==elt.ELEMENT_NODE and (elt.nodeName=="Integer" or elt.nodeName=="moby:Integer") and (elt.getAttribute("articleName")=="Length" or elt.getAttribute("moby:articleName")=="Length"):
                 t=MobyInteger()
-                t.fromMoby(elt.toxml())
+                t.fromMoby(elt)
                 self.Length=t.content
             if elt.nodeType==elt.ELEMENT_NODE and (elt.nodeName=="String" or elt.nodeName=="moby:String") and (elt.getAttribute("articleName")=="Insert code" or elt.getAttribute("moby:articleName")=="Insert code"):
                 t=MobyString()
-                t.fromMoby(elt.toxml())
+                t.fromMoby(elt)
                 self.InsertCode=t.content
             if elt.nodeType==elt.ELEMENT_NODE and (elt.nodeName=="Integer" or elt.nodeName=="moby:Integer") and (elt.getAttribute("articleName")=="Starting amino acid position" or elt.getAttribute("moby:articleName")=="Starting amino acid position"):
                 t=MobyInteger()
-                t.fromMoby(elt.toxml())
+                t.fromMoby(elt)
                 self.StartingAminoAcidPosition=t.content
             if elt.nodeType==elt.ELEMENT_NODE and (elt.nodeName=="String" or elt.nodeName=="moby:String") and (elt.getAttribute("articleName")=="Chain ID" or elt.getAttribute("moby:articleName")=="Chain ID"):
                 t=MobyString()
-                t.fromMoby(elt.toxml())
+                t.fromMoby(elt)
                 self.ChainID=t.content
             if elt.nodeType==elt.ELEMENT_NODE and (elt.nodeName=="String" or elt.nodeName=="moby:String") and (elt.getAttribute("articleName")=="PDB ID" or elt.getAttribute("moby:articleName")=="PDB ID"):
                 t=MobyString()
-                t.fromMoby(elt.toxml())
+                t.fromMoby(elt)
                 self.PDBID=t.content
\ No newline at end of file

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/ontology/SchematikonSegmentID.py,v
retrieving revision 1.4
retrieving revision 1.5
diff -u -r1.4 -r1.5
--- /home/repository/moby/moby-live/Python/bioMoby/ontology/SchematikonSegmentID.py	2005/02/01 08:52:16	1.4
+++ /home/repository/moby/moby-live/Python/bioMoby/ontology/SchematikonSegmentID.py	2005/02/01 14:20:44	1.5
@@ -27,7 +27,9 @@
         """ Load the attributes from an XML string
         """
         from bioMoby.mobyMarshal import MobyUnmarshaller
-        doc=parseString(value).firstChild
+        doc=value
+        if isinstance(value, str):
+            doc=parseString(value).firstChild
         um=MobyUnmarshaller()
         self.content=""
         self.namespace=doc.getAttribute("moby:namespace")
@@ -47,8 +49,8 @@
             if elt.nodeName=="CrossReference" or elt.nodeName=="moby:CrossReference":
                 self.__cross__=[]
                 for ref in elt.childNodes:
-                    self.__cross__.append(ref.toxml())
+                    self.__cross__.append(um.loads(ref))
             if elt.nodeType==elt.ELEMENT_NODE and (elt.nodeName=="String" or elt.nodeName=="moby:String") and (elt.getAttribute("articleName")=="ID" or elt.getAttribute("moby:articleName")=="ID"):
                 t=MobyString()
-                t.fromMoby(elt.toxml())
+                t.fromMoby(elt)
                 self.ID=t.content
\ No newline at end of file

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/ontology/SchematikonStructureAnnotation.py,v
retrieving revision 1.4
retrieving revision 1.5
diff -u -r1.4 -r1.5
--- /home/repository/moby/moby-live/Python/bioMoby/ontology/SchematikonStructureAnnotation.py	2005/02/01 08:52:16	1.4
+++ /home/repository/moby/moby-live/Python/bioMoby/ontology/SchematikonStructureAnnotation.py	2005/02/01 14:20:44	1.5
@@ -30,7 +30,9 @@
         """ Load the attributes from an XML string
         """
         from bioMoby.mobyMarshal import MobyUnmarshaller
-        doc=parseString(value).firstChild
+        doc=value
+        if isinstance(value, str):
+            doc=parseString(value).firstChild
         um=MobyUnmarshaller()
         self.content=""
         self.namespace=doc.getAttribute("moby:namespace")
@@ -50,20 +52,20 @@
             if elt.nodeName=="CrossReference" or elt.nodeName=="moby:CrossReference":
                 self.__cross__=[]
                 for ref in elt.childNodes:
-                    self.__cross__.append(ref.toxml())
+                    self.__cross__.append(um.loads(ref))
             if elt.nodeType==elt.ELEMENT_NODE and (elt.nodeName=="String" or elt.nodeName=="moby:String") and (elt.getAttribute("articleName")=="PROMOTIF gamma-turn" or elt.getAttribute("moby:articleName")=="PROMOTIF gamma-turn"):
                 t=MobyString()
-                t.fromMoby(elt.toxml())
+                t.fromMoby(elt)
                 self.PROMOTIFGammaTurn=t.content
             if elt.nodeType==elt.ELEMENT_NODE and (elt.nodeName=="String" or elt.nodeName=="moby:String") and (elt.getAttribute("articleName")=="PROMOTIF beta-turn" or elt.getAttribute("moby:articleName")=="PROMOTIF beta-turn"):
                 t=MobyString()
-                t.fromMoby(elt.toxml())
+                t.fromMoby(elt)
                 self.PROMOTIFBetaTurn=t.content
             if elt.nodeType==elt.ELEMENT_NODE and (elt.nodeName=="String" or elt.nodeName=="moby:String") and (elt.getAttribute("articleName")=="DSSP" or elt.getAttribute("moby:articleName")=="DSSP"):
                 t=MobyString()
-                t.fromMoby(elt.toxml())
+                t.fromMoby(elt)
                 self.DSSP=t.content
             if elt.nodeType==elt.ELEMENT_NODE and (elt.nodeName=="String" or elt.nodeName=="moby:String") and (elt.getAttribute("articleName")=="STRIDE" or elt.getAttribute("moby:articleName")=="STRIDE"):
                 t=MobyString()
-                t.fromMoby(elt.toxml())
+                t.fromMoby(elt)
                 self.STRIDE=t.content
\ No newline at end of file

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/ontology/SchematikonVorocodeName.py,v
retrieving revision 1.4
retrieving revision 1.5
diff -u -r1.4 -r1.5
--- /home/repository/moby/moby-live/Python/bioMoby/ontology/SchematikonVorocodeName.py	2005/02/01 08:52:16	1.4
+++ /home/repository/moby/moby-live/Python/bioMoby/ontology/SchematikonVorocodeName.py	2005/02/01 14:20:44	1.5
@@ -27,7 +27,9 @@
         """ Load the attributes from an XML string
         """
         from bioMoby.mobyMarshal import MobyUnmarshaller
-        doc=parseString(value).firstChild
+        doc=value
+        if isinstance(value, str):
+            doc=parseString(value).firstChild
         um=MobyUnmarshaller()
         self.content=""
         self.namespace=doc.getAttribute("moby:namespace")
@@ -47,8 +49,8 @@
             if elt.nodeName=="CrossReference" or elt.nodeName=="moby:CrossReference":
                 self.__cross__=[]
                 for ref in elt.childNodes:
-                    self.__cross__.append(ref.toxml())
+                    self.__cross__.append(um.loads(ref))
             if elt.nodeType==elt.ELEMENT_NODE and (elt.nodeName=="String" or elt.nodeName=="moby:String") and (elt.getAttribute("articleName")=="VorocodeName" or elt.getAttribute("moby:articleName")=="VorocodeName"):
                 t=MobyString()
-                t.fromMoby(elt.toxml())
+                t.fromMoby(elt)
                 self.VorocodeName=t.content
\ No newline at end of file

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/ontology/Scored_acronym_string.py,v
retrieving revision 1.4
retrieving revision 1.5
diff -u -r1.4 -r1.5
--- /home/repository/moby/moby-live/Python/bioMoby/ontology/Scored_acronym_string.py	2005/02/01 08:52:16	1.4
+++ /home/repository/moby/moby-live/Python/bioMoby/ontology/Scored_acronym_string.py	2005/02/01 14:20:44	1.5
@@ -30,7 +30,9 @@
         """ Load the attributes from an XML string
         """
         from bioMoby.mobyMarshal import MobyUnmarshaller
-        doc=parseString(value).firstChild
+        doc=value
+        if isinstance(value, str):
+            doc=parseString(value).firstChild
         um=MobyUnmarshaller()
         self.content=""
         self.namespace=doc.getAttribute("moby:namespace")
@@ -50,15 +52,15 @@
             if elt.nodeName=="CrossReference" or elt.nodeName=="moby:CrossReference":
                 self.__cross__=[]
                 for ref in elt.childNodes:
-                    self.__cross__.append(ref.toxml())
+                    self.__cross__.append(um.loads(ref))
             if elt.nodeType==elt.ELEMENT_NODE and (elt.nodeName=="Float" or elt.nodeName=="moby:Float") and (elt.getAttribute("articleName")=="score" or elt.getAttribute("moby:articleName")=="score"):
                 t=MobyFloat()
-                t.fromMoby(elt.toxml())
+                t.fromMoby(elt)
                 self.Score=t.content
             if elt.nodeType==elt.ELEMENT_NODE and (elt.nodeName=="Object" or elt.nodeName=="moby:Object") and (elt.getAttribute("articleName")=="string_component" or elt.getAttribute("moby:articleName")=="string_component"):
                 self.String_component=MobyObject()
-                self.String_component.fromMoby(elt.toxml())
+                self.String_component.fromMoby(elt)
             if elt.nodeType==elt.ELEMENT_NODE and (elt.nodeName=="String" or elt.nodeName=="moby:String") and (elt.getAttribute("articleName")=="acronym" or elt.getAttribute("moby:articleName")=="acronym"):
                 t=MobyString()
-                t.fromMoby(elt.toxml())
+                t.fromMoby(elt)
                 self.Acronym=t.content
\ No newline at end of file

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/ontology/SimpleAnnotatedGIFImage.py,v
retrieving revision 1.4
retrieving revision 1.5
diff -u -r1.4 -r1.5
--- /home/repository/moby/moby-live/Python/bioMoby/ontology/SimpleAnnotatedGIFImage.py	2005/02/01 08:52:16	1.4
+++ /home/repository/moby/moby-live/Python/bioMoby/ontology/SimpleAnnotatedGIFImage.py	2005/02/01 14:20:44	1.5
@@ -28,7 +28,9 @@
         """ Load the attributes from an XML string
         """
         from bioMoby.mobyMarshal import MobyUnmarshaller
-        doc=parseString(value).firstChild
+        doc=value
+        if isinstance(value, str):
+            doc=parseString(value).firstChild
         um=MobyUnmarshaller()
         self.content=""
         self.namespace=doc.getAttribute("moby:namespace")
@@ -48,8 +50,8 @@
             if elt.nodeName=="CrossReference" or elt.nodeName=="moby:CrossReference":
                 self.__cross__=[]
                 for ref in elt.childNodes:
-                    self.__cross__.append(ref.toxml())
+                    self.__cross__.append(um.loads(ref))
             if elt.nodeType==elt.ELEMENT_NODE and (elt.nodeName=="String" or elt.nodeName=="moby:String") and (elt.getAttribute("articleName")=="Description" or elt.getAttribute("moby:articleName")=="Description"):
                 t=MobyString()
-                t.fromMoby(elt.toxml())
+                t.fromMoby(elt)
                 self.Description=t.content
\ No newline at end of file

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/ontology/SimpleAnnotatedJPEGImage.py,v
retrieving revision 1.4
retrieving revision 1.5
diff -u -r1.4 -r1.5
--- /home/repository/moby/moby-live/Python/bioMoby/ontology/SimpleAnnotatedJPEGImage.py	2005/02/01 08:52:16	1.4
+++ /home/repository/moby/moby-live/Python/bioMoby/ontology/SimpleAnnotatedJPEGImage.py	2005/02/01 14:20:44	1.5
@@ -28,7 +28,9 @@
         """ Load the attributes from an XML string
         """
         from bioMoby.mobyMarshal import MobyUnmarshaller
-        doc=parseString(value).firstChild
+        doc=value
+        if isinstance(value, str):
+            doc=parseString(value).firstChild
         um=MobyUnmarshaller()
         self.content=""
         self.namespace=doc.getAttribute("moby:namespace")
@@ -49,8 +51,8 @@
             if elt.nodeName=="CrossReference" or elt.nodeName=="moby:CrossReference":
                 self.__cross__=[]
                 for ref in elt.childNodes:
-                    self.__cross__.append(ref.toxml())
+                    self.__cross__.append(um.loads(ref))
             if elt.nodeType==elt.ELEMENT_NODE and (elt.nodeName=="String" or elt.nodeName=="moby:String") and (elt.getAttribute("articleName")=="Description" or elt.getAttribute("moby:articleName")=="Description"):
                 t=MobyString()
-                t.fromMoby(elt.toxml())
+                t.fromMoby(elt)
                 self.Description.append(t.content)
\ No newline at end of file

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/ontology/Simple_key_value_pair.py,v
retrieving revision 1.4
retrieving revision 1.5
diff -u -r1.4 -r1.5
--- /home/repository/moby/moby-live/Python/bioMoby/ontology/Simple_key_value_pair.py	2005/02/01 08:52:16	1.4
+++ /home/repository/moby/moby-live/Python/bioMoby/ontology/Simple_key_value_pair.py	2005/02/01 14:20:44	1.5
@@ -28,7 +28,9 @@
         """ Load the attributes from an XML string
         """
         from bioMoby.mobyMarshal import MobyUnmarshaller
-        doc=parseString(value).firstChild
+        doc=value
+        if isinstance(value, str):
+            doc=parseString(value).firstChild
         um=MobyUnmarshaller()
         self.content=""
         self.namespace=doc.getAttribute("moby:namespace")
@@ -48,12 +50,12 @@
             if elt.nodeName=="CrossReference" or elt.nodeName=="moby:CrossReference":
                 self.__cross__=[]
                 for ref in elt.childNodes:
-                    self.__cross__.append(ref.toxml())
+                    self.__cross__.append(um.loads(ref))
             if elt.nodeType==elt.ELEMENT_NODE and (elt.nodeName=="String" or elt.nodeName=="moby:String") and (elt.getAttribute("articleName")=="value" or elt.getAttribute("moby:articleName")=="value"):
                 t=MobyString()
-                t.fromMoby(elt.toxml())
+                t.fromMoby(elt)
                 self.Value=t.content
             if elt.nodeType==elt.ELEMENT_NODE and (elt.nodeName=="String" or elt.nodeName=="moby:String") and (elt.getAttribute("articleName")=="key" or elt.getAttribute("moby:articleName")=="key"):
                 t=MobyString()
-                t.fromMoby(elt.toxml())
+                t.fromMoby(elt)
                 self.Key=t.content
\ No newline at end of file

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/ontology/Snp_allele.py,v
retrieving revision 1.4
retrieving revision 1.5
diff -u -r1.4 -r1.5
--- /home/repository/moby/moby-live/Python/bioMoby/ontology/Snp_allele.py	2005/02/01 08:52:16	1.4
+++ /home/repository/moby/moby-live/Python/bioMoby/ontology/Snp_allele.py	2005/02/01 14:20:44	1.5
@@ -23,7 +23,9 @@
         """ Load the attributes from an XML string
         """
         from bioMoby.mobyMarshal import MobyUnmarshaller
-        doc=parseString(value).firstChild
+        doc=value
+        if isinstance(value, str):
+            doc=parseString(value).firstChild
         um=MobyUnmarshaller()
         self.content=""
 
@@ -37,7 +39,7 @@
             if elt.nodeName=="CrossReference" or elt.nodeName=="moby:CrossReference":
                 self.__cross__=[]
                 for ref in elt.childNodes:
-                    self.__cross__.append(ref.toxml())
+                    self.__cross__.append(um.loads(ref))
             if elt.nodeType==elt.ELEMENT_NODE and (elt.nodeName=="DNASequence" or elt.nodeName=="moby:DNASequence") and (elt.getAttribute("articleName")=="snp_allele" or elt.getAttribute("moby:articleName")=="snp_allele"):
                 self.Snp_allele=MobyDNASequence()
-                self.Snp_allele.fromMoby(elt.toxml())
\ No newline at end of file
+                self.Snp_allele.fromMoby(elt)
\ No newline at end of file

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/ontology/Snp_genotype.py,v
retrieving revision 1.4
retrieving revision 1.5
diff -u -r1.4 -r1.5
--- /home/repository/moby/moby-live/Python/bioMoby/ontology/Snp_genotype.py	2005/02/01 08:52:16	1.4
+++ /home/repository/moby/moby-live/Python/bioMoby/ontology/Snp_genotype.py	2005/02/01 14:20:44	1.5
@@ -24,7 +24,9 @@
         """ Load the attributes from an XML string
         """
         from bioMoby.mobyMarshal import MobyUnmarshaller
-        doc=parseString(value).firstChild
+        doc=value
+        if isinstance(value, str):
+            doc=parseString(value).firstChild
         um=MobyUnmarshaller()
         self.content=""
 
@@ -38,10 +40,10 @@
             if elt.nodeName=="CrossReference" or elt.nodeName=="moby:CrossReference":
                 self.__cross__=[]
                 for ref in elt.childNodes:
-                    self.__cross__.append(ref.toxml())
+                    self.__cross__.append(um.loads(ref))
             if elt.nodeType==elt.ELEMENT_NODE and (elt.nodeName=="snp_allele" or elt.nodeName=="moby:snp_allele") and (elt.getAttribute("articleName")=="allele1" or elt.getAttribute("moby:articleName")=="allele1"):
                 self.Allele1=MobySnp_allele()
-                self.Allele1.fromMoby(elt.toxml())
+                self.Allele1.fromMoby(elt)
             if elt.nodeType==elt.ELEMENT_NODE and (elt.nodeName=="snp_allele" or elt.nodeName=="moby:snp_allele") and (elt.getAttribute("articleName")=="allele2" or elt.getAttribute("moby:articleName")=="allele2"):
                 self.Allele2=MobySnp_allele()
-                self.Allele2.fromMoby(elt.toxml())
\ No newline at end of file
+                self.Allele2.fromMoby(elt)
\ No newline at end of file

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/ontology/Study.py,v
retrieving revision 1.4
retrieving revision 1.5
diff -u -r1.4 -r1.5
--- /home/repository/moby/moby-live/Python/bioMoby/ontology/Study.py	2005/02/01 08:52:16	1.4
+++ /home/repository/moby/moby-live/Python/bioMoby/ontology/Study.py	2005/02/01 14:20:44	1.5
@@ -30,7 +30,9 @@
         """ Load the attributes from an XML string
         """
         from bioMoby.mobyMarshal import MobyUnmarshaller
-        doc=parseString(value).firstChild
+        doc=value
+        if isinstance(value, str):
+            doc=parseString(value).firstChild
         um=MobyUnmarshaller()
         self.content=""
         self.namespace=doc.getAttribute("moby:namespace")
@@ -50,16 +52,16 @@
             if elt.nodeName=="CrossReference" or elt.nodeName=="moby:CrossReference":
                 self.__cross__=[]
                 for ref in elt.childNodes:
-                    self.__cross__.append(ref.toxml())
+                    self.__cross__.append(um.loads(ref))
             if elt.nodeType==elt.ELEMENT_NODE and (elt.nodeName=="String" or elt.nodeName=="moby:String") and (elt.getAttribute("articleName")=="study_name" or elt.getAttribute("moby:articleName")=="study_name"):
                 t=MobyString()
-                t.fromMoby(elt.toxml())
+                t.fromMoby(elt)
                 self.Study_name=t.content
             if elt.nodeType==elt.ELEMENT_NODE and (elt.nodeName=="Integer" or elt.nodeName=="moby:Integer") and (elt.getAttribute("articleName")=="study_id" or elt.getAttribute("moby:articleName")=="study_id"):
                 t=MobyInteger()
-                t.fromMoby(elt.toxml())
+                t.fromMoby(elt)
                 self.Study_id=t.content
             if elt.nodeType==elt.ELEMENT_NODE and (elt.nodeName=="String" or elt.nodeName=="moby:String") and (elt.getAttribute("articleName")=="study_desc" or elt.getAttribute("moby:articleName")=="study_desc"):
                 t=MobyString()
-                t.fromMoby(elt.toxml())
+                t.fromMoby(elt)
                 self.Study_desc=t.content
\ No newline at end of file

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/ontology/TEST.py,v
retrieving revision 1.4
retrieving revision 1.5
diff -u -r1.4 -r1.5
--- /home/repository/moby/moby-live/Python/bioMoby/ontology/TEST.py	2005/02/01 08:52:16	1.4
+++ /home/repository/moby/moby-live/Python/bioMoby/ontology/TEST.py	2005/02/01 14:20:44	1.5
@@ -26,7 +26,9 @@
         """ Load the attributes from an XML string
         """
         from bioMoby.mobyMarshal import MobyUnmarshaller
-        doc=parseString(value).firstChild
+        doc=value
+        if isinstance(value, str):
+            doc=parseString(value).firstChild
         um=MobyUnmarshaller()
         self.content=""
         self.namespace=doc.getAttribute("moby:namespace")
@@ -46,4 +48,4 @@
             if elt.nodeName=="CrossReference" or elt.nodeName=="moby:CrossReference":
                 self.__cross__=[]
                 for ref in elt.childNodes:
-                    self.__cross__.append(ref.toxml())
\ No newline at end of file
+                    self.__cross__.append(um.loads(ref))
\ No newline at end of file

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/ontology/TargetP_result.py,v
retrieving revision 1.4
retrieving revision 1.5
diff -u -r1.4 -r1.5
--- /home/repository/moby/moby-live/Python/bioMoby/ontology/TargetP_result.py	2005/02/01 08:52:16	1.4
+++ /home/repository/moby/moby-live/Python/bioMoby/ontology/TargetP_result.py	2005/02/01 14:20:44	1.5
@@ -32,7 +32,9 @@
         """ Load the attributes from an XML string
         """
         from bioMoby.mobyMarshal import MobyUnmarshaller
-        doc=parseString(value).firstChild
+        doc=value
+        if isinstance(value, str):
+            doc=parseString(value).firstChild
         um=MobyUnmarshaller()
         self.content=""
         self.namespace=doc.getAttribute("moby:namespace")
@@ -52,24 +54,24 @@
             if elt.nodeName=="CrossReference" or elt.nodeName=="moby:CrossReference":
                 self.__cross__=[]
                 for ref in elt.childNodes:
-                    self.__cross__.append(ref.toxml())
+                    self.__cross__.append(um.loads(ref))
             if elt.nodeType==elt.ELEMENT_NODE and (elt.nodeName=="Float" or elt.nodeName=="moby:Float") and (elt.getAttribute("articleName")=="o_score" or elt.getAttribute("moby:articleName")=="o_score"):
                 t=MobyFloat()
-                t.fromMoby(elt.toxml())
+                t.fromMoby(elt)
                 self.O_score=t.content
             if elt.nodeType==elt.ELEMENT_NODE and (elt.nodeName=="Float" or elt.nodeName=="moby:Float") and (elt.getAttribute("articleName")=="s_score" or elt.getAttribute("moby:articleName")=="s_score"):
                 t=MobyFloat()
-                t.fromMoby(elt.toxml())
+                t.fromMoby(elt)
                 self.S_score=t.content
             if elt.nodeType==elt.ELEMENT_NODE and (elt.nodeName=="Float" or elt.nodeName=="moby:Float") and (elt.getAttribute("articleName")=="m_score" or elt.getAttribute("moby:articleName")=="m_score"):
                 t=MobyFloat()
-                t.fromMoby(elt.toxml())
+                t.fromMoby(elt)
                 self.M_score=t.content
             if elt.nodeType==elt.ELEMENT_NODE and (elt.nodeName=="Float" or elt.nodeName=="moby:Float") and (elt.getAttribute("articleName")=="c_score" or elt.getAttribute("moby:articleName")=="c_score"):
                 t=MobyFloat()
-                t.fromMoby(elt.toxml())
+                t.fromMoby(elt)
                 self.C_score=t.content
             if elt.nodeType==elt.ELEMENT_NODE and (elt.nodeName=="String" or elt.nodeName=="moby:String") and (elt.getAttribute("articleName")=="compartment" or elt.getAttribute("moby:articleName")=="compartment"):
                 t=MobyString()
-                t.fromMoby(elt.toxml())
+                t.fromMoby(elt)
                 self.Compartment=t.content
\ No newline at end of file

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/ontology/Testout.py,v
retrieving revision 1.4
retrieving revision 1.5
diff -u -r1.4 -r1.5
--- /home/repository/moby/moby-live/Python/bioMoby/ontology/Testout.py	2005/02/01 08:52:16	1.4
+++ /home/repository/moby/moby-live/Python/bioMoby/ontology/Testout.py	2005/02/01 14:20:44	1.5
@@ -31,7 +31,9 @@
         """ Load the attributes from an XML string
         """
         from bioMoby.mobyMarshal import MobyUnmarshaller
-        doc=parseString(value).firstChild
+        doc=value
+        if isinstance(value, str):
+            doc=parseString(value).firstChild
         um=MobyUnmarshaller()
         self.content=""
         self.namespace=doc.getAttribute("moby:namespace")
@@ -51,20 +53,20 @@
             if elt.nodeName=="CrossReference" or elt.nodeName=="moby:CrossReference":
                 self.__cross__=[]
                 for ref in elt.childNodes:
-                    self.__cross__.append(ref.toxml())
+                    self.__cross__.append(um.loads(ref))
             if elt.nodeType==elt.ELEMENT_NODE and (elt.nodeName=="Integer" or elt.nodeName=="moby:Integer") and (elt.getAttribute("articleName")=="gid" or elt.getAttribute("moby:articleName")=="gid"):
                 t=MobyInteger()
-                t.fromMoby(elt.toxml())
+                t.fromMoby(elt)
                 self.Gid=t.content
             if elt.nodeType==elt.ELEMENT_NODE and (elt.nodeName=="String" or elt.nodeName=="moby:String") and (elt.getAttribute("articleName")=="dvalue" or elt.getAttribute("moby:articleName")=="dvalue"):
                 t=MobyString()
-                t.fromMoby(elt.toxml())
+                t.fromMoby(elt)
                 self.Dvalue=t.content
             if elt.nodeType==elt.ELEMENT_NODE and (elt.nodeName=="Integer" or elt.nodeName=="moby:Integer") and (elt.getAttribute("articleName")=="scaleid" or elt.getAttribute("moby:articleName")=="scaleid"):
                 t=MobyInteger()
-                t.fromMoby(elt.toxml())
+                t.fromMoby(elt)
                 self.Scaleid=t.content
             if elt.nodeType==elt.ELEMENT_NODE and (elt.nodeName=="Integer" or elt.nodeName=="moby:Integer") and (elt.getAttribute("articleName")=="tmethid" or elt.getAttribute("moby:articleName")=="tmethid"):
                 t=MobyInteger()
-                t.fromMoby(elt.toxml())
+                t.fromMoby(elt)
                 self.Tmethid=t.content
\ No newline at end of file

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/ontology/TextBase64.py,v
retrieving revision 1.4
retrieving revision 1.5
diff -u -r1.4 -r1.5
--- /home/repository/moby/moby-live/Python/bioMoby/ontology/TextBase64.py	2005/02/01 08:52:16	1.4
+++ /home/repository/moby/moby-live/Python/bioMoby/ontology/TextBase64.py	2005/02/01 14:20:44	1.5
@@ -26,7 +26,9 @@
         """ Load the attributes from an XML string
         """
         from bioMoby.mobyMarshal import MobyUnmarshaller
-        doc=parseString(value).firstChild
+        doc=value
+        if isinstance(value, str):
+            doc=parseString(value).firstChild
         um=MobyUnmarshaller()
         self.content=""
         self.namespace=doc.getAttribute("moby:namespace")
@@ -46,4 +48,4 @@
             if elt.nodeName=="CrossReference" or elt.nodeName=="moby:CrossReference":
                 self.__cross__=[]
                 for ref in elt.childNodes:
-                    self.__cross__.append(ref.toxml())
\ No newline at end of file
+                    self.__cross__.append(um.loads(ref))
\ No newline at end of file

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/ontology/TextFormatted.py,v
retrieving revision 1.4
retrieving revision 1.5
diff -u -r1.4 -r1.5
--- /home/repository/moby/moby-live/Python/bioMoby/ontology/TextFormatted.py	2005/02/01 08:52:16	1.4
+++ /home/repository/moby/moby-live/Python/bioMoby/ontology/TextFormatted.py	2005/02/01 14:20:44	1.5
@@ -26,7 +26,9 @@
         """ Load the attributes from an XML string
         """
         from bioMoby.mobyMarshal import MobyUnmarshaller
-        doc=parseString(value).firstChild
+        doc=value
+        if isinstance(value, str):
+            doc=parseString(value).firstChild
         um=MobyUnmarshaller()
         self.content=""
         self.namespace=doc.getAttribute("moby:namespace")
@@ -46,4 +48,4 @@
             if elt.nodeName=="CrossReference" or elt.nodeName=="moby:CrossReference":
                 self.__cross__=[]
                 for ref in elt.childNodes:
-                    self.__cross__.append(ref.toxml())
\ No newline at end of file
+                    self.__cross__.append(um.loads(ref))
\ No newline at end of file

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/ontology/TextHtml.py,v
retrieving revision 1.4
retrieving revision 1.5
diff -u -r1.4 -r1.5
--- /home/repository/moby/moby-live/Python/bioMoby/ontology/TextHtml.py	2005/02/01 08:52:16	1.4
+++ /home/repository/moby/moby-live/Python/bioMoby/ontology/TextHtml.py	2005/02/01 14:20:44	1.5
@@ -26,7 +26,9 @@
         """ Load the attributes from an XML string
         """
         from bioMoby.mobyMarshal import MobyUnmarshaller
-        doc=parseString(value).firstChild
+        doc=value
+        if isinstance(value, str):
+            doc=parseString(value).firstChild
         um=MobyUnmarshaller()
         self.content=""
         self.namespace=doc.getAttribute("moby:namespace")
@@ -46,4 +48,4 @@
             if elt.nodeName=="CrossReference" or elt.nodeName=="moby:CrossReference":
                 self.__cross__=[]
                 for ref in elt.childNodes:
-                    self.__cross__.append(ref.toxml())
\ No newline at end of file
+                    self.__cross__.append(um.loads(ref))
\ No newline at end of file

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/ontology/TextPlain.py,v
retrieving revision 1.4
retrieving revision 1.5
diff -u -r1.4 -r1.5
--- /home/repository/moby/moby-live/Python/bioMoby/ontology/TextPlain.py	2005/02/01 08:52:16	1.4
+++ /home/repository/moby/moby-live/Python/bioMoby/ontology/TextPlain.py	2005/02/01 14:20:44	1.5
@@ -26,7 +26,9 @@
         """ Load the attributes from an XML string
         """
         from bioMoby.mobyMarshal import MobyUnmarshaller
-        doc=parseString(value).firstChild
+        doc=value
+        if isinstance(value, str):
+            doc=parseString(value).firstChild
         um=MobyUnmarshaller()
         self.content=""
         self.namespace=doc.getAttribute("moby:namespace")
@@ -46,4 +48,4 @@
             if elt.nodeName=="CrossReference" or elt.nodeName=="moby:CrossReference":
                 self.__cross__=[]
                 for ref in elt.childNodes:
-                    self.__cross__.append(ref.toxml())
\ No newline at end of file
+                    self.__cross__.append(um.loads(ref))
\ No newline at end of file

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/ontology/TextUuencoded.py,v
retrieving revision 1.4
retrieving revision 1.5
diff -u -r1.4 -r1.5
--- /home/repository/moby/moby-live/Python/bioMoby/ontology/TextUuencoded.py	2005/02/01 08:52:16	1.4
+++ /home/repository/moby/moby-live/Python/bioMoby/ontology/TextUuencoded.py	2005/02/01 14:20:44	1.5
@@ -26,7 +26,9 @@
         """ Load the attributes from an XML string
         """
         from bioMoby.mobyMarshal import MobyUnmarshaller
-        doc=parseString(value).firstChild
+        doc=value
+        if isinstance(value, str):
+            doc=parseString(value).firstChild
         um=MobyUnmarshaller()
         self.content=""
         self.namespace=doc.getAttribute("moby:namespace")
@@ -46,4 +48,4 @@
             if elt.nodeName=="CrossReference" or elt.nodeName=="moby:CrossReference":
                 self.__cross__=[]
                 for ref in elt.childNodes:
-                    self.__cross__.append(ref.toxml())
\ No newline at end of file
+                    self.__cross__.append(um.loads(ref))
\ No newline at end of file

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/ontology/TextXml.py,v
retrieving revision 1.4
retrieving revision 1.5
diff -u -r1.4 -r1.5
--- /home/repository/moby/moby-live/Python/bioMoby/ontology/TextXml.py	2005/02/01 08:52:16	1.4
+++ /home/repository/moby/moby-live/Python/bioMoby/ontology/TextXml.py	2005/02/01 14:20:44	1.5
@@ -26,7 +26,9 @@
         """ Load the attributes from an XML string
         """
         from bioMoby.mobyMarshal import MobyUnmarshaller
-        doc=parseString(value).firstChild
+        doc=value
+        if isinstance(value, str):
+            doc=parseString(value).firstChild
         um=MobyUnmarshaller()
         self.content=""
         self.namespace=doc.getAttribute("moby:namespace")
@@ -46,4 +48,4 @@
             if elt.nodeName=="CrossReference" or elt.nodeName=="moby:CrossReference":
                 self.__cross__=[]
                 for ref in elt.childNodes:
-                    self.__cross__.append(ref.toxml())
\ No newline at end of file
+                    self.__cross__.append(um.loads(ref))
\ No newline at end of file

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/ontology/Text_plain.py,v
retrieving revision 1.4
retrieving revision 1.5
diff -u -r1.4 -r1.5
--- /home/repository/moby/moby-live/Python/bioMoby/ontology/Text_plain.py	2005/02/01 08:52:16	1.4
+++ /home/repository/moby/moby-live/Python/bioMoby/ontology/Text_plain.py	2005/02/01 14:20:44	1.5
@@ -26,7 +26,9 @@
         """ Load the attributes from an XML string
         """
         from bioMoby.mobyMarshal import MobyUnmarshaller
-        doc=parseString(value).firstChild
+        doc=value
+        if isinstance(value, str):
+            doc=parseString(value).firstChild
         um=MobyUnmarshaller()
         self.content=""
         self.namespace=doc.getAttribute("moby:namespace")
@@ -46,4 +48,4 @@
             if elt.nodeName=="CrossReference" or elt.nodeName=="moby:CrossReference":
                 self.__cross__=[]
                 for ref in elt.childNodes:
-                    self.__cross__.append(ref.toxml())
\ No newline at end of file
+                    self.__cross__.append(um.loads(ref))
\ No newline at end of file

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/ontology/Trait_Details.py,v
retrieving revision 1.4
retrieving revision 1.5
diff -u -r1.4 -r1.5
--- /home/repository/moby/moby-live/Python/bioMoby/ontology/Trait_Details.py	2005/02/01 08:52:16	1.4
+++ /home/repository/moby/moby-live/Python/bioMoby/ontology/Trait_Details.py	2005/02/01 14:20:44	1.5
@@ -32,7 +32,9 @@
         """ Load the attributes from an XML string
         """
         from bioMoby.mobyMarshal import MobyUnmarshaller
-        doc=parseString(value).firstChild
+        doc=value
+        if isinstance(value, str):
+            doc=parseString(value).firstChild
         um=MobyUnmarshaller()
         self.content=""
         self.namespace=doc.getAttribute("moby:namespace")
@@ -52,24 +54,24 @@
             if elt.nodeName=="CrossReference" or elt.nodeName=="moby:CrossReference":
                 self.__cross__=[]
                 for ref in elt.childNodes:
-                    self.__cross__.append(ref.toxml())
+                    self.__cross__.append(um.loads(ref))
             if elt.nodeType==elt.ELEMENT_NODE and (elt.nodeName=="String" or elt.nodeName=="moby:String") and (elt.getAttribute("articleName")=="trait_desc" or elt.getAttribute("moby:articleName")=="trait_desc"):
                 t=MobyString()
-                t.fromMoby(elt.toxml())
+                t.fromMoby(elt)
                 self.Trait_desc=t.content
             if elt.nodeType==elt.ELEMENT_NODE and (elt.nodeName=="Integer" or elt.nodeName=="moby:Integer") and (elt.getAttribute("articleName")=="num_studies" or elt.getAttribute("moby:articleName")=="num_studies"):
                 t=MobyInteger()
-                t.fromMoby(elt.toxml())
+                t.fromMoby(elt)
                 self.Num_studies=t.content
             if elt.nodeType==elt.ELEMENT_NODE and (elt.nodeName=="String" or elt.nodeName=="moby:String") and (elt.getAttribute("articleName")=="trait_abbr" or elt.getAttribute("moby:articleName")=="trait_abbr"):
                 t=MobyString()
-                t.fromMoby(elt.toxml())
+                t.fromMoby(elt)
                 self.Trait_abbr=t.content
             if elt.nodeType==elt.ELEMENT_NODE and (elt.nodeName=="Integer" or elt.nodeName=="moby:Integer") and (elt.getAttribute("articleName")=="trait_id" or elt.getAttribute("moby:articleName")=="trait_id"):
                 t=MobyInteger()
-                t.fromMoby(elt.toxml())
+                t.fromMoby(elt)
                 self.Trait_id=t.content
             if elt.nodeType==elt.ELEMENT_NODE and (elt.nodeName=="String" or elt.nodeName=="moby:String") and (elt.getAttribute("articleName")=="trait_name" or elt.getAttribute("moby:articleName")=="trait_name"):
                 t=MobyString()
-                t.fromMoby(elt.toxml())
+                t.fromMoby(elt)
                 self.Trait_name=t.content
\ No newline at end of file

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/ontology/Tree.py,v
retrieving revision 1.4
retrieving revision 1.5
diff -u -r1.4 -r1.5
--- /home/repository/moby/moby-live/Python/bioMoby/ontology/Tree.py	2005/02/01 08:52:16	1.4
+++ /home/repository/moby/moby-live/Python/bioMoby/ontology/Tree.py	2005/02/01 14:20:44	1.5
@@ -26,7 +26,9 @@
         """ Load the attributes from an XML string
         """
         from bioMoby.mobyMarshal import MobyUnmarshaller
-        doc=parseString(value).firstChild
+        doc=value
+        if isinstance(value, str):
+            doc=parseString(value).firstChild
         um=MobyUnmarshaller()
         self.content=""
         self.namespace=doc.getAttribute("moby:namespace")
@@ -46,4 +48,4 @@
             if elt.nodeName=="CrossReference" or elt.nodeName=="moby:CrossReference":
                 self.__cross__=[]
                 for ref in elt.childNodes:
-                    self.__cross__.append(ref.toxml())
\ No newline at end of file
+                    self.__cross__.append(um.loads(ref))
\ No newline at end of file

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/ontology/TropGENE_ACCESSION.py,v
retrieving revision 1.4
retrieving revision 1.5
diff -u -r1.4 -r1.5
--- /home/repository/moby/moby-live/Python/bioMoby/ontology/TropGENE_ACCESSION.py	2005/02/01 08:52:16	1.4
+++ /home/repository/moby/moby-live/Python/bioMoby/ontology/TropGENE_ACCESSION.py	2005/02/01 14:20:44	1.5
@@ -36,7 +36,9 @@
         """ Load the attributes from an XML string
         """
         from bioMoby.mobyMarshal import MobyUnmarshaller
-        doc=parseString(value).firstChild
+        doc=value
+        if isinstance(value, str):
+            doc=parseString(value).firstChild
         um=MobyUnmarshaller()
         self.content=""
         self.namespace=doc.getAttribute("moby:namespace")
@@ -66,34 +68,34 @@
             if elt.nodeName=="CrossReference" or elt.nodeName=="moby:CrossReference":
                 self.__cross__=[]
                 for ref in elt.childNodes:
-                    self.__cross__.append(ref.toxml())
+                    self.__cross__.append(um.loads(ref))
             if elt.nodeType==elt.ELEMENT_NODE and (elt.nodeName=="TropGENE_LOCUS" or elt.nodeName=="moby:TropGENE_LOCUS") and (elt.getAttribute("articleName")=="RFLP" or elt.getAttribute("moby:articleName")=="RFLP"):
                 self.RFLP=MobyTropGENE_LOCUS()
-                self.RFLP.fromMoby(elt.toxml())
+                self.RFLP.fromMoby(elt)
             if elt.nodeType==elt.ELEMENT_NODE and (elt.nodeName=="TropGENE_LOCUS" or elt.nodeName=="moby:TropGENE_LOCUS") and (elt.getAttribute("articleName")=="AFLP" or elt.getAttribute("moby:articleName")=="AFLP"):
                 self.AFLP=MobyTropGENE_LOCUS()
-                self.AFLP.fromMoby(elt.toxml())
+                self.AFLP.fromMoby(elt)
             if elt.nodeType==elt.ELEMENT_NODE and (elt.nodeName=="TropGENE_LOCUS" or elt.nodeName=="moby:TropGENE_LOCUS") and (elt.getAttribute("articleName")=="RAPD" or elt.getAttribute("moby:articleName")=="RAPD"):
                 self.RAPD=MobyTropGENE_LOCUS()
-                self.RAPD.fromMoby(elt.toxml())
+                self.RAPD.fromMoby(elt)
             if elt.nodeType==elt.ELEMENT_NODE and (elt.nodeName=="TropGENE_LOCUS" or elt.nodeName=="moby:TropGENE_LOCUS") and (elt.getAttribute("articleName")=="Isozyme" or elt.getAttribute("moby:articleName")=="Isozyme"):
                 self.Isozyme=MobyTropGENE_LOCUS()
-                self.Isozyme.fromMoby(elt.toxml())
+                self.Isozyme.fromMoby(elt)
             if elt.nodeType==elt.ELEMENT_NODE and (elt.nodeName=="TropGENE_LOCUS" or elt.nodeName=="moby:TropGENE_LOCUS") and (elt.getAttribute("articleName")=="Polyphenol" or elt.getAttribute("moby:articleName")=="Polyphenol"):
                 self.Polyphenol=MobyTropGENE_LOCUS()
-                self.Polyphenol.fromMoby(elt.toxml())
+                self.Polyphenol.fromMoby(elt)
             if elt.nodeType==elt.ELEMENT_NODE and (elt.nodeName=="TropGENE_LOCUS" or elt.nodeName=="moby:TropGENE_LOCUS") and (elt.getAttribute("articleName")=="Morphological" or elt.getAttribute("moby:articleName")=="Morphological"):
                 self.Morphological=MobyTropGENE_LOCUS()
-                self.Morphological.fromMoby(elt.toxml())
+                self.Morphological.fromMoby(elt)
             if elt.nodeType==elt.ELEMENT_NODE and (elt.nodeName=="TropGENE_LOCUS" or elt.nodeName=="moby:TropGENE_LOCUS") and (elt.getAttribute("articleName")=="Microsatellite" or elt.getAttribute("moby:articleName")=="Microsatellite"):
                 self.Microsatellite=MobyTropGENE_LOCUS()
-                self.Microsatellite.fromMoby(elt.toxml())
+                self.Microsatellite.fromMoby(elt)
             if elt.nodeType==elt.ELEMENT_NODE and (elt.nodeName=="TropGENE_LOCUS" or elt.nodeName=="moby:TropGENE_LOCUS") and (elt.getAttribute("articleName")=="SNP" or elt.getAttribute("moby:articleName")=="SNP"):
                 self.SNP=MobyTropGENE_LOCUS()
-                self.SNP.fromMoby(elt.toxml())
+                self.SNP.fromMoby(elt)
             if elt.nodeType==elt.ELEMENT_NODE and (elt.nodeName=="TropGENE_LOCUS" or elt.nodeName=="moby:TropGENE_LOCUS") and (elt.getAttribute("articleName")=="CAPS" or elt.getAttribute("moby:articleName")=="CAPS"):
                 self.CAPS=MobyTropGENE_LOCUS()
-                self.CAPS.fromMoby(elt.toxml())
+                self.CAPS.fromMoby(elt)
             if elt.nodeType==elt.ELEMENT_NODE and (elt.nodeName=="TropGENE_LOCUS" or elt.nodeName=="moby:TropGENE_LOCUS") and (elt.getAttribute("articleName")=="TAMPL" or elt.getAttribute("moby:articleName")=="TAMPL"):
                 self.TAMPL=MobyTropGENE_LOCUS()
-                self.TAMPL.fromMoby(elt.toxml())
\ No newline at end of file
+                self.TAMPL.fromMoby(elt)
\ No newline at end of file

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/ontology/TropGENE_Diversity_Matrix.py,v
retrieving revision 1.4
retrieving revision 1.5
diff -u -r1.4 -r1.5
--- /home/repository/moby/moby-live/Python/bioMoby/ontology/TropGENE_Diversity_Matrix.py	2005/02/01 08:52:16	1.4
+++ /home/repository/moby/moby-live/Python/bioMoby/ontology/TropGENE_Diversity_Matrix.py	2005/02/01 14:20:44	1.5
@@ -26,7 +26,9 @@
         """ Load the attributes from an XML string
         """
         from bioMoby.mobyMarshal import MobyUnmarshaller
-        doc=parseString(value).firstChild
+        doc=value
+        if isinstance(value, str):
+            doc=parseString(value).firstChild
         um=MobyUnmarshaller()
         self.content=""
         self.namespace=doc.getAttribute("moby:namespace")
@@ -46,4 +48,4 @@
             if elt.nodeName=="CrossReference" or elt.nodeName=="moby:CrossReference":
                 self.__cross__=[]
                 for ref in elt.childNodes:
-                    self.__cross__.append(ref.toxml())
\ No newline at end of file
+                    self.__cross__.append(um.loads(ref))
\ No newline at end of file

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/ontology/TropGENE_LOCUS.py,v
retrieving revision 1.4
retrieving revision 1.5
diff -u -r1.4 -r1.5
--- /home/repository/moby/moby-live/Python/bioMoby/ontology/TropGENE_LOCUS.py	2005/02/01 08:52:16	1.4
+++ /home/repository/moby/moby-live/Python/bioMoby/ontology/TropGENE_LOCUS.py	2005/02/01 14:20:44	1.5
@@ -25,7 +25,9 @@
         """ Load the attributes from an XML string
         """
         from bioMoby.mobyMarshal import MobyUnmarshaller
-        doc=parseString(value).firstChild
+        doc=value
+        if isinstance(value, str):
+            doc=parseString(value).firstChild
         um=MobyUnmarshaller()
         self.content=""
         self.namespace=doc.getAttribute("moby:namespace")
@@ -45,4 +47,4 @@
             if elt.nodeName=="CrossReference" or elt.nodeName=="moby:CrossReference":
                 self.__cross__=[]
                 for ref in elt.childNodes:
-                    self.__cross__.append(ref.toxml())
\ No newline at end of file
+                    self.__cross__.append(um.loads(ref))
\ No newline at end of file

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/ontology/VirtualSequence.py,v
retrieving revision 1.4
retrieving revision 1.5
diff -u -r1.4 -r1.5
--- /home/repository/moby/moby-live/Python/bioMoby/ontology/VirtualSequence.py	2005/02/01 08:52:16	1.4
+++ /home/repository/moby/moby-live/Python/bioMoby/ontology/VirtualSequence.py	2005/02/01 14:20:44	1.5
@@ -27,7 +27,9 @@
         """ Load the attributes from an XML string
         """
         from bioMoby.mobyMarshal import MobyUnmarshaller
-        doc=parseString(value).firstChild
+        doc=value
+        if isinstance(value, str):
+            doc=parseString(value).firstChild
         um=MobyUnmarshaller()
         self.content=""
         self.namespace=doc.getAttribute("moby:namespace")
@@ -47,8 +49,8 @@
             if elt.nodeName=="CrossReference" or elt.nodeName=="moby:CrossReference":
                 self.__cross__=[]
                 for ref in elt.childNodes:
-                    self.__cross__.append(ref.toxml())
+                    self.__cross__.append(um.loads(ref))
             if elt.nodeType==elt.ELEMENT_NODE and (elt.nodeName=="Integer" or elt.nodeName=="moby:Integer") and (elt.getAttribute("articleName")=="Length" or elt.getAttribute("moby:articleName")=="Length"):
                 t=MobyInteger()
-                t.fromMoby(elt.toxml())
+                t.fromMoby(elt)
                 self.Length=t.content
\ No newline at end of file

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/ontology/WU_BLAST_Text.py,v
retrieving revision 1.4
retrieving revision 1.5
diff -u -r1.4 -r1.5
--- /home/repository/moby/moby-live/Python/bioMoby/ontology/WU_BLAST_Text.py	2005/02/01 08:52:16	1.4
+++ /home/repository/moby/moby-live/Python/bioMoby/ontology/WU_BLAST_Text.py	2005/02/01 14:20:44	1.5
@@ -26,7 +26,9 @@
         """ Load the attributes from an XML string
         """
         from bioMoby.mobyMarshal import MobyUnmarshaller
-        doc=parseString(value).firstChild
+        doc=value
+        if isinstance(value, str):
+            doc=parseString(value).firstChild
         um=MobyUnmarshaller()
         self.content=""
         self.namespace=doc.getAttribute("moby:namespace")
@@ -46,4 +48,4 @@
             if elt.nodeName=="CrossReference" or elt.nodeName=="moby:CrossReference":
                 self.__cross__=[]
                 for ref in elt.childNodes:
-                    self.__cross__.append(ref.toxml())
\ No newline at end of file
+                    self.__cross__.append(um.loads(ref))
\ No newline at end of file

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/ontology/Wildcard_Query.py,v
retrieving revision 1.4
retrieving revision 1.5
diff -u -r1.4 -r1.5
--- /home/repository/moby/moby-live/Python/bioMoby/ontology/Wildcard_Query.py	2005/02/01 08:52:16	1.4
+++ /home/repository/moby/moby-live/Python/bioMoby/ontology/Wildcard_Query.py	2005/02/01 14:20:44	1.5
@@ -30,7 +30,9 @@
         """ Load the attributes from an XML string
         """
         from bioMoby.mobyMarshal import MobyUnmarshaller
-        doc=parseString(value).firstChild
+        doc=value
+        if isinstance(value, str):
+            doc=parseString(value).firstChild
         um=MobyUnmarshaller()
         self.content=""
         self.namespace=doc.getAttribute("moby:namespace")
@@ -50,16 +52,16 @@
             if elt.nodeName=="CrossReference" or elt.nodeName=="moby:CrossReference":
                 self.__cross__=[]
                 for ref in elt.childNodes:
-                    self.__cross__.append(ref.toxml())
+                    self.__cross__.append(um.loads(ref))
             if elt.nodeType==elt.ELEMENT_NODE and (elt.nodeName=="Integer" or elt.nodeName=="moby:Integer") and (elt.getAttribute("articleName")=="end_row" or elt.getAttribute("moby:articleName")=="end_row"):
                 t=MobyInteger()
-                t.fromMoby(elt.toxml())
+                t.fromMoby(elt)
                 self.End_row=t.content
             if elt.nodeType==elt.ELEMENT_NODE and (elt.nodeName=="Integer" or elt.nodeName=="moby:Integer") and (elt.getAttribute("articleName")=="start_row" or elt.getAttribute("moby:articleName")=="start_row"):
                 t=MobyInteger()
-                t.fromMoby(elt.toxml())
+                t.fromMoby(elt)
                 self.Start_row=t.content
             if elt.nodeType==elt.ELEMENT_NODE and (elt.nodeName=="String" or elt.nodeName=="moby:String") and (elt.getAttribute("articleName")=="germplasm_name" or elt.getAttribute("moby:articleName")=="germplasm_name"):
                 t=MobyString()
-                t.fromMoby(elt.toxml())
+                t.fromMoby(elt)
                 self.Germplasm_name=t.content
\ No newline at end of file



From yanwong at pub.open-bio.org  Mon Feb  7 09:12:35 2005
From: yanwong at pub.open-bio.org (Yan Wong)
Date: Mon, 07 Feb 2005 14:12:35 -0000
Subject: [MOBY-guts] biomoby commit
Message-ID: <200502071423.j17ENYJS018965@pub.open-bio.org>


yanwong
Mon Feb  7 09:23:33 EST 2005
Update of /home/repository/moby/moby-live/Python/bioMoby/ontology
In directory pub.open-bio.org:/tmp/cvs-serv18508

Modified Files:
	Alignment.py AlleleAssociation.py Allele_freq.py 
	AminoAcidSequence.py B64_Encoded_PNG.py 
	B64_Encoded_Postscript.py B64_encoded_PDB.py 
	B64_encoded_gif.py B64_encoded_jpeg.py BLASTText.py 
	BasicGFFSequenceFeature.py ClustalAlnFormattedText.py 
	ClustalMsfFormattedText.py CommentedAASequence.py 
	CommentedDNASequence.py CommentedRNASequence.py DNASequence.py 
	DNASequenceWithGFFFeatures.py DateTime.py Decypher_Text.py 
	Edge.py EmblFlatfile.py FASTA.py FASTA_AA.py FASTA_NA.py 
	FASTA_NA_multi.py FASTA_Text.py GFF.py GFF1.py GFF2.py 
	GFF2_5.py GFF3.py GO_Term.py GenbankFlatfile.py 
	Gene_Expression_data.py GenericSequence.py GeneticElement.py 
	Genotype.py Germplasm_Details.py Germplasm_List.py 
	Global_Keyword.py HBond_Pair.py HFormatText.py 
	Haplotyping_Study_obj.py ICIS_Query.py ICIS_Query2.py 
	ICIS_Query3.py IntAct_XML.py Interaction.py 
	InteractionMethod.py Interaction_partner.py Interactor.py 
	MEME_Text.py MGIS_ACCESSION.py MMP_Locus.py MO_Term_Test.py 
	MSF.py MmCIFText.py Multi_key_value_pair.py 
	MyTestingDataType_11024145298313.py MyTree.py 
	NCBI_BLAST_Text.py NCBI_Blast_XML.py NCBI_Blast_XML_Gif.py 
	NCBI_Blast_XML_Gif_Map.py NCBI_MEME_Text.py 
	NucleotideSequence.py PDBFormattedText.py PDBText.py PDGJOB.py 
	PHDText.py PMUTText.py PSeaTextFormatted.py 
	PhenotypeDescription.py PubMedMEDLINE.py RNASequence.py 
	SINGER_ACCESSION.py Sample.py SchematikonMotifID.py 
	SchematikonMotifSupport.py SchematikonSegmentAttributes.py 
	SchematikonSegmentID.py SchematikonStructureAnnotation.py 
	SchematikonVorocodeName.py Scored_acronym_string.py 
	SimpleAnnotatedGIFImage.py SimpleAnnotatedJPEGImage.py 
	Simple_key_value_pair.py Snp_allele.py Snp_genotype.py 
	Study.py TEST.py TargetP_result.py Testout.py TextBase64.py 
	TextFormatted.py TextHtml.py TextPlain.py TextUuencoded.py 
	TextXml.py Text_plain.py Trait_Details.py Tree.py 
	TropGENE_ACCESSION.py TropGENE_Diversity_Matrix.py 
	TropGENE_LOCUS.py VirtualSequence.py WU_BLAST_Text.py 
	Wildcard_Query.py 
Log Message:


moby-live/Python/bioMoby/ontology Alignment.py,1.1,1.2 AlleleAssociation.py,1.5,1.6 Allele_freq.py,1.5,1.6 AminoAcidSequence.py,1.5,1.6 B64_Encoded_PNG.py,1.5,1.6 B64_Encoded_Postscript.py,1.5,1.6 B64_encoded_PDB.py,1.5,1.6 B64_encoded_gif.py,1.5,1.6 B64_encoded_jpeg.py,1.5,1.6 BLASTText.py,1.5,1.6 BasicGFFSequenceFeature.py,1.5,1.6 ClustalAlnFormattedText.py,1.5,1.6 ClustalMsfFormattedText.py,1.5,1.6 CommentedAASequence.py,1.5,1.6 CommentedDNASequence.py,1.5,1.6 CommentedRNASequence.py,1.5,1.6 DNASequence.py,1.5,1.6 DNASequenceWithGFFFeatures.py,1.5,1.6 DateTime.py,1.5,1.6 Decypher_Text.py,1.5,1.6 Edge.py,1.5,1.6 EmblFlatfile.py,1.5,1.6 FASTA.py,1.5,1.6 FASTA_AA.py,1.5,1.6 FASTA_NA.py,1.5,1.6 FASTA_NA_multi.py,1.1,1.2 FASTA_Text.py,1.5,1.6 GFF.py,1.5,1.6 GFF1.py,1.5,1.6 GFF2.py,1.5,1.6 GFF2_5.py,1.5,1.6 GFF3.py,1.5,1.6 GO_Term.py,1.5,1.6 GenbankFlatfile.py,1.5,1.6 Gene_Expression_data.py,1.1,1.2 GenericSequence.py,1.5,1.6 GeneticElement.py,1.5,1.6 Genotype.py,1.5,1.6 Germpl!
asm_Details.py,1.5,1.6 Germplasm_List.py,1.5,1.6 Global_Keyword.py,1.5,1.6 HBond_Pair.py,1.5,1.6 HFormatText.py,1.5,1.6 Haplotyping_Study_obj.py,1.5,1.6 ICIS_Query.py,1.5,1.6 ICIS_Query2.py,1.5,1.6 ICIS_Query3.py,1.5,1.6 IntAct_XML.py,1.5,1.6 Interaction.py,1.5,1.6 InteractionMethod.py,1.5,1.6 Interaction_partner.py,1.5,1.6 Interactor.py,1.5,1.6 MEME_Text.py,1.5,1.6 MGIS_ACCESSION.py,1.5,1.6 MMP_Locus.py,1.5,1.6 MO_Term_Test.py,1.5,1.6 MSF.py,1.1,1.2 MmCIFText.py,1.5,1.6 Multi_key_value_pair.py,1.5,1.6 MyTestingDataType_11024145298313.py,1.5,1.6 MyTree.py,1.5,1.6 NCBI_BLAST_Text.py,1.5,1.6 NCBI_Blast_XML.py,1.5,1.6 NCBI_Blast_XML_Gif.py,1.5,1.6 NCBI_Blast_XML_Gif_Map.py,1.5,1.6 NCBI_MEME_Text.py,1.5,1.6 NucleotideSequence.py,1.5,1.6 PDBFormattedText.py,1.5,1.6 PDBText.py,1.5,1.6 PDGJOB.py,1.5,1.6 PHDText.py,1.5,1.6 PMUTText.py,1.5,1.6 PSeaTextFormatted.py,1.5,1.6 PhenotypeDescription.py,1.5,1.6 PubMedMEDLINE.py,1.5,1.6 RNASequence.py,1.5,1.6 SINGER_ACCESSION.py,1.5,1.6 Sampl!
e.py,1.5,1.6 SchematikonMotifID.py,1.5,1.6 SchematikonMotifSu!
pport.py,1.5,1.6 SchematikonSegmentAttributes.py,1.5,1.6 SchematikonSegmentID.py,1.5,1.6 SchematikonStructureAnnotation.py,1.5,1.6 SchematikonVorocodeName.py,1.5,1.6 Scored_acronym_string.py,1.5,1.6 SimpleAnnotatedGIFImage.py,1.5,1.6 SimpleAnnotatedJPEGImage.py,1.5,1.6 Simple_key_value_pair.py,1.5,1.6 Snp_allele.py,1.5,1.6 Snp_genotype.py,1.5,1.6 Study.py,1.5,1.6 TEST.py,1.5,1.6 TargetP_result.py,1.5,1.6 Testout.py,1.5,1.6 TextBase64.py,1.5,1.6 TextFormatted.py,1.5,1.6 TextHtml.py,1.5,1.6 TextPlain.py,1.5,1.6 TextUuencoded.py,1.5,1.6 TextXml.py,1.5,1.6 Text_plain.py,1.5,1.6 Trait_Details.py,1.5,1.6 Tree.py,1.5,1.6 TropGENE_ACCESSION.py,1.5,1.6 TropGENE_Diversity_Matrix.py,1.5,1.6 TropGENE_LOCUS.py,1.5,1.6 VirtualSequence.py,1.5,1.6 WU_BLAST_Text.py,1.5,1.6 Wildcard_Query.py,1.5,1.6
===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/ontology/Alignment.py,v
retrieving revision 1.1
retrieving revision 1.2
diff -u -r1.1 -r1.2
--- /home/repository/moby/moby-live/Python/bioMoby/ontology/Alignment.py	2005/02/02 15:18:06	1.1
+++ /home/repository/moby/moby-live/Python/bioMoby/ontology/Alignment.py	2005/02/07 14:23:32	1.2
@@ -48,4 +48,5 @@
             if elt.nodeName=="CrossReference" or elt.nodeName=="moby:CrossReference":
                 self.__cross__=[]
                 for ref in elt.childNodes:
-                    self.__cross__.append(um.loads(ref))
\ No newline at end of file
+                    if ref.nodeType==ref.ELEMENT_NODE:
+                        self.__cross__.append(um.loadn(ref))
\ No newline at end of file

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/ontology/AlleleAssociation.py,v
retrieving revision 1.5
retrieving revision 1.6
diff -u -r1.5 -r1.6
--- /home/repository/moby/moby-live/Python/bioMoby/ontology/AlleleAssociation.py	2005/02/01 14:20:44	1.5
+++ /home/repository/moby/moby-live/Python/bioMoby/ontology/AlleleAssociation.py	2005/02/07 14:23:32	1.6
@@ -52,7 +52,8 @@
             if elt.nodeName=="CrossReference" or elt.nodeName=="moby:CrossReference":
                 self.__cross__=[]
                 for ref in elt.childNodes:
-                    self.__cross__.append(um.loads(ref))
+                    if ref.nodeType==ref.ELEMENT_NODE:
+                        self.__cross__.append(um.loadn(ref))
             if elt.nodeType==elt.ELEMENT_NODE and (elt.nodeName=="String" or elt.nodeName=="moby:String") and (elt.getAttribute("articleName")=="snp" or elt.getAttribute("moby:articleName")=="snp"):
                 t=MobyString()
                 t.fromMoby(elt)

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/ontology/Allele_freq.py,v
retrieving revision 1.5
retrieving revision 1.6
diff -u -r1.5 -r1.6
--- /home/repository/moby/moby-live/Python/bioMoby/ontology/Allele_freq.py	2005/02/01 14:20:44	1.5
+++ /home/repository/moby/moby-live/Python/bioMoby/ontology/Allele_freq.py	2005/02/07 14:23:32	1.6
@@ -46,7 +46,8 @@
             if elt.nodeName=="CrossReference" or elt.nodeName=="moby:CrossReference":
                 self.__cross__=[]
                 for ref in elt.childNodes:
-                    self.__cross__.append(um.loads(ref))
+                    if ref.nodeType==ref.ELEMENT_NODE:
+                        self.__cross__.append(um.loadn(ref))
             if elt.nodeType==elt.ELEMENT_NODE and (elt.nodeName=="Object" or elt.nodeName=="moby:Object") and (elt.getAttribute("articleName")=="panel_lsid" or elt.getAttribute("moby:articleName")=="panel_lsid"):
                 self.Panel_lsid=MobyObject()
                 self.Panel_lsid.fromMoby(elt)

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/ontology/AminoAcidSequence.py,v
retrieving revision 1.5
retrieving revision 1.6
diff -u -r1.5 -r1.6
--- /home/repository/moby/moby-live/Python/bioMoby/ontology/AminoAcidSequence.py	2005/02/01 14:20:44	1.5
+++ /home/repository/moby/moby-live/Python/bioMoby/ontology/AminoAcidSequence.py	2005/02/07 14:23:32	1.6
@@ -51,7 +51,8 @@
             if elt.nodeName=="CrossReference" or elt.nodeName=="moby:CrossReference":
                 self.__cross__=[]
                 for ref in elt.childNodes:
-                    self.__cross__.append(um.loads(ref))
+                    if ref.nodeType==ref.ELEMENT_NODE:
+                        self.__cross__.append(um.loadn(ref))
             if elt.nodeType==elt.ELEMENT_NODE and (elt.nodeName=="Integer" or elt.nodeName=="moby:Integer") and (elt.getAttribute("articleName")=="Length" or elt.getAttribute("moby:articleName")=="Length"):
                 t=MobyInteger()
                 t.fromMoby(elt)

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/ontology/B64_Encoded_PNG.py,v
retrieving revision 1.5
retrieving revision 1.6
diff -u -r1.5 -r1.6
--- /home/repository/moby/moby-live/Python/bioMoby/ontology/B64_Encoded_PNG.py	2005/02/01 14:20:44	1.5
+++ /home/repository/moby/moby-live/Python/bioMoby/ontology/B64_Encoded_PNG.py	2005/02/07 14:23:32	1.6
@@ -48,4 +48,5 @@
             if elt.nodeName=="CrossReference" or elt.nodeName=="moby:CrossReference":
                 self.__cross__=[]
                 for ref in elt.childNodes:
-                    self.__cross__.append(um.loads(ref))
\ No newline at end of file
+                    if ref.nodeType==ref.ELEMENT_NODE:
+                        self.__cross__.append(um.loadn(ref))
\ No newline at end of file

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/ontology/B64_Encoded_Postscript.py,v
retrieving revision 1.5
retrieving revision 1.6
diff -u -r1.5 -r1.6
--- /home/repository/moby/moby-live/Python/bioMoby/ontology/B64_Encoded_Postscript.py	2005/02/01 14:20:44	1.5
+++ /home/repository/moby/moby-live/Python/bioMoby/ontology/B64_Encoded_Postscript.py	2005/02/07 14:23:32	1.6
@@ -48,4 +48,5 @@
             if elt.nodeName=="CrossReference" or elt.nodeName=="moby:CrossReference":
                 self.__cross__=[]
                 for ref in elt.childNodes:
-                    self.__cross__.append(um.loads(ref))
\ No newline at end of file
+                    if ref.nodeType==ref.ELEMENT_NODE:
+                        self.__cross__.append(um.loadn(ref))
\ No newline at end of file

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/ontology/B64_encoded_PDB.py,v
retrieving revision 1.5
retrieving revision 1.6
diff -u -r1.5 -r1.6
--- /home/repository/moby/moby-live/Python/bioMoby/ontology/B64_encoded_PDB.py	2005/02/01 14:20:44	1.5
+++ /home/repository/moby/moby-live/Python/bioMoby/ontology/B64_encoded_PDB.py	2005/02/07 14:23:32	1.6
@@ -48,4 +48,5 @@
             if elt.nodeName=="CrossReference" or elt.nodeName=="moby:CrossReference":
                 self.__cross__=[]
                 for ref in elt.childNodes:
-                    self.__cross__.append(um.loads(ref))
\ No newline at end of file
+                    if ref.nodeType==ref.ELEMENT_NODE:
+                        self.__cross__.append(um.loadn(ref))
\ No newline at end of file

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/ontology/B64_encoded_gif.py,v
retrieving revision 1.5
retrieving revision 1.6
diff -u -r1.5 -r1.6
--- /home/repository/moby/moby-live/Python/bioMoby/ontology/B64_encoded_gif.py	2005/02/01 14:20:44	1.5
+++ /home/repository/moby/moby-live/Python/bioMoby/ontology/B64_encoded_gif.py	2005/02/07 14:23:32	1.6
@@ -48,4 +48,5 @@
             if elt.nodeName=="CrossReference" or elt.nodeName=="moby:CrossReference":
                 self.__cross__=[]
                 for ref in elt.childNodes:
-                    self.__cross__.append(um.loads(ref))
\ No newline at end of file
+                    if ref.nodeType==ref.ELEMENT_NODE:
+                        self.__cross__.append(um.loadn(ref))
\ No newline at end of file

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/ontology/B64_encoded_jpeg.py,v
retrieving revision 1.5
retrieving revision 1.6
diff -u -r1.5 -r1.6
--- /home/repository/moby/moby-live/Python/bioMoby/ontology/B64_encoded_jpeg.py	2005/02/01 14:20:44	1.5
+++ /home/repository/moby/moby-live/Python/bioMoby/ontology/B64_encoded_jpeg.py	2005/02/07 14:23:32	1.6
@@ -48,4 +48,5 @@
             if elt.nodeName=="CrossReference" or elt.nodeName=="moby:CrossReference":
                 self.__cross__=[]
                 for ref in elt.childNodes:
-                    self.__cross__.append(um.loads(ref))
\ No newline at end of file
+                    if ref.nodeType==ref.ELEMENT_NODE:
+                        self.__cross__.append(um.loadn(ref))
\ No newline at end of file

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/ontology/BLASTText.py,v
retrieving revision 1.5
retrieving revision 1.6
diff -u -r1.5 -r1.6
--- /home/repository/moby/moby-live/Python/bioMoby/ontology/BLASTText.py	2005/02/01 14:20:44	1.5
+++ /home/repository/moby/moby-live/Python/bioMoby/ontology/BLASTText.py	2005/02/07 14:23:32	1.6
@@ -48,4 +48,5 @@
             if elt.nodeName=="CrossReference" or elt.nodeName=="moby:CrossReference":
                 self.__cross__=[]
                 for ref in elt.childNodes:
-                    self.__cross__.append(um.loads(ref))
\ No newline at end of file
+                    if ref.nodeType==ref.ELEMENT_NODE:
+                        self.__cross__.append(um.loadn(ref))
\ No newline at end of file

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/ontology/BasicGFFSequenceFeature.py,v
retrieving revision 1.5
retrieving revision 1.6
diff -u -r1.5 -r1.6
--- /home/repository/moby/moby-live/Python/bioMoby/ontology/BasicGFFSequenceFeature.py	2005/02/01 14:20:44	1.5
+++ /home/repository/moby/moby-live/Python/bioMoby/ontology/BasicGFFSequenceFeature.py	2005/02/07 14:23:32	1.6
@@ -62,7 +62,8 @@
             if elt.nodeName=="CrossReference" or elt.nodeName=="moby:CrossReference":
                 self.__cross__=[]
                 for ref in elt.childNodes:
-                    self.__cross__.append(um.loads(ref))
+                    if ref.nodeType==ref.ELEMENT_NODE:
+                        self.__cross__.append(um.loadn(ref))
             if elt.nodeType==elt.ELEMENT_NODE and (elt.nodeName=="String" or elt.nodeName=="moby:String") and (elt.getAttribute("articleName")=="reference" or elt.getAttribute("moby:articleName")=="reference"):
                 t=MobyString()
                 t.fromMoby(elt)

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/ontology/ClustalAlnFormattedText.py,v
retrieving revision 1.5
retrieving revision 1.6
diff -u -r1.5 -r1.6
--- /home/repository/moby/moby-live/Python/bioMoby/ontology/ClustalAlnFormattedText.py	2005/02/01 14:20:44	1.5
+++ /home/repository/moby/moby-live/Python/bioMoby/ontology/ClustalAlnFormattedText.py	2005/02/07 14:23:32	1.6
@@ -48,4 +48,5 @@
             if elt.nodeName=="CrossReference" or elt.nodeName=="moby:CrossReference":
                 self.__cross__=[]
                 for ref in elt.childNodes:
-                    self.__cross__.append(um.loads(ref))
\ No newline at end of file
+                    if ref.nodeType==ref.ELEMENT_NODE:
+                        self.__cross__.append(um.loadn(ref))
\ No newline at end of file

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/ontology/ClustalMsfFormattedText.py,v
retrieving revision 1.5
retrieving revision 1.6
diff -u -r1.5 -r1.6
--- /home/repository/moby/moby-live/Python/bioMoby/ontology/ClustalMsfFormattedText.py	2005/02/01 14:20:44	1.5
+++ /home/repository/moby/moby-live/Python/bioMoby/ontology/ClustalMsfFormattedText.py	2005/02/07 14:23:32	1.6
@@ -48,4 +48,5 @@
             if elt.nodeName=="CrossReference" or elt.nodeName=="moby:CrossReference":
                 self.__cross__=[]
                 for ref in elt.childNodes:
-                    self.__cross__.append(um.loads(ref))
\ No newline at end of file
+                    if ref.nodeType==ref.ELEMENT_NODE:
+                        self.__cross__.append(um.loadn(ref))
\ No newline at end of file

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/ontology/CommentedAASequence.py,v
retrieving revision 1.5
retrieving revision 1.6
diff -u -r1.5 -r1.6
--- /home/repository/moby/moby-live/Python/bioMoby/ontology/CommentedAASequence.py	2005/02/01 14:20:44	1.5
+++ /home/repository/moby/moby-live/Python/bioMoby/ontology/CommentedAASequence.py	2005/02/07 14:23:32	1.6
@@ -52,7 +52,8 @@
             if elt.nodeName=="CrossReference" or elt.nodeName=="moby:CrossReference":
                 self.__cross__=[]
                 for ref in elt.childNodes:
-                    self.__cross__.append(um.loads(ref))
+                    if ref.nodeType==ref.ELEMENT_NODE:
+                        self.__cross__.append(um.loadn(ref))
             if elt.nodeType==elt.ELEMENT_NODE and (elt.nodeName=="Integer" or elt.nodeName=="moby:Integer") and (elt.getAttribute("articleName")=="Length" or elt.getAttribute("moby:articleName")=="Length"):
                 t=MobyInteger()
                 t.fromMoby(elt)

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/ontology/CommentedDNASequence.py,v
retrieving revision 1.5
retrieving revision 1.6
diff -u -r1.5 -r1.6
--- /home/repository/moby/moby-live/Python/bioMoby/ontology/CommentedDNASequence.py	2005/02/01 14:20:44	1.5
+++ /home/repository/moby/moby-live/Python/bioMoby/ontology/CommentedDNASequence.py	2005/02/07 14:23:32	1.6
@@ -52,7 +52,8 @@
             if elt.nodeName=="CrossReference" or elt.nodeName=="moby:CrossReference":
                 self.__cross__=[]
                 for ref in elt.childNodes:
-                    self.__cross__.append(um.loads(ref))
+                    if ref.nodeType==ref.ELEMENT_NODE:
+                        self.__cross__.append(um.loadn(ref))
             if elt.nodeType==elt.ELEMENT_NODE and (elt.nodeName=="Integer" or elt.nodeName=="moby:Integer") and (elt.getAttribute("articleName")=="Length" or elt.getAttribute("moby:articleName")=="Length"):
                 t=MobyInteger()
                 t.fromMoby(elt)

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/ontology/CommentedRNASequence.py,v
retrieving revision 1.5
retrieving revision 1.6
diff -u -r1.5 -r1.6
--- /home/repository/moby/moby-live/Python/bioMoby/ontology/CommentedRNASequence.py	2005/02/01 14:20:44	1.5
+++ /home/repository/moby/moby-live/Python/bioMoby/ontology/CommentedRNASequence.py	2005/02/07 14:23:32	1.6
@@ -52,7 +52,8 @@
             if elt.nodeName=="CrossReference" or elt.nodeName=="moby:CrossReference":
                 self.__cross__=[]
                 for ref in elt.childNodes:
-                    self.__cross__.append(um.loads(ref))
+                    if ref.nodeType==ref.ELEMENT_NODE:
+                        self.__cross__.append(um.loadn(ref))
             if elt.nodeType==elt.ELEMENT_NODE and (elt.nodeName=="Integer" or elt.nodeName=="moby:Integer") and (elt.getAttribute("articleName")=="Length" or elt.getAttribute("moby:articleName")=="Length"):
                 t=MobyInteger()
                 t.fromMoby(elt)

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/ontology/DNASequence.py,v
retrieving revision 1.5
retrieving revision 1.6
diff -u -r1.5 -r1.6
--- /home/repository/moby/moby-live/Python/bioMoby/ontology/DNASequence.py	2005/02/01 14:20:44	1.5
+++ /home/repository/moby/moby-live/Python/bioMoby/ontology/DNASequence.py	2005/02/07 14:23:32	1.6
@@ -51,7 +51,8 @@
             if elt.nodeName=="CrossReference" or elt.nodeName=="moby:CrossReference":
                 self.__cross__=[]
                 for ref in elt.childNodes:
-                    self.__cross__.append(um.loads(ref))
+                    if ref.nodeType==ref.ELEMENT_NODE:
+                        self.__cross__.append(um.loadn(ref))
             if elt.nodeType==elt.ELEMENT_NODE and (elt.nodeName=="Integer" or elt.nodeName=="moby:Integer") and (elt.getAttribute("articleName")=="Length" or elt.getAttribute("moby:articleName")=="Length"):
                 t=MobyInteger()
                 t.fromMoby(elt)

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/ontology/DNASequenceWithGFFFeatures.py,v
retrieving revision 1.5
retrieving revision 1.6
diff -u -r1.5 -r1.6
--- /home/repository/moby/moby-live/Python/bioMoby/ontology/DNASequenceWithGFFFeatures.py	2005/02/01 14:20:44	1.5
+++ /home/repository/moby/moby-live/Python/bioMoby/ontology/DNASequenceWithGFFFeatures.py	2005/02/07 14:23:33	1.6
@@ -54,7 +54,8 @@
             if elt.nodeName=="CrossReference" or elt.nodeName=="moby:CrossReference":
                 self.__cross__=[]
                 for ref in elt.childNodes:
-                    self.__cross__.append(um.loads(ref))
+                    if ref.nodeType==ref.ELEMENT_NODE:
+                        self.__cross__.append(um.loadn(ref))
             if elt.nodeType==elt.ELEMENT_NODE and (elt.nodeName=="Integer" or elt.nodeName=="moby:Integer") and (elt.getAttribute("articleName")=="Length" or elt.getAttribute("moby:articleName")=="Length"):
                 t=MobyInteger()
                 t.fromMoby(elt)

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/ontology/DateTime.py,v
retrieving revision 1.5
retrieving revision 1.6
diff -u -r1.5 -r1.6
--- /home/repository/moby/moby-live/Python/bioMoby/ontology/DateTime.py	2005/02/01 14:20:44	1.5
+++ /home/repository/moby/moby-live/Python/bioMoby/ontology/DateTime.py	2005/02/07 14:23:33	1.6
@@ -48,4 +48,5 @@
             if elt.nodeName=="CrossReference" or elt.nodeName=="moby:CrossReference":
                 self.__cross__=[]
                 for ref in elt.childNodes:
-                    self.__cross__.append(um.loads(ref))
\ No newline at end of file
+                    if ref.nodeType==ref.ELEMENT_NODE:
+                        self.__cross__.append(um.loadn(ref))
\ No newline at end of file

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/ontology/Decypher_Text.py,v
retrieving revision 1.5
retrieving revision 1.6
diff -u -r1.5 -r1.6
--- /home/repository/moby/moby-live/Python/bioMoby/ontology/Decypher_Text.py	2005/02/01 14:20:44	1.5
+++ /home/repository/moby/moby-live/Python/bioMoby/ontology/Decypher_Text.py	2005/02/07 14:23:33	1.6
@@ -48,4 +48,5 @@
             if elt.nodeName=="CrossReference" or elt.nodeName=="moby:CrossReference":
                 self.__cross__=[]
                 for ref in elt.childNodes:
-                    self.__cross__.append(um.loads(ref))
\ No newline at end of file
+                    if ref.nodeType==ref.ELEMENT_NODE:
+                        self.__cross__.append(um.loadn(ref))
\ No newline at end of file

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/ontology/Edge.py,v
retrieving revision 1.5
retrieving revision 1.6
diff -u -r1.5 -r1.6
--- /home/repository/moby/moby-live/Python/bioMoby/ontology/Edge.py	2005/02/01 14:20:44	1.5
+++ /home/repository/moby/moby-live/Python/bioMoby/ontology/Edge.py	2005/02/07 14:23:33	1.6
@@ -51,7 +51,8 @@
             if elt.nodeName=="CrossReference" or elt.nodeName=="moby:CrossReference":
                 self.__cross__=[]
                 for ref in elt.childNodes:
-                    self.__cross__.append(um.loads(ref))
+                    if ref.nodeType==ref.ELEMENT_NODE:
+                        self.__cross__.append(um.loadn(ref))
             if elt.nodeType==elt.ELEMENT_NODE and (elt.nodeName=="String" or elt.nodeName=="moby:String") and (elt.getAttribute("articleName")=="partner" or elt.getAttribute("moby:articleName")=="partner"):
                 t=MobyString()
                 t.fromMoby(elt)

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/ontology/EmblFlatfile.py,v
retrieving revision 1.5
retrieving revision 1.6
diff -u -r1.5 -r1.6
--- /home/repository/moby/moby-live/Python/bioMoby/ontology/EmblFlatfile.py	2005/02/01 14:20:44	1.5
+++ /home/repository/moby/moby-live/Python/bioMoby/ontology/EmblFlatfile.py	2005/02/07 14:23:33	1.6
@@ -48,4 +48,5 @@
             if elt.nodeName=="CrossReference" or elt.nodeName=="moby:CrossReference":
                 self.__cross__=[]
                 for ref in elt.childNodes:
-                    self.__cross__.append(um.loads(ref))
\ No newline at end of file
+                    if ref.nodeType==ref.ELEMENT_NODE:
+                        self.__cross__.append(um.loadn(ref))
\ No newline at end of file

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/ontology/FASTA.py,v
retrieving revision 1.5
retrieving revision 1.6
diff -u -r1.5 -r1.6
--- /home/repository/moby/moby-live/Python/bioMoby/ontology/FASTA.py	2005/02/01 14:20:44	1.5
+++ /home/repository/moby/moby-live/Python/bioMoby/ontology/FASTA.py	2005/02/07 14:23:33	1.6
@@ -48,4 +48,5 @@
             if elt.nodeName=="CrossReference" or elt.nodeName=="moby:CrossReference":
                 self.__cross__=[]
                 for ref in elt.childNodes:
-                    self.__cross__.append(um.loads(ref))
\ No newline at end of file
+                    if ref.nodeType==ref.ELEMENT_NODE:
+                        self.__cross__.append(um.loadn(ref))
\ No newline at end of file

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/ontology/FASTA_AA.py,v
retrieving revision 1.5
retrieving revision 1.6
diff -u -r1.5 -r1.6
--- /home/repository/moby/moby-live/Python/bioMoby/ontology/FASTA_AA.py	2005/02/01 14:20:44	1.5
+++ /home/repository/moby/moby-live/Python/bioMoby/ontology/FASTA_AA.py	2005/02/07 14:23:33	1.6
@@ -48,4 +48,5 @@
             if elt.nodeName=="CrossReference" or elt.nodeName=="moby:CrossReference":
                 self.__cross__=[]
                 for ref in elt.childNodes:
-                    self.__cross__.append(um.loads(ref))
\ No newline at end of file
+                    if ref.nodeType==ref.ELEMENT_NODE:
+                        self.__cross__.append(um.loadn(ref))
\ No newline at end of file

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/ontology/FASTA_NA.py,v
retrieving revision 1.5
retrieving revision 1.6
diff -u -r1.5 -r1.6
--- /home/repository/moby/moby-live/Python/bioMoby/ontology/FASTA_NA.py	2005/02/01 14:20:44	1.5
+++ /home/repository/moby/moby-live/Python/bioMoby/ontology/FASTA_NA.py	2005/02/07 14:23:33	1.6
@@ -48,4 +48,5 @@
             if elt.nodeName=="CrossReference" or elt.nodeName=="moby:CrossReference":
                 self.__cross__=[]
                 for ref in elt.childNodes:
-                    self.__cross__.append(um.loads(ref))
\ No newline at end of file
+                    if ref.nodeType==ref.ELEMENT_NODE:
+                        self.__cross__.append(um.loadn(ref))
\ No newline at end of file

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/ontology/FASTA_NA_multi.py,v
retrieving revision 1.1
retrieving revision 1.2
diff -u -r1.1 -r1.2
--- /home/repository/moby/moby-live/Python/bioMoby/ontology/FASTA_NA_multi.py	2005/02/02 15:20:55	1.1
+++ /home/repository/moby/moby-live/Python/bioMoby/ontology/FASTA_NA_multi.py	2005/02/07 14:23:33	1.2
@@ -48,4 +48,5 @@
             if elt.nodeName=="CrossReference" or elt.nodeName=="moby:CrossReference":
                 self.__cross__=[]
                 for ref in elt.childNodes:
-                    self.__cross__.append(um.loads(ref))
\ No newline at end of file
+                    if ref.nodeType==ref.ELEMENT_NODE:
+                        self.__cross__.append(um.loadn(ref))
\ No newline at end of file

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/ontology/FASTA_Text.py,v
retrieving revision 1.5
retrieving revision 1.6
diff -u -r1.5 -r1.6
--- /home/repository/moby/moby-live/Python/bioMoby/ontology/FASTA_Text.py	2005/02/01 14:20:44	1.5
+++ /home/repository/moby/moby-live/Python/bioMoby/ontology/FASTA_Text.py	2005/02/07 14:23:33	1.6
@@ -48,4 +48,5 @@
             if elt.nodeName=="CrossReference" or elt.nodeName=="moby:CrossReference":
                 self.__cross__=[]
                 for ref in elt.childNodes:
-                    self.__cross__.append(um.loads(ref))
\ No newline at end of file
+                    if ref.nodeType==ref.ELEMENT_NODE:
+                        self.__cross__.append(um.loadn(ref))
\ No newline at end of file

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/ontology/GFF.py,v
retrieving revision 1.5
retrieving revision 1.6
diff -u -r1.5 -r1.6
--- /home/repository/moby/moby-live/Python/bioMoby/ontology/GFF.py	2005/02/01 14:20:44	1.5
+++ /home/repository/moby/moby-live/Python/bioMoby/ontology/GFF.py	2005/02/07 14:23:33	1.6
@@ -48,4 +48,5 @@
             if elt.nodeName=="CrossReference" or elt.nodeName=="moby:CrossReference":
                 self.__cross__=[]
                 for ref in elt.childNodes:
-                    self.__cross__.append(um.loads(ref))
\ No newline at end of file
+                    if ref.nodeType==ref.ELEMENT_NODE:
+                        self.__cross__.append(um.loadn(ref))
\ No newline at end of file

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/ontology/GFF1.py,v
retrieving revision 1.5
retrieving revision 1.6
diff -u -r1.5 -r1.6
--- /home/repository/moby/moby-live/Python/bioMoby/ontology/GFF1.py	2005/02/01 14:20:44	1.5
+++ /home/repository/moby/moby-live/Python/bioMoby/ontology/GFF1.py	2005/02/07 14:23:33	1.6
@@ -48,4 +48,5 @@
             if elt.nodeName=="CrossReference" or elt.nodeName=="moby:CrossReference":
                 self.__cross__=[]
                 for ref in elt.childNodes:
-                    self.__cross__.append(um.loads(ref))
\ No newline at end of file
+                    if ref.nodeType==ref.ELEMENT_NODE:
+                        self.__cross__.append(um.loadn(ref))
\ No newline at end of file

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/ontology/GFF2.py,v
retrieving revision 1.5
retrieving revision 1.6
diff -u -r1.5 -r1.6
--- /home/repository/moby/moby-live/Python/bioMoby/ontology/GFF2.py	2005/02/01 14:20:44	1.5
+++ /home/repository/moby/moby-live/Python/bioMoby/ontology/GFF2.py	2005/02/07 14:23:33	1.6
@@ -48,4 +48,5 @@
             if elt.nodeName=="CrossReference" or elt.nodeName=="moby:CrossReference":
                 self.__cross__=[]
                 for ref in elt.childNodes:
-                    self.__cross__.append(um.loads(ref))
\ No newline at end of file
+                    if ref.nodeType==ref.ELEMENT_NODE:
+                        self.__cross__.append(um.loadn(ref))
\ No newline at end of file

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/ontology/GFF2_5.py,v
retrieving revision 1.5
retrieving revision 1.6
diff -u -r1.5 -r1.6
--- /home/repository/moby/moby-live/Python/bioMoby/ontology/GFF2_5.py	2005/02/01 14:20:44	1.5
+++ /home/repository/moby/moby-live/Python/bioMoby/ontology/GFF2_5.py	2005/02/07 14:23:33	1.6
@@ -48,4 +48,5 @@
             if elt.nodeName=="CrossReference" or elt.nodeName=="moby:CrossReference":
                 self.__cross__=[]
                 for ref in elt.childNodes:
-                    self.__cross__.append(um.loads(ref))
\ No newline at end of file
+                    if ref.nodeType==ref.ELEMENT_NODE:
+                        self.__cross__.append(um.loadn(ref))
\ No newline at end of file

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/ontology/GFF3.py,v
retrieving revision 1.5
retrieving revision 1.6
diff -u -r1.5 -r1.6
--- /home/repository/moby/moby-live/Python/bioMoby/ontology/GFF3.py	2005/02/01 14:20:44	1.5
+++ /home/repository/moby/moby-live/Python/bioMoby/ontology/GFF3.py	2005/02/07 14:23:33	1.6
@@ -48,4 +48,5 @@
             if elt.nodeName=="CrossReference" or elt.nodeName=="moby:CrossReference":
                 self.__cross__=[]
                 for ref in elt.childNodes:
-                    self.__cross__.append(um.loads(ref))
\ No newline at end of file
+                    if ref.nodeType==ref.ELEMENT_NODE:
+                        self.__cross__.append(um.loadn(ref))
\ No newline at end of file

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/ontology/GO_Term.py,v
retrieving revision 1.5
retrieving revision 1.6
diff -u -r1.5 -r1.6
--- /home/repository/moby/moby-live/Python/bioMoby/ontology/GO_Term.py	2005/02/01 14:20:44	1.5
+++ /home/repository/moby/moby-live/Python/bioMoby/ontology/GO_Term.py	2005/02/07 14:23:33	1.6
@@ -50,7 +50,8 @@
             if elt.nodeName=="CrossReference" or elt.nodeName=="moby:CrossReference":
                 self.__cross__=[]
                 for ref in elt.childNodes:
-                    self.__cross__.append(um.loads(ref))
+                    if ref.nodeType==ref.ELEMENT_NODE:
+                        self.__cross__.append(um.loadn(ref))
             if elt.nodeType==elt.ELEMENT_NODE and (elt.nodeName=="String" or elt.nodeName=="moby:String") and (elt.getAttribute("articleName")=="Term" or elt.getAttribute("moby:articleName")=="Term"):
                 t=MobyString()
                 t.fromMoby(elt)

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/ontology/GenbankFlatfile.py,v
retrieving revision 1.5
retrieving revision 1.6
diff -u -r1.5 -r1.6
--- /home/repository/moby/moby-live/Python/bioMoby/ontology/GenbankFlatfile.py	2005/02/01 14:20:44	1.5
+++ /home/repository/moby/moby-live/Python/bioMoby/ontology/GenbankFlatfile.py	2005/02/07 14:23:33	1.6
@@ -48,4 +48,5 @@
             if elt.nodeName=="CrossReference" or elt.nodeName=="moby:CrossReference":
                 self.__cross__=[]
                 for ref in elt.childNodes:
-                    self.__cross__.append(um.loads(ref))
\ No newline at end of file
+                    if ref.nodeType==ref.ELEMENT_NODE:
+                        self.__cross__.append(um.loadn(ref))
\ No newline at end of file

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/ontology/Gene_Expression_data.py,v
retrieving revision 1.1
retrieving revision 1.2
diff -u -r1.1 -r1.2
--- /home/repository/moby/moby-live/Python/bioMoby/ontology/Gene_Expression_data.py	2005/02/02 15:20:55	1.1
+++ /home/repository/moby/moby-live/Python/bioMoby/ontology/Gene_Expression_data.py	2005/02/07 14:23:33	1.2
@@ -49,7 +49,8 @@
             if elt.nodeName=="CrossReference" or elt.nodeName=="moby:CrossReference":
                 self.__cross__=[]
                 for ref in elt.childNodes:
-                    self.__cross__.append(um.loads(ref))
+                    if ref.nodeType==ref.ELEMENT_NODE:
+                        self.__cross__.append(um.loadn(ref))
             if elt.nodeType==elt.ELEMENT_NODE and (elt.nodeName=="String" or elt.nodeName=="moby:String") and (elt.getAttribute("articleName")=="Expression data" or elt.getAttribute("moby:articleName")=="Expression data"):
                 t=MobyString()
                 t.fromMoby(elt)

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/ontology/GenericSequence.py,v
retrieving revision 1.5
retrieving revision 1.6
diff -u -r1.5 -r1.6
--- /home/repository/moby/moby-live/Python/bioMoby/ontology/GenericSequence.py	2005/02/01 14:20:44	1.5
+++ /home/repository/moby/moby-live/Python/bioMoby/ontology/GenericSequence.py	2005/02/07 14:23:33	1.6
@@ -51,7 +51,8 @@
             if elt.nodeName=="CrossReference" or elt.nodeName=="moby:CrossReference":
                 self.__cross__=[]
                 for ref in elt.childNodes:
-                    self.__cross__.append(um.loads(ref))
+                    if ref.nodeType==ref.ELEMENT_NODE:
+                        self.__cross__.append(um.loadn(ref))
             if elt.nodeType==elt.ELEMENT_NODE and (elt.nodeName=="Integer" or elt.nodeName=="moby:Integer") and (elt.getAttribute("articleName")=="Length" or elt.getAttribute("moby:articleName")=="Length"):
                 t=MobyInteger()
                 t.fromMoby(elt)

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/ontology/GeneticElement.py,v
retrieving revision 1.5
retrieving revision 1.6
diff -u -r1.5 -r1.6
--- /home/repository/moby/moby-live/Python/bioMoby/ontology/GeneticElement.py	2005/02/01 14:20:44	1.5
+++ /home/repository/moby/moby-live/Python/bioMoby/ontology/GeneticElement.py	2005/02/07 14:23:33	1.6
@@ -49,7 +49,8 @@
             if elt.nodeName=="CrossReference" or elt.nodeName=="moby:CrossReference":
                 self.__cross__=[]
                 for ref in elt.childNodes:
-                    self.__cross__.append(um.loads(ref))
+                    if ref.nodeType==ref.ELEMENT_NODE:
+                        self.__cross__.append(um.loadn(ref))
             if elt.nodeType==elt.ELEMENT_NODE and (elt.nodeName=="String" or elt.nodeName=="moby:String") and (elt.getAttribute("articleName")=="GeneticElement" or elt.getAttribute("moby:articleName")=="GeneticElement"):
                 t=MobyString()
                 t.fromMoby(elt)

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/ontology/Genotype.py,v
retrieving revision 1.5
retrieving revision 1.6
diff -u -r1.5 -r1.6
--- /home/repository/moby/moby-live/Python/bioMoby/ontology/Genotype.py	2005/02/01 14:20:44	1.5
+++ /home/repository/moby/moby-live/Python/bioMoby/ontology/Genotype.py	2005/02/07 14:23:33	1.6
@@ -51,7 +51,8 @@
             if elt.nodeName=="CrossReference" or elt.nodeName=="moby:CrossReference":
                 self.__cross__=[]
                 for ref in elt.childNodes:
-                    self.__cross__.append(um.loads(ref))
+                    if ref.nodeType==ref.ELEMENT_NODE:
+                        self.__cross__.append(um.loadn(ref))
             if elt.nodeType==elt.ELEMENT_NODE and (elt.nodeName=="String" or elt.nodeName=="moby:String") and (elt.getAttribute("articleName")=="snp" or elt.getAttribute("moby:articleName")=="snp"):
                 t=MobyString()
                 t.fromMoby(elt)

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/ontology/Germplasm_Details.py,v
retrieving revision 1.5
retrieving revision 1.6
diff -u -r1.5 -r1.6
--- /home/repository/moby/moby-live/Python/bioMoby/ontology/Germplasm_Details.py	2005/02/01 14:20:44	1.5
+++ /home/repository/moby/moby-live/Python/bioMoby/ontology/Germplasm_Details.py	2005/02/07 14:23:33	1.6
@@ -57,7 +57,8 @@
             if elt.nodeName=="CrossReference" or elt.nodeName=="moby:CrossReference":
                 self.__cross__=[]
                 for ref in elt.childNodes:
-                    self.__cross__.append(um.loads(ref))
+                    if ref.nodeType==ref.ELEMENT_NODE:
+                        self.__cross__.append(um.loadn(ref))
             if elt.nodeType==elt.ELEMENT_NODE and (elt.nodeName=="Integer" or elt.nodeName=="moby:Integer") and (elt.getAttribute("articleName")=="date" or elt.getAttribute("moby:articleName")=="date"):
                 t=MobyInteger()
                 t.fromMoby(elt)

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/ontology/Germplasm_List.py,v
retrieving revision 1.5
retrieving revision 1.6
diff -u -r1.5 -r1.6
--- /home/repository/moby/moby-live/Python/bioMoby/ontology/Germplasm_List.py	2005/02/01 14:20:44	1.5
+++ /home/repository/moby/moby-live/Python/bioMoby/ontology/Germplasm_List.py	2005/02/07 14:23:33	1.6
@@ -57,7 +57,8 @@
             if elt.nodeName=="CrossReference" or elt.nodeName=="moby:CrossReference":
                 self.__cross__=[]
                 for ref in elt.childNodes:
-                    self.__cross__.append(um.loads(ref))
+                    if ref.nodeType==ref.ELEMENT_NODE:
+                        self.__cross__.append(um.loadn(ref))
             if elt.nodeType==elt.ELEMENT_NODE and (elt.nodeName=="Integer" or elt.nodeName=="moby:Integer") and (elt.getAttribute("articleName")=="germplasm_id" or elt.getAttribute("moby:articleName")=="germplasm_id"):
                 t=MobyInteger()
                 t.fromMoby(elt)

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/ontology/Global_Keyword.py,v
retrieving revision 1.5
retrieving revision 1.6
diff -u -r1.5 -r1.6
--- /home/repository/moby/moby-live/Python/bioMoby/ontology/Global_Keyword.py	2005/02/01 14:20:44	1.5
+++ /home/repository/moby/moby-live/Python/bioMoby/ontology/Global_Keyword.py	2005/02/07 14:23:33	1.6
@@ -47,4 +47,5 @@
             if elt.nodeName=="CrossReference" or elt.nodeName=="moby:CrossReference":
                 self.__cross__=[]
                 for ref in elt.childNodes:
-                    self.__cross__.append(um.loads(ref))
\ No newline at end of file
+                    if ref.nodeType==ref.ELEMENT_NODE:
+                        self.__cross__.append(um.loadn(ref))
\ No newline at end of file

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/ontology/HBond_Pair.py,v
retrieving revision 1.5
retrieving revision 1.6
diff -u -r1.5 -r1.6
--- /home/repository/moby/moby-live/Python/bioMoby/ontology/HBond_Pair.py	2005/02/01 14:20:44	1.5
+++ /home/repository/moby/moby-live/Python/bioMoby/ontology/HBond_Pair.py	2005/02/07 14:23:33	1.6
@@ -51,7 +51,8 @@
             if elt.nodeName=="CrossReference" or elt.nodeName=="moby:CrossReference":
                 self.__cross__=[]
                 for ref in elt.childNodes:
-                    self.__cross__.append(um.loads(ref))
+                    if ref.nodeType==ref.ELEMENT_NODE:
+                        self.__cross__.append(um.loadn(ref))
             if elt.nodeType==elt.ELEMENT_NODE and (elt.nodeName=="String" or elt.nodeName=="moby:String") and (elt.getAttribute("articleName")=="A" or elt.getAttribute("moby:articleName")=="A"):
                 t=MobyString()
                 t.fromMoby(elt)

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/ontology/HFormatText.py,v
retrieving revision 1.5
retrieving revision 1.6
diff -u -r1.5 -r1.6
--- /home/repository/moby/moby-live/Python/bioMoby/ontology/HFormatText.py	2005/02/01 14:20:44	1.5
+++ /home/repository/moby/moby-live/Python/bioMoby/ontology/HFormatText.py	2005/02/07 14:23:33	1.6
@@ -48,4 +48,5 @@
             if elt.nodeName=="CrossReference" or elt.nodeName=="moby:CrossReference":
                 self.__cross__=[]
                 for ref in elt.childNodes:
-                    self.__cross__.append(um.loads(ref))
\ No newline at end of file
+                    if ref.nodeType==ref.ELEMENT_NODE:
+                        self.__cross__.append(um.loadn(ref))
\ No newline at end of file

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/ontology/Haplotyping_Study_obj.py,v
retrieving revision 1.5
retrieving revision 1.6
diff -u -r1.5 -r1.6
--- /home/repository/moby/moby-live/Python/bioMoby/ontology/Haplotyping_Study_obj.py	2005/02/01 14:20:44	1.5
+++ /home/repository/moby/moby-live/Python/bioMoby/ontology/Haplotyping_Study_obj.py	2005/02/07 14:23:33	1.6
@@ -47,4 +47,5 @@
             if elt.nodeName=="CrossReference" or elt.nodeName=="moby:CrossReference":
                 self.__cross__=[]
                 for ref in elt.childNodes:
-                    self.__cross__.append(um.loads(ref))
\ No newline at end of file
+                    if ref.nodeType==ref.ELEMENT_NODE:
+                        self.__cross__.append(um.loadn(ref))
\ No newline at end of file

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/ontology/ICIS_Query.py,v
retrieving revision 1.5
retrieving revision 1.6
diff -u -r1.5 -r1.6
--- /home/repository/moby/moby-live/Python/bioMoby/ontology/ICIS_Query.py	2005/02/01 14:20:44	1.5
+++ /home/repository/moby/moby-live/Python/bioMoby/ontology/ICIS_Query.py	2005/02/07 14:23:33	1.6
@@ -52,7 +52,8 @@
             if elt.nodeName=="CrossReference" or elt.nodeName=="moby:CrossReference":
                 self.__cross__=[]
                 for ref in elt.childNodes:
-                    self.__cross__.append(um.loads(ref))
+                    if ref.nodeType==ref.ELEMENT_NODE:
+                        self.__cross__.append(um.loadn(ref))
             if elt.nodeType==elt.ELEMENT_NODE and (elt.nodeName=="Integer" or elt.nodeName=="moby:Integer") and (elt.getAttribute("articleName")=="end_row" or elt.getAttribute("moby:articleName")=="end_row"):
                 t=MobyInteger()
                 t.fromMoby(elt)

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/ontology/ICIS_Query2.py,v
retrieving revision 1.5
retrieving revision 1.6
diff -u -r1.5 -r1.6
--- /home/repository/moby/moby-live/Python/bioMoby/ontology/ICIS_Query2.py	2005/02/01 14:20:44	1.5
+++ /home/repository/moby/moby-live/Python/bioMoby/ontology/ICIS_Query2.py	2005/02/07 14:23:33	1.6
@@ -54,7 +54,8 @@
             if elt.nodeName=="CrossReference" or elt.nodeName=="moby:CrossReference":
                 self.__cross__=[]
                 for ref in elt.childNodes:
-                    self.__cross__.append(um.loads(ref))
+                    if ref.nodeType==ref.ELEMENT_NODE:
+                        self.__cross__.append(um.loadn(ref))
             if elt.nodeType==elt.ELEMENT_NODE and (elt.nodeName=="String" or elt.nodeName=="moby:String") and (elt.getAttribute("articleName")=="search_text1" or elt.getAttribute("moby:articleName")=="search_text1"):
                 t=MobyString()
                 t.fromMoby(elt)

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/ontology/ICIS_Query3.py,v
retrieving revision 1.5
retrieving revision 1.6
diff -u -r1.5 -r1.6
--- /home/repository/moby/moby-live/Python/bioMoby/ontology/ICIS_Query3.py	2005/02/01 14:20:44	1.5
+++ /home/repository/moby/moby-live/Python/bioMoby/ontology/ICIS_Query3.py	2005/02/07 14:23:33	1.6
@@ -52,7 +52,8 @@
             if elt.nodeName=="CrossReference" or elt.nodeName=="moby:CrossReference":
                 self.__cross__=[]
                 for ref in elt.childNodes:
-                    self.__cross__.append(um.loads(ref))
+                    if ref.nodeType==ref.ELEMENT_NODE:
+                        self.__cross__.append(um.loadn(ref))
             if elt.nodeType==elt.ELEMENT_NODE and (elt.nodeName=="Integer" or elt.nodeName=="moby:Integer") and (elt.getAttribute("articleName")=="search_text1" or elt.getAttribute("moby:articleName")=="search_text1"):
                 t=MobyInteger()
                 t.fromMoby(elt)

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/ontology/IntAct_XML.py,v
retrieving revision 1.5
retrieving revision 1.6
diff -u -r1.5 -r1.6
--- /home/repository/moby/moby-live/Python/bioMoby/ontology/IntAct_XML.py	2005/02/01 14:20:44	1.5
+++ /home/repository/moby/moby-live/Python/bioMoby/ontology/IntAct_XML.py	2005/02/07 14:23:33	1.6
@@ -48,4 +48,5 @@
             if elt.nodeName=="CrossReference" or elt.nodeName=="moby:CrossReference":
                 self.__cross__=[]
                 for ref in elt.childNodes:
-                    self.__cross__.append(um.loads(ref))
\ No newline at end of file
+                    if ref.nodeType==ref.ELEMENT_NODE:
+                        self.__cross__.append(um.loadn(ref))
\ No newline at end of file

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/ontology/Interaction.py,v
retrieving revision 1.5
retrieving revision 1.6
diff -u -r1.5 -r1.6
--- /home/repository/moby/moby-live/Python/bioMoby/ontology/Interaction.py	2005/02/01 14:20:44	1.5
+++ /home/repository/moby/moby-live/Python/bioMoby/ontology/Interaction.py	2005/02/07 14:23:33	1.6
@@ -53,7 +53,8 @@
             if elt.nodeName=="CrossReference" or elt.nodeName=="moby:CrossReference":
                 self.__cross__=[]
                 for ref in elt.childNodes:
-                    self.__cross__.append(um.loads(ref))
+                    if ref.nodeType==ref.ELEMENT_NODE:
+                        self.__cross__.append(um.loadn(ref))
             if elt.nodeType==elt.ELEMENT_NODE and (elt.nodeName=="String" or elt.nodeName=="moby:String") and (elt.getAttribute("articleName")=="result" or elt.getAttribute("moby:articleName")=="result"):
                 t=MobyString()
                 t.fromMoby(elt)

