From senger at dev.open-bio.org  Sun Mar  2 07:45:25 2008
From: senger at dev.open-bio.org (Martin Senger)
Date: Sun, 2 Mar 2008 07:45:25 -0500
Subject: [MOBY-guts] biomoby commit
Message-ID: <200803021245.m22CjPI4032364@dev.open-bio.org>


senger
Sun Mar  2 07:45:24 EST 2008
Update of /home/repository/moby/moby-live/Java
In directory dev.open-bio.org:/tmp/cvs-serv32345

Modified Files:
	build.xml 
Log Message:
Too Many Changes - see docs/ChangeLog

moby-live/Java build.xml,1.69,1.70
===================================================================
RCS file: /home/repository/moby/moby-live/Java/build.xml,v
retrieving revision 1.69
retrieving revision 1.70
diff -u -r1.69 -r1.70
--- /home/repository/moby/moby-live/Java/build.xml	2008/02/28 05:21:48	1.69
+++ /home/repository/moby/moby-live/Java/build.xml	2008/03/02 12:45:24	1.70
@@ -97,7 +97,6 @@
   <property name="proxySet" value=""/>
   
   <property name="dot.location" value=""/>
-  <property name="registry.cache.dir" value=""/>
   
   <!-- Classpath -->
   <path id="build.classpath">
@@ -106,12 +105,9 @@
     <fileset dir="${lib.dir}">
       <include name="*.jar"/>
     </fileset>
-    <!-- it should not be necessary anymore because
-         tools.jar are now defined in xmls/project.pom
     <fileset dir="${java.home}/../lib">
       <include name="tools.jar"/>
     </fileset>
-    -->
   </path>
           
   <!-- this differs from the ${build.classpath} by not including


From senger at dev.open-bio.org  Sun Mar  2 07:45:25 2008
From: senger at dev.open-bio.org (Martin Senger)
Date: Sun, 2 Mar 2008 07:45:25 -0500
Subject: [MOBY-guts] biomoby commit
Message-ID: <200803021245.m22CjPFH032415@dev.open-bio.org>


senger
Sun Mar  2 07:45:24 EST 2008
Update of /home/repository/moby/moby-live/Java/docs
In directory dev.open-bio.org:/tmp/cvs-serv32345/docs

Modified Files:
	ChangeLog Dashboard-NOTES.txt 
Log Message:
Too Many Changes - see docs/ChangeLog

moby-live/Java/docs ChangeLog,1.84,1.85 Dashboard-NOTES.txt,1.14,1.15
===================================================================
RCS file: /home/repository/moby/moby-live/Java/docs/ChangeLog,v
retrieving revision 1.84
retrieving revision 1.85
diff -u -r1.84 -r1.85
--- /home/repository/moby/moby-live/Java/docs/ChangeLog	2008/02/28 05:21:48	1.84
+++ /home/repository/moby/moby-live/Java/docs/ChangeLog	2008/03/02 12:45:24	1.85
@@ -1,3 +1,43 @@
+2008-03-02  Martin Senger  <martin.senger&#64;gmail.com>
+
+	* Added: new installation task (type: ant install) - it downloads
+	all needed librraies, builds the jMoby, fills the local cache and
+	starts Dashboard.
+
+	* Added: method MobyException.formatAndLog()
+
+	* Changes in Dashboard:
+	
+	  - Better support for configuration; it uses now also properties
+	  from the 'build.properties' file (which helps, for example, in
+	  finding the same registry local cache as the one used during the
+	  jMoby installation (ant install).
+
+	  - Allowing to select category when registering a new service.
+
+	  - The component layout in the MoSeS generators panel was
+	  slightly changed (the never-implemented flavours removed; more
+	  space for the console).
+
+	  - The console panels, in the append mode, now scroll better to
+	  their ends (in order to better follow what is being written
+	  there).
+
+	  - Fix the local class selector in the SimpleClient panel (before
+	  it suggested a file to select but in fact it was a class name
+	  that should be entered there).
+
+	
+2008-02-29  Martin Senger  <martin.senger&#64;gmail.com>
+
+	* Fixed: Calling various tasks from Dashboard sometimes caused a
+	mysterious NullPointerException in the SimpleAnt task. This was
+	because of a (still mysterious) bug in Ant itself. But I at least
+	found a workaround so the bug should not occur again.
+
+	* Added: New method getResource(URL url) in CentralImp class,
+	dealing with gzipped RDF resources.
+
 2008-02-28  Martin Senger  <martin.senger&#64;gmail.com>
 
 	* Fixed: the jMoby XML message parser can accept now more

===================================================================
RCS file: /home/repository/moby/moby-live/Java/docs/Dashboard-NOTES.txt,v
retrieving revision 1.14
retrieving revision 1.15
diff -u -r1.14 -r1.15
--- /home/repository/moby/moby-live/Java/docs/Dashboard-NOTES.txt	2006/10/14 20:46:55	1.14
+++ /home/repository/moby/moby-live/Java/docs/Dashboard-NOTES.txt	2008/03/02 12:45:24	1.15
@@ -15,20 +15,9 @@
 Should be done:
 ---------------
 
-* jMoby.jar for service providers should be smaller (no need for many
-  classes there - like ui...)
-
 * Dashborad should have a way to create/show XML data representing a
   data type *before* there is a service registered that uses such data
 
-* when moses panel generates datatypes they are not immediately
-  recognized by the same dashbord (e.g. in the SimpleClient panel);
-  one must restart the dashboard; it should be better to dynamically
-  extend the dashboard's classpath
-
-* add a cache action button: "show me what's would be updated if I
-  update my cache"
-
 * right-click
   - if nothing selected, it should take what is under the
     mouse (selected first), otherwise it is annoying
@@ -82,9 +71,6 @@
 
 ? move help system to Java Help; more contextual help
 
-? cache: start to work on/think of the RDF-based cache 
-? cache: remove memory-caching from CentralImpl
-
 ? Possible new panels:
   - verify registry
   - browsing in graphs


From senger at dev.open-bio.org  Sun Mar  2 07:45:25 2008
From: senger at dev.open-bio.org (Martin Senger)
Date: Sun, 2 Mar 2008 07:45:25 -0500
Subject: [MOBY-guts] biomoby commit
Message-ID: <200803021245.m22CjP3e032468@dev.open-bio.org>


senger
Sun Mar  2 07:45:25 EST 2008
Update of /home/repository/moby/moby-live/Java/src/Clients/help
In directory dev.open-bio.org:/tmp/cvs-serv32345/src/Clients/help

Added Files:
	MobyDigestClient_usage.txt 
Removed Files:
	MobyDigest_usage.txt 
Log Message:
Too Many Changes - see docs/ChangeLog

moby-live/Java/src/Clients/help MobyDigestClient_usage.txt,NONE,1.1 MobyDigest_usage.txt,1.7,NONE
rcsdiff: /home/repository/moby/moby-live/Java/src/Clients/help/RCS/MobyDigest_usage.txt,v: No such file or directory


From senger at dev.open-bio.org  Sun Mar  2 07:45:25 2008
From: senger at dev.open-bio.org (Martin Senger)
Date: Sun, 2 Mar 2008 07:45:25 -0500
Subject: [MOBY-guts] biomoby commit
Message-ID: <200803021245.m22CjPYM032393@dev.open-bio.org>


senger
Sun Mar  2 07:45:24 EST 2008
Update of /home/repository/moby/moby-live/Java/data/registrations
In directory dev.open-bio.org:/tmp/cvs-serv32345/data/registrations