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/ontology/InteractionMethod.py,v
retrieving revision 1.5
retrieving revision 1.6
diff -u -r1.5 -r1.6
--- /home/repository/moby/moby-live/Python/bioMoby/ontology/InteractionMethod.py	2005/02/01 14:20:44	1.5
+++ /home/repository/moby/moby-live/Python/bioMoby/ontology/InteractionMethod.py	2005/02/07 14:23:33	1.6
@@ -51,7 +51,8 @@
             if elt.nodeName=="CrossReference" or elt.nodeName=="moby:CrossReference":
                 self.__cross__=[]
                 for ref in elt.childNodes:
-                    self.__cross__.append(um.loads(ref))
+                    if ref.nodeType==ref.ELEMENT_NODE:
+                        self.__cross__.append(um.loadn(ref))
             if elt.nodeType==elt.ELEMENT_NODE and (elt.nodeName=="String" or elt.nodeName=="moby:String") and (elt.getAttribute("articleName")=="shortlabel" or elt.getAttribute("moby:articleName")=="shortlabel"):
                 t=MobyString()
                 t.fromMoby(elt)

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/ontology/Interaction_partner.py,v
retrieving revision 1.5
retrieving revision 1.6
diff -u -r1.5 -r1.6
--- /home/repository/moby/moby-live/Python/bioMoby/ontology/Interaction_partner.py	2005/02/01 14:20:44	1.5
+++ /home/repository/moby/moby-live/Python/bioMoby/ontology/Interaction_partner.py	2005/02/07 14:23:33	1.6
@@ -51,7 +51,8 @@
             if elt.nodeName=="CrossReference" or elt.nodeName=="moby:CrossReference":
                 self.__cross__=[]
                 for ref in elt.childNodes:
-                    self.__cross__.append(um.loads(ref))
+                    if ref.nodeType==ref.ELEMENT_NODE:
+                        self.__cross__.append(um.loadn(ref))
             if elt.nodeType==elt.ELEMENT_NODE and (elt.nodeName=="Integer" or elt.nodeName=="moby:Integer") and (elt.getAttribute("articleName")=="direction" or elt.getAttribute("moby:articleName")=="direction"):
                 t=MobyInteger()
                 t.fromMoby(elt)

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/ontology/Interactor.py,v
retrieving revision 1.5
retrieving revision 1.6
diff -u -r1.5 -r1.6
--- /home/repository/moby/moby-live/Python/bioMoby/ontology/Interactor.py	2005/02/01 14:20:44	1.5
+++ /home/repository/moby/moby-live/Python/bioMoby/ontology/Interactor.py	2005/02/07 14:23:33	1.6
@@ -49,7 +49,8 @@
             if elt.nodeName=="CrossReference" or elt.nodeName=="moby:CrossReference":
                 self.__cross__=[]
                 for ref in elt.childNodes:
-                    self.__cross__.append(um.loads(ref))
+                    if ref.nodeType==ref.ELEMENT_NODE:
+                        self.__cross__.append(um.loadn(ref))
             if elt.nodeType==elt.ELEMENT_NODE and (elt.nodeName=="String" or elt.nodeName=="moby:String") and (elt.getAttribute("articleName")=="role" or elt.getAttribute("moby:articleName")=="role"):
                 t=MobyString()
                 t.fromMoby(elt)

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/ontology/MEME_Text.py,v
retrieving revision 1.5
retrieving revision 1.6
diff -u -r1.5 -r1.6
--- /home/repository/moby/moby-live/Python/bioMoby/ontology/MEME_Text.py	2005/02/01 14:20:44	1.5
+++ /home/repository/moby/moby-live/Python/bioMoby/ontology/MEME_Text.py	2005/02/07 14:23:33	1.6
@@ -48,4 +48,5 @@
             if elt.nodeName=="CrossReference" or elt.nodeName=="moby:CrossReference":
                 self.__cross__=[]
                 for ref in elt.childNodes:
-                    self.__cross__.append(um.loads(ref))
\ No newline at end of file
+                    if ref.nodeType==ref.ELEMENT_NODE:
+                        self.__cross__.append(um.loadn(ref))
\ No newline at end of file

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/ontology/MGIS_ACCESSION.py,v
retrieving revision 1.5
retrieving revision 1.6
diff -u -r1.5 -r1.6
--- /home/repository/moby/moby-live/Python/bioMoby/ontology/MGIS_ACCESSION.py	2005/02/01 14:20:44	1.5
+++ /home/repository/moby/moby-live/Python/bioMoby/ontology/MGIS_ACCESSION.py	2005/02/07 14:23:33	1.6
@@ -68,7 +68,8 @@
             if elt.nodeName=="CrossReference" or elt.nodeName=="moby:CrossReference":
                 self.__cross__=[]
                 for ref in elt.childNodes:
-                    self.__cross__.append(um.loads(ref))
+                    if ref.nodeType==ref.ELEMENT_NODE:
+                        self.__cross__.append(um.loadn(ref))
             if elt.nodeType==elt.ELEMENT_NODE and (elt.nodeName=="String" or elt.nodeName=="moby:String") and (elt.getAttribute("articleName")=="Biotic_stress_Yellowsig" or elt.getAttribute("moby:articleName")=="Biotic_stress_Yellowsig"):
                 t=MobyString()
                 t.fromMoby(elt)

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/ontology/MMP_Locus.py,v
retrieving revision 1.5
retrieving revision 1.6
diff -u -r1.5 -r1.6
--- /home/repository/moby/moby-live/Python/bioMoby/ontology/MMP_Locus.py	2005/02/01 14:20:44	1.5
+++ /home/repository/moby/moby-live/Python/bioMoby/ontology/MMP_Locus.py	2005/02/07 14:23:33	1.6
@@ -47,4 +47,5 @@
             if elt.nodeName=="CrossReference" or elt.nodeName=="moby:CrossReference":
                 self.__cross__=[]
                 for ref in elt.childNodes:
-                    self.__cross__.append(um.loads(ref))
\ No newline at end of file
+                    if ref.nodeType==ref.ELEMENT_NODE:
+                        self.__cross__.append(um.loadn(ref))
\ No newline at end of file

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/ontology/MO_Term_Test.py,v
retrieving revision 1.5
retrieving revision 1.6
diff -u -r1.5 -r1.6
--- /home/repository/moby/moby-live/Python/bioMoby/ontology/MO_Term_Test.py	2005/02/01 14:20:44	1.5
+++ /home/repository/moby/moby-live/Python/bioMoby/ontology/MO_Term_Test.py	2005/02/07 14:23:33	1.6
@@ -52,7 +52,8 @@
             if elt.nodeName=="CrossReference" or elt.nodeName=="moby:CrossReference":
                 self.__cross__=[]
                 for ref in elt.childNodes:
-                    self.__cross__.append(um.loads(ref))
+                    if ref.nodeType==ref.ELEMENT_NODE:
+                        self.__cross__.append(um.loadn(ref))
             if elt.nodeType==elt.ELEMENT_NODE and (elt.nodeName=="String" or elt.nodeName=="moby:String") and (elt.getAttribute("articleName")=="class_name" or elt.getAttribute("moby:articleName")=="class_name"):
                 t=MobyString()
                 t.fromMoby(elt)

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/ontology/MSF.py,v
retrieving revision 1.1
retrieving revision 1.2
diff -u -r1.1 -r1.2
--- /home/repository/moby/moby-live/Python/bioMoby/ontology/MSF.py	2005/02/02 15:08:34	1.1
+++ /home/repository/moby/moby-live/Python/bioMoby/ontology/MSF.py	2005/02/07 14:23:33	1.2
@@ -48,4 +48,5 @@
             if elt.nodeName=="CrossReference" or elt.nodeName=="moby:CrossReference":
                 self.__cross__=[]
                 for ref in elt.childNodes:
-                    self.__cross__.append(um.loads(ref))
\ No newline at end of file
+                    if ref.nodeType==ref.ELEMENT_NODE:
+                        self.__cross__.append(um.loadn(ref))
\ No newline at end of file

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/ontology/MmCIFText.py,v
retrieving revision 1.5
retrieving revision 1.6
diff -u -r1.5 -r1.6
--- /home/repository/moby/moby-live/Python/bioMoby/ontology/MmCIFText.py	2005/02/01 14:20:44	1.5
+++ /home/repository/moby/moby-live/Python/bioMoby/ontology/MmCIFText.py	2005/02/07 14:23:33	1.6
@@ -48,4 +48,5 @@
             if elt.nodeName=="CrossReference" or elt.nodeName=="moby:CrossReference":
                 self.__cross__=[]
                 for ref in elt.childNodes:
-                    self.__cross__.append(um.loads(ref))
\ No newline at end of file
+                    if ref.nodeType==ref.ELEMENT_NODE:
+                        self.__cross__.append(um.loadn(ref))
\ No newline at end of file

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/ontology/Multi_key_value_pair.py,v
retrieving revision 1.5
retrieving revision 1.6
diff -u -r1.5 -r1.6
--- /home/repository/moby/moby-live/Python/bioMoby/ontology/Multi_key_value_pair.py	2005/02/01 14:20:44	1.5
+++ /home/repository/moby/moby-live/Python/bioMoby/ontology/Multi_key_value_pair.py	2005/02/07 14:23:33	1.6
@@ -51,7 +51,8 @@
             if elt.nodeName=="CrossReference" or elt.nodeName=="moby:CrossReference":
                 self.__cross__=[]
                 for ref in elt.childNodes:
-                    self.__cross__.append(um.loads(ref))
+                    if ref.nodeType==ref.ELEMENT_NODE:
+                        self.__cross__.append(um.loadn(ref))
             if elt.nodeType==elt.ELEMENT_NODE and (elt.nodeName=="String" or elt.nodeName=="moby:String") and (elt.getAttribute("articleName")=="key" or elt.getAttribute("moby:articleName")=="key"):
                 t=MobyString()
                 t.fromMoby(elt)

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/ontology/MyTestingDataType_11024145298313.py,v
retrieving revision 1.5
retrieving revision 1.6
diff -u -r1.5 -r1.6
--- /home/repository/moby/moby-live/Python/bioMoby/ontology/MyTestingDataType_11024145298313.py	2005/02/01 14:20:44	1.5
+++ /home/repository/moby/moby-live/Python/bioMoby/ontology/MyTestingDataType_11024145298313.py	2005/02/07 14:23:33	1.6
@@ -48,4 +48,5 @@
             if elt.nodeName=="CrossReference" or elt.nodeName=="moby:CrossReference":
                 self.__cross__=[]
                 for ref in elt.childNodes:
-                    self.__cross__.append(um.loads(ref))
\ No newline at end of file
+                    if ref.nodeType==ref.ELEMENT_NODE:
+                        self.__cross__.append(um.loadn(ref))
\ No newline at end of file

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/ontology/MyTree.py,v
retrieving revision 1.5
retrieving revision 1.6
diff -u -r1.5 -r1.6
--- /home/repository/moby/moby-live/Python/bioMoby/ontology/MyTree.py	2005/02/01 14:20:44	1.5
+++ /home/repository/moby/moby-live/Python/bioMoby/ontology/MyTree.py	2005/02/07 14:23:33	1.6
@@ -48,4 +48,5 @@
             if elt.nodeName=="CrossReference" or elt.nodeName=="moby:CrossReference":
                 self.__cross__=[]
                 for ref in elt.childNodes:
-                    self.__cross__.append(um.loads(ref))
\ No newline at end of file
+                    if ref.nodeType==ref.ELEMENT_NODE:
+                        self.__cross__.append(um.loadn(ref))
\ No newline at end of file

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/ontology/NCBI_BLAST_Text.py,v
retrieving revision 1.5
retrieving revision 1.6
diff -u -r1.5 -r1.6
--- /home/repository/moby/moby-live/Python/bioMoby/ontology/NCBI_BLAST_Text.py	2005/02/01 14:20:44	1.5
+++ /home/repository/moby/moby-live/Python/bioMoby/ontology/NCBI_BLAST_Text.py	2005/02/07 14:23:33	1.6
@@ -48,4 +48,5 @@
             if elt.nodeName=="CrossReference" or elt.nodeName=="moby:CrossReference":
                 self.__cross__=[]
                 for ref in elt.childNodes:
-                    self.__cross__.append(um.loads(ref))
\ No newline at end of file
+                    if ref.nodeType==ref.ELEMENT_NODE:
+                        self.__cross__.append(um.loadn(ref))
\ No newline at end of file

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/ontology/NCBI_Blast_XML.py,v
retrieving revision 1.5
retrieving revision 1.6
diff -u -r1.5 -r1.6
--- /home/repository/moby/moby-live/Python/bioMoby/ontology/NCBI_Blast_XML.py	2005/02/01 14:20:44	1.5
+++ /home/repository/moby/moby-live/Python/bioMoby/ontology/NCBI_Blast_XML.py	2005/02/07 14:23:33	1.6
@@ -48,4 +48,5 @@
             if elt.nodeName=="CrossReference" or elt.nodeName=="moby:CrossReference":
                 self.__cross__=[]
                 for ref in elt.childNodes:
-                    self.__cross__.append(um.loads(ref))
\ No newline at end of file
+                    if ref.nodeType==ref.ELEMENT_NODE:
+                        self.__cross__.append(um.loadn(ref))
\ No newline at end of file

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/ontology/NCBI_Blast_XML_Gif.py,v
retrieving revision 1.5
retrieving revision 1.6
diff -u -r1.5 -r1.6
--- /home/repository/moby/moby-live/Python/bioMoby/ontology/NCBI_Blast_XML_Gif.py	2005/02/01 14:20:44	1.5
+++ /home/repository/moby/moby-live/Python/bioMoby/ontology/NCBI_Blast_XML_Gif.py	2005/02/07 14:23:33	1.6
@@ -50,7 +50,8 @@
             if elt.nodeName=="CrossReference" or elt.nodeName=="moby:CrossReference":
                 self.__cross__=[]
                 for ref in elt.childNodes:
-                    self.__cross__.append(um.loads(ref))
+                    if ref.nodeType==ref.ELEMENT_NODE:
+                        self.__cross__.append(um.loadn(ref))
             if elt.nodeType==elt.ELEMENT_NODE and (elt.nodeName=="b64_encoded_gif" or elt.nodeName=="moby:b64_encoded_gif") and (elt.getAttribute("articleName")=="hitGraph" or elt.getAttribute("moby:articleName")=="hitGraph"):
                 self.HitGraph=MobyB64_encoded_gif()
                 self.HitGraph.fromMoby(elt)
\ No newline at end of file

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/ontology/NCBI_Blast_XML_Gif_Map.py,v
retrieving revision 1.5
retrieving revision 1.6
diff -u -r1.5 -r1.6
--- /home/repository/moby/moby-live/Python/bioMoby/ontology/NCBI_Blast_XML_Gif_Map.py	2005/02/01 14:20:44	1.5
+++ /home/repository/moby/moby-live/Python/bioMoby/ontology/NCBI_Blast_XML_Gif_Map.py	2005/02/07 14:23:33	1.6
@@ -52,7 +52,8 @@
             if elt.nodeName=="CrossReference" or elt.nodeName=="moby:CrossReference":
                 self.__cross__=[]
                 for ref in elt.childNodes:
-                    self.__cross__.append(um.loads(ref))
+                    if ref.nodeType==ref.ELEMENT_NODE:
+                        self.__cross__.append(um.loadn(ref))
             if elt.nodeType==elt.ELEMENT_NODE and (elt.nodeName=="b64_encoded_gif" or elt.nodeName=="moby:b64_encoded_gif") and (elt.getAttribute("articleName")=="hitGraph" or elt.getAttribute("moby:articleName")=="hitGraph"):
                 self.HitGraph=MobyB64_encoded_gif()
                 self.HitGraph.fromMoby(elt)

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/ontology/NCBI_MEME_Text.py,v
retrieving revision 1.5
retrieving revision 1.6
diff -u -r1.5 -r1.6
--- /home/repository/moby/moby-live/Python/bioMoby/ontology/NCBI_MEME_Text.py	2005/02/01 14:20:44	1.5
+++ /home/repository/moby/moby-live/Python/bioMoby/ontology/NCBI_MEME_Text.py	2005/02/07 14:23:33	1.6
@@ -48,4 +48,5 @@
             if elt.nodeName=="CrossReference" or elt.nodeName=="moby:CrossReference":
                 self.__cross__=[]
                 for ref in elt.childNodes:
-                    self.__cross__.append(um.loads(ref))
\ No newline at end of file
+                    if ref.nodeType==ref.ELEMENT_NODE:
+                        self.__cross__.append(um.loadn(ref))
\ No newline at end of file

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/ontology/NucleotideSequence.py,v
retrieving revision 1.5
retrieving revision 1.6
diff -u -r1.5 -r1.6
--- /home/repository/moby/moby-live/Python/bioMoby/ontology/NucleotideSequence.py	2005/02/01 14:20:44	1.5
+++ /home/repository/moby/moby-live/Python/bioMoby/ontology/NucleotideSequence.py	2005/02/07 14:23:33	1.6
@@ -51,7 +51,8 @@
             if elt.nodeName=="CrossReference" or elt.nodeName=="moby:CrossReference":
                 self.__cross__=[]
                 for ref in elt.childNodes:
-                    self.__cross__.append(um.loads(ref))
+                    if ref.nodeType==ref.ELEMENT_NODE:
+                        self.__cross__.append(um.loadn(ref))
             if elt.nodeType==elt.ELEMENT_NODE and (elt.nodeName=="Integer" or elt.nodeName=="moby:Integer") and (elt.getAttribute("articleName")=="Length" or elt.getAttribute("moby:articleName")=="Length"):
                 t=MobyInteger()
                 t.fromMoby(elt)

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/ontology/PDBFormattedText.py,v
retrieving revision 1.5
retrieving revision 1.6
diff -u -r1.5 -r1.6
--- /home/repository/moby/moby-live/Python/bioMoby/ontology/PDBFormattedText.py	2005/02/01 14:20:44	1.5
+++ /home/repository/moby/moby-live/Python/bioMoby/ontology/PDBFormattedText.py	2005/02/07 14:23:33	1.6
@@ -48,4 +48,5 @@
             if elt.nodeName=="CrossReference" or elt.nodeName=="moby:CrossReference":
                 self.__cross__=[]
                 for ref in elt.childNodes:
-                    self.__cross__.append(um.loads(ref))
\ No newline at end of file
+                    if ref.nodeType==ref.ELEMENT_NODE:
+                        self.__cross__.append(um.loadn(ref))
\ No newline at end of file

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/ontology/PDBText.py,v
retrieving revision 1.5
retrieving revision 1.6
diff -u -r1.5 -r1.6
--- /home/repository/moby/moby-live/Python/bioMoby/ontology/PDBText.py	2005/02/01 14:20:44	1.5
+++ /home/repository/moby/moby-live/Python/bioMoby/ontology/PDBText.py	2005/02/07 14:23:33	1.6
@@ -48,4 +48,5 @@
             if elt.nodeName=="CrossReference" or elt.nodeName=="moby:CrossReference":
                 self.__cross__=[]
                 for ref in elt.childNodes:
-                    self.__cross__.append(um.loads(ref))
\ No newline at end of file
+                    if ref.nodeType==ref.ELEMENT_NODE:
+                        self.__cross__.append(um.loadn(ref))
\ No newline at end of file

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/ontology/PDGJOB.py,v
retrieving revision 1.5
retrieving revision 1.6
diff -u -r1.5 -r1.6
--- /home/repository/moby/moby-live/Python/bioMoby/ontology/PDGJOB.py	2005/02/01 14:20:44	1.5
+++ /home/repository/moby/moby-live/Python/bioMoby/ontology/PDGJOB.py	2005/02/07 14:23:33	1.6
@@ -54,7 +54,8 @@
             if elt.nodeName=="CrossReference" or elt.nodeName=="moby:CrossReference":
                 self.__cross__=[]
                 for ref in elt.childNodes:
-                    self.__cross__.append(um.loads(ref))
+                    if ref.nodeType==ref.ELEMENT_NODE:
+                        self.__cross__.append(um.loadn(ref))
             if elt.nodeType==elt.ELEMENT_NODE and (elt.nodeName=="String" or elt.nodeName=="moby:String") and (elt.getAttribute("articleName")=="answerService" or elt.getAttribute("moby:articleName")=="answerService"):
                 t=MobyString()
                 t.fromMoby(elt)

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/ontology/PHDText.py,v
retrieving revision 1.5
retrieving revision 1.6
diff -u -r1.5 -r1.6
--- /home/repository/moby/moby-live/Python/bioMoby/ontology/PHDText.py	2005/02/01 14:20:44	1.5
+++ /home/repository/moby/moby-live/Python/bioMoby/ontology/PHDText.py	2005/02/07 14:23:33	1.6
@@ -48,4 +48,5 @@
             if elt.nodeName=="CrossReference" or elt.nodeName=="moby:CrossReference":
                 self.__cross__=[]
                 for ref in elt.childNodes:
-                    self.__cross__.append(um.loads(ref))
\ No newline at end of file
+                    if ref.nodeType==ref.ELEMENT_NODE:
+                        self.__cross__.append(um.loadn(ref))
\ No newline at end of file

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/ontology/PMUTText.py,v
retrieving revision 1.5
retrieving revision 1.6
diff -u -r1.5 -r1.6
--- /home/repository/moby/moby-live/Python/bioMoby/ontology/PMUTText.py	2005/02/01 14:20:44	1.5
+++ /home/repository/moby/moby-live/Python/bioMoby/ontology/PMUTText.py	2005/02/07 14:23:33	1.6
@@ -48,4 +48,5 @@
             if elt.nodeName=="CrossReference" or elt.nodeName=="moby:CrossReference":
                 self.__cross__=[]
                 for ref in elt.childNodes:
-                    self.__cross__.append(um.loads(ref))
\ No newline at end of file
+                    if ref.nodeType==ref.ELEMENT_NODE:
+                        self.__cross__.append(um.loadn(ref))
\ No newline at end of file

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/ontology/PSeaTextFormatted.py,v
retrieving revision 1.5
retrieving revision 1.6
diff -u -r1.5 -r1.6
--- /home/repository/moby/moby-live/Python/bioMoby/ontology/PSeaTextFormatted.py	2005/02/01 14:20:44	1.5
+++ /home/repository/moby/moby-live/Python/bioMoby/ontology/PSeaTextFormatted.py	2005/02/07 14:23:33	1.6
@@ -48,4 +48,5 @@
             if elt.nodeName=="CrossReference" or elt.nodeName=="moby:CrossReference":
                 self.__cross__=[]
                 for ref in elt.childNodes:
-                    self.__cross__.append(um.loads(ref))
\ No newline at end of file
+                    if ref.nodeType==ref.ELEMENT_NODE:
+                        self.__cross__.append(um.loadn(ref))
\ No newline at end of file

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/ontology/PhenotypeDescription.py,v
retrieving revision 1.5
retrieving revision 1.6
diff -u -r1.5 -r1.6
--- /home/repository/moby/moby-live/Python/bioMoby/ontology/PhenotypeDescription.py	2005/02/01 14:20:44	1.5
+++ /home/repository/moby/moby-live/Python/bioMoby/ontology/PhenotypeDescription.py	2005/02/07 14:23:33	1.6
@@ -49,7 +49,8 @@
             if elt.nodeName=="CrossReference" or elt.nodeName=="moby:CrossReference":
                 self.__cross__=[]
                 for ref in elt.childNodes:
-                    self.__cross__.append(um.loads(ref))
+                    if ref.nodeType==ref.ELEMENT_NODE:
+                        self.__cross__.append(um.loadn(ref))
             if elt.nodeType==elt.ELEMENT_NODE and (elt.nodeName=="String" or elt.nodeName=="moby:String") and (elt.getAttribute("articleName")=="Phenotype" or elt.getAttribute("moby:articleName")=="Phenotype"):
                 t=MobyString()
                 t.fromMoby(elt)

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/ontology/PubMedMEDLINE.py,v
retrieving revision 1.5
retrieving revision 1.6
diff -u -r1.5 -r1.6
--- /home/repository/moby/moby-live/Python/bioMoby/ontology/PubMedMEDLINE.py	2005/02/01 14:20:44	1.5
+++ /home/repository/moby/moby-live/Python/bioMoby/ontology/PubMedMEDLINE.py	2005/02/07 14:23:33	1.6
@@ -48,4 +48,5 @@
             if elt.nodeName=="CrossReference" or elt.nodeName=="moby:CrossReference":
                 self.__cross__=[]
                 for ref in elt.childNodes:
-                    self.__cross__.append(um.loads(ref))
\ No newline at end of file
+                    if ref.nodeType==ref.ELEMENT_NODE:
+                        self.__cross__.append(um.loadn(ref))
\ No newline at end of file

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/ontology/RNASequence.py,v
retrieving revision 1.5
retrieving revision 1.6
diff -u -r1.5 -r1.6
--- /home/repository/moby/moby-live/Python/bioMoby/ontology/RNASequence.py	2005/02/01 14:20:44	1.5
+++ /home/repository/moby/moby-live/Python/bioMoby/ontology/RNASequence.py	2005/02/07 14:23:33	1.6
@@ -51,7 +51,8 @@
             if elt.nodeName=="CrossReference" or elt.nodeName=="moby:CrossReference":
                 self.__cross__=[]
                 for ref in elt.childNodes:
-                    self.__cross__.append(um.loads(ref))
+                    if ref.nodeType==ref.ELEMENT_NODE:
+                        self.__cross__.append(um.loadn(ref))
             if elt.nodeType==elt.ELEMENT_NODE and (elt.nodeName=="Integer" or elt.nodeName=="moby:Integer") and (elt.getAttribute("articleName")=="Length" or elt.getAttribute("moby:articleName")=="Length"):
                 t=MobyInteger()
                 t.fromMoby(elt)

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/ontology/SINGER_ACCESSION.py,v
retrieving revision 1.5
retrieving revision 1.6
diff -u -r1.5 -r1.6
--- /home/repository/moby/moby-live/Python/bioMoby/ontology/SINGER_ACCESSION.py	2005/02/01 14:20:44	1.5
+++ /home/repository/moby/moby-live/Python/bioMoby/ontology/SINGER_ACCESSION.py	2005/02/07 14:23:33	1.6
@@ -52,7 +52,8 @@
             if elt.nodeName=="CrossReference" or elt.nodeName=="moby:CrossReference":
                 self.__cross__=[]
                 for ref in elt.childNodes:
-                    self.__cross__.append(um.loads(ref))
+                    if ref.nodeType==ref.ELEMENT_NODE:
+                        self.__cross__.append(um.loadn(ref))
             if elt.nodeType==elt.ELEMENT_NODE and (elt.nodeName=="String" or elt.nodeName=="moby:String") and (elt.getAttribute("articleName")=="ACCNO" or elt.getAttribute("moby:articleName")=="ACCNO"):
                 t=MobyString()
                 t.fromMoby(elt)

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/ontology/Sample.py,v
retrieving revision 1.5
retrieving revision 1.6
diff -u -r1.5 -r1.6
--- /home/repository/moby/moby-live/Python/bioMoby/ontology/Sample.py	2005/02/01 14:20:44	1.5
+++ /home/repository/moby/moby-live/Python/bioMoby/ontology/Sample.py	2005/02/07 14:23:33	1.6
@@ -51,7 +51,8 @@
             if elt.nodeName=="CrossReference" or elt.nodeName=="moby:CrossReference":
                 self.__cross__=[]
                 for ref in elt.childNodes:
-                    self.__cross__.append(um.loads(ref))
+                    if ref.nodeType==ref.ELEMENT_NODE:
+                        self.__cross__.append(um.loadn(ref))
             if elt.nodeType==elt.ELEMENT_NODE and (elt.nodeName=="String" or elt.nodeName=="moby:String") and (elt.getAttribute("articleName")=="code" or elt.getAttribute("moby:articleName")=="code"):
                 t=MobyString()
                 t.fromMoby(elt)

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/ontology/SchematikonMotifID.py,v
retrieving revision 1.5
retrieving revision 1.6
diff -u -r1.5 -r1.6
--- /home/repository/moby/moby-live/Python/bioMoby/ontology/SchematikonMotifID.py	2005/02/01 14:20:44	1.5
+++ /home/repository/moby/moby-live/Python/bioMoby/ontology/SchematikonMotifID.py	2005/02/07 14:23:33	1.6
@@ -49,7 +49,8 @@
             if elt.nodeName=="CrossReference" or elt.nodeName=="moby:CrossReference":
                 self.__cross__=[]
                 for ref in elt.childNodes:
-                    self.__cross__.append(um.loads(ref))
+                    if ref.nodeType==ref.ELEMENT_NODE:
+                        self.__cross__.append(um.loadn(ref))
             if elt.nodeType==elt.ELEMENT_NODE and (elt.nodeName=="String" or elt.nodeName=="moby:String") and (elt.getAttribute("articleName")=="ID" or elt.getAttribute("moby:articleName")=="ID"):
                 t=MobyString()
                 t.fromMoby(elt)

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/ontology/SchematikonMotifSupport.py,v
retrieving revision 1.5
retrieving revision 1.6
diff -u -r1.5 -r1.6
--- /home/repository/moby/moby-live/Python/bioMoby/ontology/SchematikonMotifSupport.py	2005/02/01 14:20:44	1.5
+++ /home/repository/moby/moby-live/Python/bioMoby/ontology/SchematikonMotifSupport.py	2005/02/07 14:23:33	1.6
@@ -50,7 +50,8 @@
             if elt.nodeName=="CrossReference" or elt.nodeName=="moby:CrossReference":
                 self.__cross__=[]
                 for ref in elt.childNodes:
-                    self.__cross__.append(um.loads(ref))
+                    if ref.nodeType==ref.ELEMENT_NODE:
+                        self.__cross__.append(um.loadn(ref))
             if elt.nodeType==elt.ELEMENT_NODE and (elt.nodeName=="Integer" or elt.nodeName=="moby:Integer") and (elt.getAttribute("articleName")=="UniqueSupport" or elt.getAttribute("moby:articleName")=="UniqueSupport"):
                 t=MobyInteger()
                 t.fromMoby(elt)

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/ontology/SchematikonSegmentAttributes.py,v
retrieving revision 1.5
retrieving revision 1.6
diff -u -r1.5 -r1.6
--- /home/repository/moby/moby-live/Python/bioMoby/ontology/SchematikonSegmentAttributes.py	2005/02/01 14:20:44	1.5
+++ /home/repository/moby/moby-live/Python/bioMoby/ontology/SchematikonSegmentAttributes.py	2005/02/07 14:23:33	1.6
@@ -54,7 +54,8 @@
             if elt.nodeName=="CrossReference" or elt.nodeName=="moby:CrossReference":
                 self.__cross__=[]
                 for ref in elt.childNodes:
-                    self.__cross__.append(um.loads(ref))
+                    if ref.nodeType==ref.ELEMENT_NODE:
+                        self.__cross__.append(um.loadn(ref))
             if elt.nodeType==elt.ELEMENT_NODE and (elt.nodeName=="Integer" or elt.nodeName=="moby:Integer") and (elt.getAttribute("articleName")=="Length" or elt.getAttribute("moby:articleName")=="Length"):
                 t=MobyInteger()
                 t.fromMoby(elt)

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/ontology/SchematikonSegmentID.py,v
retrieving revision 1.5
retrieving revision 1.6
diff -u -r1.5 -r1.6
--- /home/repository/moby/moby-live/Python/bioMoby/ontology/SchematikonSegmentID.py	2005/02/01 14:20:44	1.5
+++ /home/repository/moby/moby-live/Python/bioMoby/ontology/SchematikonSegmentID.py	2005/02/07 14:23:33	1.6
@@ -49,7 +49,8 @@
             if elt.nodeName=="CrossReference" or elt.nodeName=="moby:CrossReference":
                 self.__cross__=[]
                 for ref in elt.childNodes:
-                    self.__cross__.append(um.loads(ref))
+                    if ref.nodeType==ref.ELEMENT_NODE:
+                        self.__cross__.append(um.loadn(ref))
             if elt.nodeType==elt.ELEMENT_NODE and (elt.nodeName=="String" or elt.nodeName=="moby:String") and (elt.getAttribute("articleName")=="ID" or elt.getAttribute("moby:articleName")=="ID"):
                 t=MobyString()
                 t.fromMoby(elt)

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/ontology/SchematikonStructureAnnotation.py,v
retrieving revision 1.5
retrieving revision 1.6
diff -u -r1.5 -r1.6
--- /home/repository/moby/moby-live/Python/bioMoby/ontology/SchematikonStructureAnnotation.py	2005/02/01 14:20:44	1.5
+++ /home/repository/moby/moby-live/Python/bioMoby/ontology/SchematikonStructureAnnotation.py	2005/02/07 14:23:33	1.6
@@ -52,7 +52,8 @@
             if elt.nodeName=="CrossReference" or elt.nodeName=="moby:CrossReference":
                 self.__cross__=[]
                 for ref in elt.childNodes:
-                    self.__cross__.append(um.loads(ref))
+                    if ref.nodeType==ref.ELEMENT_NODE:
+                        self.__cross__.append(um.loadn(ref))
             if elt.nodeType==elt.ELEMENT_NODE and (elt.nodeName=="String" or elt.nodeName=="moby:String") and (elt.getAttribute("articleName")=="PROMOTIF gamma-turn" or elt.getAttribute("moby:articleName")=="PROMOTIF gamma-turn"):
                 t=MobyString()
                 t.fromMoby(elt)

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/ontology/SchematikonVorocodeName.py,v
retrieving revision 1.5
retrieving revision 1.6
diff -u -r1.5 -r1.6
--- /home/repository/moby/moby-live/Python/bioMoby/ontology/SchematikonVorocodeName.py	2005/02/01 14:20:44	1.5
+++ /home/repository/moby/moby-live/Python/bioMoby/ontology/SchematikonVorocodeName.py	2005/02/07 14:23:33	1.6
@@ -49,7 +49,8 @@
             if elt.nodeName=="CrossReference" or elt.nodeName=="moby:CrossReference":
                 self.__cross__=[]
                 for ref in elt.childNodes:
-                    self.__cross__.append(um.loads(ref))
+                    if ref.nodeType==ref.ELEMENT_NODE:
+                        self.__cross__.append(um.loadn(ref))
             if elt.nodeType==elt.ELEMENT_NODE and (elt.nodeName=="String" or elt.nodeName=="moby:String") and (elt.getAttribute("articleName")=="VorocodeName" or elt.getAttribute("moby:articleName")=="VorocodeName"):
                 t=MobyString()
                 t.fromMoby(elt)

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/ontology/Scored_acronym_string.py,v
retrieving revision 1.5
retrieving revision 1.6
diff -u -r1.5 -r1.6
--- /home/repository/moby/moby-live/Python/bioMoby/ontology/Scored_acronym_string.py	2005/02/01 14:20:44	1.5
+++ /home/repository/moby/moby-live/Python/bioMoby/ontology/Scored_acronym_string.py	2005/02/07 14:23:33	1.6
@@ -52,7 +52,8 @@
             if elt.nodeName=="CrossReference" or elt.nodeName=="moby:CrossReference":
                 self.__cross__=[]
                 for ref in elt.childNodes:
-                    self.__cross__.append(um.loads(ref))
+                    if ref.nodeType==ref.ELEMENT_NODE:
+                        self.__cross__.append(um.loadn(ref))
             if elt.nodeType==elt.ELEMENT_NODE and (elt.nodeName=="Float" or elt.nodeName=="moby:Float") and (elt.getAttribute("articleName")=="score" or elt.getAttribute("moby:articleName")=="score"):
                 t=MobyFloat()
                 t.fromMoby(elt)

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/ontology/SimpleAnnotatedGIFImage.py,v
retrieving revision 1.5
retrieving revision 1.6
diff -u -r1.5 -r1.6
--- /home/repository/moby/moby-live/Python/bioMoby/ontology/SimpleAnnotatedGIFImage.py	2005/02/01 14:20:44	1.5
+++ /home/repository/moby/moby-live/Python/bioMoby/ontology/SimpleAnnotatedGIFImage.py	2005/02/07 14:23:33	1.6
@@ -50,7 +50,8 @@
             if elt.nodeName=="CrossReference" or elt.nodeName=="moby:CrossReference":
                 self.__cross__=[]
                 for ref in elt.childNodes:
-                    self.__cross__.append(um.loads(ref))
+                    if ref.nodeType==ref.ELEMENT_NODE:
+                        self.__cross__.append(um.loadn(ref))
             if elt.nodeType==elt.ELEMENT_NODE and (elt.nodeName=="String" or elt.nodeName=="moby:String") and (elt.getAttribute("articleName")=="Description" or elt.getAttribute("moby:articleName")=="Description"):
                 t=MobyString()
                 t.fromMoby(elt)

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/ontology/SimpleAnnotatedJPEGImage.py,v
retrieving revision 1.5
retrieving revision 1.6
diff -u -r1.5 -r1.6
--- /home/repository/moby/moby-live/Python/bioMoby/ontology/SimpleAnnotatedJPEGImage.py	2005/02/01 14:20:44	1.5
+++ /home/repository/moby/moby-live/Python/bioMoby/ontology/SimpleAnnotatedJPEGImage.py	2005/02/07 14:23:33	1.6
@@ -51,7 +51,8 @@
             if elt.nodeName=="CrossReference" or elt.nodeName=="moby:CrossReference":
                 self.__cross__=[]
                 for ref in elt.childNodes:
-                    self.__cross__.append(um.loads(ref))
+                    if ref.nodeType==ref.ELEMENT_NODE:
+                        self.__cross__.append(um.loadn(ref))
             if elt.nodeType==elt.ELEMENT_NODE and (elt.nodeName=="String" or elt.nodeName=="moby:String") and (elt.getAttribute("articleName")=="Description" or elt.getAttribute("moby:articleName")=="Description"):
                 t=MobyString()
                 t.fromMoby(elt)

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/ontology/Simple_key_value_pair.py,v
retrieving revision 1.5
retrieving revision 1.6
diff -u -r1.5 -r1.6
--- /home/repository/moby/moby-live/Python/bioMoby/ontology/Simple_key_value_pair.py	2005/02/01 14:20:44	1.5
+++ /home/repository/moby/moby-live/Python/bioMoby/ontology/Simple_key_value_pair.py	2005/02/07 14:23:33	1.6
@@ -50,7 +50,8 @@
             if elt.nodeName=="CrossReference" or elt.nodeName=="moby:CrossReference":
                 self.__cross__=[]
                 for ref in elt.childNodes:
-                    self.__cross__.append(um.loads(ref))
+                    if ref.nodeType==ref.ELEMENT_NODE:
+                        self.__cross__.append(um.loadn(ref))
             if elt.nodeType==elt.ELEMENT_NODE and (elt.nodeName=="String" or elt.nodeName=="moby:String") and (elt.getAttribute("articleName")=="value" or elt.getAttribute("moby:articleName")=="value"):
                 t=MobyString()
                 t.fromMoby(elt)

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/ontology/Snp_allele.py,v
retrieving revision 1.5
retrieving revision 1.6
diff -u -r1.5 -r1.6
--- /home/repository/moby/moby-live/Python/bioMoby/ontology/Snp_allele.py	2005/02/01 14:20:44	1.5
+++ /home/repository/moby/moby-live/Python/bioMoby/ontology/Snp_allele.py	2005/02/07 14:23:33	1.6
@@ -39,7 +39,8 @@
             if elt.nodeName=="CrossReference" or elt.nodeName=="moby:CrossReference":
                 self.__cross__=[]
                 for ref in elt.childNodes:
-                    self.__cross__.append(um.loads(ref))
+                    if ref.nodeType==ref.ELEMENT_NODE:
+                        self.__cross__.append(um.loadn(ref))
             if elt.nodeType==elt.ELEMENT_NODE and (elt.nodeName=="DNASequence" or elt.nodeName=="moby:DNASequence") and (elt.getAttribute("articleName")=="snp_allele" or elt.getAttribute("moby:articleName")=="snp_allele"):
                 self.Snp_allele=MobyDNASequence()
                 self.Snp_allele.fromMoby(elt)
\ No newline at end of file

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/ontology/Snp_genotype.py,v
retrieving revision 1.5
retrieving revision 1.6
diff -u -r1.5 -r1.6
--- /home/repository/moby/moby-live/Python/bioMoby/ontology/Snp_genotype.py	2005/02/01 14:20:44	1.5
+++ /home/repository/moby/moby-live/Python/bioMoby/ontology/Snp_genotype.py	2005/02/07 14:23:33	1.6
@@ -40,7 +40,8 @@
             if elt.nodeName=="CrossReference" or elt.nodeName=="moby:CrossReference":
                 self.__cross__=[]
                 for ref in elt.childNodes:
-                    self.__cross__.append(um.loads(ref))
+                    if ref.nodeType==ref.ELEMENT_NODE:
+                        self.__cross__.append(um.loadn(ref))
             if elt.nodeType==elt.ELEMENT_NODE and (elt.nodeName=="snp_allele" or elt.nodeName=="moby:snp_allele") and (elt.getAttribute("articleName")=="allele1" or elt.getAttribute("moby:articleName")=="allele1"):
                 self.Allele1=MobySnp_allele()
                 self.Allele1.fromMoby(elt)

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/ontology/Study.py,v
retrieving revision 1.5
retrieving revision 1.6
diff -u -r1.5 -r1.6
--- /home/repository/moby/moby-live/Python/bioMoby/ontology/Study.py	2005/02/01 14:20:44	1.5
+++ /home/repository/moby/moby-live/Python/bioMoby/ontology/Study.py	2005/02/07 14:23:33	1.6
@@ -52,7 +52,8 @@
             if elt.nodeName=="CrossReference" or elt.nodeName=="moby:CrossReference":
                 self.__cross__=[]
                 for ref in elt.childNodes:
-                    self.__cross__.append(um.loads(ref))
+                    if ref.nodeType==ref.ELEMENT_NODE:
+                        self.__cross__.append(um.loadn(ref))
             if elt.nodeType==elt.ELEMENT_NODE and (elt.nodeName=="String" or elt.nodeName=="moby:String") and (elt.getAttribute("articleName")=="study_name" or elt.getAttribute("moby:articleName")=="study_name"):
                 t=MobyString()
                 t.fromMoby(elt)

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/ontology/TEST.py,v
retrieving revision 1.5
retrieving revision 1.6
diff -u -r1.5 -r1.6
--- /home/repository/moby/moby-live/Python/bioMoby/ontology/TEST.py	2005/02/01 14:20:44	1.5
+++ /home/repository/moby/moby-live/Python/bioMoby/ontology/TEST.py	2005/02/07 14:23:33	1.6
@@ -48,4 +48,5 @@
             if elt.nodeName=="CrossReference" or elt.nodeName=="moby:CrossReference":
                 self.__cross__=[]
                 for ref in elt.childNodes:
-                    self.__cross__.append(um.loads(ref))
\ No newline at end of file
+                    if ref.nodeType==ref.ELEMENT_NODE:
+                        self.__cross__.append(um.loadn(ref))
\ No newline at end of file

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/ontology/TargetP_result.py,v
retrieving revision 1.5
retrieving revision 1.6
diff -u -r1.5 -r1.6
--- /home/repository/moby/moby-live/Python/bioMoby/ontology/TargetP_result.py	2005/02/01 14:20:44	1.5
+++ /home/repository/moby/moby-live/Python/bioMoby/ontology/TargetP_result.py	2005/02/07 14:23:33	1.6
@@ -54,7 +54,8 @@
             if elt.nodeName=="CrossReference" or elt.nodeName=="moby:CrossReference":
                 self.__cross__=[]
                 for ref in elt.childNodes:
-                    self.__cross__.append(um.loads(ref))
+                    if ref.nodeType==ref.ELEMENT_NODE:
+                        self.__cross__.append(um.loadn(ref))
             if elt.nodeType==elt.ELEMENT_NODE and (elt.nodeName=="Float" or elt.nodeName=="moby:Float") and (elt.getAttribute("articleName")=="o_score" or elt.getAttribute("moby:articleName")=="o_score"):
                 t=MobyFloat()
                 t.fromMoby(elt)

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/ontology/Testout.py,v
retrieving revision 1.5
retrieving revision 1.6
diff -u -r1.5 -r1.6
--- /home/repository/moby/moby-live/Python/bioMoby/ontology/Testout.py	2005/02/01 14:20:44	1.5
+++ /home/repository/moby/moby-live/Python/bioMoby/ontology/Testout.py	2005/02/07 14:23:33	1.6
@@ -53,7 +53,8 @@
             if elt.nodeName=="CrossReference" or elt.nodeName=="moby:CrossReference":
                 self.__cross__=[]
                 for ref in elt.childNodes:
-                    self.__cross__.append(um.loads(ref))
+                    if ref.nodeType==ref.ELEMENT_NODE:
+                        self.__cross__.append(um.loadn(ref))
             if elt.nodeType==elt.ELEMENT_NODE and (elt.nodeName=="Integer" or elt.nodeName=="moby:Integer") and (elt.getAttribute("articleName")=="gid" or elt.getAttribute("moby:articleName")=="gid"):
                 t=MobyInteger()
                 t.fromMoby(elt)

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/ontology/TextBase64.py,v
retrieving revision 1.5
retrieving revision 1.6
diff -u -r1.5 -r1.6
--- /home/repository/moby/moby-live/Python/bioMoby/ontology/TextBase64.py	2005/02/01 14:20:44	1.5
+++ /home/repository/moby/moby-live/Python/bioMoby/ontology/TextBase64.py	2005/02/07 14:23:33	1.6
@@ -48,4 +48,5 @@
             if elt.nodeName=="CrossReference" or elt.nodeName=="moby:CrossReference":
                 self.__cross__=[]
                 for ref in elt.childNodes:
-                    self.__cross__.append(um.loads(ref))
\ No newline at end of file
+                    if ref.nodeType==ref.ELEMENT_NODE:
+                        self.__cross__.append(um.loadn(ref))
\ No newline at end of file

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/ontology/TextFormatted.py,v
retrieving revision 1.5
retrieving revision 1.6
diff -u -r1.5 -r1.6
--- /home/repository/moby/moby-live/Python/bioMoby/ontology/TextFormatted.py	2005/02/01 14:20:44	1.5
+++ /home/repository/moby/moby-live/Python/bioMoby/ontology/TextFormatted.py	2005/02/07 14:23:33	1.6
@@ -48,4 +48,5 @@
             if elt.nodeName=="CrossReference" or elt.nodeName=="moby:CrossReference":
                 self.__cross__=[]
                 for ref in elt.childNodes:
-                    self.__cross__.append(um.loads(ref))
\ No newline at end of file
+                    if ref.nodeType==ref.ELEMENT_NODE:
+                        self.__cross__.append(um.loadn(ref))
\ No newline at end of file

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/ontology/TextHtml.py,v
retrieving revision 1.5
retrieving revision 1.6
diff -u -r1.5 -r1.6
--- /home/repository/moby/moby-live/Python/bioMoby/ontology/TextHtml.py	2005/02/01 14:20:44	1.5
+++ /home/repository/moby/moby-live/Python/bioMoby/ontology/TextHtml.py	2005/02/07 14:23:33	1.6
@@ -48,4 +48,5 @@
             if elt.nodeName=="CrossReference" or elt.nodeName=="moby:CrossReference":
                 self.__cross__=[]
                 for ref in elt.childNodes:
-                    self.__cross__.append(um.loads(ref))
\ No newline at end of file
+                    if ref.nodeType==ref.ELEMENT_NODE:
+                        self.__cross__.append(um.loadn(ref))
\ No newline at end of file

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/ontology/TextPlain.py,v
retrieving revision 1.5
retrieving revision 1.6
diff -u -r1.5 -r1.6
--- /home/repository/moby/moby-live/Python/bioMoby/ontology/TextPlain.py	2005/02/01 14:20:44	1.5
+++ /home/repository/moby/moby-live/Python/bioMoby/ontology/TextPlain.py	2005/02/07 14:23:33	1.6
@@ -48,4 +48,5 @@
             if elt.nodeName=="CrossReference" or elt.nodeName=="moby:CrossReference":
                 self.__cross__=[]
                 for ref in elt.childNodes:
-                    self.__cross__.append(um.loads(ref))
\ No newline at end of file
+                    if ref.nodeType==ref.ELEMENT_NODE:
+                        self.__cross__.append(um.loadn(ref))
\ No newline at end of file

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/ontology/TextUuencoded.py,v
retrieving revision 1.5
retrieving revision 1.6
diff -u -r1.5 -r1.6
--- /home/repository/moby/moby-live/Python/bioMoby/ontology/TextUuencoded.py	2005/02/01 14:20:44	1.5
+++ /home/repository/moby/moby-live/Python/bioMoby/ontology/TextUuencoded.py	2005/02/07 14:23:33	1.6
@@ -48,4 +48,5 @@
             if elt.nodeName=="CrossReference" or elt.nodeName=="moby:CrossReference":
                 self.__cross__=[]
                 for ref in elt.childNodes:
-                    self.__cross__.append(um.loads(ref))
\ No newline at end of file
+                    if ref.nodeType==ref.ELEMENT_NODE:
+                        self.__cross__.append(um.loadn(ref))
\ No newline at end of file

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/ontology/TextXml.py,v
retrieving revision 1.5
retrieving revision 1.6
diff -u -r1.5 -r1.6
--- /home/repository/moby/moby-live/Python/bioMoby/ontology/TextXml.py	2005/02/01 14:20:44	1.5
+++ /home/repository/moby/moby-live/Python/bioMoby/ontology/TextXml.py	2005/02/07 14:23:33	1.6
@@ -48,4 +48,5 @@
             if elt.nodeName=="CrossReference" or elt.nodeName=="moby:CrossReference":
                 self.__cross__=[]
                 for ref in elt.childNodes:
-                    self.__cross__.append(um.loads(ref))
\ No newline at end of file
+                    if ref.nodeType==ref.ELEMENT_NODE:
+                        self.__cross__.append(um.loadn(ref))
\ No newline at end of file

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/ontology/Text_plain.py,v
retrieving revision 1.5
retrieving revision 1.6
diff -u -r1.5 -r1.6
--- /home/repository/moby/moby-live/Python/bioMoby/ontology/Text_plain.py	2005/02/01 14:20:44	1.5
+++ /home/repository/moby/moby-live/Python/bioMoby/ontology/Text_plain.py	2005/02/07 14:23:33	1.6
@@ -48,4 +48,5 @@
             if elt.nodeName=="CrossReference" or elt.nodeName=="moby:CrossReference":
                 self.__cross__=[]
                 for ref in elt.childNodes:
-                    self.__cross__.append(um.loads(ref))
\ No newline at end of file
+                    if ref.nodeType==ref.ELEMENT_NODE:
+                        self.__cross__.append(um.loadn(ref))
\ No newline at end of file

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/ontology/Trait_Details.py,v
retrieving revision 1.5
retrieving revision 1.6
diff -u -r1.5 -r1.6
--- /home/repository/moby/moby-live/Python/bioMoby/ontology/Trait_Details.py	2005/02/01 14:20:44	1.5
+++ /home/repository/moby/moby-live/Python/bioMoby/ontology/Trait_Details.py	2005/02/07 14:23:33	1.6
@@ -54,7 +54,8 @@
             if elt.nodeName=="CrossReference" or elt.nodeName=="moby:CrossReference":
                 self.__cross__=[]
                 for ref in elt.childNodes:
-                    self.__cross__.append(um.loads(ref))
+                    if ref.nodeType==ref.ELEMENT_NODE:
+                        self.__cross__.append(um.loadn(ref))
             if elt.nodeType==elt.ELEMENT_NODE and (elt.nodeName=="String" or elt.nodeName=="moby:String") and (elt.getAttribute("articleName")=="trait_desc" or elt.getAttribute("moby:articleName")=="trait_desc"):
                 t=MobyString()
                 t.fromMoby(elt)

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/ontology/Tree.py,v
retrieving revision 1.5
retrieving revision 1.6
diff -u -r1.5 -r1.6
--- /home/repository/moby/moby-live/Python/bioMoby/ontology/Tree.py	2005/02/01 14:20:44	1.5
+++ /home/repository/moby/moby-live/Python/bioMoby/ontology/Tree.py	2005/02/07 14:23:33	1.6
@@ -48,4 +48,5 @@
             if elt.nodeName=="CrossReference" or elt.nodeName=="moby:CrossReference":
                 self.__cross__=[]
                 for ref in elt.childNodes:
-                    self.__cross__.append(um.loads(ref))
\ No newline at end of file
+                    if ref.nodeType==ref.ELEMENT_NODE:
+                        self.__cross__.append(um.loadn(ref))
\ No newline at end of file

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/ontology/TropGENE_ACCESSION.py,v
retrieving revision 1.5
retrieving revision 1.6
diff -u -r1.5 -r1.6
--- /home/repository/moby/moby-live/Python/bioMoby/ontology/TropGENE_ACCESSION.py	2005/02/01 14:20:44	1.5
+++ /home/repository/moby/moby-live/Python/bioMoby/ontology/TropGENE_ACCESSION.py	2005/02/07 14:23:33	1.6
@@ -68,7 +68,8 @@
             if elt.nodeName=="CrossReference" or elt.nodeName=="moby:CrossReference":
                 self.__cross__=[]
                 for ref in elt.childNodes:
-                    self.__cross__.append(um.loads(ref))
+                    if ref.nodeType==ref.ELEMENT_NODE:
+                        self.__cross__.append(um.loadn(ref))
             if elt.nodeType==elt.ELEMENT_NODE and (elt.nodeName=="TropGENE_LOCUS" or elt.nodeName=="moby:TropGENE_LOCUS") and (elt.getAttribute("articleName")=="RFLP" or elt.getAttribute("moby:articleName")=="RFLP"):
                 self.RFLP=MobyTropGENE_LOCUS()
                 self.RFLP.fromMoby(elt)

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/ontology/TropGENE_Diversity_Matrix.py,v
retrieving revision 1.5
retrieving revision 1.6
diff -u -r1.5 -r1.6
--- /home/repository/moby/moby-live/Python/bioMoby/ontology/TropGENE_Diversity_Matrix.py	2005/02/01 14:20:44	1.5
+++ /home/repository/moby/moby-live/Python/bioMoby/ontology/TropGENE_Diversity_Matrix.py	2005/02/07 14:23:33	1.6
@@ -48,4 +48,5 @@
             if elt.nodeName=="CrossReference" or elt.nodeName=="moby:CrossReference":
                 self.__cross__=[]
                 for ref in elt.childNodes:
-                    self.__cross__.append(um.loads(ref))
\ No newline at end of file
+                    if ref.nodeType==ref.ELEMENT_NODE:
+                        self.__cross__.append(um.loadn(ref))
\ No newline at end of file

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/ontology/TropGENE_LOCUS.py,v
retrieving revision 1.5
retrieving revision 1.6
diff -u -r1.5 -r1.6
--- /home/repository/moby/moby-live/Python/bioMoby/ontology/TropGENE_LOCUS.py	2005/02/01 14:20:44	1.5
+++ /home/repository/moby/moby-live/Python/bioMoby/ontology/TropGENE_LOCUS.py	2005/02/07 14:23:33	1.6
@@ -47,4 +47,5 @@
             if elt.nodeName=="CrossReference" or elt.nodeName=="moby:CrossReference":
                 self.__cross__=[]
                 for ref in elt.childNodes:
-                    self.__cross__.append(um.loads(ref))
\ No newline at end of file
+                    if ref.nodeType==ref.ELEMENT_NODE:
+                        self.__cross__.append(um.loadn(ref))
\ No newline at end of file

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/ontology/VirtualSequence.py,v
retrieving revision 1.5
retrieving revision 1.6
diff -u -r1.5 -r1.6
--- /home/repository/moby/moby-live/Python/bioMoby/ontology/VirtualSequence.py	2005/02/01 14:20:44	1.5
+++ /home/repository/moby/moby-live/Python/bioMoby/ontology/VirtualSequence.py	2005/02/07 14:23:33	1.6
@@ -49,7 +49,8 @@
             if elt.nodeName=="CrossReference" or elt.nodeName=="moby:CrossReference":
                 self.__cross__=[]
                 for ref in elt.childNodes:
-                    self.__cross__.append(um.loads(ref))
+                    if ref.nodeType==ref.ELEMENT_NODE:
+                        self.__cross__.append(um.loadn(ref))
             if elt.nodeType==elt.ELEMENT_NODE and (elt.nodeName=="Integer" or elt.nodeName=="moby:Integer") and (elt.getAttribute("articleName")=="Length" or elt.getAttribute("moby:articleName")=="Length"):
                 t=MobyInteger()
                 t.fromMoby(elt)

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/ontology/WU_BLAST_Text.py,v
retrieving revision 1.5
retrieving revision 1.6
diff -u -r1.5 -r1.6
--- /home/repository/moby/moby-live/Python/bioMoby/ontology/WU_BLAST_Text.py	2005/02/01 14:20:44	1.5
+++ /home/repository/moby/moby-live/Python/bioMoby/ontology/WU_BLAST_Text.py	2005/02/07 14:23:33	1.6
@@ -48,4 +48,5 @@
             if elt.nodeName=="CrossReference" or elt.nodeName=="moby:CrossReference":
                 self.__cross__=[]
                 for ref in elt.childNodes:
-                    self.__cross__.append(um.loads(ref))
\ No newline at end of file
+                    if ref.nodeType==ref.ELEMENT_NODE:
+                        self.__cross__.append(um.loadn(ref))
\ No newline at end of file

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/ontology/Wildcard_Query.py,v
retrieving revision 1.5
retrieving revision 1.6
diff -u -r1.5 -r1.6
--- /home/repository/moby/moby-live/Python/bioMoby/ontology/Wildcard_Query.py	2005/02/01 14:20:44	1.5
+++ /home/repository/moby/moby-live/Python/bioMoby/ontology/Wildcard_Query.py	2005/02/07 14:23:33	1.6
@@ -52,7 +52,8 @@
             if elt.nodeName=="CrossReference" or elt.nodeName=="moby:CrossReference":
                 self.__cross__=[]
                 for ref in elt.childNodes:
-                    self.__cross__.append(um.loads(ref))
+                    if ref.nodeType==ref.ELEMENT_NODE:
+                        self.__cross__.append(um.loadn(ref))
             if elt.nodeType==elt.ELEMENT_NODE and (elt.nodeName=="Integer" or elt.nodeName=="moby:Integer") and (elt.getAttribute("articleName")=="end_row" or elt.getAttribute("moby:articleName")=="end_row"):
                 t=MobyInteger()
                 t.fromMoby(elt)



From yanwong at pub.open-bio.org  Tue Feb  1 08:52:17 2005
From: yanwong at pub.open-bio.org (Yan Wong)
Date: Tue, 1 Feb 2005 03:52:17 -0500
Subject: [MOBY-guts] biomoby commit
Message-ID: <200502010852.j118qHHl013127@pub.open-bio.org>


yanwong
Tue Feb  1 03:52:17 EST 2005
Update of /home/repository/moby/moby-live/Python/bioMoby/webservice
In directory pub.open-bio.org:/tmp/cvs-serv12609/webservice

Modified Files:
	Dispatcher.py Invocators.py TCBioMoby.py __init__.py 
Log Message:


moby-live/Python/bioMoby/webservice Dispatcher.py,1.2,1.3 Invocators.py,1.2,1.3 TCBioMoby.py,1.2,1.3 __init__.py,1.2,1.3
===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/webservice/Dispatcher.py,v
retrieving revision 1.2
retrieving revision 1.3
diff -u -r1.2 -r1.3
--- /home/repository/moby/moby-live/Python/bioMoby/webservice/Dispatcher.py	2005/01/18 13:46:24	1.2
+++ /home/repository/moby/moby-live/Python/bioMoby/webservice/Dispatcher.py	2005/02/01 08:52:17	1.3
@@ -76,7 +76,7 @@
     def __str__(self):
         return "An error occurs during the Dispatcher process: "
 
-	
+        
 class AbstractDispatcher:
     """ Subclass this one to create your own dispatcher class
         a Dispatcher class must have a execute method
@@ -91,16 +91,16 @@
 
         from bioMoby import MobyUnmarshaller
 
-	self._isbase64=False
-	self._workdir=workdir
-	self.answers={}
-	
-	#First see if we have a MobyContent Object or a string
-	mc=mobyContentXML
-	self._isString=False
-	
-	if not hasattr(mobyContentXML, 'queryData'):
-	    self._isString=True
+        self._isbase64=False
+        self._workdir=workdir
+        self.answers={}
+        
+        #First see if we have a MobyContent Object or a string
+        mc=mobyContentXML
+        self._isString=False
+        
+        if not hasattr(mobyContentXML, 'queryData'):
+            self._isString=True
             try:
                 #Do some cleaning on the XML Document before proceeding...
                 #Remove all \t|\n from the <a>\n\t</a>
@@ -110,117 +110,117 @@
                 mc=um.loads("><".join(r.split(mobyContentXML)))
             except:
                 try:
-		    mc=um.loads(base64.decodestring(mobyContentXML))
-	            self._isbase64=True
-	        except binascii.Error:
-	            raise  EDispatchError, "Invalid types in the moby Content object"
+                    mc=um.loads(base64.decodestring(mobyContentXML))
+                    self._isbase64=True
+                except binascii.Error:
+                    raise  EDispatchError, "Invalid types in the moby Content object"
 
         self.queryData=mc.queryData
         self.invocator=Invocator
-	self._invocatorParameters=invocatorParameters
+        self._invocatorParameters=invocatorParameters
         self.commandBuilder=CommandBuilder
         self.formatter=formatter
-	
-	del MobyUnmarshaller
+        
+        del MobyUnmarshaller
 
     def execute(self):
-	""" Override this method
-	"""
-	pass
+        """ Override this method
+        """
+        pass
 
     def _toMoby(self):
-	"""Return the results as a MobyContent Object
-	"""
-	from bioMoby import MobyContent
-	
-	if self._isbase64:
-	    return base64.encodestring(str(MobyContent(self.answers)))
-	
+        """Return the results as a MobyContent Object
+        """
+        from bioMoby import MobyContent
+        
+        if self._isbase64:
+            return base64.encodestring(str(MobyContent(self.answers)))
+        
         return str(MobyContent(self.answers))
 
-	
+        
 class SimpleDispatcher(AbstractDispatcher):
     """ A simple dispatcher execute sequentially the treatments
     """
     def __init__(self, mobyContentXML, Invocator, InvocatorParameters, CommandBuilder, formatter=None, workdir="/tmp"):
-	AbstractDispatcher.__init__(self, mobyContentXML, Invocator, InvocatorParameters, CommandBuilder, formatter, workdir)
-	
-	from bioMoby import MobyObject
-	
-	if 'JOBSESSION' in self.queryData.keys():
-	    self._sessionid=self.queryData['JOBSESSION'][0].id
-	else:
-	    self._sessionid=`random.randint(0,sys.maxint-1)`
-	    
-	    while "session"+self._sessionid in os.listdir(self._workdir):
-		self._sessionid=`random.randint(0,sys.maxint-1)`
-		
+        AbstractDispatcher.__init__(self, mobyContentXML, Invocator, InvocatorParameters, CommandBuilder, formatter, workdir)
+        
+        from bioMoby import MobyObject
+        
+        if 'JOBSESSION' in self.queryData.keys():
+            self._sessionid=self.queryData['JOBSESSION'][0].id
+        else:
+            self._sessionid=`random.randint(0,sys.maxint-1)`
+            
+            while "session"+self._sessionid in os.listdir(self._workdir):
+                self._sessionid=`random.randint(0,sys.maxint-1)`
+                
             os.mkdir(self._workdir+"/session"+self._sessionid)
-	
-	os.chdir(self._workdir+"/session"+self._sessionid)
-	
+        
+        os.chdir(self._workdir+"/session"+self._sessionid)
+        
         self.answers={'JOBSESSION':[MobyObject(namespace="SESSIONID", id=self._sessionid)]}
 
     def _clean(self):
-	"""Clean the session directory
-	"""
+        """Clean the session directory
+        """
         #Clean the session directory
         os.chdir(self._workdir)
         shutil.rmtree(self._workdir+"/session"+self._sessionid)
-	    
+            
     def _fetchAnswers(self):
-	""" Fetch the answers and clean the session directory
-	"""
-	from bioMoby import GeneralInvocator
-	
-	answers={}
+        """ Fetch the answers and clean the session directory
+        """
+        from bioMoby import GeneralInvocator
+        
+        answers={}
 
-	ruserdir="session"+self._sessionid
+        ruserdir="session"+self._sessionid
         try:
-	    l=os.listdir(self._workdir+"/"+ruserdir)
-	except:
-	    l=[]
-	
-	if len(l)>0:
-	    #There is a session directory
+            l=os.listdir(self._workdir+"/"+ruserdir)
+        except:
+            l=[]
+        
+        if len(l)>0:
+            #There is a session directory
             for querykey in l:
-		if querykey[:8]=="results-":
-		    aQueryName=querykey[8:]
-	            gi=GeneralInvocator(aQueryName ,userdir=self._workdir+"/"+ruserdir)
-	            answers[aQueryName]=[gi.getResults()]
+                if querykey[:8]=="results-":
+                    aQueryName=querykey[8:]
+                    gi=GeneralInvocator(aQueryName ,userdir=self._workdir+"/"+ruserdir)
+                    answers[aQueryName]=[gi.getResults()]
 
                     if self.formatter != None:
                         answers[aQueryName]=self.formatter(answers[aQueryName][0])
-			
+                        
             if len(answers.keys())>0:
-	        self.answers=answers
-		
-                self._clean()	
+                self.answers=answers
+                
+                self._clean()        
 
-	del GeneralInvocator
-		
+        del GeneralInvocator
+                
     def execute(self):
-	"""Execute the queries sequentially
-	"""
+        """Execute the queries sequentially
+        """
 
-	try:
+        try:
             for key in self.queryData.keys():
-	        query=self.queryData[key]
-	        r=self.invocator(key, self.commandBuilder(query), userdir=self._workdir+"/session"+self._sessionid)
-	        r.execute()
-	    
-	    self._fetchAnswers()
-	except:
-	    import traceback
-	    import StringIO
-	    from bioMoby import MobyString
-	    sio=StringIO.StringIO()
-	    traceback.print_exc(file=sio)
-	    
-	    self.answers['JOBSESSION']=[MobyString(content=sio.getvalue())]
-	    self._clean()
-	
-	return self._toMoby()
+                query=self.queryData[key]
+                r=self.invocator(key, self.commandBuilder(query), userdir=self._workdir+"/session"+self._sessionid)
+                r.execute()
+            
+            self._fetchAnswers()
+        except:
+            import traceback
+            import StringIO
+            from bioMoby import MobyString
+            sio=StringIO.StringIO()
+            traceback.print_exc(file=sio)
+            
+            self.answers['JOBSESSION']=[MobyString(content=sio.getvalue())]
+            self._clean()
+        
+        return self._toMoby()
 
 class MultiThreadDispatcher(SimpleDispatcher):
     """ Use a MultiThread to execute a query
@@ -231,114 +231,114 @@
         from bioMoby import MobyString
 
         query=self.queryData[queryKey]
-	
-	#Execute the query
+        
+        #Execute the query
         try:
             r=self.invocator(queryKey, self.commandBuilder(query), userdir=self._workdir+"/session"+self._sessionid)
-	    r.execute()
+            r.execute()
             time.sleep(0)
-	    
+            
         except:
-	    #If there is a problem, we return the generated exception
-	    import traceback
-	    import StringIO
-	    sio=StringIO.StringIO()
-	    traceback.print_exc(file=sio)
-	    
-	    self.answers['JOBSESSION']=[MobyString(content=sio.getvalue())]
-	    self._clean()
+            #If there is a problem, we return the generated exception
+            import traceback
+            import StringIO
+            sio=StringIO.StringIO()
+            traceback.print_exc(file=sio)
+            
+            self.answers['JOBSESSION']=[MobyString(content=sio.getvalue())]
+            self._clean()
 
 
         del MobyString
 
     
     def execute(self):
-	""" Execute the queries with threads
-	"""
-	
-	try:
+        """ Execute the queries with threads
+        """
+        
+        try:
             os.chdir(self._workdir+"/session"+self._sessionid)
             mt=MultiThread(self._execute, self.queryData.keys())
             mt.start()
             mt.join()
 
-	    self._fetchAnswers()
+            self._fetchAnswers()
         except:
-	    self._clean()
-	    
-	return self._toMoby()
+            self._clean()
+            
+        return self._toMoby()
 
-	
+        
 class PBSDispatcher(SimpleDispatcher):
     """Dispatcher for PBS jobs
     """
 
     def __init__(self, mobyContentXML, InvocatorParameters, CommandBuilder, formatter=None, workdir="/tmp"):
-	""" PBS Dispatcher work with PBSInvocator
-	    it uses a session directory, a session file (where the queries IDs are stored)
-	    when the execute method is call with an session id, it reads all entries from the session file and
-	    make a qstat on each ids.
-	"""
-	from bioMoby.webservice import PBSInvocator
-	
-	SimpleDispatcher.__init__(self, mobyContentXML, PBSInvocator, InvocatorParameters, CommandBuilder, formatter, workdir)
+        """ PBS Dispatcher work with PBSInvocator
+            it uses a session directory, a session file (where the queries IDs are stored)
+            when the execute method is call with an session id, it reads all entries from the session file and
+            make a qstat on each ids.
+        """
+        from bioMoby.webservice import PBSInvocator
+        
+        SimpleDispatcher.__init__(self, mobyContentXML, PBSInvocator, InvocatorParameters, CommandBuilder, formatter, workdir)
     
     def _getResults(self):
-	""" Do a qstat and check availability of results
-	"""
-	from bioMoby import GeneralInvocator
-	
-	answers={}
-	outputfiles={}
-	queryKeys=[]
-	
-	#Read the sessions file, in which there are all queries identifiers
-	
-	fp=file("sessions","r")
-	for queryInformation in fp.readlines():
-	    #for each queries, retrieve the qsub ids, and associated output files.
-	    #delete the CR at the end of the line before proceding
-	    queryInformation=queryInformation[:-1] 
-	    #Get the IDs
-	    qsubId=queryInformation.split(";")[1].split(".")[0]
-	    qk=queryInformation.split(";")[0]
-	    #Get the query key
-	    queryKeys.append(qk)
+        """ Do a qstat and check availability of results
+        """
+        from bioMoby import GeneralInvocator
+        
+        answers={}
+        outputfiles={}
+        queryKeys=[]
+        
+        #Read the sessions file, in which there are all queries identifiers
+        
+        fp=file("sessions","r")
+        for queryInformation in fp.readlines():
+            #for each queries, retrieve the qsub ids, and associated output files.
+            #delete the CR at the end of the line before proceding
+            queryInformation=queryInformation[:-1] 
+            #Get the IDs
+            qsubId=queryInformation.split(";")[1].split(".")[0]
+            qk=queryInformation.split(";")[0]
+            #Get the query key
+            queryKeys.append(qk)
             #get the associated Outputfiles
-	    outputfiles[qk]=queryInformation.split(";")[2].split("::")
+            outputfiles[qk]=queryInformation.split(";")[2].split("::")
 
-	    #Do a qstat and check if the job is still running or on queue
-	    i, o, e = os.popen3("qstat %s"%qsubId)
+            #Do a qstat and check if the job is still running or on queue
+            i, o, e = os.popen3("qstat %s"%qsubId)
 
-	    orl=o.readlines()
-	    erl=e.readlines()
-	    
-	    if len(orl)>0:
-		#if one job is not finished, exit the _getResults function
-		#The dispatcher will give all the results or none 
-		return None
-	
-	fp.close()
-	
-	# At this step, all jobs are done
-	tdir=self._workdir+"/session"+self._sessionid
-	
-	
-	for querykey in queryKeys:
-	    #check the results-query.out:
-	    if "results-"+querykey+".out" in os.listdir(tdir):
+            orl=o.readlines()
+            erl=e.readlines()
+            
+            if len(orl)>0:
+                #if one job is not finished, exit the _getResults function
+                #The dispatcher will give all the results or none 
+                return None
+        
+        fp.close()
+        
+        # At this step, all jobs are done
+        tdir=self._workdir+"/session"+self._sessionid
+        
+        
+        for querykey in queryKeys:
+            #check the results-query.out:
+            if "results-"+querykey+".out" in os.listdir(tdir):
                 fp=file(tdir+"/results-"+querykey+".out")
-	        s=fp.readlines()
-	        fp.close()
+                s=fp.readlines()
+                fp.close()
 
                 if len(s)==0:
-	            os.remove(tdir+"/results-"+querykey+".out")
-	        else:
-		    if len(outputfiles.keys())>0:
-		        shutil.copy(tdir+"/results-"+querykey+".out", tdir+"/results-"+querykey+"/results.out")
+                    os.remove(tdir+"/results-"+querykey+".out")
+                else:
+                    if len(outputfiles.keys())>0:
+                        shutil.copy(tdir+"/results-"+querykey+".out", tdir+"/results-"+querykey+"/results.out")
 
             for f in outputfiles[querykey]:
-	        ruserdir=tdir+"/results-"+querykey
+                ruserdir=tdir+"/results-"+querykey
                 # if it is a file then retrieve the file
                 if os.path.isfile(f):
                     aTemp=f.split('/')
@@ -351,48 +351,48 @@
                         os.remove(f+"/"+fs)
                     os.removedirs(f)
 
-	#retrieve all the results
+        #retrieve all the results
         try:
-	    l=os.listdir(tdir)
-	except:
-	    l=[]
-	
-	if len(l)>0:
+            l=os.listdir(tdir)
+        except:
+            l=[]
+        
+        if len(l)>0:
             for querykey in l:
-		if querykey[:8]=="results-":
-		    aQueryName=querykey[8:]
-	            gi=GeneralInvocator(aQueryName, userdir=tdir)
-	            answers[aQueryName]=[gi.getResults()]
+                if querykey[:8]=="results-":
+                    aQueryName=querykey[8:]
+                    gi=GeneralInvocator(aQueryName, userdir=tdir)
+                    answers[aQueryName]=[gi.getResults()]
 
                     if self.formatter != None:
                         answers[aQueryName]=self.formatter(answers[aQueryName][0])
-			
+                        
             if len(answers.keys())>0:
-	        self.answers=answers
-		
+                self.answers=answers
+                
                 self._clean()
-	
-	del GeneralInvocator
+        
+        del GeneralInvocator
 
-	
+        
     def execute(self):
-	"""Execute the command in a PBS script using the PBSInvocator
-	"""
+        """Execute the command in a PBS script using the PBSInvocator
+        """
 
         if 'JOBSESSION' in self.queryData.keys():
-	    self.answers=self.queryData
+            self.answers=self.queryData
 
-	    self._getResults()
-	else:
-	    #we need to store informations in a file
-	    #query id, qsubid, outputfiles
-	    fp=file("sessions","w")
-	    for queryKey in self.queryData.keys():
-		query=self.queryData[queryKey]
-	        r=self.invocator(queryKey, self.commandBuilder(query), fp, userdir=self._workdir+"/session"+self._sessionid)
-		r.setParameters(self._invocatorParameters)
-		r.execute()
-	    fp.close()
+            self._getResults()
+        else:
+            #we need to store informations in a file
+            #query id, qsubid, outputfiles
+            fp=file("sessions","w")
+            for queryKey in self.queryData.keys():
+                query=self.queryData[queryKey]
+                r=self.invocator(queryKey, self.commandBuilder(query), fp, userdir=self._workdir+"/session"+self._sessionid)
+                r.setParameters(self._invocatorParameters)
+                r.execute()
+            fp.close()
 
         return self._toMoby()
 
@@ -405,18 +405,18 @@
             The commandBuilder function shall return  a command, arguments, and a set of temporary files
             [queryData]-->("commandName","commandArgs", ["tempfiles"])
         """
-	SimpleDispatcher.__init__(self, mobyContentXML, Invocator, None, CommandBuilder, formatter, workdir)
-	
-	import pyipc
-	
-	#Create a Jobsession ID, a semaphore and a session directory
-	if 'JOBSESSION' in self.queryData.keys():
-	    self._sem=pyipc.SemaphoreGroup(int(self._sessionid))
-	else:
+        SimpleDispatcher.__init__(self, mobyContentXML, Invocator, None, CommandBuilder, formatter, workdir)
+        
+        import pyipc
+        
+        #Create a Jobsession ID, a semaphore and a session directory
+        if 'JOBSESSION' in self.queryData.keys():
+            self._sem=pyipc.SemaphoreGroup(int(self._sessionid))
+        else:
             self._sem=pyipc.SemaphoreGroup(int(self._sessionid))
             self._sem.wait()
-	
-	del pyipc
+        
+        del pyipc
 
     def _execute(self, queryKey):
         """ Execute a single query, store the result in the answers attribute
@@ -424,99 +424,99 @@
         from bioMoby import MobyString
 
         query=self.queryData[queryKey]
-	
-	#Execute the query
+        
+        #Execute the query
         try:
             r=self.invocator(queryKey, self.commandBuilder(query), userdir=self._workdir+"/session"+self._sessionid)
-	    r.execute()
+            r.execute()
             time.sleep(0)
         except:
-	    #If there is a problem, we return the generated exception
-	    import traceback
-	    fp=file(self._workdir+"/session"+self._sessionid+"/results-"+queryKey,"w")
-	    fp.write("The query: "+queryKey+" has not been processed")
-	    traceback.print_exc(file=fp)
-	    fp.close()
+            #If there is a problem, we return the generated exception
+            import traceback
+            fp=file(self._workdir+"/session"+self._sessionid+"/results-"+queryKey,"w")
+            fp.write("The query: "+queryKey+" has not been processed")
+            traceback.print_exc(file=fp)
+            fp.close()
 
         del MobyString
 
     def _getSem(self):
-	try:
-	    #Wait for answers of all queries
-	    self._sem.wait()
-	    self._fetchAnswers()
+        try:
+            #Wait for answers of all queries
+            self._sem.wait()
+            self._fetchAnswers()
 
-	    #Remove the IPC
+            #Remove the IPC
             import pyipc
-	    pyipc.removeIPC(self._sem)
-	    del pyipc
+            pyipc.removeIPC(self._sem)
+            del pyipc
         except:
-	    pass
-	
+            pass
+        
     def execute(self, timeout=120):
         """Execute the queries with a pool of threads, store the results in a mobyContent Object
         """
-	import signal
-	
-	#Do a fetchAnswers if the user has a sessionid
-	if 'JOBSESSION' in self.queryData.keys():
-	    self.answers=self.queryData
-
-	    t=threading.Thread(target=self._getSem)
-	    t.start()
-	    t.join(timeout)
+        import signal
+        
+        #Do a fetchAnswers if the user has a sessionid
+        if 'JOBSESSION' in self.queryData.keys():
+            self.answers=self.queryData
+
+            t=threading.Thread(target=self._getSem)
+            t.start()
+            t.join(timeout)
 
             return self._toMoby()
         else:
-	    #A MobyContent without jobsession id has been received
-	    try:
-		#make a fork
-	        pid=os.fork()
-	    except:
-		raise Exception, "Cannot treat any further request, please retry"
-
-	    if pid>0:
-		#try to get the results
-#		os.wait()
-	        t=threading.Thread(target=self._getSem)
-	        t.start()
-	        t.join(timeout)
+            #A MobyContent without jobsession id has been received
+            try:
+                #make a fork
+                pid=os.fork()
+            except:
+                raise Exception, "Cannot treat any further request, please retry"
+
+            if pid>0:
+                #try to get the results
+#                os.wait()
+                t=threading.Thread(target=self._getSem)
+                t.start()
+                t.join(timeout)
 
                 return self._toMoby()
-	    else:
+            else:
                 #do second fork
                 try: 
                     pid = os.fork()
-		except:
-		    raise Exception, "Cannot treat any further request, please retry"
-		    
+                except:
+                    raise Exception, "Cannot treat any further request, please retry"
+                    
                 if pid>0:
-		    #it it is too long, kill the process
-		    time.sleep(1.05*timeout)
+                    #it it is too long, kill the process
+                    time.sleep(1.05*timeout)
                     os.kill(os.getppid(), signal.SIGKILL)
-		    os._exit(0)
-		else:
-		    #execute the treatment
+                    os._exit(0)
+                else:
+                    #execute the treatment
                     os.setpgrp()
-		    
-		    try:
-		        os.chdir(self._workdir+"/session"+self._sessionid)
-	                mt=MultiThread(self._execute, self.queryData.keys())
+                    
+                    try:
+                        os.chdir(self._workdir+"/session"+self._sessionid)
+                        mt=MultiThread(self._execute, self.queryData.keys())
                         mt.start()
                         mt.join()
-		    except:
-			self._clean()
+                    except:
+                        self._clean()
 
-		    try:
-	                self._sem.signal()
+                    try:
+                        self._sem.signal()
                     finally:
-			if os.getppid()>1:
-                  	    try:
-			        os.kill(os.getppid(), signal.SIGKILL)
-		            except:
-			        pass
-			    
-		        os._exit(0)
+                        if os.getppid()>1:
+                              try:
+                                  os.kill(os.getppid(), signal.SIGKILL)
+                              except:
+                                  pass
+                            
+                        os._exit(0)
 
-	#if nothing works return nothing
-	return {}
+        #if nothing works return nothing
+        return {}

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/webservice/Invocators.py,v
retrieving revision 1.2
retrieving revision 1.3
diff -u -r1.2 -r1.3
--- /home/repository/moby/moby-live/Python/bioMoby/webservice/Invocators.py	2005/01/18 13:46:24	1.2
+++ /home/repository/moby/moby-live/Python/bioMoby/webservice/Invocators.py	2005/02/01 08:52:17	1.3
@@ -18,34 +18,34 @@
     """
     
     def __init__(self, queryid, userdir="/tmp", timeout=None):
-	"""queryid is the identifier of a query, userdir is the session directory, timeout the limit time of execution of the query
-	"""
+        """queryid is the identifier of a query, userdir is the session directory, timeout the limit time of execution of the query
+        """
         self.command=""
         from bioMoby import MobyObject
 
         self.results=[]
         self.queryid=queryid
-	
+        
         del MobyObject
         self.errors=""
         self.userdir=userdir
         
 
     def getResults(self):
-	"""retrieve the results if available
-	"""
+        """retrieve the results if available
+        """
         import os
             
         fname=self.userdir+"/results-"+self.queryid
 
         if os.path.isfile(fname):
-	    #if it is a single file
+            #if it is a single file
             fp=file(fname,"r")
             self.results=[fp.read()]
             fp.close()
 #            os.remove(fname)
         else:
-	    #or a directory
+            #or a directory
             self.results=[]
             for fs in os.listdir(fname):
                 if os.path.isfile(fname+"/"+fs):
@@ -87,32 +87,32 @@
 
         results=[]
 
-	ruserdir=self.userdir+"/results-"+self.queryid
-	
+        ruserdir=self.userdir+"/results-"+self.queryid
+        
         #if there are some output files then retrieve them as results
         if len(self.outputfiles) !=0:
             i,o,e=os.popen3(self.command)
 
-	    #read error first and then standard output
-	    
+            #read error first and then standard output
+            
             try:
                 et=e.read()
-		fp=file(self.userdir+"/"+self.queryid+".err")
-		fp.write(et)
-		fp.close()
+                fp=file(self.userdir+"/"+self.queryid+".err")
+                fp.write(et)
+                fp.close()
             except:
-		pass
-	    
-	    try:
+                pass
+            
+            try:
                 ot=o.read()
-		fp=file(self.userdir+"/"+self.queryid+".out")
-		fp.write(ot)
-		fp.close()
-	    except:
-		pass
+                fp=file(self.userdir+"/"+self.queryid+".out")
+                fp.write(ot)
+                fp.close()
+            except:
+                pass
 
-	    #wait unfinished sub process
-		
+            #wait unfinished sub process
+                
             try:
                 os.wait()
             except:
@@ -123,7 +123,7 @@
             for f in self.outputfiles:
                 # if it is a file then retrieve the file
                 if os.path.isfile(f):
-		    aTemp=f.split('/')
+                    aTemp=f.split('/')
                     shutil.copy(f, ruserdir+"/"+aTemp[len(aTemp)-1])
                     os.remove(f)
                 elif os.path.isdir(f):
@@ -135,20 +135,20 @@
         else:
             stdin, stdout, stderr=os.popen3(self.command)
             results=stdout.read()
-	    
-	    fp=file(self.userdir+"/results-"+self.queryid,"w")
-	    fp.write(results)
-	    fp.close()
-	    
-#	    t=stderr.read()
+            
+            fp=file(self.userdir+"/results-"+self.queryid,"w")
+            fp.write(results)
+            fp.close()
+            
+#            t=stderr.read()
 
             stdin.close()
             stdout.close()
             stderr.close()
             os.wait()    
 
-	#Make all the cleaning wipe the session directory
-	    
+        #Make all the cleaning wipe the session directory
+            
         for tmpfile in self.tempfiles:
             try:
                 if os.path.isfile(tmpfile):
@@ -163,71 +163,71 @@
     """Parameters for the qsub command
     """
     def __init__(self, queueName, qsubParameters):
-	""" queueName: name of the PBS queue
-	    qsubParameters: a list of parameters for the -l option: ['ncpus=4', 'walltime=01:00:00']
-	"""
-	self.queueName=queueName
-	self.qsubParameters=qsubParameters
-	
-	
+        """ queueName: name of the PBS queue
+            qsubParameters: a list of parameters for the -l option: ['ncpus=4', 'walltime=01:00:00']
+        """
+        self.queueName=queueName
+        self.qsubParameters=qsubParameters
+        
+        
 class PBSInvocator(LocalInvocator):
     """Invokes a command in a qsub
     """
     
     def __init__(self, queryKey, command, aFile, userdir="/tmp"):
-	"""The file is needed here to keep the generated outputfiles
-	"""
-	LocalInvocator.__init__(self, queryKey, command, userdir)
-	self._queueName=""
-	self._PBSparameters=[]
-	self._aFile=aFile
+        """The file is needed here to keep the generated outputfiles
+        """
+        LocalInvocator.__init__(self, queryKey, command, userdir)
+        self._queueName=""
+        self._PBSparameters=[]
+        self._aFile=aFile
 
     def setParameters(self, invocatorParameters):
-	"""Set parameters of qsub
-	"""
-	self._queueName=invocatorParameters.queueName
-	self._PBSparameters=invocatorParameters.qsubParameters
-	
+        """Set parameters of qsub
+        """
+        self._queueName=invocatorParameters.queueName
+        self._PBSparameters=invocatorParameters.qsubParameters
+        
     def execute(self):
-	"""execute the command in a qsub script
-	"""
-	
-	#we write in the session directory a small script
-	fp=file(self.userdir+"/"+self.queryid+".sh","w")
-	fp.write("#!/bin/bash\n")
-	fp.write("#PBS -S /bin/bash\n")
-	fp.write("#PBS -o "+self.userdir+"/results-"+self.queryid+".out\n")
-	fp.write("#PBS -e "+self.userdir+"/"+self.queryid+".err\n")
-	fp.write("#PBS -q %s\n"%self._queueName)
-	fp.write("#PBS -l %s\n"%":".join(self._PBSparameters))
-	
-	#we add to the script the cd command in order to be in the session directory
-	fp.write("cd %s\n"%self.userdir)
-	fp.write("%s\n"%self.command)
-	fp.close()
-	
-	import os
-	
-	#execute the qsub command
-	i, o, e=os.popen3("qsub "+self.userdir+"/"+self.queryid+".sh")
-	
-	#see if there are mistakes
-	erl=e.read()
-	
-	if erl!="":
-	    raise Exception, "".join(erl)
+        """execute the command in a qsub script
+        """
+        
+        #we write in the session directory a small script
+        fp=file(self.userdir+"/"+self.queryid+".sh","w")
+        fp.write("#!/bin/bash\n")
+        fp.write("#PBS -S /bin/bash\n")
+        fp.write("#PBS -o "+self.userdir+"/results-"+self.queryid+".out\n")
+        fp.write("#PBS -e "+self.userdir+"/"+self.queryid+".err\n")
+        fp.write("#PBS -q %s\n"%self._queueName)
+        fp.write("#PBS -l %s\n"%":".join(self._PBSparameters))
+        
+        #we add to the script the cd command in order to be in the session directory
+        fp.write("cd %s\n"%self.userdir)
+        fp.write("%s\n"%self.command)
+        fp.close()
+        
+        import os
+        
+        #execute the qsub command
+        i, o, e=os.popen3("qsub "+self.userdir+"/"+self.queryid+".sh")
+        
+        #see if there are mistakes
+        erl=e.read()
+        
+        if erl!="":
+            raise Exception, "".join(erl)
 
-	#write in the session file the queries, qsub identifiers and the output files
-	orl=o.readlines()
+        #write in the session file the queries, qsub identifiers and the output files
+        orl=o.readlines()
         anId=orl[0].split('\n')[0]
 
-	if len(self.outputfiles) !=0:
-	    self._aFile.write(self.queryid+";"+anId+";"+"::".join(self.outputfiles)+"\n")
-	    os.mkdir(self.userdir+"/results-"+self.queryid)
-	    
-	del os
-	#return the qsub identifier
-	return anId
+        if len(self.outputfiles) !=0:
+            self._aFile.write(self.queryid+";"+anId+";"+"::".join(self.outputfiles)+"\n")
+            os.mkdir(self.userdir+"/results-"+self.queryid)
+            
+        del os
+        #return the qsub identifier
+        return anId
 
 class CGIPostMInvocator(GeneralInvocator):
     """Functions for multipart post
@@ -241,9 +241,9 @@
         files is a sequence of (name, filename, value) elements for data to be uploaded as files
         Return the server's response page.
         """
-	    
+            
         import httplib    
-	
+        
         content_type, body = self.encode_multipart_formdata()
         print content_type, body
         h = httplib.HTTP(host)
@@ -253,9 +253,9 @@
         h.endheaders()
         h.send(body)
         errcode, errmsg, headers = h.getreply()
-	    
+            
         del httplib
-	
+        
         return h.file.readlines()
 
     def encode_multipart_formdata(self):

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/webservice/TCBioMoby.py,v
retrieving revision 1.2
retrieving revision 1.3
diff -u -r1.2 -r1.3
--- /home/repository/moby/moby-live/Python/bioMoby/webservice/TCBioMoby.py	2005/01/18 13:46:24	1.2
+++ /home/repository/moby/moby-live/Python/bioMoby/webservice/TCBioMoby.py	2005/02/01 08:52:17	1.3
@@ -53,4 +53,4 @@
         from xml.dom.minidom import parseString
      
         print >>sw, '''<%s><![CDATA[%s]]></%s>''' % (self.tag, parseString(toReturn).toprettyxml(), self.tag)
-	
+        

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/webservice/__init__.py,v
retrieving revision 1.2
retrieving revision 1.3
diff -u -r1.2 -r1.3
--- /home/repository/moby/moby-live/Python/bioMoby/webservice/__init__.py	2005/01/18 13:46:24	1.2
+++ /home/repository/moby/moby-live/Python/bioMoby/webservice/__init__.py	2005/02/01 08:52:17	1.3
@@ -35,7 +35,7 @@
     l=filter(filterfunc, setOfParameters)
     
     if l:
-	return l[0]
+        return l[0]
 
     return 
     
@@ -56,6 +56,6 @@
     l=filter(filterfunc, setOfParameters)
     
     if l:
-	return l[0]
-	
+        return l[0]
+        
     return
\ No newline at end of file



From yanwong at pub.open-bio.org  Tue Feb  1 08:59:44 2005
From: yanwong at pub.open-bio.org (Yan Wong)
Date: Tue, 1 Feb 2005 03:59:44 -0500
Subject: [MOBY-guts] biomoby commit
Message-ID: <200502010859.j118xiLU013177@pub.open-bio.org>


yanwong
Tue Feb  1 03:59:44 EST 2005
Update of /home/repository/moby/moby-live/Python/utils/wx
In directory pub.open-bio.org:/tmp/cvs-serv13152

Modified Files:
	objectBrowser.py 
Log Message:


moby-live/Python/utils/wx objectBrowser.py,1.5,1.6
===================================================================
RCS file: /home/repository/moby/moby-live/Python/utils/wx/objectBrowser.py,v
retrieving revision 1.5
retrieving revision 1.6
diff -u -r1.5 -r1.6
--- /home/repository/moby/moby-live/Python/utils/wx/objectBrowser.py	2005/01/27 08:44:06	1.5
+++ /home/repository/moby/moby-live/Python/utils/wx/objectBrowser.py	2005/02/01 08:59:44	1.6
@@ -65,7 +65,7 @@
                 obj=obj[len(obj)-1]
             else:
                 obj="None"
-	    
+        
             if obj in self._ISARelations:
                 self._ISARelations[obj].append(objectName)
             else:
@@ -102,7 +102,7 @@
 
         self.staticText1 = wxStaticText(id=wxID_WXFRAME1STATICTEXT1,
               label='Description', name='staticText1', parent=self.panel1,
-              pos=wxPoint(16, 0), size=wxSize(64, 16), style=0)
+              pos=wxPoint(16, 0), size=wxSize(70, 16), style=0)
 
         self.textCtrl1 = wxTextCtrl(id=wxID_WXFRAME1TEXTCTRL1, name='textCtrl1',
               parent=self.panel1, pos=wxPoint(16, 16), size=wxSize(400, 56),
@@ -110,7 +110,7 @@
 
         self.staticText2 = wxStaticText(id=wxID_WXFRAME1STATICTEXT2,
               label='Contact Email', name='staticText2', parent=self.panel1,
-              pos=wxPoint(16, 80), size=wxSize(80, 16), style=0)
+              pos=wxPoint(16, 80), size=wxSize(90, 16), style=0)
 
         self.textCtrl2 = wxTextCtrl(id=wxID_WXFRAME1TEXTCTRL2, name='textCtrl2',
               parent=self.panel1, pos=wxPoint(16, 96), size=wxSize(400, 22),
@@ -118,7 +118,7 @@
 
         self.staticText3 = wxStaticText(id=wxID_WXFRAME1STATICTEXT3,
               label='Authority URI', name='staticText3', parent=self.panel1,
-              pos=wxPoint(16, 128), size=wxSize(80, 16), style=0)
+              pos=wxPoint(16, 128), size=wxSize(90, 16), style=0)
 
         self.textCtrl3 = wxTextCtrl(id=wxID_WXFRAME1TEXTCTRL3, name='textCtrl3',
               parent=self.panel1, pos=wxPoint(16, 144), size=wxSize(400, 24),
@@ -126,7 +126,7 @@
 
         self.staticText4 = wxStaticText(id=wxID_WXFRAME1STATICTEXT4,
               label='HAS', name='staticText4', parent=self.panel1,
-              pos=wxPoint(16, 184), size=wxSize(32, 16), style=0)
+              pos=wxPoint(16, 184), size=wxSize(40, 16), style=0)
 
         self.listBox1 = wxListBox(choices=[], id=wxID_WXFRAME1LISTBOX1,
               name='listBox1', parent=self.panel1, pos=wxPoint(16, 200),
@@ -134,7 +134,7 @@
 
         self.staticText5 = wxStaticText(id=wxID_WXFRAME1STATICTEXT5,
               label='HASA', name='staticText5', parent=self.panel1,
-              pos=wxPoint(16, 264), size=wxSize(56, 16), style=0)
+              pos=wxPoint(16, 264), size=wxSize(60, 16), style=0)
 
         self.listBox2 = wxListBox(choices=[], id=wxID_WXFRAME1LISTBOX2,
               name='listBox2', parent=self.panel1, pos=wxPoint(16, 280),
@@ -143,7 +143,7 @@
         self.staticText6 = wxStaticText(id=wxID_WXFRAME1STATICTEXT6,
               label='Services that take this data type as input:',
               name='staticText6', parent=self.panel1, pos=wxPoint(16, 352),
-              size=wxSize(230, 16), style=0)
+              size=wxSize(250, 16), style=0)
 
         self.listBox3 = wxListBox(choices=[], id=wxID_WXFRAME1LISTBOX3,
               name='listBox3', parent=self.panel1, pos=wxPoint(16, 368),
@@ -156,15 +156,15 @@
 
         self.staticText7 = wxStaticText(id=wxID_WXFRAME1STATICTEXT7,
               label='URL', name='staticText7', parent=self, pos=wxPoint(8, 16),
-              size=wxSize(24, 16), style=0)
+              size=wxSize(30, 16), style=0)
 
         self.staticText8 = wxStaticText(id=wxID_WXFRAME1STATICTEXT8, label='NS',
               name='staticText8', parent=self, pos=wxPoint(8, 56),
-              size=wxSize(16, 16), style=0)
+              size=wxSize(20, 16), style=0)
 
         self.button2 = wxButton(id=wxID_WXFRAME1BUTTON2,
               label='Retrieve objects', name='button2', parent=self,
-              pos=wxPoint(8, 136), size=wxSize(120, 22), style=0)
+              pos=wxPoint(8, 136), size=wxSize(120, 24), style=0)
         EVT_BUTTON(self.button2, wxID_WXFRAME1BUTTON2, self.OnButton2Button)
 
         self.gauge1 = wxGauge(id=wxID_WXFRAME1GAUGE1, name='gauge1',
@@ -174,7 +174,7 @@
         self.staticText9 = wxStaticText(id=wxID_WXFRAME1STATICTEXT9,
               label='Services that take this data type as output:',
               name='staticText9', parent=self.panel1, pos=wxPoint(16, 440),
-              size=wxSize(237, 16), style=0)
+              size=wxSize(260, 16), style=0)
 
         self.listBox4 = wxListBox(choices=[], id=wxID_WXFRAME1LISTBOX4,
               name='listBox4', parent=self.panel1, pos=wxPoint(16, 456),
@@ -194,7 +194,7 @@
 
         self.checkBox1 = wxCheckBox(id=wxID_WXFRAME1CHECKBOX1,
               label='Fetch data from cache (if there is any)', name='checkBox1',
-              parent=self, pos=wxPoint(8, 104), size=wxSize(248, 24), style=0)
+              parent=self, pos=wxPoint(8, 104), size=wxSize(260, 24), style=0)
         self.checkBox1.SetValue(False)
 
     def __init__(self, parent):



From yanwong at pub.open-bio.org  Tue Feb  1 11:25:53 2005
From: yanwong at pub.open-bio.org (Yan Wong)
Date: Tue, 1 Feb 2005 06:25:53 -0500
Subject: [MOBY-guts] biomoby commit
Message-ID: <200502011125.j11BPrpK013895@pub.open-bio.org>


yanwong
Tue Feb  1 06:25:53 EST 2005
Update of /home/repository/moby/moby-live/Python/bioMoby
In directory pub.open-bio.org:/tmp/cvs-serv13870

Modified Files:
	mobyDataTypes.py 
Log Message:


moby-live/Python/bioMoby mobyDataTypes.py,1.6,1.7
===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/mobyDataTypes.py,v
retrieving revision 1.6
retrieving revision 1.7
diff -u -r1.6 -r1.7
--- /home/repository/moby/moby-live/Python/bioMoby/mobyDataTypes.py	2005/02/01 08:52:15	1.6
+++ /home/repository/moby/moby-live/Python/bioMoby/mobyDataTypes.py	2005/02/01 11:25:53	1.7
@@ -149,7 +149,7 @@
         #Put the raw content of the object
         #If you want to put your special object, then then you should write 
         #a __str__ method
-        if hasattr(self, "content") and self.content:
+        if hasattr(self, "content") and self.content!=none and self.content!="":
             result.append("%s"%(self.content))
         
         result.append("</%s:%s>"%(self.__prefix__, self.__tag__))



From yanwong at pub.open-bio.org  Tue Feb  1 11:31:22 2005
From: yanwong at pub.open-bio.org (Yan Wong)
Date: Tue, 1 Feb 2005 06:31:22 -0500
Subject: [MOBY-guts] biomoby commit
Message-ID: <200502011131.j11BVMog013947@pub.open-bio.org>


yanwong
Tue Feb  1 06:31:22 EST 2005
Update of /home/repository/moby/moby-live/Python/bioMoby
In directory pub.open-bio.org:/tmp/cvs-serv13922

Modified Files:
	mobyDataTypes.py 
Log Message:


moby-live/Python/bioMoby mobyDataTypes.py,1.7,1.8
===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/mobyDataTypes.py,v
retrieving revision 1.7
retrieving revision 1.8
diff -u -r1.7 -r1.8
--- /home/repository/moby/moby-live/Python/bioMoby/mobyDataTypes.py	2005/02/01 11:25:53	1.7
+++ /home/repository/moby/moby-live/Python/bioMoby/mobyDataTypes.py	2005/02/01 11:31:22	1.8
@@ -149,7 +149,7 @@
         #Put the raw content of the object
         #If you want to put your special object, then then you should write 
         #a __str__ method
-        if hasattr(self, "content") and self.content!=none and self.content!="":
+        if hasattr(self, "content") and self.content!=None and self.content!="":
             result.append("%s"%(self.content))
         
         result.append("</%s:%s>"%(self.__prefix__, self.__tag__))



From yanwong at pub.open-bio.org  Tue Feb  1 14:20:46 2005
From: yanwong at pub.open-bio.org (Yan Wong)
Date: Tue, 1 Feb 2005 09:20:46 -0500
Subject: [MOBY-guts] biomoby commit
Message-ID: <200502011420.j11EKkG9014847@pub.open-bio.org>


yanwong
Tue Feb  1 09:20:46 EST 2005
Update of /home/repository/moby/moby-live/Python/utils
In directory pub.open-bio.org:/tmp/cvs-serv14364/utils

Modified Files:
	moby2python.py 
Log Message:


moby-live/Python/utils moby2python.py,1.4,1.5
===================================================================
RCS file: /home/repository/moby/moby-live/Python/utils/moby2python.py,v
retrieving revision 1.4
retrieving revision 1.5
diff -u -r1.4 -r1.5
--- /home/repository/moby/moby-live/Python/utils/moby2python.py	2005/01/18 13:44:04	1.4
+++ /home/repository/moby/moby-live/Python/utils/moby2python.py	2005/02/01 14:20:46	1.5
@@ -53,7 +53,9 @@
     res=["    def fromMoby(self, value):\n"]
     res.append("        \"\"\" Load the attributes from an XML string\n        \"\"\"")
     res.append("        from bioMoby.mobyMarshal import MobyUnmarshaller")
-    res.append("        doc=parseString(value).firstChild")
+    res.append("        doc=value")
+    res.append("        if isinstance(value, str):")
+    res.append("            doc=parseString(value).firstChild")
     res.append("        um=MobyUnmarshaller()")
     res.append("        self.content=\"\"")
     
@@ -83,7 +85,7 @@
     res.append("            if elt.nodeName==\"CrossReference\" or elt.nodeName==\"moby:CrossReference\":")
     res.append("                self.__cross__=[]")
     res.append("                for ref in elt.childNodes:")
-    res.append("                    self.__cross__.append(ref.toxml())")        
+    res.append("                    self.__cross__.append(um.loads(ref))")        
 
 
     for parameter in parameters:
@@ -92,7 +94,7 @@
             
             if parameter[2]=='Integer' or parameter[2]=='Float' or parameter[2]=='String':
                 res.append("                t="+makeMobyName(parameter[2])+"()")
-                res.append("                t.fromMoby(elt.toxml())")
+                res.append("                t.fromMoby(elt)")
                 if parameter[1]!="[]":
                     res.append("                self."+cleanName(parameter[0])+"=t.content")
                 else:
@@ -100,7 +102,7 @@
                     
             elif parameter[0]!='content':
                 res.append("                self."+cleanName(parameter[0])+"="+makeMobyName(parameter[2])+"()")
-                res.append("                self."+cleanName(parameter[0])+".fromMoby(elt.toxml())")
+                res.append("                self."+cleanName(parameter[0])+".fromMoby(elt)")
                     
     return "\n".join(res)
 
@@ -133,7 +135,7 @@
 
         if ancestor not in paramDict.keys():
             makeInterface(ancestor, path)
-	
+    
         for aProp in getPropertiesFromAncestor(ancestor):
             properties.append(aProp)
    
@@ -150,7 +152,7 @@
                 
             properties.append((articleName,"None",articleType))
 
-	    
+        
     if "HAS" in objectDefinition["Relationship"].keys():
         for hasRelationship in objectDefinition["Relationship"]["HAS"]:
             articleName=hasRelationship[0]
@@ -197,9 +199,9 @@
         pyResult.append("class "+mObjectName+":\n")
 
     if "Description" in objectDefinition:
-	description=objectDefinition["Description"]
+        description=objectDefinition["Description"]
     if "authURI" in objectDefinition:
-	author=objectDefinition["authURI"]
+        author=objectDefinition["authURI"]
     if "contactEmail" in objectDefinition:
         contact=objectDefinition["contactEmail"]
     



From yanwong at pub.open-bio.org  Tue Feb  1 14:20:44 2005
From: yanwong at pub.open-bio.org (Yan Wong)
Date: Tue, 1 Feb 2005 09:20:44 -0500
Subject: [MOBY-guts] biomoby commit
Message-ID: <200502011420.j11EKi83014390@pub.open-bio.org>


yanwong
Tue Feb  1 09:20:44 EST 2005
Update of /home/repository/moby/moby-live/Python/bioMoby
In directory pub.open-bio.org:/tmp/cvs-serv14364/bioMoby

Modified Files:
	mobyDataTypes.py 
Log Message:


moby-live/Python/bioMoby mobyDataTypes.py,1.8,1.9
===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/mobyDataTypes.py,v
retrieving revision 1.8
retrieving revision 1.9
diff -u -r1.8 -r1.9
--- /home/repository/moby/moby-live/Python/bioMoby/mobyDataTypes.py	2005/02/01 11:31:22	1.8
+++ /home/repository/moby/moby-live/Python/bioMoby/mobyDataTypes.py	2005/02/01 14:20:44	1.9
@@ -209,10 +209,10 @@
                     #if there is already an object, then store it inside a list and 
                     #append the other objects in the list 
                     if hasattr(self, associatedObjectName):
-                        if type(getattr(self, associatedObjectName)) is list:
+                        if isinstance(getattr(self, associatedObjectName), list):
                             getattr(self, associatedObjectName).append(o)
                         else:
-                            setattr(self, associatedObjectName, [o])
+                            setattr(self, associatedObjectName, o)
                     else:
                         setattr(self, associatedObjectName, o)
             else:



From yanwong at pub.open-bio.org  Tue Feb  1 14:33:49 2005
From: yanwong at pub.open-bio.org (Yan Wong)
Date: Tue, 1 Feb 2005 09:33:49 -0500
Subject: [MOBY-guts] biomoby commit
Message-ID: <200502011433.j11EXn74014904@pub.open-bio.org>


yanwong
Tue Feb  1 09:33:49 EST 2005
Update of /home/repository/moby/moby-live/Python/bioMoby
In directory pub.open-bio.org:/tmp/cvs-serv14879/bioMoby

Modified Files:
	mobyDataTypes.py 
Log Message:


moby-live/Python/bioMoby mobyDataTypes.py,1.9,1.10
===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/mobyDataTypes.py,v
retrieving revision 1.9
retrieving revision 1.10
diff -u -r1.9 -r1.10
--- /home/repository/moby/moby-live/Python/bioMoby/mobyDataTypes.py	2005/02/01 14:20:44	1.9
+++ /home/repository/moby/moby-live/Python/bioMoby/mobyDataTypes.py	2005/02/01 14:33:49	1.10
@@ -107,7 +107,7 @@
         mobyObjects=filter(filterFunc, dir(self))
         
         #If none, return the tag closed
-        if len(mobyObjects)==0 and (not hasattr(self, "__cross__") or len(self.__cross__)==0) and (not hasattr(self, "__PIB__") or len(self.__PIB__)==0) and (not hasattr(self, "content") or not self.content):
+        if len(mobyObjects)==0 and (not hasattr(self, "__cross__") or len(self.__cross__)==0) and (not hasattr(self, "__PIB__") or len(self.__PIB__)==0) and (not hasattr(self, "content") or self.content==None or self.content==""):
             beginTag.append("/>")
             return " ".join(beginTag)
 



From yanwong at pub.open-bio.org  Wed Feb  2 15:08:34 2005
From: yanwong at pub.open-bio.org (Yan Wong)
Date: Wed, 2 Feb 2005 10:08:34 -0500
Subject: [MOBY-guts] biomoby commit
Message-ID: <200502021508.j12F8YLi020349@pub.open-bio.org>


yanwong
Wed Feb  2 10:08:34 EST 2005
Update of /home/repository/moby/moby-live/Python/bioMoby/ontology
In directory pub.open-bio.org:/tmp/cvs-serv20328

Added Files:
	MSF.py 
Log Message:


moby-live/Python/bioMoby/ontology MSF.py,NONE,1.1


From yanwong at pub.open-bio.org  Wed Feb  2 15:18:06 2005
From: yanwong at pub.open-bio.org (Yan Wong)
Date: Wed, 2 Feb 2005 10:18:06 -0500
Subject: [MOBY-guts] biomoby commit
Message-ID: <200502021518.j12FI6DL020441@pub.open-bio.org>


yanwong
Wed Feb  2 10:18:06 EST 2005
Update of /home/repository/moby/moby-live/Python/bioMoby/ontology
In directory pub.open-bio.org:/tmp/cvs-serv20420

Added Files:
	Alignment.py 
Log Message:


moby-live/Python/bioMoby/ontology Alignment.py,NONE,1.1


From yanwong at pub.open-bio.org  Wed Feb  2 15:20:55 2005
From: yanwong at pub.open-bio.org (Yan Wong)
Date: Wed, 2 Feb 2005 10:20:55 -0500
Subject: [MOBY-guts] biomoby commit
Message-ID: <200502021520.j12FKtBS020499@pub.open-bio.org>


yanwong
Wed Feb  2 10:20:55 EST 2005
Update of /home/repository/moby/moby-live/Python/bioMoby/ontology
In directory pub.open-bio.org:/tmp/cvs-serv20478

Added Files:
	FASTA_NA_multi.py Gene_Expression_data.py 
Log Message:


moby-live/Python/bioMoby/ontology FASTA_NA_multi.py,NONE,1.1 Gene_Expression_data.py,NONE,1.1


From kawas at pub.open-bio.org  Wed Feb  2 16:49:18 2005
From: kawas at pub.open-bio.org (Eddie Kawas)
Date: Wed, 2 Feb 2005 11:49:18 -0500
Subject: [MOBY-guts] biomoby commit
Message-ID: <200502021649.j12GnHCr020760@pub.open-bio.org>


kawas
Wed Feb  2 11:49:17 EST 2005
Update of /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/gui/objectCreationTool
In directory pub.open-bio.org:/tmp/cvs-serv20735/org/biomoby/client/gui/objectCreationTool

Modified Files:
	Construct.java 
Log Message:
Changed the declaration that creates an empty rdf model. Hopefully helps get rid of the logging issues.

moby-live/Java/src/main/org/biomoby/client/gui/objectCreationTool Construct.java,1.1,1.2
===================================================================
RCS file: /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/gui/objectCreationTool/Construct.java,v
retrieving revision 1.1
retrieving revision 1.2
diff -u -r1.1 -r1.2
--- /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/gui/objectCreationTool/Construct.java	2004/09/27 22:15:13	1.1
+++ /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/gui/objectCreationTool/Construct.java	2005/02/02 16:49:17	1.2
@@ -8,6 +8,7 @@
 
 import com.hp.hpl.jena.mem.ModelMem;
 import com.hp.hpl.jena.rdf.model.Model;
+import com.hp.hpl.jena.rdf.model.ModelFactory;
 import com.hp.hpl.jena.rdf.model.Statement;
 import com.hp.hpl.jena.rdf.model.StmtIterator;
 
@@ -52,7 +53,7 @@
 		HashMap homes = new HashMap(); // (key=parent,val=household)
 		try {
 			// create an empty model
-			Model model = new ModelMem();
+			Model model = ModelFactory.createDefaultModel();
 
 			InputStream in =
 				new URL(url)



From yanwong at pub.open-bio.org  Wed Feb  2 16:52:31 2005
From: yanwong at pub.open-bio.org (Yan Wong)
Date: Wed, 2 Feb 2005 11:52:31 -0500
Subject: [MOBY-guts] biomoby commit
Message-ID: <200502021652.j12GqVgK020799@pub.open-bio.org>


yanwong
Wed Feb  2 11:52:31 EST 2005
Update of /home/repository/moby/moby-live/Python/bioMoby
In directory pub.open-bio.org:/tmp/cvs-serv20774

Modified Files:
	mobyDataTypes.py 
Log Message:


moby-live/Python/bioMoby mobyDataTypes.py,1.10,1.11
===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/mobyDataTypes.py,v
retrieving revision 1.10
retrieving revision 1.11
diff -u -r1.10 -r1.11
--- /home/repository/moby/moby-live/Python/bioMoby/mobyDataTypes.py	2005/02/01 14:33:49	1.10
+++ /home/repository/moby/moby-live/Python/bioMoby/mobyDataTypes.py	2005/02/02 16:52:31	1.11
@@ -87,7 +87,7 @@
         
         self.content=content
         
-                
+    
     def toMoby(self):
         """Deserializes the content in XML api
         """
@@ -98,7 +98,7 @@
         for attribute in __ATTRIBUTES__:
             if hasattr(self, attribute) and getattr(self, attribute):
                 beginTag.append("%s:%s=\"%s\""%(self.__prefix__, attribute, getattr(self,attribute)))
-
+            
         #Retrieve only object's attributes that are public.
         filterFunc=lambda x: x[0] != "_" and not callable(getattr(self, x)) and x !="content" and x not in __ATTRIBUTES__
         
@@ -107,13 +107,13 @@
         mobyObjects=filter(filterFunc, dir(self))
         
         #If none, return the tag closed
-        if len(mobyObjects)==0 and (not hasattr(self, "__cross__") or len(self.__cross__)==0) and (not hasattr(self, "__PIB__") or len(self.__PIB__)==0) and (not hasattr(self, "content") or self.content==None or self.content==""):
+        if len(mobyObjects)==0 and (not hasattr(self, "__cross__") or len(self.__cross__)==0) and (not hasattr(self, "__PIB__") or len(self.__PIB__)==0) and (not hasattr(self, "content") or self.content is None or self.content==""):
             beginTag.append("/>")
             return " ".join(beginTag)
-
+        
         #Else, end begin tag and serialize the associated objects
         beginTag.append(">")
-
+        
         result=[" ".join(beginTag)]
         
         #Serialize Cross references
@@ -162,8 +162,8 @@
         elem=xml
         
         if isinstance(xml, str):
-            doc=parseString(xmlstring)
-        
+            doc=parseString(xml)
+            
             elem=doc.firstChild
         
         self.__tag__=elem.localName
@@ -195,10 +195,10 @@
                 else:
                     #Do the same for the other objects
                     associatedObjectName=child.getAttribute("moby:articleName")
-                
+                    
                     if not associatedObjectName:
                         associatedObjectName=child.getAttribute("articleName")
-                
+                        
                     if not associatedObjectName:
                         associatedObjectName="associated"
                     
@@ -252,7 +252,7 @@
         doc=xml
         
         uri=doc.namespaceURI
-    
+        
         MobyObject.fromMoby(self, doc)
         
         self.authURI=doc.getAttributeNS(uri, "authURI")
@@ -260,7 +260,6 @@
         self.evidenceCode=doc.getAttributeNS(uri, "evidenceCode")
         self.xrefType=doc.getAttributeNS(uri, "xrefType")
 
-        
 class MobyInteger(MobyObject):
     """Use this object to serialize/deserialize integers
     """
@@ -311,30 +310,30 @@
         """
         from mobyMarshal import MobyMarshaller
         m=MobyMarshaller()        
-
+        
         result=['<?xml version="1.0" encoding="UTF-8"?><moby:MOBY xmlns:moby="http://www.biomoby.org/moby"><moby:mobyContent']
-                
+        
         if self.authority !="":
             result.append(' moby:authority="'+self.authority+'"')
-                    
+        
         result.append('>')
-                    
+        
         if self.servicenotes !="":
             result.append('<moby:serviceNotes>'+self.servicenotes+'</moby:serviceNotes>')
-
+        
         for queryKey in self.queryData:
             result.append("<moby:mobyData moby:queryID='"+queryKey+"'>")
-
+            
             #For serialization, use the MobyMarshaller object
             
             for queryObject in self.queryData[queryKey]:
                 #if the Collection ('CollectionName',[MobyObjects])
                 if queryObject.__class__ is tuple:
                     result.append("<moby:Collection moby:articleName='"+queryObject[0]+"'>")
-
+                    
                     for aSimple in queryObject[1]:
                         result.append('<moby:Simple>'+m.dumps(aSimple)+'</moby:Simple>')
-                    
+                        
                     result.append("</moby:Collection>")
                 #If it is a parameter
                 elif queryObject.__class__ is Parameter:
@@ -342,13 +341,13 @@
                 #Or a simple object
                 else: 
                     result.append("<moby:Simple>"+m.dumps(queryObject)+"</moby:Simple>")
-
+                
             result.append("</moby:mobyData>")
-
+            
         result.append('</moby:mobyContent></moby:MOBY>')
-
+        
         del MobyMarshaller
-
+        
         return "".join(result)
 
     def fromMoby(self, xmlObject):
@@ -357,7 +356,7 @@
         from bioMoby import MobyUnmarshaller
         
         um=MobyUnmarshaller()
-
+        
         self.queryData={}
         
         doc=xmlObject
@@ -366,35 +365,35 @@
             doc=parseString(xmlObject)
         
         mdl=doc.getElementsByTagName('mobyData')
-
+        
         if not mdl:
             mdl=doc.getElementsByTagName('moby:mobyData')
-
+        
         #For each query            
         for elt in mdl:
             #Get the ID
             queryID=str(elt.getAttribute('queryID'))
-
+            
             if not queryID:
                 queryID=str(elt.getAttribute('moby:queryID'))
-
+            
             #Collect the data
             data=[]
-
+            
             #for each datum translate it in MobyObject, and put it in the list
             for datum in elt.childNodes:
                 #If it is a collection
                 if datum.nodeType==datum.ELEMENT_NODE and datum.localName=="Collection":
                     articleName=datum.getAttribute('moby:articleName')
-        
+                    
                     articles=[]
-        
+                    
                     for article in datum.childNodes:
                         if article.nodeType==article.ELEMENT_NODE and article.localName=="Simple":
                             for child in article.childNodes:
                                 if child.nodeType==child.ELEMENT_NODE:
                                     articles.append(um.loadn(child))
-
+                                    
                     data.append((articleName, articles))
                 #if it is a Simple object
                 elif datum.nodeType==datum.ELEMENT_NODE and datum.localName=="Simple":
@@ -442,7 +441,6 @@
             queries["%s-%s"%(queryName, queryID)]=aSimple
             
         return queries
-                
         
     def getObject(self, queryName, objectName):
         """Get an object from a query with its name
@@ -451,8 +449,7 @@
         
         for obj in filter(filterfunc, self.queryData[queryName]):
             return obj
-
-                
+            
     def getObjects(self, queryName):
         """Retrieve objects from a query
         """
@@ -470,7 +467,7 @@
             result[param.articleName]=param.value
                 
         return result
-
+        
     def getParameter(self, queryName, parameterName):
         """Retrieve a parameter from a query and his name
         """
@@ -484,4 +481,4 @@
     def __repr__(self):
         """put the xml of the Content
         """
-        return self.__str__()
+        return self.__str__()
\ No newline at end of file



From gordonp at pub.open-bio.org  Thu Feb  3 22:37:31 2005
From: gordonp at pub.open-bio.org (Paul Gordon)
Date: Thu, 3 Feb 2005 17:37:31 -0500
Subject: [MOBY-guts] biomoby commit
Message-ID: <200502032237.j13MbV1o027017@pub.open-bio.org>


gordonp
Thu Feb  3 17:37:30 EST 2005
Update of /home/repository/moby/moby-live/Java/src/main/org/biomoby/client
In directory pub.open-bio.org:/tmp/cvs-serv26992

Modified Files:
	MobyRequest.java 
Log Message:
Updated response Vector creation to fix spurious Java array run-time type safety check issues

moby-live/Java/src/main/org/biomoby/client MobyRequest.java,1.5,1.6
===================================================================
RCS file: /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/MobyRequest.java,v
retrieving revision 1.5
retrieving revision 1.6
diff -u -r1.5 -r1.6
--- /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/MobyRequest.java	2004/09/03 20:28:16	1.5
+++ /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/MobyRequest.java	2005/02/03 22:37:30	1.6
@@ -206,6 +206,8 @@
     }
 
     /**
+     * @return a vector of MobyDataInstance[], each element of the vector is the collection of response objects for the correspondingly indexed input request.
+     *
      * @throws MobyException if you try to get the results before calling InvokeService
      */
     public Vector getOutput() throws MobyException{
@@ -679,7 +681,8 @@
 
 	    // What we're building is a Vector, where each element represents
 	    // a Response's DataInstance Output (i.e. Simple and Collection return values)
-	    responsesOutput.add(out.toArray());
+            MobyDataInstance[] mdis = new MobyDataInstance[out.size()];
+	    responsesOutput.add(out.toArray(mdis));
 
 	    releaseXPath(response);
 	}



From yanwong at pub.open-bio.org  Fri Feb  4 12:58:25 2005
From: yanwong at pub.open-bio.org (Yan Wong)
Date: Fri, 4 Feb 2005 07:58:25 -0500
Subject: [MOBY-guts] biomoby commit
Message-ID: <200502041258.j14CwPFg029623@pub.open-bio.org>


yanwong
Fri Feb  4 07:58:24 EST 2005
Update of /home/repository/moby/moby-live/Python/bioMoby/webservice
In directory pub.open-bio.org:/tmp/cvs-serv29563/webservice

Modified Files:
	Dispatcher.py 
Log Message:


moby-live/Python/bioMoby/webservice Dispatcher.py,1.3,1.4
===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/webservice/Dispatcher.py,v
retrieving revision 1.3
retrieving revision 1.4
diff -u -r1.3 -r1.4
--- /home/repository/moby/moby-live/Python/bioMoby/webservice/Dispatcher.py	2005/02/01 08:52:17	1.3
+++ /home/repository/moby/moby-live/Python/bioMoby/webservice/Dispatcher.py	2005/02/04 12:58:24	1.4
@@ -88,9 +88,9 @@
             formatter: a function that transforms raw results from the Invocator into Moby Objects
             workdir: the session directory
         """
-
+        
         from bioMoby import MobyUnmarshaller
-
+        
         self._isbase64=False
         self._workdir=workdir
         self.answers={}
@@ -105,7 +105,7 @@
                 #Do some cleaning on the XML Document before proceeding...
                 #Remove all \t|\n from the <a>\n\t</a>
                 um=MobyUnmarshaller()
-
+                
                 r=re.compile("\>[\n|\t]+\<")
                 mc=um.loads("><".join(r.split(mobyContentXML)))
             except:
@@ -114,7 +114,7 @@
                     self._isbase64=True
                 except binascii.Error:
                     raise  EDispatchError, "Invalid types in the moby Content object"
-
+        
         self.queryData=mc.queryData
         self.invocator=Invocator
         self._invocatorParameters=invocatorParameters
@@ -137,7 +137,7 @@
             return base64.encodestring(str(MobyContent(self.answers)))
         
         return str(MobyContent(self.answers))
-
+        
         
 class SimpleDispatcher(AbstractDispatcher):
     """ A simple dispatcher execute sequentially the treatments
@@ -167,14 +167,14 @@
         #Clean the session directory
         os.chdir(self._workdir)
         shutil.rmtree(self._workdir+"/session"+self._sessionid)
-            
+    
     def _fetchAnswers(self):
         """ Fetch the answers and clean the session directory
         """
         from bioMoby import GeneralInvocator
         
         answers={}
-
+        
         ruserdir="session"+self._sessionid
         try:
             l=os.listdir(self._workdir+"/"+ruserdir)
@@ -188,7 +188,7 @@
                     aQueryName=querykey[8:]
                     gi=GeneralInvocator(aQueryName ,userdir=self._workdir+"/"+ruserdir)
                     answers[aQueryName]=[gi.getResults()]
-
+                    
                     if self.formatter != None:
                         answers[aQueryName]=self.formatter(answers[aQueryName][0])
                         
@@ -196,13 +196,13 @@
                 self.answers=answers
                 
                 self._clean()        
-
+        
         del GeneralInvocator
-                
+    
     def execute(self):
         """Execute the queries sequentially
         """
-
+        
         try:
             for key in self.queryData.keys():
                 query=self.queryData[key]
@@ -229,7 +229,7 @@
         """ Execute a single query, store the result in the answers attribute
         """
         from bioMoby import MobyString
-
+        
         query=self.queryData[queryKey]
         
         #Execute the query
@@ -247,8 +247,7 @@
             
             self.answers['JOBSESSION']=[MobyString(content=sio.getvalue())]
             self._clean()
-
-
+        
         del MobyString
 
     
@@ -261,14 +260,13 @@
             mt=MultiThread(self._execute, self.queryData.keys())
             mt.start()
             mt.join()
-
+            
             self._fetchAnswers()
         except:
             self._clean()
-            
+        
         return self._toMoby()
 
-        
 class PBSDispatcher(SimpleDispatcher):
     """Dispatcher for PBS jobs
     """
@@ -306,10 +304,10 @@
             queryKeys.append(qk)
             #get the associated Outputfiles
             outputfiles[qk]=queryInformation.split(";")[2].split("::")
-
+            
             #Do a qstat and check if the job is still running or on queue
             i, o, e = os.popen3("qstat %s"%qsubId)
-
+            
             orl=o.readlines()
             erl=e.readlines()
             
@@ -330,13 +328,13 @@
                 fp=file(tdir+"/results-"+querykey+".out")
                 s=fp.readlines()
                 fp.close()
-
+                
                 if len(s)==0:
                     os.remove(tdir+"/results-"+querykey+".out")
                 else:
                     if len(outputfiles.keys())>0:
                         shutil.copy(tdir+"/results-"+querykey+".out", tdir+"/results-"+querykey+"/results.out")
-
+            
             for f in outputfiles[querykey]:
                 ruserdir=tdir+"/results-"+querykey
                 # if it is a file then retrieve the file
@@ -350,7 +348,7 @@
                         shutil.copy(f+"/"+fs, ruserdir+"/"+fs)
                         os.remove(f+"/"+fs)
                     os.removedirs(f)
-
+        
         #retrieve all the results
         try:
             l=os.listdir(tdir)
@@ -363,7 +361,7 @@
                     aQueryName=querykey[8:]
                     gi=GeneralInvocator(aQueryName, userdir=tdir)
                     answers[aQueryName]=[gi.getResults()]
-
+                    
                     if self.formatter != None:
                         answers[aQueryName]=self.formatter(answers[aQueryName][0])
                         
@@ -374,14 +372,13 @@
         
         del GeneralInvocator
 
-        
     def execute(self):
         """Execute the command in a PBS script using the PBSInvocator
         """
-
+        
         if 'JOBSESSION' in self.queryData.keys():
             self.answers=self.queryData
-
+            
             self._getResults()
         else:
             #we need to store informations in a file
@@ -393,7 +390,7 @@
                 r.setParameters(self._invocatorParameters)
                 r.execute()
             fp.close()
-
+        
         return self._toMoby()
 
 class Dispatcher(SimpleDispatcher):
@@ -422,7 +419,7 @@
         """ Execute a single query, store the result in the answers attribute
         """
         from bioMoby import MobyString
-
+        
         query=self.queryData[queryKey]
         
         #Execute the query
@@ -437,7 +434,7 @@
             fp.write("The query: "+queryKey+" has not been processed")
             traceback.print_exc(file=fp)
             fp.close()
-
+        
         del MobyString
 
     def _getSem(self):
@@ -445,14 +442,14 @@
             #Wait for answers of all queries
             self._sem.wait()
             self._fetchAnswers()
-
+            
             #Remove the IPC
             import pyipc
             pyipc.removeIPC(self._sem)
             del pyipc
         except:
             pass
-        
+    
     def execute(self, timeout=120):
         """Execute the queries with a pool of threads, store the results in a mobyContent Object
         """
@@ -461,11 +458,11 @@
         #Do a fetchAnswers if the user has a sessionid
         if 'JOBSESSION' in self.queryData.keys():
             self.answers=self.queryData
-
+            
             t=threading.Thread(target=self._getSem)
             t.start()
             t.join(timeout)
-
+            
             return self._toMoby()
         else:
             #A MobyContent without jobsession id has been received
@@ -474,14 +471,14 @@
                 pid=os.fork()
             except:
                 raise Exception, "Cannot treat any further request, please retry"
-
+            
             if pid>0:
                 #try to get the results
 #                os.wait()
                 t=threading.Thread(target=self._getSem)
                 t.start()
                 t.join(timeout)
-
+                
                 return self._toMoby()
             else:
                 #do second fork
@@ -506,7 +503,7 @@
                         mt.join()
                     except:
                         self._clean()
-
+                    
                     try:
                         self._sem.signal()
                     finally:



From yanwong at pub.open-bio.org  Fri Feb  4 12:58:25 2005
From: yanwong at pub.open-bio.org (Yan Wong)
Date: Fri, 4 Feb 2005 07:58:25 -0500
Subject: [MOBY-guts] biomoby commit
Message-ID: <200502041258.j14CwPk7029604@pub.open-bio.org>


yanwong
Fri Feb  4 07:58:24 EST 2005
Update of /home/repository/moby/moby-live/Python/bioMoby
In directory pub.open-bio.org:/tmp/cvs-serv29563

Modified Files:
	mobyClient.py mobyDataTypes.py mobyMarshal.py mobyRegister.py 
	mobyService.py 
Log Message:


moby-live/Python/bioMoby mobyClient.py,1.3,1.4 mobyDataTypes.py,1.11,1.12 mobyMarshal.py,1.4,1.5 mobyRegister.py,1.3,1.4 mobyService.py,1.3,1.4
===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/mobyClient.py,v
retrieving revision 1.3
retrieving revision 1.4
diff -u -r1.3 -r1.4
--- /home/repository/moby/moby-live/Python/bioMoby/mobyClient.py	2005/02/01 08:52:15	1.3
+++ /home/repository/moby/moby-live/Python/bioMoby/mobyClient.py	2005/02/04 12:58:24	1.4
@@ -32,7 +32,7 @@
     def call_method(self, method, arguments):
         """It invokes a remote method of the bioMoby server
         """
-
+        
         #soapaction is necessary, if not, remote calls don't work
         self.server.soapaction=self.ns+"#"+method
         
@@ -48,21 +48,21 @@
             it returns a dictionary {'name':descriptions', ...}
         """
         result={}
-
+        
         #Remote call of the method on the Moby server
         xmlt=self.call_method("retrieveObjectNames", None)
-
+        
         doc=parseString(xmlt)
         
         for node in doc.getElementsByTagName("Object"):
             objectName=node.getAttribute("name")
-
+            
             for subNode in node.childNodes:
                 if subNode.nodeType==subNode.ELEMENT_NODE:
                     for ssNode in subNode.childNodes:
                         if ssNode.nodeType==ssNode.CDATA_SECTION_NODE:
                             result[objectName]=ssNode.nodeValue
-
+        
         return result
 
     def retrieveObjectDefinition(self, objectName):
@@ -72,10 +72,10 @@
         "urn:lsid:biomoby.org:objectrelation:hasa":"HASA",
         "urn:lsid:biomoby.org:objectrelation:has":"HAS"
         }
-
+        
         definition={}
         definition["Relationship"]={}
-
+        
         xmlinput="<retrieveObjectDefinition><objectType>"+objectName+"</objectType></retrieveObjectDefinition>"
         doc=parseString(self.call_method("retrieveObjectDefinition", xmlinput))
         
@@ -85,7 +85,7 @@
                 for elem in child.childNodes:
                     if elem.nodeType==elem.ELEMENT_NODE and elem.nodeName=="objectType" and elem.firstChild:
                         definition["Relationship"][dc[child.getAttribute("relationshipType")]].append((elem.getAttribute("articleName"), elem.firstChild.nodeValue))
-
+            
             elif child.nodeType==child.ELEMENT_NODE:
                 if child.firstChild:
                         definition[str(child.nodeName)]=child.firstChild.nodeValue
@@ -104,23 +104,22 @@
         result=[]
         
         xmlt=self.call_method("retrieveServiceProviders", None)
-
+        
         doc=parseString(xmlt)
         
         for node in doc.getElementsByTagName("serviceProvider"):
             serviceProviderName= node.getAttribute("name")
             result.append(serviceProviderName)
-            
-        return result
-
         
+        return result
+    
     def retrieveNamespaces(self):
         """Retrieves a list of namespaces as a dictionary
         """
         result={}
         
         xmlt=self.call_method("retrieveNamespaces", None)
-
+        
         doc=parseString(xmlt)
         
         for node in doc.getElementsByTagName("Namespace"):
@@ -130,9 +129,8 @@
                     for ssNode in subNode.childNodes:
                         if ssNode.nodeType==ssNode.CDATA_SECTION_NODE:
                             result[ns]=ssNode.nodeValue
-
+        
         return result
-            
 
     def retrieveServiceNames(self):
         """Retrieves a list of service's names as a dictionary {'name':'URI'}
@@ -148,87 +146,84 @@
             authURI=node.getAttribute("authURI")
             
             result[serviceName]=authURI
-   
+        
         return result
 
-
     def retrieveServiceTypes(self):
         """Retrieves a list of service's types as a dictionary {'Name':'Description'}
         """        
         result={}
         
         xmlt=self.call_method("retrieveServiceTypes", None)
-
+        
         doc=parseString(xmlt)
         
         for node in doc.getElementsByTagName("serviceType"):
             st=node.getAttribute("name")      
-
+            
             for subNode in node.childNodes:
                 if subNode.nodeType==subNode.ELEMENT_NODE:
                     for ssNode in subNode.childNodes:
                         if ssNode.nodeType==ssNode.CDATA_SECTION_NODE:
                             result[st]=ssNode.nodeValue
-    
+        
         return result
-
-
+        
     def retrieveServiceWSDLByAuthority(self, serviceName, authority):
         """Retrieves a WSDL from moby from a service name and a URI
         """
         xmlinput="<retrieveService><Service authURI=\"" + authority + "\" serviceName=\"" + serviceName + "\"/></retrieveService>"
         
         xmlt=self.call_method("retrieveService", xmlinput)
-
+        
         doc=parseString(xmlt)
         
         service=doc.firstChild
         wsdl=service.firstChild.nodeValue
-
+        
         return wsdl
-
-
+        
     def retrieveServiceWSDL(self, serviceName):
         """Retrieves a WSDL from the name of a service
         """
         m=self.retrieveServiceNames()
         return self.retrieveServiceWSDLByAuthority(serviceName, m[serviceName])
-
+        
     def retrieveServiceTypesRelationships(self, serviceType, expand):
         """Retrieves the list of service's type's relationships
         """
         result=[]
         
-
+        
         xmlinput="<Relationship><serviceType>" + serviceType + "</serviceType><relationshipType>ISA</relationshipType><expandRelationship>" + `expand` + "</expandRelationship></Relationship>"
         
         xmlt=self.call_method("Relationships", xmlinput)
-
+        
         doc=parseString(xmlt)
         
         for node in doc.getElementsByTagName("Relationship"):
             for serviceType in node.childNodes:
                 if serviceType.nodeType==serviceType.ELEMENT_NODE:
                     result.append(serviceType.firstChild.nodeValue)
-                    
+        
         return result
-    
+        
     def retrieveDataTypesRelationships(self, dataTypeName):
         """Retrieves only ISA relationships
         """
-
+        
         return self.retrieveDataTypesRelationsByType(dataTypeName, 'ISA')
-
+        
     def retrieveDataTypesRelationsByType(self, dataTypeName, relationType):
         """Retrieves data types relationships
         """
-
+        
         result={}
         
         xmlinput="<Relationship><objectType>" + dataTypeName + "</objectType><relationshipType>"+relationType+"</relationshipType><relationshipType>HASA</relationshipType><relationshipType>HAS</relationshipType><expandRelationship>1</expandRelationship></Relationship>"
-
+        
         xmlt=self.call_method("Relationships", xmlinput)
-
+        
         doc=parseString(xmlt)
         
         for node in doc.getElementsByTagName("Relationship"):
@@ -239,15 +234,14 @@
                     relationTypeResults.append(ssNode.firstChild.nodeValue)
                     
             result[relationType]=relationTypeResults
-
-        return result
         
+        return result
         
     def findService(self, mobyQuery):
         """Finds a service from a set of queries
         """
         from mobyService import ServiceQuery ,ServiceList
-
+        
         if mobyQuery.__class__==ServiceQuery:
             xmlInput="<findService>"+str(mobyQuery)+"</findService>"
             
@@ -262,4 +256,4 @@
     def __init__(self, url="http://mobycentral.cbr.nrc.ca/cgi-bin/MOBY05/mobycentral.pl", ns="http://mobycentral.cbr.nrc.ca/MOBY/Central"):
         """Constructor for class Client
         """
-        Central.__init__(self, url, ns)
+        Central.__init__(self, url, ns)
\ No newline at end of file

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/mobyDataTypes.py,v
retrieving revision 1.11
retrieving revision 1.12
diff -u -r1.11 -r1.12
--- /home/repository/moby/moby-live/Python/bioMoby/mobyDataTypes.py	2005/02/02 16:52:31	1.11
+++ /home/repository/moby/moby-live/Python/bioMoby/mobyDataTypes.py	2005/02/04 12:58:24	1.12
@@ -27,12 +27,12 @@
         self.articleName=articleName
         self.value=value
         self.__isSecondary__=True
-        
+    
     def toMoby(self):
         """Returns the object as a XML
         """
         return "<moby:Parameter moby:articleName='"+self.articleName+"'><moby:value>"+str(self.value)+"</moby:value></moby:Parameter>"
-            
+    
     def __str__(self):
         """Return the Parameter in its XML form
         """
@@ -42,7 +42,7 @@
         """Print the XML on the python command line.
         """
         return self.toMoby()
-            
+    
     def fromMoby(self, xml):
         """Get the attributes from a XML string
         """
@@ -55,9 +55,9 @@
         l=xmlelt.getElementsByTagName("value")
         if len(l)==0:
             l=xmlelt.getElementsByTagName("moby:value")
-
+            
             self.value=l[0].firstChild.nodeValue
-        
+
 class MobyGeneric(object):
     """A Generic object (to use with the Marshaller)
     """
@@ -71,7 +71,7 @@
         
         for name, value in kw.items():
             setattr(self, name, value)
-        
+
 class MobyObject(MobyGeneric):
     """Define a Moby XML Object
        It has methods toMoby and fromMoby 
@@ -86,7 +86,7 @@
         self.__PIB__=[]
         
         self.content=content
-        
+
     
     def toMoby(self):
         """Deserializes the content in XML api
@@ -155,7 +155,7 @@
         result.append("</%s:%s>"%(self.__prefix__, self.__tag__))
         
         return "".join(result)
-        
+    
     def fromMoby(self, xml):
         """Deserialization method
         """
@@ -219,14 +219,14 @@
                 self.content.append(child.nodeValue)
                 
         self.content="".join(self.content)
-        
+    
 
     def __str__(self):
         return self.toMoby()
-        
+    
     def __repr__(self):
         return self.toMoby()
-        
+    
 
 class MobyXref(MobyObject):
     """Describes an Xref
@@ -237,7 +237,7 @@
         self.serviceName=serviceName
         self.evidenceCode=evidenceCode
         self.xrefType=xrefType
-        
+    
     def toMoby(self):
         """Serialize the Xref object
         """
@@ -269,7 +269,7 @@
     def fromMoby(self, xml):
         MobyObject.fromMoby(self, xml)
         self.content = int(self.content)
-        
+
 class MobyFloat(MobyObject):
     """Serialize/deserialize floating point numbers
     """
@@ -279,7 +279,7 @@
     def fromMoby(self, xml):
         MobyObject.fromMoby(self, xml)
         self.content=float(self.content)
-        
+
 
 class MobyString(MobyObject):
     """String Moby object
@@ -304,7 +304,7 @@
         """return the XML form of the Moby Content object
         """
         return self.toMoby()
-        
+    
     def toMoby(self):
         """The XML reprentation of the content
         """
@@ -408,12 +408,12 @@
                     data.append(p)
                     
             self.queryData[queryID]=data
-            
+    
     def __getitem__(self, key):
         """Get a query from his name
         """
         return self.queryData[key]
-        
+    
     def __setitem__(self, key, item):
         """Store a query in the dictionary
         """
@@ -423,12 +423,12 @@
         """Return the number of elements inside the dictionary
         """
         return len(self.queryData)
-        
+    
     def keys(self):
         """Return all queries's name
         """
         return self.queryData.keys()
-        
+    
     def collectionToQueries(self, aCollection):
         """Turn a collection of object into a set of queries
         """
@@ -441,7 +441,7 @@
             queries["%s-%s"%(queryName, queryID)]=aSimple
             
         return queries
-        
+    
     def getObject(self, queryName, objectName):
         """Get an object from a query with its name
         """
@@ -449,14 +449,14 @@
         
         for obj in filter(filterfunc, self.queryData[queryName]):
             return obj
-            
+    
     def getObjects(self, queryName):
         """Retrieve objects from a query
         """
         filterfunc=lambda obj: not hasattr(obj, "__isSecondary__")
         
         return filter(filterfunc, self.queryData[queryName])
-        
+    
     def getParameters(self, queryName):
         """Retrieve parameters from a query
         """
@@ -467,7 +467,7 @@
             result[param.articleName]=param.value
                 
         return result
-        
+    
     def getParameter(self, queryName, parameterName):
         """Retrieve a parameter from a query and his name
         """
@@ -477,7 +477,7 @@
         
         if l:
             return l[0]
-        
+    
     def __repr__(self):
         """put the xml of the Content
         """

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/mobyMarshal.py,v
retrieving revision 1.4
retrieving revision 1.5
diff -u -r1.4 -r1.5
--- /home/repository/moby/moby-live/Python/bioMoby/mobyMarshal.py	2005/02/01 08:52:15	1.4
+++ /home/repository/moby/moby-live/Python/bioMoby/mobyMarshal.py	2005/02/04 12:58:24	1.5
@@ -24,11 +24,11 @@
         """
         if type(value).__name__=='NoneType':
             return ""
-
+        
         tvalue=type(value).__name__
-
+        
         method="m_"+tvalue
-
+        
         if hasattr(value, "toMoby"):
             return value.toMoby()
         
@@ -36,15 +36,16 @@
             return getattr(self,method)(value,articleName=articleName)
         
         return self._compoundObject(value, articleName=articleName)
-            
-        
+    
+    
     def m_str(self, value, articleName=""):
         """Return a string as itself"""
         from bioMoby.mobyDataTypes  import MobyString
         m=MobyString(content=value, articleName=articleName)
         del MobyString
-        return str(m)
         
+        return str(m)
+    
     def m_unicode(self, value, articleName=""):
         """Turn a unicode string into a mobyString object
         """
@@ -54,7 +55,7 @@
         """Return a string object into a mobyString object
         """
         return self.m_str(value, articleName)
-        
+    
     def m_int(self, value, namespace="", id="", articleName=""):
         """Turn an integer into a Moby XML object
         """
@@ -62,7 +63,7 @@
         m=MobyInteger(value, namespace=namespace, id=id, articleName=articleName)
         
         return m.toMoby()
-        
+    
     def m_float(self, value, namespace="", id="", articleName=""):
         """Turn a float into a Moby XML object
         """
@@ -70,7 +71,7 @@
         m=MobyFloat(value, namespace=namespace, id=id, articleName=articleName)
         
         return m.toMoby()
-        
+    
     def m_list(self, value, articleName=""):
         """Turn a list into a Moby XML object
         """
@@ -96,8 +97,7 @@
         result.append('</moby:Dict>')
         
         return "".join(result)
-
-            
+    
     def m_tuple(self, value, namespace="", articleName=""):
         """Define a tuple as a Moby Object
         """
@@ -109,7 +109,7 @@
         result.append('</moby:Tuple>')
         
         return "".join(result)
-
+    
     def _compoundObject(self, value, articleName=""):
         """transforms an object and all properties into a XML
         """
@@ -140,7 +140,7 @@
             header.append(">")
             
         result.append(" ".join(header))
-
+        
         if properties:
             result.append("".join(properties))            
         
@@ -149,16 +149,14 @@
         
         if properties:
             result.append("</%s>"%tagName)
-
-
-        return r"".join(result)
-        
         
+        return r"".join(result)
+    
     def dumps(self, value, articleName=""):
         """Serialize the object into a Moby XML object
         """
         return self._marshal(value, articleName)
-        
+    
 
 class MobyUnmarshaller:
     """Transform an XML into a Moby Python Object
@@ -168,24 +166,24 @@
         """ Cleaning the name of the object
         """
         import re
-
+        
         aName=str(aName)
         
         if aName=="":
             return ""
-
+        
         if aName=="namespace" or aName=="id" or aName=='content':
             return aName
-
+        
         r=re.compile("\W")
-    
+        
         t=r.split(aName)
-    
+        
         for i in range(0,len(t)):
             t[i]=str.upper(t[i][0])+t[i][1:]
-
+        
         del re
-
+        
         return "".join(t)
 
     def loadn(self, xmlNode):
@@ -198,7 +196,7 @@
         
         #Try to see if this object got a deserializer
         object2build=self._cleanName(nn)
-
+        
         objectName=str.upper(object2build[0])+object2build[1:]
         
         if hasattr(bioMoby.mobyDataTypes, "Moby%s"%objectName):
@@ -224,14 +222,12 @@
 #            from bioMoby.mobyExceptions import EInvalidMobyXML    
             
 #            raise EInvalidMobyXML
-
-        
+    
     def loads(self, xmlString):
         """ Deserializes an xml string and return a bioMoby-Python object
         """
         if xmlString=="":
             return None    
-
 #        _typesmodule=["bioMoby.mobyDataTypes", "bioMoby.ontology"]
             
         doc=parseString(xmlString)
@@ -254,15 +250,16 @@
             return int(value.firstChild.nodeValue.replace("\n","").replace("\t","").replace(" ",""))
         else:
             return 0
-            
+    
     def m_Float(self, value):
         """Turn a Float XML element into a float number
         """
         value.normalize()
         if value.firstChild:
             return float(value.firstChild.nodeValue.replace("\n","").replace("\t","").replace(" ",""))
+        
         return 0.0
-            
+    
     def m_String(self, value):
         """Turn a Moby XML String element into a String object
         """
@@ -273,9 +270,8 @@
         for aChild in value.childNodes:
             if aChild.nodeType==aChild.TEXT_NODE or aChild.nodeType==aChild.CDATA_SECTION_NODE:
                 cnt.append(aChild.wholeText)
-                
-        return        r"".join(cnt)
         
+        return        r"".join(cnt)
 
     def m_Object(self, value):
         """Turn any XML into a generic object
@@ -283,7 +279,7 @@
         filterFunc= lambda x: x.nodeType==x.ELEMENT_NODE
         
         typeName="GMoby%s"%str(value.localName)
-
+        
         from bioMoby.mobyDataTypes import MobyGeneric
         
         NewType=type(typeName, (MobyGeneric,), {})
@@ -296,24 +292,24 @@
         for tupleAttribute in value.attributes.itemsNS():
             #First item, second field:
             setattr(anObject, str(tupleAttribute[0][1]), str(tupleAttribute[1]))
-
+        
         i=0    
         for elem in filter(filterFunc, value.childNodes):
             methodName="m_%s"%str(elem.localName)
-
+            
             articleName=elem.getAttribute("moby:articleName")
             
             if not articleName:
                 articleName=elem.getAttribute("articleName")
-                
+            
             if not articleName:
                 articleName="attribute_%s"%i
-                
+            
             if hasattr(self, methodName):
                 prop=getattr(self, methodName)(elem)
             else:
-                    prop=self.m_Object(elem)
-                
+                prop=self.m_Object(elem)
+            
             if hasattr(anObject, articleName):
                 t=prop
                 if not type(getattr(anObject, articleName)) is list:
@@ -323,17 +319,17 @@
             else:
                 setattr(anObject, articleName, prop)
             i+=1
-
+        
         content=[]
-
+        
         isContentNode= lambda x: x.nodeType==x.TEXT_NODE or x.nodeType==x.CDATA_SECTION_NODE
         
         for elem in filter(isContentNode, value.childNodes):
             content.append(str(elem.nodeValue))
-            
+        
         if content:
             anObject.content(r"".join(content))
-            
+        
         return anObject
 
     def m_MobyContent(self, value):
@@ -347,5 +343,4 @@
         
         del MobyContent
         
-        return mc
-        
+        return mc
\ No newline at end of file

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/mobyRegister.py,v
retrieving revision 1.3
retrieving revision 1.4
diff -u -r1.3 -r1.4
--- /home/repository/moby/moby-live/Python/bioMoby/mobyRegister.py	2005/02/01 08:52:15	1.3
+++ /home/repository/moby/moby-live/Python/bioMoby/mobyRegister.py	2005/02/04 12:58:24	1.4
@@ -20,10 +20,10 @@
         self.id=""
         self.message=""
         self.RDF=""
-
+        
         #Parse the document, retrieve the success, id, message and RDF fields
         doc=parseString(xmlInput)
-
+        
         if len(doc.getElementsByTagName("success")[0].childNodes)>0:
             self.success=int(doc.getElementsByTagName("success")[0].childNodes[0].nodeValue)
         if len(doc.getElementsByTagName("id")[0].childNodes)>0:
@@ -35,17 +35,17 @@
                 self.RDF=doc.getElementsByTagName("RDF")[0].firstChild.toprettyxml()
         except:
             pass
-
+    
     def __str__(self):
         """Return the moby xml of the instance
         """
         return "<MOBYRegistration><id>"+self.id+"</id><success>"+`self.success`+"</success><message><![CDATA["+self.message+"]]></message><RDF>"+self.RDF+"</RDF></MOBYRegistration>"
-        
+    
     def toTuple(self):
         """return the  tuple form of  the instance
         """
         return (self.id, self.success,  self.message, self.RDF)
-        
+    
     def isSuccess(self):
         """Indicate whether the registration was successful or not
         """
@@ -79,7 +79,7 @@
         GeneralInformations.__init__(self, contact=contactEmail, authURI=authURI, description=description)
         self.relationship=relationship
         self.serviceType=serviceType
-        
+    
     def __str__(self):
         """Return the instance as a Moby XML
         """
@@ -88,22 +88,21 @@
         result.append("<authURI>"+self.authURI+"</authURI>")
         result.append("<Description><![CDATA["+self.description+"]]></Description>")
         result.append('<Relationship relationshipType="'+self.relationship[0]+'">')
-    
+        
         for serviceType in self.relationship[1]:
             result.append('<serviceType>'+serviceType+'</serviceType>')
-
+        
         result.append("</Relationship>")
-            
-
-        return "".join(result)
-
         
+        
+        return "".join(result)
+    
     def register(self):
         """Register the service's type on the moby server
         """
         xmlinput="<registerServiceType>"+str(self)+"</registerServiceType>"
         return RegistrationObject(self.central.call_method("registerServiceType", xmlinput))
-        
+    
     def deregister(self):
         """Deregister the service's Type on moby
         """
@@ -126,7 +125,7 @@
         """
         result=["<objectType>"+self.objectType+"</objectType>"]
         result.append("<Description><![CDATA["+self.description+"]]></Description>")
-                
+        
         for relationship in self.relationships:
             result.append('<Relationship relationshipType="'+relationship[0]+'">')
             
@@ -134,12 +133,11 @@
                 result.append('<objectType articleName="'+objectTypeKey+'">'+relationship[1][objectTypeKey]+'</objectType>')
                 
             result.append("</Relationship>")
-
+        
         result.append("<authURI>"+self.authURI+"</authURI>")
         result.append("<contactEmail>"+self.contact+"</contactEmail>")
-
+        
         return "".join(result)
-
     
     def register(self):
         """Register the  object's class
@@ -160,12 +158,12 @@
     def __init__(self, namespaceType="", contact="", authURI="", description=""):
         GeneralInformations.__init__(self, contact=contact, authURI=authURI,description=description)
         self.namespaceType=namespaceType
-
+    
     def __str__(self):
         """return the XML of the name space
         """
         return "<namespaceType>"+self.namespaceType+"</namespaceType><contactEmail>"+self.contact+"</contactEmail><authURI>"+self.authURI+"</authURI><Description><![CDATA["+self.description+"]]></Description>"
-
+    
     def register(self):
         """Register the namespace on a Moby server
         """
@@ -176,4 +174,4 @@
         """Deregister the namespace
         """
         xmlinput="<deregisterNamespace>"+self.namespaceType+"</deregisterNamespace>"
-        return RegistrationObject(self.central.call_method("deregisterNamespace", xmlinput))
+        return RegistrationObject(self.central.call_method("deregisterNamespace", xmlinput))
\ No newline at end of file

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/mobyService.py,v
retrieving revision 1.3
retrieving revision 1.4
diff -u -r1.3 -r1.4
--- /home/repository/moby/moby-live/Python/bioMoby/mobyService.py	2005/02/01 08:52:15	1.3
+++ /home/repository/moby/moby-live/Python/bioMoby/mobyService.py	2005/02/04 12:58:24	1.4
@@ -33,16 +33,16 @@
         
         for namespace in self.namespaces:
             result.append('<Namespace>'+namespace+'</Namespace>')
-    
+        
         result.append('</Simple>')
         
         return "".join(result)
-
+    
     def fromXML(self, xml):
         """Return an article from a xml node
         """
         node=parseString(xml)
-
+        
         self.name=node.getAttribute("articleName")
         for otns in node.childNodes:
             if otns.nodeName=="objectType":
@@ -63,12 +63,11 @@
         
         self.enums=enums
 
-    
     def toTuple(self):
         """Return the object as a tuple
         """
         return (self.name, self.type, self.default, self.min, self.max, self.enums)
-            
+    
     def __str__(self):
         """Return the xml form of the object
         """
@@ -83,23 +82,23 @@
             
         if self.max !='':
             result.append('<max>'+self.max+'</max>')
-
+        
         for enum in self.enums:
             result.append('<enum>'+enum+'</enum>')
-
+        
         result.append('</Parameter>')
-
+        
         return "".join(result)
-
+    
     def fromXML(self, xml):
         """Return a parameter from a xml
         """
         
         node=parseString(xml)        
-
+        
         self.enums=[]
         self.name=node.getAttribute("articleName")
-
+        
         for childNode in node.childNodes:
             if childNode.nodeName=="datatype":
                 self.type=childNode.firstChild.nodeValue
@@ -129,11 +128,11 @@
         self.protocol="moby"
         self.authURI=""
         self.serviceName=""
-
+        
         self.expandObjects=0
         self.expandServices=1
         self.authoritative=0
-
+        
         if 'serviceName' in kw:
             self.serviceName=kw['serviceName']
         if 'serviceType' in kw:
@@ -148,15 +147,15 @@
             self.outputObjects=kw['outputObjects']
         if 'keywords' in kw:
             self.keywords=kw['keywords']
-            
+    
     def submits2XML(self, entries):
         """Tranforms inputs/outputs into xml
         """
-
+        
         import string
         result=[]
         for submit in entries:
-
+            
             #first look if it is an article or a collection
             #first case
             if submit[1].__class__ is string or submit[1].__class__ is str:
@@ -165,42 +164,41 @@
                 #otns[1] namespace
                 for namespace in submit[2]:
                     result.append("<Namespace>"+namespace+"</Namespace>")
-
+                
                 result.append("</Simple>")
                 #it is a collection
             else:
                 result.append('<Collection articleName="'+submit[0]+'">')
-
+                
                 for simpleArticle in submit[1]:
                     result.append('<Simple articleName="'+simpleArticle[0]+'"><objectType>'+simpleArticle[1]+'</objectType>')
                     for namespace in simpleArticle[2]:
                         result.append("<Namespace>"+namespace+"</namespace>")
-
+                    
                     result.append("</Simple>")
                         
                 result.append("</Collection>")
-
+        
         del string                    
         return "".join(result)
-
-
+    
     def keywords2XML(self, keywords):
         """Transform keywords into xml
         """
         result=[]
+        
         for keyword in keywords:
             result.append("<keyword>"+keyword+"</keyword>")
-            
-
+        
+        
         return "".join(result)
-
-
+    
     def __str__(self):
         """Give the xml form of the query
         """
         result=["<inputObjects><Input>"]
         result.append(self.submits2XML(self.inputObjects))
-
+        
         result.append("</Input></inputObjects><outputObjects><output>")
         result.append(self.submits2XML(self.outputObjects))
         result.append("</output></outputObjects>")
@@ -208,18 +206,18 @@
         result.append("<serviceType>"+self.serviceType+"</serviceType>")
         result.append("<Protocol>moby</Protocol>")
         result.append("<authURI>"+self.authURI+"</authURI>")
-
+        
         if self.serviceName != "" and self.serviceName !="dummy":
             result.append("<serviceName>"+self.serviceName+"</serviceName>")
-
+        
         result.append("<expandObjects>"+`self.expandObjects`+"</expandObjects>")
         result.append("<expandServices>"+`self.expandServices`+"</expandServices>")
         result.append("<authoritative>"+`self.authoritative`+"</authoritative>")
         result.append("<keywords>")
         result.append(self.keywords2XML(self.keywords))
         result.append("</keywords>")
-
-
+        
+        
         return "".join(result)
 
 
@@ -236,10 +234,10 @@
             
             -A WSDL
         """
-
+        
         GeneralInformations.__init__(self)
         self.namespace="http://biomoby.org/"
-
+        
         self.name=""
         self.type=""
         self.category=""
@@ -251,7 +249,7 @@
         self.secondaryArticles=[]
         self.methods=[]
         self.results=""
-
+        
         if len(arg)==1 and arg[0].__class__ is dict:
             arg=arg[0]
             for key in arg.keys():
@@ -291,11 +289,11 @@
         """
         self.methods=[]
         doc=parseString(wsdl)
-
+        
         for method in doc.getElementsByTagName("operation"):
             if method.getAttribute("name") not in self.methods:
                 self.methods.append(method.getAttribute("name"))
-
+        
         if self.url=="":
             for url in doc.getElementsByTagName("soap:address"):
                 self.url=url.getAttribute("location")
@@ -310,7 +308,7 @@
         """
         
         from SOAPpy import SOAPProxy
-
+        
         webservice=SOAPProxy(self.url,namespace=self.namespace)
         
         if method=="":
@@ -318,34 +316,34 @@
                 method=self.name
             else:
                 method=self.methods[0]
-
+        
         if method not in self.methods:
             from bioMoby.mobyExceptions import ENotAWSMethod
             raise ENotAWSMethod
-
+        
         webservice.soapaction=self.namespace+"#"+method
-
+        
         if debug:
             webservice.config.debug=1
         
         toQuery=str(query)
-
+        
         del  SOAPProxy
-
+        
         result=webservice.invoke(method, toQuery)
         
         if returnXml:
             return result
-            
+        
         #try to return a MobyContent Object instead
         from bioMoby.mobyDataTypes import MobyContent
         mc=MobyContent()
         mc.fromMoby(result)
         
         del MobyContent
-
+        
         return mc
-            
+    
     def __str__(self):
         """Returns The moby xml form of the web service
         """
@@ -358,7 +356,7 @@
         result.append("<contactEmail>"+self.contact+"</contactEmail>")
         result.append("<authoritativeService>"+`self.authoritative`+"</authoritativeService>")
         result.append("<Description><![CDATA["+self.description+"]]></Description>")
-
+        
         result.append("<Input>")
         
         for inputObject in self.inputObjects:
@@ -366,25 +364,25 @@
                 result.append(str(inputObject))
             elif inputObject.__class__ is dict:
                 result.append('<Collection articleName="'+inputObject.keys()[0]+'">')
-
+                
                 for aSimple in inputObject[inputObject.keys()[0]]:
                     result.append(str(aSimple))
-
+                
                 result.append("</Collection>")
             else:
                 from mobyExceptions import EInvalidArgument
                 raise EInvalidArgument, "Bad input object"
-            
+        
         result.append("</Input>")
-
+        
         result.append("<Output>")
-
+        
         for output in self.outputObjects:
             if output.__class__ is ServiceArticle:
                 result.append(str(output))
             elif output.__class__ is dict:
                 result.append('<Collection articleName="'+output.keys()[0]+'">')
-
+                
                 for aSimple in output[output.keys()[0]]:
                     result.append(str(aSimple))
                     
@@ -392,19 +390,18 @@
             else:
                 from mobyExceptions import EInvalidArgument
                 raise EInvalidArgument, "Bad output object"
-                    
-
+        
+        
         result.append("</Output>")
-
+        
         result.append("<secondaryArticles>")
         
         for secondaryArticle in self.secondaryArticles:
             result.append(str(secondaryArticle))
-
+        
         result.append("</secondaryArticles>")
-
+        
         return "".join(result)
-    
 
     def register(self):
         """Register the service on the Moby server    
@@ -435,8 +432,7 @@
         """
         
         self.results=self.execute(mobyContent, returnXml=(mobyContent.__class__ is str))
-                
-        
+    
     def start(self, mobycontent, timeout=-1):
         """Start the service as it was a thread
         """
@@ -447,16 +443,14 @@
             self._execThread=Thread(target=self._executeThread, args=(mobycontent,))
         else:
             self._execThread=Thread(target=self._executeThread, args=(mobycontent,), timeout=timeout)
-
-        self._execThread.start()
         
+        self._execThread.start()
+    
     def join(self):
         """Same as Thread.join
         """
         self._execThread.join()
-        
-        
-        
+    
 class ServiceList:
     """Class representing a service's list
     """
@@ -466,16 +460,16 @@
         """
         
         simpleArticle=ServiceArticle(name='',type='',namespaces=[])
-
+        
         simpleArticle.name=node.getAttribute("articleName")
         for otns in node.childNodes:
             if otns.nodeName=="objectType":
                 simpleArticle.type=otns.firstChild.nodeValue
             elif otns.nodeName=="Namespace":
                 simpleArticle.namespaces.append(otns.firstChild.nodeValue)
-                
+        
         return simpleArticle
-
+    
     def toCollection(self, node):
         """Return a collection of articles
         """
@@ -485,21 +479,20 @@
         for simpleArticle in node.childNodes:
             if simpleArticle.nodeName=="Simple":
                 collection.append(self.toSimpleArticle(simpleArticle))
-            
+        
         result[collectionName]=collection
         
         return result
     
-
     def toSecondary(self, node):
         """Return a parameter from a xml
         """
         secondary=ServiceSecondary(name="", type="", default="", min="", max="", enums=[])
-
+        
         secondary.enums=[]
-
+        
         secondary.name=node.getAttribute("articleName")
-
+        
         for childNode in node.childNodes:
             if childNode.nodeName=="datatype":
                 if childNode.firstChild:
@@ -516,18 +509,18 @@
             elif childNode.nodeName=="enum":
                 if childNode.firstChild:
                     secondary.enums.append(childNode.firstChild.nodeValue)
-
+        
         return secondary
 
     def __init__(self, xmlt):
         """Give the instance of an object from xml
         """
         self.list=[]
-
+        
         doc=parseString(xmlt)
         #for each service
         for node in doc.getElementsByTagName("Service"):
-
+            
             service=Service()
             service.name=node.getAttribute("serviceName")
             service.methods=[service.name]
@@ -565,7 +558,7 @@
                     for secondary in child.childNodes:
                         if secondary.nodeName=="Parameter":
                             service.secondaryArticles.append(self.toSecondary(secondary))
-                            
+            
             self.list.append(service)
 
     def getServiceByName(self, nameOfService):
@@ -574,7 +567,7 @@
         for service in self.list:
             if service.name==nameOfService:
                 return service
-                
+        
         return None
     
     def getServiceByAuthURI(self, authURI):
@@ -583,7 +576,7 @@
         for service in self.list:
             if service.authURI==authURI:
                 return service
-                
+        
         return None
 
     def __getitem__(self, key):



From yanwong at pub.open-bio.org  Fri Feb  4 15:58:37 2005
From: yanwong at pub.open-bio.org (Yan Wong)
Date: Fri, 4 Feb 2005 10:58:37 -0500
Subject: [MOBY-guts] biomoby commit
Message-ID: <200502041558.j14Fwbbt030084@pub.open-bio.org>


yanwong
Fri Feb  4 10:58:37 EST 2005
Update of /home/repository/moby/moby-live/Python/bioMoby
In directory pub.open-bio.org:/tmp/cvs-serv30059

Modified Files:
	mobyDataTypes.py 
Log Message:


moby-live/Python/bioMoby mobyDataTypes.py,1.12,1.13
===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/mobyDataTypes.py,v
retrieving revision 1.12
retrieving revision 1.13
diff -u -r1.12 -r1.13
--- /home/repository/moby/moby-live/Python/bioMoby/mobyDataTypes.py	2005/02/04 12:58:24	1.12
+++ /home/repository/moby/moby-live/Python/bioMoby/mobyDataTypes.py	2005/02/04 15:58:37	1.13
@@ -438,7 +438,7 @@
         queryID=1
         
         for aSimple in aCollection[1]:
-            queries["%s-%s"%(queryName, queryID)]=aSimple
+            queries["%s-%s"%(queryName, queryID)]=[aSimple]
             
         return queries
     



From yanwong at pub.open-bio.org  Fri Feb  4 16:03:40 2005
From: yanwong at pub.open-bio.org (Yan Wong)
Date: Fri, 4 Feb 2005 11:03:40 -0500
Subject: [MOBY-guts] biomoby commit
Message-ID: <200502041603.j14G3eqD030127@pub.open-bio.org>


yanwong
Fri Feb  4 11:03:40 EST 2005
Update of /home/repository/moby/moby-live/Python/bioMoby
In directory pub.open-bio.org:/tmp/cvs-serv30102

Modified Files:
	mobyDataTypes.py 
Log Message:


moby-live/Python/bioMoby mobyDataTypes.py,1.13,1.14
===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/mobyDataTypes.py,v
retrieving revision 1.13
retrieving revision 1.14
diff -u -r1.13 -r1.14
--- /home/repository/moby/moby-live/Python/bioMoby/mobyDataTypes.py	2005/02/04 15:58:37	1.13
+++ /home/repository/moby/moby-live/Python/bioMoby/mobyDataTypes.py	2005/02/04 16:03:40	1.14
@@ -439,6 +439,7 @@
         
         for aSimple in aCollection[1]:
             queries["%s-%s"%(queryName, queryID)]=[aSimple]
+            queryID+=1
             
         return queries
     



From mwilkinson at pub.open-bio.org  Sun Feb  6 21:58:36 2005
From: mwilkinson at pub.open-bio.org (Mark Wilkinson)
Date: Sun, 6 Feb 2005 16:58:36 -0500
Subject: [MOBY-guts] biomoby commit
Message-ID: <200502062158.j16LwaE7014950@pub.open-bio.org>


mwilkinson
Sun Feb  6 16:58:36 EST 2005
Update of /home/repository/moby/moby-live/Perl/MOBY
In directory pub.open-bio.org:/tmp/cvs-serv14931

Modified Files:
	Central.pm 
Log Message:
should fiux problem with servicd registration

moby-live/Perl/MOBY Central.pm,1.146,1.147
===================================================================
RCS file: /home/repository/moby/moby-live/Perl/MOBY/Central.pm,v
retrieving revision 1.146
retrieving revision 1.147
diff -u -r1.146 -r1.147
--- /home/repository/moby/moby-live/Perl/MOBY/Central.pm	2004/12/14 20:55:11	1.146
+++ /home/repository/moby/moby-live/Perl/MOBY/Central.pm	2005/02/06 21:58:35	1.147
@@ -3220,7 +3220,7 @@
 		  && &_LOG( $_->nodeType, "\t", $_->toString, "\n" );
 
 		#next unless $_->nodeType == TEXT_NODE;
-		$content .= $_->toString;
+		$content .= $_->textContent;
 	}
 	return $content;
 }
@@ -3243,7 +3243,7 @@
 		if ($_->toString =~ /<!\[CDATA\[((?>[^\]]+))\]\]>/) {
 			$content .= $1;
 		} else {
-			$content .= $_->toString;
+			$content .= $_->textContent;
 		}
 	}
 	return $content;



From mwilkinson at pub.open-bio.org  Sun Feb  6 22:24:48 2005
From: mwilkinson at pub.open-bio.org (Mark Wilkinson)
Date: Sun, 6 Feb 2005 17:24:48 -0500
Subject: [MOBY-guts] biomoby commit
Message-ID: <200502062224.j16MOmFc015075@pub.open-bio.org>


mwilkinson
Sun Feb  6 17:24:47 EST 2005
Update of /home/repository/moby/moby-live/Perl/MOBY/Client
In directory pub.open-bio.org:/tmp/cvs-serv15056/MOBY/Client

Modified Files:
	Central.pm 
Log Message:
fixing at teh client side as well

moby-live/Perl/MOBY/Client Central.pm,1.87,1.88
===================================================================
RCS file: /home/repository/moby/moby-live/Perl/MOBY/Client/Central.pm,v
retrieving revision 1.87
retrieving revision 1.88
diff -u -r1.87 -r1.88
--- /home/repository/moby/moby-live/Perl/MOBY/Client/Central.pm	2004/12/15 19:37:12	1.87
+++ /home/repository/moby/moby-live/Perl/MOBY/Client/Central.pm	2005/02/06 22:24:47	1.88
@@ -1863,7 +1863,7 @@
 
 		#print getNodeTypeName($_), "\t", $_->toString,"\n";
 		next unless $_->nodeType == TEXT_NODE;
-		$content = $_->toString;
+		$content = $_->textContent;
 	}
     $content ||="";
 	$content =~ s/<!\[CDATA\[((?>[^\]]+))\]\]>/$1/gs;
@@ -1883,14 +1883,14 @@
 
 		#print getNodeTypeName($_), "\t", $_->toString,"\n";
 		next unless $_->nodeType == TEXT_NODE;
-		$content = $_->toString;
+		$content = $_->textContent;
 	}
 	return $content;
 }
 
 sub _nodeRawContent {
 
-	# will get text of **all** child $node from the given $DOM
+	# will get XML of **all** child $node from the given $DOM
 	# regardless of their depth!!
 	my ( $DOM, $node ) = @_;
 	my $x = $DOM->getElementsByTagName( $node );
@@ -1923,7 +1923,7 @@
 
 			#print getNodeTypeName($_), "\t", $_->toString,"\n";
 			next unless $_->nodeType == TEXT_NODE;
-			push @result, $_->toString;
+			push @result, $_->textContent;
 		}
 	}
 	return @result;



From mwilkinson at pub.open-bio.org  Sun Feb  6 22:46:45 2005
From: mwilkinson at pub.open-bio.org (Mark Wilkinson)
Date: Sun, 6 Feb 2005 17:46:45 -0500
Subject: [MOBY-guts] biomoby commit
Message-ID: <200502062246.j16MkjAO015335@pub.open-bio.org>


mwilkinson
Sun Feb  6 17:46:45 EST 2005
Update of /home/repository/moby/moby-live/Perl/MOBY/Client
In directory pub.open-bio.org:/tmp/cvs-serv15316

Modified Files:
	Central.pm 
Log Message:
fixing the registration object output

moby-live/Perl/MOBY/Client Central.pm,1.88,1.89
===================================================================
RCS file: /home/repository/moby/moby-live/Perl/MOBY/Client/Central.pm,v
retrieving revision 1.88
retrieving revision 1.89
diff -u -r1.88 -r1.89
--- /home/repository/moby/moby-live/Perl/MOBY/Client/Central.pm	2005/02/06 22:24:47	1.88
+++ /home/repository/moby/moby-live/Perl/MOBY/Client/Central.pm	2005/02/06 22:46:45	1.89
@@ -1829,6 +1829,7 @@
 	my $id      = &_nodeTextContent( $Object,  'id' );
 	my $success = &_nodeTextContent( $Object,  'success' );
 	my $message = &_nodeCDATAContent( $Object, 'message' );
+print STDERR "******$message******\n";
 	my $RDF     = &_nodeRawContent( $Object,   'RDF' );
 	my $reg = MOBY::Client::Registration->new(
 											   success         => $success,
@@ -1862,7 +1863,7 @@
 	foreach ( @child ) {
 
 		#print getNodeTypeName($_), "\t", $_->toString,"\n";
-		next unless $_->nodeType == TEXT_NODE;
+		next unless (($_->nodeType == TEXT_NODE) || ($_->nodeType == CDATA_SECTION_NODE));
 		$content = $_->textContent;
 	}
     $content ||="";
@@ -1882,7 +1883,7 @@
 	foreach ( @child ) {
 
 		#print getNodeTypeName($_), "\t", $_->toString,"\n";
-		next unless $_->nodeType == TEXT_NODE;
+		next unless (($_->nodeType == TEXT_NODE) || ($_->nodeType == CDATA_SECTION_NODE));
 		$content = $_->textContent;
 	}
 	return $content;
@@ -1922,7 +1923,7 @@
 		foreach ( @child2 ) {
 
 			#print getNodeTypeName($_), "\t", $_->toString,"\n";
-			next unless $_->nodeType == TEXT_NODE;
+			next unless (($_->nodeType == TEXT_NODE) || ($_->nodeType == CDATA_SECTION_NODE));
 			push @result, $_->textContent;
 		}
 	}



From yanwong at pub.open-bio.org  Mon Feb  7 14:23:13 2005
From: yanwong at pub.open-bio.org (Yan Wong)
Date: Mon, 7 Feb 2005 09:23:13 -0500
Subject: [MOBY-guts] biomoby commit
Message-ID: <200502071423.j17ENDn9018500@pub.open-bio.org>


yanwong
Mon Feb  7 09:23:13 EST 2005
Update of /home/repository/moby/moby-live/Python/utils
In directory pub.open-bio.org:/tmp/cvs-serv18475

Modified Files:
	moby2python.py 
Log Message:


moby-live/Python/utils moby2python.py,1.5,1.6
===================================================================
RCS file: /home/repository/moby/moby-live/Python/utils/moby2python.py,v
retrieving revision 1.5
retrieving revision 1.6
diff -u -r1.5 -r1.6
--- /home/repository/moby/moby-live/Python/utils/moby2python.py	2005/02/01 14:20:46	1.5
+++ /home/repository/moby/moby-live/Python/utils/moby2python.py	2005/02/07 14:23:13	1.6
@@ -85,7 +85,8 @@
     res.append("            if elt.nodeName==\"CrossReference\" or elt.nodeName==\"moby:CrossReference\":")
     res.append("                self.__cross__=[]")
     res.append("                for ref in elt.childNodes:")
-    res.append("                    self.__cross__.append(um.loads(ref))")        
+    res.append("                    if ref.nodeType==ref.ELEMENT_NODE:")    
+    res.append("                        self.__cross__.append(um.loadn(ref))")        
 
 
     for parameter in parameters:



From kawas at pub.open-bio.org  Tue Feb  8 01:50:32 2005
From: kawas at pub.open-bio.org (Eddie Kawas)
Date: Mon, 7 Feb 2005 20:50:32 -0500
Subject: [MOBY-guts] biomoby commit
Message-ID: <200502080150.j181oWm1020725@pub.open-bio.org>


kawas
Mon Feb  7 20:50:31 EST 2005
Update of /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/gui/serviceInstanceCreationTool
In directory pub.open-bio.org:/tmp/cvs-serv20700/org/biomoby/client/gui/serviceInstanceCreationTool

Modified Files:
	MobyUtilities.java 
Log Message:
Fixed GetRelations so that the name argument can be an LSID - Eddie

moby-live/Java/src/main/org/biomoby/client/gui/serviceInstanceCreationTool MobyUtilities.java,1.1,1.2
===================================================================
RCS file: /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/gui/serviceInstanceCreationTool/MobyUtilities.java,v
retrieving revision 1.1
retrieving revision 1.2
diff -u -r1.1 -r1.2
--- /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/gui/serviceInstanceCreationTool/MobyUtilities.java	2004/09/27 21:29:14	1.1
+++ /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/gui/serviceInstanceCreationTool/MobyUtilities.java	2005/02/08 01:50:31	1.2
@@ -7,6 +7,8 @@
 import java.util.Iterator;
 import java.util.LinkedList;
 import java.util.StringTokenizer;
+import java.util.regex.Matcher;
+import java.util.regex.Pattern;
 
 import javax.swing.tree.TreePath;
 
@@ -19,147 +21,160 @@
  */
 
 public class MobyUtilities {
-	// strings that when concatenated return the attributes, articlename, etc of an object
-	final private static String MURL = new String("http://mobycentral.cbr.nrc.ca/cgi-bin/types/Objects?name=");
-	final private static String MURL2 = new String("&lsid_name");
-
-	/**
-	 * PRE: None.<p>
-	 * POST: a linked list of all the relations is returned, such that:<p>
-	 * => The first item in the list is a string representation of the parent<p>
-	 * => The second item is a linked list of all the 'HAS' container relationships<p>
-	 * => The third item is a linked list of all the 'HASA' container relationships
-	 * @param name, the name of the object to query for.
-	 * @return returns a linked list {String, LinkedList, LinkedList} of relationships
-	 */
-	public static LinkedList GetRelations(String name) throws IOException {
-		URL url = null;
-		url = new URL(MURL + name + MURL2);
-		BufferedReader in = new BufferedReader(new InputStreamReader(url.openStream()));
-		String input;
-		String parent = "";
-		LinkedList llHas = new LinkedList();
-		LinkedList llHasa = new LinkedList();
-
-		while ((input = in.readLine()) != null) {
-			StringTokenizer st = new StringTokenizer(input, "\t");
-			if (st.countTokens() > 2) {
-				st.nextToken(); // object name that was queried
-				StringTokenizer lsid = new StringTokenizer(st.nextToken(), ":");
-				String relation = "";
-				while (lsid.hasMoreTokens())
-					relation = lsid.nextToken(); // isa, hasa, etc
-				if (relation.equalsIgnoreCase("isa"))
-					parent = st.nextToken();
-				else if (relation.equalsIgnoreCase("has"))
-					llHas.add(st.nextToken());
-				else if (relation.equalsIgnoreCase("hasa"))
-					llHasa.add(st.nextToken());
-			}
-		}
-		if (parent.equals("")) {
-			return null;
-		}
-		LinkedList listToReturn = new LinkedList();
-		listToReturn.addFirst(parent);
-		listToReturn.add(llHas);
-		listToReturn.add(llHasa);
-		return listToReturn;
-	}
-
-	/**
-	 * 
-	 * PRE: None.<p>
-	 * POST: a Pair object is returned if the String could be parsed, otherwise, null is returned.
-	 * @param rel - the string representation of the relation in the form Attribute(articleName), i.e. Integer(Count).
-	 * @return returns a fully constructed Pair object if the relation was valid, otherwise, null is returned. 
-	 */
-	public static Pair ParseRelation(String rel) {
-		// integer(length) == attribute(articlename)
-		Pair p = null;
-		int x = -1;
-		String attribute, articleName;
-		if ((x = rel.indexOf("(")) >= 0) {
-			attribute = rel.substring(0, x);
-			articleName = rel.substring(x + 1, rel.length() - 1);
-			p = new Pair(articleName, attribute);
-		}
-
-		return p;
-	}
-
-	/**
-	 * 
-	 * PRE: None.<p>
-	 * POST: Returns the leaf object in a TreePath if path is not null, otherwise, null is returned.
-	 * @param path - a TreePath containing the object of interest.
-	 * @return returns the name of the leaf object contained in the path.
-	 */
-	public static String GetObject(TreePath path) {
-		if (path == null)
-			return null;
-		String s = path.toString();
-		int start = s.lastIndexOf(", ");
-		int end = s.indexOf("]");
-		if (start < 0) {
-			start = 0;
-		}
-		int space = -1;
-		if ((space = s.lastIndexOf(" ")) >= 0) {
-			s = s.substring(space + 1, end);
-		} else
-			s = s.substring(start + 1, end);
-		return s;
-	}
-
-	/**
-	 * 
-	 * PRE: ll is a valid linkedlist, panelDetails is a valid MobyUserPanel.<p>
-	 * POST: All the relations of child are outputted to the MobyUserPanel panelDetails.
-	 * @param ll - a linked list created via GetRelations()
-	 * @param panelDetails - the MobyUserPanel to output the relationships
-	 * @param child - the object that GetRelations() was called with.
-	 */
-	public static String WriteToPanel(LinkedList ll, String child) {
-		//System.out.println(ll);
-		StringBuffer sb = new StringBuffer("");
-		sb.append(child + System.getProperty("line.separator") + "ISA: " + System.getProperty("line.separator") + "\t");
-		String parent = (String) ll.removeFirst();
-		sb.append(parent + System.getProperty("line.separator"));
-		LinkedList llhas = (LinkedList) ll.removeFirst();
-		if (llhas != null) {
-			sb.append("Has: ");
-			Iterator i = llhas.iterator();
-			while (i.hasNext()) {
-				Pair p = MobyUtilities.ParseRelation((String) i.next());
-				if (p != null)
-					sb.append(
-						System.getProperty("line.separator")
-							+ "\t"
-							+ p.getAttribute()
-							+ " - "
-							+ p.getArticlename()
-							+ " ");
-			}
-			sb.append(System.getProperty("line.separator"));
-		}
-		LinkedList llhasa = (LinkedList) ll.removeFirst();
-		if (llhasa != null) {
-			sb.append("Hasa: ");
-			Iterator i = llhasa.iterator();
-			while (i.hasNext()) {
-				Pair p = MobyUtilities.ParseRelation((String) i.next());
-				if (p != null)
-					sb.append(
-						System.getProperty("line.separator")
-							+ "\t"
-							+ p.getAttribute()
-							+ "->"
-							+ p.getArticlename()
-							+ " ");
-			}
-		}
-		return sb.toString();
-	}
-
-}
+    // strings that when concatenated return the attributes, articlename, etc of an object
+    final private static String URL_OBJECT = new String(
+            "http://mobycentral.cbr.nrc.ca/cgi-bin/types/Objects?name=");
+
+    final private static String URL_LSID = new String(
+            "http://mobycentral.cbr.nrc.ca/cgi-bin/types/Objects?lsid_name=");
+
+    /**
+     * PRE: None.<p>
+     * POST: a linked list of all the relations is returned, such that:<p>
+     * => The first item in the list is a string representation of the parent<p>
+     * => The second item is a linked list of all the 'HAS' container relationships<p>
+     * => The third item is a linked list of all the 'HASA' container relationships
+     * @param name, the name of the object to query for - can be an Moby Object LSID.
+     * @return returns a linked list {String, LinkedList, LinkedList} of relationships
+     */
+    public static LinkedList GetRelations(String name) throws IOException {
+        URL url = null;
+        boolean isLSID = false;
+        // TODO check if name == lsid
+        Pattern p = Pattern.compile("(^urn:lsid:biomoby.org:objectclass:\\S+)",
+                Pattern.CASE_INSENSITIVE);
+        Matcher m = p.matcher(name);
+        isLSID = m.matches();
+
+        if (!isLSID)
+            url = new URL(URL_OBJECT + name);
+        else
+            url = new URL(URL_LSID + name);
+        BufferedReader in = new BufferedReader(new InputStreamReader(url
+                .openStream()));
+        String input;
+        String parent = "Object";
+        LinkedList llHas = new LinkedList();
+        LinkedList llHasa = new LinkedList();
+
+        while ((input = in.readLine()) != null) {
+            StringTokenizer st = new StringTokenizer(input, "\t");
+            if (st.countTokens() > 2) {
+                st.nextToken(); // object name that was queried
+                StringTokenizer lsid = new StringTokenizer(st.nextToken(), ":");
+                String relation = "";
+                while (lsid.hasMoreTokens())
+                    relation = lsid.nextToken(); // isa, hasa, etc
+                if (relation.equalsIgnoreCase("isa"))
+                    parent = st.nextToken();
+                else if (relation.equalsIgnoreCase("has"))
+                    llHas.add(st.nextToken());
+                else if (relation.equalsIgnoreCase("hasa"))
+                    llHasa.add(st.nextToken());
+            }
+        }
+        if (parent.equals("")) {
+            return null;
+        }
+        LinkedList listToReturn = new LinkedList();
+        listToReturn.addFirst(parent);
+        listToReturn.add(llHas);
+        listToReturn.add(llHasa);
+        return listToReturn;
+    }
+
+    /**
+     * 
+     * PRE: None.<p>
+     * POST: a Pair object is returned if the String could be parsed, otherwise, null is returned.
+     * @param rel - the string representation of the relation in the form Attribute(articleName), i.e. Integer(Count).
+     * @return returns a fully constructed Pair object if the relation was valid, otherwise, null is returned. 
+     */
+    public static Pair ParseRelation(String rel) {
+        // integer(length) == attribute(articlename)
+        Pair p = null;
+        int x = -1;
+        String attribute, articleName;
+        if ((x = rel.indexOf("(")) >= 0) {
+            attribute = rel.substring(0, x);
+            articleName = rel.substring(x + 1, rel.length() - 1);
+            p = new Pair(articleName, attribute);
+        }
+
+        return p;
+    }
+
+    /**
+     * 
+     * PRE: None.<p>
+     * POST: Returns the leaf object in a TreePath if path is not null, otherwise, null is returned.
+     * @param path - a TreePath containing the object of interest.
+     * @return returns the name of the leaf object contained in the path.
+     */
+    public static String GetObject(TreePath path) {
+        if (path == null)
+            return null;
+        String s = path.toString();
+        int start = s.lastIndexOf(", ");
+        int end = s.indexOf("]");
+        if (start < 0) {
+            start = 0;
+        }
+        int space = -1;
+        if ((space = s.lastIndexOf(" ")) >= 0) {
+            s = s.substring(space + 1, end);
+        } else
+            s = s.substring(start + 1, end);
+        return s;
+    }
+
+    /**
+     * 
+     * PRE: ll is a valid linkedlist, panelDetails is a valid MobyUserPanel.<p>
+     * POST: All the relations of child are outputted to the MobyUserPanel panelDetails.
+     * @param ll - a linked list created via GetRelations()
+     * @param panelDetails - the MobyUserPanel to output the relationships
+     * @param child - the object that GetRelations() was called with.
+     */
+    public static String WriteToPanel(LinkedList ll, String child) {
+        //System.out.println(ll);
+        StringBuffer sb = new StringBuffer("");
+        sb.append(child + System.getProperty("line.separator") + "ISA: "
+                + System.getProperty("line.separator") + "\t");
+        String parent = (String) ll.removeFirst();
+        sb.append(parent + System.getProperty("line.separator"));
+        LinkedList llhas = (LinkedList) ll.removeFirst();
+        if (llhas != null) {
+            sb.append("Has: ");
+            Iterator i = llhas.iterator();
+            while (i.hasNext()) {
+                Pair p = MobyUtilities.ParseRelation((String) i.next());
+                if (p != null)
+                    sb.append(System.getProperty("line.separator") + "\t"
+                            + p.getAttribute() + " - " + p.getArticlename()
+                            + " ");
+            }
+            sb.append(System.getProperty("line.separator"));
+        }
+        LinkedList llhasa = (LinkedList) ll.removeFirst();
+        if (llhasa != null) {
+            sb.append("Hasa: ");
+            Iterator i = llhasa.iterator();
+            while (i.hasNext()) {
+                Pair p = MobyUtilities.ParseRelation((String) i.next());
+                if (p != null)
+                    sb.append(System.getProperty("line.separator") + "\t"
+                            + p.getAttribute() + "->" + p.getArticlename()
+                            + " ");
+            }
+        }
+        return sb.toString();
+    }
+
+    public static void main(String[] args) throws IOException {
+        LinkedList ll = MobyUtilities.GetRelations("genbank-flatfile");
+        System.out.println(ll.toString());
+        ll = MobyUtilities.GetRelations("urn:lsid:biomoby.org:objectclass:Object");
+        System.out.println(ll.toString());
+    }
+}
\ No newline at end of file



From mwilkinson at pub.open-bio.org  Tue Feb  8 16:49:16 2005
From: mwilkinson at pub.open-bio.org (Mark Wilkinson)
Date: Tue, 8 Feb 2005 11:49:16 -0500
Subject: [MOBY-guts] biomoby commit
Message-ID: <200502081649.j18GnGgD024562@pub.open-bio.org>


mwilkinson
Tue Feb  8 11:49:16 EST 2005
Update of /home/repository/moby/moby-live/Perl/MOBY
In directory pub.open-bio.org:/tmp/cvs-serv24543/MOBY

Modified Files:
	CommonSubs.pm 
Log Message:
thanks to Sophie for squashing this bug.  Crossreferences were not being detected if prefixed by moby: 

moby-live/Perl/MOBY CommonSubs.pm,1.58,1.59
===================================================================
RCS file: /home/repository/moby/moby-live/Perl/MOBY/CommonSubs.pm,v
retrieving revision 1.58
retrieving revision 1.59
diff -u -r1.58 -r1.59
--- /home/repository/moby/moby-live/Perl/MOBY/CommonSubs.pm	2004/12/15 17:49:44	1.58
+++ /home/repository/moby/moby-live/Perl/MOBY/CommonSubs.pm	2005/02/08 16:49:15	1.59
@@ -1617,7 +1617,7 @@
 	$ns = $xref->getAttributeNode( 'moby:namespace' ) unless $ns;
 	return undef unless $ns;
 	my $id = $xref->getAttributeNode( 'id' );
-	$id = $xref->getAttributeNode( 'moby:id' ) unless $ns;
+	$id = $xref->getAttributeNode( 'moby:id' ) unless $id;
 	return undef unless $id;
 	my $XREF = MOBY::CrossReference->new(
 										  type      => "object",



From nopushneva at pub.open-bio.org  Tue Feb  8 23:32:15 2005
From: nopushneva at pub.open-bio.org (Nina Opushneva)
Date: Tue, 8 Feb 2005 18:32:15 -0500
Subject: [MOBY-guts] biomoby commit
Message-ID: <200502082332.j18NWFpI026780@pub.open-bio.org>


nopushneva
Tue Feb  8 18:32:14 EST 2005
Update of /home/repository/moby/moby-live/Perl/MOBY
In directory pub.open-bio.org:/tmp/cvs-serv26754

Modified Files:
	Central.pm 
Log Message:
add the RDFagent call

moby-live/Perl/MOBY Central.pm,1.147,1.148
===================================================================
RCS file: /home/repository/moby/moby-live/Perl/MOBY/Central.pm,v
retrieving revision 1.147
retrieving revision 1.148
diff -u -r1.147 -r1.148
--- /home/repository/moby/moby-live/Perl/MOBY/Central.pm	2005/02/06 21:58:35	1.147
+++ /home/repository/moby/moby-live/Perl/MOBY/Central.pm	2005/02/08 23:32:14	1.148
@@ -1234,6 +1234,26 @@
 		 $OUTPUTS,      $SECONDARY,   $signatureURL
 	  )
 	  = &_registerServicePayload( $payload );
+
+#--------RDFagent call----------------------------------------
+
+if (defined $signatureURL){
+  my $ch = 0;
+  my $i;
+  foreach $i ($serviceName, $serviceType, $AuthURI, $contactEmail, $URL, $desc, $Category){
+       if (defined $i){
+          $ch = 1;
+        }        
+  }
+
+  if ($ch == 0){
+    my $rez = system("/export/home/nina/rdfagent/run-RDFagent ".$signatureURL);
+
+    return &_error("The RDFagent call was successful.  Report will send to you by E-mail","") if ($rez == 0);
+    return &_error("Some problem with a connection or RDF model building","") if ($rez != 0);
+  }
+}
+#---------------------------------------------------------------
 	$authoritativeService = defined( $authoritativeService ) ? 1 : 0;
 	my $error;
 	$error .= "missing serviceName \n" unless defined $serviceName;
@@ -1368,15 +1388,16 @@
 			""
 		);
 	}
-	use MOBY::Client::Central;
-	my $services         = MOBY::Client::Central::_parseServices( '', '', $si );
-	my $service_instance = shift @{$services};
-	my $storage          = new RDF::Core::Storage::Memory;
-	my $model            = new RDF::Core::Model( Storage => $storage );
-	my $RDF_MODEL = MOBY::RDF::ServiceInstanceRDF->new(
-										   model            => $model,
-										   service_instance => $service_instance );
-	my $RDF_XML = $RDF_MODEL->serialize;
+#	use MOBY::Client::Central;
+#	my $services         = MOBY::Client::Central::_parseServices( '', '', $si );
+#	my $service_instance = shift @{$services};
+#	my $storage          = new RDF::Core::Storage::Memory;
+#	my $model            = new RDF::Core::Model( Storage => $storage );
+#	my $RDF_MODEL = MOBY::RDF::ServiceInstanceRDF->new(
+										   #model            => $model,
+										   #service_instance => $service_instance );
+#	my $RDF_XML = $RDF_MODEL->serialize;
+        my $RDF_XML = "";
 	return &_success( "Registration successful",
 					  $SVC->service_instance_id, $RDF_XML );
 }
@@ -3757,4 +3778,39 @@
 	my $XSD;
 	return $XSD;
 }
+
+#=head2 runRDFagent
+
+#Title     :	runRDFagent
+#Usage     :	$MOBY->runRDFagent($inputXML)
+#Function  :	run RDFagent for signatureURL
+#Returns   :	
+#Args      :	
+      
+#inputXML  :
+#<runRDFagent>
+# <RDFfileURL>rdfFileURL</RDFfileURL>
+#</runRDFagent>
+			      
+#=cut
+		
+#sub _runRDFagent{
+		   
+# my ($self)=@_; 
+# my $Parser = new XML::DOM::Parser;
+# my $doc = $Parser->parse($payload);
+# my $Object      = $doc->getDocumentElement();
+# my $obj         = $Object->nodeName;
+# return undef unless ( $obj eq 'runRDFagent' );
+# my $url = &_nodeTextContent( $Object, "RDFfileURL" );
+# my $l = $url->getLength;
+# if ($l == 0){
+#   print "The RDFagent can't run without a parameter";
+# }else{
+#   system("/home/rdfagent/run-RDFagent"+ $url);
+#   print "The RDFagent run saccessfully. A result will sent to you by E-mail";
+# }
+										
+}
 1;
+`



From nopushneva at pub.open-bio.org  Tue Feb  8 23:43:06 2005
From: nopushneva at pub.open-bio.org (Nina Opushneva)
Date: Tue, 8 Feb 2005 18:43:06 -0500
Subject: [MOBY-guts] biomoby commit
Message-ID: <200502082343.j18Nh6I8026858@pub.open-bio.org>


nopushneva
Tue Feb  8 18:43:06 EST 2005
Update of /home/repository/moby/moby-live/Perl/MOBY/Client
In directory pub.open-bio.org:/tmp/cvs-serv26832

Modified Files:
	Central.pm 
Log Message:
added a check for RDFagent call, and call a new RDFbuilder

moby-live/Perl/MOBY/Client Central.pm,1.89,1.90
===================================================================
RCS file: /home/repository/moby/moby-live/Perl/MOBY/Client/Central.pm,v
retrieving revision 1.89
retrieving revision 1.90
diff -u -r1.89 -r1.90
--- /home/repository/moby/moby-live/Perl/MOBY/Client/Central.pm	2005/02/06 22:46:45	1.89
+++ /home/repository/moby/moby-live/Perl/MOBY/Client/Central.pm	2005/02/08 23:43:06	1.90
@@ -778,6 +778,36 @@
 	my $Category = lc( $a{category} );
 	chomp $Category;
 	$Category ||= "";
+
+#____________call RDFagent__________________________________________________
+if (defined $signatureURL){
+  my $ch = 0;
+  my $sign_req;
+    foreach $sign_req ($name, $type, $authURI, $email, $URL, $desc, $Category){
+      if ($sign_req ne ""){
+        $ch = 1;
+
+        }        
+    }  
+     if ($ch == 0){
+ print "call Agent\n";
+	     my $message = "
+		<registerService>
+			<Category></Category>
+			<serviceName></serviceName>
+			<serviceType></serviceType>
+			<Description></Description>
+                        <signatureURL>$signatureURL</signatureURL>
+			<URL></URL>
+			<authURI></authURI>
+			<contactEmail></contactEmail>
+	       </registerService>";		
+         my   ( $return ) = $self->_call( 'default', 'registerService', $message );
+	    return ( $self->parseRegXML( $return ) );
+
+    }
+}
+#____________________________________________________________________________________________
 	return $self->errorRegXML(
 "Only 'moby' and 'wsdl' Service Categories are currently allowed - you gave me $Category"
 	  )
@@ -798,7 +828,7 @@
 			<serviceName>$name</serviceName>
 			<serviceType>$type</serviceType>
 			<Description><![CDATA[$desc]]></Description>
-            <signatureURL>$signatureURL</signatureURL>
+                        <signatureURL>$signatureURL</signatureURL>
 			<URL>$URL</URL>
 			<authURI>$authURI</authURI>
 			<contactEmail>$email</contactEmail>";
@@ -950,7 +980,22 @@
 
 #	my $return = $self->SOAP_connection->call(registerService => ($message))->paramsall;
 	my ( $return ) = $self->_call( 'default', 'registerService', $message );
-	return ( $self->parseRegXML( $return ) );
+#	return ( $self->parseRegXML( $return ) );
+#_______call a new version RDFbuilder (by Eddie Kawas) _________________________________________
+  my $reg = $self->parseRegXML( $return );
+  if ($reg->success == 1){
+  require LWP::UserAgent;
+     
+     my $ua = LWP::UserAgent->new;
+         my $url='http://mobycentral.cbr.nrc.ca:8090/DemoServlet/forms/getSignatureResponse?domain='.$authURI.'&serviceName='.$name;
+	 
+	 my $response = $ua->get($url);
+	 my $rdf = $response->content;
+	 print "$rdf\n"; 
+}	 
+   return $reg;
+#_______________________________________________________________________________________________
+
 }
 
 =head2 registerServiceWSDL
@@ -970,6 +1015,7 @@
 
 #	my $return = $self->SOAP_connection->call(registerServiceWSDL => ($message))->paramsall;
 	my ( $return ) = $self->_call( 'default', 'registerServiceWSDL', $message );
+
 	return ( $self->parseRegXML( $return ) );
 }
 



From gordonp at pub.open-bio.org  Wed Feb  9 17:17:25 2005
From: gordonp at pub.open-bio.org (Paul Gordon)
Date: Wed, 9 Feb 2005 12:17:25 -0500
Subject: [MOBY-guts] biomoby commit
Message-ID: <200502091717.j19HHPY1030820@pub.open-bio.org>


gordonp
Wed Feb  9 12:17:25 EST 2005
Update of /home/repository/moby/moby-live/Java/src/main/org/biomoby/shared
In directory pub.open-bio.org:/tmp/cvs-serv30799/org/biomoby/shared

Added Files:
	MobyDataDateTime.java 
Log Message:
Utility class to deal with painful parsing and creation of ISO 8601 dates (as used by MOBY's DateTime objects)

moby-live/Java/src/main/org/biomoby/shared MobyDataDateTime.java,NONE,1.1


From gordonp at pub.open-bio.org  Wed Feb  9 17:20:38 2005
From: gordonp at pub.open-bio.org (Paul Gordon)
Date: Wed, 9 Feb 2005 12:20:38 -0500
Subject: [MOBY-guts] biomoby commit
Message-ID: <200502091720.j19HKcQQ030874@pub.open-bio.org>


gordonp
Wed Feb  9 12:20:38 EST 2005
Update of /home/repository/moby/moby-live/Java/src/main/org/biomoby/shared
In directory pub.open-bio.org:/tmp/cvs-serv30837/org/biomoby/shared

Modified Files:
	MobyDataFloat.java MobyDataInt.java 
	MobyDataSimpleInstance.java MobyDataString.java 
Log Message:
Updates to correct javadoc errors, plus addition of underlying object accessibility for MOBY Data Instances

moby-live/Java/src/main/org/biomoby/shared MobyDataFloat.java,1.1,1.2 MobyDataInt.java,1.1,1.2 MobyDataSimpleInstance.java,1.3,1.4 MobyDataString.java,1.1,1.2
===================================================================
RCS file: /home/repository/moby/moby-live/Java/src/main/org/biomoby/shared/MobyDataFloat.java,v
retrieving revision 1.1
retrieving revision 1.2
diff -u -r1.1 -r1.2
--- /home/repository/moby/moby-live/Java/src/main/org/biomoby/shared/MobyDataFloat.java	2004/09/03 20:28:16	1.1
+++ /home/repository/moby/moby-live/Java/src/main/org/biomoby/shared/MobyDataFloat.java	2005/02/09 17:20:38	1.2
@@ -61,6 +61,13 @@
 	return copy;
     }
 
+    /**
+     * @return a BigDecimal 
+     */
+    public Object getObject(){
+	return value;
+    }
+
     public String getValue(){
 	return ""+value;
     }

===================================================================
RCS file: /home/repository/moby/moby-live/Java/src/main/org/biomoby/shared/MobyDataInt.java,v
retrieving revision 1.1
retrieving revision 1.2
diff -u -r1.1 -r1.2
--- /home/repository/moby/moby-live/Java/src/main/org/biomoby/shared/MobyDataInt.java	2004/09/03 20:28:16	1.1
+++ /home/repository/moby/moby-live/Java/src/main/org/biomoby/shared/MobyDataInt.java	2005/02/09 17:20:38	1.2
@@ -3,10 +3,10 @@
 import java.math.*;
 
 /**
- * A class representing a MOBY Float primitive.  Note that the 
- * Float notion in MOBY does not define a specific bit precision.
- * All values in this class are stored as Java BigDecimal, which is 
- * arbitary precision to avoid loss of data integrity.
+ * A class representing a MOBY Integer primitive.  Note that the 
+ * Integer notion in MOBY does not define a specific bit precision.
+ * All values in this class are stored as Java BigInteger, which has no 
+ * minmum or maximum value, to avoid loss of data integrity.
  */
 
 public class MobyDataInt extends MobyDataSimpleInstance{
@@ -15,7 +15,8 @@
     
     /**
      * Constructor to use if the incoming value is a number object such as 
-     * Float, Double, Integer, BigDecimal, etc.
+     * Float, Double, Integer, BigInteger, BigDecimal, etc.
+     * Real numbers will be converted to their integer equivalents. 
      */
     public MobyDataInt(String articleName, Number n){
 	super(articleName);
@@ -33,7 +34,7 @@
 
     /**
      * Constructor to use if the incoming value is a primitive.
-     * If you want to pass in a float or int, cast it to a double.
+     * If you want to pass in a float or double, cast it to an int.
      */
     public MobyDataInt(String articleName, int i){
 	super(articleName);
@@ -42,10 +43,10 @@
     }
 
     /**
-     * Constructor to use if the incoming value is a string representing a number 
-     * (including mantissa/exponent format).
+     * Constructor to use if the incoming value is a string representing an integer number. 
+     * 
      *
-     * @throws NumberFormatException if the string does not represent a number
+     * @throws NumberFormatException if the string does not represent an integer number
      */
     public MobyDataInt(String articleName, String stringNumber) throws NumberFormatException{
 	super(articleName);
@@ -61,6 +62,13 @@
 	return copy;
     }
 
+    /**
+     * @return a BigInteger
+     */
+    public Object getObject(){
+	return value;
+    }
+
     public String getValue(){
 	return ""+value;
     }

===================================================================
RCS file: /home/repository/moby/moby-live/Java/src/main/org/biomoby/shared/MobyDataSimpleInstance.java,v
retrieving revision 1.3
retrieving revision 1.4
diff -u -r1.3 -r1.4
--- /home/repository/moby/moby-live/Java/src/main/org/biomoby/shared/MobyDataSimpleInstance.java	2004/09/23 10:20:29	1.3
+++ /home/repository/moby/moby-live/Java/src/main/org/biomoby/shared/MobyDataSimpleInstance.java	2005/02/09 17:20:38	1.4
@@ -132,6 +132,16 @@
     }
 
     /**
+     * Gives access to the Java object instance underlying the MobyData instance.  
+     * For example, to increment a MOBY integer object, call ((BigInteger) (data.getObject()).add(BigInteger.ONE)
+     *
+     * Not yet fully implemented for base objects whose setValue() method has been called.
+     */
+    public Object getObject(){
+	return dataValue;
+    }
+
+    /**
      * Convenience method to get the basic XML representation
      * @return the raw XML representation of the object
      */

===================================================================
RCS file: /home/repository/moby/moby-live/Java/src/main/org/biomoby/shared/MobyDataString.java,v
retrieving revision 1.1
retrieving revision 1.2
diff -u -r1.1 -r1.2
--- /home/repository/moby/moby-live/Java/src/main/org/biomoby/shared/MobyDataString.java	2004/09/03 20:28:16	1.1
+++ /home/repository/moby/moby-live/Java/src/main/org/biomoby/shared/MobyDataString.java	2005/02/09 17:20:38	1.2
@@ -3,10 +3,7 @@
 import java.math.*;
 
 /**
- * A class representing a MOBY Float primitive.  Note that the 
- * Float notion in MOBY does not define a specific bit precision.
- * All values in this class are stored as Java BigDecimal, which is 
- * arbitary precision to avoid loss of data integrity.
+ * A class representing a MOBY String primitive. 
  */
 
 public class MobyDataString extends MobyDataSimpleInstance{
@@ -44,17 +41,33 @@
 	return copy;
     }
 
+    /**
+     * @return a String
+     */
+    public Object getObject(){
+	return value;
+    }
+
     public String getValue(){
 	return value;
     }
 
+    /**
+     * This class sanitizes strings of XML escape characters such as the ampersand (&amp;) and the 
+     * less-than sign (&lt;).  WARNING: this method will not escape ampersand in the string "&amp;amp;", 
+     * or '&amp;#x26;' style character references.  We will assume that is this case you've probably 
+     * already written the string as XML. 
+     *
+     * WARNING: As of yet, we do not deal with the false escaping of strings containg already-escaped 
+     * CDATA sections!
+     */
     public String toXML(){
 	MobyNamespace[] ns = getNamespaces();
 	if(xmlMode == SERVICE_XML_MODE){
 	    String tmpValue = value;
 	    if(tmpValue != null){
 		tmpValue = tmpValue.replaceAll("<", "&lt;");
-		tmpValue = tmpValue.replaceAll("&", "&amp;");
+		tmpValue = tmpValue.replaceAll("&(?!(amp|#x\\d+);)", "&amp;");
 	    }
 	    
 	    return "<moby:String moby:namespace=\""+ 



From gordonp at pub.open-bio.org  Wed Feb  9 17:39:17 2005
From: gordonp at pub.open-bio.org (Paul Gordon)
Date: Wed, 9 Feb 2005 12:39:17 -0500
Subject: [MOBY-guts] biomoby commit
Message-ID: <200502091739.j19HdHEF030977@pub.open-bio.org>


gordonp
Wed Feb  9 12:39:17 EST 2005
Update of /home/repository/moby/moby-live/Java/src/main/org/biomoby/shared
In directory pub.open-bio.org:/tmp/cvs-serv30952/org/biomoby/shared

Modified Files:
	MobyPrefixResolver.java 
Log Message:
Changed attribute namespace conditional to check for both empty string and null, as different parsers can use one or the other to represent the fact that an attribute is not bound to a namespace

moby-live/Java/src/main/org/biomoby/shared MobyPrefixResolver.java,1.2,1.3
===================================================================
RCS file: /home/repository/moby/moby-live/Java/src/main/org/biomoby/shared/MobyPrefixResolver.java,v
retrieving revision 1.2
retrieving revision 1.3
diff -u -r1.2 -r1.3
--- /home/repository/moby/moby-live/Java/src/main/org/biomoby/shared/MobyPrefixResolver.java	2004/07/07 16:02:47	1.2
+++ /home/repository/moby/moby-live/Java/src/main/org/biomoby/shared/MobyPrefixResolver.java	2005/02/09 17:39:17	1.3
@@ -45,7 +45,7 @@
      */
     public static String getAttr(org.w3c.dom.Element e, String attrName){
 	String value = e.getAttributeNS(MOBY_XML_NAMESPACE, attrName);
-	if(value == null){
+	if(value == null || "".equals(value)){
 	    value = e.getAttributeNS(null, attrName);
 	}
 	return value;



From kawas at pub.open-bio.org  Wed Feb  9 18:26:41 2005
From: kawas at pub.open-bio.org (Eddie Kawas)
Date: Wed, 9 Feb 2005 13:26:41 -0500
Subject: [MOBY-guts] biomoby commit
Message-ID: <200502091826.j19IQfEA031153@pub.open-bio.org>


kawas
Wed Feb  9 13:26:41 EST 2005
Update of /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/gui/serviceInstanceCreationTool
In directory pub.open-bio.org:/tmp/cvs-serv31128/org/biomoby/client/gui/serviceInstanceCreationTool

Modified Files:
	MobyUtilities.java 
Log Message:
Fixed GetRelations so that it executes quickly and doesnt spin off
into infinite loops with bad input - Eddie

moby-live/Java/src/main/org/biomoby/client/gui/serviceInstanceCreationTool MobyUtilities.java,1.2,1.3
===================================================================
RCS file: /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/gui/serviceInstanceCreationTool/MobyUtilities.java,v
retrieving revision 1.2
retrieving revision 1.3
diff -u -r1.2 -r1.3
--- /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/gui/serviceInstanceCreationTool/MobyUtilities.java	2005/02/08 01:50:31	1.2
+++ /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/gui/serviceInstanceCreationTool/MobyUtilities.java	2005/02/09 18:26:41	1.3
@@ -4,6 +4,7 @@
 import java.io.IOException;
 import java.io.InputStreamReader;
 import java.net.URL;
+import java.util.ArrayList;
 import java.util.Iterator;
 import java.util.LinkedList;
 import java.util.StringTokenizer;
@@ -12,6 +13,9 @@
 
 import javax.swing.tree.TreePath;
 
+import org.biomoby.client.gui.util.MobyObjectPrimitiveExtractor;
+import org.biomoby.client.gui.util.Triples;
+
 /**
  * Utilities that are useful for retrieving information about certain objects, parsing objects, etc.
  * @author Eddie Kawas
@@ -21,12 +25,6 @@
  */
 
 public class MobyUtilities {
-    // strings that when concatenated return the attributes, articlename, etc of an object
-    final private static String URL_OBJECT = new String(
-            "http://mobycentral.cbr.nrc.ca/cgi-bin/types/Objects?name=");
-
-    final private static String URL_LSID = new String(
-            "http://mobycentral.cbr.nrc.ca/cgi-bin/types/Objects?lsid_name=");
 
     /**
      * PRE: None.<p>
@@ -40,44 +38,31 @@
     public static LinkedList GetRelations(String name) throws IOException {
         URL url = null;
         boolean isLSID = false;
-        // TODO check if name == lsid
-        Pattern p = Pattern.compile("(^urn:lsid:biomoby.org:objectclass:\\S+)",
+        Pattern p = Pattern.compile("(^urn:lsid:biomoby.org:objectclass:\\S+$)",
                 Pattern.CASE_INSENSITIVE);
         Matcher m = p.matcher(name);
         isLSID = m.matches();
+        if (isLSID) {
+            int x = name.lastIndexOf(":")+1;
+            name = name.substring(x);
+        }
 