Added Files:
	ConcatSequenceSet-registration.xml 
	ConcatSequences-registration.xml 
	HelloBiomobyWorld-registration.xml Mabuhay-registration.xml 
	README Regex.datatype.xml TestServiceNotes-registration.xml 
	TextExtract-registration.xml 
Log Message:
Too Many Changes - see docs/ChangeLog

moby-live/Java/data/registrations ConcatSequenceSet-registration.xml,NONE,1.1 ConcatSequences-registration.xml,NONE,1.1 HelloBiomobyWorld-registration.xml,NONE,1.1 Mabuhay-registration.xml,NONE,1.1 README,NONE,1.1 Regex.datatype.xml,NONE,1.1 TestServiceNotes-registration.xml,NONE,1.1 TextExtract-registration.xml,NONE,1.1

From senger at dev.open-bio.org  Sun Mar  2 07:45:25 2008
From: senger at dev.open-bio.org (Martin Senger)
Date: Sun, 2 Mar 2008 07:45:25 -0500
Subject: [MOBY-guts] biomoby commit
Message-ID: <200803021245.m22CjPJk032379@dev.open-bio.org>


senger
Sun Mar  2 07:45:24 EST 2008
Update of /home/repository/moby/moby-live/Java/data
In directory dev.open-bio.org:/tmp/cvs-serv32345/data

Removed Files:
	parser-test-input2.xml 
Log Message:
Too Many Changes - see docs/ChangeLog

moby-live/Java/data parser-test-input2.xml,1.2,NONE
rcsdiff: /home/repository/moby/moby-live/Java/data/RCS/parser-test-input2.xml,v: No such file or directory


From senger at dev.open-bio.org  Sun Mar  2 07:45:25 2008
From: senger at dev.open-bio.org (Martin Senger)
Date: Sun, 2 Mar 2008 07:45:25 -0500
Subject: [MOBY-guts] biomoby commit
Message-ID: <200803021245.m22CjPju032526@dev.open-bio.org>


senger
Sun Mar  2 07:45:25 EST 2008
Update of /home/repository/moby/moby-live/Java/src/config/dashboard/META-INF/services
In directory dev.open-bio.org:/tmp/cvs-serv32345/src/config/dashboard/META-INF/services

Modified Files:
	org.biomoby.service.dashboard.renderers.Renderer 
Log Message:
Too Many Changes - see docs/ChangeLog

moby-live/Java/src/config/dashboard/META-INF/services org.biomoby.service.dashboard.renderers.Renderer,1.3,1.4
===================================================================
RCS file: /home/repository/moby/moby-live/Java/src/config/dashboard/META-INF/services/org.biomoby.service.dashboard.renderers.Renderer,v
retrieving revision 1.3
retrieving revision 1.4
diff -u -r1.3 -r1.4
--- /home/repository/moby/moby-live/Java/src/config/dashboard/META-INF/services/org.biomoby.service.dashboard.renderers.Renderer	2006/02/19 18:42:55	1.3
+++ /home/repository/moby/moby-live/Java/src/config/dashboard/META-INF/services/org.biomoby.service.dashboard.renderers.Renderer	2008/03/02 12:45:25	1.4
@@ -2,4 +2,4 @@
 org.biomoby.service.dashboard.renderers.PlainMobyText
 org.biomoby.service.dashboard.renderers.Base64Image
 org.biomoby.service.dashboard.renderers.XMLTreeRenderer
-org.biomoby.service.dashboard.renderers.ICISPedigreeTree
+#org.biomoby.service.dashboard.renderers.ICISPedigreeTree


From senger at dev.open-bio.org  Sun Mar  2 07:45:25 2008
From: senger at dev.open-bio.org (Martin Senger)
Date: Sun, 2 Mar 2008 07:45:25 -0500
Subject: [MOBY-guts] biomoby commit
Message-ID: <200803021245.m22CjPGj032441@dev.open-bio.org>


senger
Sun Mar  2 07:45:25 EST 2008
Update of /home/repository/moby/moby-live/Java/src/Clients
In directory dev.open-bio.org:/tmp/cvs-serv32345/src/Clients

Modified Files:
	CacheRegistryClient.java MobyDigestClient.java 
	TestingCentral.java 
Log Message:
Too Many Changes - see docs/ChangeLog

moby-live/Java/src/Clients CacheRegistryClient.java,1.9,1.10 MobyDigestClient.java,1.8,1.9 TestingCentral.java,1.10,1.11
===================================================================
RCS file: /home/repository/moby/moby-live/Java/src/Clients/CacheRegistryClient.java,v
retrieving revision 1.9
retrieving revision 1.10
diff -u -r1.9 -r1.10
--- /home/repository/moby/moby-live/Java/src/Clients/CacheRegistryClient.java	2008/02/23 13:58:32	1.9
+++ /home/repository/moby/moby-live/Java/src/Clients/CacheRegistryClient.java	2008/03/02 12:45:25	1.10
@@ -16,8 +16,7 @@
 import org.biomoby.shared.event.Notifier;
 
 import org.tulsoft.tools.BaseCmdLine;
-import org.tulsoft.shared.FileUtils;
-import org.tulsoft.shared.GException;
+import org.apache.commons.lang.time.DurationFormatUtils;
 
 /**
  * This is a command-line client creating (and removing) a cache of a
@@ -65,53 +64,91 @@
 	    if (! cmd.hasOption ("-q"))
 		worker.addNotificationListener (new LogListener());
 
+	    long started, elapsed, total = 0;
+
 	    //
 	    // [re-]fill the cache
 	    //
+	    if (cmd.hasOption ("-fill") || cmd.hasOption ("-fill-n")) {
+		worker.removeFromCache (CentralCached.CACHE_PART_NAMESPACES);
+		decoration ("Retrieving namespaces...    ");
+		started = System.currentTimeMillis();
+		worker.getFullNamespaces();
+		elapsed = System.currentTimeMillis() - started;
+		total += elapsed;
+		decorationLn (DurationFormatUtils.formatDurationHMS (elapsed));
+	    }
 	    if (cmd.hasOption ("-fill") || cmd.hasOption ("-fill-d")) {
 		worker.removeFromCache (CentralCached.CACHE_PART_DATATYPES);
-		decorationLn ("Retrieving data types...");
+		decoration ("Retrieving data types...    ");
+		started = System.currentTimeMillis();
 		worker.getDataTypes();
+		elapsed = System.currentTimeMillis() - started;
+		total += elapsed;
+		decorationLn (DurationFormatUtils.formatDurationHMS (elapsed));
 	    }
 	    if (cmd.hasOption ("-fill") || cmd.hasOption ("-fill-s")) {
 		worker.removeFromCache (CentralCached.CACHE_PART_SERVICES);
-		decorationLn ("Retrieving services...");
+		decoration ("Retrieving services...      ");
+		started = System.currentTimeMillis();
 		worker.getServices();
+		elapsed = System.currentTimeMillis() - started;
+		total += elapsed;
+		decorationLn (DurationFormatUtils.formatDurationHMS (elapsed));
 	    }
 	    if (cmd.hasOption ("-fill") || cmd.hasOption ("-fill-t")) {
 		worker.removeFromCache (CentralCached.CACHE_PART_SERVICETYPES);
-		decorationLn ("Retrieving service types...");
+		decoration ("Retrieving service types... ");
+		started = System.currentTimeMillis();
 		worker.getFullServiceTypes();
-	    }
-	    if (cmd.hasOption ("-fill") || cmd.hasOption ("-fill-n")) {
-		worker.removeFromCache (CentralCached.CACHE_PART_NAMESPACES);
-		decorationLn ("Retrieving namespaces...");
-		worker.getFullNamespaces();
+		elapsed = System.currentTimeMillis() - started;
+		total += elapsed;
+		decorationLn (DurationFormatUtils.formatDurationHMS (elapsed));
 	    }
 
 	    //
 	    // update the cache
 	    //
+	    if (cmd.hasOption ("-update") || cmd.hasOption ("-update-n")) {
+		decoration ("Updating namespaces...      ");
+		started = System.currentTimeMillis();
+		worker.updateCache (CentralCached.CACHE_PART_NAMESPACES);
+		elapsed = System.currentTimeMillis() - started;
+		total += elapsed;
+		decorationLn (DurationFormatUtils.formatDurationHMS (elapsed));
+	    }
 	    if (cmd.hasOption ("-update") || cmd.hasOption ("-update-d")) {
-		decorationLn ("Updating data types...");
+		decoration ("Updating data types...      ");
+		started = System.currentTimeMillis();
 		worker.updateCache (CentralCached.CACHE_PART_DATATYPES);
+		elapsed = System.currentTimeMillis() - started;
+		total += elapsed;
+		decorationLn (DurationFormatUtils.formatDurationHMS (elapsed));
 	    }
 	    if (cmd.hasOption ("-update") || cmd.hasOption ("-update-s")) {
-		decorationLn ("Updating services...");
+		decoration ("Updating services...        ");
+		started = System.currentTimeMillis();
 		worker.updateCache (CentralCached.CACHE_PART_SERVICES);
+		elapsed = System.currentTimeMillis() - started;
+		total += elapsed;
+		decorationLn (DurationFormatUtils.formatDurationHMS (elapsed));
 	    }
 	    if (cmd.hasOption ("-update") || cmd.hasOption ("-update-t")) {
-		decorationLn ("Updating service types...");
+		decoration ("Updating service types...   ");
+		started = System.currentTimeMillis();
 		worker.updateCache (CentralCached.CACHE_PART_SERVICETYPES);
-	    }
-	    if (cmd.hasOption ("-update") || cmd.hasOption ("-update-n")) {
-		decorationLn ("Updating namespaces...");
-		worker.updateCache (CentralCached.CACHE_PART_NAMESPACES);
+		elapsed = System.currentTimeMillis() - started;
+		total += elapsed;
+		decorationLn (DurationFormatUtils.formatDurationHMS (elapsed));
 	    }
 
 	    //
 	    // remove the cache
 	    //
+	    if (cmd.hasOption ("-remove") || cmd.hasOption ("-remove-n")) {
+		worker.removeFromCache (CentralCached.CACHE_PART_NAMESPACES);
+		decorationLn ("Cache for namespaces removed.");
+	    }
 	    if (cmd.hasOption ("-remove") || cmd.hasOption ("-remove-d")) {
 		worker.removeFromCache (CentralCached.CACHE_PART_DATATYPES);
 		decorationLn ("Cache for data types removed.");
@@ -124,14 +161,15 @@
 		worker.removeFromCache (CentralCached.CACHE_PART_SERVICETYPES);
 		decorationLn ("Cache for service types removed.");
 	    }
-	    if (cmd.hasOption ("-remove") || cmd.hasOption ("-remove-n")) {
-		worker.removeFromCache (CentralCached.CACHE_PART_NAMESPACES);
-		decorationLn ("Cache for namespaces removed.");
-	    }
 
 	    //
 	    // cache info
 	    //
+	    if (cmd.hasOption ("-info") || cmd.hasOption ("-info-n")) {
+		decorationLn ("Cache for namespaces...");
+		msgln
+		    (worker.getCacheInfoFormatted (CentralCached.CACHE_PART_NAMESPACES));
+	    }
 	    if (cmd.hasOption ("-info") || cmd.hasOption ("-info-d")) {
 		decorationLn ("Cache for data types...");
 		msgln
@@ -147,11 +185,11 @@
 		msgln
 		    (worker.getCacheInfoFormatted (CentralCached.CACHE_PART_SERVICETYPES));
 	    }
-	    if (cmd.hasOption ("-info") || cmd.hasOption ("-info-n")) {
-		decorationLn ("Cache for namespaces...");
-		msgln
-		    (worker.getCacheInfoFormatted (CentralCached.CACHE_PART_NAMESPACES));
-	    }
+
+
+	    decorationLn ("Total spent time:           " +
+			  DurationFormatUtils.formatDurationHMS (total));
+
 
 	} catch (Throwable e) {
 	    processErrorAndExit (e);

===================================================================
RCS file: /home/repository/moby/moby-live/Java/src/Clients/MobyDigestClient.java,v
retrieving revision 1.8
retrieving revision 1.9
diff -u -r1.8 -r1.9
--- /home/repository/moby/moby-live/Java/src/Clients/MobyDigestClient.java	2006/02/08 17:24:13	1.8
+++ /home/repository/moby/moby-live/Java/src/Clients/MobyDigestClient.java	2008/03/02 12:45:25	1.9
@@ -6,16 +6,21 @@
 // Copyright Martin Senger (martin.senger at gmail.com).
 //
 
-import org.biomoby.shared.*;
+import org.biomoby.client.CmdLineHelper;
+import org.biomoby.shared.CentralCached;
+import org.biomoby.shared.MobyDataType;
+import org.biomoby.shared.MobyNamespace;
+import org.biomoby.shared.MobyService;
+import org.biomoby.shared.MobyServiceType;
+import org.biomoby.shared.MobyData;
+import org.biomoby.shared.MobySecondaryData;
+import org.biomoby.shared.MobyPrimaryDataSet;
 import org.biomoby.shared.event.SimpleListener;
-import org.biomoby.shared.event.Notifier;
-import org.biomoby.client.*;
 
 import org.tulsoft.tools.BaseCmdLine;
-import org.tulsoft.shared.FileUtils;
-import org.tulsoft.shared.GException;
 
 import java.util.Map;
+import java.util.Set;
 import java.util.HashSet;
 import java.util.Iterator;
 
@@ -28,22 +33,8 @@
  * @version $Id$
  */
 
-public class MobyDigestClient {
-
-    /*************************************************************************
-     * Return a help text how to use this client.
-     *************************************************************************/
-    public static String getUsage() {
-	String helpFile = "help/MobyDigest_usage.txt";
-	try {
-	    return new String (FileUtils.findAndGetBinaryFile (helpFile));
-	} catch (GException e) {
-	    return
-		"Sorry but an error occured.\n" +
-		"I cannot find the help file '" + helpFile + "'.\n" +
-		e.getMessage();
-	}
-    }
+public class MobyDigestClient
+    extends CmdLineHelper {
 
     /*************************************************************************
      *
@@ -53,38 +44,31 @@
     public static void main (String [] args) {
 	try {
 
-	    BaseCmdLine cmd = new BaseCmdLine (args, true);
-	    if (cmd.hasParam ("-help") || cmd.hasParam ("-h")) {
-		System.out.print (MobyDigestClient.getUsage());
-		System.exit (0);
-	    }
+	    BaseCmdLine cmd = getCmdLine (args, MobyDigestClient.class);
 
 	    // where is a Moby registry
-	    CentralAll worker =
-		new CentralDigestCachedImpl (cmd.getParam ("-e"),
-					     cmd.getParam ("-uri"),
-					     cmd.getParam ("-cachedir"));
+	    CentralCached worker = getCachableRegistryWorker (cmd);
 
 	    // how much to show
 	    boolean details = cmd.hasOption ("-details");
 	    boolean summary = cmd.hasOption ("-summary");
 	    boolean verbose = (cmd.hasOption ("-v") || cmd.hasOption ("-verbose"));
 	    if (verbose)
-		((Notifier)worker).addNotificationListener (new SimpleListener());
+		worker.addNotificationListener (new SimpleListener());
 