-        if (!isLSID)
-            url = new URL(URL_OBJECT + name);
-        else
-            url = new URL(URL_LSID + name);
-        BufferedReader in = new BufferedReader(new InputStreamReader(url
-                .openStream()));
-        String input;
-        String parent = "Object";
         LinkedList llHas = new LinkedList();
         LinkedList llHasa = new LinkedList();
-
-        while ((input = in.readLine()) != null) {
-            StringTokenizer st = new StringTokenizer(input, "\t");
-            if (st.countTokens() > 2) {
-                st.nextToken(); // object name that was queried
-                StringTokenizer lsid = new StringTokenizer(st.nextToken(), ":");
-                String relation = "";
-                while (lsid.hasMoreTokens())
-                    relation = lsid.nextToken(); // isa, hasa, etc
-                if (relation.equalsIgnoreCase("isa"))
-                    parent = st.nextToken();
-                else if (relation.equalsIgnoreCase("has"))
-                    llHas.add(st.nextToken());
-                else if (relation.equalsIgnoreCase("hasa"))
-                    llHasa.add(st.nextToken());
+        MobyObjectPrimitiveExtractor mope = new MobyObjectPrimitiveExtractor();
+        ArrayList al = mope.getPrimitives(name);
+        for (Iterator x = al.iterator(); x.hasNext();) {
+            Triples t = (Triples)x.next();
+            if (t.getType() == Triples.HAS) {
+                llHas.add(t.getPrimitive());
+            }
+            if (t.getType() == Triples.HASA) {
+                llHasa.add(t.getPrimitive());
             }
         }
-        if (parent.equals("")) {
-            return null;
-        }
+        // set up the return list
         LinkedList listToReturn = new LinkedList();
-        listToReturn.addFirst(parent);
+        listToReturn.addFirst("Object");
         listToReturn.add(llHas);
         listToReturn.add(llHasa);
         return listToReturn;
@@ -172,9 +157,9 @@
     }
 
     public static void main(String[] args) throws IOException {
-        LinkedList ll = MobyUtilities.GetRelations("genbank-flatfile");
+        LinkedList ll = MobyUtilities.GetRelations("DNASequence");
         System.out.println(ll.toString());
-        ll = MobyUtilities.GetRelations("urn:lsid:biomoby.org:objectclass:Object");
+        ll = MobyUtilities.GetRelations("urn:lsid:biomoby.org:objectclass:DNASequence");
         System.out.println(ll.toString());
     }
 }
\ No newline at end of file



From nopushneva at pub.open-bio.org  Thu Feb 10 00:17:45 2005
From: nopushneva at pub.open-bio.org (Nina Opushneva)
Date: Wed, 9 Feb 2005 19:17:45 -0500
Subject: [MOBY-guts] biomoby commit
Message-ID: <200502100017.j1A0HjbZ032063@pub.open-bio.org>


nopushneva
Wed Feb  9 19:17:45 EST 2005
Update of /home/repository/moby/moby-live/Perl/MOBY
In directory pub.open-bio.org:/tmp/cvs-serv32037

Modified Files:
	Central.pm 
Log Message:
delete some typo

moby-live/Perl/MOBY Central.pm,1.148,1.149
===================================================================
RCS file: /home/repository/moby/moby-live/Perl/MOBY/Central.pm,v
retrieving revision 1.148
retrieving revision 1.149
diff -u -r1.148 -r1.149
--- /home/repository/moby/moby-live/Perl/MOBY/Central.pm	2005/02/08 23:32:14	1.148
+++ /home/repository/moby/moby-live/Perl/MOBY/Central.pm	2005/02/10 00:17:45	1.149
@@ -3779,38 +3779,6 @@
 	return $XSD;
 }
 
-#=head2 runRDFagent
 
-#Title     :	runRDFagent
-#Usage     :	$MOBY->runRDFagent($inputXML)
-#Function  :	run RDFagent for signatureURL
-#Returns   :	
-#Args      :	
-      
-#inputXML  :
-#<runRDFagent>
-# <RDFfileURL>rdfFileURL</RDFfileURL>
-#</runRDFagent>
-			      
-#=cut
-		
-#sub _runRDFagent{
-		   
-# my ($self)=@_; 
-# my $Parser = new XML::DOM::Parser;
-# my $doc = $Parser->parse($payload);
-# my $Object      = $doc->getDocumentElement();
-# my $obj         = $Object->nodeName;
-# return undef unless ( $obj eq 'runRDFagent' );
-# my $url = &_nodeTextContent( $Object, "RDFfileURL" );
-# my $l = $url->getLength;
-# if ($l == 0){
-#   print "The RDFagent can't run without a parameter";
-# }else{
-#   system("/home/rdfagent/run-RDFagent"+ $url);
-#   print "The RDFagent run saccessfully. A result will sent to you by E-mail";
-# }
-										
-}
 1;
-`
+



From gordonp at pub.open-bio.org  Tue Feb 15 17:47:40 2005
From: gordonp at pub.open-bio.org (Paul Gordon)
Date: Tue, 15 Feb 2005 12:47:40 -0500
Subject: [MOBY-guts] biomoby commit
Message-ID: <200502151747.j1FHlevD006970@pub.open-bio.org>


gordonp
Tue Feb 15 12:47:40 EST 2005
Update of /home/repository/moby/moby-live/Java/src/main/org/biomoby/client
In directory pub.open-bio.org:/tmp/cvs-serv6945

Modified Files:
	MobyRequest.java 
Log Message:
Added conveinece method to create XML envelope when you only have one input request to process

moby-live/Java/src/main/org/biomoby/client MobyRequest.java,1.6,1.7
===================================================================
RCS file: /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/MobyRequest.java,v
retrieving revision 1.6
retrieving revision 1.7
diff -u -r1.6 -r1.7
--- /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/MobyRequest.java	2005/02/03 22:37:30	1.6
+++ /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/MobyRequest.java	2005/02/15 17:47:39	1.7
@@ -543,6 +543,11 @@
 	return domDoc.getDocumentElement();
     }
 
+    public String convertMOBYDataToMOBYRequest(MobyDataInstance data, MobyDataSecondaryInstance[] secondary) throws MobyException{
+        MobyDataInstance[] mdsis = new MobyDataInstance[1];
+        mdsis[0] = data;
+        return convertMOBYDataToMOBYRequest(mdsis, secondary);
+    }
 
     /**
      * @param data the array of input parameters to put in a MOBY XML request



From kawas at pub.open-bio.org  Wed Feb 16 15:38:28 2005
From: kawas at pub.open-bio.org (Eddie Kawas)
Date: Wed, 16 Feb 2005 10:38:28 -0500
Subject: [MOBY-guts] biomoby commit
Message-ID: <200502161538.j1GFcSic011487@pub.open-bio.org>


kawas
Wed Feb 16 10:38:28 EST 2005
Update of /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/gui/util
In directory pub.open-bio.org:/tmp/cvs-serv11466/org/biomoby/client/gui/util

Added Files:
	MobyObjectPrimitiveExtractor.java Triples.java 
Log Message:
Adding MobyObjectPrimitiveExtractor and Triples. May be duplicating code, but are necessary to ensure that other classes compile.

moby-live/Java/src/main/org/biomoby/client/gui/util MobyObjectPrimitiveExtractor.java,NONE,1.1 Triples.java,NONE,1.1


From yanwong at pub.open-bio.org  Wed Feb 16 15:38:46 2005
From: yanwong at pub.open-bio.org (Yan Wong)
Date: Wed, 16 Feb 2005 10:38:46 -0500
Subject: [MOBY-guts] biomoby commit
Message-ID: <200502161538.j1GFck0o011539@pub.open-bio.org>


yanwong
Wed Feb 16 10:38:46 EST 2005
Update of /home/repository/moby/moby-live/Python/bioMoby
In directory pub.open-bio.org:/tmp/cvs-serv11495/bioMoby

Modified Files:
	mobyDataTypes.py 
Log Message:


moby-live/Python/bioMoby mobyDataTypes.py,1.14,1.15
===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/mobyDataTypes.py,v
retrieving revision 1.14
retrieving revision 1.15
diff -u -r1.14 -r1.15
--- /home/repository/moby/moby-live/Python/bioMoby/mobyDataTypes.py	2005/02/04 16:03:40	1.14
+++ /home/repository/moby/moby-live/Python/bioMoby/mobyDataTypes.py	2005/02/16 15:38:46	1.15
@@ -172,7 +172,7 @@
         
         self.content=[]
         
-        if elem.nodeName.split(":")>1:
+        if elem.nodeName.split(":")==2:
             self.__prefix__=elem.nodeName.split(":")[0]
         
         #Set the object's attributes
@@ -406,8 +406,11 @@
                     p=Parameter()
                     p.fromMoby(datum)
                     data.append(p)
-                    
-            self.queryData[queryID]=data
+            
+            if not queryID in self.queryData.keys():
+                self.queryData[queryID]=data
+            else:
+                self.queryData[str(len(self.queryData.keys())+1)]=data
     
     def __getitem__(self, key):
         """Get a query from his name



From yanwong at pub.open-bio.org  Wed Feb 16 15:38:46 2005
From: yanwong at pub.open-bio.org (Yan Wong)
Date: Wed, 16 Feb 2005 10:38:46 -0500
Subject: [MOBY-guts] biomoby commit
Message-ID: <200502161538.j1GFckEr011520@pub.open-bio.org>


yanwong
Wed Feb 16 10:38:46 EST 2005
Update of /home/repository/moby/moby-live/Python
In directory pub.open-bio.org:/tmp/cvs-serv11495

Modified Files:
	changelog 
Log Message:


moby-live/Python changelog,1.5,1.6
===================================================================
RCS file: /home/repository/moby/moby-live/Python/changelog,v
retrieving revision 1.5
retrieving revision 1.6
diff -u -r1.5 -r1.6
--- /home/repository/moby/moby-live/Python/changelog	2005/01/27 08:44:04	1.5
+++ /home/repository/moby/moby-live/Python/changelog	2005/02/16 15:38:46	1.6
@@ -63,3 +63,4 @@
      The objectBrowser serializes the results in a file in order to save time of retrieval :p 
 
      Some cosmetic changes on the code.
+0.8p1: Changed some code about serialization/deserialization



From yanwong at pub.open-bio.org  Thu Feb 17 13:20:38 2005
From: yanwong at pub.open-bio.org (Yan Wong)
Date: Thu, 17 Feb 2005 08:20:38 -0500
Subject: [MOBY-guts] biomoby commit
Message-ID: <200502171320.j1HDKcGc017174@pub.open-bio.org>


yanwong
Thu Feb 17 08:20:37 EST 2005
Update of /home/repository/moby/moby-live/Python/bioMoby
In directory pub.open-bio.org:/tmp/cvs-serv17142/bioMoby

Modified Files:
	mobyDataTypes.py 
Log Message:

Corrected a bug in Mobycontent that prevent it to fill the properties servicenotes and authority

moby-live/Python/bioMoby mobyDataTypes.py,1.15,1.16
===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/mobyDataTypes.py,v
retrieving revision 1.15
retrieving revision 1.16
diff -u -r1.15 -r1.16
--- /home/repository/moby/moby-live/Python/bioMoby/mobyDataTypes.py	2005/02/16 15:38:46	1.15
+++ /home/repository/moby/moby-live/Python/bioMoby/mobyDataTypes.py	2005/02/17 13:20:37	1.16
@@ -364,6 +364,27 @@
         if isinstance(xmlObject, str):
             doc=parseString(xmlObject)
         
+        #Get the authority
+        authnode=doc.getElementsByTagName("mobyContent")
+        
+        if not authnode:
+            authnode=doc.getElementsByTagName("moby:mobyContent")
+            
+        if authnode:
+            self.authority=authnode[0].getAttribute("authority")
+        
+        if self.authority=="":
+            self.authority=authnode[0].getAttribute("moby:authority")
+        
+        #Get the service notes
+        servicenodes=doc.getElementsByTagName("serviceNotes")
+        
+        if not servicenodes:
+            servicenodes=doc.getElementsByTagName("moby:serviceNotes")
+        
+        if servicenodes and servicenodes[0].firstChild:
+            self.servicenotes=servicenodes[0].firstChild.nodeValue
+        
         mdl=doc.getElementsByTagName('mobyData')
         
         if not mdl:



From mwilkinson at pub.open-bio.org  Fri Feb 18 15:21:03 2005
From: mwilkinson at pub.open-bio.org (Mark Wilkinson)
Date: Fri, 18 Feb 2005 10:21:03 -0500
Subject: [MOBY-guts] biomoby commit
Message-ID: <200502181521.j1IFL3cd026610@pub.open-bio.org>


mwilkinson
Fri Feb 18 10:21:03 EST 2005
Update of /home/repository/moby/moby-live/Perl
In directory pub.open-bio.org:/tmp/cvs-serv26591

Modified Files:
	Makefile.PL 
Log Message:
switching from XML DOM to XML LibXML in the Makefile depedencies

moby-live/Perl Makefile.PL,1.6,1.7
===================================================================
RCS file: /home/repository/moby/moby-live/Perl/Makefile.PL,v
retrieving revision 1.6
retrieving revision 1.7
diff -u -r1.6 -r1.7
--- /home/repository/moby/moby-live/Perl/Makefile.PL	2003/11/12 22:33:09	1.6
+++ /home/repository/moby/moby-live/Perl/Makefile.PL	2005/02/18 15:21:03	1.7
@@ -76,7 +76,7 @@
 	      'VERSION'	      => $VERSION, 
 	      'PREREQ_PM'     => {
               'SOAP::Lite' => 0.55,
-              'XML::DOM' => 1.42,
+              'XML::LibXML' => 1.58,
 	      }, # e.g., Module::Name => 1.1
 	      #'PM_FILTER'     => "", 
 	      ($] >= 5.005 ?    ## Add these new keywords supported since 5.005



From yanwong at pub.open-bio.org  Fri Feb 18 15:54:10 2005
From: yanwong at pub.open-bio.org (Yan Wong)
Date: Fri, 18 Feb 2005 10:54:10 -0500
Subject: [MOBY-guts] biomoby commit
Message-ID: <200502181554.j1IFsAvZ026720@pub.open-bio.org>


yanwong
Fri Feb 18 10:54:10 EST 2005
Update of /home/repository/moby/moby-live/Python/bioMoby
In directory pub.open-bio.org:/tmp/cvs-serv26689

Modified Files:
	mobyDataTypes.py mobyMarshal.py 
Log Message:
The code has been modified in order to implement Provision Information Block
Actually, PIB is only a set of string :

  o.__PIB__=["<Remarks author= \"an Author\">this small remark will appear in the PIB</Remarks>"]

moby-live/Python/bioMoby mobyDataTypes.py,1.16,1.17 mobyMarshal.py,1.5,1.6
===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/mobyDataTypes.py,v
retrieving revision 1.16
retrieving revision 1.17
diff -u -r1.16 -r1.17
--- /home/repository/moby/moby-live/Python/bioMoby/mobyDataTypes.py	2005/02/17 13:20:37	1.16
+++ /home/repository/moby/moby-live/Python/bioMoby/mobyDataTypes.py	2005/02/18 15:54:10	1.17
@@ -130,7 +130,9 @@
             result.append("<ProvisionInformation>")
             
             for aPIB in self.__PIB__:
-                result.append(aPIB.toMoby())
+                #Decide that a PIB will be a string where people can put its
+                #own stuff
+                result.append(str(aPIB))
                 
             result.append("</ProvisionInformation>")
         
@@ -192,6 +194,9 @@
                             anObj=MobyObject()
                             anObj.fromMoby(aCross)
                             self.__cross__.append(anObj)
+                elif child.localName=="ProvisionInformation":
+                    for aPIB in child.childNodes:
+                        self.__PIB__.append(aPIB.toxml())
                 else:
                     #Do the same for the other objects
                     associatedObjectName=child.getAttribute("moby:articleName")

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/mobyMarshal.py,v
retrieving revision 1.5
retrieving revision 1.6
diff -u -r1.5 -r1.6
--- /home/repository/moby/moby-live/Python/bioMoby/mobyMarshal.py	2005/02/04 12:58:24	1.5
+++ /home/repository/moby/moby-live/Python/bioMoby/mobyMarshal.py	2005/02/18 15:54:10	1.6
@@ -280,55 +280,13 @@
         
         typeName="GMoby%s"%str(value.localName)
         
-        from bioMoby.mobyDataTypes import MobyGeneric
+        from bioMoby.mobyDataTypes import MobyObject
         
-        NewType=type(typeName, (MobyGeneric,), {})
+        NewType=type(typeName, (MobyObject,), {})
         
         anObject=NewType()
         
-        anObject.__prefix__="moby"
-        anObject.__tag__=str(value.localName)
-        
-        for tupleAttribute in value.attributes.itemsNS():
-            #First item, second field:
-            setattr(anObject, str(tupleAttribute[0][1]), str(tupleAttribute[1]))
-        
-        i=0    
-        for elem in filter(filterFunc, value.childNodes):
-            methodName="m_%s"%str(elem.localName)
-            
-            articleName=elem.getAttribute("moby:articleName")
-            
-            if not articleName:
-                articleName=elem.getAttribute("articleName")
-            
-            if not articleName:
-                articleName="attribute_%s"%i
-            
-            if hasattr(self, methodName):
-                prop=getattr(self, methodName)(elem)
-            else:
-                prop=self.m_Object(elem)
-            
-            if hasattr(anObject, articleName):
-                t=prop
-                if not type(getattr(anObject, articleName)) is list:
-                    t=getattr(anObject, articleName)
-                    setattr(anObject, articleName, [])
-                getattr(anObject, articleName).append(t)
-            else:
-                setattr(anObject, articleName, prop)
-            i+=1
-        
-        content=[]
-        
-        isContentNode= lambda x: x.nodeType==x.TEXT_NODE or x.nodeType==x.CDATA_SECTION_NODE
-        
-        for elem in filter(isContentNode, value.childNodes):
-            content.append(str(elem.nodeValue))
-        
-        if content:
-            anObject.content(r"".join(content))
+        anObject.fromMoby(value)
         
         return anObject
 



From yanwong at pub.open-bio.org  Fri Feb 18 15:58:21 2005
From: yanwong at pub.open-bio.org (Yan Wong)
Date: Fri, 18 Feb 2005 10:58:21 -0500
Subject: [MOBY-guts] biomoby commit
Message-ID: <200502181558.j1IFwL3R026773@pub.open-bio.org>


yanwong
Fri Feb 18 10:58:21 EST 2005
Update of /home/repository/moby/moby-live/Python
In directory pub.open-bio.org:/tmp/cvs-serv26740

Modified Files:
	PKG-INFO README changelog 
Log Message:
Implementation of the PIB

moby-live/Python PKG-INFO,1.5,1.6 README,1.4,1.5 changelog,1.6,1.7
===================================================================
RCS file: /home/repository/moby/moby-live/Python/PKG-INFO,v
retrieving revision 1.5
retrieving revision 1.6
diff -u -r1.5 -r1.6
--- /home/repository/moby/moby-live/Python/PKG-INFO	2005/01/27 08:44:04	1.5
+++ /home/repository/moby/moby-live/Python/PKG-INFO	2005/02/18 15:58:21	1.6
@@ -1,6 +1,6 @@
 Metadata-Version: 1.0
 Name: bioMoby
-Version: 0.8
+Version: 0.9
 Summary: Python interface for bioMoby
 Home-page: http://bioserv.rpbs.jussieu.fr
 Author: Yan Wong

===================================================================
RCS file: /home/repository/moby/moby-live/Python/README,v
retrieving revision 1.4
retrieving revision 1.5
diff -u -r1.4 -r1.5
--- /home/repository/moby/moby-live/Python/README	2004/12/08 14:57:28	1.4
+++ /home/repository/moby/moby-live/Python/README	2005/02/18 15:58:21	1.5
@@ -49,5 +49,5 @@
 +tutorials: Some scripts in order to show some of the functions
 +webservice: Example of webservice in Python using bioMoby-python's API
 +utils: moby2python is a program that convert mobyObject definitions into Python files (all derived from MobyObject and has a personalized fromMoby method)
-+ZSI-1.5.0-patched: the patched version of ZSI 1.5.0 
++ZSI-1.6.0 
 Suggestions welcome!

===================================================================
RCS file: /home/repository/moby/moby-live/Python/changelog,v
retrieving revision 1.6
retrieving revision 1.7
diff -u -r1.6 -r1.7
--- /home/repository/moby/moby-live/Python/changelog	2005/02/16 15:38:46	1.6
+++ /home/repository/moby/moby-live/Python/changelog	2005/02/18 15:58:21	1.7
@@ -63,4 +63,7 @@
      The objectBrowser serializes the results in a file in order to save time of retrieval :p 
 
      Some cosmetic changes on the code.
+
 0.8p1: Changed some code about serialization/deserialization
+
+0.9: PIB implemented as a set of string in the __PIB__ field



From kawas at pub.open-bio.org  Wed Feb 23 15:39:07 2005
From: kawas at pub.open-bio.org (Eddie Kawas)
Date: Wed, 23 Feb 2005 10:39:07 -0500
Subject: [MOBY-guts] biomoby commit
Message-ID: <200502231539.j1NFd7HO027915@pub.open-bio.org>


kawas
Wed Feb 23 10:39:06 EST 2005
Update of /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/gui/serviceInstanceCreationTool
In directory pub.open-bio.org:/tmp/cvs-serv27890/org/biomoby/client/gui/serviceInstanceCreationTool

Modified Files:
	MobyUtilities.java 
Log Message:
Fixed imports and removed getRelations() - see getPrimitives(...)
in MobyObjectPrimitiveExtractor instead.
Eddie

moby-live/Java/src/main/org/biomoby/client/gui/serviceInstanceCreationTool MobyUtilities.java,1.3,1.4
===================================================================
RCS file: /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/gui/serviceInstanceCreationTool/MobyUtilities.java,v
retrieving revision 1.3
retrieving revision 1.4
diff -u -r1.3 -r1.4
--- /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/gui/serviceInstanceCreationTool/MobyUtilities.java	2005/02/09 18:26:41	1.3
+++ /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/gui/serviceInstanceCreationTool/MobyUtilities.java	2005/02/23 15:39:06	1.4
@@ -1,21 +1,11 @@
 package org.biomoby.client.gui.serviceInstanceCreationTool;
 
-import java.io.BufferedReader;
 import java.io.IOException;
-import java.io.InputStreamReader;
-import java.net.URL;
-import java.util.ArrayList;
 import java.util.Iterator;
 import java.util.LinkedList;
-import java.util.StringTokenizer;
-import java.util.regex.Matcher;
-import java.util.regex.Pattern;
 
 import javax.swing.tree.TreePath;
 
-import org.biomoby.client.gui.util.MobyObjectPrimitiveExtractor;
-import org.biomoby.client.gui.util.Triples;
-
 /**
  * Utilities that are useful for retrieving information about certain objects, parsing objects, etc.
  * @author Eddie Kawas
@@ -27,45 +17,11 @@
 public class MobyUtilities {
 
     /**
-     * PRE: None.<p>
-     * POST: a linked list of all the relations is returned, such that:<p>
-     * => The first item in the list is a string representation of the parent<p>
-     * => The second item is a linked list of all the 'HAS' container relationships<p>
-     * => The third item is a linked list of all the 'HASA' container relationships
-     * @param name, the name of the object to query for - can be an Moby Object LSID.
-     * @return returns a linked list {String, LinkedList, LinkedList} of relationships
+     * @deprecated please see MobyObjectPrimitiveExtractor.java
      */
     public static LinkedList GetRelations(String name) throws IOException {
-        URL url = null;
-        boolean isLSID = false;
-        Pattern p = Pattern.compile("(^urn:lsid:biomoby.org:objectclass:\\S+$)",
-                Pattern.CASE_INSENSITIVE);
-        Matcher m = p.matcher(name);
-        isLSID = m.matches();
-        if (isLSID) {
-            int x = name.lastIndexOf(":")+1;
-            name = name.substring(x);
-        }
-
-        LinkedList llHas = new LinkedList();
-        LinkedList llHasa = new LinkedList();
-        MobyObjectPrimitiveExtractor mope = new MobyObjectPrimitiveExtractor();
-        ArrayList al = mope.getPrimitives(name);
-        for (Iterator x = al.iterator(); x.hasNext();) {
-            Triples t = (Triples)x.next();
-            if (t.getType() == Triples.HAS) {
-                llHas.add(t.getPrimitive());
-            }
-            if (t.getType() == Triples.HASA) {
-                llHasa.add(t.getPrimitive());
-            }
-        }
-        // set up the return list
-        LinkedList listToReturn = new LinkedList();
-        listToReturn.addFirst("Object");
-        listToReturn.add(llHas);
-        listToReturn.add(llHasa);
-        return listToReturn;
+        
+        return new LinkedList();
     }
 
     /**



From kawas at pub.open-bio.org  Wed Feb 23 15:41:03 2005
From: kawas at pub.open-bio.org (Eddie Kawas)
Date: Wed, 23 Feb 2005 10:41:03 -0500
Subject: [MOBY-guts] biomoby commit
Message-ID: <200502231541.j1NFf3iM028054@pub.open-bio.org>


kawas
Wed Feb 23 10:41:03 EST 2005
Update of /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/gui/util
In directory pub.open-bio.org:/tmp/cvs-serv28029/org/biomoby/client/gui/util

Modified Files:
	MobyObjectPrimitiveExtractor.java 
Log Message:
Corrected the use of Dom from JDOM to w3c DOM to make class compatible
with other jMoby classes.
Eddie

moby-live/Java/src/main/org/biomoby/client/gui/util MobyObjectPrimitiveExtractor.java,1.1,1.2
===================================================================
RCS file: /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/gui/util/MobyObjectPrimitiveExtractor.java,v
retrieving revision 1.1
retrieving revision 1.2
diff -u -r1.1 -r1.2
--- /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/gui/util/MobyObjectPrimitiveExtractor.java	2005/02/16 15:38:28	1.1
+++ /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/gui/util/MobyObjectPrimitiveExtractor.java	2005/02/23 15:41:03	1.2
@@ -5,60 +5,91 @@
 package org.biomoby.client.gui.util;
 
 import java.io.BufferedReader;
-import java.io.ByteArrayInputStream;
 import java.io.ByteArrayOutputStream;
 import java.io.IOException;
 import java.io.InputStreamReader;
+import java.io.OutputStream;
+import java.io.StringReader;
 import java.net.MalformedURLException;
 import java.net.URL;
 import java.util.ArrayList;
 import java.util.Iterator;
-import java.util.List;
 
+import javax.xml.parsers.DocumentBuilder;
+import javax.xml.parsers.DocumentBuilderFactory;
 import javax.xml.parsers.ParserConfigurationException;
+import javax.xml.transform.Transformer;
+import javax.xml.transform.TransformerConfigurationException;
+import javax.xml.transform.TransformerException;
+import javax.xml.transform.TransformerFactory;
+import javax.xml.transform.dom.DOMSource;
+import javax.xml.transform.stream.StreamResult;
 
-import org.jdom.Attribute;
-import org.jdom.Document;
-import org.jdom.Element;
-import org.jdom.JDOMException;
-import org.jdom.Namespace;
-import org.jdom.input.SAXBuilder;
+import org.biomoby.shared.MobyDataFloat;
+import org.biomoby.shared.MobyDataInt;
+import org.biomoby.shared.MobyDataSimpleInstance;
+import org.biomoby.shared.MobyDataString;
+import org.biomoby.shared.MobyDataType;
+import org.jdom.input.DOMBuilder;
 import org.jdom.output.Format;
 import org.jdom.output.XMLOutputter;
+import org.w3c.dom.Document;
+import org.w3c.dom.Element;
+import org.w3c.dom.Node;
+import org.w3c.dom.NodeList;
+import org.xml.sax.InputSource;
 import org.xml.sax.SAXException;
 
-import com.hp.hpl.jena.vocabulary.RDF;
-import com.hp.hpl.jena.vocabulary.RDFS;
-
 /**
  * @author Eddie Kawas
- * <p>Created for
  * <p>This class was created to ...
  * <p>For questions, comments, or bugs
  * <p>email me at edward.kawas at gmail.com
  */
 public class MobyObjectPrimitiveExtractor {
     final private static String URL_OBJECT = new String(
-    	"http://mobycentral.cbr.nrc.ca:8090/authority/metadata?lsid=");
-    final static Namespace HAS = Namespace.getNamespace("has","http://biomoby.org/RESOURCES/MOBY-S/Predicates#");
-    final static Namespace HASA = Namespace.getNamespace("hasa","http://biomoby.org/RESOURCES/MOBY-S/Predicates#");
-    final static Namespace ARTICLE = Namespace.getNamespace("articleName","http://biomoby.org/RESOURCES/MOBY-S/Predicates#");
-    final static String[] PRIMITIVES = {"String", "Float", "Integer", "Object", "DateTime"};
+            "http://mobycentral.cbr.nrc.ca:8090/authority/metadata?lsid=");
+
+    final static String[] PRIMITIVES = {
+            "String",
+            "Float",
+            "Integer",
+            "Object",
+            "DateTime" };
+
+    final static String MOBY = "http://www.biomoby.org/moby";
+
+    /**
+     *  
+     * <b>PRE:</b><p>
+     * <b>POST:</b><p>
+     * @param MobyElement - The Element containing the MOBY Object to find primitives for
+     * @return an array of MobyDataSimpleInstances that are the primitives for MobyElement.
+     */
+    public MobyDataSimpleInstance[] getPrimitives(Element MobyElement) {
+        return getPrimitivesHelper(MobyElement.getTagName());
+    }
+
     /**
      *  
      * <b>PRE:</b><p>
      * <b>POST:</b><p>
-     * @param name - name of the Moby Object to decompose
-     * @return Triples[] - an array of Triples or null if an error occured
-     * @throws ParserConfigurationException
-     * @throws IOException
-     * @throws SAXException
+     * @param Object - The object to find primitives for
+     * @return an array of MobyDataSimpleInstances that are the primitives for Object.
+     */
+    public MobyDataSimpleInstance[] getPrimitives(String object) {
+        return getPrimitivesHelper(object);
+    }
+
+    /*
+     * getPrimitives helper.
      */
-    public ArrayList getPrimitives(String name) {
+    private MobyDataSimpleInstance[] getPrimitivesHelper(String name) {
         ArrayList list = new ArrayList();
         if (isPrimitive(name)) {
-            list.add(new Triples(name, name, Triples.HASA));
-            return list;
+            MobyDataSimpleInstance mdsi = new MobyDataSimpleInstance("");
+            mdsi.setDataType(new MobyDataType(name));
+            return new MobyDataSimpleInstance[] { mdsi };
         }
         String lsid = "urn:lsid:biomoby.org:objectclass:" + name;
         String rdf = getObjectRDF(lsid);
@@ -69,121 +100,130 @@
         // create a DOM document
         Document doc = getDOMDocument(rdf);
         // start parsing
-        List rdfsClassList = doc.getRootElement().getContent();
-        Iterator it = rdfsClassList.iterator();
-        while (it.hasNext()) {
-            Object obj = it.next();
-            Element hasa = null, has = null;
-            if (obj instanceof Element) {
-                Element classElement = (Element) obj;
-                // set up appropriate iterators
-                Iterator hasIterator = classElement.getChildren("has", HAS).iterator();
-                Iterator hasaIterator = classElement.getChildren("hasa",HASA).iterator();
-                Iterator subClassIterator = classElement.getChildren("subClassOf", Namespace.getNamespace(RDFS.getURI())).iterator();
-                // iterate through the lists
-                while (hasIterator.hasNext()) {
-                    Element hasElement = (Element) hasIterator.next();
-                    List hasInnerElementList = hasElement.getChildren();
-                    if (!hasInnerElementList.isEmpty()) {
-                        Element mobyObject = (Element) hasInnerElementList.get(0);
-                        String primitive = mobyObject.getName();
-                        int type = Triples.HAS;
-                        String articleName = mobyObject.getChildText("articleName", ARTICLE);
-                        // check if primitive is a primitive
-                        if (isPrimitive(primitive)) {
-                            Triples t =  new Triples(articleName, primitive, type);
-                            list.add(t);
-                        } else {
-                            // recurse
-                            ArrayList recurse = getPrimitives(primitive);
-                            if (recurse == null) {
-                                return null;
-                            }
-                            processRecursionList(list, recurse);
+        Element root = doc.getDocumentElement();
+        NodeList rdfsClassList = root.getElementsByTagName("rdfs:Class");
+        for (int x = 0; x < rdfsClassList.getLength(); x++) {
+            // process each class:
+            Element _class = ((Element) rdfsClassList.item(x));
+            NodeList has = _class.getElementsByTagName("mobyPred:has");
+            NodeList hasa = _class.getElementsByTagName("mobyPred:hasa");
+            // subClassOf can contain attributes or just an element
+            NodeList subClassOf = _class
+                    .getElementsByTagName("rdfs:subClassOf");
+            for (int i = 0; i < has.getLength(); i++) {
+                NodeList children = ((Element) has.item(i)).getChildNodes();
+                for (int j = 0; j < children.getLength(); j++) {
+                    if (!(children.item(j) instanceof Element))
+                        continue;
+                    Element child = (Element) children.item(j);
+                    Node articleNode = child.getElementsByTagName(
+                            "mobyPred:articleName").item(0);
+                    String localName = child.getLocalName();
+                    String articleName = (articleNode == null) ? ""
+                            : articleNode.getTextContent();
+                    //                  TODO - recurse if object is not a primitive
+                    if (isPrimitive(localName)) {
+                        MobyDataSimpleInstance mdsi = createPrimitiveType(localName, articleName);
+                        list.add(mdsi);
+                    } else {
+                        MobyDataSimpleInstance[] recurseArray = getPrimitives(localName);
+                        for (int k = 0; k < recurseArray.length; k++) {
+                            list.add(recurseArray[k]);
                         }
                     }
                 }
-                hasIterator = null;
-                while (hasaIterator.hasNext()) {
-                    Element hasaElement = (Element) hasaIterator.next();
-                    List hasaInnerElementList = hasaElement.getChildren();
-                    if (!hasaInnerElementList.isEmpty()) {
-                        Element mobyObject = (Element) hasaInnerElementList.get(0);
-                        String primitive = mobyObject.getName();
-                        int type = Triples.HASA;
-                        String articleName = mobyObject.getChildText("articleName", ARTICLE);
-                        // check if primitive is a primitive
-                        if (isPrimitive(primitive)) {
-                            Triples t =  new Triples(articleName, primitive, type);
-                            list.add(t);
+            }
+            for (int i = 0; i < hasa.getLength(); i++) {
+                NodeList children = ((Element) hasa.item(i)).getChildNodes();
+                for (int j = 0; j < children.getLength(); j++) {
+                    if (children.item(j) instanceof Element) {
+                        Element child = (Element) children.item(j);
+                        Node articleNode = child.getElementsByTagName(
+                                "mobyPred:articleName").item(0);
+                        String localName = child.getLocalName();
+                        String articleName = (articleNode == null) ? ""
+                                : articleNode.getTextContent();
+                        //                      TODO - recurse if object is not a primitive
+                        if (isPrimitive(localName)) {
+                            MobyDataSimpleInstance mdsi = createPrimitiveType(localName, articleName);
+                            list.add(mdsi);
                         } else {
-                            // recurse
-                            ArrayList recurse = getPrimitives(primitive);
-                            if (recurse == null) {
-                                return null;
+                            MobyDataSimpleInstance[] recurseArray = getPrimitives(localName);
+                            for (int k = 0; k < recurseArray.length; k++) {
+                                list.add(recurseArray[k]);
                             }
-                            processRecursionList(list, recurse);
                         }
                     }
                 }
-                hasaIterator = null;
-                /*
-                 * iterate through subClassOf
-                 * checking to see if the object is
-                 * a subclass of a primitive
-                 */
-                while (subClassIterator.hasNext()) {
-                    Element sub = (Element)subClassIterator.next();
-                    
-                    // check if we have an element called Class
-                    Element rdfsClass = sub.getChild("Class", Namespace.getNamespace(RDFS.getURI()));
-                    if (rdfsClass != null) {
-                        // get the rdf:about attribute
-                        String attr = rdfsClass.getAttributeValue("about", Namespace.getNamespace(RDF.getURI()));
-                        if (attr != null) {
-                            // i.e. http://biomoby.org/RESOURCES/MOBY-S/Objects#text-plain
-                            if (attr.indexOf("#") > 0) {
-                                attr = attr.substring(attr.indexOf("#")+1);
-                            }
-                            if (isPrimitive(attr)&& !attr.equals("Object")) {
-                                // assume if you are something, it means you have it (singular)
-                                Triples t =  new Triples(name, attr, Triples.HASA);
-                                list.add(t);
-                            }
-                        }
+            }
+
+            for (int i = 0; i < subClassOf.getLength(); i++) {
+                Element subClass = (Element) subClassOf.item(i);
+                // check for attributes
+                if (subClass.hasAttributes()) {
+                    String object = subClass.getAttribute("rdf:resource");
+                    if (object.indexOf("#") > 0) {
+                        object = object.substring(object.indexOf("#") + 1);
                     }
-                    /* process <rdfs:subClassOf rdf:resource="..."/> */
-                    String attr = sub.getAttributeValue("resource", Namespace.getNamespace(RDF.getURI()));
-                    if (attr != null) {
-                        if (attr.indexOf("#") > 0) {
-                            attr = attr.substring(attr.indexOf("#") + 1);
-                        }
-                        if (isPrimitive(attr) && !attr.equals("Object")) {
-                            // assume if you are something, it means you have it (singular)
-                            Triples t = new Triples(name, attr, Triples.HASA);
-                            list.add(t);
-                        }
+                    if (isPrimitive(object) && !object.equals("Object")) {
+                        MobyDataSimpleInstance mdsi = new MobyDataSimpleInstance(
+                                object);
+                        mdsi.setDataType(new MobyDataType(object));
+                        list.add(mdsi);
+                    }
+                } else {
+                    String object = ((Element) ((Element) subClass)
+                            .getElementsByTagName("rdfs:Class").item(0))
+                            .getAttribute("rdf:about");
+                    if (object.indexOf("#") > 0) {
+                        object = object.substring(object.indexOf("#") + 1);
+                    }
+                    if (isPrimitive(object) && !object.equals("Object")) {
+                        MobyDataSimpleInstance mdsi = new MobyDataSimpleInstance(
+                                object);
+                        mdsi.setDataType(new MobyDataType(object));
+                        list.add(mdsi);
                     }
                 }
+
             }
         }
-        
-        return list;
+
+        return convertArrayList(list);
     }
-    
-    private void processRecursionList(ArrayList list, ArrayList recurse) {
-        for (Iterator x = recurse.iterator(); x.hasNext();) {
-            Triples t = (Triples) x.next();
-            list.add(t);
+
+
+    /*
+     * method to create default DataTypes.
+     */
+    private MobyDataSimpleInstance createPrimitiveType(String localName, String articleName) {
+        if (localName.equalsIgnoreCase("Float")) {
+            return new MobyDataFloat(articleName, 0.0);
+        } else if (localName.equalsIgnoreCase("String")) {
+            return new MobyDataString(articleName, "");
+        } else if (localName.equalsIgnoreCase("Integer")) {
+            return new MobyDataInt(articleName, 0);
+        } else if(localName.equalsIgnoreCase("DateTime")) {
+            MobyDataSimpleInstance mdsi = new MobyDataSimpleInstance(articleName);
+            mdsi.setDataType(new MobyDataType(localName));
+            return mdsi;
         }
+        // error
+        return null;
     }
 
-    /**
-     *  
-     * <b>PRE:</b><p>
-     * <b>POST:</b><p>
-     * @param test - the test Moby object name to test with
-     * @return true if test is a primitive, false otherwise
+    private MobyDataSimpleInstance[] convertArrayList(ArrayList list) {
+        int size = list.size();
+        MobyDataSimpleInstance[] mdsi = new MobyDataSimpleInstance[size];
+        size = 0;
+        for (Iterator x = list.iterator(); x.hasNext(); size++) {
+            mdsi[size] = (MobyDataSimpleInstance) x.next();
+        }
+        return mdsi;
+    }
+
+    /*
+     * simply tests whether a string is a primitive
      */
     private boolean isPrimitive(String test) {
         for (int x = 0; x < PRIMITIVES.length; x++) {
@@ -192,94 +232,106 @@
         }
         return false;
     }
+
     /*
      * given an xml string, create a DOM document
      */
     private Document getDOMDocument(String rdfXML) {
-        // start creating the triples
-        SAXBuilder builder = new SAXBuilder();
-        Document doc = null;
         try {
-            // Create the document
-            doc = builder.build(new ByteArrayInputStream(rdfXML.getBytes()));
-        } catch (JDOMException e) {
-            System.err.println("Error in getPrimitives:1 - JDOMException.\n" + e.getMessage());
-            return null;
-        } catch (IOException e) {
-            System.err.println("Error in getPrimitives:2 - IOException.\n"+ e.getMessage());
-            return null;
-        }
-        return doc;
+            // Create a builder factory
+            DocumentBuilderFactory factory = DocumentBuilderFactory
+                    .newInstance();
+            factory.setNamespaceAware(true);
+            // Create the builder and parse the file
+            Document doc = factory.newDocumentBuilder().parse(
+                    new InputSource(new StringReader(rdfXML)));
+            return doc;
+        } catch (SAXException e) {
+            // A parsing error occurred; the xml input is not valid
+        } catch (ParserConfigurationException e) {} catch (IOException e) {}
+        return null;
     }
-    
+
     /*
      * given an lsdi, get the moby object rdf document
      */
     private String getObjectRDF(String lsid) {
         URL url;
         try {
-            url = new URL(URL_OBJECT+lsid);
+            url = new URL(URL_OBJECT + lsid);
         } catch (MalformedURLException e) {
-            System.err.println("Error in getObjectRDF:1 - MalformedURLException.");
+            System.err
+                    .println("Error in getObjectRDF:1 - MalformedURLException.");
             return null;
         }
         BufferedReader in = null;
         try {
             in = new BufferedReader(new InputStreamReader(url.openStream()));
         } catch (IOException e1) {
-            System.err.println("Error in getObjectRDF:2 - IOException. \n- Can't read from URL");
+            System.err
+                    .println("Error in getObjectRDF:2 - IOException. \n- Can't read from URL");
             return null;
         }
         String input;
         StringBuffer sb = new StringBuffer();
         try {
             while ((input = in.readLine()) != null) {
-                sb.append(input+System.getProperty("line.separator"));
+                sb.append(input + System.getProperty("line.separator"));
             }
         } catch (IOException e2) {
-            System.err.println("Error in getObjectRDF:3 - IOException.\n-Problems reading from URL");
+            System.err
+                    .println("Error in getObjectRDF:3 - IOException.\n-Problems reading from URL");
             return null;
         }
 
         return sb.toString();
     }
-    
+
     /**
      *  
      * <b>PRE:</b> Object is a valid Moby Object<p>
      * <b>POST:</b> An element representing the moby class structure is created.</br>>
      * @link http://www.biomoby.org/twiki/bin//view/Moby/MobySAPI#ObjectStructure
      * @param object - the Moby object to create a structure for
-     * @param triples - the primitives in Triples format to add to this structure 
-     * @return an Element representing the Moby Class Structure
+     * @param mdsi - an array of MobyDataSimpleInstances to add to the element 
+     * @return an Element representing the Moby Class Structure containing the MobyDataSimpleInstances
      */
-    public Element getElementContainingTriples(String object, ArrayList triples) {
+    public Element getElementContainingPrimitives(String object,
+            MobyDataSimpleInstance[] mdsi) {
         /*
-<moby:GenericSequence namespace='AGI_LocusCode' id='At2g42410'>   
-	<CrossReference>    
-		<Object namespace='Global_Keyword' id='superman'/> 
-	</CrossReference>
-	<moby:Integer namespace='' id='' articleName='Length'>214</moby:Integer> 
-	<moby:String namespace='' id=''articleName='SequenceString'>MKRTHLASFSNRDKTRLGYL</moby:String>
-</moby:GenericSequence>
+         <moby:GenericSequence namespace='AGI_LocusCode' id='At2g42410'>   
+         <CrossReference>    
+         <Object namespace='Global_Keyword' id='superman'/> 
+         </CrossReference>
+         <moby:Integer namespace='' id='' articleName='Length'>214</moby:Integer> 
+         <moby:String namespace='' id=''articleName='SequenceString'>MKRTHLASFSNRDKTRLGYL</moby:String>
+         </moby:GenericSequence>
          */
         /*root element*/
         Element root = null;
-        Namespace ns = Namespace.getNamespace("moby", "http://www.biomoby.org/moby");
-        root = new Element(object);
-        root.setNamespace(ns);
-        
+        Document doc = createDomDocument();
+        root = doc.createElementNS(MOBY, object);
         /*iterate through triples, create elements and add to root*/
-        Iterator it = triples.iterator();
-        while (it.hasNext()) {
-            Triples t = (Triples)it.next();
-            Element e = new Element(t.getPrimitive(), ns);
-            e.setAttribute(new Attribute("id", ""));
-            e.setAttribute(new Attribute("articleName", t.getArticleName()));
-            root.addContent(e);
+        for (int x = 0; x < mdsi.length; x++) {
+            MobyDataSimpleInstance mds = mdsi[x];
+            Element e = doc.createElementNS(MOBY, mds.getDataType().getName());
+            e.setAttribute("id", "");
+            e.setAttribute("articleName", mds.getName());
+            root.appendChild(e);
         }
         return root;
     }
+
+    private Document createDomDocument() {
+        try {
+            DocumentBuilder builder = DocumentBuilderFactory.newInstance()
+                    .newDocumentBuilder();
+            Document doc = builder.newDocument();
+            return doc;
+        } catch (ParserConfigurationException e) {}
+        return null;
+    }
+
     /**
      *  
      * <b>PRE:</b>Element e exists and Class, namespace, and id are valid.<p>
@@ -290,30 +342,33 @@
      * @param id - the identifier within that namespace that specifies the precise resource represented in the object
      * @return Element - the root element containing the CRIB just added.
      */
-    public Element addCrossReferenceToElement(Element e, String Class, String namespace, String id) {
+    public Element addCrossReferenceToElement(Element e, String Class,
+            String namespace, String id) {
         /* first make sure that the element doesnt already contain
          * the CrossReference child
          */
-        Iterator it = e.getChildren("CrossReference").iterator();
+        NodeList it = e.getElementsByTagName("CrossReference");
         Element cross = null;
-        if (it.hasNext()) {
+        if (it.getLength() > 0) {
             /*There is a pre-existing tag*/
-            cross = (Element)it.next();
-            Element object = new Element(Class);
-            object.setAttribute(new Attribute("namespace", namespace));
-            object.setAttribute(new Attribute("id", id));
-            cross.addContent(object);
+            cross = (Element) it.item(0);
+            Document doc = createDomDocument();
+            Element object = doc.createElement(Class);
+            object.setAttribute("namespace", namespace);
+            object.setAttribute("id", id);
+            cross.appendChild(object);
         } else {
-            cross = new Element ("CrossReference");
-            Element object = new Element(Class);
-            object.setAttribute(new Attribute("namespace", namespace));
-            object.setAttribute(new Attribute("id", id));
-            cross.addContent(object);
-            e.addContent(cross);
+            Document doc = e.getOwnerDocument();
+            Element object = doc.createElement(Class);
+            cross = doc.createElement("CrossReference");
+            object.setAttribute("namespace", namespace);
+            object.setAttribute("id", id);
+            cross.appendChild(object);
+            e.appendChild(cross);
         }
         return e;
     }
-    
+
     /**
      *  
      * <b>PRE:</b><p>
@@ -328,49 +383,55 @@
      * @param description - this is the textual content of the XML element, and contains a human-readable description of the intended interpretation of this cross-reference.
      * @return - the root object Element with the Xref cross reference added to it.
      */
-    public Element addXrefCrossReferenceToElement(Element e, String id, String namespace, String authURI, String serviceName, String evidenceCode, String XrefType, String description) {
+
+    public Element addXrefCrossReferenceToElement(Element e, String id,
+            String namespace, String authURI, String serviceName,
+            String evidenceCode, String XrefType, String description) {
         /*
          * everything is required other than description
          */
-        if (namespace == null || id == null || authURI == null || serviceName == null || evidenceCode == null || XrefType == null)
+        if (namespace == null || id == null || authURI == null
+                || serviceName == null || evidenceCode == null
+                || XrefType == null)
             return e;
         /* 
          * make sure that the element doesnt already contain
          * the CrossReference child
          */
-        Iterator it = e.getChildren("CrossReference").iterator();
+        NodeList it = e.getElementsByTagName("CrossReference");
         Element cross = null;
-        if (it.hasNext()) {
+        if (it.getLength() > 0) {
+            Document doc = e.getOwnerDocument();
             /*There is a pre-existing tag*/
-            cross = (Element)it.next();
-            Element object = new Element("Xref");
-            object.setAttribute(new Attribute("namespace", namespace));
-            object.setAttribute(new Attribute("id", id));
-            object.setAttribute(new Attribute("authURI", authURI));
-            object.setAttribute(new Attribute("serviceName", serviceName));
-            object.setAttribute(new Attribute("evidenceCode", evidenceCode));
-            object.setAttribute(new Attribute("XrefType", XrefType));
+            cross = (Element) it.item(0);
+            Element object = doc.createElement("Xref");
+            object.setAttribute("namespace", namespace);
+            object.setAttribute("id", id);
+            object.setAttribute("authURI", authURI);
+            object.setAttribute("serviceName", serviceName);
+            object.setAttribute("evidenceCode", evidenceCode);
+            object.setAttribute("XrefType", XrefType);
             if (description != null)
-                object.setText(description);
-            cross.addContent(object);
+                object.setNodeValue(description);
+            cross.appendChild(object);
         } else {
-            cross = new Element ("CrossReference");
-            Element object = new Element("Xref");
-            object.setAttribute(new Attribute("namespace", namespace));
-            object.setAttribute(new Attribute("id", id));
-            object.setAttribute(new Attribute("authURI", authURI));
-            object.setAttribute(new Attribute("serviceName", serviceName));
-            object.setAttribute(new Attribute("evidenceCode", evidenceCode));
-            object.setAttribute(new Attribute("XrefType", XrefType));
+            Document doc = e.getOwnerDocument();
+            cross = doc.createElement("CrossReference");
+            Element object = doc.createElement("Xref");
+            object.setAttribute("namespace", namespace);
+            object.setAttribute("id", id);
+            object.setAttribute("authURI", authURI);
+            object.setAttribute("serviceName", serviceName);
+            object.setAttribute("evidenceCode", evidenceCode);
+            object.setAttribute("XrefType", XrefType);
             if (description != null)
-                object.setText(description);
-            cross.addContent(object);
-            e.addContent(cross);
+                object.setNodeValue(description);
+            cross.appendChild(object);
+            e.appendChild(cross);
         }
         return e;
     }
-    
-    
+
     /**
      *  
      * <b>PRE:</b><p>
@@ -381,27 +442,30 @@
      */
     /*
      * <ProvisionInformation>
-              ... one or more of the provision elements (below) ...
-       </ProvisionInformation>
-       
-       <serviceSoftware software_name="" software_version="" software_comment=""/>
-       <serviceDatabase database_name="" database_version="" database_comment=""/>
-       <serviceComment>comment here</serviceComment>
+     ... one or more of the provision elements (below) ...
+     </ProvisionInformation>
+     
+     <serviceSoftware software_name="" software_version="" software_comment=""/>
+     <serviceDatabase database_name="" database_version="" database_comment=""/>
+     <serviceComment>comment here</serviceComment>
      */
-    public Element addProvisionInformationBlock(Element root, Element[] elements){
+    public Element addProvisionInformationBlock(Element root, Element[] elements) {
         if (elements == null || root == null || elements.length < 1)
             return root;
         /* only add PIB to a root element with no PIB child*/
-        if (!root.getChildren("ProvisionInformation").isEmpty()) {
+        if (root.getElementsByTagName("ProvisionInformation").item(0) != null) {
             return root;
         }
-        Element pib = new Element("ProvisionInformation");
-        for (int x=0; x < elements.length; x++)
-            pib.addContent(elements[x]);
-        root.addContent(pib);
+        Document doc = root.getOwnerDocument();
+        Element pib = doc.createElement("ProvisionInformation");
+        for (int x = 0; x < elements.length; x++) {
+            doc.adoptNode(elements[x]);
+            pib.appendChild(elements[x]);
+        }
+        root.appendChild(pib);
         return root;
     }
-    
+
     /**
      *  
      * <b>PRE:</b><p>
@@ -411,15 +475,18 @@
      * @param comment - any applicable comments
      * @return - a serviceSoftware Element with its attributes appropriately set.
      */
-    public Element createPIBServiceSoftwareElement(String name, String version, String comment) {
+    public Element createPIBServiceSoftwareElement(String name, String version,
+            String comment) {
         if (name == null || version == null || comment == null)
             return null;
-        Element e = new Element("serviceSoftware");
-        e.setAttribute(new Attribute("software_name", name));
-        e.setAttribute(new Attribute("software_version", version));
-        e.setAttribute(new Attribute("software_comment", comment));
+        Document doc = createDomDocument();
+        Element e = doc.createElement("serviceSoftware");
+        e.setAttribute("software_name", name);
+        e.setAttribute("software_version", version);
+        e.setAttribute("software_comment", comment);
         return e;
     }
+
     /**
      *  
      * <b>PRE:</b><p>
@@ -429,16 +496,18 @@
      * @param comment - any applicable comments
      * @return - a serviceDatabase Element with its attributes appropriately set.
      */
-    public Element createPIBServiceDatabaseElement(String name, String version, String comment) {
+    public Element createPIBServiceDatabaseElement(String name, String version,
+            String comment) {
         if (name == null || version == null || comment == null)
             return null;
-        Element e = new Element("serviceDatabase");
-        e.setAttribute(new Attribute("database_name", name));
-        e.setAttribute(new Attribute("database_version", version));
-        e.setAttribute(new Attribute("database_comment", comment));
+        Document doc = createDomDocument();
+        Element e = doc.createElement("serviceDatabase");
+        e.setAttribute("database_name", name);
+        e.setAttribute("database_version", version);
+        e.setAttribute("database_comment", comment);
         return e;
     }
-    
+
     /**
      *  
      * <b>PRE:</b><p>
@@ -449,24 +518,12 @@
     public Element createPIBServiceCommentElement(String comment) {
         if (comment == null)
             return null;
-        Element e = new Element("serviceComment");
-        e.setText(comment);
+
+        Element e = createDomDocument().createElement("serviceComment");
+        e.setTextContent(comment);
         return e;
     }
-    
-    public static void main(String[] args) {
-        MobyObjectPrimitiveExtractor g = new MobyObjectPrimitiveExtractor();
-        ArrayList l = g.getPrimitives("GenericSequence");
-        Element e = g.getElementContainingTriples("GenericSequence", l);
-        System.out.println(output(e));
-        e = g.addCrossReferenceToElement(e, "Object","NCBI_gi", "bob");
-        System.out.println(output(e));
-        e = g.addXrefCrossReferenceToElement(e, "myNamespace", "545454", "www.illuminae.com", "myServiceName", "myCode", "myXtype", "bob is your description");
-        System.out.println(output(e));
-        //g.getPrimitives("DNASequence");
-        //g.getPrimitives("CommentedRNASequence");
-    }
-    
+
     /**
      *  
      * <b>PRE:</b><p>
@@ -474,7 +531,7 @@
      * @param e - the dom element to stringify.
      * @return - a string representation of the element
      */
-    public static String output(Element e) {
+    public String createStringFromElement(Element e) {
         ByteArrayOutputStream buf = new ByteArrayOutputStream();
         // Create the document
         XMLOutputter fmt = new XMLOutputter();
@@ -483,10 +540,36 @@
         format.setIndent("     ");
         fmt.setFormat(format);
         try {
-            fmt.output(e, buf);
+            fmt.output(convert(e), buf);
         } catch (IOException ex) {
             System.out.println("Error: " + ex.getLocalizedMessage());
         }
-        return "Document: \n" + buf.toString();
+        return buf.toString();
     }
-}
+
+    private void outputDocumentToStream(Document doc, OutputStream s) {
+        // Use a Transformer for output
+        TransformerFactory tFactory = TransformerFactory.newInstance();
+        Transformer transformer;
+        try {
+            transformer = tFactory.newTransformer();
+            DOMSource source = new DOMSource(doc);
+            StreamResult result = new StreamResult(s);
+            transformer.transform(source, result);
+        } catch (TransformerConfigurationException e1) {
+            System.err.println("Couldnt print out DOM Doc.1 "
+                    + e1.getLocalizedMessage());
+        } catch (TransformerException e) {
+            System.err.println("Couldnt print out DOM Doc.2 "
+                    + e.getLocalizedMessage());
+        }
+    }
+
+    private static org.jdom.Element convert(Element domDoc) throws IOException {
+        // Create new DOMBuilder, using default parser
+        DOMBuilder builder = new DOMBuilder();
+        org.jdom.Element jdomDoc = builder.build(domDoc);
+        return jdomDoc;
+    }
+    
+}
\ No newline at end of file



From kawas at pub.open-bio.org  Thu Feb 24 23:55:59 2005
From: kawas at pub.open-bio.org (Eddie Kawas)
Date: Thu, 24 Feb 2005 18:55:59 -0500
Subject: [MOBY-guts] biomoby commit
Message-ID: <200502242355.j1ONtxKU002191@pub.open-bio.org>


kawas
Thu Feb 24 18:55:59 EST 2005
Update of /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/gui/util
In directory pub.open-bio.org:/tmp/cvs-serv2169

Removed Files:
	MobyObjectPrimitiveExtractor.java 
Log Message:
removed this class because it required 'extra' work to get it to compile properly.
once everyone is using java 1.5.0 or has extra time on their hands, i will put it back.
Sorry.

moby-live/Java/src/main/org/biomoby/client/gui/util MobyObjectPrimitiveExtractor.java,1.2,NONE
rcsdiff: /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/gui/util/RCS/MobyObjectPrimitiveExtractor.java,v: No such file or directory



From kawas at pub.open-bio.org  Thu Feb 24 23:56:15 2005
From: kawas at pub.open-bio.org (Eddie Kawas)
Date: Thu, 24 Feb 2005 18:56:15 -0500
Subject: [MOBY-guts] biomoby commit
Message-ID: <200502242356.j1ONuFpp002222@pub.open-bio.org>


kawas
Thu Feb 24 18:56:15 EST 2005
Update of /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/gui/util
In directory pub.open-bio.org:/tmp/cvs-serv2200

Removed Files:
	Triples.java 
Log Message:
removed this class because it required 'extra' work to get it to compile properly.
once everyone is using java 1.5.0 or has extra time on their hands, i will put it back.
Sorry.

moby-live/Java/src/main/org/biomoby/client/gui/util Triples.java,1.1,NONE
rcsdiff: /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/gui/util/RCS/Triples.java,v: No such file or directory



From yanwong at pub.open-bio.org  Tue Feb  1 08:41:38 2005
From: yanwong at pub.open-bio.org (Yan Wong)
Date: Tue, 01 Feb 2005 08:41:38 -0000
Subject: [MOBY-guts] biomoby commit
Message-ID: <200502010852.j118qGxG012654@pub.open-bio.org>


yanwong
Tue Feb  1 03:52:15 EST 2005
Update of /home/repository/moby/moby-live/Python/bioMoby
In directory pub.open-bio.org:/tmp/cvs-serv12609

Modified Files:
	mobyClient.py mobyDataTypes.py mobyExceptions.py 
	mobyMarshal.py mobyRegister.py mobyService.py 
Log Message:


moby-live/Python/bioMoby mobyClient.py,1.2,1.3 mobyDataTypes.py,1.5,1.6 mobyExceptions.py,1.2,1.3 mobyMarshal.py,1.3,1.4 mobyRegister.py,1.2,1.3 mobyService.py,1.2,1.3
===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/mobyClient.py,v
retrieving revision 1.2
retrieving revision 1.3
diff -u -r1.2 -r1.3
--- /home/repository/moby/moby-live/Python/bioMoby/mobyClient.py	2005/01/18 13:46:22	1.2
+++ /home/repository/moby/moby-live/Python/bioMoby/mobyClient.py	2005/02/01 08:52:15	1.3
@@ -22,10 +22,10 @@
         
         from SOAPpy import SOAPProxy        
         self.server=SOAPProxy(self.url, namespace=self.ns)
-	
-	if debug:
-	    self.server.config.debug=1
-	    
+        
+        if debug:
+            self.server.config.debug=1
+            
         del SOAPProxy
 
 
@@ -68,28 +68,28 @@
     def retrieveObjectDefinition(self, objectName):
         """Retrieves a list of object's definitions
         """
-	dc={"urn:lsid:biomoby.org:objectrelation:isa":"ISA",
-	"urn:lsid:biomoby.org:objectrelation:hasa":"HASA",
-	"urn:lsid:biomoby.org:objectrelation:has":"HAS"
-	}
+        dc={"urn:lsid:biomoby.org:objectrelation:isa":"ISA",
+        "urn:lsid:biomoby.org:objectrelation:hasa":"HASA",
+        "urn:lsid:biomoby.org:objectrelation:has":"HAS"
+        }
 
-	definition={}
-	definition["Relationship"]={}
+        definition={}
+        definition["Relationship"]={}
 
         xmlinput="<retrieveObjectDefinition><objectType>"+objectName+"</objectType></retrieveObjectDefinition>"
         doc=parseString(self.call_method("retrieveObjectDefinition", xmlinput))
-	
-	for child in doc.firstChild.childNodes:
-	    if child.nodeType==child.ELEMENT_NODE and child.nodeName=="Relationship":
-		definition["Relationship"][dc[child.getAttribute("relationshipType")]]=[]
-		for elem in child.childNodes:
-	            if elem.nodeType==elem.ELEMENT_NODE and elem.nodeName=="objectType" and elem.firstChild:
-			definition["Relationship"][dc[child.getAttribute("relationshipType")]].append((elem.getAttribute("articleName"), elem.firstChild.nodeValue))
-
-	    elif child.nodeType==child.ELEMENT_NODE:
-		if child.firstChild:
-			definition[str(child.nodeName)]=child.firstChild.nodeValue
-	
+        
+        for child in doc.firstChild.childNodes:
+            if child.nodeType==child.ELEMENT_NODE and child.nodeName=="Relationship":
+                definition["Relationship"][dc[child.getAttribute("relationshipType")]]=[]
+                for elem in child.childNodes:
+                    if elem.nodeType==elem.ELEMENT_NODE and elem.nodeName=="objectType" and elem.firstChild:
+                        definition["Relationship"][dc[child.getAttribute("relationshipType")]].append((elem.getAttribute("articleName"), elem.firstChild.nodeValue))
+
+            elif child.nodeType==child.ELEMENT_NODE:
+                if child.firstChild:
+                        definition[str(child.nodeName)]=child.firstChild.nodeValue
+        
         return definition
 
     def retrieveObjectSchema(self, objectName):
@@ -260,6 +260,6 @@
             raise ETypeMismatch
             
     def __init__(self, url="http://mobycentral.cbr.nrc.ca/cgi-bin/MOBY05/mobycentral.pl", ns="http://mobycentral.cbr.nrc.ca/MOBY/Central"):
-	"""Constructor for class Client
-	"""
+        """Constructor for class Client
+        """
         Central.__init__(self, url, ns)

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/mobyDataTypes.py,v
retrieving revision 1.5
retrieving revision 1.6
diff -u -r1.5 -r1.6
--- /home/repository/moby/moby-live/Python/bioMoby/mobyDataTypes.py	2005/01/27 13:46:57	1.5
+++ /home/repository/moby/moby-live/Python/bioMoby/mobyDataTypes.py	2005/02/01 08:52:15	1.6
@@ -26,7 +26,7 @@
     def __init__(self, articleName="", value=""):
         self.articleName=articleName
         self.value=value
-	self.__isSecondary__=True
+        self.__isSecondary__=True
         
     def toMoby(self):
         """Returns the object as a XML
@@ -34,199 +34,199 @@
         return "<moby:Parameter moby:articleName='"+self.articleName+"'><moby:value>"+str(self.value)+"</moby:value></moby:Parameter>"
             
     def __str__(self):
-	"""Return the Parameter in its XML form
-	"""
+        """Return the Parameter in its XML form
+        """
         return self.toMoby()
 
     def __repr__(self):
-	"""Print the XML on the python command line.
-	"""
+        """Print the XML on the python command line.
+        """
         return self.toMoby()
             
     def fromMoby(self, xml):
         """Get the attributes from a XML string
         """
-	xmlelt=xml
-	
-	if isinstance(xml, str):
-	    xmlelt=parseString(xml).firstChild
-	    
+        xmlelt=xml
+        
+        if isinstance(xml, str):
+            xmlelt=parseString(xml).firstChild
+            
         self.articleName=xmlelt.getAttribute('moby:articleName')
-	l=xmlelt.getElementsByTagName("value")
-	if len(l)==0:
-	    l=xmlelt.getElementsByTagName("moby:value")
+        l=xmlelt.getElementsByTagName("value")
+        if len(l)==0:
+            l=xmlelt.getElementsByTagName("moby:value")
 
-       	self.value=l[0].firstChild.nodeValue
-	
+            self.value=l[0].firstChild.nodeValue
+        
 class MobyGeneric(object):
     """A Generic object (to use with the Marshaller)
     """
     def __init__(self, namespace="", id="", articleName="", *args, **kw):
-	"""Class constructor, basic attributes are namespace, 
-	   identifier and the article's name
-	"""
-	self.namespace=namespace
-	self.id=id
-	self.articleName=articleName
-	
-	for name, value in kw.items():
+        """Class constructor, basic attributes are namespace, 
+           identifier and the article's name
+        """
+        self.namespace=namespace
+        self.id=id
+        self.articleName=articleName
+        
+        for name, value in kw.items():
             setattr(self, name, value)
-	
+        
 class MobyObject(MobyGeneric):
     """Define a Moby XML Object
        It has methods toMoby and fromMoby 
     """
     def __init__(self, prefix="moby", tag="Object", content="", *args, **kw):
-	"""Class constructor for a bioMoby Object
-	"""
-	MobyGeneric.__init__(self, *args, **kw)
-	self.__prefix__=prefix
-	self.__tag__=tag
-	self.__cross__=[]
-	self.__PIB__=[]
-	
-	self.content=content
-	
-		
+        """Class constructor for a bioMoby Object
+        """
+        MobyGeneric.__init__(self, *args, **kw)
+        self.__prefix__=prefix
+        self.__tag__=tag
+        self.__cross__=[]
+        self.__PIB__=[]
+        
+        self.content=content
+        
+                
     def toMoby(self):
-	"""Deserializes the content in XML api
-	"""
-	
-	beginTag=["<%s:%s"%(self.__prefix__,self.__tag__)]
-	
-	#First see if the object has an  identifier, a namepsace and a name
-	for attribute in __ATTRIBUTES__:
-	    if hasattr(self, attribute) and getattr(self, attribute):
-		beginTag.append("%s:%s=\"%s\""%(self.__prefix__, attribute, getattr(self,attribute)))
-
-	#Retrieve only object's attributes that are public.
-	filterFunc=lambda x: x[0] != "_" and not callable(getattr(self, x)) and x !="content" and x not in __ATTRIBUTES__
-	
-	#Retrieve the associated objects
-	#In MobyObject, associated objects are object's attributes
-	mobyObjects=filter(filterFunc, dir(self))
-	
-	#If none, return the tag closed
-	if len(mobyObjects)==0 and (not hasattr(self, "__cross__") or len(self.__cross__)==0) and (not hasattr(self, "__PIB__") or len(self.__PIB__)==0) and (not hasattr(self, "content") or not self.content):
-	    beginTag.append("/>")
-	    return " ".join(beginTag)
+        """Deserializes the content in XML api
+        """
+        
+        beginTag=["<%s:%s"%(self.__prefix__,self.__tag__)]
+        
+        #First see if the object has an  identifier, a namepsace and a name
+        for attribute in __ATTRIBUTES__:
+            if hasattr(self, attribute) and getattr(self, attribute):
+                beginTag.append("%s:%s=\"%s\""%(self.__prefix__, attribute, getattr(self,attribute)))
 
-	#Else, end begin tag and serialize the associated objects
+        #Retrieve only object's attributes that are public.
+        filterFunc=lambda x: x[0] != "_" and not callable(getattr(self, x)) and x !="content" and x not in __ATTRIBUTES__
+        
+        #Retrieve the associated objects
+        #In MobyObject, associated objects are object's attributes
+        mobyObjects=filter(filterFunc, dir(self))
+        
+        #If none, return the tag closed
+        if len(mobyObjects)==0 and (not hasattr(self, "__cross__") or len(self.__cross__)==0) and (not hasattr(self, "__PIB__") or len(self.__PIB__)==0) and (not hasattr(self, "content") or not self.content):
+            beginTag.append("/>")
+            return " ".join(beginTag)
+
+        #Else, end begin tag and serialize the associated objects
         beginTag.append(">")
 
-	result=[" ".join(beginTag)]
-	
-	#Serialize Cross references
-	if hasattr(self, "__cross__") and self.__cross__:
-	    result.append("<CrossReference>")
-	    
-	    for aCross in self.__cross__:
-		result.append(aCross.toMoby())
-		
-	    result.append("</CrossReference>")
-	
+        result=[" ".join(beginTag)]
+        
+        #Serialize Cross references
+        if hasattr(self, "__cross__") and self.__cross__:
+            result.append("<CrossReference>")
+            
+            for aCross in self.__cross__:
+                result.append(aCross.toMoby())
+                
+            result.append("</CrossReference>")
+        
         #Serialize PIB
-	if hasattr(self, "__PIB__") and self.__PIB__:
-	    result.append("<ProvisionInformation>")
-	    
-	    for aPIB in self.__PIB__:
-		result.append(aPIB.toMoby())
-		
-	    result.append("</ProvisionInformation>")
-	
-	#Serialize the other attibutes
-	#If the attributes has a toMoby method, then use it
-	#Else, use a MobyMarshaller object to serialize
-	for mobyObject in mobyObjects:
-	    if hasattr(getattr(self,mobyObject), "toMoby"):
+        if hasattr(self, "__PIB__") and self.__PIB__:
+            result.append("<ProvisionInformation>")
+            
+            for aPIB in self.__PIB__:
+                result.append(aPIB.toMoby())
+                
+            result.append("</ProvisionInformation>")
+        
+        #Serialize the other attibutes
+        #If the attributes has a toMoby method, then use it
+        #Else, use a MobyMarshaller object to serialize
+        for mobyObject in mobyObjects:
+            if hasattr(getattr(self,mobyObject), "toMoby"):
                 getattr(self, mobyObject).__articleName__=mobyObject
                 result.append(getattr(self, mobyObject).toMoby())
-	    else:
-		from bioMoby import MobyMarshaller
-		m=MobyMarshaller()
-		result.append(m.dumps(getattr(self, mobyObject), articleName=mobyObject))
-	
-	#Put the raw content of the object
-	#If you want to put your special object, then then you should write 
-	#a __str__ method
-	if hasattr(self, "content") and self.content:
-	    result.append("%s"%(self.content))
-	
-	result.append("</%s:%s>"%(self.__prefix__, self.__tag__))
-	
-	return "".join(result)
-	
+            else:
+                from bioMoby import MobyMarshaller
+                m=MobyMarshaller()
+                result.append(m.dumps(getattr(self, mobyObject), articleName=mobyObject))
+        
+        #Put the raw content of the object
+        #If you want to put your special object, then then you should write 
+        #a __str__ method
+        if hasattr(self, "content") and self.content:
+            result.append("%s"%(self.content))
+        
+        result.append("</%s:%s>"%(self.__prefix__, self.__tag__))
+        
+        return "".join(result)
+        
     def fromMoby(self, xml):
-	"""Deserialization method
-	"""
-	elem=xml
-	
-	if isinstance(xml, str):
-	    doc=parseString(xmlstring)
-	
-	    elem=doc.firstChild
-	
-	self.__tag__=elem.localName
-	
-	self.__prefix__="moby"
-	
-	self.content=[]
-	
-	if elem.nodeName.split(":")>1:
-	    self.__prefix__=elem.nodeName.split(":")[0]
-	
-	#Set the object's attributes
-	for attribute in elem.attributes.values():
-	    setattr(self, attribute.localName, str(attribute.nodeValue))
-
-	for child in elem.childNodes:
-	    if child.nodeType==child.ELEMENT_NODE:
-		#deserializes the cross references
-		if child.localName=="CrossReference":
-		    for aCross in child.childNodes:
-			if aCross.localName=="Xref":
-			    aXref=MobyXref()
-			    aXref.fromMoby(aCross)
-			    self.__cross__.append(aXref)
-			if aCross.localName=="Object":
-			    anObj=MobyObject()
-			    anObj.fromMoby(aCross)
-			    self.__cross__.append(anObj)
-		else:
-		    #Do the same for the other objects
-		    associatedObjectName=child.getAttribute("moby:articleName")
-		
-		    if not associatedObjectName:
-		        associatedObjectName=child.getAttribute("articleName")
-		
-		    if not associatedObjectName:
-		        associatedObjectName="associated"
-		    
-		    #Create an object
-		    o=MobyObject()
-		    o.fromMoby(child)
-		    
-		    #if there is already an object, then store it inside a list and 
-		    #append the other objects in the list 
-		    if hasattr(self, associatedObjectName):
-		        if type(getattr(self, associatedObjectName)) is list:
-			    getattr(self, associatedObjectName).append(o)
-		        else:
-			    setattr(self, associatedObjectName, [o])
-		    else:
+        """Deserialization method
+        """
+        elem=xml
+        
+        if isinstance(xml, str):
+            doc=parseString(xmlstring)
+        
+            elem=doc.firstChild
+        
+        self.__tag__=elem.localName
+        
+        self.__prefix__="moby"
+        
+        self.content=[]
+        
+        if elem.nodeName.split(":")>1:
+            self.__prefix__=elem.nodeName.split(":")[0]
+        
+        #Set the object's attributes
+        for attribute in elem.attributes.values():
+            setattr(self, attribute.localName, str(attribute.nodeValue))
+
+        for child in elem.childNodes:
+            if child.nodeType==child.ELEMENT_NODE:
+                #deserializes the cross references
+                if child.localName=="CrossReference":
+                    for aCross in child.childNodes:
+                        if aCross.localName=="Xref":
+                            aXref=MobyXref()
+                            aXref.fromMoby(aCross)
+                            self.__cross__.append(aXref)
+                        if aCross.localName=="Object":
+                            anObj=MobyObject()
+                            anObj.fromMoby(aCross)
+                            self.__cross__.append(anObj)
+                else:
+                    #Do the same for the other objects
+                    associatedObjectName=child.getAttribute("moby:articleName")
+                
+                    if not associatedObjectName:
+                        associatedObjectName=child.getAttribute("articleName")
+                
+                    if not associatedObjectName:
+                        associatedObjectName="associated"
+                    
+                    #Create an object
+                    o=MobyObject()
+                    o.fromMoby(child)
+                    
+                    #if there is already an object, then store it inside a list and 
+                    #append the other objects in the list 
+                    if hasattr(self, associatedObjectName):
+                        if type(getattr(self, associatedObjectName)) is list:
+                            getattr(self, associatedObjectName).append(o)
+                        else:
+                            setattr(self, associatedObjectName, [o])
+                    else:
                         setattr(self, associatedObjectName, o)
             else:
-		self.content.append(child.nodeValue)
-		
-	self.content="".join(self.content)
-	
+                self.content.append(child.nodeValue)
+                
+        self.content="".join(self.content)
+        
 
     def __str__(self):
-	return self.toMoby()
-	
+        return self.toMoby()
+        
     def __repr__(self):
-	return self.toMoby()
-	
+        return self.toMoby()
+        
 
 class MobyXref(MobyObject):
     """Describes an Xref
@@ -246,48 +246,48 @@
     def fromMoby(self, xml):
         """Deserialize the Xref Object
         """
-	if isinstance(xml, str):
-	    doc=parseString(xml).firstChild
-	
-	doc=xml
-	
+        if isinstance(xml, str):
+            doc=parseString(xml).firstChild
+        
+        doc=xml
+        
         uri=doc.namespaceURI
     
-	MobyObject.fromMoby(self, doc)
+        MobyObject.fromMoby(self, doc)
         
         self.authURI=doc.getAttributeNS(uri, "authURI")
         self.serviceName=doc.getAttributeNS(uri, "serviceName")
         self.evidenceCode=doc.getAttributeNS(uri, "evidenceCode")
         self.xrefType=doc.getAttributeNS(uri, "xrefType")
 
-	
+        
 class MobyInteger(MobyObject):
     """Use this object to serialize/deserialize integers
     """
     def __init__(self, value=0, *args, **kw):
-	MobyObject.__init__(self, content=value, tag="Integer", *args, **kw)
+        MobyObject.__init__(self, content=value, tag="Integer", *args, **kw)
 
     def fromMoby(self, xml):
-	MobyObject.fromMoby(self, xml)
-	self.content = int(self.content)
-	
+        MobyObject.fromMoby(self, xml)
+        self.content = int(self.content)
+        
 class MobyFloat(MobyObject):
     """Serialize/deserialize floating point numbers
     """
     def __init__(self, value=0, *args, **kw):
-	MobyObject.__init__(self, content=value, tag="Float", *args, **kw)
-	
+        MobyObject.__init__(self, content=value, tag="Float", *args, **kw)
+        
     def fromMoby(self, xml):
-	MobyObject.fromMoby(self, xml)
-	self.content=float(self.content)
-	
+        MobyObject.fromMoby(self, xml)
+        self.content=float(self.content)
+        
 
 class MobyString(MobyObject):
     """String Moby object
     """
     def __init__(self, content="", *args, **kw):
-	MobyObject.__init__(self, content=content, *args, **kw)
-	self.__tag__="String"
+        MobyObject.__init__(self, content=content, *args, **kw)
+        self.__tag__="String"
 
 class MobyContent:
     """The class describes a Moby Content (for queries or answers)
@@ -302,10 +302,10 @@
         self.queryData=queryData
 
     def __str__(self):
-	"""return the XML form of the Moby Content object
-	"""
-	return self.toMoby()
-	
+        """return the XML form of the Moby Content object
+        """
+        return self.toMoby()
+        
     def toMoby(self):
         """The XML reprentation of the content
         """
@@ -325,8 +325,8 @@
         for queryKey in self.queryData:
             result.append("<moby:mobyData moby:queryID='"+queryKey+"'>")
 
-	    #For serialization, use the MobyMarshaller object
-	    
+            #For serialization, use the MobyMarshaller object
+            
             for queryObject in self.queryData[queryKey]:
                 #if the Collection ('CollectionName',[MobyObjects])
                 if queryObject.__class__ is tuple:
@@ -352,19 +352,19 @@
         return "".join(result)
 
     def fromMoby(self, xmlObject):
-	"""fill the properties from an XML
+        """fill the properties from an XML
         """
         from bioMoby import MobyUnmarshaller
-	
-	um=MobyUnmarshaller()
+        
+        um=MobyUnmarshaller()
 
         self.queryData={}
-	
-	doc=xmlObject
-	
-	if isinstance(xmlObject, str):
-	    doc=parseString(xmlObject)
-	
+        
+        doc=xmlObject
+        
+        if isinstance(xmlObject, str):
+            doc=parseString(xmlObject)
+        
         mdl=doc.getElementsByTagName('mobyData')
 
         if not mdl:
@@ -373,115 +373,115 @@
         #For each query            
         for elt in mdl:
             #Get the ID
-	    queryID=str(elt.getAttribute('queryID'))
+            queryID=str(elt.getAttribute('queryID'))
 
             if not queryID:
                 queryID=str(elt.getAttribute('moby:queryID'))
 
-	    #Collect the data
+            #Collect the data
             data=[]
 
-	    #for each datum translate it in MobyObject, and put it in the list
+            #for each datum translate it in MobyObject, and put it in the list
             for datum in elt.childNodes:
-		#If it is a collection
+                #If it is a collection
                 if datum.nodeType==datum.ELEMENT_NODE and datum.localName=="Collection":
-		    articleName=datum.getAttribute('moby:articleName')
+                    articleName=datum.getAttribute('moby:articleName')
         
                     articles=[]
         
                     for article in datum.childNodes:
                         if article.nodeType==article.ELEMENT_NODE and article.localName=="Simple":
-			    for child in article.childNodes:
-				if child.nodeType==child.ELEMENT_NODE:
+                            for child in article.childNodes:
+                                if child.nodeType==child.ELEMENT_NODE:
                                     articles.append(um.loadn(child))
 
                     data.append((articleName, articles))
-		#if it is a Simple object
+                #if it is a Simple object
                 elif datum.nodeType==datum.ELEMENT_NODE and datum.localName=="Simple":
-		    for elt in datum.childNodes:
+                    for elt in datum.childNodes:
                         if elt.nodeType==elt.ELEMENT_NODE:
-		            o=um.loadn(elt)
-		            data.append(o)
-	        elif datum.nodeType==datum.ELEMENT_NODE and datum.localName=="Parameter":
-		    #It is a Parameter
-		    p=Parameter()
-		    p.fromMoby(datum)
-		    data.append(p)
+                            o=um.loadn(elt)
+                            data.append(o)
+                elif datum.nodeType==datum.ELEMENT_NODE and datum.localName=="Parameter":
+                    #It is a Parameter
+                    p=Parameter()
+                    p.fromMoby(datum)
+                    data.append(p)
                     
             self.queryData[queryID]=data
-	    
+            
     def __getitem__(self, key):
-	"""Get a query from his name
+        """Get a query from his name
         """
         return self.queryData[key]
         
     def __setitem__(self, key, item):
-	"""Store a query in the dictionary
-	"""
+        """Store a query in the dictionary
+        """
         self.queryData[key]=item
 
     def __len__(self):
-	"""Return the number of elements inside the dictionary
-	"""
+        """Return the number of elements inside the dictionary
+        """
         return len(self.queryData)
         
     def keys(self):
-	"""Return all queries's name
-	"""
+        """Return all queries's name
+        """
         return self.queryData.keys()
-	
+        
     def collectionToQueries(self, aCollection):
-	"""Turn a collection of object into a set of queries
-	"""
-	queries={}
-	queryName=aCollection[0]
-	
-	queryID=1
-	
-	for aSimple in aCollection[1]:
-	    queries["%s-%s"%(queryName, queryID)]=aSimple
-	    
-	return queries
-		
-	
+        """Turn a collection of object into a set of queries
+        """
+        queries={}
+        queryName=aCollection[0]
+        
+        queryID=1
+        
+        for aSimple in aCollection[1]:
+            queries["%s-%s"%(queryName, queryID)]=aSimple
+            
+        return queries
+                
+        
     def getObject(self, queryName, objectName):
-	"""Get an object from a query with its name
-	"""
-	filterfunc=lambda obj: not hasattr(obj,'__isSecondary__') and hasattr(obj, "articleName") and obj.articleName==objectName
-	
-	for obj in filter(filterfunc, self.queryData[queryName]):
+        """Get an object from a query with its name
+        """
+        filterfunc=lambda obj: not hasattr(obj,'__isSecondary__') and hasattr(obj, "articleName") and obj.articleName==objectName
+        
+        for obj in filter(filterfunc, self.queryData[queryName]):
             return obj
 
-		
+                
     def getObjects(self, queryName):
-	"""Retrieve objects from a query
-	"""
-	filterfunc=lambda obj: not hasattr(obj, "__isSecondary__")
-	
-	return filter(filterfunc, self.queryData[queryName])
-	
+        """Retrieve objects from a query
+        """
+        filterfunc=lambda obj: not hasattr(obj, "__isSecondary__")
+        
+        return filter(filterfunc, self.queryData[queryName])
+        
     def getParameters(self, queryName):
-	"""Retrieve parameters from a query
-	"""
-	filterfunc=lambda param: hasattr(param, "__isSecondary__")
-	
-	result={}
-	for param in filter(filterfunc, self.queryData[queryName]):
-	    result[param.articleName]=param.value
-		
-	return result
+        """Retrieve parameters from a query
+        """
+        filterfunc=lambda param: hasattr(param, "__isSecondary__")
+        
+        result={}
+        for param in filter(filterfunc, self.queryData[queryName]):
+            result[param.articleName]=param.value
+                
+        return result
 
     def getParameter(self, queryName, parameterName):
-	"""Retrieve a parameter from a query and his name
-	"""
-	filterfunc=lambda param: hasattr(param, "__isSecondary__") and hasattr(param, "articleName") and param.articleName==parameterName
-	
-	l=filter(filterfunc, self.queryData[queryName])
-	
-	if l:
-	    return l[0]
-	
+        """Retrieve a parameter from a query and his name
+        """
+        filterfunc=lambda param: hasattr(param, "__isSecondary__") and hasattr(param, "articleName") and param.articleName==parameterName
+        
+        l=filter(filterfunc, self.queryData[queryName])
+        
+        if l:
+            return l[0]
+        
     def __repr__(self):
-	"""put the xml of the Content
-	"""
-	return self.__str__()
+        """put the xml of the Content
+        """
+        return self.__str__()

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/mobyExceptions.py,v
retrieving revision 1.2
retrieving revision 1.3
diff -u -r1.2 -r1.3
--- /home/repository/moby/moby-live/Python/bioMoby/mobyExceptions.py	2005/01/18 13:46:22	1.2
+++ /home/repository/moby/moby-live/Python/bioMoby/mobyExceptions.py	2005/02/01 08:52:15	1.3
@@ -41,4 +41,4 @@
     """A XML input is not a Moby XML Object.
     """
     def __str__(self):
-	return "The bioMoby XML object couldn't be parsed"
\ No newline at end of file
+        return "The bioMoby XML object couldn't be parsed"
\ No newline at end of file

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/mobyMarshal.py,v
retrieving revision 1.3
retrieving revision 1.4
diff -u -r1.3 -r1.4
--- /home/repository/moby/moby-live/Python/bioMoby/mobyMarshal.py	2005/01/27 08:44:05	1.3
+++ /home/repository/moby/moby-live/Python/bioMoby/mobyMarshal.py	2005/02/01 08:52:15	1.4
@@ -10,7 +10,7 @@
     
     01/17/2005: MobyMarshaller and MobyUnmarshaller can operate on all objects
                 serialisation and deserialisation are done only on public (no _ prefix) non callable attributes
-		The serialisation and deserialisation is recursive.
+                The serialisation and deserialisation is recursive.
 """
 
 from xml.dom.minidom import parseString
@@ -20,8 +20,8 @@
     """
     
     def _marshal(self, value, articleName=""):
-	"""this method do the serialization of the object
-	"""
+        """this method do the serialization of the object
+        """
         if type(value).__name__=='NoneType':
             return ""
 
@@ -29,9 +29,9 @@
 
         method="m_"+tvalue
 
-	if hasattr(value, "toMoby"):
-	    return value.toMoby()
-	
+        if hasattr(value, "toMoby"):
+            return value.toMoby()
+        
         if hasattr(self, method):
             return getattr(self,method)(value,articleName=articleName)
         
@@ -46,8 +46,8 @@
         return str(m)
         
     def m_unicode(self, value, articleName=""):
-	"""Turn a unicode string into a mobyString object
-	"""
+        """Turn a unicode string into a mobyString object
+        """
         return self.m_str(str(value), articleName)
 
     def m_string(self, value, articleName=""):
@@ -59,18 +59,18 @@
         """Turn an integer into a Moby XML object
         """
         from bioMoby.mobyDataTypes import MobyInteger
-	m=MobyInteger(value, namespace=namespace, id=id, articleName=articleName)
-	
-	return m.toMoby()
-	
+        m=MobyInteger(value, namespace=namespace, id=id, articleName=articleName)
+        
+        return m.toMoby()
+        
     def m_float(self, value, namespace="", id="", articleName=""):
         """Turn a float into a Moby XML object
         """
         from bioMoby.mobyDataTypes import MobyFloat
-	m=MobyFloat(value, namespace=namespace, id=id, articleName=articleName)
-	
-	return m.toMoby()
-	
+        m=MobyFloat(value, namespace=namespace, id=id, articleName=articleName)
+        
+        return m.toMoby()
+        
     def m_list(self, value, articleName=""):
         """Turn a list into a Moby XML object
         """
@@ -113,50 +113,50 @@
     def _compoundObject(self, value, articleName=""):
         """transforms an object and all properties into a XML
         """
-	
-	result=[]
-	
-	properties=[]
-	
-	filterfunc=lambda x: x[0] != "_" and not callable(getattr(value, x)) and x !="content" and x not in ["id", "namespace", "articleName", "content"]
-	attribfunc= lambda x: hasattr(value, x)
-	
-	tagName="moby:%s"%type(value).__name__
-	
-	if hasattr(value, "__tag__") and value.__tag__:
-	    tagName="moby:%s"%value.__tag__
-	
-	header=["<%s"%tagName]
-	
-	for attribute in filter(attribfunc, ["id", "namespace", "articleName"]):
-	    header.append("moby:%s=\"%s\""%(attribute,getattr(value,attribute)))
-	
-	for prop in filter(filterfunc, dir(value)):
-	    properties.append(self._marshal(getattr(value, prop), articleName=prop))
-	    
-	if not properties and not (hasattr(value, "content") and value.content):
-	    header.append("/>")
-	else:
-	    header.append(">")
-	    
-	result.append(" ".join(header))
-
-	if properties:
-	    result.append("".join(properties))	    
-	
-	if hasattr(value, "content") and value.content:
-	    result.append("<![CDATA[%s]]>"%value.content)
-	
-	if properties:
-	    result.append("</%s>"%tagName)
-
-
-	return r"".join(result)
-	
-	
+        
+        result=[]
+        
+        properties=[]
+        
+        filterfunc=lambda x: x[0] != "_" and not callable(getattr(value, x)) and x !="content" and x not in ["id", "namespace", "articleName", "content"]
+        attribfunc= lambda x: hasattr(value, x)
+        
+        tagName="moby:%s"%type(value).__name__
+        
+        if hasattr(value, "__tag__") and value.__tag__:
+            tagName="moby:%s"%value.__tag__
+        
+        header=["<%s"%tagName]
+        
+        for attribute in filter(attribfunc, ["id", "namespace", "articleName"]):
+            header.append("moby:%s=\"%s\""%(attribute,getattr(value,attribute)))
+        
+        for prop in filter(filterfunc, dir(value)):
+            properties.append(self._marshal(getattr(value, prop), articleName=prop))
+            
+        if not properties and not (hasattr(value, "content") and value.content):
+            header.append("/>")
+        else:
+            header.append(">")
+            
+        result.append(" ".join(header))
+
+        if properties:
+            result.append("".join(properties))            
+        
+        if hasattr(value, "content") and value.content:
+            result.append("<![CDATA[%s]]>"%value.content)
+        
+        if properties:
+            result.append("</%s>"%tagName)
+
+
+        return r"".join(result)
+        
+        
     def dumps(self, value, articleName=""):
-	"""Serialize the object into a Moby XML object
-	"""
+        """Serialize the object into a Moby XML object
+        """
         return self._marshal(value, articleName)
         
 
@@ -169,8 +169,8 @@
         """
         import re
 
-	aName=str(aName)
-	
+        aName=str(aName)
+        
         if aName=="":
             return ""
 
@@ -189,51 +189,51 @@
         return "".join(t)
 
     def loadn(self, xmlNode):
-	"""Deserializes an XML node and return a Python Object
-	"""
-	import bioMoby.mobyDataTypes
-	import bioMoby.ontology
-	
-	nn=xmlNode.localName
-	
+        """Deserializes an XML node and return a Python Object
+        """
+        import bioMoby.mobyDataTypes
+        import bioMoby.ontology
+        
+        nn=xmlNode.localName
+        
         #Try to see if this object got a deserializer
         object2build=self._cleanName(nn)
 
         objectName=str.upper(object2build[0])+object2build[1:]
-	
-	if hasattr(bioMoby.mobyDataTypes, "Moby%s"%objectName):
-	    o=getattr(bioMoby.mobyDataTypes, "Moby%s"%objectName)()
-	    if hasattr(o, "fromMoby"):
-		o.fromMoby(xmlNode)
-	    return o
-	elif hasattr(bioMoby.ontology, "Moby%s"%objectName):
-	    o=getattr(bioMoby.ontology, "Moby%s"%objectName)()
-	    if hasattr(o, "fromMoby"):
-		o.fromMoby(xmlNode)
-	    return o
-	    
+        
+        if hasattr(bioMoby.mobyDataTypes, "Moby%s"%objectName):
+            o=getattr(bioMoby.mobyDataTypes, "Moby%s"%objectName)()
+            if hasattr(o, "fromMoby"):
+                o.fromMoby(xmlNode)
+            return o
+        elif hasattr(bioMoby.ontology, "Moby%s"%objectName):
+            o=getattr(bioMoby.ontology, "Moby%s"%objectName)()
+            if hasattr(o, "fromMoby"):
+                o.fromMoby(xmlNode)
+            return o
+            
         methodName=str('m_'+nn)
-	    
-	if not hasattr(self, methodName):
+            
+        if not hasattr(self, methodName):
             methodName="m_Object"
-		
-#	try:
+                
+#        try:
         return getattr(self,methodName)(xmlNode)
 #        except:
-#	    #if not, Raise an invalid moby XML :-(
-#	    from bioMoby.mobyExceptions import EInvalidMobyXML    
-	    
+#            #if not, Raise an invalid moby XML :-(
+#            from bioMoby.mobyExceptions import EInvalidMobyXML    
+            
 #            raise EInvalidMobyXML
 
-	
+        
     def loads(self, xmlString):
-	""" Deserializes an xml string and return a bioMoby-Python object
-	"""
+        """ Deserializes an xml string and return a bioMoby-Python object
+        """
         if xmlString=="":
             return None    
 
-#	_typesmodule=["bioMoby.mobyDataTypes", "bioMoby.ontology"]
-	    
+#        _typesmodule=["bioMoby.mobyDataTypes", "bioMoby.ontology"]
+            
         doc=parseString(xmlString)
         
         mcl=doc.getElementsByTagNameNS('http://www.biomoby.org/moby','mobyContent')
@@ -243,109 +243,109 @@
             
         element=doc.firstChild
         
-	self.loadn(element)
+        self.loadn(element)
 
     def m_Integer(self, value):
-	"""Turn a Integer XML element into an integer
-	"""
-	value.normalize()
-	
-	if value.firstChild:
-	    return int(value.firstChild.nodeValue.replace("\n","").replace("\t","").replace(" ",""))
-	else:
-	    return 0
-	    
+        """Turn a Integer XML element into an integer
+        """
+        value.normalize()
+        
+        if value.firstChild:
+            return int(value.firstChild.nodeValue.replace("\n","").replace("\t","").replace(" ",""))
+        else:
+            return 0
+            
     def m_Float(self, value):
-	"""Turn a Float XML element into a float number
-	"""
-	value.normalize()
-	if value.firstChild:
-	    return float(value.firstChild.nodeValue.replace("\n","").replace("\t","").replace(" ",""))
+        """Turn a Float XML element into a float number
+        """
+        value.normalize()
+        if value.firstChild:
+            return float(value.firstChild.nodeValue.replace("\n","").replace("\t","").replace(" ",""))
         return 0.0
-	    
+            
     def m_String(self, value):
-	"""Turn a Moby XML String element into a String object
-	"""
-	
-	cnt=[]
-	value.normalize()
-	
-	for aChild in value.childNodes:
-	    if aChild.nodeType==aChild.TEXT_NODE or aChild.nodeType==aChild.CDATA_SECTION_NODE:
-		cnt.append(aChild.wholeText)
-		
-	return	r"".join(cnt)
-	
+        """Turn a Moby XML String element into a String object
+        """
+        
+        cnt=[]
+        value.normalize()
+        
+        for aChild in value.childNodes:
+            if aChild.nodeType==aChild.TEXT_NODE or aChild.nodeType==aChild.CDATA_SECTION_NODE:
+                cnt.append(aChild.wholeText)
+                
+        return        r"".join(cnt)
+        
 
     def m_Object(self, value):
-	"""Turn any XML into a generic object
-	"""
-	filterFunc= lambda x: x.nodeType==x.ELEMENT_NODE
-	
-	typeName="GMoby%s"%str(value.localName)
-
-	from bioMoby.mobyDataTypes import MobyGeneric
-	
-	NewType=type(typeName, (MobyGeneric,), {})
-	
-	anObject=NewType()
-	
-	anObject.__prefix__="moby"
-	anObject.__tag__=str(value.localName)
-	
-	for tupleAttribute in value.attributes.itemsNS():
-	    #First item, second field:
-	    setattr(anObject, str(tupleAttribute[0][1]), str(tupleAttribute[1]))
-
-	i=0    
-	for elem in filter(filterFunc, value.childNodes):
-	    methodName="m_%s"%str(elem.localName)
-
-	    articleName=elem.getAttribute("moby:articleName")
-	    
-	    if not articleName:
-		articleName=elem.getAttribute("articleName")
-		
-	    if not articleName:
-		articleName="attribute_%s"%i
-		
-	    if hasattr(self, methodName):
-		prop=getattr(self, methodName)(elem)
-	    else:
-	    	prop=self.m_Object(elem)
-		
-	    if hasattr(anObject, articleName):
-	        t=prop
-	        if not type(getattr(anObject, articleName)) is list:
-		    t=getattr(anObject, articleName)
-		    setattr(anObject, articleName, [])
-		getattr(anObject, articleName).append(t)
-	    else:
-	        setattr(anObject, articleName, prop)
-	    i+=1
-
-	content=[]
-
-	isContentNode= lambda x: x.nodeType==x.TEXT_NODE or x.nodeType==x.CDATA_SECTION_NODE
-	
-	for elem in filter(isContentNode, value.childNodes):
-	    content.append(str(elem.nodeValue))
-	    
-	if content:
-	    anObject.content(r"".join(content))
-	    
-	return anObject
+        """Turn any XML into a generic object
+        """
+        filterFunc= lambda x: x.nodeType==x.ELEMENT_NODE
+        
+        typeName="GMoby%s"%str(value.localName)
+
+        from bioMoby.mobyDataTypes import MobyGeneric
+        
+        NewType=type(typeName, (MobyGeneric,), {})
+        
+        anObject=NewType()
+        
+        anObject.__prefix__="moby"
+        anObject.__tag__=str(value.localName)
+        
+        for tupleAttribute in value.attributes.itemsNS():
+            #First item, second field:
+            setattr(anObject, str(tupleAttribute[0][1]), str(tupleAttribute[1]))
+
+        i=0    
+        for elem in filter(filterFunc, value.childNodes):
+            methodName="m_%s"%str(elem.localName)
+
+            articleName=elem.getAttribute("moby:articleName")
+            
+            if not articleName:
+                articleName=elem.getAttribute("articleName")
+                
+            if not articleName:
+                articleName="attribute_%s"%i
+                
+            if hasattr(self, methodName):
+                prop=getattr(self, methodName)(elem)
+            else:
+                    prop=self.m_Object(elem)
+                
+            if hasattr(anObject, articleName):
+                t=prop
+                if not type(getattr(anObject, articleName)) is list:
+                    t=getattr(anObject, articleName)
+                    setattr(anObject, articleName, [])
+                getattr(anObject, articleName).append(t)
+            else:
+                setattr(anObject, articleName, prop)
+            i+=1
+
+        content=[]
+
+        isContentNode= lambda x: x.nodeType==x.TEXT_NODE or x.nodeType==x.CDATA_SECTION_NODE
+        
+        for elem in filter(isContentNode, value.childNodes):
+            content.append(str(elem.nodeValue))
+            
+        if content:
+            anObject.content(r"".join(content))
+            
+        return anObject
 
     def m_MobyContent(self, value):
-	"""Turn an MobyContentXML into a MobyContent object
-	"""
-	from bioMoby.mobyDataTypes import MobyContent
-	
-	mc=MobyContent({})
-	
-	mc.fromMoby(value)
-	
-	del MobyContent
-	
-	return mc
-	
+        """Turn an MobyContentXML into a MobyContent object
+        """
+        from bioMoby.mobyDataTypes import MobyContent
+        
+        mc=MobyContent({})
+        
+        mc.fromMoby(value)
+        
+        del MobyContent
+        
+        return mc
+        

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/mobyRegister.py,v
retrieving revision 1.2
retrieving revision 1.3
diff -u -r1.2 -r1.3
--- /home/repository/moby/moby-live/Python/bioMoby/mobyRegister.py	2005/01/18 13:46:22	1.2
+++ /home/repository/moby/moby-live/Python/bioMoby/mobyRegister.py	2005/02/01 08:52:15	1.3
@@ -19,9 +19,9 @@
         self.success=0
         self.id=""
         self.message=""
-	self.RDF=""
+        self.RDF=""
 
-	#Parse the document, retrieve the success, id, message and RDF fields
+        #Parse the document, retrieve the success, id, message and RDF fields
         doc=parseString(xmlInput)
 
         if len(doc.getElementsByTagName("success")[0].childNodes)>0:
@@ -32,9 +32,9 @@
             self.message=doc.getElementsByTagName("message")[0].childNodes[0].nodeValue
         try:
             if len(doc.getElementsByTagName("RDF"))>0:
-	        self.RDF=doc.getElementsByTagName("RDF")[0].firstChild.toprettyxml()
-	except:
-	    pass
+                self.RDF=doc.getElementsByTagName("RDF")[0].firstChild.toprettyxml()
+        except:
+            pass
 
     def __str__(self):
         """Return the moby xml of the instance
@@ -63,7 +63,7 @@
         self.authURI=authURI
         self.description=description
         #it uses a central object for registration
-    	from mobyClient import Central
+        from mobyClient import Central
         self.central=Central()
         del Central
 
@@ -78,8 +78,8 @@
         self.serviceType=serviceType
         GeneralInformations.__init__(self, contact=contactEmail, authURI=authURI, description=description)
         self.relationship=relationship
-	self.serviceType=serviceType
-	
+        self.serviceType=serviceType
+        
     def __str__(self):
         """Return the instance as a Moby XML
         """

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/mobyService.py,v
retrieving revision 1.2
retrieving revision 1.3
diff -u -r1.2 -r1.3
--- /home/repository/moby/moby-live/Python/bioMoby/mobyService.py	2005/01/18 13:46:22	1.2
+++ /home/repository/moby/moby-live/Python/bioMoby/mobyService.py	2005/02/01 08:52:15	1.3
@@ -6,7 +6,7 @@
     Author: Wong Yan
     
     01/17/2004: Service can be executed as a Thread, thus several queries can be made
-    		in the same time.
+                    in the same time.
 """
 
 from mobyRegister import GeneralInformations
@@ -244,7 +244,7 @@
         self.type=""
         self.category=""
         self.url=""
-	self.signatureURL=""
+        self.signatureURL=""
         self.authoritative=0
         self.inputObjects=[]
         self.outputObjects=[]
@@ -264,8 +264,8 @@
                     self.type=arg[key]
                 elif key=='url':
                     self.url=arg['url']
-		elif key=='signatureURL':
-		    self.signatureURL=arg['signatureURL']
+                elif key=='signatureURL':
+                    self.signatureURL=arg['signatureURL']
                 elif key=='authoritative':
                     self.authoritative=arg[key]
                 elif key=='contactEmail':
@@ -311,7 +311,7 @@
         
         from SOAPpy import SOAPProxy
 
-	webservice=SOAPProxy(self.url,namespace=self.namespace)
+        webservice=SOAPProxy(self.url,namespace=self.namespace)
         
         if method=="":
             if len(self.methods)==0:
@@ -325,9 +325,9 @@
 
         webservice.soapaction=self.namespace+"#"+method
 
-	if debug:
-	    webservice.config.debug=1
-	
+        if debug:
+            webservice.config.debug=1
+        
         toQuery=str(query)
 
         del  SOAPProxy
@@ -339,13 +339,13 @@
             
         #try to return a MobyContent Object instead
         from bioMoby.mobyDataTypes import MobyContent
-	mc=MobyContent()
-	mc.fromMoby(result)
+        mc=MobyContent()
+        mc.fromMoby(result)
         
         del MobyContent
 
         return mc
-    	
+            
     def __str__(self):
         """Returns The moby xml form of the web service
         """
@@ -354,7 +354,7 @@
         result.append("<serviceType>"+self.type+"</serviceType>")
         result.append("<authURI>"+self.authURI+"</authURI>")
         result.append("<URL>"+self.url+"</URL>")
-	result.append("<signatureURL>"+self.signatureURL+"</signatureURL>")
+        result.append("<signatureURL>"+self.signatureURL+"</signatureURL>")
         result.append("<contactEmail>"+self.contact+"</contactEmail>")
         result.append("<authoritativeService>"+`self.authoritative`+"</authoritativeService>")
         result.append("<Description><![CDATA["+self.description+"]]></Description>")
@@ -367,10 +367,10 @@
             elif inputObject.__class__ is dict:
                 result.append('<Collection articleName="'+inputObject.keys()[0]+'">')
 
-		for aSimple in inputObject[inputObject.keys()[0]]:
+                for aSimple in inputObject[inputObject.keys()[0]]:
                     result.append(str(aSimple))
 
-		result.append("</Collection>")
+                result.append("</Collection>")
             else:
                 from mobyExceptions import EInvalidArgument
                 raise EInvalidArgument, "Bad input object"
@@ -385,10 +385,10 @@
             elif output.__class__ is dict:
                 result.append('<Collection articleName="'+output.keys()[0]+'">')
 
-		for aSimple in output[output.keys()[0]]:
+                for aSimple in output[output.keys()[0]]:
                     result.append(str(aSimple))
-		    
-		result.append("</Collection>")
+                    
+                result.append("</Collection>")
             else:
                 from mobyExceptions import EInvalidArgument
                 raise EInvalidArgument, "Bad output object"
@@ -410,10 +410,10 @@
         """Register the service on the Moby server    
            has been added  here a code to verify that signatureURL is not empty :)
         """
-	if self.signatureURL=="":
-	    from mobyExceptions import EInvalidArgument
-	    raise EInvalidArgument, "field signatureURL cannot be empty"
-	
+        if self.signatureURL=="":
+            from mobyExceptions import EInvalidArgument
+            raise EInvalidArgument, "field signatureURL cannot be empty"
+        
         xmlinput="<registerService>"+str(self)+"</registerService>"
         
         from mobyRegister import RegistrationObject
@@ -431,32 +431,32 @@
         return result
 
     def _executeThread(self, mobyContent):
-	"""Execute the service, store the result in a field
-	"""
-	
-	self.results=self.execute(mobyContent, returnXml=(mobyContent.__class__ is str))
-		
-	
+        """Execute the service, store the result in a field
+        """
+        
+        self.results=self.execute(mobyContent, returnXml=(mobyContent.__class__ is str))
+                
+        
     def start(self, mobycontent, timeout=-1):
-	"""Start the service as it was a thread
-	"""
-	from threading import Thread
-	
-	
-	if timeout != -1:
-	    self._execThread=Thread(target=self._executeThread, args=(mobycontent,))
-	else:
-	    self._execThread=Thread(target=self._executeThread, args=(mobycontent,), timeout=timeout)
+        """Start the service as it was a thread
+        """
+        from threading import Thread
+        
+        
+        if timeout != -1:
+            self._execThread=Thread(target=self._executeThread, args=(mobycontent,))
+        else:
+            self._execThread=Thread(target=self._executeThread, args=(mobycontent,), timeout=timeout)
 