 	    // read (sometimes all) data types and their relationships
 	    if (cmd.hasOption ("-d")) {
 		if (details) {
 		    MobyDataType[] dataTypes = worker.getDataTypes();
 		    for (int i = 0; i < dataTypes.length; i++) {
-			System.out.println (dataTypes[i].toString());
-			System.out.println ("---");
+			msgln (dataTypes[i].toString());
+			msgln ("---");
 		    }
 		} else {
 		    Map dataTypeNames = worker.getDataTypeNames();
 		    for (Iterator it = dataTypeNames.entrySet().iterator(); it.hasNext(); ) {
 			Map.Entry entry = (Map.Entry)it.next();
-			System.out.println (entry.getKey());
+			msgln (entry.getKey());
 		    }
 		}
 	    }
@@ -94,9 +78,9 @@
 		MobyServiceType[] serviceTypes = worker.getFullServiceTypes();
 		for (int i = 0; i < serviceTypes.length; i++) {
 		    if (details)
-			System.out.println (serviceTypes[i]);
+			msgln (serviceTypes[i]);
 		    else
-			System.out.println (serviceTypes[i].getName());
+			msgln (serviceTypes[i].getName());
 		}
 	    }
 
@@ -106,21 +90,21 @@
 		    MobyService[] services = worker.getServices();
 		    if (details) {
 			for (int i = 0; i < services.length; i++) {
-			    System.out.println (services[i]);
-			    System.out.println ("---");
+			    msgln (services[i]);
+			    msgln ("---");
 			}
 		    } else {  // summary
-			System.out.println
+			msgln
 			    ("#Prim\t#Sec\tSType\t#Out\tInColl\tOutColl\tService\tAuthority");
 			for (int i = 0; i < services.length; i++) {
 			    MobyService service = services[i];
 			    MobyData[] pInputs = service.getPrimaryInputs();
 			    MobyData[] sInputs = service.getSecondaryInputs();
 			    MobyData[] outputs = service.getPrimaryOutputs();
-			    System.out.print (pInputs.length + "\t");
-			    System.out.print (sInputs.length + "\t");
+			    msg (pInputs.length + "\t");
+			    msg (sInputs.length + "\t");
 			    StringBuffer buf = new StringBuffer();
-			    HashSet set = new HashSet();
+			    Set<String> set = new HashSet<String>();
 			    for (int j = 0; j < sInputs.length; j++) {
 				String abbrev =
 				    ( ((MobySecondaryData)sInputs[j]).getDataType()
@@ -130,8 +114,8 @@
 				    set.add (abbrev);
 				}
 			    }
-			    System.out.print (buf + "\t");
-			    System.out.print (outputs.length + "\t");
+			    msg (buf + "\t");
+			    msg (outputs.length + "\t");
 			    boolean found = false;
 			    for (int j = 0; j < pInputs.length; j++) {
 				if (pInputs[j] instanceof MobyPrimaryDataSet) {
@@ -139,7 +123,7 @@
 				    break;
 				}
 			    }
-			    System.out.print (found + "\t");
+			    msg (found + "\t");
 			    found = false;
 			    for (int j = 0; j < outputs.length; j++) {
 				if (outputs[j] instanceof MobyPrimaryDataSet) {
@@ -147,10 +131,9 @@
 				    break;
 				}
 			    }
-			    System.out.print (found + "\t");
-			    System.out.print (service.getName() + "\t");
- 			    System.out.print (service.getAuthority());
-			    System.out.println();
+			    msg (found + "\t");
+			    msg (service.getName() + "\t");
+ 			    msgln (service.getAuthority());
 			}
 		    }
 		} else {
@@ -160,7 +143,7 @@
 			String authority = (String)entry.getKey();
 			String[] names = (String[])entry.getValue();
 			for (int i = 0; i < names.length; i++) {
-			    System.out.println (names[i] + " (" + authority + ")");
+			    msgln (names[i] + " (" + authority + ")");
 			}
 		    }
 		}
@@ -171,16 +154,14 @@
 		MobyNamespace[] namespaces = worker.getFullNamespaces();
 		for (int i = 0; i < namespaces.length; i++) {
 		    if (details)
-			System.out.println (namespaces[i]);
+			msgln (namespaces[i]);
 		    else
-			System.out.println (namespaces[i].getName());
+			msgln (namespaces[i].getName());
 		}
 	    }
 
-	} catch (Exception e) {
-	    System.err.println ("===ERROR===");
-	    e.printStackTrace();
-	    System.err.println ("===========");
+	} catch (Throwable e) {
+	    processErrorAndExit (e);
 	}
     }
 }

===================================================================
RCS file: /home/repository/moby/moby-live/Java/src/Clients/TestingCentral.java,v
retrieving revision 1.10
retrieving revision 1.11
diff -u -r1.10 -r1.11
--- /home/repository/moby/moby-live/Java/src/Clients/TestingCentral.java	2006/12/07 18:41:00	1.10
+++ /home/repository/moby/moby-live/Java/src/Clients/TestingCentral.java	2008/03/02 12:45:25	1.11
@@ -94,8 +94,8 @@
         }
 	if (type.equalsIgnoreCase ("Integer")) {
 	    data.setDefaultValue ("123");
-	    data.setMaximumValue (234);
-	    data.setMinimumValue (23);
+	    data.setMaxValue     ("234");
+	    data.setMinValue     ("23");
 	    data.addAllowedValue ("30");
 	    data.addAllowedValue ("40");
 	    data.addAllowedValue ("50");


From senger at dev.open-bio.org  Sun Mar  2 07:45:26 2008
From: senger at dev.open-bio.org (Martin Senger)
Date: Sun, 2 Mar 2008 07:45:26 -0500
Subject: [MOBY-guts] biomoby commit
Message-ID: <200803021245.m22CjQGl032570@dev.open-bio.org>


senger
Sun Mar  2 07:45:25 EST 2008
Update of /home/repository/moby/moby-live/Java/src/main/org/biomoby/client
In directory dev.open-bio.org:/tmp/cvs-serv32345/src/main/org/biomoby/client

Modified Files:
	CentralImpl.java 
Log Message:
Too Many Changes - see docs/ChangeLog

moby-live/Java/src/main/org/biomoby/client CentralImpl.java,1.53,1.54
===================================================================
RCS file: /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/CentralImpl.java,v
retrieving revision 1.53
retrieving revision 1.54
diff -u -r1.53 -r1.54
--- /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/CentralImpl.java	2008/02/28 16:58:56	1.53
+++ /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/CentralImpl.java	2008/03/02 12:45:25	1.54
@@ -21,6 +21,7 @@
 import org.biomoby.shared.NoSuccessException;
 import org.biomoby.shared.PendingCurationException;
 import org.biomoby.shared.MobyResourceRef;
+import org.biomoby.shared.Utils;
 
 import javax.xml.parsers.DocumentBuilderFactory;
 import javax.xml.parsers.DocumentBuilder;
@@ -772,7 +773,8 @@
 	    Element elem = (Element)list.item (i);
 	    String name = elem.getAttribute ("name");
 	    String auth = elem.getAttribute ("authURI");
-	    Vector v = (results.containsKey (auth) ? (Vector)results.get (auth) : new Vector());
+	    Vector<Object> v =
+		(results.containsKey (auth) ? (Vector)results.get (auth) : new Vector<Object>());
 	    if (onlyNames) {
 		v.addElement (name);
 	    } else {
@@ -1597,7 +1599,7 @@
 	throws MobyException {
 
 	// parse returned XML
-	Vector v = new Vector();
+	Vector<String> v = new Vector<String>();
 	Document document = loadDocument (new ByteArrayInputStream (result.getBytes()));
 	NodeList list = document.getElementsByTagName ("Relationship");
 	for (int i = 0; i < list.getLength(); i++) {
@@ -1661,7 +1663,7 @@
 	    Element elem = (Element)list.item (i);
 	    String relType = elem.getAttribute ("relationshipType");
 	    NodeList children = elem.getChildNodes();
-	    Vector v = new Vector();
+	    Vector<String> v = new Vector<String>();
 	    for (int j = 0; j < children.getLength(); j++) {
 		if (children.item (j).getNodeName().equals ("objectType")) {
 		    v.addElement (getFirstValue (children.item (j)));
@@ -1707,7 +1709,7 @@
 			    });
 