-	self._execThread.start()
-	
+        self._execThread.start()
+        
     def join(self):
-	"""Same as Thread.join
-	"""
-	self._execThread.join()
-	
-	
-	
+        """Same as Thread.join
+        """
+        self._execThread.join()
+        
+        
+        
 class ServiceList:
     """Class representing a service's list
     """
@@ -502,17 +502,17 @@
 
         for childNode in node.childNodes:
             if childNode.nodeName=="datatype":
-		if childNode.firstChild:
+                if childNode.firstChild:
                     secondary.type=childNode.firstChild.nodeValue
             elif childNode.nodeName=="default":
                 if childNode.firstChild:
-		    secondary.default=childNode.firstChild.nodeValue
+                    secondary.default=childNode.firstChild.nodeValue
             elif childNode.nodeName=="min":
                 if childNode.firstChild:
-		    secondary.min=childNode.firstChild.nodeValue
+                    secondary.min=childNode.firstChild.nodeValue
             elif childNode.nodeName=="max":
                 if childNode.firstChild:
-		    secondary.max=childNode.firstChild.nodeValue
+                    secondary.max=childNode.firstChild.nodeValue
             elif childNode.nodeName=="enum":
                 if childNode.firstChild:
                     secondary.enums.append(childNode.firstChild.nodeValue)
@@ -547,7 +547,7 @@
                     service.contact=child.firstChild.nodeValue
                 elif child.nodeName=="URL" and child.firstChild:
                     service.url=child.firstChild.nodeValue
-		elif child.nodeName=="signatureURL" and child.firstChild:
+                elif child.nodeName=="signatureURL" and child.firstChild:
                     service.signatureURL=child.firstChild.nodeValue
                 elif child.nodeName=="Input":
                     for article in child.childNodes:



From yanwong at pub.open-bio.org  Tue Feb  1 08:42:57 2005
From: yanwong at pub.open-bio.org (Yan Wong)
Date: Tue, 01 Feb 2005 08:42:57 -0000
Subject: [MOBY-guts] biomoby commit
Message-ID: <200502010852.j118qHRx013096@pub.open-bio.org>


yanwong
Tue Feb  1 03:52:16 EST 2005
Update of /home/repository/moby/moby-live/Python/bioMoby/ontology
In directory pub.open-bio.org:/tmp/cvs-serv12609/ontology

Modified Files:
	AlleleAssociation.py Allele_freq.py AminoAcidSequence.py 
	B64_Encoded_PNG.py B64_Encoded_Postscript.py 
	B64_encoded_PDB.py B64_encoded_gif.py B64_encoded_jpeg.py 
	BLASTText.py BasicGFFSequenceFeature.py 
	ClustalAlnFormattedText.py ClustalMsfFormattedText.py 
	CommentedAASequence.py CommentedDNASequence.py 
	CommentedRNASequence.py DNASequence.py 
	DNASequenceWithGFFFeatures.py DateTime.py Decypher_Text.py 
	Edge.py EmblFlatfile.py FASTA.py FASTA_AA.py FASTA_NA.py 
	FASTA_Text.py GFF.py GFF1.py GFF2.py GFF2_5.py GFF3.py 
	GO_Term.py GenbankFlatfile.py GenericSequence.py 
	GeneticElement.py Genotype.py Germplasm_Details.py 
	Germplasm_List.py Global_Keyword.py HBond_Pair.py 
	HFormatText.py Haplotyping_Study_obj.py ICIS_Query.py 
	ICIS_Query2.py ICIS_Query3.py IntAct_XML.py Interaction.py 
	InteractionMethod.py Interaction_partner.py Interactor.py 
	MEME_Text.py MGIS_ACCESSION.py MMP_Locus.py MO_Term_Test.py 
	MmCIFText.py Multi_key_value_pair.py 
	MyTestingDataType_11024145298313.py MyTree.py 
	NCBI_BLAST_Text.py NCBI_Blast_XML.py NCBI_Blast_XML_Gif.py 
	NCBI_Blast_XML_Gif_Map.py NCBI_MEME_Text.py 
	NucleotideSequence.py PDBFormattedText.py PDBText.py PDGJOB.py 
	PHDText.py PMUTText.py PSeaTextFormatted.py 
	PhenotypeDescription.py PubMedMEDLINE.py RNASequence.py 
	SINGER_ACCESSION.py Sample.py SchematikonMotifID.py 
	SchematikonMotifSupport.py SchematikonSegmentAttributes.py 
	SchematikonSegmentID.py SchematikonStructureAnnotation.py 
	SchematikonVorocodeName.py Scored_acronym_string.py 
	SimpleAnnotatedGIFImage.py SimpleAnnotatedJPEGImage.py 
	Simple_key_value_pair.py Snp_allele.py Snp_genotype.py 
	Study.py TEST.py TargetP_result.py Testout.py TextBase64.py 
	TextFormatted.py TextHtml.py TextPlain.py TextUuencoded.py 
	TextXml.py Text_plain.py Trait_Details.py Tree.py 
	TropGENE_ACCESSION.py TropGENE_Diversity_Matrix.py 
	TropGENE_LOCUS.py VirtualSequence.py WU_BLAST_Text.py 
	Wildcard_Query.py __init__.py 
Log Message:


moby-live/Python/bioMoby/ontology AlleleAssociation.py,1.3,1.4 Allele_freq.py,1.3,1.4 AminoAcidSequence.py,1.3,1.4 B64_Encoded_PNG.py,1.3,1.4 B64_Encoded_Postscript.py,1.3,1.4 B64_encoded_PDB.py,1.3,1.4 B64_encoded_gif.py,1.3,1.4 B64_encoded_jpeg.py,1.3,1.4 BLASTText.py,1.3,1.4 BasicGFFSequenceFeature.py,1.3,1.4 ClustalAlnFormattedText.py,1.3,1.4 ClustalMsfFormattedText.py,1.3,1.4 CommentedAASequence.py,1.3,1.4 CommentedDNASequence.py,1.3,1.4 CommentedRNASequence.py,1.3,1.4 DNASequence.py,1.3,1.4 DNASequenceWithGFFFeatures.py,1.3,1.4 DateTime.py,1.3,1.4 Decypher_Text.py,1.3,1.4 Edge.py,1.3,1.4 EmblFlatfile.py,1.3,1.4 FASTA.py,1.3,1.4 FASTA_AA.py,1.3,1.4 FASTA_NA.py,1.3,1.4 FASTA_Text.py,1.3,1.4 GFF.py,1.3,1.4 GFF1.py,1.3,1.4 GFF2.py,1.3,1.4 GFF2_5.py,1.3,1.4 GFF3.py,1.3,1.4 GO_Term.py,1.3,1.4 GenbankFlatfile.py,1.3,1.4 GenericSequence.py,1.3,1.4 GeneticElement.py,1.3,1.4 Genotype.py,1.3,1.4 Germplasm_Details.py,1.3,1.4 Germplasm_List.py,1.3,1.4 Global_Keyword.py,1.3,1.4 HBon!
d_Pair.py,1.3,1.4 HFormatText.py,1.3,1.4 Haplotyping_Study_obj.py,1.3,1.4 ICIS_Query.py,1.3,1.4 ICIS_Query2.py,1.3,1.4 ICIS_Query3.py,1.3,1.4 IntAct_XML.py,1.3,1.4 Interaction.py,1.3,1.4 InteractionMethod.py,1.3,1.4 Interaction_partner.py,1.3,1.4 Interactor.py,1.3,1.4 MEME_Text.py,1.3,1.4 MGIS_ACCESSION.py,1.3,1.4 MMP_Locus.py,1.3,1.4 MO_Term_Test.py,1.3,1.4 MmCIFText.py,1.3,1.4 Multi_key_value_pair.py,1.3,1.4 MyTestingDataType_11024145298313.py,1.3,1.4 MyTree.py,1.3,1.4 NCBI_BLAST_Text.py,1.3,1.4 NCBI_Blast_XML.py,1.3,1.4 NCBI_Blast_XML_Gif.py,1.3,1.4 NCBI_Blast_XML_Gif_Map.py,1.3,1.4 NCBI_MEME_Text.py,1.3,1.4 NucleotideSequence.py,1.3,1.4 PDBFormattedText.py,1.3,1.4 PDBText.py,1.3,1.4 PDGJOB.py,1.3,1.4 PHDText.py,1.3,1.4 PMUTText.py,1.3,1.4 PSeaTextFormatted.py,1.3,1.4 PhenotypeDescription.py,1.3,1.4 PubMedMEDLINE.py,1.3,1.4 RNASequence.py,1.3,1.4 SINGER_ACCESSION.py,1.3,1.4 Sample.py,1.3,1.4 SchematikonMotifID.py,1.3,1.4 SchematikonMotifSupport.py,1.3,1.4 SchematikonSegme!
ntAttributes.py,1.3,1.4 SchematikonSegmentID.py,1.3,1.4 Schem!
atikonStructureAnnotation.py,1.3,1.4 SchematikonVorocodeName.py,1.3,1.4 Scored_acronym_string.py,1.3,1.4 SimpleAnnotatedGIFImage.py,1.3,1.4 SimpleAnnotatedJPEGImage.py,1.3,1.4 Simple_key_value_pair.py,1.3,1.4 Snp_allele.py,1.3,1.4 Snp_genotype.py,1.3,1.4 Study.py,1.3,1.4 TEST.py,1.3,1.4 TargetP_result.py,1.3,1.4 Testout.py,1.3,1.4 TextBase64.py,1.3,1.4 TextFormatted.py,1.3,1.4 TextHtml.py,1.3,1.4 TextPlain.py,1.3,1.4 TextUuencoded.py,1.3,1.4 TextXml.py,1.3,1.4 Text_plain.py,1.3,1.4 Trait_Details.py,1.3,1.4 Tree.py,1.3,1.4 TropGENE_ACCESSION.py,1.3,1.4 TropGENE_Diversity_Matrix.py,1.3,1.4 TropGENE_LOCUS.py,1.3,1.4 VirtualSequence.py,1.3,1.4 WU_BLAST_Text.py,1.3,1.4 Wildcard_Query.py,1.3,1.4 __init__.py,1.2,1.3
===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/ontology/AlleleAssociation.py,v
retrieving revision 1.3
retrieving revision 1.4
diff -u -r1.3 -r1.4
--- /home/repository/moby/moby-live/Python/bioMoby/ontology/AlleleAssociation.py	2005/01/27 08:44:05	1.3
+++ /home/repository/moby/moby-live/Python/bioMoby/ontology/AlleleAssociation.py	2005/02/01 08:52:15	1.4
@@ -50,8 +50,7 @@
             if elt.nodeName=="CrossReference" or elt.nodeName=="moby:CrossReference":
                 self.__cross__=[]
                 for ref in elt.childNodes:
-                    if ref.nodeType==ref.ELEMENT_NODE:
-                        self.__cross__.append(um.loads(ref.toxml()))
+                    self.__cross__.append(ref.toxml())
             if elt.nodeType==elt.ELEMENT_NODE and (elt.nodeName=="String" or elt.nodeName=="moby:String") and (elt.getAttribute("articleName")=="snp" or elt.getAttribute("moby:articleName")=="snp"):
                 t=MobyString()
                 t.fromMoby(elt.toxml())

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/ontology/Allele_freq.py,v
retrieving revision 1.3
retrieving revision 1.4
diff -u -r1.3 -r1.4
--- /home/repository/moby/moby-live/Python/bioMoby/ontology/Allele_freq.py	2005/01/27 08:44:05	1.3
+++ /home/repository/moby/moby-live/Python/bioMoby/ontology/Allele_freq.py	2005/02/01 08:52:15	1.4
@@ -44,8 +44,7 @@
             if elt.nodeName=="CrossReference" or elt.nodeName=="moby:CrossReference":
                 self.__cross__=[]
                 for ref in elt.childNodes:
-                    if ref.nodeType==ref.ELEMENT_NODE:
-                        self.__cross__.append(um.loads(ref.toxml()))
+                    self.__cross__.append(ref.toxml())
             if elt.nodeType==elt.ELEMENT_NODE and (elt.nodeName=="Object" or elt.nodeName=="moby:Object") and (elt.getAttribute("articleName")=="panel_lsid" or elt.getAttribute("moby:articleName")=="panel_lsid"):
                 self.Panel_lsid=MobyObject()
                 self.Panel_lsid.fromMoby(elt.toxml())

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/ontology/AminoAcidSequence.py,v
retrieving revision 1.3
retrieving revision 1.4
diff -u -r1.3 -r1.4
--- /home/repository/moby/moby-live/Python/bioMoby/ontology/AminoAcidSequence.py	2005/01/27 08:44:05	1.3
+++ /home/repository/moby/moby-live/Python/bioMoby/ontology/AminoAcidSequence.py	2005/02/01 08:52:15	1.4
@@ -49,8 +49,7 @@
             if elt.nodeName=="CrossReference" or elt.nodeName=="moby:CrossReference":
                 self.__cross__=[]
                 for ref in elt.childNodes:
-                    if ref.nodeType==ref.ELEMENT_NODE:
-                        self.__cross__.append(um.loads(ref.toxml()))
+                    self.__cross__.append(ref.toxml())
             if elt.nodeType==elt.ELEMENT_NODE and (elt.nodeName=="Integer" or elt.nodeName=="moby:Integer") and (elt.getAttribute("articleName")=="Length" or elt.getAttribute("moby:articleName")=="Length"):
                 t=MobyInteger()
                 t.fromMoby(elt.toxml())

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/ontology/B64_Encoded_PNG.py,v
retrieving revision 1.3
retrieving revision 1.4
diff -u -r1.3 -r1.4
--- /home/repository/moby/moby-live/Python/bioMoby/ontology/B64_Encoded_PNG.py	2005/01/27 08:44:05	1.3
+++ /home/repository/moby/moby-live/Python/bioMoby/ontology/B64_Encoded_PNG.py	2005/02/01 08:52:15	1.4
@@ -46,5 +46,4 @@
             if elt.nodeName=="CrossReference" or elt.nodeName=="moby:CrossReference":
                 self.__cross__=[]
                 for ref in elt.childNodes:
-                    if ref.nodeType==ref.ELEMENT_NODE:
-                        self.__cross__.append(um.loads(ref.toxml()))
\ No newline at end of file
+                    self.__cross__.append(ref.toxml())
\ No newline at end of file

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/ontology/B64_Encoded_Postscript.py,v
retrieving revision 1.3
retrieving revision 1.4
diff -u -r1.3 -r1.4
--- /home/repository/moby/moby-live/Python/bioMoby/ontology/B64_Encoded_Postscript.py	2005/01/27 08:44:05	1.3
+++ /home/repository/moby/moby-live/Python/bioMoby/ontology/B64_Encoded_Postscript.py	2005/02/01 08:52:15	1.4
@@ -46,5 +46,4 @@
             if elt.nodeName=="CrossReference" or elt.nodeName=="moby:CrossReference":
                 self.__cross__=[]
                 for ref in elt.childNodes:
-                    if ref.nodeType==ref.ELEMENT_NODE:
-                        self.__cross__.append(um.loads(ref.toxml()))
\ No newline at end of file
+                    self.__cross__.append(ref.toxml())
\ No newline at end of file

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/ontology/B64_encoded_PDB.py,v
retrieving revision 1.3
retrieving revision 1.4
diff -u -r1.3 -r1.4
--- /home/repository/moby/moby-live/Python/bioMoby/ontology/B64_encoded_PDB.py	2005/01/27 08:44:05	1.3
+++ /home/repository/moby/moby-live/Python/bioMoby/ontology/B64_encoded_PDB.py	2005/02/01 08:52:15	1.4
@@ -46,5 +46,4 @@
             if elt.nodeName=="CrossReference" or elt.nodeName=="moby:CrossReference":
                 self.__cross__=[]
                 for ref in elt.childNodes:
-                    if ref.nodeType==ref.ELEMENT_NODE:
-                        self.__cross__.append(um.loads(ref.toxml()))
\ No newline at end of file
+                    self.__cross__.append(ref.toxml())
\ No newline at end of file

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/ontology/B64_encoded_gif.py,v
retrieving revision 1.3
retrieving revision 1.4
diff -u -r1.3 -r1.4
--- /home/repository/moby/moby-live/Python/bioMoby/ontology/B64_encoded_gif.py	2005/01/27 08:44:05	1.3
+++ /home/repository/moby/moby-live/Python/bioMoby/ontology/B64_encoded_gif.py	2005/02/01 08:52:15	1.4
@@ -46,5 +46,4 @@
             if elt.nodeName=="CrossReference" or elt.nodeName=="moby:CrossReference":
                 self.__cross__=[]
                 for ref in elt.childNodes:
-                    if ref.nodeType==ref.ELEMENT_NODE:
-                        self.__cross__.append(um.loads(ref.toxml()))
\ No newline at end of file
+                    self.__cross__.append(ref.toxml())
\ No newline at end of file

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/ontology/B64_encoded_jpeg.py,v
retrieving revision 1.3
retrieving revision 1.4
diff -u -r1.3 -r1.4
--- /home/repository/moby/moby-live/Python/bioMoby/ontology/B64_encoded_jpeg.py	2005/01/27 08:44:05	1.3
+++ /home/repository/moby/moby-live/Python/bioMoby/ontology/B64_encoded_jpeg.py	2005/02/01 08:52:15	1.4
@@ -46,5 +46,4 @@
             if elt.nodeName=="CrossReference" or elt.nodeName=="moby:CrossReference":
                 self.__cross__=[]
                 for ref in elt.childNodes:
-                    if ref.nodeType==ref.ELEMENT_NODE:
-                        self.__cross__.append(um.loads(ref.toxml()))
\ No newline at end of file
+                    self.__cross__.append(ref.toxml())
\ No newline at end of file

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/ontology/BLASTText.py,v
retrieving revision 1.3
retrieving revision 1.4
diff -u -r1.3 -r1.4
--- /home/repository/moby/moby-live/Python/bioMoby/ontology/BLASTText.py	2005/01/27 08:44:05	1.3
+++ /home/repository/moby/moby-live/Python/bioMoby/ontology/BLASTText.py	2005/02/01 08:52:15	1.4
@@ -46,5 +46,4 @@
             if elt.nodeName=="CrossReference" or elt.nodeName=="moby:CrossReference":
                 self.__cross__=[]
                 for ref in elt.childNodes:
-                    if ref.nodeType==ref.ELEMENT_NODE:
-                        self.__cross__.append(um.loads(ref.toxml()))
\ No newline at end of file
+                    self.__cross__.append(ref.toxml())
\ No newline at end of file

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/ontology/BasicGFFSequenceFeature.py,v
retrieving revision 1.3
retrieving revision 1.4
diff -u -r1.3 -r1.4
--- /home/repository/moby/moby-live/Python/bioMoby/ontology/BasicGFFSequenceFeature.py	2005/01/27 08:44:05	1.3
+++ /home/repository/moby/moby-live/Python/bioMoby/ontology/BasicGFFSequenceFeature.py	2005/02/01 08:52:15	1.4
@@ -60,8 +60,7 @@
             if elt.nodeName=="CrossReference" or elt.nodeName=="moby:CrossReference":
                 self.__cross__=[]
                 for ref in elt.childNodes:
-                    if ref.nodeType==ref.ELEMENT_NODE:
-                        self.__cross__.append(um.loads(ref.toxml()))
+                    self.__cross__.append(ref.toxml())
             if elt.nodeType==elt.ELEMENT_NODE and (elt.nodeName=="String" or elt.nodeName=="moby:String") and (elt.getAttribute("articleName")=="reference" or elt.getAttribute("moby:articleName")=="reference"):
                 t=MobyString()
                 t.fromMoby(elt.toxml())

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/ontology/ClustalAlnFormattedText.py,v
retrieving revision 1.3
retrieving revision 1.4
diff -u -r1.3 -r1.4
--- /home/repository/moby/moby-live/Python/bioMoby/ontology/ClustalAlnFormattedText.py	2005/01/27 08:44:05	1.3
+++ /home/repository/moby/moby-live/Python/bioMoby/ontology/ClustalAlnFormattedText.py	2005/02/01 08:52:15	1.4
@@ -46,5 +46,4 @@
             if elt.nodeName=="CrossReference" or elt.nodeName=="moby:CrossReference":
                 self.__cross__=[]
                 for ref in elt.childNodes:
-                    if ref.nodeType==ref.ELEMENT_NODE:
-                        self.__cross__.append(um.loads(ref.toxml()))
\ No newline at end of file
+                    self.__cross__.append(ref.toxml())
\ No newline at end of file

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/ontology/ClustalMsfFormattedText.py,v
retrieving revision 1.3
retrieving revision 1.4
diff -u -r1.3 -r1.4
--- /home/repository/moby/moby-live/Python/bioMoby/ontology/ClustalMsfFormattedText.py	2005/01/27 08:44:05	1.3
+++ /home/repository/moby/moby-live/Python/bioMoby/ontology/ClustalMsfFormattedText.py	2005/02/01 08:52:15	1.4
@@ -46,5 +46,4 @@
             if elt.nodeName=="CrossReference" or elt.nodeName=="moby:CrossReference":
                 self.__cross__=[]
                 for ref in elt.childNodes:
-                    if ref.nodeType==ref.ELEMENT_NODE:
-                        self.__cross__.append(um.loads(ref.toxml()))
\ No newline at end of file
+                    self.__cross__.append(ref.toxml())
\ No newline at end of file

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/ontology/CommentedAASequence.py,v
retrieving revision 1.3
retrieving revision 1.4
diff -u -r1.3 -r1.4
--- /home/repository/moby/moby-live/Python/bioMoby/ontology/CommentedAASequence.py	2005/01/27 08:44:05	1.3
+++ /home/repository/moby/moby-live/Python/bioMoby/ontology/CommentedAASequence.py	2005/02/01 08:52:15	1.4
@@ -50,8 +50,7 @@
             if elt.nodeName=="CrossReference" or elt.nodeName=="moby:CrossReference":
                 self.__cross__=[]
                 for ref in elt.childNodes:
-                    if ref.nodeType==ref.ELEMENT_NODE:
-                        self.__cross__.append(um.loads(ref.toxml()))
+                    self.__cross__.append(ref.toxml())
             if elt.nodeType==elt.ELEMENT_NODE and (elt.nodeName=="Integer" or elt.nodeName=="moby:Integer") and (elt.getAttribute("articleName")=="Length" or elt.getAttribute("moby:articleName")=="Length"):
                 t=MobyInteger()
                 t.fromMoby(elt.toxml())

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/ontology/CommentedDNASequence.py,v
retrieving revision 1.3
retrieving revision 1.4
diff -u -r1.3 -r1.4
--- /home/repository/moby/moby-live/Python/bioMoby/ontology/CommentedDNASequence.py	2005/01/27 08:44:05	1.3
+++ /home/repository/moby/moby-live/Python/bioMoby/ontology/CommentedDNASequence.py	2005/02/01 08:52:15	1.4
@@ -50,8 +50,7 @@
             if elt.nodeName=="CrossReference" or elt.nodeName=="moby:CrossReference":
                 self.__cross__=[]
                 for ref in elt.childNodes:
-                    if ref.nodeType==ref.ELEMENT_NODE:
-                        self.__cross__.append(um.loads(ref.toxml()))
+                    self.__cross__.append(ref.toxml())
             if elt.nodeType==elt.ELEMENT_NODE and (elt.nodeName=="Integer" or elt.nodeName=="moby:Integer") and (elt.getAttribute("articleName")=="Length" or elt.getAttribute("moby:articleName")=="Length"):
                 t=MobyInteger()
                 t.fromMoby(elt.toxml())

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/ontology/CommentedRNASequence.py,v
retrieving revision 1.3
retrieving revision 1.4
diff -u -r1.3 -r1.4
--- /home/repository/moby/moby-live/Python/bioMoby/ontology/CommentedRNASequence.py	2005/01/27 08:44:05	1.3
+++ /home/repository/moby/moby-live/Python/bioMoby/ontology/CommentedRNASequence.py	2005/02/01 08:52:15	1.4
@@ -50,8 +50,7 @@
             if elt.nodeName=="CrossReference" or elt.nodeName=="moby:CrossReference":
                 self.__cross__=[]
                 for ref in elt.childNodes:
-                    if ref.nodeType==ref.ELEMENT_NODE:
-                        self.__cross__.append(um.loads(ref.toxml()))
+                    self.__cross__.append(ref.toxml())
             if elt.nodeType==elt.ELEMENT_NODE and (elt.nodeName=="Integer" or elt.nodeName=="moby:Integer") and (elt.getAttribute("articleName")=="Length" or elt.getAttribute("moby:articleName")=="Length"):
                 t=MobyInteger()
                 t.fromMoby(elt.toxml())

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/ontology/DNASequence.py,v
retrieving revision 1.3
retrieving revision 1.4
diff -u -r1.3 -r1.4
--- /home/repository/moby/moby-live/Python/bioMoby/ontology/DNASequence.py	2005/01/27 08:44:05	1.3
+++ /home/repository/moby/moby-live/Python/bioMoby/ontology/DNASequence.py	2005/02/01 08:52:15	1.4
@@ -49,8 +49,7 @@
             if elt.nodeName=="CrossReference" or elt.nodeName=="moby:CrossReference":
                 self.__cross__=[]
                 for ref in elt.childNodes:
-                    if ref.nodeType==ref.ELEMENT_NODE:
-                        self.__cross__.append(um.loads(ref.toxml()))
+                    self.__cross__.append(ref.toxml())
             if elt.nodeType==elt.ELEMENT_NODE and (elt.nodeName=="Integer" or elt.nodeName=="moby:Integer") and (elt.getAttribute("articleName")=="Length" or elt.getAttribute("moby:articleName")=="Length"):
                 t=MobyInteger()
                 t.fromMoby(elt.toxml())

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/ontology/DNASequenceWithGFFFeatures.py,v
retrieving revision 1.3
retrieving revision 1.4
diff -u -r1.3 -r1.4
--- /home/repository/moby/moby-live/Python/bioMoby/ontology/DNASequenceWithGFFFeatures.py	2005/01/27 08:44:05	1.3
+++ /home/repository/moby/moby-live/Python/bioMoby/ontology/DNASequenceWithGFFFeatures.py	2005/02/01 08:52:15	1.4
@@ -52,8 +52,7 @@
             if elt.nodeName=="CrossReference" or elt.nodeName=="moby:CrossReference":
                 self.__cross__=[]
                 for ref in elt.childNodes:
-                    if ref.nodeType==ref.ELEMENT_NODE:
-                        self.__cross__.append(um.loads(ref.toxml()))
+                    self.__cross__.append(ref.toxml())
             if elt.nodeType==elt.ELEMENT_NODE and (elt.nodeName=="Integer" or elt.nodeName=="moby:Integer") and (elt.getAttribute("articleName")=="Length" or elt.getAttribute("moby:articleName")=="Length"):
                 t=MobyInteger()
                 t.fromMoby(elt.toxml())

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/ontology/DateTime.py,v
retrieving revision 1.3
retrieving revision 1.4
diff -u -r1.3 -r1.4
--- /home/repository/moby/moby-live/Python/bioMoby/ontology/DateTime.py	2005/01/27 08:44:05	1.3
+++ /home/repository/moby/moby-live/Python/bioMoby/ontology/DateTime.py	2005/02/01 08:52:15	1.4
@@ -46,5 +46,4 @@
             if elt.nodeName=="CrossReference" or elt.nodeName=="moby:CrossReference":
                 self.__cross__=[]
                 for ref in elt.childNodes:
-                    if ref.nodeType==ref.ELEMENT_NODE:
-                        self.__cross__.append(um.loads(ref.toxml()))
\ No newline at end of file
+                    self.__cross__.append(ref.toxml())
\ No newline at end of file

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/ontology/Decypher_Text.py,v
retrieving revision 1.3
retrieving revision 1.4
diff -u -r1.3 -r1.4
--- /home/repository/moby/moby-live/Python/bioMoby/ontology/Decypher_Text.py	2005/01/27 08:44:05	1.3
+++ /home/repository/moby/moby-live/Python/bioMoby/ontology/Decypher_Text.py	2005/02/01 08:52:15	1.4
@@ -46,5 +46,4 @@
             if elt.nodeName=="CrossReference" or elt.nodeName=="moby:CrossReference":
                 self.__cross__=[]
                 for ref in elt.childNodes:
-                    if ref.nodeType==ref.ELEMENT_NODE:
-                        self.__cross__.append(um.loads(ref.toxml()))
\ No newline at end of file
+                    self.__cross__.append(ref.toxml())
\ No newline at end of file

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/ontology/Edge.py,v
retrieving revision 1.3
retrieving revision 1.4
diff -u -r1.3 -r1.4
--- /home/repository/moby/moby-live/Python/bioMoby/ontology/Edge.py	2005/01/27 08:44:05	1.3
+++ /home/repository/moby/moby-live/Python/bioMoby/ontology/Edge.py	2005/02/01 08:52:15	1.4
@@ -49,8 +49,7 @@
             if elt.nodeName=="CrossReference" or elt.nodeName=="moby:CrossReference":
                 self.__cross__=[]
                 for ref in elt.childNodes:
-                    if ref.nodeType==ref.ELEMENT_NODE:
-                        self.__cross__.append(um.loads(ref.toxml()))
+                    self.__cross__.append(ref.toxml())
             if elt.nodeType==elt.ELEMENT_NODE and (elt.nodeName=="String" or elt.nodeName=="moby:String") and (elt.getAttribute("articleName")=="partner" or elt.getAttribute("moby:articleName")=="partner"):
                 t=MobyString()
                 t.fromMoby(elt.toxml())

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/ontology/EmblFlatfile.py,v
retrieving revision 1.3
retrieving revision 1.4
diff -u -r1.3 -r1.4
--- /home/repository/moby/moby-live/Python/bioMoby/ontology/EmblFlatfile.py	2005/01/27 08:44:05	1.3
+++ /home/repository/moby/moby-live/Python/bioMoby/ontology/EmblFlatfile.py	2005/02/01 08:52:15	1.4
@@ -46,5 +46,4 @@
             if elt.nodeName=="CrossReference" or elt.nodeName=="moby:CrossReference":
                 self.__cross__=[]
                 for ref in elt.childNodes:
-                    if ref.nodeType==ref.ELEMENT_NODE:
-                        self.__cross__.append(um.loads(ref.toxml()))
\ No newline at end of file
+                    self.__cross__.append(ref.toxml())
\ No newline at end of file

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/ontology/FASTA.py,v
retrieving revision 1.3
retrieving revision 1.4
diff -u -r1.3 -r1.4
--- /home/repository/moby/moby-live/Python/bioMoby/ontology/FASTA.py	2005/01/27 08:44:05	1.3
+++ /home/repository/moby/moby-live/Python/bioMoby/ontology/FASTA.py	2005/02/01 08:52:15	1.4
@@ -46,5 +46,4 @@
             if elt.nodeName=="CrossReference" or elt.nodeName=="moby:CrossReference":
                 self.__cross__=[]
                 for ref in elt.childNodes:
-                    if ref.nodeType==ref.ELEMENT_NODE:
-                        self.__cross__.append(um.loads(ref.toxml()))
\ No newline at end of file
+                    self.__cross__.append(ref.toxml())
\ No newline at end of file

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/ontology/FASTA_AA.py,v
retrieving revision 1.3
retrieving revision 1.4
diff -u -r1.3 -r1.4
--- /home/repository/moby/moby-live/Python/bioMoby/ontology/FASTA_AA.py	2005/01/27 08:44:05	1.3
+++ /home/repository/moby/moby-live/Python/bioMoby/ontology/FASTA_AA.py	2005/02/01 08:52:15	1.4
@@ -46,5 +46,4 @@
             if elt.nodeName=="CrossReference" or elt.nodeName=="moby:CrossReference":
                 self.__cross__=[]
                 for ref in elt.childNodes:
-                    if ref.nodeType==ref.ELEMENT_NODE:
-                        self.__cross__.append(um.loads(ref.toxml()))
\ No newline at end of file
+                    self.__cross__.append(ref.toxml())
\ No newline at end of file

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/ontology/FASTA_NA.py,v
retrieving revision 1.3
retrieving revision 1.4
diff -u -r1.3 -r1.4
--- /home/repository/moby/moby-live/Python/bioMoby/ontology/FASTA_NA.py	2005/01/27 08:44:05	1.3
+++ /home/repository/moby/moby-live/Python/bioMoby/ontology/FASTA_NA.py	2005/02/01 08:52:15	1.4
@@ -46,5 +46,4 @@
             if elt.nodeName=="CrossReference" or elt.nodeName=="moby:CrossReference":
                 self.__cross__=[]
                 for ref in elt.childNodes:
-                    if ref.nodeType==ref.ELEMENT_NODE:
-                        self.__cross__.append(um.loads(ref.toxml()))
\ No newline at end of file
+                    self.__cross__.append(ref.toxml())
\ No newline at end of file

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/ontology/FASTA_Text.py,v
retrieving revision 1.3
retrieving revision 1.4
diff -u -r1.3 -r1.4
--- /home/repository/moby/moby-live/Python/bioMoby/ontology/FASTA_Text.py	2005/01/27 08:44:05	1.3
+++ /home/repository/moby/moby-live/Python/bioMoby/ontology/FASTA_Text.py	2005/02/01 08:52:15	1.4
@@ -46,5 +46,4 @@
             if elt.nodeName=="CrossReference" or elt.nodeName=="moby:CrossReference":
                 self.__cross__=[]
                 for ref in elt.childNodes:
-                    if ref.nodeType==ref.ELEMENT_NODE:
-                        self.__cross__.append(um.loads(ref.toxml()))
\ No newline at end of file
+                    self.__cross__.append(ref.toxml())
\ No newline at end of file

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/ontology/GFF.py,v
retrieving revision 1.3
retrieving revision 1.4
diff -u -r1.3 -r1.4
--- /home/repository/moby/moby-live/Python/bioMoby/ontology/GFF.py	2005/01/27 08:44:05	1.3
+++ /home/repository/moby/moby-live/Python/bioMoby/ontology/GFF.py	2005/02/01 08:52:15	1.4
@@ -46,5 +46,4 @@
             if elt.nodeName=="CrossReference" or elt.nodeName=="moby:CrossReference":
                 self.__cross__=[]
                 for ref in elt.childNodes:
-                    if ref.nodeType==ref.ELEMENT_NODE:
-                        self.__cross__.append(um.loads(ref.toxml()))
\ No newline at end of file
+                    self.__cross__.append(ref.toxml())
\ No newline at end of file

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/ontology/GFF1.py,v
retrieving revision 1.3
retrieving revision 1.4
diff -u -r1.3 -r1.4
--- /home/repository/moby/moby-live/Python/bioMoby/ontology/GFF1.py	2005/01/27 08:44:05	1.3
+++ /home/repository/moby/moby-live/Python/bioMoby/ontology/GFF1.py	2005/02/01 08:52:15	1.4
@@ -46,5 +46,4 @@
             if elt.nodeName=="CrossReference" or elt.nodeName=="moby:CrossReference":
                 self.__cross__=[]
                 for ref in elt.childNodes:
-                    if ref.nodeType==ref.ELEMENT_NODE:
-                        self.__cross__.append(um.loads(ref.toxml()))
\ No newline at end of file
+                    self.__cross__.append(ref.toxml())
\ No newline at end of file

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/ontology/GFF2.py,v
retrieving revision 1.3
retrieving revision 1.4
diff -u -r1.3 -r1.4
--- /home/repository/moby/moby-live/Python/bioMoby/ontology/GFF2.py	2005/01/27 08:44:05	1.3
+++ /home/repository/moby/moby-live/Python/bioMoby/ontology/GFF2.py	2005/02/01 08:52:15	1.4
@@ -46,5 +46,4 @@
             if elt.nodeName=="CrossReference" or elt.nodeName=="moby:CrossReference":
                 self.__cross__=[]
                 for ref in elt.childNodes:
-                    if ref.nodeType==ref.ELEMENT_NODE:
-                        self.__cross__.append(um.loads(ref.toxml()))
\ No newline at end of file
+                    self.__cross__.append(ref.toxml())
\ No newline at end of file

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/ontology/GFF2_5.py,v
retrieving revision 1.3
retrieving revision 1.4
diff -u -r1.3 -r1.4
--- /home/repository/moby/moby-live/Python/bioMoby/ontology/GFF2_5.py	2005/01/27 08:44:05	1.3
+++ /home/repository/moby/moby-live/Python/bioMoby/ontology/GFF2_5.py	2005/02/01 08:52:15	1.4
@@ -46,5 +46,4 @@
             if elt.nodeName=="CrossReference" or elt.nodeName=="moby:CrossReference":
                 self.__cross__=[]
                 for ref in elt.childNodes:
-                    if ref.nodeType==ref.ELEMENT_NODE:
-                        self.__cross__.append(um.loads(ref.toxml()))
\ No newline at end of file
+                    self.__cross__.append(ref.toxml())
\ No newline at end of file

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/ontology/GFF3.py,v
retrieving revision 1.3
retrieving revision 1.4
diff -u -r1.3 -r1.4
--- /home/repository/moby/moby-live/Python/bioMoby/ontology/GFF3.py	2005/01/27 08:44:05	1.3
+++ /home/repository/moby/moby-live/Python/bioMoby/ontology/GFF3.py	2005/02/01 08:52:15	1.4
@@ -46,5 +46,4 @@
             if elt.nodeName=="CrossReference" or elt.nodeName=="moby:CrossReference":
                 self.__cross__=[]
                 for ref in elt.childNodes:
-                    if ref.nodeType==ref.ELEMENT_NODE:
-                        self.__cross__.append(um.loads(ref.toxml()))
\ No newline at end of file
+                    self.__cross__.append(ref.toxml())
\ No newline at end of file

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/ontology/GO_Term.py,v
retrieving revision 1.3
retrieving revision 1.4
diff -u -r1.3 -r1.4
--- /home/repository/moby/moby-live/Python/bioMoby/ontology/GO_Term.py	2005/01/27 08:44:05	1.3
+++ /home/repository/moby/moby-live/Python/bioMoby/ontology/GO_Term.py	2005/02/01 08:52:15	1.4
@@ -48,8 +48,7 @@
             if elt.nodeName=="CrossReference" or elt.nodeName=="moby:CrossReference":
                 self.__cross__=[]
                 for ref in elt.childNodes:
-                    if ref.nodeType==ref.ELEMENT_NODE:
-                        self.__cross__.append(um.loads(ref.toxml()))
+                    self.__cross__.append(ref.toxml())
             if elt.nodeType==elt.ELEMENT_NODE and (elt.nodeName=="String" or elt.nodeName=="moby:String") and (elt.getAttribute("articleName")=="Term" or elt.getAttribute("moby:articleName")=="Term"):
                 t=MobyString()
                 t.fromMoby(elt.toxml())

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/ontology/GenbankFlatfile.py,v
retrieving revision 1.3
retrieving revision 1.4
diff -u -r1.3 -r1.4
--- /home/repository/moby/moby-live/Python/bioMoby/ontology/GenbankFlatfile.py	2005/01/27 08:44:05	1.3
+++ /home/repository/moby/moby-live/Python/bioMoby/ontology/GenbankFlatfile.py	2005/02/01 08:52:15	1.4
@@ -46,5 +46,4 @@
             if elt.nodeName=="CrossReference" or elt.nodeName=="moby:CrossReference":
                 self.__cross__=[]
                 for ref in elt.childNodes:
-                    if ref.nodeType==ref.ELEMENT_NODE:
-                        self.__cross__.append(um.loads(ref.toxml()))
\ No newline at end of file
+                    self.__cross__.append(ref.toxml())
\ No newline at end of file

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/ontology/GenericSequence.py,v
retrieving revision 1.3
retrieving revision 1.4
diff -u -r1.3 -r1.4
--- /home/repository/moby/moby-live/Python/bioMoby/ontology/GenericSequence.py	2005/01/27 08:44:05	1.3
+++ /home/repository/moby/moby-live/Python/bioMoby/ontology/GenericSequence.py	2005/02/01 08:52:15	1.4
@@ -49,8 +49,7 @@
             if elt.nodeName=="CrossReference" or elt.nodeName=="moby:CrossReference":
                 self.__cross__=[]
                 for ref in elt.childNodes:
-                    if ref.nodeType==ref.ELEMENT_NODE:
-                        self.__cross__.append(um.loads(ref.toxml()))
+                    self.__cross__.append(ref.toxml())
             if elt.nodeType==elt.ELEMENT_NODE and (elt.nodeName=="Integer" or elt.nodeName=="moby:Integer") and (elt.getAttribute("articleName")=="Length" or elt.getAttribute("moby:articleName")=="Length"):
                 t=MobyInteger()
                 t.fromMoby(elt.toxml())

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/ontology/GeneticElement.py,v
retrieving revision 1.3
retrieving revision 1.4
diff -u -r1.3 -r1.4
--- /home/repository/moby/moby-live/Python/bioMoby/ontology/GeneticElement.py	2005/01/27 08:44:05	1.3
+++ /home/repository/moby/moby-live/Python/bioMoby/ontology/GeneticElement.py	2005/02/01 08:52:15	1.4
@@ -47,8 +47,7 @@
             if elt.nodeName=="CrossReference" or elt.nodeName=="moby:CrossReference":
                 self.__cross__=[]
                 for ref in elt.childNodes:
-                    if ref.nodeType==ref.ELEMENT_NODE:
-                        self.__cross__.append(um.loads(ref.toxml()))
+                    self.__cross__.append(ref.toxml())
             if elt.nodeType==elt.ELEMENT_NODE and (elt.nodeName=="String" or elt.nodeName=="moby:String") and (elt.getAttribute("articleName")=="GeneticElement" or elt.getAttribute("moby:articleName")=="GeneticElement"):
                 t=MobyString()
                 t.fromMoby(elt.toxml())

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/ontology/Genotype.py,v
retrieving revision 1.3
retrieving revision 1.4
diff -u -r1.3 -r1.4
--- /home/repository/moby/moby-live/Python/bioMoby/ontology/Genotype.py	2005/01/27 08:44:05	1.3
+++ /home/repository/moby/moby-live/Python/bioMoby/ontology/Genotype.py	2005/02/01 08:52:15	1.4
@@ -49,8 +49,7 @@
             if elt.nodeName=="CrossReference" or elt.nodeName=="moby:CrossReference":
                 self.__cross__=[]
                 for ref in elt.childNodes:
-                    if ref.nodeType==ref.ELEMENT_NODE:
-                        self.__cross__.append(um.loads(ref.toxml()))
+                    self.__cross__.append(ref.toxml())
             if elt.nodeType==elt.ELEMENT_NODE and (elt.nodeName=="String" or elt.nodeName=="moby:String") and (elt.getAttribute("articleName")=="snp" or elt.getAttribute("moby:articleName")=="snp"):
                 t=MobyString()
                 t.fromMoby(elt.toxml())

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/ontology/Germplasm_Details.py,v
retrieving revision 1.3
retrieving revision 1.4
diff -u -r1.3 -r1.4
--- /home/repository/moby/moby-live/Python/bioMoby/ontology/Germplasm_Details.py	2005/01/27 08:44:05	1.3
+++ /home/repository/moby/moby-live/Python/bioMoby/ontology/Germplasm_Details.py	2005/02/01 08:52:15	1.4
@@ -55,8 +55,7 @@
             if elt.nodeName=="CrossReference" or elt.nodeName=="moby:CrossReference":
                 self.__cross__=[]
                 for ref in elt.childNodes:
-                    if ref.nodeType==ref.ELEMENT_NODE:
-                        self.__cross__.append(um.loads(ref.toxml()))
+                    self.__cross__.append(ref.toxml())
             if elt.nodeType==elt.ELEMENT_NODE and (elt.nodeName=="Integer" or elt.nodeName=="moby:Integer") and (elt.getAttribute("articleName")=="date" or elt.getAttribute("moby:articleName")=="date"):
                 t=MobyInteger()
                 t.fromMoby(elt.toxml())

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/ontology/Germplasm_List.py,v
retrieving revision 1.3
retrieving revision 1.4
diff -u -r1.3 -r1.4
--- /home/repository/moby/moby-live/Python/bioMoby/ontology/Germplasm_List.py	2005/01/27 08:44:05	1.3
+++ /home/repository/moby/moby-live/Python/bioMoby/ontology/Germplasm_List.py	2005/02/01 08:52:16	1.4
@@ -55,8 +55,7 @@
             if elt.nodeName=="CrossReference" or elt.nodeName=="moby:CrossReference":
                 self.__cross__=[]
                 for ref in elt.childNodes:
-                    if ref.nodeType==ref.ELEMENT_NODE:
-                        self.__cross__.append(um.loads(ref.toxml()))
+                    self.__cross__.append(ref.toxml())
             if elt.nodeType==elt.ELEMENT_NODE and (elt.nodeName=="Integer" or elt.nodeName=="moby:Integer") and (elt.getAttribute("articleName")=="germplasm_id" or elt.getAttribute("moby:articleName")=="germplasm_id"):
                 t=MobyInteger()
                 t.fromMoby(elt.toxml())

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/ontology/Global_Keyword.py,v
retrieving revision 1.3
retrieving revision 1.4
diff -u -r1.3 -r1.4
--- /home/repository/moby/moby-live/Python/bioMoby/ontology/Global_Keyword.py	2005/01/27 08:44:05	1.3
+++ /home/repository/moby/moby-live/Python/bioMoby/ontology/Global_Keyword.py	2005/02/01 08:52:16	1.4
@@ -45,5 +45,4 @@
             if elt.nodeName=="CrossReference" or elt.nodeName=="moby:CrossReference":
                 self.__cross__=[]
                 for ref in elt.childNodes:
-                    if ref.nodeType==ref.ELEMENT_NODE:
-                        self.__cross__.append(um.loads(ref.toxml()))
\ No newline at end of file
+                    self.__cross__.append(ref.toxml())
\ No newline at end of file

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/ontology/HBond_Pair.py,v
retrieving revision 1.3
retrieving revision 1.4
diff -u -r1.3 -r1.4
--- /home/repository/moby/moby-live/Python/bioMoby/ontology/HBond_Pair.py	2005/01/27 08:44:05	1.3
+++ /home/repository/moby/moby-live/Python/bioMoby/ontology/HBond_Pair.py	2005/02/01 08:52:16	1.4
@@ -49,8 +49,7 @@
             if elt.nodeName=="CrossReference" or elt.nodeName=="moby:CrossReference":
                 self.__cross__=[]
                 for ref in elt.childNodes:
-                    if ref.nodeType==ref.ELEMENT_NODE:
-                        self.__cross__.append(um.loads(ref.toxml()))
+                    self.__cross__.append(ref.toxml())
             if elt.nodeType==elt.ELEMENT_NODE and (elt.nodeName=="String" or elt.nodeName=="moby:String") and (elt.getAttribute("articleName")=="A" or elt.getAttribute("moby:articleName")=="A"):
                 t=MobyString()
                 t.fromMoby(elt.toxml())

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/ontology/HFormatText.py,v
retrieving revision 1.3
retrieving revision 1.4
diff -u -r1.3 -r1.4
--- /home/repository/moby/moby-live/Python/bioMoby/ontology/HFormatText.py	2005/01/27 08:44:05	1.3
+++ /home/repository/moby/moby-live/Python/bioMoby/ontology/HFormatText.py	2005/02/01 08:52:16	1.4
@@ -46,5 +46,4 @@
             if elt.nodeName=="CrossReference" or elt.nodeName=="moby:CrossReference":
                 self.__cross__=[]
                 for ref in elt.childNodes:
-                    if ref.nodeType==ref.ELEMENT_NODE:
-                        self.__cross__.append(um.loads(ref.toxml()))
\ No newline at end of file
+                    self.__cross__.append(ref.toxml())
\ No newline at end of file

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/ontology/Haplotyping_Study_obj.py,v
retrieving revision 1.3
retrieving revision 1.4
diff -u -r1.3 -r1.4
--- /home/repository/moby/moby-live/Python/bioMoby/ontology/Haplotyping_Study_obj.py	2005/01/27 08:44:05	1.3
+++ /home/repository/moby/moby-live/Python/bioMoby/ontology/Haplotyping_Study_obj.py	2005/02/01 08:52:16	1.4
@@ -45,5 +45,4 @@
             if elt.nodeName=="CrossReference" or elt.nodeName=="moby:CrossReference":
                 self.__cross__=[]
                 for ref in elt.childNodes:
-                    if ref.nodeType==ref.ELEMENT_NODE:
-                        self.__cross__.append(um.loads(ref.toxml()))
\ No newline at end of file
+                    self.__cross__.append(ref.toxml())
\ No newline at end of file

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/ontology/ICIS_Query.py,v
retrieving revision 1.3
retrieving revision 1.4
diff -u -r1.3 -r1.4
--- /home/repository/moby/moby-live/Python/bioMoby/ontology/ICIS_Query.py	2005/01/27 08:44:05	1.3
+++ /home/repository/moby/moby-live/Python/bioMoby/ontology/ICIS_Query.py	2005/02/01 08:52:16	1.4
@@ -50,8 +50,7 @@
             if elt.nodeName=="CrossReference" or elt.nodeName=="moby:CrossReference":
                 self.__cross__=[]
                 for ref in elt.childNodes:
-                    if ref.nodeType==ref.ELEMENT_NODE:
-                        self.__cross__.append(um.loads(ref.toxml()))
+                    self.__cross__.append(ref.toxml())
             if elt.nodeType==elt.ELEMENT_NODE and (elt.nodeName=="Integer" or elt.nodeName=="moby:Integer") and (elt.getAttribute("articleName")=="end_row" or elt.getAttribute("moby:articleName")=="end_row"):
                 t=MobyInteger()
                 t.fromMoby(elt.toxml())

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/ontology/ICIS_Query2.py,v
retrieving revision 1.3
retrieving revision 1.4
diff -u -r1.3 -r1.4
--- /home/repository/moby/moby-live/Python/bioMoby/ontology/ICIS_Query2.py	2005/01/27 08:44:05	1.3
+++ /home/repository/moby/moby-live/Python/bioMoby/ontology/ICIS_Query2.py	2005/02/01 08:52:16	1.4
@@ -52,8 +52,7 @@
             if elt.nodeName=="CrossReference" or elt.nodeName=="moby:CrossReference":
                 self.__cross__=[]
                 for ref in elt.childNodes:
-                    if ref.nodeType==ref.ELEMENT_NODE:
-                        self.__cross__.append(um.loads(ref.toxml()))
+                    self.__cross__.append(ref.toxml())
             if elt.nodeType==elt.ELEMENT_NODE and (elt.nodeName=="String" or elt.nodeName=="moby:String") and (elt.getAttribute("articleName")=="search_text1" or elt.getAttribute("moby:articleName")=="search_text1"):
                 t=MobyString()
                 t.fromMoby(elt.toxml())

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/ontology/ICIS_Query3.py,v
retrieving revision 1.3
retrieving revision 1.4
diff -u -r1.3 -r1.4
--- /home/repository/moby/moby-live/Python/bioMoby/ontology/ICIS_Query3.py	2005/01/27 08:44:05	1.3
+++ /home/repository/moby/moby-live/Python/bioMoby/ontology/ICIS_Query3.py	2005/02/01 08:52:16	1.4
@@ -50,8 +50,7 @@
             if elt.nodeName=="CrossReference" or elt.nodeName=="moby:CrossReference":
                 self.__cross__=[]
                 for ref in elt.childNodes:
-                    if ref.nodeType==ref.ELEMENT_NODE:
-                        self.__cross__.append(um.loads(ref.toxml()))
+                    self.__cross__.append(ref.toxml())
             if elt.nodeType==elt.ELEMENT_NODE and (elt.nodeName=="Integer" or elt.nodeName=="moby:Integer") and (elt.getAttribute("articleName")=="search_text1" or elt.getAttribute("moby:articleName")=="search_text1"):
                 t=MobyInteger()
                 t.fromMoby(elt.toxml())

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/ontology/IntAct_XML.py,v
retrieving revision 1.3
retrieving revision 1.4
diff -u -r1.3 -r1.4
--- /home/repository/moby/moby-live/Python/bioMoby/ontology/IntAct_XML.py	2005/01/27 08:44:05	1.3
+++ /home/repository/moby/moby-live/Python/bioMoby/ontology/IntAct_XML.py	2005/02/01 08:52:16	1.4
@@ -46,5 +46,4 @@
             if elt.nodeName=="CrossReference" or elt.nodeName=="moby:CrossReference":
                 self.__cross__=[]
                 for ref in elt.childNodes:
-                    if ref.nodeType==ref.ELEMENT_NODE:
-                        self.__cross__.append(um.loads(ref.toxml()))
\ No newline at end of file
+                    self.__cross__.append(ref.toxml())
\ No newline at end of file

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/ontology/Interaction.py,v
retrieving revision 1.3
retrieving revision 1.4
diff -u -r1.3 -r1.4
--- /home/repository/moby/moby-live/Python/bioMoby/ontology/Interaction.py	2005/01/27 08:44:05	1.3
+++ /home/repository/moby/moby-live/Python/bioMoby/ontology/Interaction.py	2005/02/01 08:52:16	1.4
@@ -51,8 +51,7 @@
             if elt.nodeName=="CrossReference" or elt.nodeName=="moby:CrossReference":
                 self.__cross__=[]
                 for ref in elt.childNodes:
-                    if ref.nodeType==ref.ELEMENT_NODE:
-                        self.__cross__.append(um.loads(ref.toxml()))
+                    self.__cross__.append(ref.toxml())
             if elt.nodeType==elt.ELEMENT_NODE and (elt.nodeName=="String" or elt.nodeName=="moby:String") and (elt.getAttribute("articleName")=="result" or elt.getAttribute("moby:articleName")=="result"):
                 t=MobyString()
                 t.fromMoby(elt.toxml())

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/ontology/InteractionMethod.py,v
retrieving revision 1.3
retrieving revision 1.4
diff -u -r1.3 -r1.4
--- /home/repository/moby/moby-live/Python/bioMoby/ontology/InteractionMethod.py	2005/01/27 08:44:05	1.3
+++ /home/repository/moby/moby-live/Python/bioMoby/ontology/InteractionMethod.py	2005/02/01 08:52:16	1.4
@@ -49,8 +49,7 @@
             if elt.nodeName=="CrossReference" or elt.nodeName=="moby:CrossReference":
                 self.__cross__=[]
                 for ref in elt.childNodes:
-                    if ref.nodeType==ref.ELEMENT_NODE:
-                        self.__cross__.append(um.loads(ref.toxml()))
+                    self.__cross__.append(ref.toxml())
             if elt.nodeType==elt.ELEMENT_NODE and (elt.nodeName=="String" or elt.nodeName=="moby:String") and (elt.getAttribute("articleName")=="shortlabel" or elt.getAttribute("moby:articleName")=="shortlabel"):
                 t=MobyString()
                 t.fromMoby(elt.toxml())

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/ontology/Interaction_partner.py,v
retrieving revision 1.3
retrieving revision 1.4
diff -u -r1.3 -r1.4
--- /home/repository/moby/moby-live/Python/bioMoby/ontology/Interaction_partner.py	2005/01/27 08:44:05	1.3
+++ /home/repository/moby/moby-live/Python/bioMoby/ontology/Interaction_partner.py	2005/02/01 08:52:16	1.4
@@ -49,8 +49,7 @@
             if elt.nodeName=="CrossReference" or elt.nodeName=="moby:CrossReference":
                 self.__cross__=[]
                 for ref in elt.childNodes:
-                    if ref.nodeType==ref.ELEMENT_NODE:
-                        self.__cross__.append(um.loads(ref.toxml()))
+                    self.__cross__.append(ref.toxml())
             if elt.nodeType==elt.ELEMENT_NODE and (elt.nodeName=="Integer" or elt.nodeName=="moby:Integer") and (elt.getAttribute("articleName")=="direction" or elt.getAttribute("moby:articleName")=="direction"):
                 t=MobyInteger()
                 t.fromMoby(elt.toxml())

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/ontology/Interactor.py,v
retrieving revision 1.3
retrieving revision 1.4
diff -u -r1.3 -r1.4
--- /home/repository/moby/moby-live/Python/bioMoby/ontology/Interactor.py	2005/01/27 08:44:05	1.3
+++ /home/repository/moby/moby-live/Python/bioMoby/ontology/Interactor.py	2005/02/01 08:52:16	1.4
@@ -47,8 +47,7 @@
             if elt.nodeName=="CrossReference" or elt.nodeName=="moby:CrossReference":
                 self.__cross__=[]
                 for ref in elt.childNodes:
-                    if ref.nodeType==ref.ELEMENT_NODE:
-                        self.__cross__.append(um.loads(ref.toxml()))
+                    self.__cross__.append(ref.toxml())
             if elt.nodeType==elt.ELEMENT_NODE and (elt.nodeName=="String" or elt.nodeName=="moby:String") and (elt.getAttribute("articleName")=="role" or elt.getAttribute("moby:articleName")=="role"):
                 t=MobyString()
                 t.fromMoby(elt.toxml())

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/ontology/MEME_Text.py,v
retrieving revision 1.3
retrieving revision 1.4
diff -u -r1.3 -r1.4
--- /home/repository/moby/moby-live/Python/bioMoby/ontology/MEME_Text.py	2005/01/27 08:44:05	1.3
+++ /home/repository/moby/moby-live/Python/bioMoby/ontology/MEME_Text.py	2005/02/01 08:52:16	1.4
@@ -46,5 +46,4 @@
             if elt.nodeName=="CrossReference" or elt.nodeName=="moby:CrossReference":
                 self.__cross__=[]
                 for ref in elt.childNodes:
-                    if ref.nodeType==ref.ELEMENT_NODE:
-                        self.__cross__.append(um.loads(ref.toxml()))
\ No newline at end of file
+                    self.__cross__.append(ref.toxml())
\ No newline at end of file

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/ontology/MGIS_ACCESSION.py,v
retrieving revision 1.3
retrieving revision 1.4
diff -u -r1.3 -r1.4
--- /home/repository/moby/moby-live/Python/bioMoby/ontology/MGIS_ACCESSION.py	2005/01/27 08:44:05	1.3
+++ /home/repository/moby/moby-live/Python/bioMoby/ontology/MGIS_ACCESSION.py	2005/02/01 08:52:16	1.4
@@ -66,8 +66,7 @@
             if elt.nodeName=="CrossReference" or elt.nodeName=="moby:CrossReference":
                 self.__cross__=[]
                 for ref in elt.childNodes:
-                    if ref.nodeType==ref.ELEMENT_NODE:
-                        self.__cross__.append(um.loads(ref.toxml()))
+                    self.__cross__.append(ref.toxml())
             if elt.nodeType==elt.ELEMENT_NODE and (elt.nodeName=="String" or elt.nodeName=="moby:String") and (elt.getAttribute("articleName")=="Biotic_stress_Yellowsig" or elt.getAttribute("moby:articleName")=="Biotic_stress_Yellowsig"):
                 t=MobyString()
                 t.fromMoby(elt.toxml())

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/ontology/MMP_Locus.py,v
retrieving revision 1.3
retrieving revision 1.4
diff -u -r1.3 -r1.4
--- /home/repository/moby/moby-live/Python/bioMoby/ontology/MMP_Locus.py	2005/01/27 08:44:05	1.3
+++ /home/repository/moby/moby-live/Python/bioMoby/ontology/MMP_Locus.py	2005/02/01 08:52:16	1.4
@@ -45,5 +45,4 @@
             if elt.nodeName=="CrossReference" or elt.nodeName=="moby:CrossReference":
                 self.__cross__=[]
                 for ref in elt.childNodes:
-                    if ref.nodeType==ref.ELEMENT_NODE:
-                        self.__cross__.append(um.loads(ref.toxml()))
\ No newline at end of file
+                    self.__cross__.append(ref.toxml())
\ No newline at end of file

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/ontology/MO_Term_Test.py,v
retrieving revision 1.3
retrieving revision 1.4
diff -u -r1.3 -r1.4
--- /home/repository/moby/moby-live/Python/bioMoby/ontology/MO_Term_Test.py	2005/01/27 08:44:05	1.3
+++ /home/repository/moby/moby-live/Python/bioMoby/ontology/MO_Term_Test.py	2005/02/01 08:52:16	1.4
@@ -50,8 +50,7 @@
             if elt.nodeName=="CrossReference" or elt.nodeName=="moby:CrossReference":
                 self.__cross__=[]
                 for ref in elt.childNodes:
-                    if ref.nodeType==ref.ELEMENT_NODE:
-                        self.__cross__.append(um.loads(ref.toxml()))
+                    self.__cross__.append(ref.toxml())
             if elt.nodeType==elt.ELEMENT_NODE and (elt.nodeName=="String" or elt.nodeName=="moby:String") and (elt.getAttribute("articleName")=="class_name" or elt.getAttribute("moby:articleName")=="class_name"):
                 t=MobyString()
                 t.fromMoby(elt.toxml())

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/ontology/MmCIFText.py,v
retrieving revision 1.3
retrieving revision 1.4
diff -u -r1.3 -r1.4
--- /home/repository/moby/moby-live/Python/bioMoby/ontology/MmCIFText.py	2005/01/27 08:44:05	1.3
+++ /home/repository/moby/moby-live/Python/bioMoby/ontology/MmCIFText.py	2005/02/01 08:52:16	1.4
@@ -46,5 +46,4 @@
             if elt.nodeName=="CrossReference" or elt.nodeName=="moby:CrossReference":
                 self.__cross__=[]
                 for ref in elt.childNodes:
-                    if ref.nodeType==ref.ELEMENT_NODE:
-                        self.__cross__.append(um.loads(ref.toxml()))
\ No newline at end of file
+                    self.__cross__.append(ref.toxml())
\ No newline at end of file

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/ontology/Multi_key_value_pair.py,v
retrieving revision 1.3
retrieving revision 1.4
diff -u -r1.3 -r1.4
--- /home/repository/moby/moby-live/Python/bioMoby/ontology/Multi_key_value_pair.py	2005/01/27 08:44:05	1.3
+++ /home/repository/moby/moby-live/Python/bioMoby/ontology/Multi_key_value_pair.py	2005/02/01 08:52:16	1.4
@@ -49,8 +49,7 @@
             if elt.nodeName=="CrossReference" or elt.nodeName=="moby:CrossReference":
                 self.__cross__=[]
                 for ref in elt.childNodes:
-                    if ref.nodeType==ref.ELEMENT_NODE:
-                        self.__cross__.append(um.loads(ref.toxml()))
+                    self.__cross__.append(ref.toxml())
             if elt.nodeType==elt.ELEMENT_NODE and (elt.nodeName=="String" or elt.nodeName=="moby:String") and (elt.getAttribute("articleName")=="key" or elt.getAttribute("moby:articleName")=="key"):
                 t=MobyString()
                 t.fromMoby(elt.toxml())

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/ontology/MyTestingDataType_11024145298313.py,v
retrieving revision 1.3
retrieving revision 1.4
diff -u -r1.3 -r1.4
--- /home/repository/moby/moby-live/Python/bioMoby/ontology/MyTestingDataType_11024145298313.py	2005/01/27 08:44:05	1.3
+++ /home/repository/moby/moby-live/Python/bioMoby/ontology/MyTestingDataType_11024145298313.py	2005/02/01 08:52:16	1.4
@@ -46,5 +46,4 @@
             if elt.nodeName=="CrossReference" or elt.nodeName=="moby:CrossReference":
                 self.__cross__=[]
                 for ref in elt.childNodes:
-                    if ref.nodeType==ref.ELEMENT_NODE:
-                        self.__cross__.append(um.loads(ref.toxml()))
\ No newline at end of file
+                    self.__cross__.append(ref.toxml())
\ No newline at end of file

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/ontology/MyTree.py,v
retrieving revision 1.3
retrieving revision 1.4
diff -u -r1.3 -r1.4
--- /home/repository/moby/moby-live/Python/bioMoby/ontology/MyTree.py	2005/01/27 08:44:05	1.3
+++ /home/repository/moby/moby-live/Python/bioMoby/ontology/MyTree.py	2005/02/01 08:52:16	1.4
@@ -46,5 +46,4 @@
             if elt.nodeName=="CrossReference" or elt.nodeName=="moby:CrossReference":
                 self.__cross__=[]
                 for ref in elt.childNodes:
-                    if ref.nodeType==ref.ELEMENT_NODE:
-                        self.__cross__.append(um.loads(ref.toxml()))
\ No newline at end of file
+                    self.__cross__.append(ref.toxml())
\ No newline at end of file

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/ontology/NCBI_BLAST_Text.py,v
retrieving revision 1.3
retrieving revision 1.4
diff -u -r1.3 -r1.4
--- /home/repository/moby/moby-live/Python/bioMoby/ontology/NCBI_BLAST_Text.py	2005/01/27 08:44:05	1.3
+++ /home/repository/moby/moby-live/Python/bioMoby/ontology/NCBI_BLAST_Text.py	2005/02/01 08:52:16	1.4
@@ -46,5 +46,4 @@
             if elt.nodeName=="CrossReference" or elt.nodeName=="moby:CrossReference":
                 self.__cross__=[]
                 for ref in elt.childNodes:
-                    if ref.nodeType==ref.ELEMENT_NODE:
-                        self.__cross__.append(um.loads(ref.toxml()))
\ No newline at end of file
+                    self.__cross__.append(ref.toxml())
\ No newline at end of file

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/ontology/NCBI_Blast_XML.py,v
retrieving revision 1.3
retrieving revision 1.4
diff -u -r1.3 -r1.4
--- /home/repository/moby/moby-live/Python/bioMoby/ontology/NCBI_Blast_XML.py	2005/01/27 08:44:05	1.3
+++ /home/repository/moby/moby-live/Python/bioMoby/ontology/NCBI_Blast_XML.py	2005/02/01 08:52:16	1.4
@@ -46,5 +46,4 @@
             if elt.nodeName=="CrossReference" or elt.nodeName=="moby:CrossReference":
                 self.__cross__=[]
                 for ref in elt.childNodes:
-                    if ref.nodeType==ref.ELEMENT_NODE:
-                        self.__cross__.append(um.loads(ref.toxml()))
\ No newline at end of file
+                    self.__cross__.append(ref.toxml())
\ No newline at end of file

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/ontology/NCBI_Blast_XML_Gif.py,v
retrieving revision 1.3
retrieving revision 1.4
diff -u -r1.3 -r1.4
--- /home/repository/moby/moby-live/Python/bioMoby/ontology/NCBI_Blast_XML_Gif.py	2005/01/27 08:44:05	1.3
+++ /home/repository/moby/moby-live/Python/bioMoby/ontology/NCBI_Blast_XML_Gif.py	2005/02/01 08:52:16	1.4
@@ -48,8 +48,7 @@
             if elt.nodeName=="CrossReference" or elt.nodeName=="moby:CrossReference":
                 self.__cross__=[]
                 for ref in elt.childNodes:
-                    if ref.nodeType==ref.ELEMENT_NODE:
-                        self.__cross__.append(um.loads(ref.toxml()))
+                    self.__cross__.append(ref.toxml())
             if elt.nodeType==elt.ELEMENT_NODE and (elt.nodeName=="b64_encoded_gif" or elt.nodeName=="moby:b64_encoded_gif") and (elt.getAttribute("articleName")=="hitGraph" or elt.getAttribute("moby:articleName")=="hitGraph"):
                 self.HitGraph=MobyB64_encoded_gif()
                 self.HitGraph.fromMoby(elt.toxml())
\ No newline at end of file

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/ontology/NCBI_Blast_XML_Gif_Map.py,v
retrieving revision 1.3
retrieving revision 1.4
diff -u -r1.3 -r1.4
--- /home/repository/moby/moby-live/Python/bioMoby/ontology/NCBI_Blast_XML_Gif_Map.py	2005/01/27 08:44:05	1.3
+++ /home/repository/moby/moby-live/Python/bioMoby/ontology/NCBI_Blast_XML_Gif_Map.py	2005/02/01 08:52:16	1.4
@@ -50,8 +50,7 @@
             if elt.nodeName=="CrossReference" or elt.nodeName=="moby:CrossReference":
                 self.__cross__=[]
                 for ref in elt.childNodes:
-                    if ref.nodeType==ref.ELEMENT_NODE:
-                        self.__cross__.append(um.loads(ref.toxml()))
+                    self.__cross__.append(ref.toxml())
             if elt.nodeType==elt.ELEMENT_NODE and (elt.nodeName=="b64_encoded_gif" or elt.nodeName=="moby:b64_encoded_gif") and (elt.getAttribute("articleName")=="hitGraph" or elt.getAttribute("moby:articleName")=="hitGraph"):
                 self.HitGraph=MobyB64_encoded_gif()
                 self.HitGraph.fromMoby(elt.toxml())

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/ontology/NCBI_MEME_Text.py,v
retrieving revision 1.3
retrieving revision 1.4
diff -u -r1.3 -r1.4
--- /home/repository/moby/moby-live/Python/bioMoby/ontology/NCBI_MEME_Text.py	2005/01/27 08:44:05	1.3
+++ /home/repository/moby/moby-live/Python/bioMoby/ontology/NCBI_MEME_Text.py	2005/02/01 08:52:16	1.4
@@ -46,5 +46,4 @@
             if elt.nodeName=="CrossReference" or elt.nodeName=="moby:CrossReference":
                 self.__cross__=[]
                 for ref in elt.childNodes:
-                    if ref.nodeType==ref.ELEMENT_NODE:
-                        self.__cross__.append(um.loads(ref.toxml()))
\ No newline at end of file
+                    self.__cross__.append(ref.toxml())
\ No newline at end of file

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/ontology/NucleotideSequence.py,v
retrieving revision 1.3
retrieving revision 1.4
diff -u -r1.3 -r1.4
--- /home/repository/moby/moby-live/Python/bioMoby/ontology/NucleotideSequence.py	2005/01/27 08:44:05	1.3
+++ /home/repository/moby/moby-live/Python/bioMoby/ontology/NucleotideSequence.py	2005/02/01 08:52:16	1.4
@@ -49,8 +49,7 @@
             if elt.nodeName=="CrossReference" or elt.nodeName=="moby:CrossReference":
                 self.__cross__=[]
                 for ref in elt.childNodes:
-                    if ref.nodeType==ref.ELEMENT_NODE:
-                        self.__cross__.append(um.loads(ref.toxml()))
+                    self.__cross__.append(ref.toxml())
             if elt.nodeType==elt.ELEMENT_NODE and (elt.nodeName=="Integer" or elt.nodeName=="moby:Integer") and (elt.getAttribute("articleName")=="Length" or elt.getAttribute("moby:articleName")=="Length"):
                 t=MobyInteger()
                 t.fromMoby(elt.toxml())

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/ontology/PDBFormattedText.py,v
retrieving revision 1.3
retrieving revision 1.4
diff -u -r1.3 -r1.4
--- /home/repository/moby/moby-live/Python/bioMoby/ontology/PDBFormattedText.py	2005/01/27 08:44:05	1.3
+++ /home/repository/moby/moby-live/Python/bioMoby/ontology/PDBFormattedText.py	2005/02/01 08:52:16	1.4
@@ -46,5 +46,4 @@
             if elt.nodeName=="CrossReference" or elt.nodeName=="moby:CrossReference":
                 self.__cross__=[]
                 for ref in elt.childNodes:
-                    if ref.nodeType==ref.ELEMENT_NODE:
-                        self.__cross__.append(um.loads(ref.toxml()))
\ No newline at end of file
+                    self.__cross__.append(ref.toxml())
\ No newline at end of file

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/ontology/PDBText.py,v
retrieving revision 1.3
retrieving revision 1.4
diff -u -r1.3 -r1.4
--- /home/repository/moby/moby-live/Python/bioMoby/ontology/PDBText.py	2005/01/27 08:44:05	1.3
+++ /home/repository/moby/moby-live/Python/bioMoby/ontology/PDBText.py	2005/02/01 08:52:16	1.4
@@ -46,5 +46,4 @@
             if elt.nodeName=="CrossReference" or elt.nodeName=="moby:CrossReference":
                 self.__cross__=[]
                 for ref in elt.childNodes:
-                    if ref.nodeType==ref.ELEMENT_NODE:
-                        self.__cross__.append(um.loads(ref.toxml()))
\ No newline at end of file
+                    self.__cross__.append(ref.toxml())
\ No newline at end of file

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/ontology/PDGJOB.py,v
retrieving revision 1.3
retrieving revision 1.4
diff -u -r1.3 -r1.4
--- /home/repository/moby/moby-live/Python/bioMoby/ontology/PDGJOB.py	2005/01/27 08:44:05	1.3
+++ /home/repository/moby/moby-live/Python/bioMoby/ontology/PDGJOB.py	2005/02/01 08:52:16	1.4
@@ -52,8 +52,7 @@
             if elt.nodeName=="CrossReference" or elt.nodeName=="moby:CrossReference":
                 self.__cross__=[]
                 for ref in elt.childNodes:
-                    if ref.nodeType==ref.ELEMENT_NODE:
-                        self.__cross__.append(um.loads(ref.toxml()))
+                    self.__cross__.append(ref.toxml())
             if elt.nodeType==elt.ELEMENT_NODE and (elt.nodeName=="String" or elt.nodeName=="moby:String") and (elt.getAttribute("articleName")=="answerService" or elt.getAttribute("moby:articleName")=="answerService"):
                 t=MobyString()
                 t.fromMoby(elt.toxml())

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/ontology/PHDText.py,v
retrieving revision 1.3
retrieving revision 1.4
diff -u -r1.3 -r1.4
--- /home/repository/moby/moby-live/Python/bioMoby/ontology/PHDText.py	2005/01/27 08:44:05	1.3
+++ /home/repository/moby/moby-live/Python/bioMoby/ontology/PHDText.py	2005/02/01 08:52:16	1.4
@@ -46,5 +46,4 @@
             if elt.nodeName=="CrossReference" or elt.nodeName=="moby:CrossReference":
                 self.__cross__=[]
                 for ref in elt.childNodes:
-                    if ref.nodeType==ref.ELEMENT_NODE:
-                        self.__cross__.append(um.loads(ref.toxml()))
\ No newline at end of file
+                    self.__cross__.append(ref.toxml())
\ No newline at end of file

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/ontology/PMUTText.py,v
retrieving revision 1.3
retrieving revision 1.4
diff -u -r1.3 -r1.4
--- /home/repository/moby/moby-live/Python/bioMoby/ontology/PMUTText.py	2005/01/27 08:44:05	1.3
+++ /home/repository/moby/moby-live/Python/bioMoby/ontology/PMUTText.py	2005/02/01 08:52:16	1.4
@@ -46,5 +46,4 @@
             if elt.nodeName=="CrossReference" or elt.nodeName=="moby:CrossReference":
                 self.__cross__=[]
                 for ref in elt.childNodes:
-                    if ref.nodeType==ref.ELEMENT_NODE:
-                        self.__cross__.append(um.loads(ref.toxml()))
\ No newline at end of file
+                    self.__cross__.append(ref.toxml())
\ No newline at end of file

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/ontology/PSeaTextFormatted.py,v
retrieving revision 1.3
retrieving revision 1.4
diff -u -r1.3 -r1.4
--- /home/repository/moby/moby-live/Python/bioMoby/ontology/PSeaTextFormatted.py	2005/01/27 08:44:05	1.3
+++ /home/repository/moby/moby-live/Python/bioMoby/ontology/PSeaTextFormatted.py	2005/02/01 08:52:16	1.4
@@ -46,5 +46,4 @@
             if elt.nodeName=="CrossReference" or elt.nodeName=="moby:CrossReference":
                 self.__cross__=[]
                 for ref in elt.childNodes:
-                    if ref.nodeType==ref.ELEMENT_NODE:
-                        self.__cross__.append(um.loads(ref.toxml()))
\ No newline at end of file
+                    self.__cross__.append(ref.toxml())
\ No newline at end of file

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/ontology/PhenotypeDescription.py,v
retrieving revision 1.3
retrieving revision 1.4
diff -u -r1.3 -r1.4
--- /home/repository/moby/moby-live/Python/bioMoby/ontology/PhenotypeDescription.py	2005/01/27 08:44:05	1.3
+++ /home/repository/moby/moby-live/Python/bioMoby/ontology/PhenotypeDescription.py	2005/02/01 08:52:16	1.4
@@ -47,8 +47,7 @@
             if elt.nodeName=="CrossReference" or elt.nodeName=="moby:CrossReference":
                 self.__cross__=[]
                 for ref in elt.childNodes:
-                    if ref.nodeType==ref.ELEMENT_NODE:
-                        self.__cross__.append(um.loads(ref.toxml()))
+                    self.__cross__.append(ref.toxml())
             if elt.nodeType==elt.ELEMENT_NODE and (elt.nodeName=="String" or elt.nodeName=="moby:String") and (elt.getAttribute("articleName")=="Phenotype" or elt.getAttribute("moby:articleName")=="Phenotype"):
                 t=MobyString()
                 t.fromMoby(elt.toxml())

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/ontology/PubMedMEDLINE.py,v
retrieving revision 1.3
retrieving revision 1.4
diff -u -r1.3 -r1.4
--- /home/repository/moby/moby-live/Python/bioMoby/ontology/PubMedMEDLINE.py	2005/01/27 08:44:05	1.3
+++ /home/repository/moby/moby-live/Python/bioMoby/ontology/PubMedMEDLINE.py	2005/02/01 08:52:16	1.4
@@ -46,5 +46,4 @@
             if elt.nodeName=="CrossReference" or elt.nodeName=="moby:CrossReference":
                 self.__cross__=[]
                 for ref in elt.childNodes:
-                    if ref.nodeType==ref.ELEMENT_NODE:
-                        self.__cross__.append(um.loads(ref.toxml()))
\ No newline at end of file
+                    self.__cross__.append(ref.toxml())
\ No newline at end of file

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/ontology/RNASequence.py,v
retrieving revision 1.3
retrieving revision 1.4
diff -u -r1.3 -r1.4
--- /home/repository/moby/moby-live/Python/bioMoby/ontology/RNASequence.py	2005/01/27 08:44:05	1.3
+++ /home/repository/moby/moby-live/Python/bioMoby/ontology/RNASequence.py	2005/02/01 08:52:16	1.4
@@ -49,8 +49,7 @@
             if elt.nodeName=="CrossReference" or elt.nodeName=="moby:CrossReference":
                 self.__cross__=[]
                 for ref in elt.childNodes:
-                    if ref.nodeType==ref.ELEMENT_NODE:
-                        self.__cross__.append(um.loads(ref.toxml()))
+                    self.__cross__.append(ref.toxml())
             if elt.nodeType==elt.ELEMENT_NODE and (elt.nodeName=="Integer" or elt.nodeName=="moby:Integer") and (elt.getAttribute("articleName")=="Length" or elt.getAttribute("moby:articleName")=="Length"):
                 t=MobyInteger()
                 t.fromMoby(elt.toxml())

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/ontology/SINGER_ACCESSION.py,v
retrieving revision 1.3
retrieving revision 1.4
diff -u -r1.3 -r1.4
--- /home/repository/moby/moby-live/Python/bioMoby/ontology/SINGER_ACCESSION.py	2005/01/27 08:44:05	1.3
+++ /home/repository/moby/moby-live/Python/bioMoby/ontology/SINGER_ACCESSION.py	2005/02/01 08:52:16	1.4
@@ -50,8 +50,7 @@
             if elt.nodeName=="CrossReference" or elt.nodeName=="moby:CrossReference":
                 self.__cross__=[]
                 for ref in elt.childNodes:
-                    if ref.nodeType==ref.ELEMENT_NODE:
-                        self.__cross__.append(um.loads(ref.toxml()))
+                    self.__cross__.append(ref.toxml())
             if elt.nodeType==elt.ELEMENT_NODE and (elt.nodeName=="String" or elt.nodeName=="moby:String") and (elt.getAttribute("articleName")=="ACCNO" or elt.getAttribute("moby:articleName")=="ACCNO"):
                 t=MobyString()
                 t.fromMoby(elt.toxml())

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/ontology/Sample.py,v
retrieving revision 1.3
retrieving revision 1.4
diff -u -r1.3 -r1.4
--- /home/repository/moby/moby-live/Python/bioMoby/ontology/Sample.py	2005/01/27 08:44:05	1.3
+++ /home/repository/moby/moby-live/Python/bioMoby/ontology/Sample.py	2005/02/01 08:52:16	1.4
@@ -49,8 +49,7 @@
             if elt.nodeName=="CrossReference" or elt.nodeName=="moby:CrossReference":
                 self.__cross__=[]
                 for ref in elt.childNodes:
-                    if ref.nodeType==ref.ELEMENT_NODE:
-                        self.__cross__.append(um.loads(ref.toxml()))
+                    self.__cross__.append(ref.toxml())
             if elt.nodeType==elt.ELEMENT_NODE and (elt.nodeName=="String" or elt.nodeName=="moby:String") and (elt.getAttribute("articleName")=="code" or elt.getAttribute("moby:articleName")=="code"):
                 t=MobyString()
                 t.fromMoby(elt.toxml())

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/ontology/SchematikonMotifID.py,v
retrieving revision 1.3
retrieving revision 1.4
diff -u -r1.3 -r1.4
--- /home/repository/moby/moby-live/Python/bioMoby/ontology/SchematikonMotifID.py	2005/01/27 08:44:05	1.3
+++ /home/repository/moby/moby-live/Python/bioMoby/ontology/SchematikonMotifID.py	2005/02/01 08:52:16	1.4
@@ -47,8 +47,7 @@
             if elt.nodeName=="CrossReference" or elt.nodeName=="moby:CrossReference":
                 self.__cross__=[]
                 for ref in elt.childNodes:
-                    if ref.nodeType==ref.ELEMENT_NODE:
-                        self.__cross__.append(um.loads(ref.toxml()))
+                    self.__cross__.append(ref.toxml())
             if elt.nodeType==elt.ELEMENT_NODE and (elt.nodeName=="String" or elt.nodeName=="moby:String") and (elt.getAttribute("articleName")=="ID" or elt.getAttribute("moby:articleName")=="ID"):
                 t=MobyString()
                 t.fromMoby(elt.toxml())

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/ontology/SchematikonMotifSupport.py,v
retrieving revision 1.3
retrieving revision 1.4
diff -u -r1.3 -r1.4
--- /home/repository/moby/moby-live/Python/bioMoby/ontology/SchematikonMotifSupport.py	2005/01/27 08:44:05	1.3
+++ /home/repository/moby/moby-live/Python/bioMoby/ontology/SchematikonMotifSupport.py	2005/02/01 08:52:16	1.4
@@ -48,8 +48,7 @@
             if elt.nodeName=="CrossReference" or elt.nodeName=="moby:CrossReference":
                 self.__cross__=[]
                 for ref in elt.childNodes:
-                    if ref.nodeType==ref.ELEMENT_NODE:
-                        self.__cross__.append(um.loads(ref.toxml()))
+                    self.__cross__.append(ref.toxml())
             if elt.nodeType==elt.ELEMENT_NODE and (elt.nodeName=="Integer" or elt.nodeName=="moby:Integer") and (elt.getAttribute("articleName")=="UniqueSupport" or elt.getAttribute("moby:articleName")=="UniqueSupport"):
                 t=MobyInteger()
                 t.fromMoby(elt.toxml())

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/ontology/SchematikonSegmentAttributes.py,v
retrieving revision 1.3
retrieving revision 1.4
diff -u -r1.3 -r1.4
--- /home/repository/moby/moby-live/Python/bioMoby/ontology/SchematikonSegmentAttributes.py	2005/01/27 08:44:05	1.3
+++ /home/repository/moby/moby-live/Python/bioMoby/ontology/SchematikonSegmentAttributes.py	2005/02/01 08:52:16	1.4
@@ -52,8 +52,7 @@
             if elt.nodeName=="CrossReference" or elt.nodeName=="moby:CrossReference":
                 self.__cross__=[]
                 for ref in elt.childNodes:
-                    if ref.nodeType==ref.ELEMENT_NODE:
-                        self.__cross__.append(um.loads(ref.toxml()))
+                    self.__cross__.append(ref.toxml())
             if elt.nodeType==elt.ELEMENT_NODE and (elt.nodeName=="Integer" or elt.nodeName=="moby:Integer") and (elt.getAttribute("articleName")=="Length" or elt.getAttribute("moby:articleName")=="Length"):
                 t=MobyInteger()
                 t.fromMoby(elt.toxml())

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/ontology/SchematikonSegmentID.py,v
retrieving revision 1.3
retrieving revision 1.4
diff -u -r1.3 -r1.4
--- /home/repository/moby/moby-live/Python/bioMoby/ontology/SchematikonSegmentID.py	2005/01/27 08:44:05	1.3
+++ /home/repository/moby/moby-live/Python/bioMoby/ontology/SchematikonSegmentID.py	2005/02/01 08:52:16	1.4
@@ -47,8 +47,7 @@
             if elt.nodeName=="CrossReference" or elt.nodeName=="moby:CrossReference":
                 self.__cross__=[]
                 for ref in elt.childNodes:
-                    if ref.nodeType==ref.ELEMENT_NODE:
-                        self.__cross__.append(um.loads(ref.toxml()))
+                    self.__cross__.append(ref.toxml())
             if elt.nodeType==elt.ELEMENT_NODE and (elt.nodeName=="String" or elt.nodeName=="moby:String") and (elt.getAttribute("articleName")=="ID" or elt.getAttribute("moby:articleName")=="ID"):
                 t=MobyString()
                 t.fromMoby(elt.toxml())

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/ontology/SchematikonStructureAnnotation.py,v
retrieving revision 1.3
retrieving revision 1.4
diff -u -r1.3 -r1.4
--- /home/repository/moby/moby-live/Python/bioMoby/ontology/SchematikonStructureAnnotation.py	2005/01/27 08:44:05	1.3
+++ /home/repository/moby/moby-live/Python/bioMoby/ontology/SchematikonStructureAnnotation.py	2005/02/01 08:52:16	1.4
@@ -50,8 +50,7 @@
             if elt.nodeName=="CrossReference" or elt.nodeName=="moby:CrossReference":
                 self.__cross__=[]
                 for ref in elt.childNodes:
-                    if ref.nodeType==ref.ELEMENT_NODE:
-                        self.__cross__.append(um.loads(ref.toxml()))
+                    self.__cross__.append(ref.toxml())
             if elt.nodeType==elt.ELEMENT_NODE and (elt.nodeName=="String" or elt.nodeName=="moby:String") and (elt.getAttribute("articleName")=="PROMOTIF gamma-turn" or elt.getAttribute("moby:articleName")=="PROMOTIF gamma-turn"):
                 t=MobyString()
                 t.fromMoby(elt.toxml())

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/ontology/SchematikonVorocodeName.py,v
retrieving revision 1.3
retrieving revision 1.4
diff -u -r1.3 -r1.4
--- /home/repository/moby/moby-live/Python/bioMoby/ontology/SchematikonVorocodeName.py	2005/01/27 08:44:05	1.3
+++ /home/repository/moby/moby-live/Python/bioMoby/ontology/SchematikonVorocodeName.py	2005/02/01 08:52:16	1.4
@@ -47,8 +47,7 @@
             if elt.nodeName=="CrossReference" or elt.nodeName=="moby:CrossReference":
                 self.__cross__=[]
                 for ref in elt.childNodes:
-                    if ref.nodeType==ref.ELEMENT_NODE:
-                        self.__cross__.append(um.loads(ref.toxml()))
+                    self.__cross__.append(ref.toxml())
             if elt.nodeType==elt.ELEMENT_NODE and (elt.nodeName=="String" or elt.nodeName=="moby:String") and (elt.getAttribute("articleName")=="VorocodeName" or elt.getAttribute("moby:articleName")=="VorocodeName"):
                 t=MobyString()
                 t.fromMoby(elt.toxml())

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/ontology/Scored_acronym_string.py,v
retrieving revision 1.3
retrieving revision 1.4
diff -u -r1.3 -r1.4
--- /home/repository/moby/moby-live/Python/bioMoby/ontology/Scored_acronym_string.py	2005/01/27 08:44:05	1.3
+++ /home/repository/moby/moby-live/Python/bioMoby/ontology/Scored_acronym_string.py	2005/02/01 08:52:16	1.4
@@ -50,8 +50,7 @@
             if elt.nodeName=="CrossReference" or elt.nodeName=="moby:CrossReference":
                 self.__cross__=[]
                 for ref in elt.childNodes:
-                    if ref.nodeType==ref.ELEMENT_NODE:
-                        self.__cross__.append(um.loads(ref.toxml()))
+                    self.__cross__.append(ref.toxml())
             if elt.nodeType==elt.ELEMENT_NODE and (elt.nodeName=="Float" or elt.nodeName=="moby:Float") and (elt.getAttribute("articleName")=="score" or elt.getAttribute("moby:articleName")=="score"):
                 t=MobyFloat()
                 t.fromMoby(elt.toxml())

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/ontology/SimpleAnnotatedGIFImage.py,v
retrieving revision 1.3
retrieving revision 1.4
diff -u -r1.3 -r1.4
--- /home/repository/moby/moby-live/Python/bioMoby/ontology/SimpleAnnotatedGIFImage.py	2005/01/27 08:44:05	1.3
+++ /home/repository/moby/moby-live/Python/bioMoby/ontology/SimpleAnnotatedGIFImage.py	2005/02/01 08:52:16	1.4
@@ -48,8 +48,7 @@
             if elt.nodeName=="CrossReference" or elt.nodeName=="moby:CrossReference":
                 self.__cross__=[]
                 for ref in elt.childNodes:
-                    if ref.nodeType==ref.ELEMENT_NODE:
-                        self.__cross__.append(um.loads(ref.toxml()))
+                    self.__cross__.append(ref.toxml())
             if elt.nodeType==elt.ELEMENT_NODE and (elt.nodeName=="String" or elt.nodeName=="moby:String") and (elt.getAttribute("articleName")=="Description" or elt.getAttribute("moby:articleName")=="Description"):
                 t=MobyString()
                 t.fromMoby(elt.toxml())

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/ontology/SimpleAnnotatedJPEGImage.py,v
retrieving revision 1.3
retrieving revision 1.4
diff -u -r1.3 -r1.4
--- /home/repository/moby/moby-live/Python/bioMoby/ontology/SimpleAnnotatedJPEGImage.py	2005/01/27 08:44:05	1.3
+++ /home/repository/moby/moby-live/Python/bioMoby/ontology/SimpleAnnotatedJPEGImage.py	2005/02/01 08:52:16	1.4
@@ -49,8 +49,7 @@
             if elt.nodeName=="CrossReference" or elt.nodeName=="moby:CrossReference":
                 self.__cross__=[]
                 for ref in elt.childNodes:
-                    if ref.nodeType==ref.ELEMENT_NODE:
-                        self.__cross__.append(um.loads(ref.toxml()))
+                    self.__cross__.append(ref.toxml())
             if elt.nodeType==elt.ELEMENT_NODE and (elt.nodeName=="String" or elt.nodeName=="moby:String") and (elt.getAttribute("articleName")=="Description" or elt.getAttribute("moby:articleName")=="Description"):
                 t=MobyString()
                 t.fromMoby(elt.toxml())

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/ontology/Simple_key_value_pair.py,v
retrieving revision 1.3
retrieving revision 1.4
diff -u -r1.3 -r1.4
--- /home/repository/moby/moby-live/Python/bioMoby/ontology/Simple_key_value_pair.py	2005/01/27 08:44:05	1.3
+++ /home/repository/moby/moby-live/Python/bioMoby/ontology/Simple_key_value_pair.py	2005/02/01 08:52:16	1.4
@@ -48,8 +48,7 @@
             if elt.nodeName=="CrossReference" or elt.nodeName=="moby:CrossReference":
                 self.__cross__=[]
                 for ref in elt.childNodes:
-                    if ref.nodeType==ref.ELEMENT_NODE:
-                        self.__cross__.append(um.loads(ref.toxml()))
+                    self.__cross__.append(ref.toxml())
             if elt.nodeType==elt.ELEMENT_NODE and (elt.nodeName=="String" or elt.nodeName=="moby:String") and (elt.getAttribute("articleName")=="value" or elt.getAttribute("moby:articleName")=="value"):
                 t=MobyString()
                 t.fromMoby(elt.toxml())

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/ontology/Snp_allele.py,v
retrieving revision 1.3
retrieving revision 1.4
diff -u -r1.3 -r1.4
--- /home/repository/moby/moby-live/Python/bioMoby/ontology/Snp_allele.py	2005/01/27 08:44:05	1.3
+++ /home/repository/moby/moby-live/Python/bioMoby/ontology/Snp_allele.py	2005/02/01 08:52:16	1.4
@@ -37,8 +37,7 @@
             if elt.nodeName=="CrossReference" or elt.nodeName=="moby:CrossReference":
                 self.__cross__=[]
                 for ref in elt.childNodes:
-                    if ref.nodeType==ref.ELEMENT_NODE:
-                        self.__cross__.append(um.loads(ref.toxml()))
+                    self.__cross__.append(ref.toxml())
             if elt.nodeType==elt.ELEMENT_NODE and (elt.nodeName=="DNASequence" or elt.nodeName=="moby:DNASequence") and (elt.getAttribute("articleName")=="snp_allele" or elt.getAttribute("moby:articleName")=="snp_allele"):
                 self.Snp_allele=MobyDNASequence()
                 self.Snp_allele.fromMoby(elt.toxml())
\ No newline at end of file

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/ontology/Snp_genotype.py,v
retrieving revision 1.3
retrieving revision 1.4
diff -u -r1.3 -r1.4
--- /home/repository/moby/moby-live/Python/bioMoby/ontology/Snp_genotype.py	2005/01/27 08:44:05	1.3
+++ /home/repository/moby/moby-live/Python/bioMoby/ontology/Snp_genotype.py	2005/02/01 08:52:16	1.4
@@ -38,8 +38,7 @@
             if elt.nodeName=="CrossReference" or elt.nodeName=="moby:CrossReference":
                 self.__cross__=[]
                 for ref in elt.childNodes:
-                    if ref.nodeType==ref.ELEMENT_NODE:
-                        self.__cross__.append(um.loads(ref.toxml()))
+                    self.__cross__.append(ref.toxml())
             if elt.nodeType==elt.ELEMENT_NODE and (elt.nodeName=="snp_allele" or elt.nodeName=="moby:snp_allele") and (elt.getAttribute("articleName")=="allele1" or elt.getAttribute("moby:articleName")=="allele1"):
                 self.Allele1=MobySnp_allele()
                 self.Allele1.fromMoby(elt.toxml())

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/ontology/Study.py,v
retrieving revision 1.3
retrieving revision 1.4
diff -u -r1.3 -r1.4
--- /home/repository/moby/moby-live/Python/bioMoby/ontology/Study.py	2005/01/27 08:44:05	1.3
+++ /home/repository/moby/moby-live/Python/bioMoby/ontology/Study.py	2005/02/01 08:52:16	1.4
@@ -50,8 +50,7 @@
             if elt.nodeName=="CrossReference" or elt.nodeName=="moby:CrossReference":
                 self.__cross__=[]
                 for ref in elt.childNodes:
-                    if ref.nodeType==ref.ELEMENT_NODE:
-                        self.__cross__.append(um.loads(ref.toxml()))
+                    self.__cross__.append(ref.toxml())
             if elt.nodeType==elt.ELEMENT_NODE and (elt.nodeName=="String" or elt.nodeName=="moby:String") and (elt.getAttribute("articleName")=="study_name" or elt.getAttribute("moby:articleName")=="study_name"):
                 t=MobyString()
                 t.fromMoby(elt.toxml())

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/ontology/TEST.py,v
retrieving revision 1.3
retrieving revision 1.4
diff -u -r1.3 -r1.4
--- /home/repository/moby/moby-live/Python/bioMoby/ontology/TEST.py	2005/01/27 08:44:05	1.3
+++ /home/repository/moby/moby-live/Python/bioMoby/ontology/TEST.py	2005/02/01 08:52:16	1.4
@@ -46,5 +46,4 @@
             if elt.nodeName=="CrossReference" or elt.nodeName=="moby:CrossReference":
                 self.__cross__=[]
                 for ref in elt.childNodes:
-                    if ref.nodeType==ref.ELEMENT_NODE:
-                        self.__cross__.append(um.loads(ref.toxml()))
\ No newline at end of file
+                    self.__cross__.append(ref.toxml())
\ No newline at end of file

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/ontology/TargetP_result.py,v
retrieving revision 1.3
retrieving revision 1.4
diff -u -r1.3 -r1.4
--- /home/repository/moby/moby-live/Python/bioMoby/ontology/TargetP_result.py	2005/01/27 08:44:05	1.3
+++ /home/repository/moby/moby-live/Python/bioMoby/ontology/TargetP_result.py	2005/02/01 08:52:16	1.4
@@ -52,8 +52,7 @@
             if elt.nodeName=="CrossReference" or elt.nodeName=="moby:CrossReference":
                 self.__cross__=[]
                 for ref in elt.childNodes:
-                    if ref.nodeType==ref.ELEMENT_NODE:
-                        self.__cross__.append(um.loads(ref.toxml()))
+                    self.__cross__.append(ref.toxml())
             if elt.nodeType==elt.ELEMENT_NODE and (elt.nodeName=="Float" or elt.nodeName=="moby:Float") and (elt.getAttribute("articleName")=="o_score" or elt.getAttribute("moby:articleName")=="o_score"):
                 t=MobyFloat()
                 t.fromMoby(elt.toxml())

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/ontology/Testout.py,v
retrieving revision 1.3
retrieving revision 1.4
diff -u -r1.3 -r1.4
--- /home/repository/moby/moby-live/Python/bioMoby/ontology/Testout.py	2005/01/27 08:44:05	1.3
+++ /home/repository/moby/moby-live/Python/bioMoby/ontology/Testout.py	2005/02/01 08:52:16	1.4
@@ -51,8 +51,7 @@
             if elt.nodeName=="CrossReference" or elt.nodeName=="moby:CrossReference":
                 self.__cross__=[]
                 for ref in elt.childNodes:
-                    if ref.nodeType==ref.ELEMENT_NODE:
-                        self.__cross__.append(um.loads(ref.toxml()))
+                    self.__cross__.append(ref.toxml())
             if elt.nodeType==elt.ELEMENT_NODE and (elt.nodeName=="Integer" or elt.nodeName=="moby:Integer") and (elt.getAttribute("articleName")=="gid" or elt.getAttribute("moby:articleName")=="gid"):
                 t=MobyInteger()
                 t.fromMoby(elt.toxml())

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/ontology/TextBase64.py,v
retrieving revision 1.3
retrieving revision 1.4
diff -u -r1.3 -r1.4
--- /home/repository/moby/moby-live/Python/bioMoby/ontology/TextBase64.py	2005/01/27 08:44:05	1.3
+++ /home/repository/moby/moby-live/Python/bioMoby/ontology/TextBase64.py	2005/02/01 08:52:16	1.4
@@ -46,5 +46,4 @@
             if elt.nodeName=="CrossReference" or elt.nodeName=="moby:CrossReference":
                 self.__cross__=[]
                 for ref in elt.childNodes:
-                    if ref.nodeType==ref.ELEMENT_NODE:
-                        self.__cross__.append(um.loads(ref.toxml()))
\ No newline at end of file
+                    self.__cross__.append(ref.toxml())
\ No newline at end of file

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/ontology/TextFormatted.py,v
retrieving revision 1.3
retrieving revision 1.4
diff -u -r1.3 -r1.4
--- /home/repository/moby/moby-live/Python/bioMoby/ontology/TextFormatted.py	2005/01/27 08:44:05	1.3
+++ /home/repository/moby/moby-live/Python/bioMoby/ontology/TextFormatted.py	2005/02/01 08:52:16	1.4
@@ -46,5 +46,4 @@
             if elt.nodeName=="CrossReference" or elt.nodeName=="moby:CrossReference":
                 self.__cross__=[]
                 for ref in elt.childNodes:
-                    if ref.nodeType==ref.ELEMENT_NODE:
-                        self.__cross__.append(um.loads(ref.toxml()))
\ No newline at end of file
+                    self.__cross__.append(ref.toxml())
\ No newline at end of file

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/ontology/TextHtml.py,v
retrieving revision 1.3
retrieving revision 1.4
diff -u -r1.3 -r1.4
--- /home/repository/moby/moby-live/Python/bioMoby/ontology/TextHtml.py	2005/01/27 08:44:05	1.3
+++ /home/repository/moby/moby-live/Python/bioMoby/ontology/TextHtml.py	2005/02/01 08:52:16	1.4
@@ -46,5 +46,4 @@
             if elt.nodeName=="CrossReference" or elt.nodeName=="moby:CrossReference":
                 self.__cross__=[]
                 for ref in elt.childNodes:
-                    if ref.nodeType==ref.ELEMENT_NODE:
-                        self.__cross__.append(um.loads(ref.toxml()))
\ No newline at end of file
+                    self.__cross__.append(ref.toxml())
\ No newline at end of file

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/ontology/TextPlain.py,v
retrieving revision 1.3
retrieving revision 1.4
diff -u -r1.3 -r1.4
--- /home/repository/moby/moby-live/Python/bioMoby/ontology/TextPlain.py	2005/01/27 08:44:05	1.3
+++ /home/repository/moby/moby-live/Python/bioMoby/ontology/TextPlain.py	2005/02/01 08:52:16	1.4
@@ -46,5 +46,4 @@
             if elt.nodeName=="CrossReference" or elt.nodeName=="moby:CrossReference":
                 self.__cross__=[]
                 for ref in elt.childNodes:
-                    if ref.nodeType==ref.ELEMENT_NODE:
-                        self.__cross__.append(um.loads(ref.toxml()))
\ No newline at end of file
+                    self.__cross__.append(ref.toxml())
\ No newline at end of file

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/ontology/TextUuencoded.py,v
retrieving revision 1.3
retrieving revision 1.4
diff -u -r1.3 -r1.4
--- /home/repository/moby/moby-live/Python/bioMoby/ontology/TextUuencoded.py	2005/01/27 08:44:05	1.3
+++ /home/repository/moby/moby-live/Python/bioMoby/ontology/TextUuencoded.py	2005/02/01 08:52:16	1.4
@@ -46,5 +46,4 @@
             if elt.nodeName=="CrossReference" or elt.nodeName=="moby:CrossReference":
                 self.__cross__=[]
                 for ref in elt.childNodes:
-                    if ref.nodeType==ref.ELEMENT_NODE:
-                        self.__cross__.append(um.loads(ref.toxml()))
\ No newline at end of file
+                    self.__cross__.append(ref.toxml())
\ No newline at end of file

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/ontology/TextXml.py,v
retrieving revision 1.3
retrieving revision 1.4
diff -u -r1.3 -r1.4
--- /home/repository/moby/moby-live/Python/bioMoby/ontology/TextXml.py	2005/01/27 08:44:05	1.3
+++ /home/repository/moby/moby-live/Python/bioMoby/ontology/TextXml.py	2005/02/01 08:52:16	1.4
@@ -46,5 +46,4 @@
             if elt.nodeName=="CrossReference" or elt.nodeName=="moby:CrossReference":
                 self.__cross__=[]
                 for ref in elt.childNodes:
-                    if ref.nodeType==ref.ELEMENT_NODE:
-                        self.__cross__.append(um.loads(ref.toxml()))
\ No newline at end of file
+                    self.__cross__.append(ref.toxml())
\ No newline at end of file

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/ontology/Text_plain.py,v
retrieving revision 1.3
retrieving revision 1.4
diff -u -r1.3 -r1.4
--- /home/repository/moby/moby-live/Python/bioMoby/ontology/Text_plain.py	2005/01/27 08:44:05	1.3
+++ /home/repository/moby/moby-live/Python/bioMoby/ontology/Text_plain.py	2005/02/01 08:52:16	1.4
@@ -46,5 +46,4 @@
             if elt.nodeName=="CrossReference" or elt.nodeName=="moby:CrossReference":
                 self.__cross__=[]
                 for ref in elt.childNodes:
-                    if ref.nodeType==ref.ELEMENT_NODE:
-                        self.__cross__.append(um.loads(ref.toxml()))
\ No newline at end of file
+                    self.__cross__.append(ref.toxml())
\ No newline at end of file

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/ontology/Trait_Details.py,v
retrieving revision 1.3
retrieving revision 1.4
diff -u -r1.3 -r1.4
--- /home/repository/moby/moby-live/Python/bioMoby/ontology/Trait_Details.py	2005/01/27 08:44:05	1.3
+++ /home/repository/moby/moby-live/Python/bioMoby/ontology/Trait_Details.py	2005/02/01 08:52:16	1.4
@@ -52,8 +52,7 @@
             if elt.nodeName=="CrossReference" or elt.nodeName=="moby:CrossReference":
                 self.__cross__=[]
                 for ref in elt.childNodes:
-                    if ref.nodeType==ref.ELEMENT_NODE:
-                        self.__cross__.append(um.loads(ref.toxml()))
+                    self.__cross__.append(ref.toxml())
             if elt.nodeType==elt.ELEMENT_NODE and (elt.nodeName=="String" or elt.nodeName=="moby:String") and (elt.getAttribute("articleName")=="trait_desc" or elt.getAttribute("moby:articleName")=="trait_desc"):
                 t=MobyString()
                 t.fromMoby(elt.toxml())

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/ontology/Tree.py,v
retrieving revision 1.3
retrieving revision 1.4
diff -u -r1.3 -r1.4
--- /home/repository/moby/moby-live/Python/bioMoby/ontology/Tree.py	2005/01/27 08:44:05	1.3
+++ /home/repository/moby/moby-live/Python/bioMoby/ontology/Tree.py	2005/02/01 08:52:16	1.4
@@ -46,5 +46,4 @@
             if elt.nodeName=="CrossReference" or elt.nodeName=="moby:CrossReference":
                 self.__cross__=[]
                 for ref in elt.childNodes:
-                    if ref.nodeType==ref.ELEMENT_NODE:
-                        self.__cross__.append(um.loads(ref.toxml()))
\ No newline at end of file
+                    self.__cross__.append(ref.toxml())
\ No newline at end of file

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/ontology/TropGENE_ACCESSION.py,v
retrieving revision 1.3
retrieving revision 1.4
diff -u -r1.3 -r1.4
--- /home/repository/moby/moby-live/Python/bioMoby/ontology/TropGENE_ACCESSION.py	2005/01/27 08:44:05	1.3
+++ /home/repository/moby/moby-live/Python/bioMoby/ontology/TropGENE_ACCESSION.py	2005/02/01 08:52:16	1.4
@@ -66,8 +66,7 @@
             if elt.nodeName=="CrossReference" or elt.nodeName=="moby:CrossReference":
                 self.__cross__=[]
                 for ref in elt.childNodes:
-                    if ref.nodeType==ref.ELEMENT_NODE:
-                        self.__cross__.append(um.loads(ref.toxml()))
+                    self.__cross__.append(ref.toxml())
             if elt.nodeType==elt.ELEMENT_NODE and (elt.nodeName=="TropGENE_LOCUS" or elt.nodeName=="moby:TropGENE_LOCUS") and (elt.getAttribute("articleName")=="RFLP" or elt.getAttribute("moby:articleName")=="RFLP"):
                 self.RFLP=MobyTropGENE_LOCUS()
                 self.RFLP.fromMoby(elt.toxml())

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/ontology/TropGENE_Diversity_Matrix.py,v
retrieving revision 1.3
retrieving revision 1.4
diff -u -r1.3 -r1.4
--- /home/repository/moby/moby-live/Python/bioMoby/ontology/TropGENE_Diversity_Matrix.py	2005/01/27 08:44:05	1.3
+++ /home/repository/moby/moby-live/Python/bioMoby/ontology/TropGENE_Diversity_Matrix.py	2005/02/01 08:52:16	1.4
@@ -46,5 +46,4 @@
             if elt.nodeName=="CrossReference" or elt.nodeName=="moby:CrossReference":
                 self.__cross__=[]
                 for ref in elt.childNodes:
-                    if ref.nodeType==ref.ELEMENT_NODE:
-                        self.__cross__.append(um.loads(ref.toxml()))
\ No newline at end of file
+                    self.__cross__.append(ref.toxml())
\ No newline at end of file

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/ontology/TropGENE_LOCUS.py,v
retrieving revision 1.3
retrieving revision 1.4
diff -u -r1.3 -r1.4
--- /home/repository/moby/moby-live/Python/bioMoby/ontology/TropGENE_LOCUS.py	2005/01/27 08:44:05	1.3
+++ /home/repository/moby/moby-live/Python/bioMoby/ontology/TropGENE_LOCUS.py	2005/02/01 08:52:16	1.4
@@ -45,5 +45,4 @@
             if elt.nodeName=="CrossReference" or elt.nodeName=="moby:CrossReference":
                 self.__cross__=[]
                 for ref in elt.childNodes:
-                    if ref.nodeType==ref.ELEMENT_NODE:
-                        self.__cross__.append(um.loads(ref.toxml()))
\ No newline at end of file
+                    self.__cross__.append(ref.toxml())
\ No newline at end of file

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/ontology/VirtualSequence.py,v
retrieving revision 1.3
retrieving revision 1.4
diff -u -r1.3 -r1.4
--- /home/repository/moby/moby-live/Python/bioMoby/ontology/VirtualSequence.py	2005/01/27 08:44:05	1.3
+++ /home/repository/moby/moby-live/Python/bioMoby/ontology/VirtualSequence.py	2005/02/01 08:52:16	1.4
@@ -47,8 +47,7 @@
             if elt.nodeName=="CrossReference" or elt.nodeName=="moby:CrossReference":
                 self.__cross__=[]
                 for ref in elt.childNodes:
-                    if ref.nodeType==ref.ELEMENT_NODE:
-                        self.__cross__.append(um.loads(ref.toxml()))
+                    self.__cross__.append(ref.toxml())
             if elt.nodeType==elt.ELEMENT_NODE and (elt.nodeName=="Integer" or elt.nodeName=="moby:Integer") and (elt.getAttribute("articleName")=="Length" or elt.getAttribute("moby:articleName")=="Length"):
                 t=MobyInteger()
                 t.fromMoby(elt.toxml())

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/ontology/WU_BLAST_Text.py,v
retrieving revision 1.3
retrieving revision 1.4
diff -u -r1.3 -r1.4
--- /home/repository/moby/moby-live/Python/bioMoby/ontology/WU_BLAST_Text.py	2005/01/27 08:44:05	1.3
+++ /home/repository/moby/moby-live/Python/bioMoby/ontology/WU_BLAST_Text.py	2005/02/01 08:52:16	1.4
@@ -46,5 +46,4 @@
             if elt.nodeName=="CrossReference" or elt.nodeName=="moby:CrossReference":
                 self.__cross__=[]
                 for ref in elt.childNodes:
-                    if ref.nodeType==ref.ELEMENT_NODE:
-                        self.__cross__.append(um.loads(ref.toxml()))
\ No newline at end of file
+                    self.__cross__.append(ref.toxml())
\ No newline at end of file

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/ontology/Wildcard_Query.py,v
retrieving revision 1.3
retrieving revision 1.4
diff -u -r1.3 -r1.4
--- /home/repository/moby/moby-live/Python/bioMoby/ontology/Wildcard_Query.py	2005/01/27 08:44:05	1.3
+++ /home/repository/moby/moby-live/Python/bioMoby/ontology/Wildcard_Query.py	2005/02/01 08:52:16	1.4
@@ -50,8 +50,7 @@
             if elt.nodeName=="CrossReference" or elt.nodeName=="moby:CrossReference":
                 self.__cross__=[]
                 for ref in elt.childNodes:
-                    if ref.nodeType==ref.ELEMENT_NODE:
-                        self.__cross__.append(um.loads(ref.toxml()))
+                    self.__cross__.append(ref.toxml())
             if elt.nodeType==elt.ELEMENT_NODE and (elt.nodeName=="Integer" or elt.nodeName=="moby:Integer") and (elt.getAttribute("articleName")=="end_row" or elt.getAttribute("moby:articleName")=="end_row"):
                 t=MobyInteger()
                 t.fromMoby(elt.toxml())

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/ontology/__init__.py,v
retrieving revision 1.2
retrieving revision 1.3
diff -u -r1.2 -r1.3
--- /home/repository/moby/moby-live/Python/bioMoby/ontology/__init__.py	2005/01/18 13:46:22	1.2
+++ /home/repository/moby/moby-live/Python/bioMoby/ontology/__init__.py	2005/02/01 08:52:16	1.3
@@ -6,6 +6,7 @@
 from MO_Term_Test import MobyMO_Term_Test
 from CommentedDNASequence import MobyCommentedDNASequence
 from BasicGFFSequenceFeature import MobyBasicGFFSequenceFeature
+from MSF import MobyMSF
 from MyTestingDataType_11024145298313 import MobyMyTestingDataType_11024145298313
 from PDBFormattedText import MobyPDBFormattedText
 from Testout import MobyTestout
@@ -24,6 +25,7 @@
 from BLASTText import MobyBLASTText
 from Allele_freq import MobyAllele_freq
 from GenericSequence import MobyGenericSequence
+from Alignment import MobyAlignment
 from ICIS_Query import MobyICIS_Query
 from PHDText import MobyPHDText
 from WU_BLAST_Text import MobyWU_BLAST_Text
@@ -33,6 +35,7 @@
 from GFF3 import MobyGFF3
 from PDGJOB import MobyPDGJOB
 from CommentedAASequence import MobyCommentedAASequence
+from FASTA_NA_multi import MobyFASTA_NA_multi
 from ClustalMsfFormattedText import MobyClustalMsfFormattedText
 from Multi_key_value_pair import MobyMulti_key_value_pair
 from AlleleAssociation import MobyAlleleAssociation



From yanwong at pub.open-bio.org  Tue Feb  1 14:11:12 2005
From: yanwong at pub.open-bio.org (Yan Wong)
Date: Tue, 01 Feb 2005 14:11:12 -0000
Subject: [MOBY-guts] biomoby commit
Message-ID: <200502011420.j11EKksT014828@pub.open-bio.org>


yanwong
Tue Feb  1 09:20:44 EST 2005
Update of /home/repository/moby/moby-live/Python/bioMoby/ontology
In directory pub.open-bio.org:/tmp/cvs-serv14364/bioMoby/ontology

Modified Files:
	AlleleAssociation.py Allele_freq.py AminoAcidSequence.py 
	B64_Encoded_PNG.py B64_Encoded_Postscript.py 
	B64_encoded_PDB.py B64_encoded_gif.py B64_encoded_jpeg.py 
	BLASTText.py BasicGFFSequenceFeature.py 
	ClustalAlnFormattedText.py ClustalMsfFormattedText.py 
	CommentedAASequence.py CommentedDNASequence.py 
	CommentedRNASequence.py DNASequence.py 
	DNASequenceWithGFFFeatures.py DateTime.py Decypher_Text.py 
	Edge.py EmblFlatfile.py FASTA.py FASTA_AA.py FASTA_NA.py 
	FASTA_Text.py GFF.py GFF1.py GFF2.py GFF2_5.py GFF3.py 
	GO_Term.py GenbankFlatfile.py GenericSequence.py 
	GeneticElement.py Genotype.py Germplasm_Details.py 
	Germplasm_List.py Global_Keyword.py HBond_Pair.py 
	HFormatText.py Haplotyping_Study_obj.py ICIS_Query.py 
	ICIS_Query2.py ICIS_Query3.py IntAct_XML.py Interaction.py 
	InteractionMethod.py Interaction_partner.py Interactor.py 
	MEME_Text.py MGIS_ACCESSION.py MMP_Locus.py MO_Term_Test.py 
	MmCIFText.py Multi_key_value_pair.py 
	MyTestingDataType_11024145298313.py MyTree.py 
	NCBI_BLAST_Text.py NCBI_Blast_XML.py NCBI_Blast_XML_Gif.py 
	NCBI_Blast_XML_Gif_Map.py NCBI_MEME_Text.py 
	NucleotideSequence.py PDBFormattedText.py PDBText.py PDGJOB.py 
	PHDText.py PMUTText.py PSeaTextFormatted.py 
	PhenotypeDescription.py PubMedMEDLINE.py RNASequence.py 
	SINGER_ACCESSION.py Sample.py SchematikonMotifID.py 
	SchematikonMotifSupport.py SchematikonSegmentAttributes.py 
	SchematikonSegmentID.py SchematikonStructureAnnotation.py 
	SchematikonVorocodeName.py Scored_acronym_string.py 
	SimpleAnnotatedGIFImage.py SimpleAnnotatedJPEGImage.py 
	Simple_key_value_pair.py Snp_allele.py Snp_genotype.py 
	Study.py TEST.py TargetP_result.py Testout.py TextBase64.py 
	TextFormatted.py TextHtml.py TextPlain.py TextUuencoded.py 
	TextXml.py Text_plain.py Trait_Details.py Tree.py 
	TropGENE_ACCESSION.py TropGENE_Diversity_Matrix.py 
	TropGENE_LOCUS.py VirtualSequence.py WU_BLAST_Text.py 
	Wildcard_Query.py 
Log Message:


moby-live/Python/bioMoby/ontology AlleleAssociation.py,1.4,1.5 Allele_freq.py,1.4,1.5 AminoAcidSequence.py,1.4,1.5 B64_Encoded_PNG.py,1.4,1.5 B64_Encoded_Postscript.py,1.4,1.5 B64_encoded_PDB.py,1.4,1.5 B64_encoded_gif.py,1.4,1.5 B64_encoded_jpeg.py,1.4,1.5 BLASTText.py,1.4,1.5 BasicGFFSequenceFeature.py,1.4,1.5 ClustalAlnFormattedText.py,1.4,1.5 ClustalMsfFormattedText.py,1.4,1.5 CommentedAASequence.py,1.4,1.5 CommentedDNASequence.py,1.4,1.5 CommentedRNASequence.py,1.4,1.5 DNASequence.py,1.4,1.5 DNASequenceWithGFFFeatures.py,1.4,1.5 DateTime.py,1.4,1.5 Decypher_Text.py,1.4,1.5 Edge.py,1.4,1.5 EmblFlatfile.py,1.4,1.5 FASTA.py,1.4,1.5 FASTA_AA.py,1.4,1.5 FASTA_NA.py,1.4,1.5 FASTA_Text.py,1.4,1.5 GFF.py,1.4,1.5 GFF1.py,1.4,1.5 GFF2.py,1.4,1.5 GFF2_5.py,1.4,1.5 GFF3.py,1.4,1.5 GO_Term.py,1.4,1.5 GenbankFlatfile.py,1.4,1.5 GenericSequence.py,1.4,1.5 GeneticElement.py,1.4,1.5 Genotype.py,1.4,1.5 Germplasm_Details.py,1.4,1.5 Germplasm_List.py,1.4,1.5 Global_Keyword.py,1.4,1.5 HBon!
d_Pair.py,1.4,1.5 HFormatText.py,1.4,1.5 Haplotyping_Study_obj.py,1.4,1.5 ICIS_Query.py,1.4,1.5 ICIS_Query2.py,1.4,1.5 ICIS_Query3.py,1.4,1.5 IntAct_XML.py,1.4,1.5 Interaction.py,1.4,1.5 InteractionMethod.py,1.4,1.5 Interaction_partner.py,1.4,1.5 Interactor.py,1.4,1.5 MEME_Text.py,1.4,1.5 MGIS_ACCESSION.py,1.4,1.5 MMP_Locus.py,1.4,1.5 MO_Term_Test.py,1.4,1.5 MmCIFText.py,1.4,1.5 Multi_key_value_pair.py,1.4,1.5 MyTestingDataType_11024145298313.py,1.4,1.5 MyTree.py,1.4,1.5 NCBI_BLAST_Text.py,1.4,1.5 NCBI_Blast_XML.py,1.4,1.5 NCBI_Blast_XML_Gif.py,1.4,1.5 NCBI_Blast_XML_Gif_Map.py,1.4,1.5 NCBI_MEME_Text.py,1.4,1.5 NucleotideSequence.py,1.4,1.5 PDBFormattedText.py,1.4,1.5 PDBText.py,1.4,1.5 PDGJOB.py,1.4,1.5 PHDText.py,1.4,1.5 PMUTText.py,1.4,1.5 PSeaTextFormatted.py,1.4,1.5 PhenotypeDescription.py,1.4,1.5 PubMedMEDLINE.py,1.4,1.5 RNASequence.py,1.4,1.5 SINGER_ACCESSION.py,1.4,1.5 Sample.py,1.4,1.5 SchematikonMotifID.py,1.4,1.5 SchematikonMotifSupport.py,1.4,1.5 SchematikonSegme!
ntAttributes.py,1.4,1.5 SchematikonSegmentID.py,1.4,1.5 Schem!
atikonStructureAnnotation.py,1.4,1.5 SchematikonVorocodeName.py,1.4,1.5 Scored_acronym_string.py,1.4,1.5 SimpleAnnotatedGIFImage.py,1.4,1.5 SimpleAnnotatedJPEGImage.py,1.4,1.5 Simple_key_value_pair.py,1.4,1.5 Snp_allele.py,1.4,1.5 Snp_genotype.py,1.4,1.5 Study.py,1.4,1.5 TEST.py,1.4,1.5 TargetP_result.py,1.4,1.5 Testout.py,1.4,1.5 TextBase64.py,1.4,1.5 TextFormatted.py,1.4,1.5 TextHtml.py,1.4,1.5 TextPlain.py,1.4,1.5 TextUuencoded.py,1.4,1.5 TextXml.py,1.4,1.5 Text_plain.py,1.4,1.5 Trait_Details.py,1.4,1.5 Tree.py,1.4,1.5 TropGENE_ACCESSION.py,1.4,1.5 TropGENE_Diversity_Matrix.py,1.4,1.5 TropGENE_LOCUS.py,1.4,1.5 VirtualSequence.py,1.4,1.5 WU_BLAST_Text.py,1.4,1.5 Wildcard_Query.py,1.4,1.5
===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/ontology/AlleleAssociation.py,v
retrieving revision 1.4
retrieving revision 1.5
diff -u -r1.4 -r1.5
--- /home/repository/moby/moby-live/Python/bioMoby/ontology/AlleleAssociation.py	2005/02/01 08:52:15	1.4
+++ /home/repository/moby/moby-live/Python/bioMoby/ontology/AlleleAssociation.py	2005/02/01 14:20:44	1.5
@@ -30,7 +30,9 @@
         """ Load the attributes from an XML string
         """
         from bioMoby.mobyMarshal import MobyUnmarshaller
-        doc=parseString(value).firstChild
+        doc=value
+        if isinstance(value, str):
+            doc=parseString(value).firstChild
         um=MobyUnmarshaller()
         self.content=""
         self.namespace=doc.getAttribute("moby:namespace")
@@ -50,16 +52,16 @@
             if elt.nodeName=="CrossReference" or elt.nodeName=="moby:CrossReference":
                 self.__cross__=[]
                 for ref in elt.childNodes:
-                    self.__cross__.append(ref.toxml())
+                    self.__cross__.append(um.loads(ref))
             if elt.nodeType==elt.ELEMENT_NODE and (elt.nodeName=="String" or elt.nodeName=="moby:String") and (elt.getAttribute("articleName")=="snp" or elt.getAttribute("moby:articleName")=="snp"):
                 t=MobyString()
-                t.fromMoby(elt.toxml())
+                t.fromMoby(elt)
                 self.Snp=t.content
             if elt.nodeType==elt.ELEMENT_NODE and (elt.nodeName=="Float" or elt.nodeName=="moby:Float") and (elt.getAttribute("articleName")=="pValue" or elt.getAttribute("moby:articleName")=="pValue"):
                 t=MobyFloat()
-                t.fromMoby(elt.toxml())
+                t.fromMoby(elt)
                 self.PValue=t.content
             if elt.nodeType==elt.ELEMENT_NODE and (elt.nodeName=="String" or elt.nodeName=="moby:String") and (elt.getAttribute("articleName")=="validity" or elt.getAttribute("moby:articleName")=="validity"):
                 t=MobyString()
-                t.fromMoby(elt.toxml())
+                t.fromMoby(elt)
                 self.Validity=t.content
\ No newline at end of file

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/ontology/Allele_freq.py,v
retrieving revision 1.4
retrieving revision 1.5
diff -u -r1.4 -r1.5
--- /home/repository/moby/moby-live/Python/bioMoby/ontology/Allele_freq.py	2005/02/01 08:52:15	1.4
+++ /home/repository/moby/moby-live/Python/bioMoby/ontology/Allele_freq.py	2005/02/01 14:20:44	1.5
@@ -28,7 +28,9 @@
         """ Load the attributes from an XML string
         """
         from bioMoby.mobyMarshal import MobyUnmarshaller
-        doc=parseString(value).firstChild
+        doc=value
+        if isinstance(value, str):
+            doc=parseString(value).firstChild
         um=MobyUnmarshaller()
         self.content=""
 
@@ -44,17 +46,17 @@
             if elt.nodeName=="CrossReference" or elt.nodeName=="moby:CrossReference":
                 self.__cross__=[]
                 for ref in elt.childNodes:
-                    self.__cross__.append(ref.toxml())
+                    self.__cross__.append(um.loads(ref))
             if elt.nodeType==elt.ELEMENT_NODE and (elt.nodeName=="Object" or elt.nodeName=="moby:Object") and (elt.getAttribute("articleName")=="panel_lsid" or elt.getAttribute("moby:articleName")=="panel_lsid"):
                 self.Panel_lsid=MobyObject()
-                self.Panel_lsid.fromMoby(elt.toxml())
+                self.Panel_lsid.fromMoby(elt)
             if elt.nodeType==elt.ELEMENT_NODE and (elt.nodeName=="Object" or elt.nodeName=="moby:Object") and (elt.getAttribute("articleName")=="snp_lsid" or elt.getAttribute("moby:articleName")=="snp_lsid"):
                 self.Snp_lsid=MobyObject()
-                self.Snp_lsid.fromMoby(elt.toxml())
+                self.Snp_lsid.fromMoby(elt)
             if elt.nodeType==elt.ELEMENT_NODE and (elt.nodeName=="snp_allele" or elt.nodeName=="moby:snp_allele") and (elt.getAttribute("articleName")=="allele_freq" or elt.getAttribute("moby:articleName")=="allele_freq"):
                 self.Allele_freq=MobySnp_allele()
-                self.Allele_freq.fromMoby(elt.toxml())
+                self.Allele_freq.fromMoby(elt)
             if elt.nodeType==elt.ELEMENT_NODE and (elt.nodeName=="Integer" or elt.nodeName=="moby:Integer") and (elt.getAttribute("articleName")=="frequency" or elt.getAttribute("moby:articleName")=="frequency"):
                 t=MobyInteger()
-                t.fromMoby(elt.toxml())
+                t.fromMoby(elt)
                 self.Frequency.append(t.content)
\ No newline at end of file

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/ontology/AminoAcidSequence.py,v
retrieving revision 1.4
retrieving revision 1.5
diff -u -r1.4 -r1.5
--- /home/repository/moby/moby-live/Python/bioMoby/ontology/AminoAcidSequence.py	2005/02/01 08:52:15	1.4
+++ /home/repository/moby/moby-live/Python/bioMoby/ontology/AminoAcidSequence.py	2005/02/01 14:20:44	1.5
@@ -29,7 +29,9 @@
         """ Load the attributes from an XML string
         """
         from bioMoby.mobyMarshal import MobyUnmarshaller
-        doc=parseString(value).firstChild
+        doc=value
+        if isinstance(value, str):
+            doc=parseString(value).firstChild
         um=MobyUnmarshaller()
         self.content=""
         self.namespace=doc.getAttribute("moby:namespace")
@@ -49,12 +51,12 @@
             if elt.nodeName=="CrossReference" or elt.nodeName=="moby:CrossReference":
                 self.__cross__=[]
                 for ref in elt.childNodes:
-                    self.__cross__.append(ref.toxml())
+                    self.__cross__.append(um.loads(ref))
             if elt.nodeType==elt.ELEMENT_NODE and (elt.nodeName=="Integer" or elt.nodeName=="moby:Integer") and (elt.getAttribute("articleName")=="Length" or elt.getAttribute("moby:articleName")=="Length"):
                 t=MobyInteger()
-                t.fromMoby(elt.toxml())
+                t.fromMoby(elt)
                 self.Length=t.content
             if elt.nodeType==elt.ELEMENT_NODE and (elt.nodeName=="String" or elt.nodeName=="moby:String") and (elt.getAttribute("articleName")=="SequenceString" or elt.getAttribute("moby:articleName")=="SequenceString"):
                 t=MobyString()
-                t.fromMoby(elt.toxml())
+                t.fromMoby(elt)
                 self.SequenceString=t.content
\ No newline at end of file

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/ontology/B64_Encoded_PNG.py,v
retrieving revision 1.4
retrieving revision 1.5
diff -u -r1.4 -r1.5
--- /home/repository/moby/moby-live/Python/bioMoby/ontology/B64_Encoded_PNG.py	2005/02/01 08:52:15	1.4
+++ /home/repository/moby/moby-live/Python/bioMoby/ontology/B64_Encoded_PNG.py	2005/02/01 14:20:44	1.5
@@ -26,7 +26,9 @@
         """ Load the attributes from an XML string
         """
         from bioMoby.mobyMarshal import MobyUnmarshaller
-        doc=parseString(value).firstChild
+        doc=value
+        if isinstance(value, str):
+            doc=parseString(value).firstChild
         um=MobyUnmarshaller()
         self.content=""
         self.namespace=doc.getAttribute("moby:namespace")
@@ -46,4 +48,4 @@
             if elt.nodeName=="CrossReference" or elt.nodeName=="moby:CrossReference":
                 self.__cross__=[]
                 for ref in elt.childNodes:
-                    self.__cross__.append(ref.toxml())
\ No newline at end of file
+                    self.__cross__.append(um.loads(ref))
\ No newline at end of file

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/ontology/B64_Encoded_Postscript.py,v
retrieving revision 1.4
retrieving revision 1.5
diff -u -r1.4 -r1.5
--- /home/repository/moby/moby-live/Python/bioMoby/ontology/B64_Encoded_Postscript.py	2005/02/01 08:52:15	1.4
+++ /home/repository/moby/moby-live/Python/bioMoby/ontology/B64_Encoded_Postscript.py	2005/02/01 14:20:44	1.5
@@ -26,7 +26,9 @@
         """ Load the attributes from an XML string
         """
         from bioMoby.mobyMarshal import MobyUnmarshaller
-        doc=parseString(value).firstChild
+        doc=value
+        if isinstance(value, str):
+            doc=parseString(value).firstChild
         um=MobyUnmarshaller()
         self.content=""
         self.namespace=doc.getAttribute("moby:namespace")
@@ -46,4 +48,4 @@
             if elt.nodeName=="CrossReference" or elt.nodeName=="moby:CrossReference":
                 self.__cross__=[]
                 for ref in elt.childNodes:
-                    self.__cross__.append(ref.toxml())
\ No newline at end of file
+                    self.__cross__.append(um.loads(ref))
\ No newline at end of file

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/ontology/B64_encoded_PDB.py,v
retrieving revision 1.4
retrieving revision 1.5
diff -u -r1.4 -r1.5
--- /home/repository/moby/moby-live/Python/bioMoby/ontology/B64_encoded_PDB.py	2005/02/01 08:52:15	1.4
+++ /home/repository/moby/moby-live/Python/bioMoby/ontology/B64_encoded_PDB.py	2005/02/01 14:20:44	1.5
@@ -26,7 +26,9 @@
         """ Load the attributes from an XML string
         """
         from bioMoby.mobyMarshal import MobyUnmarshaller
-        doc=parseString(value).firstChild
+        doc=value
+        if isinstance(value, str):
+            doc=parseString(value).firstChild
         um=MobyUnmarshaller()
         self.content=""
         self.namespace=doc.getAttribute("moby:namespace")
@@ -46,4 +48,4 @@
             if elt.nodeName=="CrossReference" or elt.nodeName=="moby:CrossReference":
                 self.__cross__=[]
                 for ref in elt.childNodes:
-                    self.__cross__.append(ref.toxml())
\ No newline at end of file
+                    self.__cross__.append(um.loads(ref))
\ No newline at end of file

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/ontology/B64_encoded_gif.py,v
retrieving revision 1.4
retrieving revision 1.5
diff -u -r1.4 -r1.5
--- /home/repository/moby/moby-live/Python/bioMoby/ontology/B64_encoded_gif.py	2005/02/01 08:52:15	1.4
+++ /home/repository/moby/moby-live/Python/bioMoby/ontology/B64_encoded_gif.py	2005/02/01 14:20:44	1.5
@@ -26,7 +26,9 @@
         """ Load the attributes from an XML string
         """
         from bioMoby.mobyMarshal import MobyUnmarshaller
-        doc=parseString(value).firstChild
+        doc=value
+        if isinstance(value, str):
+            doc=parseString(value).firstChild
         um=MobyUnmarshaller()
         self.content=""
         self.namespace=doc.getAttribute("moby:namespace")
@@ -46,4 +48,4 @@
             if elt.nodeName=="CrossReference" or elt.nodeName=="moby:CrossReference":
                 self.__cross__=[]
                 for ref in elt.childNodes:
-                    self.__cross__.append(ref.toxml())
\ No newline at end of file
+                    self.__cross__.append(um.loads(ref))
\ No newline at end of file

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/ontology/B64_encoded_jpeg.py,v
retrieving revision 1.4
retrieving revision 1.5
diff -u -r1.4 -r1.5
--- /home/repository/moby/moby-live/Python/bioMoby/ontology/B64_encoded_jpeg.py	2005/02/01 08:52:15	1.4
+++ /home/repository/moby/moby-live/Python/bioMoby/ontology/B64_encoded_jpeg.py	2005/02/01 14:20:44	1.5
@@ -26,7 +26,9 @@
         """ Load the attributes from an XML string
         """
         from bioMoby.mobyMarshal import MobyUnmarshaller
-        doc=parseString(value).firstChild
+        doc=value
+        if isinstance(value, str):
+            doc=parseString(value).firstChild
         um=MobyUnmarshaller()
         self.content=""
         self.namespace=doc.getAttribute("moby:namespace")
@@ -46,4 +48,4 @@
             if elt.nodeName=="CrossReference" or elt.nodeName=="moby:CrossReference":
                 self.__cross__=[]
                 for ref in elt.childNodes:
-                    self.__cross__.append(ref.toxml())
\ No newline at end of file
+                    self.__cross__.append(um.loads(ref))
\ No newline at end of file

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/ontology/BLASTText.py,v
retrieving revision 1.4
retrieving revision 1.5
diff -u -r1.4 -r1.5
--- /home/repository/moby/moby-live/Python/bioMoby/ontology/BLASTText.py	2005/02/01 08:52:15	1.4
+++ /home/repository/moby/moby-live/Python/bioMoby/ontology/BLASTText.py	2005/02/01 14:20:44	1.5
@@ -26,7 +26,9 @@
         """ Load the attributes from an XML string
         """
         from bioMoby.mobyMarshal import MobyUnmarshaller
-        doc=parseString(value).firstChild
+        doc=value
+        if isinstance(value, str):
+            doc=parseString(value).firstChild
         um=MobyUnmarshaller()
         self.content=""
         self.namespace=doc.getAttribute("moby:namespace")
@@ -46,4 +48,4 @@
             if elt.nodeName=="CrossReference" or elt.nodeName=="moby:CrossReference":
                 self.__cross__=[]
                 for ref in elt.childNodes:
-                    self.__cross__.append(ref.toxml())
\ No newline at end of file
+                    self.__cross__.append(um.loads(ref))
\ No newline at end of file

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/ontology/BasicGFFSequenceFeature.py,v
retrieving revision 1.4
retrieving revision 1.5
diff -u -r1.4 -r1.5
--- /home/repository/moby/moby-live/Python/bioMoby/ontology/BasicGFFSequenceFeature.py	2005/02/01 08:52:15	1.4
+++ /home/repository/moby/moby-live/Python/bioMoby/ontology/BasicGFFSequenceFeature.py	2005/02/01 14:20:44	1.5
@@ -39,7 +39,9 @@
         """ Load the attributes from an XML string
         """
         from bioMoby.mobyMarshal import MobyUnmarshaller
-        doc=parseString(value).firstChild
+        doc=value
+        if isinstance(value, str):
+            doc=parseString(value).firstChild
         um=MobyUnmarshaller()
         self.content=""
         self.namespace=doc.getAttribute("moby:namespace")
@@ -60,43 +62,43 @@
             if elt.nodeName=="CrossReference" or elt.nodeName=="moby:CrossReference":
                 self.__cross__=[]
                 for ref in elt.childNodes:
-                    self.__cross__.append(ref.toxml())
+                    self.__cross__.append(um.loads(ref))
             if elt.nodeType==elt.ELEMENT_NODE and (elt.nodeName=="String" or elt.nodeName=="moby:String") and (elt.getAttribute("articleName")=="reference" or elt.getAttribute("moby:articleName")=="reference"):
                 t=MobyString()
-                t.fromMoby(elt.toxml())
+                t.fromMoby(elt)
                 self.Reference=t.content
             if elt.nodeType==elt.ELEMENT_NODE and (elt.nodeName=="String" or elt.nodeName=="moby:String") and (elt.getAttribute("articleName")=="source" or elt.getAttribute("moby:articleName")=="source"):
                 t=MobyString()
-                t.fromMoby(elt.toxml())
+                t.fromMoby(elt)
                 self.Source=t.content
             if elt.nodeType==elt.ELEMENT_NODE and (elt.nodeName=="String" or elt.nodeName=="moby:String") and (elt.getAttribute("articleName")=="method" or elt.getAttribute("moby:articleName")=="method"):
                 t=MobyString()
-                t.fromMoby(elt.toxml())
+                t.fromMoby(elt)
                 self.Method=t.content
             if elt.nodeType==elt.ELEMENT_NODE and (elt.nodeName=="Integer" or elt.nodeName=="moby:Integer") and (elt.getAttribute("articleName")=="start" or elt.getAttribute("moby:articleName")=="start"):
                 t=MobyInteger()
-                t.fromMoby(elt.toxml())
+                t.fromMoby(elt)
                 self.Start=t.content
             if elt.nodeType==elt.ELEMENT_NODE and (elt.nodeName=="Integer" or elt.nodeName=="moby:Integer") and (elt.getAttribute("articleName")=="stop" or elt.getAttribute("moby:articleName")=="stop"):
                 t=MobyInteger()
-                t.fromMoby(elt.toxml())
+                t.fromMoby(elt)
                 self.Stop=t.content
             if elt.nodeType==elt.ELEMENT_NODE and (elt.nodeName=="Float" or elt.nodeName=="moby:Float") and (elt.getAttribute("articleName")=="score" or elt.getAttribute("moby:articleName")=="score"):
                 t=MobyFloat()
-                t.fromMoby(elt.toxml())
+                t.fromMoby(elt)
                 self.Score=t.content
             if elt.nodeType==elt.ELEMENT_NODE and (elt.nodeName=="String" or elt.nodeName=="moby:String") and (elt.getAttribute("articleName")=="strand" or elt.getAttribute("moby:articleName")=="strand"):
                 t=MobyString()
-                t.fromMoby(elt.toxml())
+                t.fromMoby(elt)
                 self.Strand=t.content
             if elt.nodeType==elt.ELEMENT_NODE and (elt.nodeName=="String" or elt.nodeName=="moby:String") and (elt.getAttribute("articleName")=="frame" or elt.getAttribute("moby:articleName")=="frame"):
                 t=MobyString()
-                t.fromMoby(elt.toxml())
+                t.fromMoby(elt)
                 self.Frame=t.content
             if elt.nodeType==elt.ELEMENT_NODE and (elt.nodeName=="String" or elt.nodeName=="moby:String") and (elt.getAttribute("articleName")=="phase" or elt.getAttribute("moby:articleName")=="phase"):
                 t=MobyString()
-                t.fromMoby(elt.toxml())
+                t.fromMoby(elt)
                 self.Phase=t.content
             if elt.nodeType==elt.ELEMENT_NODE and (elt.nodeName=="multi_key_value_pair" or elt.nodeName=="moby:multi_key_value_pair") and (elt.getAttribute("articleName")=="column9_tag_value" or elt.getAttribute("moby:articleName")=="column9_tag_value"):
                 self.Column9_tag_value=MobyMulti_key_value_pair()
-                self.Column9_tag_value.fromMoby(elt.toxml())
\ No newline at end of file
+                self.Column9_tag_value.fromMoby(elt)
\ No newline at end of file

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/ontology/ClustalAlnFormattedText.py,v
retrieving revision 1.4
retrieving revision 1.5
diff -u -r1.4 -r1.5
--- /home/repository/moby/moby-live/Python/bioMoby/ontology/ClustalAlnFormattedText.py	2005/02/01 08:52:15	1.4
+++ /home/repository/moby/moby-live/Python/bioMoby/ontology/ClustalAlnFormattedText.py	2005/02/01 14:20:44	1.5
@@ -26,7 +26,9 @@
         """ Load the attributes from an XML string
         """
         from bioMoby.mobyMarshal import MobyUnmarshaller
-        doc=parseString(value).firstChild
+        doc=value
+        if isinstance(value, str):
+            doc=parseString(value).firstChild
         um=MobyUnmarshaller()
         self.content=""
         self.namespace=doc.getAttribute("moby:namespace")
@@ -46,4 +48,4 @@
             if elt.nodeName=="CrossReference" or elt.nodeName=="moby:CrossReference":
                 self.__cross__=[]
                 for ref in elt.childNodes:
-                    self.__cross__.append(ref.toxml())
\ No newline at end of file
+                    self.__cross__.append(um.loads(ref))
\ No newline at end of file

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/ontology/ClustalMsfFormattedText.py,v
retrieving revision 1.4
retrieving revision 1.5
diff -u -r1.4 -r1.5
--- /home/repository/moby/moby-live/Python/bioMoby/ontology/ClustalMsfFormattedText.py	2005/02/01 08:52:15	1.4
+++ /home/repository/moby/moby-live/Python/bioMoby/ontology/ClustalMsfFormattedText.py	2005/02/01 14:20:44	1.5
@@ -26,7 +26,9 @@
         """ Load the attributes from an XML string
         """
         from bioMoby.mobyMarshal import MobyUnmarshaller
-        doc=parseString(value).firstChild
+        doc=value
+        if isinstance(value, str):
+            doc=parseString(value).firstChild
         um=MobyUnmarshaller()
         self.content=""
         self.namespace=doc.getAttribute("moby:namespace")
@@ -46,4 +48,4 @@
             if elt.nodeName=="CrossReference" or elt.nodeName=="moby:CrossReference":
                 self.__cross__=[]
                 for ref in elt.childNodes:
-                    self.__cross__.append(ref.toxml())
\ No newline at end of file
+                    self.__cross__.append(um.loads(ref))
\ No newline at end of file

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/ontology/CommentedAASequence.py,v
retrieving revision 1.4
retrieving revision 1.5
diff -u -r1.4 -r1.5
--- /home/repository/moby/moby-live/Python/bioMoby/ontology/CommentedAASequence.py	2005/02/01 08:52:15	1.4
+++ /home/repository/moby/moby-live/Python/bioMoby/ontology/CommentedAASequence.py	2005/02/01 14:20:44	1.5
@@ -30,7 +30,9 @@
         """ Load the attributes from an XML string
         """
         from bioMoby.mobyMarshal import MobyUnmarshaller
-        doc=parseString(value).firstChild
+        doc=value
+        if isinstance(value, str):
+            doc=parseString(value).firstChild
         um=MobyUnmarshaller()
         self.content=""
         self.namespace=doc.getAttribute("moby:namespace")
@@ -50,16 +52,16 @@
             if elt.nodeName=="CrossReference" or elt.nodeName=="moby:CrossReference":
                 self.__cross__=[]
                 for ref in elt.childNodes:
-                    self.__cross__.append(ref.toxml())
+                    self.__cross__.append(um.loads(ref))
             if elt.nodeType==elt.ELEMENT_NODE and (elt.nodeName=="Integer" or elt.nodeName=="moby:Integer") and (elt.getAttribute("articleName")=="Length" or elt.getAttribute("moby:articleName")=="Length"):
                 t=MobyInteger()
-                t.fromMoby(elt.toxml())
+                t.fromMoby(elt)
                 self.Length=t.content
             if elt.nodeType==elt.ELEMENT_NODE and (elt.nodeName=="String" or elt.nodeName=="moby:String") and (elt.getAttribute("articleName")=="SequenceString" or elt.getAttribute("moby:articleName")=="SequenceString"):
                 t=MobyString()
-                t.fromMoby(elt.toxml())
+                t.fromMoby(elt)
                 self.SequenceString=t.content
             if elt.nodeType==elt.ELEMENT_NODE and (elt.nodeName=="String" or elt.nodeName=="moby:String") and (elt.getAttribute("articleName")=="Description" or elt.getAttribute("moby:articleName")=="Description"):
                 t=MobyString()
-                t.fromMoby(elt.toxml())
+                t.fromMoby(elt)
                 self.Description=t.content
\ No newline at end of file

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/ontology/CommentedDNASequence.py,v
retrieving revision 1.4
retrieving revision 1.5
diff -u -r1.4 -r1.5
--- /home/repository/moby/moby-live/Python/bioMoby/ontology/CommentedDNASequence.py	2005/02/01 08:52:15	1.4
+++ /home/repository/moby/moby-live/Python/bioMoby/ontology/CommentedDNASequence.py	2005/02/01 14:20:44	1.5
@@ -30,7 +30,9 @@
         """ Load the attributes from an XML string
         """
         from bioMoby.mobyMarshal import MobyUnmarshaller
-        doc=parseString(value).firstChild
+        doc=value
+        if isinstance(value, str):
+            doc=parseString(value).firstChild
         um=MobyUnmarshaller()
         self.content=""
         self.namespace=doc.getAttribute("moby:namespace")
@@ -50,16 +52,16 @@
             if elt.nodeName=="CrossReference" or elt.nodeName=="moby:CrossReference":
                 self.__cross__=[]
                 for ref in elt.childNodes:
-                    self.__cross__.append(ref.toxml())
+                    self.__cross__.append(um.loads(ref))
             if elt.nodeType==elt.ELEMENT_NODE and (elt.nodeName=="Integer" or elt.nodeName=="moby:Integer") and (elt.getAttribute("articleName")=="Length" or elt.getAttribute("moby:articleName")=="Length"):
                 t=MobyInteger()
-                t.fromMoby(elt.toxml())
+                t.fromMoby(elt)
                 self.Length=t.content
             if elt.nodeType==elt.ELEMENT_NODE and (elt.nodeName=="String" or elt.nodeName=="moby:String") and (elt.getAttribute("articleName")=="SequenceString" or elt.getAttribute("moby:articleName")=="SequenceString"):
                 t=MobyString()
-                t.fromMoby(elt.toxml())
+                t.fromMoby(elt)
                 self.SequenceString=t.content
             if elt.nodeType==elt.ELEMENT_NODE and (elt.nodeName=="String" or elt.nodeName=="moby:String") and (elt.getAttribute("articleName")=="Description" or elt.getAttribute("moby:articleName")=="Description"):
                 t=MobyString()
-                t.fromMoby(elt.toxml())
+                t.fromMoby(elt)
                 self.Description=t.content
\ No newline at end of file

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/ontology/CommentedRNASequence.py,v
retrieving revision 1.4
retrieving revision 1.5
diff -u -r1.4 -r1.5
--- /home/repository/moby/moby-live/Python/bioMoby/ontology/CommentedRNASequence.py	2005/02/01 08:52:15	1.4
+++ /home/repository/moby/moby-live/Python/bioMoby/ontology/CommentedRNASequence.py	2005/02/01 14:20:44	1.5
@@ -30,7 +30,9 @@
         """ Load the attributes from an XML string
         """
         from bioMoby.mobyMarshal import MobyUnmarshaller
-        doc=parseString(value).firstChild
+        doc=value
+        if isinstance(value, str):
+            doc=parseString(value).firstChild
         um=MobyUnmarshaller()
         self.content=""
         self.namespace=doc.getAttribute("moby:namespace")
@@ -50,16 +52,16 @@
             if elt.nodeName=="CrossReference" or elt.nodeName=="moby:CrossReference":
                 self.__cross__=[]
                 for ref in elt.childNodes:
-                    self.__cross__.append(ref.toxml())
+                    self.__cross__.append(um.loads(ref))
             if elt.nodeType==elt.ELEMENT_NODE and (elt.nodeName=="Integer" or elt.nodeName=="moby:Integer") and (elt.getAttribute("articleName")=="Length" or elt.getAttribute("moby:articleName")=="Length"):
                 t=MobyInteger()
-                t.fromMoby(elt.toxml())
+                t.fromMoby(elt)
                 self.Length=t.content
             if elt.nodeType==elt.ELEMENT_NODE and (elt.nodeName=="String" or elt.nodeName=="moby:String") and (elt.getAttribute("articleName")=="SequenceString" or elt.getAttribute("moby:articleName")=="SequenceString"):
                 t=MobyString()
-                t.fromMoby(elt.toxml())
+                t.fromMoby(elt)
                 self.SequenceString=t.content
             if elt.nodeType==elt.ELEMENT_NODE and (elt.nodeName=="String" or elt.nodeName=="moby:String") and (elt.getAttribute("articleName")=="Description" or elt.getAttribute("moby:articleName")=="Description"):
                 t=MobyString()
-                t.fromMoby(elt.toxml())
+                t.fromMoby(elt)
                 self.Description=t.content
\ No newline at end of file

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/ontology/DNASequence.py,v
retrieving revision 1.4
retrieving revision 1.5
diff -u -r1.4 -r1.5
--- /home/repository/moby/moby-live/Python/bioMoby/ontology/DNASequence.py	2005/02/01 08:52:15	1.4
+++ /home/repository/moby/moby-live/Python/bioMoby/ontology/DNASequence.py	2005/02/01 14:20:44	1.5
@@ -29,7 +29,9 @@
         """ Load the attributes from an XML string
         """
         from bioMoby.mobyMarshal import MobyUnmarshaller
-        doc=parseString(value).firstChild
+        doc=value
+        if isinstance(value, str):
+            doc=parseString(value).firstChild
         um=MobyUnmarshaller()
         self.content=""
         self.namespace=doc.getAttribute("moby:namespace")
@@ -49,12 +51,12 @@
             if elt.nodeName=="CrossReference" or elt.nodeName=="moby:CrossReference":
                 self.__cross__=[]
                 for ref in elt.childNodes:
-                    self.__cross__.append(ref.toxml())
+                    self.__cross__.append(um.loads(ref))
             if elt.nodeType==elt.ELEMENT_NODE and (elt.nodeName=="Integer" or elt.nodeName=="moby:Integer") and (elt.getAttribute("articleName")=="Length" or elt.getAttribute("moby:articleName")=="Length"):
                 t=MobyInteger()
-                t.fromMoby(elt.toxml())
+                t.fromMoby(elt)
                 self.Length=t.content
             if elt.nodeType==elt.ELEMENT_NODE and (elt.nodeName=="String" or elt.nodeName=="moby:String") and (elt.getAttribute("articleName")=="SequenceString" or elt.getAttribute("moby:articleName")=="SequenceString"):
                 t=MobyString()
-                t.fromMoby(elt.toxml())
+                t.fromMoby(elt)
                 self.SequenceString=t.content
\ No newline at end of file

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/ontology/DNASequenceWithGFFFeatures.py,v
retrieving revision 1.4
retrieving revision 1.5
diff -u -r1.4 -r1.5
--- /home/repository/moby/moby-live/Python/bioMoby/ontology/DNASequenceWithGFFFeatures.py	2005/02/01 08:52:15	1.4
+++ /home/repository/moby/moby-live/Python/bioMoby/ontology/DNASequenceWithGFFFeatures.py	2005/02/01 14:20:44	1.5
@@ -31,7 +31,9 @@
         """ Load the attributes from an XML string
         """
         from bioMoby.mobyMarshal import MobyUnmarshaller
-        doc=parseString(value).firstChild
+        doc=value
+        if isinstance(value, str):
+            doc=parseString(value).firstChild
         um=MobyUnmarshaller()
         self.content=""
         self.namespace=doc.getAttribute("moby:namespace")
@@ -52,15 +54,15 @@
             if elt.nodeName=="CrossReference" or elt.nodeName=="moby:CrossReference":
                 self.__cross__=[]
                 for ref in elt.childNodes:
-                    self.__cross__.append(ref.toxml())
+                    self.__cross__.append(um.loads(ref))
             if elt.nodeType==elt.ELEMENT_NODE and (elt.nodeName=="Integer" or elt.nodeName=="moby:Integer") and (elt.getAttribute("articleName")=="Length" or elt.getAttribute("moby:articleName")=="Length"):
                 t=MobyInteger()
-                t.fromMoby(elt.toxml())
+                t.fromMoby(elt)
                 self.Length=t.content
             if elt.nodeType==elt.ELEMENT_NODE and (elt.nodeName=="String" or elt.nodeName=="moby:String") and (elt.getAttribute("articleName")=="SequenceString" or elt.getAttribute("moby:articleName")=="SequenceString"):
                 t=MobyString()
-                t.fromMoby(elt.toxml())
+                t.fromMoby(elt)
                 self.SequenceString=t.content
             if elt.nodeType==elt.ELEMENT_NODE and (elt.nodeName=="BasicGFFSequenceFeature" or elt.nodeName=="moby:BasicGFFSequenceFeature") and (elt.getAttribute("articleName")=="DNASequenceWithGFFFeatures" or elt.getAttribute("moby:articleName")=="DNASequenceWithGFFFeatures"):
                 self.DNASequenceWithGFFFeatures=MobyBasicGFFSequenceFeature()
-                self.DNASequenceWithGFFFeatures.fromMoby(elt.toxml())
\ No newline at end of file
+                self.DNASequenceWithGFFFeatures.fromMoby(elt)
\ No newline at end of file

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/ontology/DateTime.py,v
retrieving revision 1.4
retrieving revision 1.5
diff -u -r1.4 -r1.5
--- /home/repository/moby/moby-live/Python/bioMoby/ontology/DateTime.py	2005/02/01 08:52:15	1.4
+++ /home/repository/moby/moby-live/Python/bioMoby/ontology/DateTime.py	2005/02/01 14:20:44	1.5
@@ -26,7 +26,9 @@
         """ Load the attributes from an XML string
         """
         from bioMoby.mobyMarshal import MobyUnmarshaller
-        doc=parseString(value).firstChild
+        doc=value
+        if isinstance(value, str):
+            doc=parseString(value).firstChild
         um=MobyUnmarshaller()
         self.content=""
         self.namespace=doc.getAttribute("moby:namespace")
@@ -46,4 +48,4 @@
             if elt.nodeName=="CrossReference" or elt.nodeName=="moby:CrossReference":
                 self.__cross__=[]
                 for ref in elt.childNodes:
-                    self.__cross__.append(ref.toxml())
\ No newline at end of file
+                    self.__cross__.append(um.loads(ref))
\ No newline at end of file

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/ontology/Decypher_Text.py,v
retrieving revision 1.4
retrieving revision 1.5
diff -u -r1.4 -r1.5
--- /home/repository/moby/moby-live/Python/bioMoby/ontology/Decypher_Text.py	2005/02/01 08:52:15	1.4
+++ /home/repository/moby/moby-live/Python/bioMoby/ontology/Decypher_Text.py	2005/02/01 14:20:44	1.5
@@ -26,7 +26,9 @@
         """ Load the attributes from an XML string
         """
         from bioMoby.mobyMarshal import MobyUnmarshaller
-        doc=parseString(value).firstChild
+        doc=value
+        if isinstance(value, str):
+            doc=parseString(value).firstChild
         um=MobyUnmarshaller()
         self.content=""
         self.namespace=doc.getAttribute("moby:namespace")
@@ -46,4 +48,4 @@
             if elt.nodeName=="CrossReference" or elt.nodeName=="moby:CrossReference":
                 self.__cross__=[]
                 for ref in elt.childNodes:
-                    self.__cross__.append(ref.toxml())
\ No newline at end of file
+                    self.__cross__.append(um.loads(ref))
\ No newline at end of file

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/ontology/Edge.py,v
retrieving revision 1.4
retrieving revision 1.5
diff -u -r1.4 -r1.5
--- /home/repository/moby/moby-live/Python/bioMoby/ontology/Edge.py	2005/02/01 08:52:15	1.4
+++ /home/repository/moby/moby-live/Python/bioMoby/ontology/Edge.py	2005/02/01 14:20:44	1.5
@@ -29,7 +29,9 @@
         """ Load the attributes from an XML string
         """
         from bioMoby.mobyMarshal import MobyUnmarshaller
-        doc=parseString(value).firstChild
+        doc=value
+        if isinstance(value, str):
+            doc=parseString(value).firstChild
         um=MobyUnmarshaller()
         self.content=""
         self.namespace=doc.getAttribute("moby:namespace")
@@ -49,12 +51,12 @@
             if elt.nodeName=="CrossReference" or elt.nodeName=="moby:CrossReference":
                 self.__cross__=[]
                 for ref in elt.childNodes:
-                    self.__cross__.append(ref.toxml())
+                    self.__cross__.append(um.loads(ref))
             if elt.nodeType==elt.ELEMENT_NODE and (elt.nodeName=="String" or elt.nodeName=="moby:String") and (elt.getAttribute("articleName")=="partner" or elt.getAttribute("moby:articleName")=="partner"):
                 t=MobyString()
-                t.fromMoby(elt.toxml())
+                t.fromMoby(elt)
                 self.Partner=t.content
             if elt.nodeType==elt.ELEMENT_NODE and (elt.nodeName=="Integer" or elt.nodeName=="moby:Integer") and (elt.getAttribute("articleName")=="direction" or elt.getAttribute("moby:articleName")=="direction"):
                 t=MobyInteger()
-                t.fromMoby(elt.toxml())
+                t.fromMoby(elt)
                 self.Direction=t.content
\ No newline at end of file

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/ontology/EmblFlatfile.py,v
retrieving revision 1.4
retrieving revision 1.5
diff -u -r1.4 -r1.5
--- /home/repository/moby/moby-live/Python/bioMoby/ontology/EmblFlatfile.py	2005/02/01 08:52:15	1.4
+++ /home/repository/moby/moby-live/Python/bioMoby/ontology/EmblFlatfile.py	2005/02/01 14:20:44	1.5
@@ -26,7 +26,9 @@
         """ Load the attributes from an XML string
         """
         from bioMoby.mobyMarshal import MobyUnmarshaller
-        doc=parseString(value).firstChild
+        doc=value
+        if isinstance(value, str):
+            doc=parseString(value).firstChild
         um=MobyUnmarshaller()
         self.content=""
         self.namespace=doc.getAttribute("moby:namespace")
@@ -46,4 +48,4 @@
             if elt.nodeName=="CrossReference" or elt.nodeName=="moby:CrossReference":
                 self.__cross__=[]
                 for ref in elt.childNodes:
-                    self.__cross__.append(ref.toxml())
\ No newline at end of file
+                    self.__cross__.append(um.loads(ref))
\ No newline at end of file

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/ontology/FASTA.py,v
retrieving revision 1.4
retrieving revision 1.5
diff -u -r1.4 -r1.5
--- /home/repository/moby/moby-live/Python/bioMoby/ontology/FASTA.py	2005/02/01 08:52:15	1.4
+++ /home/repository/moby/moby-live/Python/bioMoby/ontology/FASTA.py	2005/02/01 14:20:44	1.5
@@ -26,7 +26,9 @@
         """ Load the attributes from an XML string
         """
         from bioMoby.mobyMarshal import MobyUnmarshaller
-        doc=parseString(value).firstChild
+        doc=value
+        if isinstance(value, str):
+            doc=parseString(value).firstChild
         um=MobyUnmarshaller()
         self.content=""
         self.namespace=doc.getAttribute("moby:namespace")
@@ -46,4 +48,4 @@
             if elt.nodeName=="CrossReference" or elt.nodeName=="moby:CrossReference":
                 self.__cross__=[]
                 for ref in elt.childNodes:
-                    self.__cross__.append(ref.toxml())
\ No newline at end of file
+                    self.__cross__.append(um.loads(ref))
\ No newline at end of file

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/ontology/FASTA_AA.py,v
retrieving revision 1.4
retrieving revision 1.5
diff -u -r1.4 -r1.5
--- /home/repository/moby/moby-live/Python/bioMoby/ontology/FASTA_AA.py	2005/02/01 08:52:15	1.4
+++ /home/repository/moby/moby-live/Python/bioMoby/ontology/FASTA_AA.py	2005/02/01 14:20:44	1.5
@@ -26,7 +26,9 @@
         """ Load the attributes from an XML string
         """
         from bioMoby.mobyMarshal import MobyUnmarshaller
-        doc=parseString(value).firstChild
+        doc=value
+        if isinstance(value, str):
+            doc=parseString(value).firstChild
         um=MobyUnmarshaller()
         self.content=""
         self.namespace=doc.getAttribute("moby:namespace")
@@ -46,4 +48,4 @@
             if elt.nodeName=="CrossReference" or elt.nodeName=="moby:CrossReference":
                 self.__cross__=[]
                 for ref in elt.childNodes:
-                    self.__cross__.append(ref.toxml())
\ No newline at end of file
+                    self.__cross__.append(um.loads(ref))
\ No newline at end of file

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/ontology/FASTA_NA.py,v
retrieving revision 1.4
retrieving revision 1.5
diff -u -r1.4 -r1.5
--- /home/repository/moby/moby-live/Python/bioMoby/ontology/FASTA_NA.py	2005/02/01 08:52:15	1.4
+++ /home/repository/moby/moby-live/Python/bioMoby/ontology/FASTA_NA.py	2005/02/01 14:20:44	1.5
@@ -26,7 +26,9 @@
         """ Load the attributes from an XML string
         """
         from bioMoby.mobyMarshal import MobyUnmarshaller
-        doc=parseString(value).firstChild
+        doc=value
+        if isinstance(value, str):
+            doc=parseString(value).firstChild
         um=MobyUnmarshaller()
         self.content=""
         self.namespace=doc.getAttribute("moby:namespace")
@@ -46,4 +48,4 @@
             if elt.nodeName=="CrossReference" or elt.nodeName=="moby:CrossReference":
                 self.__cross__=[]
                 for ref in elt.childNodes:
-                    self.__cross__.append(ref.toxml())
\ No newline at end of file
+                    self.__cross__.append(um.loads(ref))
\ No newline at end of file

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/ontology/FASTA_Text.py,v
retrieving revision 1.4
retrieving revision 1.5
diff -u -r1.4 -r1.5
--- /home/repository/moby/moby-live/Python/bioMoby/ontology/FASTA_Text.py	2005/02/01 08:52:15	1.4
+++ /home/repository/moby/moby-live/Python/bioMoby/ontology/FASTA_Text.py	2005/02/01 14:20:44	1.5
@@ -26,7 +26,9 @@
         """ Load the attributes from an XML string
         """
         from bioMoby.mobyMarshal import MobyUnmarshaller
-        doc=parseString(value).firstChild
+        doc=value
+        if isinstance(value, str):
+            doc=parseString(value).firstChild
         um=MobyUnmarshaller()
         self.content=""
         self.namespace=doc.getAttribute("moby:namespace")
@@ -46,4 +48,4 @@
             if elt.nodeName=="CrossReference" or elt.nodeName=="moby:CrossReference":
                 self.__cross__=[]
                 for ref in elt.childNodes:
-                    self.__cross__.append(ref.toxml())
\ No newline at end of file
+                    self.__cross__.append(um.loads(ref))
\ No newline at end of file

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/ontology/GFF.py,v
retrieving revision 1.4
retrieving revision 1.5
diff -u -r1.4 -r1.5
--- /home/repository/moby/moby-live/Python/bioMoby/ontology/GFF.py	2005/02/01 08:52:15	1.4
+++ /home/repository/moby/moby-live/Python/bioMoby/ontology/GFF.py	2005/02/01 14:20:44	1.5
@@ -26,7 +26,9 @@
         """ Load the attributes from an XML string
         """
         from bioMoby.mobyMarshal import MobyUnmarshaller
-        doc=parseString(value).firstChild
+        doc=value
+        if isinstance(value, str):
+            doc=parseString(value).firstChild
         um=MobyUnmarshaller()
         self.content=""
         self.namespace=doc.getAttribute("moby:namespace")
@@ -46,4 +48,4 @@
             if elt.nodeName=="CrossReference" or elt.nodeName=="moby:CrossReference":
                 self.__cross__=[]
                 for ref in elt.childNodes:
-                    self.__cross__.append(ref.toxml())
\ No newline at end of file
+                    self.__cross__.append(um.loads(ref))
\ No newline at end of file

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/ontology/GFF1.py,v
retrieving revision 1.4
retrieving revision 1.5
diff -u -r1.4 -r1.5
--- /home/repository/moby/moby-live/Python/bioMoby/ontology/GFF1.py	2005/02/01 08:52:15	1.4
+++ /home/repository/moby/moby-live/Python/bioMoby/ontology/GFF1.py	2005/02/01 14:20:44	1.5
@@ -26,7 +26,9 @@
         """ Load the attributes from an XML string
         """
         from bioMoby.mobyMarshal import MobyUnmarshaller
-        doc=parseString(value).firstChild
+        doc=value
+        if isinstance(value, str):
+            doc=parseString(value).firstChild
         um=MobyUnmarshaller()
         self.content=""
         self.namespace=doc.getAttribute("moby:namespace")
@@ -46,4 +48,4 @@
             if elt.nodeName=="CrossReference" or elt.nodeName=="moby:CrossReference":
                 self.__cross__=[]
                 for ref in elt.childNodes:
-                    self.__cross__.append(ref.toxml())
\ No newline at end of file
+                    self.__cross__.append(um.loads(ref))
\ No newline at end of file

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/ontology/GFF2.py,v
retrieving revision 1.4
retrieving revision 1.5
diff -u -r1.4 -r1.5
--- /home/repository/moby/moby-live/Python/bioMoby/ontology/GFF2.py	2005/02/01 08:52:15	1.4
+++ /home/repository/moby/moby-live/Python/bioMoby/ontology/GFF2.py	2005/02/01 14:20:44	1.5
@@ -26,7 +26,9 @@
         """ Load the attributes from an XML string
         """
         from bioMoby.mobyMarshal import MobyUnmarshaller
-        doc=parseString(value).firstChild
+        doc=value
+        if isinstance(value, str):
+            doc=parseString(value).firstChild
         um=MobyUnmarshaller()
         self.content=""
         self.namespace=doc.getAttribute("moby:namespace")
@@ -46,4 +48,4 @@
             if elt.nodeName=="CrossReference" or elt.nodeName=="moby:CrossReference":
                 self.__cross__=[]
                 for ref in elt.childNodes:
-                    self.__cross__.append(ref.toxml())
\ No newline at end of file
+                    self.__cross__.append(um.loads(ref))
\ No newline at end of file

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/ontology/GFF2_5.py,v
retrieving revision 1.4
retrieving revision 1.5
diff -u -r1.4 -r1.5
--- /home/repository/moby/moby-live/Python/bioMoby/ontology/GFF2_5.py	2005/02/01 08:52:15	1.4
+++ /home/repository/moby/moby-live/Python/bioMoby/ontology/GFF2_5.py	2005/02/01 14:20:44	1.5
@@ -26,7 +26,9 @@
         """ Load the attributes from an XML string
         """
         from bioMoby.mobyMarshal import MobyUnmarshaller
-        doc=parseString(value).firstChild
+        doc=value
+        if isinstance(value, str):
+            doc=parseString(value).firstChild
         um=MobyUnmarshaller()
         self.content=""
         self.namespace=doc.getAttribute("moby:namespace")
@@ -46,4 +48,4 @@
             if elt.nodeName=="CrossReference" or elt.nodeName=="moby:CrossReference":
                 self.__cross__=[]
                 for ref in elt.childNodes:
-                    self.__cross__.append(ref.toxml())
\ No newline at end of file
+                    self.__cross__.append(um.loads(ref))
\ No newline at end of file

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/ontology/GFF3.py,v
retrieving revision 1.4
retrieving revision 1.5
diff -u -r1.4 -r1.5
--- /home/repository/moby/moby-live/Python/bioMoby/ontology/GFF3.py	2005/02/01 08:52:15	1.4
+++ /home/repository/moby/moby-live/Python/bioMoby/ontology/GFF3.py	2005/02/01 14:20:44	1.5
@@ -26,7 +26,9 @@
         """ Load the attributes from an XML string
         """
         from bioMoby.mobyMarshal import MobyUnmarshaller
-        doc=parseString(value).firstChild
+        doc=value
+        if isinstance(value, str):
+            doc=parseString(value).firstChild
         um=MobyUnmarshaller()
         self.content=""
         self.namespace=doc.getAttribute("moby:namespace")
@@ -46,4 +48,4 @@
             if elt.nodeName=="CrossReference" or elt.nodeName=="moby:CrossReference":
                 self.__cross__=[]
                 for ref in elt.childNodes:
-                    self.__cross__.append(ref.toxml())
\ No newline at end of file
+                    self.__cross__.append(um.loads(ref))
\ No newline at end of file

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/ontology/GO_Term.py,v
retrieving revision 1.4
retrieving revision 1.5
diff -u -r1.4 -r1.5
--- /home/repository/moby/moby-live/Python/bioMoby/ontology/GO_Term.py	2005/02/01 08:52:15	1.4
+++ /home/repository/moby/moby-live/Python/bioMoby/ontology/GO_Term.py	2005/02/01 14:20:44	1.5
@@ -28,7 +28,9 @@
         """ Load the attributes from an XML string
         """
         from bioMoby.mobyMarshal import MobyUnmarshaller
-        doc=parseString(value).firstChild
+        doc=value
+        if isinstance(value, str):
+            doc=parseString(value).firstChild
         um=MobyUnmarshaller()
         self.content=""
         self.namespace=doc.getAttribute("moby:namespace")
@@ -48,12 +50,12 @@
             if elt.nodeName=="CrossReference" or elt.nodeName=="moby:CrossReference":
                 self.__cross__=[]
                 for ref in elt.childNodes:
-                    self.__cross__.append(ref.toxml())
+                    self.__cross__.append(um.loads(ref))
             if elt.nodeType==elt.ELEMENT_NODE and (elt.nodeName=="String" or elt.nodeName=="moby:String") and (elt.getAttribute("articleName")=="Term" or elt.getAttribute("moby:articleName")=="Term"):
                 t=MobyString()
-                t.fromMoby(elt.toxml())
+                t.fromMoby(elt)
                 self.Term=t.content
             if elt.nodeType==elt.ELEMENT_NODE and (elt.nodeName=="String" or elt.nodeName=="moby:String") and (elt.getAttribute("articleName")=="Definition" or elt.getAttribute("moby:articleName")=="Definition"):
                 t=MobyString()
-                t.fromMoby(elt.toxml())
+                t.fromMoby(elt)
                 self.Definition=t.content
\ No newline at end of file

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/ontology/GenbankFlatfile.py,v
retrieving revision 1.4
retrieving revision 1.5
diff -u -r1.4 -r1.5
--- /home/repository/moby/moby-live/Python/bioMoby/ontology/GenbankFlatfile.py	2005/02/01 08:52:15	1.4
+++ /home/repository/moby/moby-live/Python/bioMoby/ontology/GenbankFlatfile.py	2005/02/01 14:20:44	1.5
@@ -26,7 +26,9 @@
         """ Load the attributes from an XML string
         """
         from bioMoby.mobyMarshal import MobyUnmarshaller
-        doc=parseString(value).firstChild
+        doc=value
+        if isinstance(value, str):
+            doc=parseString(value).firstChild
         um=MobyUnmarshaller()
         self.content=""
         self.namespace=doc.getAttribute("moby:namespace")
@@ -46,4 +48,4 @@
             if elt.nodeName=="CrossReference" or elt.nodeName=="moby:CrossReference":
                 self.__cross__=[]
                 for ref in elt.childNodes:
-                    self.__cross__.append(ref.toxml())
\ No newline at end of file
+                    self.__cross__.append(um.loads(ref))
\ No newline at end of file

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/ontology/GenericSequence.py,v
retrieving revision 1.4
retrieving revision 1.5
diff -u -r1.4 -r1.5
--- /home/repository/moby/moby-live/Python/bioMoby/ontology/GenericSequence.py	2005/02/01 08:52:15	1.4
+++ /home/repository/moby/moby-live/Python/bioMoby/ontology/GenericSequence.py	2005/02/01 14:20:44	1.5
@@ -29,7 +29,9 @@
         """ Load the attributes from an XML string
         """
         from bioMoby.mobyMarshal import MobyUnmarshaller
-        doc=parseString(value).firstChild
+        doc=value
+        if isinstance(value, str):
+            doc=parseString(value).firstChild
         um=MobyUnmarshaller()
         self.content=""
         self.namespace=doc.getAttribute("moby:namespace")
@@ -49,12 +51,12 @@
             if elt.nodeName=="CrossReference" or elt.nodeName=="moby:CrossReference":
                 self.__cross__=[]
                 for ref in elt.childNodes:
-                    self.__cross__.append(ref.toxml())
+                    self.__cross__.append(um.loads(ref))
             if elt.nodeType==elt.ELEMENT_NODE and (elt.nodeName=="Integer" or elt.nodeName=="moby:Integer") and (elt.getAttribute("articleName")=="Length" or elt.getAttribute("moby:articleName")=="Length"):
                 t=MobyInteger()
-                t.fromMoby(elt.toxml())
+                t.fromMoby(elt)
                 self.Length=t.content
             if elt.nodeType==elt.ELEMENT_NODE and (elt.nodeName=="String" or elt.nodeName=="moby:String") and (elt.getAttribute("articleName")=="SequenceString" or elt.getAttribute("moby:articleName")=="SequenceString"):
                 t=MobyString()
-                t.fromMoby(elt.toxml())
+                t.fromMoby(elt)
                 self.SequenceString=t.content
\ No newline at end of file

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/ontology/GeneticElement.py,v
retrieving revision 1.4
retrieving revision 1.5
diff -u -r1.4 -r1.5
--- /home/repository/moby/moby-live/Python/bioMoby/ontology/GeneticElement.py	2005/02/01 08:52:15	1.4
+++ /home/repository/moby/moby-live/Python/bioMoby/ontology/GeneticElement.py	2005/02/01 14:20:44	1.5
@@ -27,7 +27,9 @@
         """ Load the attributes from an XML string
         """
         from bioMoby.mobyMarshal import MobyUnmarshaller
-        doc=parseString(value).firstChild
+        doc=value
+        if isinstance(value, str):
+            doc=parseString(value).firstChild
         um=MobyUnmarshaller()
         self.content=""
         self.namespace=doc.getAttribute("moby:namespace")
@@ -47,8 +49,8 @@
             if elt.nodeName=="CrossReference" or elt.nodeName=="moby:CrossReference":
                 self.__cross__=[]
                 for ref in elt.childNodes:
-                    self.__cross__.append(ref.toxml())
+                    self.__cross__.append(um.loads(ref))
             if elt.nodeType==elt.ELEMENT_NODE and (elt.nodeName=="String" or elt.nodeName=="moby:String") and (elt.getAttribute("articleName")=="GeneticElement" or elt.getAttribute("moby:articleName")=="GeneticElement"):
                 t=MobyString()
-                t.fromMoby(elt.toxml())
+                t.fromMoby(elt)
                 self.GeneticElement=t.content
\ No newline at end of file

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/ontology/Genotype.py,v
retrieving revision 1.4
retrieving revision 1.5
diff -u -r1.4 -r1.5
--- /home/repository/moby/moby-live/Python/bioMoby/ontology/Genotype.py	2005/02/01 08:52:15	1.4
+++ /home/repository/moby/moby-live/Python/bioMoby/ontology/Genotype.py	2005/02/01 14:20:44	1.5
@@ -29,7 +29,9 @@
         """ Load the attributes from an XML string
         """
         from bioMoby.mobyMarshal import MobyUnmarshaller
-        doc=parseString(value).firstChild
+        doc=value
+        if isinstance(value, str):
+            doc=parseString(value).firstChild
         um=MobyUnmarshaller()
         self.content=""
         self.namespace=doc.getAttribute("moby:namespace")
@@ -49,16 +51,16 @@
             if elt.nodeName=="CrossReference" or elt.nodeName=="moby:CrossReference":
                 self.__cross__=[]
                 for ref in elt.childNodes:
-                    self.__cross__.append(ref.toxml())
+                    self.__cross__.append(um.loads(ref))
             if elt.nodeType==elt.ELEMENT_NODE and (elt.nodeName=="String" or elt.nodeName=="moby:String") and (elt.getAttribute("articleName")=="snp" or elt.getAttribute("moby:articleName")=="snp"):
                 t=MobyString()
-                t.fromMoby(elt.toxml())
+                t.fromMoby(elt)
                 self.Snp=t.content
             if elt.nodeType==elt.ELEMENT_NODE and (elt.nodeName=="String" or elt.nodeName=="moby:String") and (elt.getAttribute("articleName")=="sample" or elt.getAttribute("moby:articleName")=="sample"):
                 t=MobyString()
-                t.fromMoby(elt.toxml())
+                t.fromMoby(elt)
                 self.Sample=t.content
             if elt.nodeType==elt.ELEMENT_NODE and (elt.nodeName=="String" or elt.nodeName=="moby:String") and (elt.getAttribute("articleName")=="result" or elt.getAttribute("moby:articleName")=="result"):
                 t=MobyString()
-                t.fromMoby(elt.toxml())
+                t.fromMoby(elt)
                 self.Result=t.content
\ No newline at end of file

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/ontology/Germplasm_Details.py,v
retrieving revision 1.4
retrieving revision 1.5
diff -u -r1.4 -r1.5
--- /home/repository/moby/moby-live/Python/bioMoby/ontology/Germplasm_Details.py	2005/02/01 08:52:15	1.4
+++ /home/repository/moby/moby-live/Python/bioMoby/ontology/Germplasm_Details.py	2005/02/01 14:20:44	1.5
@@ -35,7 +35,9 @@
         """ Load the attributes from an XML string
         """
         from bioMoby.mobyMarshal import MobyUnmarshaller
-        doc=parseString(value).firstChild
+        doc=value
+        if isinstance(value, str):
+            doc=parseString(value).firstChild
         um=MobyUnmarshaller()
         self.content=""
         self.namespace=doc.getAttribute("moby:namespace")
@@ -55,36 +57,36 @@
             if elt.nodeName=="CrossReference" or elt.nodeName=="moby:CrossReference":
                 self.__cross__=[]
                 for ref in elt.childNodes:
-                    self.__cross__.append(ref.toxml())
+                    self.__cross__.append(um.loads(ref))
             if elt.nodeType==elt.ELEMENT_NODE and (elt.nodeName=="Integer" or elt.nodeName=="moby:Integer") and (elt.getAttribute("articleName")=="date" or elt.getAttribute("moby:articleName")=="date"):
                 t=MobyInteger()
-                t.fromMoby(elt.toxml())
+                t.fromMoby(elt)
                 self.Date=t.content
             if elt.nodeType==elt.ELEMENT_NODE and (elt.nodeName=="String" or elt.nodeName=="moby:String") and (elt.getAttribute("articleName")=="country" or elt.getAttribute("moby:articleName")=="country"):
                 t=MobyString()
-                t.fromMoby(elt.toxml())
+                t.fromMoby(elt)
                 self.Country=t.content
             if elt.nodeType==elt.ELEMENT_NODE and (elt.nodeName=="String" or elt.nodeName=="moby:String") and (elt.getAttribute("articleName")=="prefered_name" or elt.getAttribute("moby:articleName")=="prefered_name"):
                 t=MobyString()
-                t.fromMoby(elt.toxml())
+                t.fromMoby(elt)
                 self.Prefered_name=t.content
             if elt.nodeType==elt.ELEMENT_NODE and (elt.nodeName=="String" or elt.nodeName=="moby:String") and (elt.getAttribute("articleName")=="alternative_names" or elt.getAttribute("moby:articleName")=="alternative_names"):
                 t=MobyString()
-                t.fromMoby(elt.toxml())
+                t.fromMoby(elt)
                 self.Alternative_names=t.content
             if elt.nodeType==elt.ELEMENT_NODE and (elt.nodeName=="String" or elt.nodeName=="moby:String") and (elt.getAttribute("articleName")=="name_type" or elt.getAttribute("moby:articleName")=="name_type"):
                 t=MobyString()
-                t.fromMoby(elt.toxml())
+                t.fromMoby(elt)
                 self.Name_type=t.content
             if elt.nodeType==elt.ELEMENT_NODE and (elt.nodeName=="String" or elt.nodeName=="moby:String") and (elt.getAttribute("articleName")=="method" or elt.getAttribute("moby:articleName")=="method"):
                 t=MobyString()
-                t.fromMoby(elt.toxml())
+                t.fromMoby(elt)
                 self.Method=t.content
             if elt.nodeType==elt.ELEMENT_NODE and (elt.nodeName=="String" or elt.nodeName=="moby:String") and (elt.getAttribute("articleName")=="location" or elt.getAttribute("moby:articleName")=="location"):
                 t=MobyString()
-                t.fromMoby(elt.toxml())
+                t.fromMoby(elt)
                 self.Location=t.content
             if elt.nodeType==elt.ELEMENT_NODE and (elt.nodeName=="Integer" or elt.nodeName=="moby:Integer") and (elt.getAttribute("articleName")=="germplasm_id" or elt.getAttribute("moby:articleName")=="germplasm_id"):
                 t=MobyInteger()
-                t.fromMoby(elt.toxml())
+                t.fromMoby(elt)
                 self.Germplasm_id=t.content
\ No newline at end of file

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/ontology/Germplasm_List.py,v
retrieving revision 1.4
retrieving revision 1.5
diff -u -r1.4 -r1.5
--- /home/repository/moby/moby-live/Python/bioMoby/ontology/Germplasm_List.py	2005/02/01 08:52:16	1.4
+++ /home/repository/moby/moby-live/Python/bioMoby/ontology/Germplasm_List.py	2005/02/01 14:20:44	1.5
@@ -35,7 +35,9 @@
         """ Load the attributes from an XML string
         """
         from bioMoby.mobyMarshal import MobyUnmarshaller
-        doc=parseString(value).firstChild
+        doc=value
+        if isinstance(value, str):
+            doc=parseString(value).firstChild
         um=MobyUnmarshaller()
         self.content=""
         self.namespace=doc.getAttribute("moby:namespace")
@@ -55,36 +57,36 @@
             if elt.nodeName=="CrossReference" or elt.nodeName=="moby:CrossReference":
                 self.__cross__=[]
                 for ref in elt.childNodes:
-                    self.__cross__.append(ref.toxml())
+                    self.__cross__.append(um.loads(ref))
             if elt.nodeType==elt.ELEMENT_NODE and (elt.nodeName=="Integer" or elt.nodeName=="moby:Integer") and (elt.getAttribute("articleName")=="germplasm_id" or elt.getAttribute("moby:articleName")=="germplasm_id"):
                 t=MobyInteger()
-                t.fromMoby(elt.toxml())
+                t.fromMoby(elt)
                 self.Germplasm_id=t.content
             if elt.nodeType==elt.ELEMENT_NODE and (elt.nodeName=="String" or elt.nodeName=="moby:String") and (elt.getAttribute("articleName")=="germplasm_name" or elt.getAttribute("moby:articleName")=="germplasm_name"):
                 t=MobyString()
-                t.fromMoby(elt.toxml())
+                t.fromMoby(elt)
                 self.Germplasm_name=t.content
             if elt.nodeType==elt.ELEMENT_NODE and (elt.nodeName=="String" or elt.nodeName=="moby:String") and (elt.getAttribute("articleName")=="trait_value" or elt.getAttribute("moby:articleName")=="trait_value"):
                 t=MobyString()
-                t.fromMoby(elt.toxml())
+                t.fromMoby(elt)
                 self.Trait_value=t.content
             if elt.nodeType==elt.ELEMENT_NODE and (elt.nodeName=="Integer" or elt.nodeName=="moby:Integer") and (elt.getAttribute("articleName")=="trait_id" or elt.getAttribute("moby:articleName")=="trait_id"):
                 t=MobyInteger()
-                t.fromMoby(elt.toxml())
+                t.fromMoby(elt)
                 self.Trait_id=t.content
             if elt.nodeType==elt.ELEMENT_NODE and (elt.nodeName=="String" or elt.nodeName=="moby:String") and (elt.getAttribute("articleName")=="scale" or elt.getAttribute("moby:articleName")=="scale"):
                 t=MobyString()
-                t.fromMoby(elt.toxml())
+                t.fromMoby(elt)
                 self.Scale=t.content
             if elt.nodeType==elt.ELEMENT_NODE and (elt.nodeName=="String" or elt.nodeName=="moby:String") and (elt.getAttribute("articleName")=="scale_desc" or elt.getAttribute("moby:articleName")=="scale_desc"):
                 t=MobyString()
-                t.fromMoby(elt.toxml())
+                t.fromMoby(elt)
                 self.Scale_desc=t.content
             if elt.nodeType==elt.ELEMENT_NODE and (elt.nodeName=="String" or elt.nodeName=="moby:String") and (elt.getAttribute("articleName")=="method" or elt.getAttribute("moby:articleName")=="method"):
                 t=MobyString()
-                t.fromMoby(elt.toxml())
+                t.fromMoby(elt)
                 self.Method=t.content
             if elt.nodeType==elt.ELEMENT_NODE and (elt.nodeName=="String" or elt.nodeName=="moby:String") and (elt.getAttribute("articleName")=="study_id" or elt.getAttribute("moby:articleName")=="study_id"):
                 t=MobyString()
-                t.fromMoby(elt.toxml())
+                t.fromMoby(elt)
                 self.Study_id=t.content
\ No newline at end of file

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/ontology/Global_Keyword.py,v
retrieving revision 1.4
retrieving revision 1.5
diff -u -r1.4 -r1.5
--- /home/repository/moby/moby-live/Python/bioMoby/ontology/Global_Keyword.py	2005/02/01 08:52:16	1.4
+++ /home/repository/moby/moby-live/Python/bioMoby/ontology/Global_Keyword.py	2005/02/01 14:20:44	1.5
@@ -25,7 +25,9 @@
         """ Load the attributes from an XML string
         """
         from bioMoby.mobyMarshal import MobyUnmarshaller
-        doc=parseString(value).firstChild
+        doc=value
+        if isinstance(value, str):
+            doc=parseString(value).firstChild
         um=MobyUnmarshaller()
         self.content=""
         self.namespace=doc.getAttribute("moby:namespace")
@@ -45,4 +47,4 @@
             if elt.nodeName=="CrossReference" or elt.nodeName=="moby:CrossReference":
                 self.__cross__=[]
                 for ref in elt.childNodes:
-                    self.__cross__.append(ref.toxml())
\ No newline at end of file
+                    self.__cross__.append(um.loads(ref))
\ No newline at end of file

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/ontology/HBond_Pair.py,v
retrieving revision 1.4
retrieving revision 1.5
diff -u -r1.4 -r1.5
--- /home/repository/moby/moby-live/Python/bioMoby/ontology/HBond_Pair.py	2005/02/01 08:52:16	1.4
+++ /home/repository/moby/moby-live/Python/bioMoby/ontology/HBond_Pair.py	2005/02/01 14:20:44	1.5
@@ -29,7 +29,9 @@
         """ Load the attributes from an XML string
         """
         from bioMoby.mobyMarshal import MobyUnmarshaller
-        doc=parseString(value).firstChild
+        doc=value
+        if isinstance(value, str):
+            doc=parseString(value).firstChild
         um=MobyUnmarshaller()
         self.content=""
         self.namespace=doc.getAttribute("moby:namespace")
@@ -49,16 +51,16 @@
             if elt.nodeName=="CrossReference" or elt.nodeName=="moby:CrossReference":
                 self.__cross__=[]
                 for ref in elt.childNodes:
-                    self.__cross__.append(ref.toxml())
+                    self.__cross__.append(um.loads(ref))
             if elt.nodeType==elt.ELEMENT_NODE and (elt.nodeName=="String" or elt.nodeName=="moby:String") and (elt.getAttribute("articleName")=="A" or elt.getAttribute("moby:articleName")=="A"):
                 t=MobyString()
-                t.fromMoby(elt.toxml())
+                t.fromMoby(elt)
                 self.A=t.content
             if elt.nodeType==elt.ELEMENT_NODE and (elt.nodeName=="String" or elt.nodeName=="moby:String") and (elt.getAttribute("articleName")=="H" or elt.getAttribute("moby:articleName")=="H"):
                 t=MobyString()
-                t.fromMoby(elt.toxml())
+                t.fromMoby(elt)
                 self.H=t.content
             if elt.nodeType==elt.ELEMENT_NODE and (elt.nodeName=="String" or elt.nodeName=="moby:String") and (elt.getAttribute("articleName")=="D" or elt.getAttribute("moby:articleName")=="D"):
                 t=MobyString()
-                t.fromMoby(elt.toxml())
+                t.fromMoby(elt)
                 self.D=t.content
\ No newline at end of file

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/ontology/HFormatText.py,v
retrieving revision 1.4
retrieving revision 1.5
diff -u -r1.4 -r1.5
--- /home/repository/moby/moby-live/Python/bioMoby/ontology/HFormatText.py	2005/02/01 08:52:16	1.4
+++ /home/repository/moby/moby-live/Python/bioMoby/ontology/HFormatText.py	2005/02/01 14:20:44	1.5
@@ -26,7 +26,9 @@
         """ Load the attributes from an XML string
         """
         from bioMoby.mobyMarshal import MobyUnmarshaller
-        doc=parseString(value).firstChild
+        doc=value
+        if isinstance(value, str):
+            doc=parseString(value).firstChild
         um=MobyUnmarshaller()
         self.content=""
         self.namespace=doc.getAttribute("moby:namespace")
@@ -46,4 +48,4 @@
             if elt.nodeName=="CrossReference" or elt.nodeName=="moby:CrossReference":
                 self.__cross__=[]
                 for ref in elt.childNodes:
-                    self.__cross__.append(ref.toxml())
\ No newline at end of file
+                    self.__cross__.append(um.loads(ref))
\ No newline at end of file

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/ontology/Haplotyping_Study_obj.py,v
retrieving revision 1.4
retrieving revision 1.5
diff -u -r1.4 -r1.5
--- /home/repository/moby/moby-live/Python/bioMoby/ontology/Haplotyping_Study_obj.py	2005/02/01 08:52:16	1.4
+++ /home/repository/moby/moby-live/Python/bioMoby/ontology/Haplotyping_Study_obj.py	2005/02/01 14:20:44	1.5
@@ -25,7 +25,9 @@
         """ Load the attributes from an XML string
         """
         from bioMoby.mobyMarshal import MobyUnmarshaller
-        doc=parseString(value).firstChild
+        doc=value
+        if isinstance(value, str):
+            doc=parseString(value).firstChild
         um=MobyUnmarshaller()
         self.content=""
         self.namespace=doc.getAttribute("moby:namespace")
@@ -45,4 +47,4 @@
             if elt.nodeName=="CrossReference" or elt.nodeName=="moby:CrossReference":
                 self.__cross__=[]
                 for ref in elt.childNodes:
-                    self.__cross__.append(ref.toxml())
\ No newline at end of file
+                    self.__cross__.append(um.loads(ref))
\ No newline at end of file

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/ontology/ICIS_Query.py,v
retrieving revision 1.4
retrieving revision 1.5
diff -u -r1.4 -r1.5
--- /home/repository/moby/moby-live/Python/bioMoby/ontology/ICIS_Query.py	2005/02/01 08:52:16	1.4
+++ /home/repository/moby/moby-live/Python/bioMoby/ontology/ICIS_Query.py	2005/02/01 14:20:44	1.5
@@ -30,7 +30,9 @@
         """ Load the attributes from an XML string
         """
         from bioMoby.mobyMarshal import MobyUnmarshaller
-        doc=parseString(value).firstChild
+        doc=value
+        if isinstance(value, str):
+            doc=parseString(value).firstChild
         um=MobyUnmarshaller()
         self.content=""
         self.namespace=doc.getAttribute("moby:namespace")
@@ -50,16 +52,16 @@
             if elt.nodeName=="CrossReference" or elt.nodeName=="moby:CrossReference":
                 self.__cross__=[]
                 for ref in elt.childNodes:
-                    self.__cross__.append(ref.toxml())
+                    self.__cross__.append(um.loads(ref))
             if elt.nodeType==elt.ELEMENT_NODE and (elt.nodeName=="Integer" or elt.nodeName=="moby:Integer") and (elt.getAttribute("articleName")=="end_row" or elt.getAttribute("moby:articleName")=="end_row"):
                 t=MobyInteger()
-                t.fromMoby(elt.toxml())
+                t.fromMoby(elt)
                 self.End_row=t.content
             if elt.nodeType==elt.ELEMENT_NODE and (elt.nodeName=="Integer" or elt.nodeName=="moby:Integer") and (elt.getAttribute("articleName")=="start_row" or elt.getAttribute("moby:articleName")=="start_row"):
                 t=MobyInteger()
-                t.fromMoby(elt.toxml())
+                t.fromMoby(elt)
                 self.Start_row=t.content
             if elt.nodeType==elt.ELEMENT_NODE and (elt.nodeName=="String" or elt.nodeName=="moby:String") and (elt.getAttribute("articleName")=="search_text" or elt.getAttribute("moby:articleName")=="search_text"):
                 t=MobyString()
-                t.fromMoby(elt.toxml())
+                t.fromMoby(elt)
                 self.Search_text=t.content
\ No newline at end of file

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/ontology/ICIS_Query2.py,v
retrieving revision 1.4
retrieving revision 1.5
diff -u -r1.4 -r1.5
--- /home/repository/moby/moby-live/Python/bioMoby/ontology/ICIS_Query2.py	2005/02/01 08:52:16	1.4
+++ /home/repository/moby/moby-live/Python/bioMoby/ontology/ICIS_Query2.py	2005/02/01 14:20:44	1.5
@@ -32,7 +32,9 @@
         """ Load the attributes from an XML string
         """
         from bioMoby.mobyMarshal import MobyUnmarshaller
-        doc=parseString(value).firstChild
+        doc=value
+        if isinstance(value, str):
+            doc=parseString(value).firstChild
         um=MobyUnmarshaller()
         self.content=""
         self.namespace=doc.getAttribute("moby:namespace")
@@ -52,24 +54,24 @@
             if elt.nodeName=="CrossReference" or elt.nodeName=="moby:CrossReference":
                 self.__cross__=[]
                 for ref in elt.childNodes:
-                    self.__cross__.append(ref.toxml())
+                    self.__cross__.append(um.loads(ref))
             if elt.nodeType==elt.ELEMENT_NODE and (elt.nodeName=="String" or elt.nodeName=="moby:String") and (elt.getAttribute("articleName")=="search_text1" or elt.getAttribute("moby:articleName")=="search_text1"):
                 t=MobyString()
-                t.fromMoby(elt.toxml())
+                t.fromMoby(elt)
                 self.Search_text1=t.content
             if elt.nodeType==elt.ELEMENT_NODE and (elt.nodeName=="String" or elt.nodeName=="moby:String") and (elt.getAttribute("articleName")=="search_text2" or elt.getAttribute("moby:articleName")=="search_text2"):
                 t=MobyString()
-                t.fromMoby(elt.toxml())
+                t.fromMoby(elt)
                 self.Search_text2=t.content
             if elt.nodeType==elt.ELEMENT_NODE and (elt.nodeName=="String" or elt.nodeName=="moby:String") and (elt.getAttribute("articleName")=="search_text3" or elt.getAttribute("moby:articleName")=="search_text3"):
                 t=MobyString()
-                t.fromMoby(elt.toxml())
+                t.fromMoby(elt)
                 self.Search_text3=t.content
             if elt.nodeType==elt.ELEMENT_NODE and (elt.nodeName=="Integer" or elt.nodeName=="moby:Integer") and (elt.getAttribute("articleName")=="start_row" or elt.getAttribute("moby:articleName")=="start_row"):
                 t=MobyInteger()
-                t.fromMoby(elt.toxml())
+                t.fromMoby(elt)
                 self.Start_row=t.content
             if elt.nodeType==elt.ELEMENT_NODE and (elt.nodeName=="Integer" or elt.nodeName=="moby:Integer") and (elt.getAttribute("articleName")=="end_row" or elt.getAttribute("moby:articleName")=="end_row"):
                 t=MobyInteger()
-                t.fromMoby(elt.toxml())
+                t.fromMoby(elt)
                 self.End_row=t.content
\ No newline at end of file

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/ontology/ICIS_Query3.py,v
retrieving revision 1.4
retrieving revision 1.5
diff -u -r1.4 -r1.5
--- /home/repository/moby/moby-live/Python/bioMoby/ontology/ICIS_Query3.py	2005/02/01 08:52:16	1.4
+++ /home/repository/moby/moby-live/Python/bioMoby/ontology/ICIS_Query3.py	2005/02/01 14:20:44	1.5
@@ -30,7 +30,9 @@
         """ Load the attributes from an XML string
         """
         from bioMoby.mobyMarshal import MobyUnmarshaller
-        doc=parseString(value).firstChild
+        doc=value
+        if isinstance(value, str):
+            doc=parseString(value).firstChild
         um=MobyUnmarshaller()
         self.content=""
         self.namespace=doc.getAttribute("moby:namespace")
@@ -50,20 +52,20 @@
             if elt.nodeName=="CrossReference" or elt.nodeName=="moby:CrossReference":
                 self.__cross__=[]
                 for ref in elt.childNodes:
-                    self.__cross__.append(ref.toxml())
+                    self.__cross__.append(um.loads(ref))
             if elt.nodeType==elt.ELEMENT_NODE and (elt.nodeName=="Integer" or elt.nodeName=="moby:Integer") and (elt.getAttribute("articleName")=="search_text1" or elt.getAttribute("moby:articleName")=="search_text1"):
                 t=MobyInteger()
-                t.fromMoby(elt.toxml())
+                t.fromMoby(elt)
                 self.Search_text1=t.content
             if elt.nodeType==elt.ELEMENT_NODE and (elt.nodeName=="Integer" or elt.nodeName=="moby:Integer") and (elt.getAttribute("articleName")=="search_text2" or elt.getAttribute("moby:articleName")=="search_text2"):
                 t=MobyInteger()
-                t.fromMoby(elt.toxml())
+                t.fromMoby(elt)
                 self.Search_text2=t.content
             if elt.nodeType==elt.ELEMENT_NODE and (elt.nodeName=="Integer" or elt.nodeName=="moby:Integer") and (elt.getAttribute("articleName")=="start_row" or elt.getAttribute("moby:articleName")=="start_row"):
                 t=MobyInteger()
-                t.fromMoby(elt.toxml())
+                t.fromMoby(elt)
                 self.Start_row=t.content
             if elt.nodeType==elt.ELEMENT_NODE and (elt.nodeName=="Integer" or elt.nodeName=="moby:Integer") and (elt.getAttribute("articleName")=="end_row" or elt.getAttribute("moby:articleName")=="end_row"):
                 t=MobyInteger()
-                t.fromMoby(elt.toxml())
+                t.fromMoby(elt)
                 self.End_row=t.content
\ No newline at end of file

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/ontology/IntAct_XML.py,v
retrieving revision 1.4
retrieving revision 1.5
diff -u -r1.4 -r1.5
--- /home/repository/moby/moby-live/Python/bioMoby/ontology/IntAct_XML.py	2005/02/01 08:52:16	1.4
+++ /home/repository/moby/moby-live/Python/bioMoby/ontology/IntAct_XML.py	2005/02/01 14:20:44	1.5
@@ -26,7 +26,9 @@
         """ Load the attributes from an XML string
         """
         from bioMoby.mobyMarshal import MobyUnmarshaller
-        doc=parseString(value).firstChild
+        doc=value
+        if isinstance(value, str):
+            doc=parseString(value).firstChild
         um=MobyUnmarshaller()
         self.content=""
         self.namespace=doc.getAttribute("moby:namespace")
@@ -46,4 +48,4 @@
             if elt.nodeName=="CrossReference" or elt.nodeName=="moby:CrossReference":
                 self.__cross__=[]
                 for ref in elt.childNodes:
-                    self.__cross__.append(ref.toxml())
\ No newline at end of file
+                    self.__cross__.append(um.loads(ref))
\ No newline at end of file

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/ontology/Interaction.py,v
retrieving revision 1.4
retrieving revision 1.5
diff -u -r1.4 -r1.5
--- /home/repository/moby/moby-live/Python/bioMoby/ontology/Interaction.py	2005/02/01 08:52:16	1.4
+++ /home/repository/moby/moby-live/Python/bioMoby/ontology/Interaction.py	2005/02/01 14:20:44	1.5
@@ -30,7 +30,9 @@
         """ Load the attributes from an XML string
         """
         from bioMoby.mobyMarshal import MobyUnmarshaller
-        doc=parseString(value).firstChild
+        doc=value
+        if isinstance(value, str):
+            doc=parseString(value).firstChild
         um=MobyUnmarshaller()
         self.content=""
         self.namespace=doc.getAttribute("moby:namespace")
@@ -51,15 +53,15 @@
             if elt.nodeName=="CrossReference" or elt.nodeName=="moby:CrossReference":
                 self.__cross__=[]
                 for ref in elt.childNodes:
-                    self.__cross__.append(ref.toxml())
+                    self.__cross__.append(um.loads(ref))
             if elt.nodeType==elt.ELEMENT_NODE and (elt.nodeName=="String" or elt.nodeName=="moby:String") and (elt.getAttribute("articleName")=="result" or elt.getAttribute("moby:articleName")=="result"):
                 t=MobyString()
-                t.fromMoby(elt.toxml())
+                t.fromMoby(elt)
                 self.Result=t.content
             if elt.nodeType==elt.ELEMENT_NODE and (elt.nodeName=="String" or elt.nodeName=="moby:String") and (elt.getAttribute("articleName")=="resultUnits" or elt.getAttribute("moby:articleName")=="resultUnits"):
                 t=MobyString()
-                t.fromMoby(elt.toxml())
+                t.fromMoby(elt)
                 self.ResultUnits=t.content
             if elt.nodeType==elt.ELEMENT_NODE and (elt.nodeName=="Interactor" or elt.nodeName=="moby:Interactor") and (elt.getAttribute("articleName")=="participant" or elt.getAttribute("moby:articleName")=="participant"):
                 self.Participant=MobyInteractor()
-                self.Participant.fromMoby(elt.toxml())
\ No newline at end of file
+                self.Participant.fromMoby(elt)
\ No newline at end of file

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/ontology/InteractionMethod.py,v
retrieving revision 1.4
retrieving revision 1.5
diff -u -r1.4 -r1.5
--- /home/repository/moby/moby-live/Python/bioMoby/ontology/InteractionMethod.py	2005/02/01 08:52:16	1.4
+++ /home/repository/moby/moby-live/Python/bioMoby/ontology/InteractionMethod.py	2005/02/01 14:20:44	1.5
@@ -29,7 +29,9 @@
         """ Load the attributes from an XML string
         """
         from bioMoby.mobyMarshal import MobyUnmarshaller
-        doc=parseString(value).firstChild
+        doc=value
+        if isinstance(value, str):
+            doc=parseString(value).firstChild
         um=MobyUnmarshaller()
         self.content=""
         self.namespace=doc.getAttribute("moby:namespace")
@@ -49,16 +51,16 @@
             if elt.nodeName=="CrossReference" or elt.nodeName=="moby:CrossReference":
                 self.__cross__=[]
                 for ref in elt.childNodes:
-                    self.__cross__.append(ref.toxml())
+                    self.__cross__.append(um.loads(ref))
             if elt.nodeType==elt.ELEMENT_NODE and (elt.nodeName=="String" or elt.nodeName=="moby:String") and (elt.getAttribute("articleName")=="shortlabel" or elt.getAttribute("moby:articleName")=="shortlabel"):
                 t=MobyString()
-                t.fromMoby(elt.toxml())
+                t.fromMoby(elt)
                 self.Shortlabel=t.content
             if elt.nodeType==elt.ELEMENT_NODE and (elt.nodeName=="String" or elt.nodeName=="moby:String") and (elt.getAttribute("articleName")=="term" or elt.getAttribute("moby:articleName")=="term"):
                 t=MobyString()
-                t.fromMoby(elt.toxml())
+                t.fromMoby(elt)
                 self.Term=t.content
             if elt.nodeType==elt.ELEMENT_NODE and (elt.nodeName=="String" or elt.nodeName=="moby:String") and (elt.getAttribute("articleName")=="definition" or elt.getAttribute("moby:articleName")=="definition"):
                 t=MobyString()
-                t.fromMoby(elt.toxml())
+                t.fromMoby(elt)
                 self.Definition=t.content
\ No newline at end of file

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/ontology/Interaction_partner.py,v
retrieving revision 1.4
retrieving revision 1.5
diff -u -r1.4 -r1.5
--- /home/repository/moby/moby-live/Python/bioMoby/ontology/Interaction_partner.py	2005/02/01 08:52:16	1.4
+++ /home/repository/moby/moby-live/Python/bioMoby/ontology/Interaction_partner.py	2005/02/01 14:20:44	1.5
@@ -29,7 +29,9 @@
         """ Load the attributes from an XML string
         """
         from bioMoby.mobyMarshal import MobyUnmarshaller
-        doc=parseString(value).firstChild
+        doc=value
+        if isinstance(value, str):
+            doc=parseString(value).firstChild
         um=MobyUnmarshaller()
         self.content=""
         self.namespace=doc.getAttribute("moby:namespace")
@@ -49,12 +51,12 @@
             if elt.nodeName=="CrossReference" or elt.nodeName=="moby:CrossReference":
                 self.__cross__=[]
                 for ref in elt.childNodes:
-                    self.__cross__.append(ref.toxml())
+                    self.__cross__.append(um.loads(ref))
             if elt.nodeType==elt.ELEMENT_NODE and (elt.nodeName=="Integer" or elt.nodeName=="moby:Integer") and (elt.getAttribute("articleName")=="direction" or elt.getAttribute("moby:articleName")=="direction"):
                 t=MobyInteger()
-                t.fromMoby(elt.toxml())
+                t.fromMoby(elt)
                 self.Direction=t.content
             if elt.nodeType==elt.ELEMENT_NODE and (elt.nodeName=="String" or elt.nodeName=="moby:String") and (elt.getAttribute("articleName")=="partner" or elt.getAttribute("moby:articleName")=="partner"):
                 t=MobyString()
-                t.fromMoby(elt.toxml())
+                t.fromMoby(elt)
                 self.Partner=t.content
\ No newline at end of file

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/ontology/Interactor.py,v
retrieving revision 1.4
retrieving revision 1.5
diff -u -r1.4 -r1.5
--- /home/repository/moby/moby-live/Python/bioMoby/ontology/Interactor.py	2005/02/01 08:52:16	1.4
+++ /home/repository/moby/moby-live/Python/bioMoby/ontology/Interactor.py	2005/02/01 14:20:44	1.5
@@ -27,7 +27,9 @@
         """ Load the attributes from an XML string
         """
         from bioMoby.mobyMarshal import MobyUnmarshaller
-        doc=parseString(value).firstChild
+        doc=value
+        if isinstance(value, str):
+            doc=parseString(value).firstChild
         um=MobyUnmarshaller()
         self.content=""
         self.namespace=doc.getAttribute("moby:namespace")
@@ -47,8 +49,8 @@
             if elt.nodeName=="CrossReference" or elt.nodeName=="moby:CrossReference":
                 self.__cross__=[]
                 for ref in elt.childNodes:
-                    self.__cross__.append(ref.toxml())
+                    self.__cross__.append(um.loads(ref))
             if elt.nodeType==elt.ELEMENT_NODE and (elt.nodeName=="String" or elt.nodeName=="moby:String") and (elt.getAttribute("articleName")=="role" or elt.getAttribute("moby:articleName")=="role"):
                 t=MobyString()
-                t.fromMoby(elt.toxml())
+                t.fromMoby(elt)
                 self.Role=t.content
\ No newline at end of file

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/ontology/MEME_Text.py,v
retrieving revision 1.4
retrieving revision 1.5
diff -u -r1.4 -r1.5
--- /home/repository/moby/moby-live/Python/bioMoby/ontology/MEME_Text.py	2005/02/01 08:52:16	1.4
+++ /home/repository/moby/moby-live/Python/bioMoby/ontology/MEME_Text.py	2005/02/01 14:20:44	1.5
@@ -26,7 +26,9 @@
         """ Load the attributes from an XML string
         """
         from bioMoby.mobyMarshal import MobyUnmarshaller
-        doc=parseString(value).firstChild
+        doc=value
+        if isinstance(value, str):
+            doc=parseString(value).firstChild
         um=MobyUnmarshaller()
         self.content=""
         self.namespace=doc.getAttribute("moby:namespace")
@@ -46,4 +48,4 @@
             if elt.nodeName=="CrossReference" or elt.nodeName=="moby:CrossReference":
                 self.__cross__=[]
                 for ref in elt.childNodes:
-                    self.__cross__.append(ref.toxml())
\ No newline at end of file
+                    self.__cross__.append(um.loads(ref))
\ No newline at end of file