 	// parse returned XML
-	Vector v = new Vector();
+	Vector<String> v = new Vector<String>();
 	Document document = loadDocument (new ByteArrayInputStream (result.getBytes()));
 	NodeList list = document.getElementsByTagName ("Relationship");
 
@@ -1755,11 +1757,11 @@
      * Parses and imports the following XML.
      * <pre>
      * &lt;resourceURLs&gt;
-     *   &lt;Resource name="Service"         url="..." type="..."/&gt;
-     *   &lt;Resource name="Object"          url="..." type="..."/&gt;
-     *   &lt;Resource name="Namespace"       url="..." type="..."/&gt;
-     *   &lt;Resource name="ServiceInstance" url="..." type="..."/&gt;
-     *   &lt;Resource name="Full"            url="..." type="..."/&gt;
+     *   &lt;Resource name="Service"         url="..." /&gt;
+     *   &lt;Resource name="Object"          url="..." /&gt;
+     *   &lt;Resource name="Namespace"       url="..." /&gt;
+     *   &lt;Resource name="ServiceInstance" url="..." /&gt;
+     *   &lt;Resource name="Full"            url="..." /&gt;
      * &lt;/resourceURLs&gt;
      * </pre>
      *************************************************************************/
@@ -1775,7 +1777,7 @@
 					new Object[] {});
 
 	// parse returned XML
-	Vector v = new Vector();
+	Vector<MobyResourceRef> v = new Vector<MobyResourceRef>();
 	Document document = loadDocument (new ByteArrayInputStream (result.getBytes()));
 	NodeList list = document.getElementsByTagName ("Resource");
 	for (int i = 0; i < list.getLength(); i++) {
@@ -1809,12 +1811,7 @@
 	MobyResourceRef[] resourceRefs = getResourceRefs();
 	for (int i = 0; i < resourceRefs.length; i++) {
 	    if (resourceName.equalsIgnoreCase (resourceRefs[i].getResourceName())) {
-		URL url = resourceRefs[i].getResourceLocation();
-		try {
-		    return url.openStream();
-		} catch (java.io.IOException e2) {
-		    throw new MobyException (e2.toString(), e2);
-		}
+		return Utils.getInputStream (resourceRefs[i].getResourceLocation());
 	    }
 	}
 	throw new MobyException ("No resource found for '" + resourceName + "'.");


From senger at dev.open-bio.org  Sun Mar  2 07:45:25 2008
From: senger at dev.open-bio.org (Martin Senger)
Date: Sun, 2 Mar 2008 07:45:25 -0500
Subject: [MOBY-guts] biomoby commit
Message-ID: <200803021245.m22CjPEW032550@dev.open-bio.org>


senger
Sun Mar  2 07:45:25 EST 2008
Update of /home/repository/moby/moby-live/Java/src/config/templates
In directory dev.open-bio.org:/tmp/cvs-serv32345/src/config/templates

Modified Files:
	ServiceSkeletonTemplate.java 
Log Message:
Too Many Changes - see docs/ChangeLog

moby-live/Java/src/config/templates ServiceSkeletonTemplate.java,1.3,1.4
===================================================================
RCS file: /home/repository/moby/moby-live/Java/src/config/templates/ServiceSkeletonTemplate.java,v
retrieving revision 1.3
retrieving revision 1.4
diff -u -r1.3 -r1.4
--- /home/repository/moby/moby-live/Java/src/config/templates/ServiceSkeletonTemplate.java	2005/11/15 03:25:51	1.3
+++ /home/repository/moby/moby-live/Java/src/config/templates/ServiceSkeletonTemplate.java	2008/03/02 12:45:25	1.4
@@ -47,8 +47,10 @@
 
 	MobyPackage mobyOutput = null;
 	try {
+
+            @FALLBACK_CODE@
 	    // reading the whole input
-	    MobyPackage mobyInput = MobyPackage.createFromXML (data, "@FALLBACK_TYPE@");
+	    MobyPackage mobyInput = MobyPackage.createFromXML (data, fallback);
 
 	    // prepare an output object
 	    mobyOutput = prepareOutput (mobyInput);


From senger at dev.open-bio.org  Sun Mar  2 07:45:25 2008
From: senger at dev.open-bio.org (Martin Senger)
Date: Sun, 2 Mar 2008 07:45:25 -0500
Subject: [MOBY-guts] biomoby commit
Message-ID: <200803021245.m22CjPDc032504@dev.open-bio.org>


senger
Sun Mar  2 07:45:25 EST 2008
Update of /home/repository/moby/moby-live/Java/src/config
In directory dev.open-bio.org:/tmp/cvs-serv32345/src/config

Modified Files:
	run-any-client run-dashboard run-dashboard.bat 
Log Message:
Too Many Changes - see docs/ChangeLog

moby-live/Java/src/config run-any-client,1.9,1.10 run-dashboard,1.8,1.9 run-dashboard.bat,1.7,1.8
===================================================================
RCS file: /home/repository/moby/moby-live/Java/src/config/run-any-client,v
retrieving revision 1.9
retrieving revision 1.10
diff -u -r1.9 -r1.10
--- /home/repository/moby/moby-live/Java/src/config/run-any-client	2008/02/14 06:13:36	1.9
+++ /home/repository/moby/moby-live/Java/src/config/run-any-client	2008/03/02 12:45:25	1.10
@@ -7,14 +7,29 @@
 #  $Id$
 # ----------------------------------------------------
 
+# --- setup JAVA_HOME (needed to get to the tools.jar)
+if [ -z "$JAVA_HOME" ] ; then
+  JAVA=`which java`
+  if [ -z "$JAVA" ] ; then
+    echo "Cannot find JAVA. Please set your PATH."
+    exit 1
+  else
+      JAVA_BIN=`dirname $JAVA`
+      JAVA_HOME=$JAVA_BIN/..
+      export JAVA_HOME
+  fi
+fi
+
 PROJECT_HOME=@PROJECT_HOME@
 LIBS_PATH=@PROJECT_DEPS@
 
 CLASSPATH=$LIBS_PATH
+CLASSPATH=${JAVA_HOME}/lib/tools.jar:$CLASSPATH
 CLASSPATH=${PROJECT_HOME}/build/others/datatypes:$CLASSPATH
 CLASSPATH=${PROJECT_HOME}/build/others/skeletons:$CLASSPATH
 CLASSPATH=${PROJECT_HOME}/build/others/samples:$CLASSPATH
 CLASSPATH=${PROJECT_HOME}/build/classes:$CLASSPATH
 CLASSPATH=${PROJECT_HOME}/build/Clients:$CLASSPATH
 
-exec java -cp $CLASSPATH @LOG4J@ "$@"
+JAVA=$JAVA_HOME/bin/java
+exec $JAVA -cp $CLASSPATH @LOG4J@ "$@"

===================================================================
RCS file: /home/repository/moby/moby-live/Java/src/config/run-dashboard,v
retrieving revision 1.8
retrieving revision 1.9
diff -u -r1.8 -r1.9
--- /home/repository/moby/moby-live/Java/src/config/run-dashboard	2008/02/22 00:54:30	1.8
+++ /home/repository/moby/moby-live/Java/src/config/run-dashboard	2008/03/02 12:45:25	1.9
@@ -4,10 +4,25 @@
 #
 #  $Id$
 # ----------------------------------------------------
+
+# --- setup JAVA_HOME (needed to get to the tools.jar for compilation)
+if [ -z "$JAVA_HOME" ] ; then
+  JAVA=`which java`
+  if [ -z "$JAVA" ] ; then
+    echo "Cannot find JAVA. Please set your PATH."
+    exit 1
+  else
+      JAVA_BIN=`dirname $JAVA`
+      JAVA_HOME=$JAVA_BIN/..
+      export JAVA_HOME
+  fi
+fi
+
 PROJECT_HOME=@PROJECT_HOME@
 LIBS_PATH=@PROJECT_DEPS@
 
 CLASSPATH=$LIBS_PATH
+CLASSPATH=${JAVA_HOME}/lib/tools.jar:$CLASSPATH
 CLASSPATH=${PROJECT_HOME}/build/others/datatypes:$CLASSPATH
 CLASSPATH=${PROJECT_HOME}/build/others/skeletons:$CLASSPATH
 CLASSPATH=${PROJECT_HOME}/build/others/samples:$CLASSPATH
@@ -15,4 +30,5 @@
 CLASSPATH=${PROJECT_HOME}/build/classes:$CLASSPATH
 CLASSPATH=${PROJECT_HOME}/build/Clients:$CLASSPATH
 
-exec java -Xms32m -Xmx256m -cp $CLASSPATH @LOG4J@ org.biomoby.service.dashboard.Dashboard "$@"
+JAVA=$JAVA_HOME/bin/java
+exec $JAVA -Xms32m -Xmx256m -cp $CLASSPATH @LOG4J@ org.biomoby.service.dashboard.Dashboard "$@"

===================================================================
RCS file: /home/repository/moby/moby-live/Java/src/config/run-dashboard.bat,v
retrieving revision 1.7
retrieving revision 1.8
diff -u -r1.7 -r1.8
--- /home/repository/moby/moby-live/Java/src/config/run-dashboard.bat	2008/02/14 06:13:36	1.7
+++ /home/repository/moby/moby-live/Java/src/config/run-dashboard.bat	2008/03/02 12:45:25	1.8
@@ -1,10 +1,20 @@
 @echo off
 
+if NOT "%JAVA_HOME%"=="" goto javadone
+echo =======================================================
+echo Setup the JAVA_HOME environment variable.
+echo Hint (for XP): Click Start -- Control Panel -- System.
+echo Then click Advanced, then click "Environment Variables".
+echo ========================================================
+goto end
+:javadone
+
 set "PROJECT_HOME=@PROJECT_HOME@"
 set "PROJECT_DEPS=@PROJECT_DEPS@"
 cd "%PROJECT_HOME%"
 set CP=
 set CP=%PROJECT_DEPS%;%CP%
+set "CP=%JAVA_HOME%\lib\tools.jar;%CP%"
 set CP=build\classes;%CP%
 set CP=build\Clients;%CP%
 set CP=build\others\datatypes;%CP%
@@ -12,4 +22,7 @@
 set CP=build\others\samples;%CP%
 set CP=build\lib\dashboard-config.jar;%CP%
 
-java -classpath "%CP%" @LOG4J@ org.biomoby.service.dashboard.Dashboard  %*
+set "JAVA=%JAVA_HOME%\bin\java"
+"%JAVA%" -classpath "%CP%" @LOG4J@ org.biomoby.service.dashboard.Dashboard  %*
+
+java -Xms32m -Xmx256m -classpath "%CP%" @LOG4J@ org.biomoby.service.dashboard.Dashboard  %*


From senger at dev.open-bio.org  Sun Mar  2 07:49:33 2008
From: senger at dev.open-bio.org (Martin Senger)
Date: Sun, 2 Mar 2008 07:49:33 -0500
Subject: [MOBY-guts] biomoby commit
Message-ID: <200803021249.m22CnXpT000482@dev.open-bio.org>


senger
Sun Mar  2 07:49:33 EST 2008
Update of /home/repository/moby/moby-live/Java/src/Clients
In directory dev.open-bio.org:/tmp/cvs-serv467/src/Clients

Added Files:
	TestAntWorker2.java 
Log Message:

moby-live/Java/src/Clients TestAntWorker2.java,NONE,1.1

From senger at dev.open-bio.org  Sun Mar  2 07:49:33 2008
From: senger at dev.open-bio.org (Martin Senger)
Date: Sun, 2 Mar 2008 07:49:33 -0500
Subject: [MOBY-guts] biomoby commit
Message-ID: <200803021249.m22CnXSd000498@dev.open-bio.org>


senger
Sun Mar  2 07:49:33 EST 2008
Update of /home/repository/moby/moby-live/Java/src/samples/org/jmoby/tutorial/service
In directory dev.open-bio.org:/tmp/cvs-serv467/src/samples/org/jmoby/tutorial/service

Added Files:
	ConcatSequenceSetImpl.java ConcatSequencesImpl.java 
Log Message:

moby-live/Java/src/samples/org/jmoby/tutorial/service ConcatSequenceSetImpl.java,NONE,1.1 ConcatSequencesImpl.java,NONE,1.1

From senger at dev.open-bio.org  Sun Mar  2 07:49:33 2008
From: senger at dev.open-bio.org (Martin Senger)
Date: Sun, 2 Mar 2008 07:49:33 -0500
Subject: [MOBY-guts] biomoby commit
Message-ID: <200803021249.m22CnXYd000512@dev.open-bio.org>


senger
Sun Mar  2 07:49:33 EST 2008
Update of /home/repository/moby/moby-live/Java/src/test/junit-resources
In directory dev.open-bio.org:/tmp/cvs-serv467/src/test/junit-resources

Added Files:
	ConcatSequences-input.xml 
Log Message:

moby-live/Java/src/test/junit-resources ConcatSequences-input.xml,NONE,1.1

From senger at dev.open-bio.org  Sun Mar  2 07:45:27 2008
From: senger at dev.open-bio.org (Martin Senger)
Date: Sun, 2 Mar 2008 07:45:27 -0500
Subject: [MOBY-guts] biomoby commit
Message-ID: <200803021245.m22CjROo000382@dev.open-bio.org>


senger
Sun Mar  2 07:45:27 EST 2008
Update of /home/repository/moby/moby-live/Java/src/test/junit-resources
In directory dev.open-bio.org:/tmp/cvs-serv32345/src/test/junit-resources

Removed Files:
	parser-test-output-1.xml parser-test-output-2.xml 
	parser-test-output-3.xml parser-test-output-4.xml 
Log Message:
Too Many Changes - see docs/ChangeLog

moby-live/Java/src/test/junit-resources parser-test-output-1.xml,1.1,NONE parser-test-output-2.xml,1.1,NONE parser-test-output-3.xml,1.1,NONE parser-test-output-4.xml,1.1,NONE
rcsdiff: /home/repository/moby/moby-live/Java/src/test/junit-resources/RCS/parser-test-output-1.xml,v: No such file or directory

rcsdiff: /home/repository/moby/moby-live/Java/src/test/junit-resources/RCS/parser-test-output-2.xml,v: No such file or directory

rcsdiff: /home/repository/moby/moby-live/Java/src/test/junit-resources/RCS/parser-test-output-3.xml,v: No such file or directory

rcsdiff: /home/repository/moby/moby-live/Java/src/test/junit-resources/RCS/parser-test-output-4.xml,v: No such file or directory


From senger at dev.open-bio.org  Sun Mar  2 07:45:26 2008
From: senger at dev.open-bio.org (Martin Senger)
Date: Sun, 2 Mar 2008 07:45:26 -0500
Subject: [MOBY-guts] biomoby commit
Message-ID: <200803021245.m22CjQpT032592@dev.open-bio.org>


senger
Sun Mar  2 07:45:26 EST 2008
Update of /home/repository/moby/moby-live/Java/src/main/org/biomoby/service
In directory dev.open-bio.org:/tmp/cvs-serv32345/src/main/org/biomoby/service