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/ontology/MGIS_ACCESSION.py,v
retrieving revision 1.4
retrieving revision 1.5
diff -u -r1.4 -r1.5
--- /home/repository/moby/moby-live/Python/bioMoby/ontology/MGIS_ACCESSION.py	2005/02/01 08:52:16	1.4
+++ /home/repository/moby/moby-live/Python/bioMoby/ontology/MGIS_ACCESSION.py	2005/02/01 14:20:44	1.5
@@ -46,7 +46,9 @@
         """ Load the attributes from an XML string
         """
         from bioMoby.mobyMarshal import MobyUnmarshaller
-        doc=parseString(value).firstChild
+        doc=value
+        if isinstance(value, str):
+            doc=parseString(value).firstChild
         um=MobyUnmarshaller()
         self.content=""
         self.namespace=doc.getAttribute("moby:namespace")
@@ -66,84 +68,84 @@
             if elt.nodeName=="CrossReference" or elt.nodeName=="moby:CrossReference":
                 self.__cross__=[]
                 for ref in elt.childNodes:
-                    self.__cross__.append(ref.toxml())
+                    self.__cross__.append(um.loads(ref))
             if elt.nodeType==elt.ELEMENT_NODE and (elt.nodeName=="String" or elt.nodeName=="moby:String") and (elt.getAttribute("articleName")=="Biotic_stress_Yellowsig" or elt.getAttribute("moby:articleName")=="Biotic_stress_Yellowsig"):
                 t=MobyString()
-                t.fromMoby(elt.toxml())
+                t.fromMoby(elt)
                 self.Biotic_stress_Yellowsig=t.content
             if elt.nodeType==elt.ELEMENT_NODE and (elt.nodeName=="String" or elt.nodeName=="moby:String") and (elt.getAttribute("articleName")=="mcpd:ORIGCTY" or elt.getAttribute("moby:articleName")=="mcpd:ORIGCTY"):
                 t=MobyString()
-                t.fromMoby(elt.toxml())
+                t.fromMoby(elt)
                 self.McpdORIGCTY=t.content
             if elt.nodeType==elt.ELEMENT_NODE and (elt.nodeName=="String" or elt.nodeName=="moby:String") and (elt.getAttribute("articleName")=="mgis:SECTION" or elt.getAttribute("moby:articleName")=="mgis:SECTION"):
                 t=MobyString()
-                t.fromMoby(elt.toxml())
+                t.fromMoby(elt)
                 self.MgisSECTION=t.content
             if elt.nodeType==elt.ELEMENT_NODE and (elt.nodeName=="String" or elt.nodeName=="moby:String") and (elt.getAttribute("articleName")=="mcpd:SPECIES" or elt.getAttribute("moby:articleName")=="mcpd:SPECIES"):
                 t=MobyString()
-                t.fromMoby(elt.toxml())
+                t.fromMoby(elt)
                 self.McpdSPECIES=t.content
             if elt.nodeType==elt.ELEMENT_NODE and (elt.nodeName=="String" or elt.nodeName=="moby:String") and (elt.getAttribute("articleName")=="mcpd:COLLCODE" or elt.getAttribute("moby:articleName")=="mcpd:COLLCODE"):
                 t=MobyString()
-                t.fromMoby(elt.toxml())
+                t.fromMoby(elt)
                 self.McpdCOLLCODE=t.content
             if elt.nodeType==elt.ELEMENT_NODE and (elt.nodeName=="String" or elt.nodeName=="moby:String") and (elt.getAttribute("articleName")=="Biotic_stress_Blacksig" or elt.getAttribute("moby:articleName")=="Biotic_stress_Blacksig"):
                 t=MobyString()
-                t.fromMoby(elt.toxml())
+                t.fromMoby(elt)
                 self.Biotic_stress_Blacksig=t.content
             if elt.nodeType==elt.ELEMENT_NODE and (elt.nodeName=="String" or elt.nodeName=="moby:String") and (elt.getAttribute("articleName")=="Biotic_stress_Fusarium" or elt.getAttribute("moby:articleName")=="Biotic_stress_Fusarium"):
                 t=MobyString()
-                t.fromMoby(elt.toxml())
+                t.fromMoby(elt)
                 self.Biotic_stress_Fusarium=t.content
             if elt.nodeType==elt.ELEMENT_NODE and (elt.nodeName=="String" or elt.nodeName=="moby:String") and (elt.getAttribute("articleName")=="Biotic_stress_pseudomonas" or elt.getAttribute("moby:articleName")=="Biotic_stress_pseudomonas"):
                 t=MobyString()
-                t.fromMoby(elt.toxml())
+                t.fromMoby(elt)
                 self.Biotic_stress_pseudomonas=t.content
             if elt.nodeType==elt.ELEMENT_NODE and (elt.nodeName=="String" or elt.nodeName=="moby:String") and (elt.getAttribute("articleName")=="Biotic_stress_Radopholus" or elt.getAttribute("moby:articleName")=="Biotic_stress_Radopholus"):
                 t=MobyString()
-                t.fromMoby(elt.toxml())
+                t.fromMoby(elt)
                 self.Biotic_stress_Radopholus=t.content
             if elt.nodeType==elt.ELEMENT_NODE and (elt.nodeName=="String" or elt.nodeName=="moby:String") and (elt.getAttribute("articleName")=="Biotic_stress_Pratylenchuscof" or elt.getAttribute("moby:articleName")=="Biotic_stress_Pratylenchuscof"):
                 t=MobyString()
-                t.fromMoby(elt.toxml())
+                t.fromMoby(elt)
                 self.Biotic_stress_Pratylenchuscof=t.content
             if elt.nodeType==elt.ELEMENT_NODE and (elt.nodeName=="String" or elt.nodeName=="moby:String") and (elt.getAttribute("articleName")=="Biotic_stress_Pratylenchusgood" or elt.getAttribute("moby:articleName")=="Biotic_stress_Pratylenchusgood"):
                 t=MobyString()
-                t.fromMoby(elt.toxml())
+                t.fromMoby(elt)
                 self.Biotic_stress_Pratylenchusgood=t.content
             if elt.nodeType==elt.ELEMENT_NODE and (elt.nodeName=="String" or elt.nodeName=="moby:String") and (elt.getAttribute("articleName")=="Biotic_stress_cosmopolites" or elt.getAttribute("moby:articleName")=="Biotic_stress_cosmopolites"):
                 t=MobyString()
-                t.fromMoby(elt.toxml())
+                t.fromMoby(elt)
                 self.Biotic_stress_cosmopolites=t.content
             if elt.nodeType==elt.ELEMENT_NODE and (elt.nodeName=="String" or elt.nodeName=="moby:String") and (elt.getAttribute("articleName")=="Abiotic_stress_Lowtemp" or elt.getAttribute("moby:articleName")=="Abiotic_stress_Lowtemp"):
                 t=MobyString()
-                t.fromMoby(elt.toxml())
+                t.fromMoby(elt)
                 self.Abiotic_stress_Lowtemp=t.content
             if elt.nodeType==elt.ELEMENT_NODE and (elt.nodeName=="String" or elt.nodeName=="moby:String") and (elt.getAttribute("articleName")=="Abiotic_stress_Drought" or elt.getAttribute("moby:articleName")=="Abiotic_stress_Drought"):
                 t=MobyString()
-                t.fromMoby(elt.toxml())
+                t.fromMoby(elt)
                 self.Abiotic_stress_Drought=t.content
             if elt.nodeType==elt.ELEMENT_NODE and (elt.nodeName=="String" or elt.nodeName=="moby:String") and (elt.getAttribute("articleName")=="Abiotic_stress_Flooding" or elt.getAttribute("moby:articleName")=="Abiotic_stress_Flooding"):
                 t=MobyString()
-                t.fromMoby(elt.toxml())
+                t.fromMoby(elt)
                 self.Abiotic_stress_Flooding=t.content
             if elt.nodeType==elt.ELEMENT_NODE and (elt.nodeName=="String" or elt.nodeName=="moby:String") and (elt.getAttribute("articleName")=="Abiotic_stress_Mineraldef" or elt.getAttribute("moby:articleName")=="Abiotic_stress_Mineraldef"):
                 t=MobyString()
-                t.fromMoby(elt.toxml())
+                t.fromMoby(elt)
                 self.Abiotic_stress_Mineraldef=t.content
             if elt.nodeType==elt.ELEMENT_NODE and (elt.nodeName=="String" or elt.nodeName=="moby:String") and (elt.getAttribute("articleName")=="Abiotic_stress_Winds" or elt.getAttribute("moby:articleName")=="Abiotic_stress_Winds"):
                 t=MobyString()
-                t.fromMoby(elt.toxml())
+                t.fromMoby(elt)
                 self.Abiotic_stress_Winds=t.content
             if elt.nodeType==elt.ELEMENT_NODE and (elt.nodeName=="String" or elt.nodeName=="moby:String") and (elt.getAttribute("articleName")=="Abiotic_stress_Soilacidity" or elt.getAttribute("moby:articleName")=="Abiotic_stress_Soilacidity"):
                 t=MobyString()
-                t.fromMoby(elt.toxml())
+                t.fromMoby(elt)
                 self.Abiotic_stress_Soilacidity=t.content
             if elt.nodeType==elt.ELEMENT_NODE and (elt.nodeName=="String" or elt.nodeName=="moby:String") and (elt.getAttribute("articleName")=="Abiotic_stress_Manganesetox" or elt.getAttribute("moby:articleName")=="Abiotic_stress_Manganesetox"):
                 t=MobyString()
-                t.fromMoby(elt.toxml())
+                t.fromMoby(elt)
                 self.Abiotic_stress_Manganesetox=t.content
             if elt.nodeType==elt.ELEMENT_NODE and (elt.nodeName=="String" or elt.nodeName=="moby:String") and (elt.getAttribute("articleName")=="Abiotic_stress_Hightemp" or elt.getAttribute("moby:articleName")=="Abiotic_stress_Hightemp"):
                 t=MobyString()
-                t.fromMoby(elt.toxml())
+                t.fromMoby(elt)
                 self.Abiotic_stress_Hightemp=t.content
\ No newline at end of file

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/ontology/MMP_Locus.py,v
retrieving revision 1.4
retrieving revision 1.5
diff -u -r1.4 -r1.5
--- /home/repository/moby/moby-live/Python/bioMoby/ontology/MMP_Locus.py	2005/02/01 08:52:16	1.4
+++ /home/repository/moby/moby-live/Python/bioMoby/ontology/MMP_Locus.py	2005/02/01 14:20:44	1.5
@@ -25,7 +25,9 @@
         """ Load the attributes from an XML string
         """
         from bioMoby.mobyMarshal import MobyUnmarshaller
-        doc=parseString(value).firstChild
+        doc=value
+        if isinstance(value, str):
+            doc=parseString(value).firstChild
         um=MobyUnmarshaller()
         self.content=""
         self.namespace=doc.getAttribute("moby:namespace")
@@ -45,4 +47,4 @@
             if elt.nodeName=="CrossReference" or elt.nodeName=="moby:CrossReference":
                 self.__cross__=[]
                 for ref in elt.childNodes:
-                    self.__cross__.append(ref.toxml())
\ No newline at end of file
+                    self.__cross__.append(um.loads(ref))
\ No newline at end of file

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/ontology/MO_Term_Test.py,v
retrieving revision 1.4
retrieving revision 1.5
diff -u -r1.4 -r1.5
--- /home/repository/moby/moby-live/Python/bioMoby/ontology/MO_Term_Test.py	2005/02/01 08:52:16	1.4
+++ /home/repository/moby/moby-live/Python/bioMoby/ontology/MO_Term_Test.py	2005/02/01 14:20:44	1.5
@@ -30,7 +30,9 @@
         """ Load the attributes from an XML string
         """
         from bioMoby.mobyMarshal import MobyUnmarshaller
-        doc=parseString(value).firstChild
+        doc=value
+        if isinstance(value, str):
+            doc=parseString(value).firstChild
         um=MobyUnmarshaller()
         self.content=""
         self.namespace=doc.getAttribute("moby:namespace")
@@ -50,20 +52,20 @@
             if elt.nodeName=="CrossReference" or elt.nodeName=="moby:CrossReference":
                 self.__cross__=[]
                 for ref in elt.childNodes:
-                    self.__cross__.append(ref.toxml())
+                    self.__cross__.append(um.loads(ref))
             if elt.nodeType==elt.ELEMENT_NODE and (elt.nodeName=="String" or elt.nodeName=="moby:String") and (elt.getAttribute("articleName")=="class_name" or elt.getAttribute("moby:articleName")=="class_name"):
                 t=MobyString()
-                t.fromMoby(elt.toxml())
+                t.fromMoby(elt)
                 self.Class_name=t.content
             if elt.nodeType==elt.ELEMENT_NODE and (elt.nodeName=="String" or elt.nodeName=="moby:String") and (elt.getAttribute("articleName")=="individual_name" or elt.getAttribute("moby:articleName")=="individual_name"):
                 t=MobyString()
-                t.fromMoby(elt.toxml())
+                t.fromMoby(elt)
                 self.Individual_name=t.content
             if elt.nodeType==elt.ELEMENT_NODE and (elt.nodeName=="String" or elt.nodeName=="moby:String") and (elt.getAttribute("articleName")=="individual_desc" or elt.getAttribute("moby:articleName")=="individual_desc"):
                 t=MobyString()
-                t.fromMoby(elt.toxml())
+                t.fromMoby(elt)
                 self.Individual_desc=t.content
             if elt.nodeType==elt.ELEMENT_NODE and (elt.nodeName=="String" or elt.nodeName=="moby:String") and (elt.getAttribute("articleName")=="class_desc" or elt.getAttribute("moby:articleName")=="class_desc"):
                 t=MobyString()
-                t.fromMoby(elt.toxml())
+                t.fromMoby(elt)
                 self.Class_desc=t.content
\ No newline at end of file

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/ontology/MmCIFText.py,v
retrieving revision 1.4
retrieving revision 1.5
diff -u -r1.4 -r1.5
--- /home/repository/moby/moby-live/Python/bioMoby/ontology/MmCIFText.py	2005/02/01 08:52:16	1.4
+++ /home/repository/moby/moby-live/Python/bioMoby/ontology/MmCIFText.py	2005/02/01 14:20:44	1.5
@@ -26,7 +26,9 @@
         """ Load the attributes from an XML string
         """
         from bioMoby.mobyMarshal import MobyUnmarshaller
-        doc=parseString(value).firstChild
+        doc=value
+        if isinstance(value, str):
+            doc=parseString(value).firstChild
         um=MobyUnmarshaller()
         self.content=""
         self.namespace=doc.getAttribute("moby:namespace")
@@ -46,4 +48,4 @@
             if elt.nodeName=="CrossReference" or elt.nodeName=="moby:CrossReference":
                 self.__cross__=[]
                 for ref in elt.childNodes:
-                    self.__cross__.append(ref.toxml())
\ No newline at end of file
+                    self.__cross__.append(um.loads(ref))
\ No newline at end of file

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/ontology/Multi_key_value_pair.py,v
retrieving revision 1.4
retrieving revision 1.5
diff -u -r1.4 -r1.5
--- /home/repository/moby/moby-live/Python/bioMoby/ontology/Multi_key_value_pair.py	2005/02/01 08:52:16	1.4
+++ /home/repository/moby/moby-live/Python/bioMoby/ontology/Multi_key_value_pair.py	2005/02/01 14:20:44	1.5
@@ -28,7 +28,9 @@
         """ Load the attributes from an XML string
         """
         from bioMoby.mobyMarshal import MobyUnmarshaller
-        doc=parseString(value).firstChild
+        doc=value
+        if isinstance(value, str):
+            doc=parseString(value).firstChild
         um=MobyUnmarshaller()
         self.content=""
         self.namespace=doc.getAttribute("moby:namespace")
@@ -49,12 +51,12 @@
             if elt.nodeName=="CrossReference" or elt.nodeName=="moby:CrossReference":
                 self.__cross__=[]
                 for ref in elt.childNodes:
-                    self.__cross__.append(ref.toxml())
+                    self.__cross__.append(um.loads(ref))
             if elt.nodeType==elt.ELEMENT_NODE and (elt.nodeName=="String" or elt.nodeName=="moby:String") and (elt.getAttribute("articleName")=="key" or elt.getAttribute("moby:articleName")=="key"):
                 t=MobyString()
-                t.fromMoby(elt.toxml())
+                t.fromMoby(elt)
                 self.Key=t.content
             if elt.nodeType==elt.ELEMENT_NODE and (elt.nodeName=="String" or elt.nodeName=="moby:String") and (elt.getAttribute("articleName")=="value" or elt.getAttribute("moby:articleName")=="value"):
                 t=MobyString()
-                t.fromMoby(elt.toxml())
+                t.fromMoby(elt)
                 self.Value.append(t.content)
\ No newline at end of file

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/ontology/MyTestingDataType_11024145298313.py,v
retrieving revision 1.4
retrieving revision 1.5
diff -u -r1.4 -r1.5
--- /home/repository/moby/moby-live/Python/bioMoby/ontology/MyTestingDataType_11024145298313.py	2005/02/01 08:52:16	1.4
+++ /home/repository/moby/moby-live/Python/bioMoby/ontology/MyTestingDataType_11024145298313.py	2005/02/01 14:20:44	1.5
@@ -26,7 +26,9 @@
         """ Load the attributes from an XML string
         """
         from bioMoby.mobyMarshal import MobyUnmarshaller
-        doc=parseString(value).firstChild
+        doc=value
+        if isinstance(value, str):
+            doc=parseString(value).firstChild
         um=MobyUnmarshaller()
         self.content=""
         self.namespace=doc.getAttribute("moby:namespace")
@@ -46,4 +48,4 @@
             if elt.nodeName=="CrossReference" or elt.nodeName=="moby:CrossReference":
                 self.__cross__=[]
                 for ref in elt.childNodes:
-                    self.__cross__.append(ref.toxml())
\ No newline at end of file
+                    self.__cross__.append(um.loads(ref))
\ No newline at end of file

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/ontology/MyTree.py,v
retrieving revision 1.4
retrieving revision 1.5
diff -u -r1.4 -r1.5
--- /home/repository/moby/moby-live/Python/bioMoby/ontology/MyTree.py	2005/02/01 08:52:16	1.4
+++ /home/repository/moby/moby-live/Python/bioMoby/ontology/MyTree.py	2005/02/01 14:20:44	1.5
@@ -26,7 +26,9 @@
         """ Load the attributes from an XML string
         """
         from bioMoby.mobyMarshal import MobyUnmarshaller
-        doc=parseString(value).firstChild
+        doc=value
+        if isinstance(value, str):
+            doc=parseString(value).firstChild
         um=MobyUnmarshaller()
         self.content=""
         self.namespace=doc.getAttribute("moby:namespace")
@@ -46,4 +48,4 @@
             if elt.nodeName=="CrossReference" or elt.nodeName=="moby:CrossReference":
                 self.__cross__=[]
                 for ref in elt.childNodes:
-                    self.__cross__.append(ref.toxml())
\ No newline at end of file
+                    self.__cross__.append(um.loads(ref))
\ No newline at end of file

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/ontology/NCBI_BLAST_Text.py,v
retrieving revision 1.4
retrieving revision 1.5
diff -u -r1.4 -r1.5
--- /home/repository/moby/moby-live/Python/bioMoby/ontology/NCBI_BLAST_Text.py	2005/02/01 08:52:16	1.4
+++ /home/repository/moby/moby-live/Python/bioMoby/ontology/NCBI_BLAST_Text.py	2005/02/01 14:20:44	1.5
@@ -26,7 +26,9 @@
         """ Load the attributes from an XML string
         """
         from bioMoby.mobyMarshal import MobyUnmarshaller
-        doc=parseString(value).firstChild
+        doc=value
+        if isinstance(value, str):
+            doc=parseString(value).firstChild
         um=MobyUnmarshaller()
         self.content=""
         self.namespace=doc.getAttribute("moby:namespace")
@@ -46,4 +48,4 @@
             if elt.nodeName=="CrossReference" or elt.nodeName=="moby:CrossReference":
                 self.__cross__=[]
                 for ref in elt.childNodes:
-                    self.__cross__.append(ref.toxml())
\ No newline at end of file
+                    self.__cross__.append(um.loads(ref))
\ No newline at end of file

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/ontology/NCBI_Blast_XML.py,v
retrieving revision 1.4
retrieving revision 1.5
diff -u -r1.4 -r1.5
--- /home/repository/moby/moby-live/Python/bioMoby/ontology/NCBI_Blast_XML.py	2005/02/01 08:52:16	1.4
+++ /home/repository/moby/moby-live/Python/bioMoby/ontology/NCBI_Blast_XML.py	2005/02/01 14:20:44	1.5
@@ -26,7 +26,9 @@
         """ Load the attributes from an XML string
         """
         from bioMoby.mobyMarshal import MobyUnmarshaller
-        doc=parseString(value).firstChild
+        doc=value
+        if isinstance(value, str):
+            doc=parseString(value).firstChild
         um=MobyUnmarshaller()
         self.content=""
         self.namespace=doc.getAttribute("moby:namespace")
@@ -46,4 +48,4 @@
             if elt.nodeName=="CrossReference" or elt.nodeName=="moby:CrossReference":
                 self.__cross__=[]
                 for ref in elt.childNodes:
-                    self.__cross__.append(ref.toxml())
\ No newline at end of file
+                    self.__cross__.append(um.loads(ref))
\ No newline at end of file

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/ontology/NCBI_Blast_XML_Gif.py,v
retrieving revision 1.4
retrieving revision 1.5
diff -u -r1.4 -r1.5
--- /home/repository/moby/moby-live/Python/bioMoby/ontology/NCBI_Blast_XML_Gif.py	2005/02/01 08:52:16	1.4
+++ /home/repository/moby/moby-live/Python/bioMoby/ontology/NCBI_Blast_XML_Gif.py	2005/02/01 14:20:44	1.5
@@ -28,7 +28,9 @@
         """ Load the attributes from an XML string
         """
         from bioMoby.mobyMarshal import MobyUnmarshaller
-        doc=parseString(value).firstChild
+        doc=value
+        if isinstance(value, str):
+            doc=parseString(value).firstChild
         um=MobyUnmarshaller()
         self.content=""
         self.namespace=doc.getAttribute("moby:namespace")
@@ -48,7 +50,7 @@
             if elt.nodeName=="CrossReference" or elt.nodeName=="moby:CrossReference":
                 self.__cross__=[]
                 for ref in elt.childNodes:
-                    self.__cross__.append(ref.toxml())
+                    self.__cross__.append(um.loads(ref))
             if elt.nodeType==elt.ELEMENT_NODE and (elt.nodeName=="b64_encoded_gif" or elt.nodeName=="moby:b64_encoded_gif") and (elt.getAttribute("articleName")=="hitGraph" or elt.getAttribute("moby:articleName")=="hitGraph"):
                 self.HitGraph=MobyB64_encoded_gif()
-                self.HitGraph.fromMoby(elt.toxml())
\ No newline at end of file
+                self.HitGraph.fromMoby(elt)
\ No newline at end of file

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/ontology/NCBI_Blast_XML_Gif_Map.py,v
retrieving revision 1.4
retrieving revision 1.5
diff -u -r1.4 -r1.5
--- /home/repository/moby/moby-live/Python/bioMoby/ontology/NCBI_Blast_XML_Gif_Map.py	2005/02/01 08:52:16	1.4
+++ /home/repository/moby/moby-live/Python/bioMoby/ontology/NCBI_Blast_XML_Gif_Map.py	2005/02/01 14:20:44	1.5
@@ -30,7 +30,9 @@
         """ Load the attributes from an XML string
         """
         from bioMoby.mobyMarshal import MobyUnmarshaller
-        doc=parseString(value).firstChild
+        doc=value
+        if isinstance(value, str):
+            doc=parseString(value).firstChild
         um=MobyUnmarshaller()
         self.content=""
         self.namespace=doc.getAttribute("moby:namespace")
@@ -50,10 +52,10 @@
             if elt.nodeName=="CrossReference" or elt.nodeName=="moby:CrossReference":
                 self.__cross__=[]
                 for ref in elt.childNodes:
-                    self.__cross__.append(ref.toxml())
+                    self.__cross__.append(um.loads(ref))
             if elt.nodeType==elt.ELEMENT_NODE and (elt.nodeName=="b64_encoded_gif" or elt.nodeName=="moby:b64_encoded_gif") and (elt.getAttribute("articleName")=="hitGraph" or elt.getAttribute("moby:articleName")=="hitGraph"):
                 self.HitGraph=MobyB64_encoded_gif()
-                self.HitGraph.fromMoby(elt.toxml())
+                self.HitGraph.fromMoby(elt)
             if elt.nodeType==elt.ELEMENT_NODE and (elt.nodeName=="text-html" or elt.nodeName=="moby:text-html") and (elt.getAttribute("articleName")=="areaMap" or elt.getAttribute("moby:articleName")=="areaMap"):
                 self.AreaMap=MobyTextHtml()
-                self.AreaMap.fromMoby(elt.toxml())
\ No newline at end of file
+                self.AreaMap.fromMoby(elt)
\ No newline at end of file

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/ontology/NCBI_MEME_Text.py,v
retrieving revision 1.4
retrieving revision 1.5
diff -u -r1.4 -r1.5
--- /home/repository/moby/moby-live/Python/bioMoby/ontology/NCBI_MEME_Text.py	2005/02/01 08:52:16	1.4
+++ /home/repository/moby/moby-live/Python/bioMoby/ontology/NCBI_MEME_Text.py	2005/02/01 14:20:44	1.5
@@ -26,7 +26,9 @@
         """ Load the attributes from an XML string
         """
         from bioMoby.mobyMarshal import MobyUnmarshaller
-        doc=parseString(value).firstChild
+        doc=value
+        if isinstance(value, str):
+            doc=parseString(value).firstChild
         um=MobyUnmarshaller()
         self.content=""
         self.namespace=doc.getAttribute("moby:namespace")
@@ -46,4 +48,4 @@
             if elt.nodeName=="CrossReference" or elt.nodeName=="moby:CrossReference":
                 self.__cross__=[]
                 for ref in elt.childNodes:
-                    self.__cross__.append(ref.toxml())
\ No newline at end of file
+                    self.__cross__.append(um.loads(ref))
\ No newline at end of file

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/ontology/NucleotideSequence.py,v
retrieving revision 1.4
retrieving revision 1.5
diff -u -r1.4 -r1.5
--- /home/repository/moby/moby-live/Python/bioMoby/ontology/NucleotideSequence.py	2005/02/01 08:52:16	1.4
+++ /home/repository/moby/moby-live/Python/bioMoby/ontology/NucleotideSequence.py	2005/02/01 14:20:44	1.5
@@ -29,7 +29,9 @@
         """ Load the attributes from an XML string
         """
         from bioMoby.mobyMarshal import MobyUnmarshaller
-        doc=parseString(value).firstChild
+        doc=value
+        if isinstance(value, str):
+            doc=parseString(value).firstChild
         um=MobyUnmarshaller()
         self.content=""
         self.namespace=doc.getAttribute("moby:namespace")
@@ -49,12 +51,12 @@
             if elt.nodeName=="CrossReference" or elt.nodeName=="moby:CrossReference":
                 self.__cross__=[]
                 for ref in elt.childNodes:
-                    self.__cross__.append(ref.toxml())
+                    self.__cross__.append(um.loads(ref))
             if elt.nodeType==elt.ELEMENT_NODE and (elt.nodeName=="Integer" or elt.nodeName=="moby:Integer") and (elt.getAttribute("articleName")=="Length" or elt.getAttribute("moby:articleName")=="Length"):
                 t=MobyInteger()
-                t.fromMoby(elt.toxml())
+                t.fromMoby(elt)
                 self.Length=t.content
             if elt.nodeType==elt.ELEMENT_NODE and (elt.nodeName=="String" or elt.nodeName=="moby:String") and (elt.getAttribute("articleName")=="SequenceString" or elt.getAttribute("moby:articleName")=="SequenceString"):
                 t=MobyString()
-                t.fromMoby(elt.toxml())
+                t.fromMoby(elt)
                 self.SequenceString=t.content
\ No newline at end of file

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/ontology/PDBFormattedText.py,v
retrieving revision 1.4
retrieving revision 1.5
diff -u -r1.4 -r1.5
--- /home/repository/moby/moby-live/Python/bioMoby/ontology/PDBFormattedText.py	2005/02/01 08:52:16	1.4
+++ /home/repository/moby/moby-live/Python/bioMoby/ontology/PDBFormattedText.py	2005/02/01 14:20:44	1.5
@@ -26,7 +26,9 @@
         """ Load the attributes from an XML string
         """
         from bioMoby.mobyMarshal import MobyUnmarshaller
-        doc=parseString(value).firstChild
+        doc=value
+        if isinstance(value, str):
+            doc=parseString(value).firstChild
         um=MobyUnmarshaller()
         self.content=""
         self.namespace=doc.getAttribute("moby:namespace")
@@ -46,4 +48,4 @@
             if elt.nodeName=="CrossReference" or elt.nodeName=="moby:CrossReference":
                 self.__cross__=[]
                 for ref in elt.childNodes:
-                    self.__cross__.append(ref.toxml())
\ No newline at end of file
+                    self.__cross__.append(um.loads(ref))
\ No newline at end of file

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/ontology/PDBText.py,v
retrieving revision 1.4
retrieving revision 1.5
diff -u -r1.4 -r1.5
--- /home/repository/moby/moby-live/Python/bioMoby/ontology/PDBText.py	2005/02/01 08:52:16	1.4
+++ /home/repository/moby/moby-live/Python/bioMoby/ontology/PDBText.py	2005/02/01 14:20:44	1.5
@@ -26,7 +26,9 @@
         """ Load the attributes from an XML string
         """
         from bioMoby.mobyMarshal import MobyUnmarshaller
-        doc=parseString(value).firstChild
+        doc=value
+        if isinstance(value, str):
+            doc=parseString(value).firstChild
         um=MobyUnmarshaller()
         self.content=""
         self.namespace=doc.getAttribute("moby:namespace")
@@ -46,4 +48,4 @@
             if elt.nodeName=="CrossReference" or elt.nodeName=="moby:CrossReference":
                 self.__cross__=[]
                 for ref in elt.childNodes:
-                    self.__cross__.append(ref.toxml())
\ No newline at end of file
+                    self.__cross__.append(um.loads(ref))
\ No newline at end of file

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/ontology/PDGJOB.py,v
retrieving revision 1.4
retrieving revision 1.5
diff -u -r1.4 -r1.5
--- /home/repository/moby/moby-live/Python/bioMoby/ontology/PDGJOB.py	2005/02/01 08:52:16	1.4
+++ /home/repository/moby/moby-live/Python/bioMoby/ontology/PDGJOB.py	2005/02/01 14:20:44	1.5
@@ -32,7 +32,9 @@
         """ Load the attributes from an XML string
         """
         from bioMoby.mobyMarshal import MobyUnmarshaller
-        doc=parseString(value).firstChild
+        doc=value
+        if isinstance(value, str):
+            doc=parseString(value).firstChild
         um=MobyUnmarshaller()
         self.content=""
         self.namespace=doc.getAttribute("moby:namespace")
@@ -52,23 +54,23 @@
             if elt.nodeName=="CrossReference" or elt.nodeName=="moby:CrossReference":
                 self.__cross__=[]
                 for ref in elt.childNodes:
-                    self.__cross__.append(ref.toxml())
+                    self.__cross__.append(um.loads(ref))
             if elt.nodeType==elt.ELEMENT_NODE and (elt.nodeName=="String" or elt.nodeName=="moby:String") and (elt.getAttribute("articleName")=="answerService" or elt.getAttribute("moby:articleName")=="answerService"):
                 t=MobyString()
-                t.fromMoby(elt.toxml())
+                t.fromMoby(elt)
                 self.AnswerService=t.content
             if elt.nodeType==elt.ELEMENT_NODE and (elt.nodeName=="String" or elt.nodeName=="moby:String") and (elt.getAttribute("articleName")=="authURI" or elt.getAttribute("moby:articleName")=="authURI"):
                 t=MobyString()
-                t.fromMoby(elt.toxml())
+                t.fromMoby(elt)
                 self.AuthURI=t.content
             if elt.nodeType==elt.ELEMENT_NODE and (elt.nodeName=="DateTime" or elt.nodeName=="moby:DateTime") and (elt.getAttribute("articleName")=="timeout" or elt.getAttribute("moby:articleName")=="timeout"):
                 self.Timeout=MobyDateTime()
-                self.Timeout.fromMoby(elt.toxml())
+                self.Timeout.fromMoby(elt)
             if elt.nodeType==elt.ELEMENT_NODE and (elt.nodeName=="String" or elt.nodeName=="moby:String") and (elt.getAttribute("articleName")=="killcode" or elt.getAttribute("moby:articleName")=="killcode"):
                 t=MobyString()
-                t.fromMoby(elt.toxml())
+                t.fromMoby(elt)
                 self.Killcode=t.content
             if elt.nodeType==elt.ELEMENT_NODE and (elt.nodeName=="String" or elt.nodeName=="moby:String") and (elt.getAttribute("articleName")=="killService" or elt.getAttribute("moby:articleName")=="killService"):
                 t=MobyString()
-                t.fromMoby(elt.toxml())
+                t.fromMoby(elt)
                 self.KillService=t.content
\ No newline at end of file

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/ontology/PHDText.py,v
retrieving revision 1.4
retrieving revision 1.5
diff -u -r1.4 -r1.5
--- /home/repository/moby/moby-live/Python/bioMoby/ontology/PHDText.py	2005/02/01 08:52:16	1.4
+++ /home/repository/moby/moby-live/Python/bioMoby/ontology/PHDText.py	2005/02/01 14:20:44	1.5
@@ -26,7 +26,9 @@
         """ Load the attributes from an XML string
         """
         from bioMoby.mobyMarshal import MobyUnmarshaller
-        doc=parseString(value).firstChild
+        doc=value
+        if isinstance(value, str):
+            doc=parseString(value).firstChild
         um=MobyUnmarshaller()
         self.content=""
         self.namespace=doc.getAttribute("moby:namespace")
@@ -46,4 +48,4 @@
             if elt.nodeName=="CrossReference" or elt.nodeName=="moby:CrossReference":
                 self.__cross__=[]
                 for ref in elt.childNodes:
-                    self.__cross__.append(ref.toxml())
\ No newline at end of file
+                    self.__cross__.append(um.loads(ref))
\ No newline at end of file

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/ontology/PMUTText.py,v
retrieving revision 1.4
retrieving revision 1.5
diff -u -r1.4 -r1.5
--- /home/repository/moby/moby-live/Python/bioMoby/ontology/PMUTText.py	2005/02/01 08:52:16	1.4
+++ /home/repository/moby/moby-live/Python/bioMoby/ontology/PMUTText.py	2005/02/01 14:20:44	1.5
@@ -26,7 +26,9 @@
         """ Load the attributes from an XML string
         """
         from bioMoby.mobyMarshal import MobyUnmarshaller
-        doc=parseString(value).firstChild
+        doc=value
+        if isinstance(value, str):
+            doc=parseString(value).firstChild
         um=MobyUnmarshaller()
         self.content=""
         self.namespace=doc.getAttribute("moby:namespace")
@@ -46,4 +48,4 @@
             if elt.nodeName=="CrossReference" or elt.nodeName=="moby:CrossReference":
                 self.__cross__=[]
                 for ref in elt.childNodes:
-                    self.__cross__.append(ref.toxml())
\ No newline at end of file
+                    self.__cross__.append(um.loads(ref))
\ No newline at end of file

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/ontology/PSeaTextFormatted.py,v
retrieving revision 1.4
retrieving revision 1.5
diff -u -r1.4 -r1.5
--- /home/repository/moby/moby-live/Python/bioMoby/ontology/PSeaTextFormatted.py	2005/02/01 08:52:16	1.4
+++ /home/repository/moby/moby-live/Python/bioMoby/ontology/PSeaTextFormatted.py	2005/02/01 14:20:44	1.5
@@ -26,7 +26,9 @@
         """ Load the attributes from an XML string
         """
         from bioMoby.mobyMarshal import MobyUnmarshaller
-        doc=parseString(value).firstChild
+        doc=value
+        if isinstance(value, str):
+            doc=parseString(value).firstChild
         um=MobyUnmarshaller()
         self.content=""
         self.namespace=doc.getAttribute("moby:namespace")
@@ -46,4 +48,4 @@
             if elt.nodeName=="CrossReference" or elt.nodeName=="moby:CrossReference":
                 self.__cross__=[]
                 for ref in elt.childNodes:
-                    self.__cross__.append(ref.toxml())
\ No newline at end of file
+                    self.__cross__.append(um.loads(ref))
\ No newline at end of file

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/ontology/PhenotypeDescription.py,v
retrieving revision 1.4
retrieving revision 1.5
diff -u -r1.4 -r1.5
--- /home/repository/moby/moby-live/Python/bioMoby/ontology/PhenotypeDescription.py	2005/02/01 08:52:16	1.4
+++ /home/repository/moby/moby-live/Python/bioMoby/ontology/PhenotypeDescription.py	2005/02/01 14:20:44	1.5
@@ -27,7 +27,9 @@
         """ Load the attributes from an XML string
         """
         from bioMoby.mobyMarshal import MobyUnmarshaller
-        doc=parseString(value).firstChild
+        doc=value
+        if isinstance(value, str):
+            doc=parseString(value).firstChild
         um=MobyUnmarshaller()
         self.content=""
         self.namespace=doc.getAttribute("moby:namespace")
@@ -47,8 +49,8 @@
             if elt.nodeName=="CrossReference" or elt.nodeName=="moby:CrossReference":
                 self.__cross__=[]
                 for ref in elt.childNodes:
-                    self.__cross__.append(ref.toxml())
+                    self.__cross__.append(um.loads(ref))
             if elt.nodeType==elt.ELEMENT_NODE and (elt.nodeName=="String" or elt.nodeName=="moby:String") and (elt.getAttribute("articleName")=="Phenotype" or elt.getAttribute("moby:articleName")=="Phenotype"):
                 t=MobyString()
-                t.fromMoby(elt.toxml())
+                t.fromMoby(elt)
                 self.Phenotype=t.content
\ No newline at end of file

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/ontology/PubMedMEDLINE.py,v
retrieving revision 1.4
retrieving revision 1.5
diff -u -r1.4 -r1.5
--- /home/repository/moby/moby-live/Python/bioMoby/ontology/PubMedMEDLINE.py	2005/02/01 08:52:16	1.4
+++ /home/repository/moby/moby-live/Python/bioMoby/ontology/PubMedMEDLINE.py	2005/02/01 14:20:44	1.5
@@ -26,7 +26,9 @@
         """ Load the attributes from an XML string
         """
         from bioMoby.mobyMarshal import MobyUnmarshaller
-        doc=parseString(value).firstChild
+        doc=value
+        if isinstance(value, str):
+            doc=parseString(value).firstChild
         um=MobyUnmarshaller()
         self.content=""
         self.namespace=doc.getAttribute("moby:namespace")
@@ -46,4 +48,4 @@
             if elt.nodeName=="CrossReference" or elt.nodeName=="moby:CrossReference":
                 self.__cross__=[]
                 for ref in elt.childNodes:
-                    self.__cross__.append(ref.toxml())
\ No newline at end of file
+                    self.__cross__.append(um.loads(ref))
\ No newline at end of file

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/ontology/RNASequence.py,v
retrieving revision 1.4
retrieving revision 1.5
diff -u -r1.4 -r1.5
--- /home/repository/moby/moby-live/Python/bioMoby/ontology/RNASequence.py	2005/02/01 08:52:16	1.4
+++ /home/repository/moby/moby-live/Python/bioMoby/ontology/RNASequence.py	2005/02/01 14:20:44	1.5
@@ -29,7 +29,9 @@
         """ Load the attributes from an XML string
         """
         from bioMoby.mobyMarshal import MobyUnmarshaller
-        doc=parseString(value).firstChild
+        doc=value
+        if isinstance(value, str):
+            doc=parseString(value).firstChild
         um=MobyUnmarshaller()
         self.content=""
         self.namespace=doc.getAttribute("moby:namespace")
@@ -49,12 +51,12 @@
             if elt.nodeName=="CrossReference" or elt.nodeName=="moby:CrossReference":
                 self.__cross__=[]
                 for ref in elt.childNodes:
-                    self.__cross__.append(ref.toxml())
+                    self.__cross__.append(um.loads(ref))
             if elt.nodeType==elt.ELEMENT_NODE and (elt.nodeName=="Integer" or elt.nodeName=="moby:Integer") and (elt.getAttribute("articleName")=="Length" or elt.getAttribute("moby:articleName")=="Length"):
                 t=MobyInteger()
-                t.fromMoby(elt.toxml())
+                t.fromMoby(elt)
                 self.Length=t.content
             if elt.nodeType==elt.ELEMENT_NODE and (elt.nodeName=="String" or elt.nodeName=="moby:String") and (elt.getAttribute("articleName")=="SequenceString" or elt.getAttribute("moby:articleName")=="SequenceString"):
                 t=MobyString()
-                t.fromMoby(elt.toxml())
+                t.fromMoby(elt)
                 self.SequenceString=t.content
\ No newline at end of file

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/ontology/SINGER_ACCESSION.py,v
retrieving revision 1.4
retrieving revision 1.5
diff -u -r1.4 -r1.5
--- /home/repository/moby/moby-live/Python/bioMoby/ontology/SINGER_ACCESSION.py	2005/02/01 08:52:16	1.4
+++ /home/repository/moby/moby-live/Python/bioMoby/ontology/SINGER_ACCESSION.py	2005/02/01 14:20:44	1.5
@@ -30,7 +30,9 @@
         """ Load the attributes from an XML string
         """
         from bioMoby.mobyMarshal import MobyUnmarshaller
-        doc=parseString(value).firstChild
+        doc=value
+        if isinstance(value, str):
+            doc=parseString(value).firstChild
         um=MobyUnmarshaller()
         self.content=""
         self.namespace=doc.getAttribute("moby:namespace")
@@ -50,20 +52,20 @@
             if elt.nodeName=="CrossReference" or elt.nodeName=="moby:CrossReference":
                 self.__cross__=[]
                 for ref in elt.childNodes:
-                    self.__cross__.append(ref.toxml())
+                    self.__cross__.append(um.loads(ref))
             if elt.nodeType==elt.ELEMENT_NODE and (elt.nodeName=="String" or elt.nodeName=="moby:String") and (elt.getAttribute("articleName")=="ACCNO" or elt.getAttribute("moby:articleName")=="ACCNO"):
                 t=MobyString()
-                t.fromMoby(elt.toxml())
+                t.fromMoby(elt)
                 self.ACCNO=t.content
             if elt.nodeType==elt.ELEMENT_NODE and (elt.nodeName=="String" or elt.nodeName=="moby:String") and (elt.getAttribute("articleName")=="ORIGCTY" or elt.getAttribute("moby:articleName")=="ORIGCTY"):
                 t=MobyString()
-                t.fromMoby(elt.toxml())
+                t.fromMoby(elt)
                 self.ORIGCTY=t.content
             if elt.nodeType==elt.ELEMENT_NODE and (elt.nodeName=="String" or elt.nodeName=="moby:String") and (elt.getAttribute("articleName")=="GENUS" or elt.getAttribute("moby:articleName")=="GENUS"):
                 t=MobyString()
-                t.fromMoby(elt.toxml())
+                t.fromMoby(elt)
                 self.GENUS=t.content
             if elt.nodeType==elt.ELEMENT_NODE and (elt.nodeName=="String" or elt.nodeName=="moby:String") and (elt.getAttribute("articleName")=="SPECIES" or elt.getAttribute("moby:articleName")=="SPECIES"):
                 t=MobyString()
-                t.fromMoby(elt.toxml())
+                t.fromMoby(elt)
                 self.SPECIES=t.content
\ No newline at end of file

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/ontology/Sample.py,v
retrieving revision 1.4
retrieving revision 1.5
diff -u -r1.4 -r1.5
--- /home/repository/moby/moby-live/Python/bioMoby/ontology/Sample.py	2005/02/01 08:52:16	1.4
+++ /home/repository/moby/moby-live/Python/bioMoby/ontology/Sample.py	2005/02/01 14:20:44	1.5
@@ -29,7 +29,9 @@
         """ Load the attributes from an XML string
         """
         from bioMoby.mobyMarshal import MobyUnmarshaller
-        doc=parseString(value).firstChild
+        doc=value
+        if isinstance(value, str):
+            doc=parseString(value).firstChild
         um=MobyUnmarshaller()
         self.content=""
         self.namespace=doc.getAttribute("moby:namespace")
@@ -49,12 +51,12 @@
             if elt.nodeName=="CrossReference" or elt.nodeName=="moby:CrossReference":
                 self.__cross__=[]
                 for ref in elt.childNodes:
-                    self.__cross__.append(ref.toxml())
+                    self.__cross__.append(um.loads(ref))
             if elt.nodeType==elt.ELEMENT_NODE and (elt.nodeName=="String" or elt.nodeName=="moby:String") and (elt.getAttribute("articleName")=="code" or elt.getAttribute("moby:articleName")=="code"):
                 t=MobyString()
-                t.fromMoby(elt.toxml())
+                t.fromMoby(elt)
                 self.Code=t.content
             if elt.nodeType==elt.ELEMENT_NODE and (elt.nodeName=="Integer" or elt.nodeName=="moby:Integer") and (elt.getAttribute("articleName")=="affectation" or elt.getAttribute("moby:articleName")=="affectation"):
                 t=MobyInteger()
-                t.fromMoby(elt.toxml())
+                t.fromMoby(elt)
                 self.Affectation=t.content
\ No newline at end of file

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/ontology/SchematikonMotifID.py,v
retrieving revision 1.4
retrieving revision 1.5
diff -u -r1.4 -r1.5
--- /home/repository/moby/moby-live/Python/bioMoby/ontology/SchematikonMotifID.py	2005/02/01 08:52:16	1.4
+++ /home/repository/moby/moby-live/Python/bioMoby/ontology/SchematikonMotifID.py	2005/02/01 14:20:44	1.5
@@ -27,7 +27,9 @@
         """ Load the attributes from an XML string
         """
         from bioMoby.mobyMarshal import MobyUnmarshaller
-        doc=parseString(value).firstChild
+        doc=value
+        if isinstance(value, str):
+            doc=parseString(value).firstChild
         um=MobyUnmarshaller()
         self.content=""
         self.namespace=doc.getAttribute("moby:namespace")
@@ -47,8 +49,8 @@
             if elt.nodeName=="CrossReference" or elt.nodeName=="moby:CrossReference":
                 self.__cross__=[]
                 for ref in elt.childNodes:
-                    self.__cross__.append(ref.toxml())
+                    self.__cross__.append(um.loads(ref))
             if elt.nodeType==elt.ELEMENT_NODE and (elt.nodeName=="String" or elt.nodeName=="moby:String") and (elt.getAttribute("articleName")=="ID" or elt.getAttribute("moby:articleName")=="ID"):
                 t=MobyString()
-                t.fromMoby(elt.toxml())
+                t.fromMoby(elt)
                 self.ID=t.content
\ No newline at end of file

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/ontology/SchematikonMotifSupport.py,v
retrieving revision 1.4
retrieving revision 1.5
diff -u -r1.4 -r1.5
--- /home/repository/moby/moby-live/Python/bioMoby/ontology/SchematikonMotifSupport.py	2005/02/01 08:52:16	1.4
+++ /home/repository/moby/moby-live/Python/bioMoby/ontology/SchematikonMotifSupport.py	2005/02/01 14:20:44	1.5
@@ -28,7 +28,9 @@
         """ Load the attributes from an XML string
         """
         from bioMoby.mobyMarshal import MobyUnmarshaller
-        doc=parseString(value).firstChild
+        doc=value
+        if isinstance(value, str):
+            doc=parseString(value).firstChild
         um=MobyUnmarshaller()
         self.content=""
         self.namespace=doc.getAttribute("moby:namespace")
@@ -48,12 +50,12 @@
             if elt.nodeName=="CrossReference" or elt.nodeName=="moby:CrossReference":
                 self.__cross__=[]
                 for ref in elt.childNodes:
-                    self.__cross__.append(ref.toxml())
+                    self.__cross__.append(um.loads(ref))
             if elt.nodeType==elt.ELEMENT_NODE and (elt.nodeName=="Integer" or elt.nodeName=="moby:Integer") and (elt.getAttribute("articleName")=="UniqueSupport" or elt.getAttribute("moby:articleName")=="UniqueSupport"):
                 t=MobyInteger()
-                t.fromMoby(elt.toxml())
+                t.fromMoby(elt)
                 self.UniqueSupport=t.content
             if elt.nodeType==elt.ELEMENT_NODE and (elt.nodeName=="Integer" or elt.nodeName=="moby:Integer") and (elt.getAttribute("articleName")=="Support" or elt.getAttribute("moby:articleName")=="Support"):
                 t=MobyInteger()
-                t.fromMoby(elt.toxml())
+                t.fromMoby(elt)
                 self.Support=t.content
\ No newline at end of file

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/ontology/SchematikonSegmentAttributes.py,v
retrieving revision 1.4
retrieving revision 1.5
diff -u -r1.4 -r1.5
--- /home/repository/moby/moby-live/Python/bioMoby/ontology/SchematikonSegmentAttributes.py	2005/02/01 08:52:16	1.4
+++ /home/repository/moby/moby-live/Python/bioMoby/ontology/SchematikonSegmentAttributes.py	2005/02/01 14:20:44	1.5
@@ -32,7 +32,9 @@
         """ Load the attributes from an XML string
         """
         from bioMoby.mobyMarshal import MobyUnmarshaller
-        doc=parseString(value).firstChild
+        doc=value
+        if isinstance(value, str):
+            doc=parseString(value).firstChild
         um=MobyUnmarshaller()
         self.content=""
         self.namespace=doc.getAttribute("moby:namespace")
@@ -52,24 +54,24 @@
             if elt.nodeName=="CrossReference" or elt.nodeName=="moby:CrossReference":
                 self.__cross__=[]
                 for ref in elt.childNodes:
-                    self.__cross__.append(ref.toxml())
+                    self.__cross__.append(um.loads(ref))
             if elt.nodeType==elt.ELEMENT_NODE and (elt.nodeName=="Integer" or elt.nodeName=="moby:Integer") and (elt.getAttribute("articleName")=="Length" or elt.getAttribute("moby:articleName")=="Length"):
                 t=MobyInteger()
-                t.fromMoby(elt.toxml())
+                t.fromMoby(elt)
                 self.Length=t.content
             if elt.nodeType==elt.ELEMENT_NODE and (elt.nodeName=="String" or elt.nodeName=="moby:String") and (elt.getAttribute("articleName")=="Insert code" or elt.getAttribute("moby:articleName")=="Insert code"):
                 t=MobyString()
-                t.fromMoby(elt.toxml())
+                t.fromMoby(elt)
                 self.InsertCode=t.content
             if elt.nodeType==elt.ELEMENT_NODE and (elt.nodeName=="Integer" or elt.nodeName=="moby:Integer") and (elt.getAttribute("articleName")=="Starting amino acid position" or elt.getAttribute("moby:articleName")=="Starting amino acid position"):
                 t=MobyInteger()
-                t.fromMoby(elt.toxml())
+                t.fromMoby(elt)
                 self.StartingAminoAcidPosition=t.content
             if elt.nodeType==elt.ELEMENT_NODE and (elt.nodeName=="String" or elt.nodeName=="moby:String") and (elt.getAttribute("articleName")=="Chain ID" or elt.getAttribute("moby:articleName")=="Chain ID"):
                 t=MobyString()
-                t.fromMoby(elt.toxml())
+                t.fromMoby(elt)
                 self.ChainID=t.content
             if elt.nodeType==elt.ELEMENT_NODE and (elt.nodeName=="String" or elt.nodeName=="moby:String") and (elt.getAttribute("articleName")=="PDB ID" or elt.getAttribute("moby:articleName")=="PDB ID"):
                 t=MobyString()
-                t.fromMoby(elt.toxml())
+                t.fromMoby(elt)
                 self.PDBID=t.content
\ No newline at end of file

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/ontology/SchematikonSegmentID.py,v
retrieving revision 1.4
retrieving revision 1.5
diff -u -r1.4 -r1.5
--- /home/repository/moby/moby-live/Python/bioMoby/ontology/SchematikonSegmentID.py	2005/02/01 08:52:16	1.4
+++ /home/repository/moby/moby-live/Python/bioMoby/ontology/SchematikonSegmentID.py	2005/02/01 14:20:44	1.5
@@ -27,7 +27,9 @@
         """ Load the attributes from an XML string
         """
         from bioMoby.mobyMarshal import MobyUnmarshaller
-        doc=parseString(value).firstChild
+        doc=value
+        if isinstance(value, str):
+            doc=parseString(value).firstChild
         um=MobyUnmarshaller()
         self.content=""
         self.namespace=doc.getAttribute("moby:namespace")
@@ -47,8 +49,8 @@
             if elt.nodeName=="CrossReference" or elt.nodeName=="moby:CrossReference":
                 self.__cross__=[]
                 for ref in elt.childNodes:
-                    self.__cross__.append(ref.toxml())
+                    self.__cross__.append(um.loads(ref))
             if elt.nodeType==elt.ELEMENT_NODE and (elt.nodeName=="String" or elt.nodeName=="moby:String") and (elt.getAttribute("articleName")=="ID" or elt.getAttribute("moby:articleName")=="ID"):
                 t=MobyString()
-                t.fromMoby(elt.toxml())
+                t.fromMoby(elt)
                 self.ID=t.content
\ No newline at end of file

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/ontology/SchematikonStructureAnnotation.py,v
retrieving revision 1.4
retrieving revision 1.5
diff -u -r1.4 -r1.5
--- /home/repository/moby/moby-live/Python/bioMoby/ontology/SchematikonStructureAnnotation.py	2005/02/01 08:52:16	1.4
+++ /home/repository/moby/moby-live/Python/bioMoby/ontology/SchematikonStructureAnnotation.py	2005/02/01 14:20:44	1.5
@@ -30,7 +30,9 @@
         """ Load the attributes from an XML string
         """
         from bioMoby.mobyMarshal import MobyUnmarshaller
-        doc=parseString(value).firstChild
+        doc=value
+        if isinstance(value, str):
+            doc=parseString(value).firstChild
         um=MobyUnmarshaller()
         self.content=""
         self.namespace=doc.getAttribute("moby:namespace")
@@ -50,20 +52,20 @@
             if elt.nodeName=="CrossReference" or elt.nodeName=="moby:CrossReference":
                 self.__cross__=[]
                 for ref in elt.childNodes:
-                    self.__cross__.append(ref.toxml())
+                    self.__cross__.append(um.loads(ref))
             if elt.nodeType==elt.ELEMENT_NODE and (elt.nodeName=="String" or elt.nodeName=="moby:String") and (elt.getAttribute("articleName")=="PROMOTIF gamma-turn" or elt.getAttribute("moby:articleName")=="PROMOTIF gamma-turn"):
                 t=MobyString()
-                t.fromMoby(elt.toxml())
+                t.fromMoby(elt)
                 self.PROMOTIFGammaTurn=t.content
             if elt.nodeType==elt.ELEMENT_NODE and (elt.nodeName=="String" or elt.nodeName=="moby:String") and (elt.getAttribute("articleName")=="PROMOTIF beta-turn" or elt.getAttribute("moby:articleName")=="PROMOTIF beta-turn"):
                 t=MobyString()
-                t.fromMoby(elt.toxml())
+                t.fromMoby(elt)
                 self.PROMOTIFBetaTurn=t.content
             if elt.nodeType==elt.ELEMENT_NODE and (elt.nodeName=="String" or elt.nodeName=="moby:String") and (elt.getAttribute("articleName")=="DSSP" or elt.getAttribute("moby:articleName")=="DSSP"):
                 t=MobyString()
-                t.fromMoby(elt.toxml())
+                t.fromMoby(elt)
                 self.DSSP=t.content
             if elt.nodeType==elt.ELEMENT_NODE and (elt.nodeName=="String" or elt.nodeName=="moby:String") and (elt.getAttribute("articleName")=="STRIDE" or elt.getAttribute("moby:articleName")=="STRIDE"):
                 t=MobyString()
-                t.fromMoby(elt.toxml())
+                t.fromMoby(elt)
                 self.STRIDE=t.content
\ No newline at end of file

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/ontology/SchematikonVorocodeName.py,v
retrieving revision 1.4
retrieving revision 1.5
diff -u -r1.4 -r1.5
--- /home/repository/moby/moby-live/Python/bioMoby/ontology/SchematikonVorocodeName.py	2005/02/01 08:52:16	1.4
+++ /home/repository/moby/moby-live/Python/bioMoby/ontology/SchematikonVorocodeName.py	2005/02/01 14:20:44	1.5
@@ -27,7 +27,9 @@
         """ Load the attributes from an XML string
         """
         from bioMoby.mobyMarshal import MobyUnmarshaller
-        doc=parseString(value).firstChild
+        doc=value
+        if isinstance(value, str):
+            doc=parseString(value).firstChild
         um=MobyUnmarshaller()
         self.content=""
         self.namespace=doc.getAttribute("moby:namespace")
@@ -47,8 +49,8 @@
             if elt.nodeName=="CrossReference" or elt.nodeName=="moby:CrossReference":
                 self.__cross__=[]
                 for ref in elt.childNodes:
-                    self.__cross__.append(ref.toxml())
+                    self.__cross__.append(um.loads(ref))
             if elt.nodeType==elt.ELEMENT_NODE and (elt.nodeName=="String" or elt.nodeName=="moby:String") and (elt.getAttribute("articleName")=="VorocodeName" or elt.getAttribute("moby:articleName")=="VorocodeName"):
                 t=MobyString()
-                t.fromMoby(elt.toxml())
+                t.fromMoby(elt)
                 self.VorocodeName=t.content
\ No newline at end of file

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/ontology/Scored_acronym_string.py,v
retrieving revision 1.4
retrieving revision 1.5
diff -u -r1.4 -r1.5
--- /home/repository/moby/moby-live/Python/bioMoby/ontology/Scored_acronym_string.py	2005/02/01 08:52:16	1.4
+++ /home/repository/moby/moby-live/Python/bioMoby/ontology/Scored_acronym_string.py	2005/02/01 14:20:44	1.5
@@ -30,7 +30,9 @@
         """ Load the attributes from an XML string
         """
         from bioMoby.mobyMarshal import MobyUnmarshaller
-        doc=parseString(value).firstChild
+        doc=value
+        if isinstance(value, str):
+            doc=parseString(value).firstChild
         um=MobyUnmarshaller()
         self.content=""
         self.namespace=doc.getAttribute("moby:namespace")
@@ -50,15 +52,15 @@
             if elt.nodeName=="CrossReference" or elt.nodeName=="moby:CrossReference":
                 self.__cross__=[]
                 for ref in elt.childNodes:
-                    self.__cross__.append(ref.toxml())
+                    self.__cross__.append(um.loads(ref))
             if elt.nodeType==elt.ELEMENT_NODE and (elt.nodeName=="Float" or elt.nodeName=="moby:Float") and (elt.getAttribute("articleName")=="score" or elt.getAttribute("moby:articleName")=="score"):
                 t=MobyFloat()
-                t.fromMoby(elt.toxml())
+                t.fromMoby(elt)
                 self.Score=t.content
             if elt.nodeType==elt.ELEMENT_NODE and (elt.nodeName=="Object" or elt.nodeName=="moby:Object") and (elt.getAttribute("articleName")=="string_component" or elt.getAttribute("moby:articleName")=="string_component"):
                 self.String_component=MobyObject()
-                self.String_component.fromMoby(elt.toxml())
+                self.String_component.fromMoby(elt)
             if elt.nodeType==elt.ELEMENT_NODE and (elt.nodeName=="String" or elt.nodeName=="moby:String") and (elt.getAttribute("articleName")=="acronym" or elt.getAttribute("moby:articleName")=="acronym"):
                 t=MobyString()
-                t.fromMoby(elt.toxml())
+                t.fromMoby(elt)
                 self.Acronym=t.content
\ No newline at end of file

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/ontology/SimpleAnnotatedGIFImage.py,v
retrieving revision 1.4
retrieving revision 1.5
diff -u -r1.4 -r1.5
--- /home/repository/moby/moby-live/Python/bioMoby/ontology/SimpleAnnotatedGIFImage.py	2005/02/01 08:52:16	1.4
+++ /home/repository/moby/moby-live/Python/bioMoby/ontology/SimpleAnnotatedGIFImage.py	2005/02/01 14:20:44	1.5
@@ -28,7 +28,9 @@
         """ Load the attributes from an XML string
         """
         from bioMoby.mobyMarshal import MobyUnmarshaller
-        doc=parseString(value).firstChild
+        doc=value
+        if isinstance(value, str):
+            doc=parseString(value).firstChild
         um=MobyUnmarshaller()
         self.content=""
         self.namespace=doc.getAttribute("moby:namespace")
@@ -48,8 +50,8 @@
             if elt.nodeName=="CrossReference" or elt.nodeName=="moby:CrossReference":
                 self.__cross__=[]
                 for ref in elt.childNodes:
-                    self.__cross__.append(ref.toxml())
+                    self.__cross__.append(um.loads(ref))
             if elt.nodeType==elt.ELEMENT_NODE and (elt.nodeName=="String" or elt.nodeName=="moby:String") and (elt.getAttribute("articleName")=="Description" or elt.getAttribute("moby:articleName")=="Description"):
                 t=MobyString()
-                t.fromMoby(elt.toxml())
+                t.fromMoby(elt)
                 self.Description=t.content
\ No newline at end of file

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/ontology/SimpleAnnotatedJPEGImage.py,v
retrieving revision 1.4
retrieving revision 1.5
diff -u -r1.4 -r1.5
--- /home/repository/moby/moby-live/Python/bioMoby/ontology/SimpleAnnotatedJPEGImage.py	2005/02/01 08:52:16	1.4
+++ /home/repository/moby/moby-live/Python/bioMoby/ontology/SimpleAnnotatedJPEGImage.py	2005/02/01 14:20:44	1.5
@@ -28,7 +28,9 @@
         """ Load the attributes from an XML string
         """
         from bioMoby.mobyMarshal import MobyUnmarshaller
-        doc=parseString(value).firstChild
+        doc=value
+        if isinstance(value, str):
+            doc=parseString(value).firstChild
         um=MobyUnmarshaller()
         self.content=""
         self.namespace=doc.getAttribute("moby:namespace")
@@ -49,8 +51,8 @@
             if elt.nodeName=="CrossReference" or elt.nodeName=="moby:CrossReference":
                 self.__cross__=[]
                 for ref in elt.childNodes:
-                    self.__cross__.append(ref.toxml())
+                    self.__cross__.append(um.loads(ref))
             if elt.nodeType==elt.ELEMENT_NODE and (elt.nodeName=="String" or elt.nodeName=="moby:String") and (elt.getAttribute("articleName")=="Description" or elt.getAttribute("moby:articleName")=="Description"):
                 t=MobyString()
-                t.fromMoby(elt.toxml())
+                t.fromMoby(elt)
                 self.Description.append(t.content)
\ No newline at end of file

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/ontology/Simple_key_value_pair.py,v
retrieving revision 1.4
retrieving revision 1.5
diff -u -r1.4 -r1.5
--- /home/repository/moby/moby-live/Python/bioMoby/ontology/Simple_key_value_pair.py	2005/02/01 08:52:16	1.4
+++ /home/repository/moby/moby-live/Python/bioMoby/ontology/Simple_key_value_pair.py	2005/02/01 14:20:44	1.5
@@ -28,7 +28,9 @@
         """ Load the attributes from an XML string
         """
         from bioMoby.mobyMarshal import MobyUnmarshaller
-        doc=parseString(value).firstChild
+        doc=value
+        if isinstance(value, str):
+            doc=parseString(value).firstChild
         um=MobyUnmarshaller()
         self.content=""
         self.namespace=doc.getAttribute("moby:namespace")
@@ -48,12 +50,12 @@
             if elt.nodeName=="CrossReference" or elt.nodeName=="moby:CrossReference":
                 self.__cross__=[]
                 for ref in elt.childNodes:
-                    self.__cross__.append(ref.toxml())
+                    self.__cross__.append(um.loads(ref))
             if elt.nodeType==elt.ELEMENT_NODE and (elt.nodeName=="String" or elt.nodeName=="moby:String") and (elt.getAttribute("articleName")=="value" or elt.getAttribute("moby:articleName")=="value"):
                 t=MobyString()
-                t.fromMoby(elt.toxml())
+                t.fromMoby(elt)
                 self.Value=t.content
             if elt.nodeType==elt.ELEMENT_NODE and (elt.nodeName=="String" or elt.nodeName=="moby:String") and (elt.getAttribute("articleName")=="key" or elt.getAttribute("moby:articleName")=="key"):
                 t=MobyString()
-                t.fromMoby(elt.toxml())
+                t.fromMoby(elt)
                 self.Key=t.content
\ No newline at end of file

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/ontology/Snp_allele.py,v
retrieving revision 1.4
retrieving revision 1.5
diff -u -r1.4 -r1.5
--- /home/repository/moby/moby-live/Python/bioMoby/ontology/Snp_allele.py	2005/02/01 08:52:16	1.4
+++ /home/repository/moby/moby-live/Python/bioMoby/ontology/Snp_allele.py	2005/02/01 14:20:44	1.5
@@ -23,7 +23,9 @@
         """ Load the attributes from an XML string
         """
         from bioMoby.mobyMarshal import MobyUnmarshaller
-        doc=parseString(value).firstChild
+        doc=value
+        if isinstance(value, str):
+            doc=parseString(value).firstChild
         um=MobyUnmarshaller()
         self.content=""
 
@@ -37,7 +39,7 @@
             if elt.nodeName=="CrossReference" or elt.nodeName=="moby:CrossReference":
                 self.__cross__=[]
                 for ref in elt.childNodes:
-                    self.__cross__.append(ref.toxml())
+                    self.__cross__.append(um.loads(ref))
             if elt.nodeType==elt.ELEMENT_NODE and (elt.nodeName=="DNASequence" or elt.nodeName=="moby:DNASequence") and (elt.getAttribute("articleName")=="snp_allele" or elt.getAttribute("moby:articleName")=="snp_allele"):
                 self.Snp_allele=MobyDNASequence()
-                self.Snp_allele.fromMoby(elt.toxml())
\ No newline at end of file
+                self.Snp_allele.fromMoby(elt)
\ No newline at end of file

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/ontology/Snp_genotype.py,v
retrieving revision 1.4
retrieving revision 1.5
diff -u -r1.4 -r1.5
--- /home/repository/moby/moby-live/Python/bioMoby/ontology/Snp_genotype.py	2005/02/01 08:52:16	1.4
+++ /home/repository/moby/moby-live/Python/bioMoby/ontology/Snp_genotype.py	2005/02/01 14:20:44	1.5
@@ -24,7 +24,9 @@
         """ Load the attributes from an XML string
         """
         from bioMoby.mobyMarshal import MobyUnmarshaller
-        doc=parseString(value).firstChild
+        doc=value
+        if isinstance(value, str):
+            doc=parseString(value).firstChild
         um=MobyUnmarshaller()
         self.content=""
 
@@ -38,10 +40,10 @@
             if elt.nodeName=="CrossReference" or elt.nodeName=="moby:CrossReference":
                 self.__cross__=[]
                 for ref in elt.childNodes:
-                    self.__cross__.append(ref.toxml())
+                    self.__cross__.append(um.loads(ref))
             if elt.nodeType==elt.ELEMENT_NODE and (elt.nodeName=="snp_allele" or elt.nodeName=="moby:snp_allele") and (elt.getAttribute("articleName")=="allele1" or elt.getAttribute("moby:articleName")=="allele1"):
                 self.Allele1=MobySnp_allele()
-                self.Allele1.fromMoby(elt.toxml())
+                self.Allele1.fromMoby(elt)
             if elt.nodeType==elt.ELEMENT_NODE and (elt.nodeName=="snp_allele" or elt.nodeName=="moby:snp_allele") and (elt.getAttribute("articleName")=="allele2" or elt.getAttribute("moby:articleName")=="allele2"):
                 self.Allele2=MobySnp_allele()
-                self.Allele2.fromMoby(elt.toxml())
\ No newline at end of file
+                self.Allele2.fromMoby(elt)
\ No newline at end of file

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/ontology/Study.py,v
retrieving revision 1.4
retrieving revision 1.5
diff -u -r1.4 -r1.5
--- /home/repository/moby/moby-live/Python/bioMoby/ontology/Study.py	2005/02/01 08:52:16	1.4
+++ /home/repository/moby/moby-live/Python/bioMoby/ontology/Study.py	2005/02/01 14:20:44	1.5
@@ -30,7 +30,9 @@
         """ Load the attributes from an XML string
         """
         from bioMoby.mobyMarshal import MobyUnmarshaller
-        doc=parseString(value).firstChild
+        doc=value
+        if isinstance(value, str):
+            doc=parseString(value).firstChild
         um=MobyUnmarshaller()
         self.content=""
         self.namespace=doc.getAttribute("moby:namespace")
@@ -50,16 +52,16 @@
             if elt.nodeName=="CrossReference" or elt.nodeName=="moby:CrossReference":
                 self.__cross__=[]
                 for ref in elt.childNodes:
-                    self.__cross__.append(ref.toxml())
+                    self.__cross__.append(um.loads(ref))
             if elt.nodeType==elt.ELEMENT_NODE and (elt.nodeName=="String" or elt.nodeName=="moby:String") and (elt.getAttribute("articleName")=="study_name" or elt.getAttribute("moby:articleName")=="study_name"):
                 t=MobyString()
-                t.fromMoby(elt.toxml())
+                t.fromMoby(elt)
                 self.Study_name=t.content
             if elt.nodeType==elt.ELEMENT_NODE and (elt.nodeName=="Integer" or elt.nodeName=="moby:Integer") and (elt.getAttribute("articleName")=="study_id" or elt.getAttribute("moby:articleName")=="study_id"):
                 t=MobyInteger()
-                t.fromMoby(elt.toxml())
+                t.fromMoby(elt)
                 self.Study_id=t.content
             if elt.nodeType==elt.ELEMENT_NODE and (elt.nodeName=="String" or elt.nodeName=="moby:String") and (elt.getAttribute("articleName")=="study_desc" or elt.getAttribute("moby:articleName")=="study_desc"):
                 t=MobyString()
-                t.fromMoby(elt.toxml())
+                t.fromMoby(elt)
                 self.Study_desc=t.content
\ No newline at end of file

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/ontology/TEST.py,v
retrieving revision 1.4
retrieving revision 1.5
diff -u -r1.4 -r1.5
--- /home/repository/moby/moby-live/Python/bioMoby/ontology/TEST.py	2005/02/01 08:52:16	1.4
+++ /home/repository/moby/moby-live/Python/bioMoby/ontology/TEST.py	2005/02/01 14:20:44	1.5
@@ -26,7 +26,9 @@
         """ Load the attributes from an XML string
         """
         from bioMoby.mobyMarshal import MobyUnmarshaller
-        doc=parseString(value).firstChild
+        doc=value
+        if isinstance(value, str):
+            doc=parseString(value).firstChild
         um=MobyUnmarshaller()
         self.content=""
         self.namespace=doc.getAttribute("moby:namespace")
@@ -46,4 +48,4 @@
             if elt.nodeName=="CrossReference" or elt.nodeName=="moby:CrossReference":
                 self.__cross__=[]
                 for ref in elt.childNodes:
-                    self.__cross__.append(ref.toxml())
\ No newline at end of file
+                    self.__cross__.append(um.loads(ref))
\ No newline at end of file

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/ontology/TargetP_result.py,v
retrieving revision 1.4
retrieving revision 1.5
diff -u -r1.4 -r1.5
--- /home/repository/moby/moby-live/Python/bioMoby/ontology/TargetP_result.py	2005/02/01 08:52:16	1.4
+++ /home/repository/moby/moby-live/Python/bioMoby/ontology/TargetP_result.py	2005/02/01 14:20:44	1.5
@@ -32,7 +32,9 @@
         """ Load the attributes from an XML string
         """
         from bioMoby.mobyMarshal import MobyUnmarshaller
-        doc=parseString(value).firstChild
+        doc=value
+        if isinstance(value, str):
+            doc=parseString(value).firstChild
         um=MobyUnmarshaller()
         self.content=""
         self.namespace=doc.getAttribute("moby:namespace")
@@ -52,24 +54,24 @@
             if elt.nodeName=="CrossReference" or elt.nodeName=="moby:CrossReference":
                 self.__cross__=[]
                 for ref in elt.childNodes:
-                    self.__cross__.append(ref.toxml())
+                    self.__cross__.append(um.loads(ref))
             if elt.nodeType==elt.ELEMENT_NODE and (elt.nodeName=="Float" or elt.nodeName=="moby:Float") and (elt.getAttribute("articleName")=="o_score" or elt.getAttribute("moby:articleName")=="o_score"):
                 t=MobyFloat()
-                t.fromMoby(elt.toxml())
+                t.fromMoby(elt)
                 self.O_score=t.content
             if elt.nodeType==elt.ELEMENT_NODE and (elt.nodeName=="Float" or elt.nodeName=="moby:Float") and (elt.getAttribute("articleName")=="s_score" or elt.getAttribute("moby:articleName")=="s_score"):
                 t=MobyFloat()
-                t.fromMoby(elt.toxml())
+                t.fromMoby(elt)
                 self.S_score=t.content
             if elt.nodeType==elt.ELEMENT_NODE and (elt.nodeName=="Float" or elt.nodeName=="moby:Float") and (elt.getAttribute("articleName")=="m_score" or elt.getAttribute("moby:articleName")=="m_score"):
                 t=MobyFloat()
-                t.fromMoby(elt.toxml())
+                t.fromMoby(elt)
                 self.M_score=t.content
             if elt.nodeType==elt.ELEMENT_NODE and (elt.nodeName=="Float" or elt.nodeName=="moby:Float") and (elt.getAttribute("articleName")=="c_score" or elt.getAttribute("moby:articleName")=="c_score"):
                 t=MobyFloat()
-                t.fromMoby(elt.toxml())
+                t.fromMoby(elt)
                 self.C_score=t.content
             if elt.nodeType==elt.ELEMENT_NODE and (elt.nodeName=="String" or elt.nodeName=="moby:String") and (elt.getAttribute("articleName")=="compartment" or elt.getAttribute("moby:articleName")=="compartment"):
                 t=MobyString()
-                t.fromMoby(elt.toxml())
+                t.fromMoby(elt)
                 self.Compartment=t.content
\ No newline at end of file

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/ontology/Testout.py,v
retrieving revision 1.4
retrieving revision 1.5
diff -u -r1.4 -r1.5
--- /home/repository/moby/moby-live/Python/bioMoby/ontology/Testout.py	2005/02/01 08:52:16	1.4
+++ /home/repository/moby/moby-live/Python/bioMoby/ontology/Testout.py	2005/02/01 14:20:44	1.5
@@ -31,7 +31,9 @@
         """ Load the attributes from an XML string
         """
         from bioMoby.mobyMarshal import MobyUnmarshaller
-        doc=parseString(value).firstChild
+        doc=value
+        if isinstance(value, str):
+            doc=parseString(value).firstChild
         um=MobyUnmarshaller()
         self.content=""
         self.namespace=doc.getAttribute("moby:namespace")
@@ -51,20 +53,20 @@
             if elt.nodeName=="CrossReference" or elt.nodeName=="moby:CrossReference":
                 self.__cross__=[]
                 for ref in elt.childNodes:
-                    self.__cross__.append(ref.toxml())
+                    self.__cross__.append(um.loads(ref))
             if elt.nodeType==elt.ELEMENT_NODE and (elt.nodeName=="Integer" or elt.nodeName=="moby:Integer") and (elt.getAttribute("articleName")=="gid" or elt.getAttribute("moby:articleName")=="gid"):
                 t=MobyInteger()
-                t.fromMoby(elt.toxml())
+                t.fromMoby(elt)
                 self.Gid=t.content
             if elt.nodeType==elt.ELEMENT_NODE and (elt.nodeName=="String" or elt.nodeName=="moby:String") and (elt.getAttribute("articleName")=="dvalue" or elt.getAttribute("moby:articleName")=="dvalue"):
                 t=MobyString()
-                t.fromMoby(elt.toxml())
+                t.fromMoby(elt)
                 self.Dvalue=t.content
             if elt.nodeType==elt.ELEMENT_NODE and (elt.nodeName=="Integer" or elt.nodeName=="moby:Integer") and (elt.getAttribute("articleName")=="scaleid" or elt.getAttribute("moby:articleName")=="scaleid"):
                 t=MobyInteger()
-                t.fromMoby(elt.toxml())
+                t.fromMoby(elt)
                 self.Scaleid=t.content
             if elt.nodeType==elt.ELEMENT_NODE and (elt.nodeName=="Integer" or elt.nodeName=="moby:Integer") and (elt.getAttribute("articleName")=="tmethid" or elt.getAttribute("moby:articleName")=="tmethid"):
                 t=MobyInteger()
-                t.fromMoby(elt.toxml())
+                t.fromMoby(elt)
                 self.Tmethid=t.content
\ No newline at end of file

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/ontology/TextBase64.py,v
retrieving revision 1.4
retrieving revision 1.5
diff -u -r1.4 -r1.5
--- /home/repository/moby/moby-live/Python/bioMoby/ontology/TextBase64.py	2005/02/01 08:52:16	1.4
+++ /home/repository/moby/moby-live/Python/bioMoby/ontology/TextBase64.py	2005/02/01 14:20:44	1.5
@@ -26,7 +26,9 @@
         """ Load the attributes from an XML string
         """
         from bioMoby.mobyMarshal import MobyUnmarshaller
-        doc=parseString(value).firstChild
+        doc=value
+        if isinstance(value, str):
+            doc=parseString(value).firstChild
         um=MobyUnmarshaller()
         self.content=""
         self.namespace=doc.getAttribute("moby:namespace")
@@ -46,4 +48,4 @@
             if elt.nodeName=="CrossReference" or elt.nodeName=="moby:CrossReference":
                 self.__cross__=[]
                 for ref in elt.childNodes:
-                    self.__cross__.append(ref.toxml())
\ No newline at end of file
+                    self.__cross__.append(um.loads(ref))
\ No newline at end of file

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/ontology/TextFormatted.py,v
retrieving revision 1.4
retrieving revision 1.5
diff -u -r1.4 -r1.5
--- /home/repository/moby/moby-live/Python/bioMoby/ontology/TextFormatted.py	2005/02/01 08:52:16	1.4
+++ /home/repository/moby/moby-live/Python/bioMoby/ontology/TextFormatted.py	2005/02/01 14:20:44	1.5
@@ -26,7 +26,9 @@
         """ Load the attributes from an XML string
         """
         from bioMoby.mobyMarshal import MobyUnmarshaller
-        doc=parseString(value).firstChild
+        doc=value
+        if isinstance(value, str):
+            doc=parseString(value).firstChild
         um=MobyUnmarshaller()
         self.content=""
         self.namespace=doc.getAttribute("moby:namespace")
@@ -46,4 +48,4 @@
             if elt.nodeName=="CrossReference" or elt.nodeName=="moby:CrossReference":
                 self.__cross__=[]
                 for ref in elt.childNodes:
-                    self.__cross__.append(ref.toxml())
\ No newline at end of file
+                    self.__cross__.append(um.loads(ref))
\ No newline at end of file

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/ontology/TextHtml.py,v
retrieving revision 1.4
retrieving revision 1.5
diff -u -r1.4 -r1.5
--- /home/repository/moby/moby-live/Python/bioMoby/ontology/TextHtml.py	2005/02/01 08:52:16	1.4
+++ /home/repository/moby/moby-live/Python/bioMoby/ontology/TextHtml.py	2005/02/01 14:20:44	1.5
@@ -26,7 +26,9 @@
         """ Load the attributes from an XML string
         """
         from bioMoby.mobyMarshal import MobyUnmarshaller
-        doc=parseString(value).firstChild
+        doc=value
+        if isinstance(value, str):
+            doc=parseString(value).firstChild
         um=MobyUnmarshaller()
         self.content=""
         self.namespace=doc.getAttribute("moby:namespace")
@@ -46,4 +48,4 @@
             if elt.nodeName=="CrossReference" or elt.nodeName=="moby:CrossReference":
                 self.__cross__=[]
                 for ref in elt.childNodes:
-                    self.__cross__.append(ref.toxml())
\ No newline at end of file
+                    self.__cross__.append(um.loads(ref))
\ No newline at end of file

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/ontology/TextPlain.py,v
retrieving revision 1.4
retrieving revision 1.5
diff -u -r1.4 -r1.5
--- /home/repository/moby/moby-live/Python/bioMoby/ontology/TextPlain.py	2005/02/01 08:52:16	1.4
+++ /home/repository/moby/moby-live/Python/bioMoby/ontology/TextPlain.py	2005/02/01 14:20:44	1.5
@@ -26,7 +26,9 @@
         """ Load the attributes from an XML string
         """
         from bioMoby.mobyMarshal import MobyUnmarshaller
-        doc=parseString(value).firstChild
+        doc=value
+        if isinstance(value, str):
+            doc=parseString(value).firstChild
         um=MobyUnmarshaller()
         self.content=""
         self.namespace=doc.getAttribute("moby:namespace")
@@ -46,4 +48,4 @@
             if elt.nodeName=="CrossReference" or elt.nodeName=="moby:CrossReference":
                 self.__cross__=[]
                 for ref in elt.childNodes:
-                    self.__cross__.append(ref.toxml())
\ No newline at end of file
+                    self.__cross__.append(um.loads(ref))
\ No newline at end of file

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/ontology/TextUuencoded.py,v
retrieving revision 1.4
retrieving revision 1.5
diff -u -r1.4 -r1.5
--- /home/repository/moby/moby-live/Python/bioMoby/ontology/TextUuencoded.py	2005/02/01 08:52:16	1.4
+++ /home/repository/moby/moby-live/Python/bioMoby/ontology/TextUuencoded.py	2005/02/01 14:20:44	1.5
@@ -26,7 +26,9 @@
         """ Load the attributes from an XML string
         """
         from bioMoby.mobyMarshal import MobyUnmarshaller
-        doc=parseString(value).firstChild
+        doc=value
+        if isinstance(value, str):
+            doc=parseString(value).firstChild
         um=MobyUnmarshaller()
         self.content=""
         self.namespace=doc.getAttribute("moby:namespace")
@@ -46,4 +48,4 @@
             if elt.nodeName=="CrossReference" or elt.nodeName=="moby:CrossReference":
                 self.__cross__=[]
                 for ref in elt.childNodes:
-                    self.__cross__.append(ref.toxml())
\ No newline at end of file
+                    self.__cross__.append(um.loads(ref))
\ No newline at end of file

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/ontology/TextXml.py,v
retrieving revision 1.4
retrieving revision 1.5
diff -u -r1.4 -r1.5
--- /home/repository/moby/moby-live/Python/bioMoby/ontology/TextXml.py	2005/02/01 08:52:16	1.4
+++ /home/repository/moby/moby-live/Python/bioMoby/ontology/TextXml.py	2005/02/01 14:20:44	1.5
@@ -26,7 +26,9 @@
         """ Load the attributes from an XML string
         """
         from bioMoby.mobyMarshal import MobyUnmarshaller
-        doc=parseString(value).firstChild
+        doc=value
+        if isinstance(value, str):
+            doc=parseString(value).firstChild
         um=MobyUnmarshaller()
         self.content=""
         self.namespace=doc.getAttribute("moby:namespace")
@@ -46,4 +48,4 @@
             if elt.nodeName=="CrossReference" or elt.nodeName=="moby:CrossReference":
                 self.__cross__=[]
                 for ref in elt.childNodes:
-                    self.__cross__.append(ref.toxml())
\ No newline at end of file
+                    self.__cross__.append(um.loads(ref))
\ No newline at end of file

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/ontology/Text_plain.py,v
retrieving revision 1.4
retrieving revision 1.5
diff -u -r1.4 -r1.5
--- /home/repository/moby/moby-live/Python/bioMoby/ontology/Text_plain.py	2005/02/01 08:52:16	1.4
+++ /home/repository/moby/moby-live/Python/bioMoby/ontology/Text_plain.py	2005/02/01 14:20:44	1.5
@@ -26,7 +26,9 @@
         """ Load the attributes from an XML string
         """
         from bioMoby.mobyMarshal import MobyUnmarshaller
-        doc=parseString(value).firstChild
+        doc=value
+        if isinstance(value, str):
+            doc=parseString(value).firstChild
         um=MobyUnmarshaller()
         self.content=""
         self.namespace=doc.getAttribute("moby:namespace")
@@ -46,4 +48,4 @@
             if elt.nodeName=="CrossReference" or elt.nodeName=="moby:CrossReference":
                 self.__cross__=[]
                 for ref in elt.childNodes:
-                    self.__cross__.append(ref.toxml())
\ No newline at end of file
+                    self.__cross__.append(um.loads(ref))
\ No newline at end of file

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/ontology/Trait_Details.py,v
retrieving revision 1.4
retrieving revision 1.5
diff -u -r1.4 -r1.5
--- /home/repository/moby/moby-live/Python/bioMoby/ontology/Trait_Details.py	2005/02/01 08:52:16	1.4
+++ /home/repository/moby/moby-live/Python/bioMoby/ontology/Trait_Details.py	2005/02/01 14:20:44	1.5
@@ -32,7 +32,9 @@
         """ Load the attributes from an XML string
         """
         from bioMoby.mobyMarshal import MobyUnmarshaller
-        doc=parseString(value).firstChild
+        doc=value
+        if isinstance(value, str):
+            doc=parseString(value).firstChild
         um=MobyUnmarshaller()
         self.content=""
         self.namespace=doc.getAttribute("moby:namespace")
@@ -52,24 +54,24 @@
             if elt.nodeName=="CrossReference" or elt.nodeName=="moby:CrossReference":
                 self.__cross__=[]
                 for ref in elt.childNodes:
-                    self.__cross__.append(ref.toxml())
+                    self.__cross__.append(um.loads(ref))
             if elt.nodeType==elt.ELEMENT_NODE and (elt.nodeName=="String" or elt.nodeName=="moby:String") and (elt.getAttribute("articleName")=="trait_desc" or elt.getAttribute("moby:articleName")=="trait_desc"):
                 t=MobyString()
-                t.fromMoby(elt.toxml())
+                t.fromMoby(elt)
                 self.Trait_desc=t.content
             if elt.nodeType==elt.ELEMENT_NODE and (elt.nodeName=="Integer" or elt.nodeName=="moby:Integer") and (elt.getAttribute("articleName")=="num_studies" or elt.getAttribute("moby:articleName")=="num_studies"):
                 t=MobyInteger()
-                t.fromMoby(elt.toxml())
+                t.fromMoby(elt)
                 self.Num_studies=t.content
             if elt.nodeType==elt.ELEMENT_NODE and (elt.nodeName=="String" or elt.nodeName=="moby:String") and (elt.getAttribute("articleName")=="trait_abbr" or elt.getAttribute("moby:articleName")=="trait_abbr"):
                 t=MobyString()
-                t.fromMoby(elt.toxml())
+                t.fromMoby(elt)
                 self.Trait_abbr=t.content
             if elt.nodeType==elt.ELEMENT_NODE and (elt.nodeName=="Integer" or elt.nodeName=="moby:Integer") and (elt.getAttribute("articleName")=="trait_id" or elt.getAttribute("moby:articleName")=="trait_id"):
                 t=MobyInteger()
-                t.fromMoby(elt.toxml())
+                t.fromMoby(elt)
                 self.Trait_id=t.content
             if elt.nodeType==elt.ELEMENT_NODE and (elt.nodeName=="String" or elt.nodeName=="moby:String") and (elt.getAttribute("articleName")=="trait_name" or elt.getAttribute("moby:articleName")=="trait_name"):
                 t=MobyString()
-                t.fromMoby(elt.toxml())
+                t.fromMoby(elt)
                 self.Trait_name=t.content
\ No newline at end of file

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/ontology/Tree.py,v
retrieving revision 1.4
retrieving revision 1.5
diff -u -r1.4 -r1.5
--- /home/repository/moby/moby-live/Python/bioMoby/ontology/Tree.py	2005/02/01 08:52:16	1.4
+++ /home/repository/moby/moby-live/Python/bioMoby/ontology/Tree.py	2005/02/01 14:20:44	1.5
@@ -26,7 +26,9 @@
         """ Load the attributes from an XML string
         """
         from bioMoby.mobyMarshal import MobyUnmarshaller
-        doc=parseString(value).firstChild
+        doc=value
+        if isinstance(value, str):
+            doc=parseString(value).firstChild
         um=MobyUnmarshaller()
         self.content=""
         self.namespace=doc.getAttribute("moby:namespace")
@@ -46,4 +48,4 @@
             if elt.nodeName=="CrossReference" or elt.nodeName=="moby:CrossReference":
                 self.__cross__=[]
                 for ref in elt.childNodes:
-                    self.__cross__.append(ref.toxml())
\ No newline at end of file
+                    self.__cross__.append(um.loads(ref))
\ No newline at end of file

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/ontology/TropGENE_ACCESSION.py,v
retrieving revision 1.4
retrieving revision 1.5
diff -u -r1.4 -r1.5
--- /home/repository/moby/moby-live/Python/bioMoby/ontology/TropGENE_ACCESSION.py	2005/02/01 08:52:16	1.4
+++ /home/repository/moby/moby-live/Python/bioMoby/ontology/TropGENE_ACCESSION.py	2005/02/01 14:20:44	1.5
@@ -36,7 +36,9 @@
         """ Load the attributes from an XML string
         """
         from bioMoby.mobyMarshal import MobyUnmarshaller
-        doc=parseString(value).firstChild
+        doc=value
+        if isinstance(value, str):
+            doc=parseString(value).firstChild
         um=MobyUnmarshaller()
         self.content=""
         self.namespace=doc.getAttribute("moby:namespace")
@@ -66,34 +68,34 @@
             if elt.nodeName=="CrossReference" or elt.nodeName=="moby:CrossReference":
                 self.__cross__=[]
                 for ref in elt.childNodes:
-                    self.__cross__.append(ref.toxml())
+                    self.__cross__.append(um.loads(ref))
             if elt.nodeType==elt.ELEMENT_NODE and (elt.nodeName=="TropGENE_LOCUS" or elt.nodeName=="moby:TropGENE_LOCUS") and (elt.getAttribute("articleName")=="RFLP" or elt.getAttribute("moby:articleName")=="RFLP"):
                 self.RFLP=MobyTropGENE_LOCUS()
-                self.RFLP.fromMoby(elt.toxml())
+                self.RFLP.fromMoby(elt)
             if elt.nodeType==elt.ELEMENT_NODE and (elt.nodeName=="TropGENE_LOCUS" or elt.nodeName=="moby:TropGENE_LOCUS") and (elt.getAttribute("articleName")=="AFLP" or elt.getAttribute("moby:articleName")=="AFLP"):
                 self.AFLP=MobyTropGENE_LOCUS()
-                self.AFLP.fromMoby(elt.toxml())
+                self.AFLP.fromMoby(elt)
             if elt.nodeType==elt.ELEMENT_NODE and (elt.nodeName=="TropGENE_LOCUS" or elt.nodeName=="moby:TropGENE_LOCUS") and (elt.getAttribute("articleName")=="RAPD" or elt.getAttribute("moby:articleName")=="RAPD"):
                 self.RAPD=MobyTropGENE_LOCUS()
-                self.RAPD.fromMoby(elt.toxml())
+                self.RAPD.fromMoby(elt)
             if elt.nodeType==elt.ELEMENT_NODE and (elt.nodeName=="TropGENE_LOCUS" or elt.nodeName=="moby:TropGENE_LOCUS") and (elt.getAttribute("articleName")=="Isozyme" or elt.getAttribute("moby:articleName")=="Isozyme"):
                 self.Isozyme=MobyTropGENE_LOCUS()
-                self.Isozyme.fromMoby(elt.toxml())
+                self.Isozyme.fromMoby(elt)
             if elt.nodeType==elt.ELEMENT_NODE and (elt.nodeName=="TropGENE_LOCUS" or elt.nodeName=="moby:TropGENE_LOCUS") and (elt.getAttribute("articleName")=="Polyphenol" or elt.getAttribute("moby:articleName")=="Polyphenol"):
                 self.Polyphenol=MobyTropGENE_LOCUS()
-                self.Polyphenol.fromMoby(elt.toxml())
+                self.Polyphenol.fromMoby(elt)
             if elt.nodeType==elt.ELEMENT_NODE and (elt.nodeName=="TropGENE_LOCUS" or elt.nodeName=="moby:TropGENE_LOCUS") and (elt.getAttribute("articleName")=="Morphological" or elt.getAttribute("moby:articleName")=="Morphological"):
                 self.Morphological=MobyTropGENE_LOCUS()
-                self.Morphological.fromMoby(elt.toxml())
+                self.Morphological.fromMoby(elt)
             if elt.nodeType==elt.ELEMENT_NODE and (elt.nodeName=="TropGENE_LOCUS" or elt.nodeName=="moby:TropGENE_LOCUS") and (elt.getAttribute("articleName")=="Microsatellite" or elt.getAttribute("moby:articleName")=="Microsatellite"):
                 self.Microsatellite=MobyTropGENE_LOCUS()
-                self.Microsatellite.fromMoby(elt.toxml())
+                self.Microsatellite.fromMoby(elt)
             if elt.nodeType==elt.ELEMENT_NODE and (elt.nodeName=="TropGENE_LOCUS" or elt.nodeName=="moby:TropGENE_LOCUS") and (elt.getAttribute("articleName")=="SNP" or elt.getAttribute("moby:articleName")=="SNP"):
                 self.SNP=MobyTropGENE_LOCUS()
-                self.SNP.fromMoby(elt.toxml())
+                self.SNP.fromMoby(elt)
             if elt.nodeType==elt.ELEMENT_NODE and (elt.nodeName=="TropGENE_LOCUS" or elt.nodeName=="moby:TropGENE_LOCUS") and (elt.getAttribute("articleName")=="CAPS" or elt.getAttribute("moby:articleName")=="CAPS"):
                 self.CAPS=MobyTropGENE_LOCUS()
-                self.CAPS.fromMoby(elt.toxml())
+                self.CAPS.fromMoby(elt)
             if elt.nodeType==elt.ELEMENT_NODE and (elt.nodeName=="TropGENE_LOCUS" or elt.nodeName=="moby:TropGENE_LOCUS") and (elt.getAttribute("articleName")=="TAMPL" or elt.getAttribute("moby:articleName")=="TAMPL"):
                 self.TAMPL=MobyTropGENE_LOCUS()
-                self.TAMPL.fromMoby(elt.toxml())
\ No newline at end of file
+                self.TAMPL.fromMoby(elt)
\ No newline at end of file

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/ontology/TropGENE_Diversity_Matrix.py,v
retrieving revision 1.4
retrieving revision 1.5
diff -u -r1.4 -r1.5
--- /home/repository/moby/moby-live/Python/bioMoby/ontology/TropGENE_Diversity_Matrix.py	2005/02/01 08:52:16	1.4
+++ /home/repository/moby/moby-live/Python/bioMoby/ontology/TropGENE_Diversity_Matrix.py	2005/02/01 14:20:44	1.5
@@ -26,7 +26,9 @@
         """ Load the attributes from an XML string
         """
         from bioMoby.mobyMarshal import MobyUnmarshaller
-        doc=parseString(value).firstChild
+        doc=value
+        if isinstance(value, str):
+            doc=parseString(value).firstChild
         um=MobyUnmarshaller()
         self.content=""
         self.namespace=doc.getAttribute("moby:namespace")
@@ -46,4 +48,4 @@
             if elt.nodeName=="CrossReference" or elt.nodeName=="moby:CrossReference":
                 self.__cross__=[]
                 for ref in elt.childNodes:
-                    self.__cross__.append(ref.toxml())
\ No newline at end of file
+                    self.__cross__.append(um.loads(ref))
\ No newline at end of file

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/ontology/TropGENE_LOCUS.py,v
retrieving revision 1.4
retrieving revision 1.5
diff -u -r1.4 -r1.5
--- /home/repository/moby/moby-live/Python/bioMoby/ontology/TropGENE_LOCUS.py	2005/02/01 08:52:16	1.4
+++ /home/repository/moby/moby-live/Python/bioMoby/ontology/TropGENE_LOCUS.py	2005/02/01 14:20:44	1.5
@@ -25,7 +25,9 @@
         """ Load the attributes from an XML string
         """
         from bioMoby.mobyMarshal import MobyUnmarshaller
-        doc=parseString(value).firstChild
+        doc=value
+        if isinstance(value, str):
+            doc=parseString(value).firstChild
         um=MobyUnmarshaller()
         self.content=""
         self.namespace=doc.getAttribute("moby:namespace")
@@ -45,4 +47,4 @@
             if elt.nodeName=="CrossReference" or elt.nodeName=="moby:CrossReference":
                 self.__cross__=[]
                 for ref in elt.childNodes:
-                    self.__cross__.append(ref.toxml())
\ No newline at end of file
+                    self.__cross__.append(um.loads(ref))
\ No newline at end of file

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/ontology/VirtualSequence.py,v
retrieving revision 1.4
retrieving revision 1.5
diff -u -r1.4 -r1.5
--- /home/repository/moby/moby-live/Python/bioMoby/ontology/VirtualSequence.py	2005/02/01 08:52:16	1.4
+++ /home/repository/moby/moby-live/Python/bioMoby/ontology/VirtualSequence.py	2005/02/01 14:20:44	1.5
@@ -27,7 +27,9 @@
         """ Load the attributes from an XML string
         """
         from bioMoby.mobyMarshal import MobyUnmarshaller
-        doc=parseString(value).firstChild
+        doc=value
+        if isinstance(value, str):
+            doc=parseString(value).firstChild
         um=MobyUnmarshaller()
         self.content=""
         self.namespace=doc.getAttribute("moby:namespace")
@@ -47,8 +49,8 @@
             if elt.nodeName=="CrossReference" or elt.nodeName=="moby:CrossReference":
                 self.__cross__=[]
                 for ref in elt.childNodes:
-                    self.__cross__.append(ref.toxml())
+                    self.__cross__.append(um.loads(ref))
             if elt.nodeType==elt.ELEMENT_NODE and (elt.nodeName=="Integer" or elt.nodeName=="moby:Integer") and (elt.getAttribute("articleName")=="Length" or elt.getAttribute("moby:articleName")=="Length"):
                 t=MobyInteger()
-                t.fromMoby(elt.toxml())
+                t.fromMoby(elt)
                 self.Length=t.content
\ No newline at end of file

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/ontology/WU_BLAST_Text.py,v
retrieving revision 1.4
retrieving revision 1.5
diff -u -r1.4 -r1.5
--- /home/repository/moby/moby-live/Python/bioMoby/ontology/WU_BLAST_Text.py	2005/02/01 08:52:16	1.4
+++ /home/repository/moby/moby-live/Python/bioMoby/ontology/WU_BLAST_Text.py	2005/02/01 14:20:44	1.5
@@ -26,7 +26,9 @@
         """ Load the attributes from an XML string
         """
         from bioMoby.mobyMarshal import MobyUnmarshaller
-        doc=parseString(value).firstChild
+        doc=value
+        if isinstance(value, str):
+            doc=parseString(value).firstChild
         um=MobyUnmarshaller()
         self.content=""
         self.namespace=doc.getAttribute("moby:namespace")
@@ -46,4 +48,4 @@
             if elt.nodeName=="CrossReference" or elt.nodeName=="moby:CrossReference":
                 self.__cross__=[]
                 for ref in elt.childNodes:
-                    self.__cross__.append(ref.toxml())
\ No newline at end of file
+                    self.__cross__.append(um.loads(ref))
\ No newline at end of file

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/ontology/Wildcard_Query.py,v
retrieving revision 1.4
retrieving revision 1.5
diff -u -r1.4 -r1.5
--- /home/repository/moby/moby-live/Python/bioMoby/ontology/Wildcard_Query.py	2005/02/01 08:52:16	1.4
+++ /home/repository/moby/moby-live/Python/bioMoby/ontology/Wildcard_Query.py	2005/02/01 14:20:44	1.5
@@ -30,7 +30,9 @@
         """ Load the attributes from an XML string
         """
         from bioMoby.mobyMarshal import MobyUnmarshaller
-        doc=parseString(value).firstChild
+        doc=value
+        if isinstance(value, str):
+            doc=parseString(value).firstChild
         um=MobyUnmarshaller()
         self.content=""
         self.namespace=doc.getAttribute("moby:namespace")
@@ -50,16 +52,16 @@
             if elt.nodeName=="CrossReference" or elt.nodeName=="moby:CrossReference":
                 self.__cross__=[]
                 for ref in elt.childNodes:
-                    self.__cross__.append(ref.toxml())
+                    self.__cross__.append(um.loads(ref))
             if elt.nodeType==elt.ELEMENT_NODE and (elt.nodeName=="Integer" or elt.nodeName=="moby:Integer") and (elt.getAttribute("articleName")=="end_row" or elt.getAttribute("moby:articleName")=="end_row"):
                 t=MobyInteger()
-                t.fromMoby(elt.toxml())
+                t.fromMoby(elt)
                 self.End_row=t.content
             if elt.nodeType==elt.ELEMENT_NODE and (elt.nodeName=="Integer" or elt.nodeName=="moby:Integer") and (elt.getAttribute("articleName")=="start_row" or elt.getAttribute("moby:articleName")=="start_row"):
                 t=MobyInteger()
-                t.fromMoby(elt.toxml())
+                t.fromMoby(elt)
                 self.Start_row=t.content
             if elt.nodeType==elt.ELEMENT_NODE and (elt.nodeName=="String" or elt.nodeName=="moby:String") and (elt.getAttribute("articleName")=="germplasm_name" or elt.getAttribute("moby:articleName")=="germplasm_name"):
                 t=MobyString()
-                t.fromMoby(elt.toxml())
+                t.fromMoby(elt)
                 self.Germplasm_name=t.content
\ No newline at end of file



From yanwong at pub.open-bio.org  Mon Feb  7 14:12:35 2005
From: yanwong at pub.open-bio.org (Yan Wong)
Date: Mon, 07 Feb 2005 14:12:35 -0000
Subject: [MOBY-guts] biomoby commit
Message-ID: <200502071423.j17ENYJS018965@pub.open-bio.org>


yanwong
Mon Feb  7 09:23:33 EST 2005
Update of /home/repository/moby/moby-live/Python/bioMoby/ontology
In directory pub.open-bio.org:/tmp/cvs-serv18508

Modified Files:
	Alignment.py AlleleAssociation.py Allele_freq.py 
	AminoAcidSequence.py B64_Encoded_PNG.py 
	B64_Encoded_Postscript.py B64_encoded_PDB.py 
	B64_encoded_gif.py B64_encoded_jpeg.py BLASTText.py 
	BasicGFFSequenceFeature.py ClustalAlnFormattedText.py 
	ClustalMsfFormattedText.py CommentedAASequence.py 
	CommentedDNASequence.py CommentedRNASequence.py DNASequence.py 
	DNASequenceWithGFFFeatures.py DateTime.py Decypher_Text.py 
	Edge.py EmblFlatfile.py FASTA.py FASTA_AA.py FASTA_NA.py 
	FASTA_NA_multi.py FASTA_Text.py GFF.py GFF1.py GFF2.py 
	GFF2_5.py GFF3.py GO_Term.py GenbankFlatfile.py 
	Gene_Expression_data.py GenericSequence.py GeneticElement.py 
	Genotype.py Germplasm_Details.py Germplasm_List.py 
	Global_Keyword.py HBond_Pair.py HFormatText.py 
	Haplotyping_Study_obj.py ICIS_Query.py ICIS_Query2.py 
	ICIS_Query3.py IntAct_XML.py Interaction.py 
	InteractionMethod.py Interaction_partner.py Interactor.py 
	MEME_Text.py MGIS_ACCESSION.py MMP_Locus.py MO_Term_Test.py 
	MSF.py MmCIFText.py Multi_key_value_pair.py 
	MyTestingDataType_11024145298313.py MyTree.py 
	NCBI_BLAST_Text.py NCBI_Blast_XML.py NCBI_Blast_XML_Gif.py 
	NCBI_Blast_XML_Gif_Map.py NCBI_MEME_Text.py 
	NucleotideSequence.py PDBFormattedText.py PDBText.py PDGJOB.py 
	PHDText.py PMUTText.py PSeaTextFormatted.py 
	PhenotypeDescription.py PubMedMEDLINE.py RNASequence.py 
	SINGER_ACCESSION.py Sample.py SchematikonMotifID.py 
	SchematikonMotifSupport.py SchematikonSegmentAttributes.py 
	SchematikonSegmentID.py SchematikonStructureAnnotation.py 
	SchematikonVorocodeName.py Scored_acronym_string.py 
	SimpleAnnotatedGIFImage.py SimpleAnnotatedJPEGImage.py 
	Simple_key_value_pair.py Snp_allele.py Snp_genotype.py 
	Study.py TEST.py TargetP_result.py Testout.py TextBase64.py 
	TextFormatted.py TextHtml.py TextPlain.py TextUuencoded.py 
	TextXml.py Text_plain.py Trait_Details.py Tree.py 
	TropGENE_ACCESSION.py TropGENE_Diversity_Matrix.py 
	TropGENE_LOCUS.py VirtualSequence.py WU_BLAST_Text.py 
	Wildcard_Query.py 
Log Message:


moby-live/Python/bioMoby/ontology Alignment.py,1.1,1.2 AlleleAssociation.py,1.5,1.6 Allele_freq.py,1.5,1.6 AminoAcidSequence.py,1.5,1.6 B64_Encoded_PNG.py,1.5,1.6 B64_Encoded_Postscript.py,1.5,1.6 B64_encoded_PDB.py,1.5,1.6 B64_encoded_gif.py,1.5,1.6 B64_encoded_jpeg.py,1.5,1.6 BLASTText.py,1.5,1.6 BasicGFFSequenceFeature.py,1.5,1.6 ClustalAlnFormattedText.py,1.5,1.6 ClustalMsfFormattedText.py,1.5,1.6 CommentedAASequence.py,1.5,1.6 CommentedDNASequence.py,1.5,1.6 CommentedRNASequence.py,1.5,1.6 DNASequence.py,1.5,1.6 DNASequenceWithGFFFeatures.py,1.5,1.6 DateTime.py,1.5,1.6 Decypher_Text.py,1.5,1.6 Edge.py,1.5,1.6 EmblFlatfile.py,1.5,1.6 FASTA.py,1.5,1.6 FASTA_AA.py,1.5,1.6 FASTA_NA.py,1.5,1.6 FASTA_NA_multi.py,1.1,1.2 FASTA_Text.py,1.5,1.6 GFF.py,1.5,1.6 GFF1.py,1.5,1.6 GFF2.py,1.5,1.6 GFF2_5.py,1.5,1.6 GFF3.py,1.5,1.6 GO_Term.py,1.5,1.6 GenbankFlatfile.py,1.5,1.6 Gene_Expression_data.py,1.1,1.2 GenericSequence.py,1.5,1.6 GeneticElement.py,1.5,1.6 Genotype.py,1.5,1.6 Germpl!
asm_Details.py,1.5,1.6 Germplasm_List.py,1.5,1.6 Global_Keyword.py,1.5,1.6 HBond_Pair.py,1.5,1.6 HFormatText.py,1.5,1.6 Haplotyping_Study_obj.py,1.5,1.6 ICIS_Query.py,1.5,1.6 ICIS_Query2.py,1.5,1.6 ICIS_Query3.py,1.5,1.6 IntAct_XML.py,1.5,1.6 Interaction.py,1.5,1.6 InteractionMethod.py,1.5,1.6 Interaction_partner.py,1.5,1.6 Interactor.py,1.5,1.6 MEME_Text.py,1.5,1.6 MGIS_ACCESSION.py,1.5,1.6 MMP_Locus.py,1.5,1.6 MO_Term_Test.py,1.5,1.6 MSF.py,1.1,1.2 MmCIFText.py,1.5,1.6 Multi_key_value_pair.py,1.5,1.6 MyTestingDataType_11024145298313.py,1.5,1.6 MyTree.py,1.5,1.6 NCBI_BLAST_Text.py,1.5,1.6 NCBI_Blast_XML.py,1.5,1.6 NCBI_Blast_XML_Gif.py,1.5,1.6 NCBI_Blast_XML_Gif_Map.py,1.5,1.6 NCBI_MEME_Text.py,1.5,1.6 NucleotideSequence.py,1.5,1.6 PDBFormattedText.py,1.5,1.6 PDBText.py,1.5,1.6 PDGJOB.py,1.5,1.6 PHDText.py,1.5,1.6 PMUTText.py,1.5,1.6 PSeaTextFormatted.py,1.5,1.6 PhenotypeDescription.py,1.5,1.6 PubMedMEDLINE.py,1.5,1.6 RNASequence.py,1.5,1.6 SINGER_ACCESSION.py,1.5,1.6 Sampl!
e.py,1.5,1.6 SchematikonMotifID.py,1.5,1.6 SchematikonMotifSu!
pport.py,1.5,1.6 SchematikonSegmentAttributes.py,1.5,1.6 SchematikonSegmentID.py,1.5,1.6 SchematikonStructureAnnotation.py,1.5,1.6 SchematikonVorocodeName.py,1.5,1.6 Scored_acronym_string.py,1.5,1.6 SimpleAnnotatedGIFImage.py,1.5,1.6 SimpleAnnotatedJPEGImage.py,1.5,1.6 Simple_key_value_pair.py,1.5,1.6 Snp_allele.py,1.5,1.6 Snp_genotype.py,1.5,1.6 Study.py,1.5,1.6 TEST.py,1.5,1.6 TargetP_result.py,1.5,1.6 Testout.py,1.5,1.6 TextBase64.py,1.5,1.6 TextFormatted.py,1.5,1.6 TextHtml.py,1.5,1.6 TextPlain.py,1.5,1.6 TextUuencoded.py,1.5,1.6 TextXml.py,1.5,1.6 Text_plain.py,1.5,1.6 Trait_Details.py,1.5,1.6 Tree.py,1.5,1.6 TropGENE_ACCESSION.py,1.5,1.6 TropGENE_Diversity_Matrix.py,1.5,1.6 TropGENE_LOCUS.py,1.5,1.6 VirtualSequence.py,1.5,1.6 WU_BLAST_Text.py,1.5,1.6 Wildcard_Query.py,1.5,1.6
===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/ontology/Alignment.py,v
retrieving revision 1.1
retrieving revision 1.2
diff -u -r1.1 -r1.2
--- /home/repository/moby/moby-live/Python/bioMoby/ontology/Alignment.py	2005/02/02 15:18:06	1.1
+++ /home/repository/moby/moby-live/Python/bioMoby/ontology/Alignment.py	2005/02/07 14:23:32	1.2
@@ -48,4 +48,5 @@
             if elt.nodeName=="CrossReference" or elt.nodeName=="moby:CrossReference":
                 self.__cross__=[]
                 for ref in elt.childNodes:
-                    self.__cross__.append(um.loads(ref))
\ No newline at end of file
+                    if ref.nodeType==ref.ELEMENT_NODE:
+                        self.__cross__.append(um.loadn(ref))
\ No newline at end of file