Modified Files:
	BaseService.java 
Log Message:
Too Many Changes - see docs/ChangeLog

moby-live/Java/src/main/org/biomoby/service BaseService.java,1.8,1.9
===================================================================
RCS file: /home/repository/moby/moby-live/Java/src/main/org/biomoby/service/BaseService.java,v
retrieving revision 1.8
retrieving revision 1.9
diff -u -r1.8 -r1.9
--- /home/repository/moby/moby-live/Java/src/main/org/biomoby/service/BaseService.java	2007/05/27 19:18:17	1.8
+++ /home/repository/moby/moby-live/Java/src/main/org/biomoby/service/BaseService.java	2008/03/02 12:45:26	1.9
@@ -85,9 +85,9 @@
 <pre> public class AServiceImpl
     extends A_ServiceSkel {
 
-    public boolean processIt (MobyJob request,
-			      MobyJob response,
-			      MobyPackage outputContext)
+    public void processIt (MobyJob request,
+		           MobyJob response,
+			   MobyPackage outputContext)
 	throws MobyException {
 
         // this is how to get input data
@@ -96,7 +96,6 @@
 
         // this is an example of a trivial "business logic"
 	response.setData (new MobyInteger (seq.length()));
-	return true;
     }
 }</pre>
  * </td></tr></table><p>


From senger at dev.open-bio.org  Sun Mar  2 07:45:27 2008
From: senger at dev.open-bio.org (Martin Senger)
Date: Sun, 2 Mar 2008 07:45:27 -0500
Subject: [MOBY-guts] biomoby commit
Message-ID: <200803021245.m22CjRFn000314@dev.open-bio.org>


senger
Sun Mar  2 07:45:26 EST 2008
Update of /home/repository/moby/moby-live/Java/src/samples/org/jmoby/tutorial/service
In directory dev.open-bio.org:/tmp/cvs-serv32345/src/samples/org/jmoby/tutorial/service

Modified Files:
	MabuhayImpl.java 
Log Message:
Too Many Changes - see docs/ChangeLog

moby-live/Java/src/samples/org/jmoby/tutorial/service MabuhayImpl.java,1.1,1.2
===================================================================
RCS file: /home/repository/moby/moby-live/Java/src/samples/org/jmoby/tutorial/service/MabuhayImpl.java,v
retrieving revision 1.1
retrieving revision 1.2
diff -u -r1.1 -r1.2
--- /home/repository/moby/moby-live/Java/src/samples/org/jmoby/tutorial/service/MabuhayImpl.java	2005/08/26 06:27:05	1.1
+++ /home/repository/moby/moby-live/Java/src/samples/org/jmoby/tutorial/service/MabuhayImpl.java	2008/03/02 12:45:26	1.2
@@ -93,7 +93,7 @@
 	}
 
 	// match pattern against all possible values we have
-	Vector v = new Vector();
+	Vector<simple_key_value_pair> v = new Vector<simple_key_value_pair>();
 	Matcher matcher = pattern.matcher ("");
 	for (int i = 0; i < languages.length; i++) {
  	    matcher.reset (languages[i]);
@@ -124,8 +124,8 @@
 	    ("resources/mabuhay.file");
 	if (ins != null) {
 	    try {
-		Vector l = new Vector (3000);
-		Vector h = new Vector (3000);
+		Vector<String> l = new Vector<String> (3000);
+		Vector<String> h = new Vector<String> (3000);
 		BufferedReader data = new BufferedReader (new InputStreamReader (ins));
 		String line;
 		while ((line = data.readLine()) != null) {


From senger at dev.open-bio.org  Sun Mar  2 07:45:26 2008
From: senger at dev.open-bio.org (Martin Senger)
Date: Sun, 2 Mar 2008 07:45:26 -0500
Subject: [MOBY-guts] biomoby commit
Message-ID: <200803021245.m22CjQJW032742@dev.open-bio.org>


senger
Sun Mar  2 07:45:26 EST 2008
Update of /home/repository/moby/moby-live/Java/src/main/org/biomoby/shared/datatypes
In directory dev.open-bio.org:/tmp/cvs-serv32345/src/main/org/biomoby/shared/datatypes

Modified Files:
	MobyObject.java 
Log Message:
Too Many Changes - see docs/ChangeLog

moby-live/Java/src/main/org/biomoby/shared/datatypes MobyObject.java,1.6,1.7
===================================================================
RCS file: /home/repository/moby/moby-live/Java/src/main/org/biomoby/shared/datatypes/MobyObject.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/shared/datatypes/MobyObject.java	2006/07/07 04:12:40	1.6
+++ /home/repository/moby/moby-live/Java/src/main/org/biomoby/shared/datatypes/MobyObject.java	2008/03/02 12:45:26	1.7
@@ -100,8 +100,7 @@
      * @return a formatted string
      *************************************************************************/
     public String toString() {
-	StringBuffer buf = new StringBuffer();
-// 	buf.append (Utils.simpleClassName (this.getClass().getName()));
+	StringBuilder buf = new StringBuilder();
 	buf.append (getMobyTypeName());
 	if (! name.equals (""))      buf.append (", Article name: " + name);
 	if (! id.equals (""))        buf.append (", Id: " + id);
@@ -112,7 +111,7 @@
 	    buf.append (((MobyXref)en.nextElement()).format (1));
 	}
 	if (! value.equals (""))     buf.append ("   Value: " + value + "\n");
-	return new String (buf);
+	return new String (buf.toString());
     }
 
     /**************************************************************************


From senger at dev.open-bio.org  Sun Mar  2 07:45:27 2008
From: senger at dev.open-bio.org (Martin Senger)
Date: Sun, 2 Mar 2008 07:45:27 -0500
Subject: [MOBY-guts] biomoby commit
Message-ID: <200803021245.m22CjReI000346@dev.open-bio.org>


senger
Sun Mar  2 07:45:27 EST 2008
Update of /home/repository/moby/moby-live/Java/src/support
In directory dev.open-bio.org:/tmp/cvs-serv32345/src/support

Removed Files:
	README _README.FIRST_ run-any-client run-any-client.bat 
	run-cache-client run-cache-client.bat run-cmdline-client 
	run-cmdline-client.bat run-digest-client run-digest-client.bat 
	run-graphs-client run-graphs-client.bat run-testing-central 
	run-testing-central.bat 
Log Message:
Too Many Changes - see docs/ChangeLog

moby-live/Java/src/support README,1.5,NONE _README.FIRST_,1.2,NONE run-any-client,1.1,NONE run-any-client.bat,1.2,NONE run-cache-client,1.1,NONE run-cache-client.bat,1.2,NONE run-cmdline-client,1.1,NONE run-cmdline-client.bat,1.2,NONE run-digest-client,1.1,NONE run-digest-client.bat,1.2,NONE run-graphs-client,1.1,NONE run-graphs-client.bat,1.2,NONE run-testing-central,1.1,NONE run-testing-central.bat,1.2,NONE
rcsdiff: /home/repository/moby/moby-live/Java/src/support/RCS/README,v: No such file or directory

rcsdiff: /home/repository/moby/moby-live/Java/src/support/RCS/_README.FIRST_,v: No such file or directory

rcsdiff: /home/repository/moby/moby-live/Java/src/support/RCS/run-any-client,v: No such file or directory

rcsdiff: /home/repository/moby/moby-live/Java/src/support/RCS/run-any-client.bat,v: No such file or directory

rcsdiff: /home/repository/moby/moby-live/Java/src/support/RCS/run-cache-client,v: No such file or directory

rcsdiff: /home/repository/moby/moby-live/Java/src/support/RCS/run-cache-client.bat,v: No such file or directory

rcsdiff: /home/repository/moby/moby-live/Java/src/support/RCS/run-cmdline-client,v: No such file or directory

rcsdiff: /home/repository/moby/moby-live/Java/src/support/RCS/run-cmdline-client.bat,v: No such file or directory

rcsdiff: /home/repository/moby/moby-live/Java/src/support/RCS/run-digest-client,v: No such file or directory

rcsdiff: /home/repository/moby/moby-live/Java/src/support/RCS/run-digest-client.bat,v: No such file or directory

rcsdiff: /home/repository/moby/moby-live/Java/src/support/RCS/run-graphs-client,v: No such file or directory

rcsdiff: /home/repository/moby/moby-live/Java/src/support/RCS/run-graphs-client.bat,v: No such file or directory

rcsdiff: /home/repository/moby/moby-live/Java/src/support/RCS/run-testing-central,v: No such file or directory

rcsdiff: /home/repository/moby/moby-live/Java/src/support/RCS/run-testing-central.bat,v: No such file or directory