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/ontology/AlleleAssociation.py,v
retrieving revision 1.5
retrieving revision 1.6
diff -u -r1.5 -r1.6
--- /home/repository/moby/moby-live/Python/bioMoby/ontology/AlleleAssociation.py	2005/02/01 14:20:44	1.5
+++ /home/repository/moby/moby-live/Python/bioMoby/ontology/AlleleAssociation.py	2005/02/07 14:23:32	1.6
@@ -52,7 +52,8 @@
             if elt.nodeName=="CrossReference" or elt.nodeName=="moby:CrossReference":
                 self.__cross__=[]
                 for ref in elt.childNodes:
-                    self.__cross__.append(um.loads(ref))
+                    if ref.nodeType==ref.ELEMENT_NODE:
+                        self.__cross__.append(um.loadn(ref))
             if elt.nodeType==elt.ELEMENT_NODE and (elt.nodeName=="String" or elt.nodeName=="moby:String") and (elt.getAttribute("articleName")=="snp" or elt.getAttribute("moby:articleName")=="snp"):
                 t=MobyString()
                 t.fromMoby(elt)

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/ontology/Allele_freq.py,v
retrieving revision 1.5
retrieving revision 1.6
diff -u -r1.5 -r1.6
--- /home/repository/moby/moby-live/Python/bioMoby/ontology/Allele_freq.py	2005/02/01 14:20:44	1.5
+++ /home/repository/moby/moby-live/Python/bioMoby/ontology/Allele_freq.py	2005/02/07 14:23:32	1.6
@@ -46,7 +46,8 @@
             if elt.nodeName=="CrossReference" or elt.nodeName=="moby:CrossReference":
                 self.__cross__=[]
                 for ref in elt.childNodes:
-                    self.__cross__.append(um.loads(ref))
+                    if ref.nodeType==ref.ELEMENT_NODE:
+                        self.__cross__.append(um.loadn(ref))
             if elt.nodeType==elt.ELEMENT_NODE and (elt.nodeName=="Object" or elt.nodeName=="moby:Object") and (elt.getAttribute("articleName")=="panel_lsid" or elt.getAttribute("moby:articleName")=="panel_lsid"):
                 self.Panel_lsid=MobyObject()
                 self.Panel_lsid.fromMoby(elt)

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/ontology/AminoAcidSequence.py,v
retrieving revision 1.5
retrieving revision 1.6
diff -u -r1.5 -r1.6
--- /home/repository/moby/moby-live/Python/bioMoby/ontology/AminoAcidSequence.py	2005/02/01 14:20:44	1.5
+++ /home/repository/moby/moby-live/Python/bioMoby/ontology/AminoAcidSequence.py	2005/02/07 14:23:32	1.6
@@ -51,7 +51,8 @@
             if elt.nodeName=="CrossReference" or elt.nodeName=="moby:CrossReference":
                 self.__cross__=[]
                 for ref in elt.childNodes:
-                    self.__cross__.append(um.loads(ref))
+                    if ref.nodeType==ref.ELEMENT_NODE:
+                        self.__cross__.append(um.loadn(ref))
             if elt.nodeType==elt.ELEMENT_NODE and (elt.nodeName=="Integer" or elt.nodeName=="moby:Integer") and (elt.getAttribute("articleName")=="Length" or elt.getAttribute("moby:articleName")=="Length"):
                 t=MobyInteger()
                 t.fromMoby(elt)

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/ontology/B64_Encoded_PNG.py,v
retrieving revision 1.5
retrieving revision 1.6
diff -u -r1.5 -r1.6
--- /home/repository/moby/moby-live/Python/bioMoby/ontology/B64_Encoded_PNG.py	2005/02/01 14:20:44	1.5
+++ /home/repository/moby/moby-live/Python/bioMoby/ontology/B64_Encoded_PNG.py	2005/02/07 14:23:32	1.6
@@ -48,4 +48,5 @@
             if elt.nodeName=="CrossReference" or elt.nodeName=="moby:CrossReference":
                 self.__cross__=[]
                 for ref in elt.childNodes:
-                    self.__cross__.append(um.loads(ref))
\ No newline at end of file
+                    if ref.nodeType==ref.ELEMENT_NODE:
+                        self.__cross__.append(um.loadn(ref))
\ No newline at end of file

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/ontology/B64_Encoded_Postscript.py,v
retrieving revision 1.5
retrieving revision 1.6
diff -u -r1.5 -r1.6
--- /home/repository/moby/moby-live/Python/bioMoby/ontology/B64_Encoded_Postscript.py	2005/02/01 14:20:44	1.5
+++ /home/repository/moby/moby-live/Python/bioMoby/ontology/B64_Encoded_Postscript.py	2005/02/07 14:23:32	1.6
@@ -48,4 +48,5 @@
             if elt.nodeName=="CrossReference" or elt.nodeName=="moby:CrossReference":
                 self.__cross__=[]
                 for ref in elt.childNodes:
-                    self.__cross__.append(um.loads(ref))
\ No newline at end of file
+                    if ref.nodeType==ref.ELEMENT_NODE:
+                        self.__cross__.append(um.loadn(ref))
\ No newline at end of file

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/ontology/B64_encoded_PDB.py,v
retrieving revision 1.5
retrieving revision 1.6
diff -u -r1.5 -r1.6
--- /home/repository/moby/moby-live/Python/bioMoby/ontology/B64_encoded_PDB.py	2005/02/01 14:20:44	1.5
+++ /home/repository/moby/moby-live/Python/bioMoby/ontology/B64_encoded_PDB.py	2005/02/07 14:23:32	1.6
@@ -48,4 +48,5 @@
             if elt.nodeName=="CrossReference" or elt.nodeName=="moby:CrossReference":
                 self.__cross__=[]
                 for ref in elt.childNodes:
-                    self.__cross__.append(um.loads(ref))
\ No newline at end of file
+                    if ref.nodeType==ref.ELEMENT_NODE:
+                        self.__cross__.append(um.loadn(ref))
\ No newline at end of file

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/ontology/B64_encoded_gif.py,v
retrieving revision 1.5
retrieving revision 1.6
diff -u -r1.5 -r1.6
--- /home/repository/moby/moby-live/Python/bioMoby/ontology/B64_encoded_gif.py	2005/02/01 14:20:44	1.5
+++ /home/repository/moby/moby-live/Python/bioMoby/ontology/B64_encoded_gif.py	2005/02/07 14:23:32	1.6
@@ -48,4 +48,5 @@
             if elt.nodeName=="CrossReference" or elt.nodeName=="moby:CrossReference":
                 self.__cross__=[]
                 for ref in elt.childNodes:
-                    self.__cross__.append(um.loads(ref))
\ No newline at end of file
+                    if ref.nodeType==ref.ELEMENT_NODE:
+                        self.__cross__.append(um.loadn(ref))
\ No newline at end of file

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/ontology/B64_encoded_jpeg.py,v
retrieving revision 1.5
retrieving revision 1.6
diff -u -r1.5 -r1.6
--- /home/repository/moby/moby-live/Python/bioMoby/ontology/B64_encoded_jpeg.py	2005/02/01 14:20:44	1.5
+++ /home/repository/moby/moby-live/Python/bioMoby/ontology/B64_encoded_jpeg.py	2005/02/07 14:23:32	1.6
@@ -48,4 +48,5 @@
             if elt.nodeName=="CrossReference" or elt.nodeName=="moby:CrossReference":
                 self.__cross__=[]
                 for ref in elt.childNodes:
-                    self.__cross__.append(um.loads(ref))
\ No newline at end of file
+                    if ref.nodeType==ref.ELEMENT_NODE:
+                        self.__cross__.append(um.loadn(ref))
\ No newline at end of file

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/ontology/BLASTText.py,v
retrieving revision 1.5
retrieving revision 1.6
diff -u -r1.5 -r1.6
--- /home/repository/moby/moby-live/Python/bioMoby/ontology/BLASTText.py	2005/02/01 14:20:44	1.5
+++ /home/repository/moby/moby-live/Python/bioMoby/ontology/BLASTText.py	2005/02/07 14:23:32	1.6
@@ -48,4 +48,5 @@
             if elt.nodeName=="CrossReference" or elt.nodeName=="moby:CrossReference":
                 self.__cross__=[]
                 for ref in elt.childNodes:
-                    self.__cross__.append(um.loads(ref))
\ No newline at end of file
+                    if ref.nodeType==ref.ELEMENT_NODE:
+                        self.__cross__.append(um.loadn(ref))
\ No newline at end of file

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/ontology/BasicGFFSequenceFeature.py,v
retrieving revision 1.5
retrieving revision 1.6
diff -u -r1.5 -r1.6
--- /home/repository/moby/moby-live/Python/bioMoby/ontology/BasicGFFSequenceFeature.py	2005/02/01 14:20:44	1.5
+++ /home/repository/moby/moby-live/Python/bioMoby/ontology/BasicGFFSequenceFeature.py	2005/02/07 14:23:32	1.6
@@ -62,7 +62,8 @@
             if elt.nodeName=="CrossReference" or elt.nodeName=="moby:CrossReference":
                 self.__cross__=[]
                 for ref in elt.childNodes:
-                    self.__cross__.append(um.loads(ref))
+                    if ref.nodeType==ref.ELEMENT_NODE:
+                        self.__cross__.append(um.loadn(ref))
             if elt.nodeType==elt.ELEMENT_NODE and (elt.nodeName=="String" or elt.nodeName=="moby:String") and (elt.getAttribute("articleName")=="reference" or elt.getAttribute("moby:articleName")=="reference"):
                 t=MobyString()
                 t.fromMoby(elt)

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/ontology/ClustalAlnFormattedText.py,v
retrieving revision 1.5
retrieving revision 1.6
diff -u -r1.5 -r1.6
--- /home/repository/moby/moby-live/Python/bioMoby/ontology/ClustalAlnFormattedText.py	2005/02/01 14:20:44	1.5
+++ /home/repository/moby/moby-live/Python/bioMoby/ontology/ClustalAlnFormattedText.py	2005/02/07 14:23:32	1.6
@@ -48,4 +48,5 @@
             if elt.nodeName=="CrossReference" or elt.nodeName=="moby:CrossReference":
                 self.__cross__=[]
                 for ref in elt.childNodes:
-                    self.__cross__.append(um.loads(ref))
\ No newline at end of file
+                    if ref.nodeType==ref.ELEMENT_NODE:
+                        self.__cross__.append(um.loadn(ref))
\ No newline at end of file

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/ontology/ClustalMsfFormattedText.py,v
retrieving revision 1.5
retrieving revision 1.6
diff -u -r1.5 -r1.6
--- /home/repository/moby/moby-live/Python/bioMoby/ontology/ClustalMsfFormattedText.py	2005/02/01 14:20:44	1.5
+++ /home/repository/moby/moby-live/Python/bioMoby/ontology/ClustalMsfFormattedText.py	2005/02/07 14:23:32	1.6
@@ -48,4 +48,5 @@
             if elt.nodeName=="CrossReference" or elt.nodeName=="moby:CrossReference":
                 self.__cross__=[]
                 for ref in elt.childNodes:
-                    self.__cross__.append(um.loads(ref))
\ No newline at end of file
+                    if ref.nodeType==ref.ELEMENT_NODE:
+                        self.__cross__.append(um.loadn(ref))
\ No newline at end of file

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/ontology/CommentedAASequence.py,v
retrieving revision 1.5
retrieving revision 1.6
diff -u -r1.5 -r1.6
--- /home/repository/moby/moby-live/Python/bioMoby/ontology/CommentedAASequence.py	2005/02/01 14:20:44	1.5
+++ /home/repository/moby/moby-live/Python/bioMoby/ontology/CommentedAASequence.py	2005/02/07 14:23:32	1.6
@@ -52,7 +52,8 @@
             if elt.nodeName=="CrossReference" or elt.nodeName=="moby:CrossReference":
                 self.__cross__=[]
                 for ref in elt.childNodes:
-                    self.__cross__.append(um.loads(ref))
+                    if ref.nodeType==ref.ELEMENT_NODE:
+                        self.__cross__.append(um.loadn(ref))
             if elt.nodeType==elt.ELEMENT_NODE and (elt.nodeName=="Integer" or elt.nodeName=="moby:Integer") and (elt.getAttribute("articleName")=="Length" or elt.getAttribute("moby:articleName")=="Length"):
                 t=MobyInteger()
                 t.fromMoby(elt)

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/ontology/CommentedDNASequence.py,v
retrieving revision 1.5
retrieving revision 1.6
diff -u -r1.5 -r1.6
--- /home/repository/moby/moby-live/Python/bioMoby/ontology/CommentedDNASequence.py	2005/02/01 14:20:44	1.5
+++ /home/repository/moby/moby-live/Python/bioMoby/ontology/CommentedDNASequence.py	2005/02/07 14:23:32	1.6
@@ -52,7 +52,8 @@
             if elt.nodeName=="CrossReference" or elt.nodeName=="moby:CrossReference":
                 self.__cross__=[]
                 for ref in elt.childNodes:
-                    self.__cross__.append(um.loads(ref))
+                    if ref.nodeType==ref.ELEMENT_NODE:
+                        self.__cross__.append(um.loadn(ref))
             if elt.nodeType==elt.ELEMENT_NODE and (elt.nodeName=="Integer" or elt.nodeName=="moby:Integer") and (elt.getAttribute("articleName")=="Length" or elt.getAttribute("moby:articleName")=="Length"):
                 t=MobyInteger()
                 t.fromMoby(elt)

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/ontology/CommentedRNASequence.py,v
retrieving revision 1.5
retrieving revision 1.6
diff -u -r1.5 -r1.6
--- /home/repository/moby/moby-live/Python/bioMoby/ontology/CommentedRNASequence.py	2005/02/01 14:20:44	1.5
+++ /home/repository/moby/moby-live/Python/bioMoby/ontology/CommentedRNASequence.py	2005/02/07 14:23:32	1.6
@@ -52,7 +52,8 @@
             if elt.nodeName=="CrossReference" or elt.nodeName=="moby:CrossReference":
                 self.__cross__=[]
                 for ref in elt.childNodes:
-                    self.__cross__.append(um.loads(ref))
+                    if ref.nodeType==ref.ELEMENT_NODE:
+                        self.__cross__.append(um.loadn(ref))
             if elt.nodeType==elt.ELEMENT_NODE and (elt.nodeName=="Integer" or elt.nodeName=="moby:Integer") and (elt.getAttribute("articleName")=="Length" or elt.getAttribute("moby:articleName")=="Length"):
                 t=MobyInteger()
                 t.fromMoby(elt)

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/ontology/DNASequence.py,v
retrieving revision 1.5
retrieving revision 1.6
diff -u -r1.5 -r1.6
--- /home/repository/moby/moby-live/Python/bioMoby/ontology/DNASequence.py	2005/02/01 14:20:44	1.5
+++ /home/repository/moby/moby-live/Python/bioMoby/ontology/DNASequence.py	2005/02/07 14:23:32	1.6
@@ -51,7 +51,8 @@
             if elt.nodeName=="CrossReference" or elt.nodeName=="moby:CrossReference":
                 self.__cross__=[]
                 for ref in elt.childNodes:
-                    self.__cross__.append(um.loads(ref))
+                    if ref.nodeType==ref.ELEMENT_NODE:
+                        self.__cross__.append(um.loadn(ref))
             if elt.nodeType==elt.ELEMENT_NODE and (elt.nodeName=="Integer" or elt.nodeName=="moby:Integer") and (elt.getAttribute("articleName")=="Length" or elt.getAttribute("moby:articleName")=="Length"):
                 t=MobyInteger()
                 t.fromMoby(elt)

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/ontology/DNASequenceWithGFFFeatures.py,v
retrieving revision 1.5
retrieving revision 1.6
diff -u -r1.5 -r1.6
--- /home/repository/moby/moby-live/Python/bioMoby/ontology/DNASequenceWithGFFFeatures.py	2005/02/01 14:20:44	1.5
+++ /home/repository/moby/moby-live/Python/bioMoby/ontology/DNASequenceWithGFFFeatures.py	2005/02/07 14:23:33	1.6
@@ -54,7 +54,8 @@
             if elt.nodeName=="CrossReference" or elt.nodeName=="moby:CrossReference":
                 self.__cross__=[]
                 for ref in elt.childNodes:
-                    self.__cross__.append(um.loads(ref))
+                    if ref.nodeType==ref.ELEMENT_NODE:
+                        self.__cross__.append(um.loadn(ref))
             if elt.nodeType==elt.ELEMENT_NODE and (elt.nodeName=="Integer" or elt.nodeName=="moby:Integer") and (elt.getAttribute("articleName")=="Length" or elt.getAttribute("moby:articleName")=="Length"):
                 t=MobyInteger()
                 t.fromMoby(elt)

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/ontology/DateTime.py,v
retrieving revision 1.5
retrieving revision 1.6
diff -u -r1.5 -r1.6
--- /home/repository/moby/moby-live/Python/bioMoby/ontology/DateTime.py	2005/02/01 14:20:44	1.5
+++ /home/repository/moby/moby-live/Python/bioMoby/ontology/DateTime.py	2005/02/07 14:23:33	1.6
@@ -48,4 +48,5 @@
             if elt.nodeName=="CrossReference" or elt.nodeName=="moby:CrossReference":
                 self.__cross__=[]
                 for ref in elt.childNodes:
-                    self.__cross__.append(um.loads(ref))
\ No newline at end of file
+                    if ref.nodeType==ref.ELEMENT_NODE:
+                        self.__cross__.append(um.loadn(ref))
\ No newline at end of file

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/ontology/Decypher_Text.py,v
retrieving revision 1.5
retrieving revision 1.6
diff -u -r1.5 -r1.6
--- /home/repository/moby/moby-live/Python/bioMoby/ontology/Decypher_Text.py	2005/02/01 14:20:44	1.5
+++ /home/repository/moby/moby-live/Python/bioMoby/ontology/Decypher_Text.py	2005/02/07 14:23:33	1.6
@@ -48,4 +48,5 @@
             if elt.nodeName=="CrossReference" or elt.nodeName=="moby:CrossReference":
                 self.__cross__=[]
                 for ref in elt.childNodes:
-                    self.__cross__.append(um.loads(ref))
\ No newline at end of file
+                    if ref.nodeType==ref.ELEMENT_NODE:
+                        self.__cross__.append(um.loadn(ref))
\ No newline at end of file

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/ontology/Edge.py,v
retrieving revision 1.5
retrieving revision 1.6
diff -u -r1.5 -r1.6
--- /home/repository/moby/moby-live/Python/bioMoby/ontology/Edge.py	2005/02/01 14:20:44	1.5
+++ /home/repository/moby/moby-live/Python/bioMoby/ontology/Edge.py	2005/02/07 14:23:33	1.6
@@ -51,7 +51,8 @@
             if elt.nodeName=="CrossReference" or elt.nodeName=="moby:CrossReference":
                 self.__cross__=[]
                 for ref in elt.childNodes:
-                    self.__cross__.append(um.loads(ref))
+                    if ref.nodeType==ref.ELEMENT_NODE:
+                        self.__cross__.append(um.loadn(ref))
             if elt.nodeType==elt.ELEMENT_NODE and (elt.nodeName=="String" or elt.nodeName=="moby:String") and (elt.getAttribute("articleName")=="partner" or elt.getAttribute("moby:articleName")=="partner"):
                 t=MobyString()
                 t.fromMoby(elt)

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/ontology/EmblFlatfile.py,v
retrieving revision 1.5
retrieving revision 1.6
diff -u -r1.5 -r1.6
--- /home/repository/moby/moby-live/Python/bioMoby/ontology/EmblFlatfile.py	2005/02/01 14:20:44	1.5
+++ /home/repository/moby/moby-live/Python/bioMoby/ontology/EmblFlatfile.py	2005/02/07 14:23:33	1.6
@@ -48,4 +48,5 @@
             if elt.nodeName=="CrossReference" or elt.nodeName=="moby:CrossReference":
                 self.__cross__=[]
                 for ref in elt.childNodes:
-                    self.__cross__.append(um.loads(ref))
\ No newline at end of file
+                    if ref.nodeType==ref.ELEMENT_NODE:
+                        self.__cross__.append(um.loadn(ref))
\ No newline at end of file

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/ontology/FASTA.py,v
retrieving revision 1.5
retrieving revision 1.6
diff -u -r1.5 -r1.6
--- /home/repository/moby/moby-live/Python/bioMoby/ontology/FASTA.py	2005/02/01 14:20:44	1.5
+++ /home/repository/moby/moby-live/Python/bioMoby/ontology/FASTA.py	2005/02/07 14:23:33	1.6
@@ -48,4 +48,5 @@
             if elt.nodeName=="CrossReference" or elt.nodeName=="moby:CrossReference":
                 self.__cross__=[]
                 for ref in elt.childNodes:
-                    self.__cross__.append(um.loads(ref))
\ No newline at end of file
+                    if ref.nodeType==ref.ELEMENT_NODE:
+                        self.__cross__.append(um.loadn(ref))
\ No newline at end of file

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/ontology/FASTA_AA.py,v
retrieving revision 1.5
retrieving revision 1.6
diff -u -r1.5 -r1.6
--- /home/repository/moby/moby-live/Python/bioMoby/ontology/FASTA_AA.py	2005/02/01 14:20:44	1.5
+++ /home/repository/moby/moby-live/Python/bioMoby/ontology/FASTA_AA.py	2005/02/07 14:23:33	1.6
@@ -48,4 +48,5 @@
             if elt.nodeName=="CrossReference" or elt.nodeName=="moby:CrossReference":
                 self.__cross__=[]
                 for ref in elt.childNodes:
-                    self.__cross__.append(um.loads(ref))
\ No newline at end of file
+                    if ref.nodeType==ref.ELEMENT_NODE:
+                        self.__cross__.append(um.loadn(ref))
\ No newline at end of file

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/ontology/FASTA_NA.py,v
retrieving revision 1.5
retrieving revision 1.6
diff -u -r1.5 -r1.6
--- /home/repository/moby/moby-live/Python/bioMoby/ontology/FASTA_NA.py	2005/02/01 14:20:44	1.5
+++ /home/repository/moby/moby-live/Python/bioMoby/ontology/FASTA_NA.py	2005/02/07 14:23:33	1.6
@@ -48,4 +48,5 @@
             if elt.nodeName=="CrossReference" or elt.nodeName=="moby:CrossReference":
                 self.__cross__=[]
                 for ref in elt.childNodes:
-                    self.__cross__.append(um.loads(ref))
\ No newline at end of file
+                    if ref.nodeType==ref.ELEMENT_NODE:
+                        self.__cross__.append(um.loadn(ref))
\ No newline at end of file

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/ontology/FASTA_NA_multi.py,v
retrieving revision 1.1
retrieving revision 1.2
diff -u -r1.1 -r1.2
--- /home/repository/moby/moby-live/Python/bioMoby/ontology/FASTA_NA_multi.py	2005/02/02 15:20:55	1.1
+++ /home/repository/moby/moby-live/Python/bioMoby/ontology/FASTA_NA_multi.py	2005/02/07 14:23:33	1.2
@@ -48,4 +48,5 @@
             if elt.nodeName=="CrossReference" or elt.nodeName=="moby:CrossReference":
                 self.__cross__=[]
                 for ref in elt.childNodes:
-                    self.__cross__.append(um.loads(ref))
\ No newline at end of file
+                    if ref.nodeType==ref.ELEMENT_NODE:
+                        self.__cross__.append(um.loadn(ref))
\ No newline at end of file

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/ontology/FASTA_Text.py,v
retrieving revision 1.5
retrieving revision 1.6
diff -u -r1.5 -r1.6
--- /home/repository/moby/moby-live/Python/bioMoby/ontology/FASTA_Text.py	2005/02/01 14:20:44	1.5
+++ /home/repository/moby/moby-live/Python/bioMoby/ontology/FASTA_Text.py	2005/02/07 14:23:33	1.6
@@ -48,4 +48,5 @@
             if elt.nodeName=="CrossReference" or elt.nodeName=="moby:CrossReference":
                 self.__cross__=[]
                 for ref in elt.childNodes:
-                    self.__cross__.append(um.loads(ref))
\ No newline at end of file
+                    if ref.nodeType==ref.ELEMENT_NODE:
+                        self.__cross__.append(um.loadn(ref))
\ No newline at end of file

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/ontology/GFF.py,v
retrieving revision 1.5
retrieving revision 1.6
diff -u -r1.5 -r1.6
--- /home/repository/moby/moby-live/Python/bioMoby/ontology/GFF.py	2005/02/01 14:20:44	1.5
+++ /home/repository/moby/moby-live/Python/bioMoby/ontology/GFF.py	2005/02/07 14:23:33	1.6
@@ -48,4 +48,5 @@
             if elt.nodeName=="CrossReference" or elt.nodeName=="moby:CrossReference":
                 self.__cross__=[]
                 for ref in elt.childNodes:
-                    self.__cross__.append(um.loads(ref))
\ No newline at end of file
+                    if ref.nodeType==ref.ELEMENT_NODE:
+                        self.__cross__.append(um.loadn(ref))
\ No newline at end of file

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/ontology/GFF1.py,v
retrieving revision 1.5
retrieving revision 1.6
diff -u -r1.5 -r1.6
--- /home/repository/moby/moby-live/Python/bioMoby/ontology/GFF1.py	2005/02/01 14:20:44	1.5
+++ /home/repository/moby/moby-live/Python/bioMoby/ontology/GFF1.py	2005/02/07 14:23:33	1.6
@@ -48,4 +48,5 @@
             if elt.nodeName=="CrossReference" or elt.nodeName=="moby:CrossReference":
                 self.__cross__=[]
                 for ref in elt.childNodes:
-                    self.__cross__.append(um.loads(ref))
\ No newline at end of file
+                    if ref.nodeType==ref.ELEMENT_NODE:
+                        self.__cross__.append(um.loadn(ref))
\ No newline at end of file

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/ontology/GFF2.py,v
retrieving revision 1.5
retrieving revision 1.6
diff -u -r1.5 -r1.6
--- /home/repository/moby/moby-live/Python/bioMoby/ontology/GFF2.py	2005/02/01 14:20:44	1.5
+++ /home/repository/moby/moby-live/Python/bioMoby/ontology/GFF2.py	2005/02/07 14:23:33	1.6
@@ -48,4 +48,5 @@
             if elt.nodeName=="CrossReference" or elt.nodeName=="moby:CrossReference":
                 self.__cross__=[]
                 for ref in elt.childNodes:
-                    self.__cross__.append(um.loads(ref))
\ No newline at end of file
+                    if ref.nodeType==ref.ELEMENT_NODE:
+                        self.__cross__.append(um.loadn(ref))
\ No newline at end of file

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/ontology/GFF2_5.py,v
retrieving revision 1.5
retrieving revision 1.6
diff -u -r1.5 -r1.6
--- /home/repository/moby/moby-live/Python/bioMoby/ontology/GFF2_5.py	2005/02/01 14:20:44	1.5
+++ /home/repository/moby/moby-live/Python/bioMoby/ontology/GFF2_5.py	2005/02/07 14:23:33	1.6
@@ -48,4 +48,5 @@
             if elt.nodeName=="CrossReference" or elt.nodeName=="moby:CrossReference":
                 self.__cross__=[]
                 for ref in elt.childNodes:
-                    self.__cross__.append(um.loads(ref))
\ No newline at end of file
+                    if ref.nodeType==ref.ELEMENT_NODE:
+                        self.__cross__.append(um.loadn(ref))
\ No newline at end of file

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/ontology/GFF3.py,v
retrieving revision 1.5
retrieving revision 1.6
diff -u -r1.5 -r1.6
--- /home/repository/moby/moby-live/Python/bioMoby/ontology/GFF3.py	2005/02/01 14:20:44	1.5
+++ /home/repository/moby/moby-live/Python/bioMoby/ontology/GFF3.py	2005/02/07 14:23:33	1.6
@@ -48,4 +48,5 @@
             if elt.nodeName=="CrossReference" or elt.nodeName=="moby:CrossReference":
                 self.__cross__=[]
                 for ref in elt.childNodes:
-                    self.__cross__.append(um.loads(ref))
\ No newline at end of file
+                    if ref.nodeType==ref.ELEMENT_NODE:
+                        self.__cross__.append(um.loadn(ref))
\ No newline at end of file

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/ontology/GO_Term.py,v
retrieving revision 1.5
retrieving revision 1.6
diff -u -r1.5 -r1.6
--- /home/repository/moby/moby-live/Python/bioMoby/ontology/GO_Term.py	2005/02/01 14:20:44	1.5
+++ /home/repository/moby/moby-live/Python/bioMoby/ontology/GO_Term.py	2005/02/07 14:23:33	1.6
@@ -50,7 +50,8 @@
             if elt.nodeName=="CrossReference" or elt.nodeName=="moby:CrossReference":
                 self.__cross__=[]
                 for ref in elt.childNodes:
-                    self.__cross__.append(um.loads(ref))
+                    if ref.nodeType==ref.ELEMENT_NODE:
+                        self.__cross__.append(um.loadn(ref))
             if elt.nodeType==elt.ELEMENT_NODE and (elt.nodeName=="String" or elt.nodeName=="moby:String") and (elt.getAttribute("articleName")=="Term" or elt.getAttribute("moby:articleName")=="Term"):
                 t=MobyString()
                 t.fromMoby(elt)

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/ontology/GenbankFlatfile.py,v
retrieving revision 1.5
retrieving revision 1.6
diff -u -r1.5 -r1.6
--- /home/repository/moby/moby-live/Python/bioMoby/ontology/GenbankFlatfile.py	2005/02/01 14:20:44	1.5
+++ /home/repository/moby/moby-live/Python/bioMoby/ontology/GenbankFlatfile.py	2005/02/07 14:23:33	1.6
@@ -48,4 +48,5 @@
             if elt.nodeName=="CrossReference" or elt.nodeName=="moby:CrossReference":
                 self.__cross__=[]
                 for ref in elt.childNodes:
-                    self.__cross__.append(um.loads(ref))
\ No newline at end of file
+                    if ref.nodeType==ref.ELEMENT_NODE:
+                        self.__cross__.append(um.loadn(ref))
\ No newline at end of file

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/ontology/Gene_Expression_data.py,v
retrieving revision 1.1
retrieving revision 1.2
diff -u -r1.1 -r1.2
--- /home/repository/moby/moby-live/Python/bioMoby/ontology/Gene_Expression_data.py	2005/02/02 15:20:55	1.1
+++ /home/repository/moby/moby-live/Python/bioMoby/ontology/Gene_Expression_data.py	2005/02/07 14:23:33	1.2
@@ -49,7 +49,8 @@
             if elt.nodeName=="CrossReference" or elt.nodeName=="moby:CrossReference":
                 self.__cross__=[]
                 for ref in elt.childNodes:
-                    self.__cross__.append(um.loads(ref))
+                    if ref.nodeType==ref.ELEMENT_NODE:
+                        self.__cross__.append(um.loadn(ref))
             if elt.nodeType==elt.ELEMENT_NODE and (elt.nodeName=="String" or elt.nodeName=="moby:String") and (elt.getAttribute("articleName")=="Expression data" or elt.getAttribute("moby:articleName")=="Expression data"):
                 t=MobyString()
                 t.fromMoby(elt)

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/ontology/GenericSequence.py,v
retrieving revision 1.5
retrieving revision 1.6
diff -u -r1.5 -r1.6
--- /home/repository/moby/moby-live/Python/bioMoby/ontology/GenericSequence.py	2005/02/01 14:20:44	1.5
+++ /home/repository/moby/moby-live/Python/bioMoby/ontology/GenericSequence.py	2005/02/07 14:23:33	1.6
@@ -51,7 +51,8 @@
             if elt.nodeName=="CrossReference" or elt.nodeName=="moby:CrossReference":
                 self.__cross__=[]
                 for ref in elt.childNodes:
-                    self.__cross__.append(um.loads(ref))
+                    if ref.nodeType==ref.ELEMENT_NODE:
+                        self.__cross__.append(um.loadn(ref))
             if elt.nodeType==elt.ELEMENT_NODE and (elt.nodeName=="Integer" or elt.nodeName=="moby:Integer") and (elt.getAttribute("articleName")=="Length" or elt.getAttribute("moby:articleName")=="Length"):
                 t=MobyInteger()
                 t.fromMoby(elt)

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/ontology/GeneticElement.py,v
retrieving revision 1.5
retrieving revision 1.6
diff -u -r1.5 -r1.6
--- /home/repository/moby/moby-live/Python/bioMoby/ontology/GeneticElement.py	2005/02/01 14:20:44	1.5
+++ /home/repository/moby/moby-live/Python/bioMoby/ontology/GeneticElement.py	2005/02/07 14:23:33	1.6
@@ -49,7 +49,8 @@
             if elt.nodeName=="CrossReference" or elt.nodeName=="moby:CrossReference":
                 self.__cross__=[]
                 for ref in elt.childNodes:
-                    self.__cross__.append(um.loads(ref))
+                    if ref.nodeType==ref.ELEMENT_NODE:
+                        self.__cross__.append(um.loadn(ref))
             if elt.nodeType==elt.ELEMENT_NODE and (elt.nodeName=="String" or elt.nodeName=="moby:String") and (elt.getAttribute("articleName")=="GeneticElement" or elt.getAttribute("moby:articleName")=="GeneticElement"):
                 t=MobyString()
                 t.fromMoby(elt)

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/ontology/Genotype.py,v
retrieving revision 1.5
retrieving revision 1.6
diff -u -r1.5 -r1.6
--- /home/repository/moby/moby-live/Python/bioMoby/ontology/Genotype.py	2005/02/01 14:20:44	1.5
+++ /home/repository/moby/moby-live/Python/bioMoby/ontology/Genotype.py	2005/02/07 14:23:33	1.6
@@ -51,7 +51,8 @@
             if elt.nodeName=="CrossReference" or elt.nodeName=="moby:CrossReference":
                 self.__cross__=[]
                 for ref in elt.childNodes:
-                    self.__cross__.append(um.loads(ref))
+                    if ref.nodeType==ref.ELEMENT_NODE:
+                        self.__cross__.append(um.loadn(ref))
             if elt.nodeType==elt.ELEMENT_NODE and (elt.nodeName=="String" or elt.nodeName=="moby:String") and (elt.getAttribute("articleName")=="snp" or elt.getAttribute("moby:articleName")=="snp"):
                 t=MobyString()
                 t.fromMoby(elt)

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/ontology/Germplasm_Details.py,v
retrieving revision 1.5
retrieving revision 1.6
diff -u -r1.5 -r1.6
--- /home/repository/moby/moby-live/Python/bioMoby/ontology/Germplasm_Details.py	2005/02/01 14:20:44	1.5
+++ /home/repository/moby/moby-live/Python/bioMoby/ontology/Germplasm_Details.py	2005/02/07 14:23:33	1.6
@@ -57,7 +57,8 @@
             if elt.nodeName=="CrossReference" or elt.nodeName=="moby:CrossReference":
                 self.__cross__=[]
                 for ref in elt.childNodes:
-                    self.__cross__.append(um.loads(ref))
+                    if ref.nodeType==ref.ELEMENT_NODE:
+                        self.__cross__.append(um.loadn(ref))
             if elt.nodeType==elt.ELEMENT_NODE and (elt.nodeName=="Integer" or elt.nodeName=="moby:Integer") and (elt.getAttribute("articleName")=="date" or elt.getAttribute("moby:articleName")=="date"):
                 t=MobyInteger()
                 t.fromMoby(elt)

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/ontology/Germplasm_List.py,v
retrieving revision 1.5
retrieving revision 1.6
diff -u -r1.5 -r1.6
--- /home/repository/moby/moby-live/Python/bioMoby/ontology/Germplasm_List.py	2005/02/01 14:20:44	1.5
+++ /home/repository/moby/moby-live/Python/bioMoby/ontology/Germplasm_List.py	2005/02/07 14:23:33	1.6
@@ -57,7 +57,8 @@
             if elt.nodeName=="CrossReference" or elt.nodeName=="moby:CrossReference":
                 self.__cross__=[]
                 for ref in elt.childNodes:
-                    self.__cross__.append(um.loads(ref))
+                    if ref.nodeType==ref.ELEMENT_NODE:
+                        self.__cross__.append(um.loadn(ref))
             if elt.nodeType==elt.ELEMENT_NODE and (elt.nodeName=="Integer" or elt.nodeName=="moby:Integer") and (elt.getAttribute("articleName")=="germplasm_id" or elt.getAttribute("moby:articleName")=="germplasm_id"):
                 t=MobyInteger()
                 t.fromMoby(elt)

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/ontology/Global_Keyword.py,v
retrieving revision 1.5
retrieving revision 1.6
diff -u -r1.5 -r1.6
--- /home/repository/moby/moby-live/Python/bioMoby/ontology/Global_Keyword.py	2005/02/01 14:20:44	1.5
+++ /home/repository/moby/moby-live/Python/bioMoby/ontology/Global_Keyword.py	2005/02/07 14:23:33	1.6
@@ -47,4 +47,5 @@
             if elt.nodeName=="CrossReference" or elt.nodeName=="moby:CrossReference":
                 self.__cross__=[]
                 for ref in elt.childNodes:
-                    self.__cross__.append(um.loads(ref))
\ No newline at end of file
+                    if ref.nodeType==ref.ELEMENT_NODE:
+                        self.__cross__.append(um.loadn(ref))
\ No newline at end of file

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/ontology/HBond_Pair.py,v
retrieving revision 1.5
retrieving revision 1.6
diff -u -r1.5 -r1.6
--- /home/repository/moby/moby-live/Python/bioMoby/ontology/HBond_Pair.py	2005/02/01 14:20:44	1.5
+++ /home/repository/moby/moby-live/Python/bioMoby/ontology/HBond_Pair.py	2005/02/07 14:23:33	1.6
@@ -51,7 +51,8 @@
             if elt.nodeName=="CrossReference" or elt.nodeName=="moby:CrossReference":
                 self.__cross__=[]
                 for ref in elt.childNodes:
-                    self.__cross__.append(um.loads(ref))
+                    if ref.nodeType==ref.ELEMENT_NODE:
+                        self.__cross__.append(um.loadn(ref))
             if elt.nodeType==elt.ELEMENT_NODE and (elt.nodeName=="String" or elt.nodeName=="moby:String") and (elt.getAttribute("articleName")=="A" or elt.getAttribute("moby:articleName")=="A"):
                 t=MobyString()
                 t.fromMoby(elt)

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/ontology/HFormatText.py,v
retrieving revision 1.5
retrieving revision 1.6
diff -u -r1.5 -r1.6
--- /home/repository/moby/moby-live/Python/bioMoby/ontology/HFormatText.py	2005/02/01 14:20:44	1.5
+++ /home/repository/moby/moby-live/Python/bioMoby/ontology/HFormatText.py	2005/02/07 14:23:33	1.6
@@ -48,4 +48,5 @@
             if elt.nodeName=="CrossReference" or elt.nodeName=="moby:CrossReference":
                 self.__cross__=[]
                 for ref in elt.childNodes:
-                    self.__cross__.append(um.loads(ref))
\ No newline at end of file
+                    if ref.nodeType==ref.ELEMENT_NODE:
+                        self.__cross__.append(um.loadn(ref))
\ No newline at end of file

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/ontology/Haplotyping_Study_obj.py,v
retrieving revision 1.5
retrieving revision 1.6
diff -u -r1.5 -r1.6
--- /home/repository/moby/moby-live/Python/bioMoby/ontology/Haplotyping_Study_obj.py	2005/02/01 14:20:44	1.5
+++ /home/repository/moby/moby-live/Python/bioMoby/ontology/Haplotyping_Study_obj.py	2005/02/07 14:23:33	1.6
@@ -47,4 +47,5 @@
             if elt.nodeName=="CrossReference" or elt.nodeName=="moby:CrossReference":
                 self.__cross__=[]
                 for ref in elt.childNodes:
-                    self.__cross__.append(um.loads(ref))
\ No newline at end of file
+                    if ref.nodeType==ref.ELEMENT_NODE:
+                        self.__cross__.append(um.loadn(ref))
\ No newline at end of file

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/ontology/ICIS_Query.py,v
retrieving revision 1.5
retrieving revision 1.6
diff -u -r1.5 -r1.6
--- /home/repository/moby/moby-live/Python/bioMoby/ontology/ICIS_Query.py	2005/02/01 14:20:44	1.5
+++ /home/repository/moby/moby-live/Python/bioMoby/ontology/ICIS_Query.py	2005/02/07 14:23:33	1.6
@@ -52,7 +52,8 @@
             if elt.nodeName=="CrossReference" or elt.nodeName=="moby:CrossReference":
                 self.__cross__=[]
                 for ref in elt.childNodes:
-                    self.__cross__.append(um.loads(ref))
+                    if ref.nodeType==ref.ELEMENT_NODE:
+                        self.__cross__.append(um.loadn(ref))
             if elt.nodeType==elt.ELEMENT_NODE and (elt.nodeName=="Integer" or elt.nodeName=="moby:Integer") and (elt.getAttribute("articleName")=="end_row" or elt.getAttribute("moby:articleName")=="end_row"):
                 t=MobyInteger()
                 t.fromMoby(elt)

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/ontology/ICIS_Query2.py,v
retrieving revision 1.5
retrieving revision 1.6
diff -u -r1.5 -r1.6
--- /home/repository/moby/moby-live/Python/bioMoby/ontology/ICIS_Query2.py	2005/02/01 14:20:44	1.5
+++ /home/repository/moby/moby-live/Python/bioMoby/ontology/ICIS_Query2.py	2005/02/07 14:23:33	1.6
@@ -54,7 +54,8 @@
             if elt.nodeName=="CrossReference" or elt.nodeName=="moby:CrossReference":
                 self.__cross__=[]
                 for ref in elt.childNodes:
-                    self.__cross__.append(um.loads(ref))
+                    if ref.nodeType==ref.ELEMENT_NODE:
+                        self.__cross__.append(um.loadn(ref))
             if elt.nodeType==elt.ELEMENT_NODE and (elt.nodeName=="String" or elt.nodeName=="moby:String") and (elt.getAttribute("articleName")=="search_text1" or elt.getAttribute("moby:articleName")=="search_text1"):
                 t=MobyString()
                 t.fromMoby(elt)

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/ontology/ICIS_Query3.py,v
retrieving revision 1.5
retrieving revision 1.6
diff -u -r1.5 -r1.6
--- /home/repository/moby/moby-live/Python/bioMoby/ontology/ICIS_Query3.py	2005/02/01 14:20:44	1.5
+++ /home/repository/moby/moby-live/Python/bioMoby/ontology/ICIS_Query3.py	2005/02/07 14:23:33	1.6
@@ -52,7 +52,8 @@
             if elt.nodeName=="CrossReference" or elt.nodeName=="moby:CrossReference":
                 self.__cross__=[]
                 for ref in elt.childNodes:
-                    self.__cross__.append(um.loads(ref))
+                    if ref.nodeType==ref.ELEMENT_NODE:
+                        self.__cross__.append(um.loadn(ref))
             if elt.nodeType==elt.ELEMENT_NODE and (elt.nodeName=="Integer" or elt.nodeName=="moby:Integer") and (elt.getAttribute("articleName")=="search_text1" or elt.getAttribute("moby:articleName")=="search_text1"):
                 t=MobyInteger()
                 t.fromMoby(elt)

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/ontology/IntAct_XML.py,v
retrieving revision 1.5
retrieving revision 1.6
diff -u -r1.5 -r1.6
--- /home/repository/moby/moby-live/Python/bioMoby/ontology/IntAct_XML.py	2005/02/01 14:20:44	1.5
+++ /home/repository/moby/moby-live/Python/bioMoby/ontology/IntAct_XML.py	2005/02/07 14:23:33	1.6
@@ -48,4 +48,5 @@
             if elt.nodeName=="CrossReference" or elt.nodeName=="moby:CrossReference":
                 self.__cross__=[]
                 for ref in elt.childNodes:
-                    self.__cross__.append(um.loads(ref))
\ No newline at end of file
+                    if ref.nodeType==ref.ELEMENT_NODE:
+                        self.__cross__.append(um.loadn(ref))
\ No newline at end of file

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/ontology/Interaction.py,v
retrieving revision 1.5
retrieving revision 1.6
diff -u -r1.5 -r1.6
--- /home/repository/moby/moby-live/Python/bioMoby/ontology/Interaction.py	2005/02/01 14:20:44	1.5
+++ /home/repository/moby/moby-live/Python/bioMoby/ontology/Interaction.py	2005/02/07 14:23:33	1.6
@@ -53,7 +53,8 @@
             if elt.nodeName=="CrossReference" or elt.nodeName=="moby:CrossReference":
                 self.__cross__=[]
                 for ref in elt.childNodes:
-                    self.__cross__.append(um.loads(ref))
+                    if ref.nodeType==ref.ELEMENT_NODE:
+                        self.__cross__.append(um.loadn(ref))
             if elt.nodeType==elt.ELEMENT_NODE and (elt.nodeName=="String" or elt.nodeName=="moby:String") and (elt.getAttribute("articleName")=="result" or elt.getAttribute("moby:articleName")=="result"):
                 t=MobyString()
                 t.fromMoby(elt)

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/ontology/InteractionMethod.py,v
retrieving revision 1.5
retrieving revision 1.6
diff -u -r1.5 -r1.6
--- /home/repository/moby/moby-live/Python/bioMoby/ontology/InteractionMethod.py	2005/02/01 14:20:44	1.5
+++ /home/repository/moby/moby-live/Python/bioMoby/ontology/InteractionMethod.py	2005/02/07 14:23:33	1.6
@@ -51,7 +51,8 @@
             if elt.nodeName=="CrossReference" or elt.nodeName=="moby:CrossReference":
                 self.__cross__=[]
                 for ref in elt.childNodes:
-                    self.__cross__.append(um.loads(ref))
+                    if ref.nodeType==ref.ELEMENT_NODE:
+                        self.__cross__.append(um.loadn(ref))
             if elt.nodeType==elt.ELEMENT_NODE and (elt.nodeName=="String" or elt.nodeName=="moby:String") and (elt.getAttribute("articleName")=="shortlabel" or elt.getAttribute("moby:articleName")=="shortlabel"):
                 t=MobyString()
                 t.fromMoby(elt)

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/ontology/Interaction_partner.py,v
retrieving revision 1.5
retrieving revision 1.6
diff -u -r1.5 -r1.6
--- /home/repository/moby/moby-live/Python/bioMoby/ontology/Interaction_partner.py	2005/02/01 14:20:44	1.5
+++ /home/repository/moby/moby-live/Python/bioMoby/ontology/Interaction_partner.py	2005/02/07 14:23:33	1.6
@@ -51,7 +51,8 @@
             if elt.nodeName=="CrossReference" or elt.nodeName=="moby:CrossReference":
                 self.__cross__=[]
                 for ref in elt.childNodes:
-                    self.__cross__.append(um.loads(ref))
+                    if ref.nodeType==ref.ELEMENT_NODE:
+                        self.__cross__.append(um.loadn(ref))
             if elt.nodeType==elt.ELEMENT_NODE and (elt.nodeName=="Integer" or elt.nodeName=="moby:Integer") and (elt.getAttribute("articleName")=="direction" or elt.getAttribute("moby:articleName")=="direction"):
                 t=MobyInteger()
                 t.fromMoby(elt)

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/ontology/Interactor.py,v
retrieving revision 1.5
retrieving revision 1.6
diff -u -r1.5 -r1.6
--- /home/repository/moby/moby-live/Python/bioMoby/ontology/Interactor.py	2005/02/01 14:20:44	1.5
+++ /home/repository/moby/moby-live/Python/bioMoby/ontology/Interactor.py	2005/02/07 14:23:33	1.6
@@ -49,7 +49,8 @@
             if elt.nodeName=="CrossReference" or elt.nodeName=="moby:CrossReference":
                 self.__cross__=[]
                 for ref in elt.childNodes:
-                    self.__cross__.append(um.loads(ref))
+                    if ref.nodeType==ref.ELEMENT_NODE:
+                        self.__cross__.append(um.loadn(ref))
             if elt.nodeType==elt.ELEMENT_NODE and (elt.nodeName=="String" or elt.nodeName=="moby:String") and (elt.getAttribute("articleName")=="role" or elt.getAttribute("moby:articleName")=="role"):
                 t=MobyString()
                 t.fromMoby(elt)

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/ontology/MEME_Text.py,v
retrieving revision 1.5
retrieving revision 1.6
diff -u -r1.5 -r1.6
--- /home/repository/moby/moby-live/Python/bioMoby/ontology/MEME_Text.py	2005/02/01 14:20:44	1.5
+++ /home/repository/moby/moby-live/Python/bioMoby/ontology/MEME_Text.py	2005/02/07 14:23:33	1.6
@@ -48,4 +48,5 @@
             if elt.nodeName=="CrossReference" or elt.nodeName=="moby:CrossReference":
                 self.__cross__=[]
                 for ref in elt.childNodes:
-                    self.__cross__.append(um.loads(ref))
\ No newline at end of file
+                    if ref.nodeType==ref.ELEMENT_NODE:
+                        self.__cross__.append(um.loadn(ref))
\ No newline at end of file

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/ontology/MGIS_ACCESSION.py,v
retrieving revision 1.5
retrieving revision 1.6
diff -u -r1.5 -r1.6
--- /home/repository/moby/moby-live/Python/bioMoby/ontology/MGIS_ACCESSION.py	2005/02/01 14:20:44	1.5
+++ /home/repository/moby/moby-live/Python/bioMoby/ontology/MGIS_ACCESSION.py	2005/02/07 14:23:33	1.6
@@ -68,7 +68,8 @@
             if elt.nodeName=="CrossReference" or elt.nodeName=="moby:CrossReference":
                 self.__cross__=[]
                 for ref in elt.childNodes:
-                    self.__cross__.append(um.loads(ref))
+                    if ref.nodeType==ref.ELEMENT_NODE:
+                        self.__cross__.append(um.loadn(ref))
             if elt.nodeType==elt.ELEMENT_NODE and (elt.nodeName=="String" or elt.nodeName=="moby:String") and (elt.getAttribute("articleName")=="Biotic_stress_Yellowsig" or elt.getAttribute("moby:articleName")=="Biotic_stress_Yellowsig"):
                 t=MobyString()
                 t.fromMoby(elt)

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/ontology/MMP_Locus.py,v
retrieving revision 1.5
retrieving revision 1.6
diff -u -r1.5 -r1.6
--- /home/repository/moby/moby-live/Python/bioMoby/ontology/MMP_Locus.py	2005/02/01 14:20:44	1.5
+++ /home/repository/moby/moby-live/Python/bioMoby/ontology/MMP_Locus.py	2005/02/07 14:23:33	1.6
@@ -47,4 +47,5 @@
             if elt.nodeName=="CrossReference" or elt.nodeName=="moby:CrossReference":
                 self.__cross__=[]
                 for ref in elt.childNodes:
-                    self.__cross__.append(um.loads(ref))
\ No newline at end of file
+                    if ref.nodeType==ref.ELEMENT_NODE:
+                        self.__cross__.append(um.loadn(ref))
\ No newline at end of file

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/ontology/MO_Term_Test.py,v
retrieving revision 1.5
retrieving revision 1.6
diff -u -r1.5 -r1.6
--- /home/repository/moby/moby-live/Python/bioMoby/ontology/MO_Term_Test.py	2005/02/01 14:20:44	1.5
+++ /home/repository/moby/moby-live/Python/bioMoby/ontology/MO_Term_Test.py	2005/02/07 14:23:33	1.6
@@ -52,7 +52,8 @@
             if elt.nodeName=="CrossReference" or elt.nodeName=="moby:CrossReference":
                 self.__cross__=[]
                 for ref in elt.childNodes:
-                    self.__cross__.append(um.loads(ref))
+                    if ref.nodeType==ref.ELEMENT_NODE:
+                        self.__cross__.append(um.loadn(ref))
             if elt.nodeType==elt.ELEMENT_NODE and (elt.nodeName=="String" or elt.nodeName=="moby:String") and (elt.getAttribute("articleName")=="class_name" or elt.getAttribute("moby:articleName")=="class_name"):
                 t=MobyString()
                 t.fromMoby(elt)

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/ontology/MSF.py,v
retrieving revision 1.1
retrieving revision 1.2
diff -u -r1.1 -r1.2
--- /home/repository/moby/moby-live/Python/bioMoby/ontology/MSF.py	2005/02/02 15:08:34	1.1
+++ /home/repository/moby/moby-live/Python/bioMoby/ontology/MSF.py	2005/02/07 14:23:33	1.2
@@ -48,4 +48,5 @@
             if elt.nodeName=="CrossReference" or elt.nodeName=="moby:CrossReference":
                 self.__cross__=[]
                 for ref in elt.childNodes:
-                    self.__cross__.append(um.loads(ref))
\ No newline at end of file
+                    if ref.nodeType==ref.ELEMENT_NODE:
+                        self.__cross__.append(um.loadn(ref))
\ No newline at end of file

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/ontology/MmCIFText.py,v
retrieving revision 1.5
retrieving revision 1.6
diff -u -r1.5 -r1.6
--- /home/repository/moby/moby-live/Python/bioMoby/ontology/MmCIFText.py	2005/02/01 14:20:44	1.5
+++ /home/repository/moby/moby-live/Python/bioMoby/ontology/MmCIFText.py	2005/02/07 14:23:33	1.6
@@ -48,4 +48,5 @@
             if elt.nodeName=="CrossReference" or elt.nodeName=="moby:CrossReference":
                 self.__cross__=[]
                 for ref in elt.childNodes:
-                    self.__cross__.append(um.loads(ref))
\ No newline at end of file
+                    if ref.nodeType==ref.ELEMENT_NODE:
+                        self.__cross__.append(um.loadn(ref))
\ No newline at end of file

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/ontology/Multi_key_value_pair.py,v
retrieving revision 1.5
retrieving revision 1.6
diff -u -r1.5 -r1.6
--- /home/repository/moby/moby-live/Python/bioMoby/ontology/Multi_key_value_pair.py	2005/02/01 14:20:44	1.5
+++ /home/repository/moby/moby-live/Python/bioMoby/ontology/Multi_key_value_pair.py	2005/02/07 14:23:33	1.6
@@ -51,7 +51,8 @@
             if elt.nodeName=="CrossReference" or elt.nodeName=="moby:CrossReference":
                 self.__cross__=[]
                 for ref in elt.childNodes:
-                    self.__cross__.append(um.loads(ref))
+                    if ref.nodeType==ref.ELEMENT_NODE:
+                        self.__cross__.append(um.loadn(ref))
             if elt.nodeType==elt.ELEMENT_NODE and (elt.nodeName=="String" or elt.nodeName=="moby:String") and (elt.getAttribute("articleName")=="key" or elt.getAttribute("moby:articleName")=="key"):
                 t=MobyString()
                 t.fromMoby(elt)

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/ontology/MyTestingDataType_11024145298313.py,v
retrieving revision 1.5
retrieving revision 1.6
diff -u -r1.5 -r1.6
--- /home/repository/moby/moby-live/Python/bioMoby/ontology/MyTestingDataType_11024145298313.py	2005/02/01 14:20:44	1.5
+++ /home/repository/moby/moby-live/Python/bioMoby/ontology/MyTestingDataType_11024145298313.py	2005/02/07 14:23:33	1.6
@@ -48,4 +48,5 @@
             if elt.nodeName=="CrossReference" or elt.nodeName=="moby:CrossReference":
                 self.__cross__=[]
                 for ref in elt.childNodes:
-                    self.__cross__.append(um.loads(ref))
\ No newline at end of file
+                    if ref.nodeType==ref.ELEMENT_NODE:
+                        self.__cross__.append(um.loadn(ref))
\ No newline at end of file

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/ontology/MyTree.py,v
retrieving revision 1.5
retrieving revision 1.6
diff -u -r1.5 -r1.6
--- /home/repository/moby/moby-live/Python/bioMoby/ontology/MyTree.py	2005/02/01 14:20:44	1.5
+++ /home/repository/moby/moby-live/Python/bioMoby/ontology/MyTree.py	2005/02/07 14:23:33	1.6
@@ -48,4 +48,5 @@
             if elt.nodeName=="CrossReference" or elt.nodeName=="moby:CrossReference":
                 self.__cross__=[]
                 for ref in elt.childNodes:
-                    self.__cross__.append(um.loads(ref))
\ No newline at end of file
+                    if ref.nodeType==ref.ELEMENT_NODE:
+                        self.__cross__.append(um.loadn(ref))
\ No newline at end of file

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/ontology/NCBI_BLAST_Text.py,v
retrieving revision 1.5
retrieving revision 1.6
diff -u -r1.5 -r1.6
--- /home/repository/moby/moby-live/Python/bioMoby/ontology/NCBI_BLAST_Text.py	2005/02/01 14:20:44	1.5
+++ /home/repository/moby/moby-live/Python/bioMoby/ontology/NCBI_BLAST_Text.py	2005/02/07 14:23:33	1.6
@@ -48,4 +48,5 @@
             if elt.nodeName=="CrossReference" or elt.nodeName=="moby:CrossReference":
                 self.__cross__=[]
                 for ref in elt.childNodes:
-                    self.__cross__.append(um.loads(ref))
\ No newline at end of file
+                    if ref.nodeType==ref.ELEMENT_NODE:
+                        self.__cross__.append(um.loadn(ref))
\ No newline at end of file

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/ontology/NCBI_Blast_XML.py,v
retrieving revision 1.5
retrieving revision 1.6
diff -u -r1.5 -r1.6
--- /home/repository/moby/moby-live/Python/bioMoby/ontology/NCBI_Blast_XML.py	2005/02/01 14:20:44	1.5
+++ /home/repository/moby/moby-live/Python/bioMoby/ontology/NCBI_Blast_XML.py	2005/02/07 14:23:33	1.6
@@ -48,4 +48,5 @@
             if elt.nodeName=="CrossReference" or elt.nodeName=="moby:CrossReference":
                 self.__cross__=[]
                 for ref in elt.childNodes:
-                    self.__cross__.append(um.loads(ref))
\ No newline at end of file
+                    if ref.nodeType==ref.ELEMENT_NODE:
+                        self.__cross__.append(um.loadn(ref))
\ No newline at end of file

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/ontology/NCBI_Blast_XML_Gif.py,v
retrieving revision 1.5
retrieving revision 1.6
diff -u -r1.5 -r1.6
--- /home/repository/moby/moby-live/Python/bioMoby/ontology/NCBI_Blast_XML_Gif.py	2005/02/01 14:20:44	1.5
+++ /home/repository/moby/moby-live/Python/bioMoby/ontology/NCBI_Blast_XML_Gif.py	2005/02/07 14:23:33	1.6
@@ -50,7 +50,8 @@
             if elt.nodeName=="CrossReference" or elt.nodeName=="moby:CrossReference":
                 self.__cross__=[]
                 for ref in elt.childNodes:
-                    self.__cross__.append(um.loads(ref))
+                    if ref.nodeType==ref.ELEMENT_NODE:
+                        self.__cross__.append(um.loadn(ref))
             if elt.nodeType==elt.ELEMENT_NODE and (elt.nodeName=="b64_encoded_gif" or elt.nodeName=="moby:b64_encoded_gif") and (elt.getAttribute("articleName")=="hitGraph" or elt.getAttribute("moby:articleName")=="hitGraph"):
                 self.HitGraph=MobyB64_encoded_gif()
                 self.HitGraph.fromMoby(elt)
\ No newline at end of file

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/ontology/NCBI_Blast_XML_Gif_Map.py,v
retrieving revision 1.5
retrieving revision 1.6
diff -u -r1.5 -r1.6
--- /home/repository/moby/moby-live/Python/bioMoby/ontology/NCBI_Blast_XML_Gif_Map.py	2005/02/01 14:20:44	1.5
+++ /home/repository/moby/moby-live/Python/bioMoby/ontology/NCBI_Blast_XML_Gif_Map.py	2005/02/07 14:23:33	1.6
@@ -52,7 +52,8 @@
             if elt.nodeName=="CrossReference" or elt.nodeName=="moby:CrossReference":
                 self.__cross__=[]
                 for ref in elt.childNodes:
-                    self.__cross__.append(um.loads(ref))
+                    if ref.nodeType==ref.ELEMENT_NODE:
+                        self.__cross__.append(um.loadn(ref))
             if elt.nodeType==elt.ELEMENT_NODE and (elt.nodeName=="b64_encoded_gif" or elt.nodeName=="moby:b64_encoded_gif") and (elt.getAttribute("articleName")=="hitGraph" or elt.getAttribute("moby:articleName")=="hitGraph"):
                 self.HitGraph=MobyB64_encoded_gif()
                 self.HitGraph.fromMoby(elt)

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/ontology/NCBI_MEME_Text.py,v
retrieving revision 1.5
retrieving revision 1.6
diff -u -r1.5 -r1.6
--- /home/repository/moby/moby-live/Python/bioMoby/ontology/NCBI_MEME_Text.py	2005/02/01 14:20:44	1.5
+++ /home/repository/moby/moby-live/Python/bioMoby/ontology/NCBI_MEME_Text.py	2005/02/07 14:23:33	1.6
@@ -48,4 +48,5 @@
             if elt.nodeName=="CrossReference" or elt.nodeName=="moby:CrossReference":
                 self.__cross__=[]
                 for ref in elt.childNodes:
-                    self.__cross__.append(um.loads(ref))
\ No newline at end of file
+                    if ref.nodeType==ref.ELEMENT_NODE:
+                        self.__cross__.append(um.loadn(ref))
\ No newline at end of file

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/ontology/NucleotideSequence.py,v
retrieving revision 1.5
retrieving revision 1.6
diff -u -r1.5 -r1.6
--- /home/repository/moby/moby-live/Python/bioMoby/ontology/NucleotideSequence.py	2005/02/01 14:20:44	1.5
+++ /home/repository/moby/moby-live/Python/bioMoby/ontology/NucleotideSequence.py	2005/02/07 14:23:33	1.6
@@ -51,7 +51,8 @@
             if elt.nodeName=="CrossReference" or elt.nodeName=="moby:CrossReference":
                 self.__cross__=[]
                 for ref in elt.childNodes:
-                    self.__cross__.append(um.loads(ref))
+                    if ref.nodeType==ref.ELEMENT_NODE:
+                        self.__cross__.append(um.loadn(ref))
             if elt.nodeType==elt.ELEMENT_NODE and (elt.nodeName=="Integer" or elt.nodeName=="moby:Integer") and (elt.getAttribute("articleName")=="Length" or elt.getAttribute("moby:articleName")=="Length"):
                 t=MobyInteger()
                 t.fromMoby(elt)

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/ontology/PDBFormattedText.py,v
retrieving revision 1.5
retrieving revision 1.6
diff -u -r1.5 -r1.6
--- /home/repository/moby/moby-live/Python/bioMoby/ontology/PDBFormattedText.py	2005/02/01 14:20:44	1.5
+++ /home/repository/moby/moby-live/Python/bioMoby/ontology/PDBFormattedText.py	2005/02/07 14:23:33	1.6
@@ -48,4 +48,5 @@
             if elt.nodeName=="CrossReference" or elt.nodeName=="moby:CrossReference":
                 self.__cross__=[]
                 for ref in elt.childNodes:
-                    self.__cross__.append(um.loads(ref))
\ No newline at end of file
+                    if ref.nodeType==ref.ELEMENT_NODE:
+                        self.__cross__.append(um.loadn(ref))
\ No newline at end of file

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/ontology/PDBText.py,v
retrieving revision 1.5
retrieving revision 1.6
diff -u -r1.5 -r1.6
--- /home/repository/moby/moby-live/Python/bioMoby/ontology/PDBText.py	2005/02/01 14:20:44	1.5
+++ /home/repository/moby/moby-live/Python/bioMoby/ontology/PDBText.py	2005/02/07 14:23:33	1.6
@@ -48,4 +48,5 @@
             if elt.nodeName=="CrossReference" or elt.nodeName=="moby:CrossReference":
                 self.__cross__=[]
                 for ref in elt.childNodes:
-                    self.__cross__.append(um.loads(ref))
\ No newline at end of file
+                    if ref.nodeType==ref.ELEMENT_NODE:
+                        self.__cross__.append(um.loadn(ref))
\ No newline at end of file

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/ontology/PDGJOB.py,v
retrieving revision 1.5
retrieving revision 1.6
diff -u -r1.5 -r1.6
--- /home/repository/moby/moby-live/Python/bioMoby/ontology/PDGJOB.py	2005/02/01 14:20:44	1.5
+++ /home/repository/moby/moby-live/Python/bioMoby/ontology/PDGJOB.py	2005/02/07 14:23:33	1.6
@@ -54,7 +54,8 @@
             if elt.nodeName=="CrossReference" or elt.nodeName=="moby:CrossReference":
                 self.__cross__=[]
                 for ref in elt.childNodes:
-                    self.__cross__.append(um.loads(ref))
+                    if ref.nodeType==ref.ELEMENT_NODE:
+                        self.__cross__.append(um.loadn(ref))
             if elt.nodeType==elt.ELEMENT_NODE and (elt.nodeName=="String" or elt.nodeName=="moby:String") and (elt.getAttribute("articleName")=="answerService" or elt.getAttribute("moby:articleName")=="answerService"):
                 t=MobyString()
                 t.fromMoby(elt)

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/ontology/PHDText.py,v
retrieving revision 1.5
retrieving revision 1.6
diff -u -r1.5 -r1.6
--- /home/repository/moby/moby-live/Python/bioMoby/ontology/PHDText.py	2005/02/01 14:20:44	1.5
+++ /home/repository/moby/moby-live/Python/bioMoby/ontology/PHDText.py	2005/02/07 14:23:33	1.6
@@ -48,4 +48,5 @@
             if elt.nodeName=="CrossReference" or elt.nodeName=="moby:CrossReference":
                 self.__cross__=[]
                 for ref in elt.childNodes:
-                    self.__cross__.append(um.loads(ref))
\ No newline at end of file
+                    if ref.nodeType==ref.ELEMENT_NODE:
+                        self.__cross__.append(um.loadn(ref))
\ No newline at end of file

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/ontology/PMUTText.py,v
retrieving revision 1.5
retrieving revision 1.6
diff -u -r1.5 -r1.6
--- /home/repository/moby/moby-live/Python/bioMoby/ontology/PMUTText.py	2005/02/01 14:20:44	1.5
+++ /home/repository/moby/moby-live/Python/bioMoby/ontology/PMUTText.py	2005/02/07 14:23:33	1.6
@@ -48,4 +48,5 @@
             if elt.nodeName=="CrossReference" or elt.nodeName=="moby:CrossReference":
                 self.__cross__=[]
                 for ref in elt.childNodes:
-                    self.__cross__.append(um.loads(ref))
\ No newline at end of file
+                    if ref.nodeType==ref.ELEMENT_NODE:
+                        self.__cross__.append(um.loadn(ref))
\ No newline at end of file

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/ontology/PSeaTextFormatted.py,v
retrieving revision 1.5
retrieving revision 1.6
diff -u -r1.5 -r1.6
--- /home/repository/moby/moby-live/Python/bioMoby/ontology/PSeaTextFormatted.py	2005/02/01 14:20:44	1.5
+++ /home/repository/moby/moby-live/Python/bioMoby/ontology/PSeaTextFormatted.py	2005/02/07 14:23:33	1.6
@@ -48,4 +48,5 @@
             if elt.nodeName=="CrossReference" or elt.nodeName=="moby:CrossReference":
                 self.__cross__=[]
                 for ref in elt.childNodes:
-                    self.__cross__.append(um.loads(ref))
\ No newline at end of file
+                    if ref.nodeType==ref.ELEMENT_NODE:
+                        self.__cross__.append(um.loadn(ref))
\ No newline at end of file

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/ontology/PhenotypeDescription.py,v
retrieving revision 1.5
retrieving revision 1.6
diff -u -r1.5 -r1.6
--- /home/repository/moby/moby-live/Python/bioMoby/ontology/PhenotypeDescription.py	2005/02/01 14:20:44	1.5
+++ /home/repository/moby/moby-live/Python/bioMoby/ontology/PhenotypeDescription.py	2005/02/07 14:23:33	1.6
@@ -49,7 +49,8 @@
             if elt.nodeName=="CrossReference" or elt.nodeName=="moby:CrossReference":
                 self.__cross__=[]
                 for ref in elt.childNodes:
-                    self.__cross__.append(um.loads(ref))
+                    if ref.nodeType==ref.ELEMENT_NODE:
+                        self.__cross__.append(um.loadn(ref))
             if elt.nodeType==elt.ELEMENT_NODE and (elt.nodeName=="String" or elt.nodeName=="moby:String") and (elt.getAttribute("articleName")=="Phenotype" or elt.getAttribute("moby:articleName")=="Phenotype"):
                 t=MobyString()
                 t.fromMoby(elt)

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/ontology/PubMedMEDLINE.py,v
retrieving revision 1.5
retrieving revision 1.6
diff -u -r1.5 -r1.6
--- /home/repository/moby/moby-live/Python/bioMoby/ontology/PubMedMEDLINE.py	2005/02/01 14:20:44	1.5
+++ /home/repository/moby/moby-live/Python/bioMoby/ontology/PubMedMEDLINE.py	2005/02/07 14:23:33	1.6
@@ -48,4 +48,5 @@
             if elt.nodeName=="CrossReference" or elt.nodeName=="moby:CrossReference":
                 self.__cross__=[]
                 for ref in elt.childNodes:
-                    self.__cross__.append(um.loads(ref))
\ No newline at end of file
+                    if ref.nodeType==ref.ELEMENT_NODE:
+                        self.__cross__.append(um.loadn(ref))
\ No newline at end of file

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/ontology/RNASequence.py,v
retrieving revision 1.5
retrieving revision 1.6
diff -u -r1.5 -r1.6
--- /home/repository/moby/moby-live/Python/bioMoby/ontology/RNASequence.py	2005/02/01 14:20:44	1.5
+++ /home/repository/moby/moby-live/Python/bioMoby/ontology/RNASequence.py	2005/02/07 14:23:33	1.6
@@ -51,7 +51,8 @@
             if elt.nodeName=="CrossReference" or elt.nodeName=="moby:CrossReference":
                 self.__cross__=[]
                 for ref in elt.childNodes:
-                    self.__cross__.append(um.loads(ref))
+                    if ref.nodeType==ref.ELEMENT_NODE:
+                        self.__cross__.append(um.loadn(ref))
             if elt.nodeType==elt.ELEMENT_NODE and (elt.nodeName=="Integer" or elt.nodeName=="moby:Integer") and (elt.getAttribute("articleName")=="Length" or elt.getAttribute("moby:articleName")=="Length"):
                 t=MobyInteger()
                 t.fromMoby(elt)

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/ontology/SINGER_ACCESSION.py,v
retrieving revision 1.5
retrieving revision 1.6
diff -u -r1.5 -r1.6
--- /home/repository/moby/moby-live/Python/bioMoby/ontology/SINGER_ACCESSION.py	2005/02/01 14:20:44	1.5
+++ /home/repository/moby/moby-live/Python/bioMoby/ontology/SINGER_ACCESSION.py	2005/02/07 14:23:33	1.6
@@ -52,7 +52,8 @@
             if elt.nodeName=="CrossReference" or elt.nodeName=="moby:CrossReference":
                 self.__cross__=[]
                 for ref in elt.childNodes:
-                    self.__cross__.append(um.loads(ref))
+                    if ref.nodeType==ref.ELEMENT_NODE:
+                        self.__cross__.append(um.loadn(ref))
             if elt.nodeType==elt.ELEMENT_NODE and (elt.nodeName=="String" or elt.nodeName=="moby:String") and (elt.getAttribute("articleName")=="ACCNO" or elt.getAttribute("moby:articleName")=="ACCNO"):
                 t=MobyString()
                 t.fromMoby(elt)

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/ontology/Sample.py,v
retrieving revision 1.5
retrieving revision 1.6
diff -u -r1.5 -r1.6
--- /home/repository/moby/moby-live/Python/bioMoby/ontology/Sample.py	2005/02/01 14:20:44	1.5
+++ /home/repository/moby/moby-live/Python/bioMoby/ontology/Sample.py	2005/02/07 14:23:33	1.6
@@ -51,7 +51,8 @@
             if elt.nodeName=="CrossReference" or elt.nodeName=="moby:CrossReference":
                 self.__cross__=[]
                 for ref in elt.childNodes:
-                    self.__cross__.append(um.loads(ref))
+                    if ref.nodeType==ref.ELEMENT_NODE:
+                        self.__cross__.append(um.loadn(ref))
             if elt.nodeType==elt.ELEMENT_NODE and (elt.nodeName=="String" or elt.nodeName=="moby:String") and (elt.getAttribute("articleName")=="code" or elt.getAttribute("moby:articleName")=="code"):
                 t=MobyString()
                 t.fromMoby(elt)

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/ontology/SchematikonMotifID.py,v
retrieving revision 1.5
retrieving revision 1.6
diff -u -r1.5 -r1.6
--- /home/repository/moby/moby-live/Python/bioMoby/ontology/SchematikonMotifID.py	2005/02/01 14:20:44	1.5
+++ /home/repository/moby/moby-live/Python/bioMoby/ontology/SchematikonMotifID.py	2005/02/07 14:23:33	1.6
@@ -49,7 +49,8 @@
             if elt.nodeName=="CrossReference" or elt.nodeName=="moby:CrossReference":
                 self.__cross__=[]
                 for ref in elt.childNodes:
-                    self.__cross__.append(um.loads(ref))
+                    if ref.nodeType==ref.ELEMENT_NODE:
+                        self.__cross__.append(um.loadn(ref))
             if elt.nodeType==elt.ELEMENT_NODE and (elt.nodeName=="String" or elt.nodeName=="moby:String") and (elt.getAttribute("articleName")=="ID" or elt.getAttribute("moby:articleName")=="ID"):
                 t=MobyString()
                 t.fromMoby(elt)

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/ontology/SchematikonMotifSupport.py,v
retrieving revision 1.5
retrieving revision 1.6
diff -u -r1.5 -r1.6
--- /home/repository/moby/moby-live/Python/bioMoby/ontology/SchematikonMotifSupport.py	2005/02/01 14:20:44	1.5
+++ /home/repository/moby/moby-live/Python/bioMoby/ontology/SchematikonMotifSupport.py	2005/02/07 14:23:33	1.6
@@ -50,7 +50,8 @@
             if elt.nodeName=="CrossReference" or elt.nodeName=="moby:CrossReference":
                 self.__cross__=[]
                 for ref in elt.childNodes:
-                    self.__cross__.append(um.loads(ref))
+                    if ref.nodeType==ref.ELEMENT_NODE:
+                        self.__cross__.append(um.loadn(ref))
             if elt.nodeType==elt.ELEMENT_NODE and (elt.nodeName=="Integer" or elt.nodeName=="moby:Integer") and (elt.getAttribute("articleName")=="UniqueSupport" or elt.getAttribute("moby:articleName")=="UniqueSupport"):
                 t=MobyInteger()
                 t.fromMoby(elt)

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/ontology/SchematikonSegmentAttributes.py,v
retrieving revision 1.5
retrieving revision 1.6
diff -u -r1.5 -r1.6
--- /home/repository/moby/moby-live/Python/bioMoby/ontology/SchematikonSegmentAttributes.py	2005/02/01 14:20:44	1.5
+++ /home/repository/moby/moby-live/Python/bioMoby/ontology/SchematikonSegmentAttributes.py	2005/02/07 14:23:33	1.6
@@ -54,7 +54,8 @@
             if elt.nodeName=="CrossReference" or elt.nodeName=="moby:CrossReference":
                 self.__cross__=[]
                 for ref in elt.childNodes:
-                    self.__cross__.append(um.loads(ref))
+                    if ref.nodeType==ref.ELEMENT_NODE:
+                        self.__cross__.append(um.loadn(ref))
             if elt.nodeType==elt.ELEMENT_NODE and (elt.nodeName=="Integer" or elt.nodeName=="moby:Integer") and (elt.getAttribute("articleName")=="Length" or elt.getAttribute("moby:articleName")=="Length"):
                 t=MobyInteger()
                 t.fromMoby(elt)

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/ontology/SchematikonSegmentID.py,v
retrieving revision 1.5
retrieving revision 1.6
diff -u -r1.5 -r1.6
--- /home/repository/moby/moby-live/Python/bioMoby/ontology/SchematikonSegmentID.py	2005/02/01 14:20:44	1.5
+++ /home/repository/moby/moby-live/Python/bioMoby/ontology/SchematikonSegmentID.py	2005/02/07 14:23:33	1.6
@@ -49,7 +49,8 @@
             if elt.nodeName=="CrossReference" or elt.nodeName=="moby:CrossReference":
                 self.__cross__=[]
                 for ref in elt.childNodes:
-                    self.__cross__.append(um.loads(ref))
+                    if ref.nodeType==ref.ELEMENT_NODE:
+                        self.__cross__.append(um.loadn(ref))
             if elt.nodeType==elt.ELEMENT_NODE and (elt.nodeName=="String" or elt.nodeName=="moby:String") and (elt.getAttribute("articleName")=="ID" or elt.getAttribute("moby:articleName")=="ID"):
                 t=MobyString()
                 t.fromMoby(elt)

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/ontology/SchematikonStructureAnnotation.py,v
retrieving revision 1.5
retrieving revision 1.6
diff -u -r1.5 -r1.6
--- /home/repository/moby/moby-live/Python/bioMoby/ontology/SchematikonStructureAnnotation.py	2005/02/01 14:20:44	1.5
+++ /home/repository/moby/moby-live/Python/bioMoby/ontology/SchematikonStructureAnnotation.py	2005/02/07 14:23:33	1.6
@@ -52,7 +52,8 @@
             if elt.nodeName=="CrossReference" or elt.nodeName=="moby:CrossReference":
                 self.__cross__=[]
                 for ref in elt.childNodes:
-                    self.__cross__.append(um.loads(ref))
+                    if ref.nodeType==ref.ELEMENT_NODE:
+                        self.__cross__.append(um.loadn(ref))
             if elt.nodeType==elt.ELEMENT_NODE and (elt.nodeName=="String" or elt.nodeName=="moby:String") and (elt.getAttribute("articleName")=="PROMOTIF gamma-turn" or elt.getAttribute("moby:articleName")=="PROMOTIF gamma-turn"):
                 t=MobyString()
                 t.fromMoby(elt)

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/ontology/SchematikonVorocodeName.py,v
retrieving revision 1.5
retrieving revision 1.6
diff -u -r1.5 -r1.6
--- /home/repository/moby/moby-live/Python/bioMoby/ontology/SchematikonVorocodeName.py	2005/02/01 14:20:44	1.5
+++ /home/repository/moby/moby-live/Python/bioMoby/ontology/SchematikonVorocodeName.py	2005/02/07 14:23:33	1.6
@@ -49,7 +49,8 @@
             if elt.nodeName=="CrossReference" or elt.nodeName=="moby:CrossReference":
                 self.__cross__=[]
                 for ref in elt.childNodes:
-                    self.__cross__.append(um.loads(ref))
+                    if ref.nodeType==ref.ELEMENT_NODE:
+                        self.__cross__.append(um.loadn(ref))
             if elt.nodeType==elt.ELEMENT_NODE and (elt.nodeName=="String" or elt.nodeName=="moby:String") and (elt.getAttribute("articleName")=="VorocodeName" or elt.getAttribute("moby:articleName")=="VorocodeName"):
                 t=MobyString()
                 t.fromMoby(elt)

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/ontology/Scored_acronym_string.py,v
retrieving revision 1.5
retrieving revision 1.6
diff -u -r1.5 -r1.6
--- /home/repository/moby/moby-live/Python/bioMoby/ontology/Scored_acronym_string.py	2005/02/01 14:20:44	1.5
+++ /home/repository/moby/moby-live/Python/bioMoby/ontology/Scored_acronym_string.py	2005/02/07 14:23:33	1.6
@@ -52,7 +52,8 @@
             if elt.nodeName=="CrossReference" or elt.nodeName=="moby:CrossReference":
                 self.__cross__=[]
                 for ref in elt.childNodes:
-                    self.__cross__.append(um.loads(ref))
+                    if ref.nodeType==ref.ELEMENT_NODE:
+                        self.__cross__.append(um.loadn(ref))
             if elt.nodeType==elt.ELEMENT_NODE and (elt.nodeName=="Float" or elt.nodeName=="moby:Float") and (elt.getAttribute("articleName")=="score" or elt.getAttribute("moby:articleName")=="score"):
                 t=MobyFloat()
                 t.fromMoby(elt)

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/ontology/SimpleAnnotatedGIFImage.py,v
retrieving revision 1.5
retrieving revision 1.6
diff -u -r1.5 -r1.6
--- /home/repository/moby/moby-live/Python/bioMoby/ontology/SimpleAnnotatedGIFImage.py	2005/02/01 14:20:44	1.5
+++ /home/repository/moby/moby-live/Python/bioMoby/ontology/SimpleAnnotatedGIFImage.py	2005/02/07 14:23:33	1.6
@@ -50,7 +50,8 @@
             if elt.nodeName=="CrossReference" or elt.nodeName=="moby:CrossReference":
                 self.__cross__=[]
                 for ref in elt.childNodes:
-                    self.__cross__.append(um.loads(ref))
+                    if ref.nodeType==ref.ELEMENT_NODE:
+                        self.__cross__.append(um.loadn(ref))
             if elt.nodeType==elt.ELEMENT_NODE and (elt.nodeName=="String" or elt.nodeName=="moby:String") and (elt.getAttribute("articleName")=="Description" or elt.getAttribute("moby:articleName")=="Description"):
                 t=MobyString()
                 t.fromMoby(elt)

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/ontology/SimpleAnnotatedJPEGImage.py,v
retrieving revision 1.5
retrieving revision 1.6
diff -u -r1.5 -r1.6
--- /home/repository/moby/moby-live/Python/bioMoby/ontology/SimpleAnnotatedJPEGImage.py	2005/02/01 14:20:44	1.5
+++ /home/repository/moby/moby-live/Python/bioMoby/ontology/SimpleAnnotatedJPEGImage.py	2005/02/07 14:23:33	1.6
@@ -51,7 +51,8 @@
             if elt.nodeName=="CrossReference" or elt.nodeName=="moby:CrossReference":
                 self.__cross__=[]
                 for ref in elt.childNodes:
-                    self.__cross__.append(um.loads(ref))
+                    if ref.nodeType==ref.ELEMENT_NODE:
+                        self.__cross__.append(um.loadn(ref))
             if elt.nodeType==elt.ELEMENT_NODE and (elt.nodeName=="String" or elt.nodeName=="moby:String") and (elt.getAttribute("articleName")=="Description" or elt.getAttribute("moby:articleName")=="Description"):
                 t=MobyString()
                 t.fromMoby(elt)

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/ontology/Simple_key_value_pair.py,v
retrieving revision 1.5
retrieving revision 1.6
diff -u -r1.5 -r1.6
--- /home/repository/moby/moby-live/Python/bioMoby/ontology/Simple_key_value_pair.py	2005/02/01 14:20:44	1.5
+++ /home/repository/moby/moby-live/Python/bioMoby/ontology/Simple_key_value_pair.py	2005/02/07 14:23:33	1.6
@@ -50,7 +50,8 @@
             if elt.nodeName=="CrossReference" or elt.nodeName=="moby:CrossReference":
                 self.__cross__=[]
                 for ref in elt.childNodes:
-                    self.__cross__.append(um.loads(ref))
+                    if ref.nodeType==ref.ELEMENT_NODE:
+                        self.__cross__.append(um.loadn(ref))
             if elt.nodeType==elt.ELEMENT_NODE and (elt.nodeName=="String" or elt.nodeName=="moby:String") and (elt.getAttribute("articleName")=="value" or elt.getAttribute("moby:articleName")=="value"):
                 t=MobyString()
                 t.fromMoby(elt)

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/ontology/Snp_allele.py,v
retrieving revision 1.5
retrieving revision 1.6
diff -u -r1.5 -r1.6
--- /home/repository/moby/moby-live/Python/bioMoby/ontology/Snp_allele.py	2005/02/01 14:20:44	1.5
+++ /home/repository/moby/moby-live/Python/bioMoby/ontology/Snp_allele.py	2005/02/07 14:23:33	1.6
@@ -39,7 +39,8 @@
             if elt.nodeName=="CrossReference" or elt.nodeName=="moby:CrossReference":
                 self.__cross__=[]
                 for ref in elt.childNodes:
-                    self.__cross__.append(um.loads(ref))
+                    if ref.nodeType==ref.ELEMENT_NODE:
+                        self.__cross__.append(um.loadn(ref))
             if elt.nodeType==elt.ELEMENT_NODE and (elt.nodeName=="DNASequence" or elt.nodeName=="moby:DNASequence") and (elt.getAttribute("articleName")=="snp_allele" or elt.getAttribute("moby:articleName")=="snp_allele"):
                 self.Snp_allele=MobyDNASequence()
                 self.Snp_allele.fromMoby(elt)
\ No newline at end of file

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/ontology/Snp_genotype.py,v
retrieving revision 1.5
retrieving revision 1.6
diff -u -r1.5 -r1.6
--- /home/repository/moby/moby-live/Python/bioMoby/ontology/Snp_genotype.py	2005/02/01 14:20:44	1.5
+++ /home/repository/moby/moby-live/Python/bioMoby/ontology/Snp_genotype.py	2005/02/07 14:23:33	1.6
@@ -40,7 +40,8 @@
             if elt.nodeName=="CrossReference" or elt.nodeName=="moby:CrossReference":
                 self.__cross__=[]
                 for ref in elt.childNodes:
-                    self.__cross__.append(um.loads(ref))
+                    if ref.nodeType==ref.ELEMENT_NODE:
+                        self.__cross__.append(um.loadn(ref))
             if elt.nodeType==elt.ELEMENT_NODE and (elt.nodeName=="snp_allele" or elt.nodeName=="moby:snp_allele") and (elt.getAttribute("articleName")=="allele1" or elt.getAttribute("moby:articleName")=="allele1"):
                 self.Allele1=MobySnp_allele()
                 self.Allele1.fromMoby(elt)

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/ontology/Study.py,v
retrieving revision 1.5
retrieving revision 1.6
diff -u -r1.5 -r1.6
--- /home/repository/moby/moby-live/Python/bioMoby/ontology/Study.py	2005/02/01 14:20:44	1.5
+++ /home/repository/moby/moby-live/Python/bioMoby/ontology/Study.py	2005/02/07 14:23:33	1.6
@@ -52,7 +52,8 @@
             if elt.nodeName=="CrossReference" or elt.nodeName=="moby:CrossReference":
                 self.__cross__=[]
                 for ref in elt.childNodes:
-                    self.__cross__.append(um.loads(ref))
+                    if ref.nodeType==ref.ELEMENT_NODE:
+                        self.__cross__.append(um.loadn(ref))
             if elt.nodeType==elt.ELEMENT_NODE and (elt.nodeName=="String" or elt.nodeName=="moby:String") and (elt.getAttribute("articleName")=="study_name" or elt.getAttribute("moby:articleName")=="study_name"):
                 t=MobyString()
                 t.fromMoby(elt)

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/ontology/TEST.py,v
retrieving revision 1.5
retrieving revision 1.6
diff -u -r1.5 -r1.6
--- /home/repository/moby/moby-live/Python/bioMoby/ontology/TEST.py	2005/02/01 14:20:44	1.5
+++ /home/repository/moby/moby-live/Python/bioMoby/ontology/TEST.py	2005/02/07 14:23:33	1.6
@@ -48,4 +48,5 @@
             if elt.nodeName=="CrossReference" or elt.nodeName=="moby:CrossReference":
                 self.__cross__=[]
                 for ref in elt.childNodes:
-                    self.__cross__.append(um.loads(ref))
\ No newline at end of file
+                    if ref.nodeType==ref.ELEMENT_NODE:
+                        self.__cross__.append(um.loadn(ref))
\ No newline at end of file

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/ontology/TargetP_result.py,v
retrieving revision 1.5
retrieving revision 1.6
diff -u -r1.5 -r1.6
--- /home/repository/moby/moby-live/Python/bioMoby/ontology/TargetP_result.py	2005/02/01 14:20:44	1.5
+++ /home/repository/moby/moby-live/Python/bioMoby/ontology/TargetP_result.py	2005/02/07 14:23:33	1.6
@@ -54,7 +54,8 @@
             if elt.nodeName=="CrossReference" or elt.nodeName=="moby:CrossReference":
                 self.__cross__=[]
                 for ref in elt.childNodes:
-                    self.__cross__.append(um.loads(ref))
+                    if ref.nodeType==ref.ELEMENT_NODE:
+                        self.__cross__.append(um.loadn(ref))
             if elt.nodeType==elt.ELEMENT_NODE and (elt.nodeName=="Float" or elt.nodeName=="moby:Float") and (elt.getAttribute("articleName")=="o_score" or elt.getAttribute("moby:articleName")=="o_score"):
                 t=MobyFloat()
                 t.fromMoby(elt)

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/ontology/Testout.py,v
retrieving revision 1.5
retrieving revision 1.6
diff -u -r1.5 -r1.6
--- /home/repository/moby/moby-live/Python/bioMoby/ontology/Testout.py	2005/02/01 14:20:44	1.5
+++ /home/repository/moby/moby-live/Python/bioMoby/ontology/Testout.py	2005/02/07 14:23:33	1.6
@@ -53,7 +53,8 @@
             if elt.nodeName=="CrossReference" or elt.nodeName=="moby:CrossReference":
                 self.__cross__=[]
                 for ref in elt.childNodes:
-                    self.__cross__.append(um.loads(ref))
+                    if ref.nodeType==ref.ELEMENT_NODE:
+                        self.__cross__.append(um.loadn(ref))
             if elt.nodeType==elt.ELEMENT_NODE and (elt.nodeName=="Integer" or elt.nodeName=="moby:Integer") and (elt.getAttribute("articleName")=="gid" or elt.getAttribute("moby:articleName")=="gid"):
                 t=MobyInteger()
                 t.fromMoby(elt)

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/ontology/TextBase64.py,v
retrieving revision 1.5
retrieving revision 1.6
diff -u -r1.5 -r1.6
--- /home/repository/moby/moby-live/Python/bioMoby/ontology/TextBase64.py	2005/02/01 14:20:44	1.5
+++ /home/repository/moby/moby-live/Python/bioMoby/ontology/TextBase64.py	2005/02/07 14:23:33	1.6
@@ -48,4 +48,5 @@
             if elt.nodeName=="CrossReference" or elt.nodeName=="moby:CrossReference":
                 self.__cross__=[]
                 for ref in elt.childNodes:
-                    self.__cross__.append(um.loads(ref))
\ No newline at end of file
+                    if ref.nodeType==ref.ELEMENT_NODE:
+                        self.__cross__.append(um.loadn(ref))
\ No newline at end of file

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/ontology/TextFormatted.py,v
retrieving revision 1.5
retrieving revision 1.6
diff -u -r1.5 -r1.6
--- /home/repository/moby/moby-live/Python/bioMoby/ontology/TextFormatted.py	2005/02/01 14:20:44	1.5
+++ /home/repository/moby/moby-live/Python/bioMoby/ontology/TextFormatted.py	2005/02/07 14:23:33	1.6
@@ -48,4 +48,5 @@
             if elt.nodeName=="CrossReference" or elt.nodeName=="moby:CrossReference":
                 self.__cross__=[]
                 for ref in elt.childNodes:
-                    self.__cross__.append(um.loads(ref))
\ No newline at end of file
+                    if ref.nodeType==ref.ELEMENT_NODE:
+                        self.__cross__.append(um.loadn(ref))
\ No newline at end of file

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/ontology/TextHtml.py,v
retrieving revision 1.5
retrieving revision 1.6
diff -u -r1.5 -r1.6
--- /home/repository/moby/moby-live/Python/bioMoby/ontology/TextHtml.py	2005/02/01 14:20:44	1.5
+++ /home/repository/moby/moby-live/Python/bioMoby/ontology/TextHtml.py	2005/02/07 14:23:33	1.6
@@ -48,4 +48,5 @@
             if elt.nodeName=="CrossReference" or elt.nodeName=="moby:CrossReference":
                 self.__cross__=[]
                 for ref in elt.childNodes:
-                    self.__cross__.append(um.loads(ref))
\ No newline at end of file
+                    if ref.nodeType==ref.ELEMENT_NODE:
+                        self.__cross__.append(um.loadn(ref))
\ No newline at end of file

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/ontology/TextPlain.py,v
retrieving revision 1.5
retrieving revision 1.6
diff -u -r1.5 -r1.6
--- /home/repository/moby/moby-live/Python/bioMoby/ontology/TextPlain.py	2005/02/01 14:20:44	1.5
+++ /home/repository/moby/moby-live/Python/bioMoby/ontology/TextPlain.py	2005/02/07 14:23:33	1.6
@@ -48,4 +48,5 @@
             if elt.nodeName=="CrossReference" or elt.nodeName=="moby:CrossReference":
                 self.__cross__=[]
                 for ref in elt.childNodes:
-                    self.__cross__.append(um.loads(ref))
\ No newline at end of file
+                    if ref.nodeType==ref.ELEMENT_NODE:
+                        self.__cross__.append(um.loadn(ref))
\ No newline at end of file

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/ontology/TextUuencoded.py,v
retrieving revision 1.5
retrieving revision 1.6
diff -u -r1.5 -r1.6
--- /home/repository/moby/moby-live/Python/bioMoby/ontology/TextUuencoded.py	2005/02/01 14:20:44	1.5
+++ /home/repository/moby/moby-live/Python/bioMoby/ontology/TextUuencoded.py	2005/02/07 14:23:33	1.6
@@ -48,4 +48,5 @@
             if elt.nodeName=="CrossReference" or elt.nodeName=="moby:CrossReference":
                 self.__cross__=[]
                 for ref in elt.childNodes:
-                    self.__cross__.append(um.loads(ref))
\ No newline at end of file
+                    if ref.nodeType==ref.ELEMENT_NODE:
+                        self.__cross__.append(um.loadn(ref))
\ No newline at end of file

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/ontology/TextXml.py,v
retrieving revision 1.5
retrieving revision 1.6
diff -u -r1.5 -r1.6
--- /home/repository/moby/moby-live/Python/bioMoby/ontology/TextXml.py	2005/02/01 14:20:44	1.5
+++ /home/repository/moby/moby-live/Python/bioMoby/ontology/TextXml.py	2005/02/07 14:23:33	1.6
@@ -48,4 +48,5 @@
             if elt.nodeName=="CrossReference" or elt.nodeName=="moby:CrossReference":
                 self.__cross__=[]
                 for ref in elt.childNodes:
-                    self.__cross__.append(um.loads(ref))
\ No newline at end of file
+                    if ref.nodeType==ref.ELEMENT_NODE:
+                        self.__cross__.append(um.loadn(ref))
\ No newline at end of file

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/ontology/Text_plain.py,v
retrieving revision 1.5
retrieving revision 1.6
diff -u -r1.5 -r1.6
--- /home/repository/moby/moby-live/Python/bioMoby/ontology/Text_plain.py	2005/02/01 14:20:44	1.5
+++ /home/repository/moby/moby-live/Python/bioMoby/ontology/Text_plain.py	2005/02/07 14:23:33	1.6
@@ -48,4 +48,5 @@
             if elt.nodeName=="CrossReference" or elt.nodeName=="moby:CrossReference":
                 self.__cross__=[]
                 for ref in elt.childNodes:
-                    self.__cross__.append(um.loads(ref))
\ No newline at end of file
+                    if ref.nodeType==ref.ELEMENT_NODE:
+                        self.__cross__.append(um.loadn(ref))
\ No newline at end of file

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/ontology/Trait_Details.py,v
retrieving revision 1.5
retrieving revision 1.6
diff -u -r1.5 -r1.6
--- /home/repository/moby/moby-live/Python/bioMoby/ontology/Trait_Details.py	2005/02/01 14:20:44	1.5
+++ /home/repository/moby/moby-live/Python/bioMoby/ontology/Trait_Details.py	2005/02/07 14:23:33	1.6
@@ -54,7 +54,8 @@
             if elt.nodeName=="CrossReference" or elt.nodeName=="moby:CrossReference":
                 self.__cross__=[]
                 for ref in elt.childNodes:
-                    self.__cross__.append(um.loads(ref))
+                    if ref.nodeType==ref.ELEMENT_NODE:
+                        self.__cross__.append(um.loadn(ref))
             if elt.nodeType==elt.ELEMENT_NODE and (elt.nodeName=="String" or elt.nodeName=="moby:String") and (elt.getAttribute("articleName")=="trait_desc" or elt.getAttribute("moby:articleName")=="trait_desc"):
                 t=MobyString()
                 t.fromMoby(elt)

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/ontology/Tree.py,v
retrieving revision 1.5
retrieving revision 1.6
diff -u -r1.5 -r1.6
--- /home/repository/moby/moby-live/Python/bioMoby/ontology/Tree.py	2005/02/01 14:20:44	1.5
+++ /home/repository/moby/moby-live/Python/bioMoby/ontology/Tree.py	2005/02/07 14:23:33	1.6
@@ -48,4 +48,5 @@
             if elt.nodeName=="CrossReference" or elt.nodeName=="moby:CrossReference":
                 self.__cross__=[]
                 for ref in elt.childNodes:
-                    self.__cross__.append(um.loads(ref))
\ No newline at end of file
+                    if ref.nodeType==ref.ELEMENT_NODE:
+                        self.__cross__.append(um.loadn(ref))
\ No newline at end of file

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/ontology/TropGENE_ACCESSION.py,v
retrieving revision 1.5
retrieving revision 1.6
diff -u -r1.5 -r1.6
--- /home/repository/moby/moby-live/Python/bioMoby/ontology/TropGENE_ACCESSION.py	2005/02/01 14:20:44	1.5
+++ /home/repository/moby/moby-live/Python/bioMoby/ontology/TropGENE_ACCESSION.py	2005/02/07 14:23:33	1.6
@@ -68,7 +68,8 @@
             if elt.nodeName=="CrossReference" or elt.nodeName=="moby:CrossReference":
                 self.__cross__=[]
                 for ref in elt.childNodes:
-                    self.__cross__.append(um.loads(ref))
+                    if ref.nodeType==ref.ELEMENT_NODE:
+                        self.__cross__.append(um.loadn(ref))
             if elt.nodeType==elt.ELEMENT_NODE and (elt.nodeName=="TropGENE_LOCUS" or elt.nodeName=="moby:TropGENE_LOCUS") and (elt.getAttribute("articleName")=="RFLP" or elt.getAttribute("moby:articleName")=="RFLP"):
                 self.RFLP=MobyTropGENE_LOCUS()
                 self.RFLP.fromMoby(elt)

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/ontology/TropGENE_Diversity_Matrix.py,v
retrieving revision 1.5
retrieving revision 1.6
diff -u -r1.5 -r1.6
--- /home/repository/moby/moby-live/Python/bioMoby/ontology/TropGENE_Diversity_Matrix.py	2005/02/01 14:20:44	1.5
+++ /home/repository/moby/moby-live/Python/bioMoby/ontology/TropGENE_Diversity_Matrix.py	2005/02/07 14:23:33	1.6
@@ -48,4 +48,5 @@
             if elt.nodeName=="CrossReference" or elt.nodeName=="moby:CrossReference":
                 self.__cross__=[]
                 for ref in elt.childNodes:
-                    self.__cross__.append(um.loads(ref))
\ No newline at end of file
+                    if ref.nodeType==ref.ELEMENT_NODE:
+                        self.__cross__.append(um.loadn(ref))
\ No newline at end of file

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/ontology/TropGENE_LOCUS.py,v
retrieving revision 1.5
retrieving revision 1.6
diff -u -r1.5 -r1.6
--- /home/repository/moby/moby-live/Python/bioMoby/ontology/TropGENE_LOCUS.py	2005/02/01 14:20:44	1.5
+++ /home/repository/moby/moby-live/Python/bioMoby/ontology/TropGENE_LOCUS.py	2005/02/07 14:23:33	1.6
@@ -47,4 +47,5 @@
             if elt.nodeName=="CrossReference" or elt.nodeName=="moby:CrossReference":
                 self.__cross__=[]
                 for ref in elt.childNodes:
-                    self.__cross__.append(um.loads(ref))
\ No newline at end of file
+                    if ref.nodeType==ref.ELEMENT_NODE:
+                        self.__cross__.append(um.loadn(ref))
\ No newline at end of file

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/ontology/VirtualSequence.py,v
retrieving revision 1.5
retrieving revision 1.6
diff -u -r1.5 -r1.6
--- /home/repository/moby/moby-live/Python/bioMoby/ontology/VirtualSequence.py	2005/02/01 14:20:44	1.5
+++ /home/repository/moby/moby-live/Python/bioMoby/ontology/VirtualSequence.py	2005/02/07 14:23:33	1.6
@@ -49,7 +49,8 @@
             if elt.nodeName=="CrossReference" or elt.nodeName=="moby:CrossReference":
                 self.__cross__=[]
                 for ref in elt.childNodes:
-                    self.__cross__.append(um.loads(ref))
+                    if ref.nodeType==ref.ELEMENT_NODE:
+                        self.__cross__.append(um.loadn(ref))
             if elt.nodeType==elt.ELEMENT_NODE and (elt.nodeName=="Integer" or elt.nodeName=="moby:Integer") and (elt.getAttribute("articleName")=="Length" or elt.getAttribute("moby:articleName")=="Length"):
                 t=MobyInteger()
                 t.fromMoby(elt)

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/ontology/WU_BLAST_Text.py,v
retrieving revision 1.5
retrieving revision 1.6
diff -u -r1.5 -r1.6
--- /home/repository/moby/moby-live/Python/bioMoby/ontology/WU_BLAST_Text.py	2005/02/01 14:20:44	1.5
+++ /home/repository/moby/moby-live/Python/bioMoby/ontology/WU_BLAST_Text.py	2005/02/07 14:23:33	1.6
@@ -48,4 +48,5 @@
             if elt.nodeName=="CrossReference" or elt.nodeName=="moby:CrossReference":
                 self.__cross__=[]
                 for ref in elt.childNodes:
-                    self.__cross__.append(um.loads(ref))
\ No newline at end of file
+                    if ref.nodeType==ref.ELEMENT_NODE:
+                        self.__cross__.append(um.loadn(ref))
\ No newline at end of file

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/ontology/Wildcard_Query.py,v
retrieving revision 1.5
retrieving revision 1.6
diff -u -r1.5 -r1.6
--- /home/repository/moby/moby-live/Python/bioMoby/ontology/Wildcard_Query.py	2005/02/01 14:20:44	1.5
+++ /home/repository/moby/moby-live/Python/bioMoby/ontology/Wildcard_Query.py	2005/02/07 14:23:33	1.6
@@ -52,7 +52,8 @@
             if elt.nodeName=="CrossReference" or elt.nodeName=="moby:CrossReference":
                 self.__cross__=[]
                 for ref in elt.childNodes:
-                    self.__cross__.append(um.loads(ref))
+                    if ref.nodeType==ref.ELEMENT_NODE:
+                        self.__cross__.append(um.loadn(ref))
             if elt.nodeType==elt.ELEMENT_NODE and (elt.nodeName=="Integer" or elt.nodeName=="moby:Integer") and (elt.getAttribute("articleName")=="end_row" or elt.getAttribute("moby:articleName")=="end_row"):
                 t=MobyInteger()
                 t.fromMoby(elt)