From senger at dev.open-bio.org  Sun Mar  2 07:45:26 2008
From: senger at dev.open-bio.org (Martin Senger)
Date: Sun, 2 Mar 2008 07:45:26 -0500
Subject: [MOBY-guts] biomoby commit
Message-ID: <200803021245.m22CjQUS032722@dev.open-bio.org>


senger
Sun Mar  2 07:45:26 EST 2008
Update of /home/repository/moby/moby-live/Java/src/main/org/biomoby/shared
In directory dev.open-bio.org:/tmp/cvs-serv32345/src/main/org/biomoby/shared

Modified Files:
	MobyException.java MobyResourceRef.java MobyService.java 
Log Message:
Too Many Changes - see docs/ChangeLog

moby-live/Java/src/main/org/biomoby/shared MobyException.java,1.4,1.5 MobyResourceRef.java,1.4,1.5 MobyService.java,1.23,1.24
===================================================================
RCS file: /home/repository/moby/moby-live/Java/src/main/org/biomoby/shared/MobyException.java,v
retrieving revision 1.4
retrieving revision 1.5
diff -u -r1.4 -r1.5
--- /home/repository/moby/moby-live/Java/src/main/org/biomoby/shared/MobyException.java	2005/11/15 03:25:51	1.4
+++ /home/repository/moby/moby-live/Java/src/main/org/biomoby/shared/MobyException.java	2008/03/02 12:45:26	1.5
@@ -47,20 +47,8 @@
     public MobyException (String s, Throwable e) {
 	super (s, e);
 	if (e != null) {
-	    boolean seriousError =
-		( (e instanceof java.lang.NullPointerException)              ||
-		  (e instanceof java.lang.ClassCastException)                ||
-		  (e instanceof java.lang.reflect.InvocationTargetException) ||
-		  (e instanceof java.lang.ClassNotFoundException) );
-	    if (seriousError || log.isDebugEnabled()) {
-		StringWriter sw = new StringWriter (500);
-		e.printStackTrace (new PrintWriter (sw));
-		if (seriousError)
-		    log.error (sw.toString());
-		else
-		    log.debug (sw.toString());
-	    }
-	}
+ 	    formatAndLog (e, log);
+ 	}
     }
 
     /******************************************************************************
@@ -75,4 +63,28 @@
 	return getCause();
     }
 
+    /******************************************************************************
+     * Format given exception 'e' depending on how serious it it. In
+     * same cases add stack trace. Log the result in the given
+     * 'log'. <p>
+     *
+     * @param e an exception to be formatted and logged
+     * @param log where to log it
+     ******************************************************************************/
+    public static void formatAndLog (Throwable e,
+				     org.apache.commons.logging.Log log) {
+	boolean seriousError =
+	    (e instanceof java.lang.RuntimeException);
+	if (seriousError || log.isDebugEnabled()) {
+	    StringWriter sw = new StringWriter (500);
+	    e.printStackTrace (new PrintWriter (sw));
+	    if (seriousError)
+		log.error (sw.toString());
+	    else
+		log.debug (sw.toString());
+	} else {
+	    log.error (e.getMessage());
+	}
+    }
+    
 }

===================================================================
RCS file: /home/repository/moby/moby-live/Java/src/main/org/biomoby/shared/MobyResourceRef.java,v
retrieving revision 1.4
retrieving revision 1.5
diff -u -r1.4 -r1.5
--- /home/repository/moby/moby-live/Java/src/main/org/biomoby/shared/MobyResourceRef.java	2006/07/07 23:27:27	1.4
+++ /home/repository/moby/moby-live/Java/src/main/org/biomoby/shared/MobyResourceRef.java	2008/03/02 12:45:26	1.5
@@ -65,7 +65,11 @@
     }
 
     /**
-     * Return resource content type.
+     * Return resource content type. 
+     *
+     * @deprecated Biomoby registry never gives the content type
+     * back. Therefore, this method does not have anything reasonable
+     * to return.
      */
     public String getResourceContentType() {
 	return contentType;

===================================================================
RCS file: /home/repository/moby/moby-live/Java/src/main/org/biomoby/shared/MobyService.java,v
retrieving revision 1.23
retrieving revision 1.24
diff -u -r1.23 -r1.24
--- /home/repository/moby/moby-live/Java/src/main/org/biomoby/shared/MobyService.java	2008/01/07 22:01:09	1.23
+++ /home/repository/moby/moby-live/Java/src/main/org/biomoby/shared/MobyService.java	2008/03/02 12:45:26	1.24
@@ -67,6 +67,13 @@
     /** Name of a category for asynchornous BioMoby services. */
     public static final String CATEGORY_MOBY_ASYNC = "moby-async";
 
+    /** Name of a category for document/literal BioMoby services. */
+    public static final String CATEGORY_MOBY_DOCLIT = "doc-literal";
+
+    /** Name of a category for asynchronous document/literal BioMoby
+     * services. */
+    public static final String CATEGORY_MOBY_DOCLIT_ASYNC = "doc-literal-async";
+
     /** A suffix added to a service name in order to make a method
      * name that submits input to an asynchronous service.
      */
@@ -601,6 +608,8 @@
     }
 
     public boolean isAsynchronous(){
-	return category.equals (CATEGORY_MOBY_ASYNC);
+	return
+	    category.equals (CATEGORY_MOBY_ASYNC) ||
+	    category.equals (CATEGORY_MOBY_DOCLIT_ASYNC);
     }
 }


From senger at dev.open-bio.org  Sun Mar  2 07:45:27 2008
From: senger at dev.open-bio.org (Martin Senger)
Date: Sun, 2 Mar 2008 07:45:27 -0500
Subject: [MOBY-guts] biomoby commit
Message-ID: <200803021245.m22CjRA5000364@dev.open-bio.org>


senger
Sun Mar  2 07:45:27 EST 2008
Update of /home/repository/moby/moby-live/Java/src/test/java/org/biomoby/shared/parser
In directory dev.open-bio.org:/tmp/cvs-serv32345/src/test/java/org/biomoby/shared/parser

Modified Files:
	MobyParserTest.java 
Log Message:
Too Many Changes - see docs/ChangeLog

moby-live/Java/src/test/java/org/biomoby/shared/parser MobyParserTest.java,1.1,1.2
===================================================================
RCS file: /home/repository/moby/moby-live/Java/src/test/java/org/biomoby/shared/parser/MobyParserTest.java,v
retrieving revision 1.1
retrieving revision 1.2
diff -u -r1.1 -r1.2
--- /home/repository/moby/moby-live/Java/src/test/java/org/biomoby/shared/parser/MobyParserTest.java	2008/02/28 05:21:48	1.1
+++ /home/repository/moby/moby-live/Java/src/test/java/org/biomoby/shared/parser/MobyParserTest.java	2008/03/02 12:45:27	1.2
@@ -1,4 +1,4 @@
-// MobyParserTestCase.java
+// MobyParserTest.java
 //
 // Created: February 2008
 //
@@ -20,17 +20,21 @@
 package org.biomoby.shared.parser;
 
 import org.biomoby.shared.MobyException;
+import org.biomoby.shared.datatypes.*;
 
 import org.junit.Before;
 import org.junit.Test;
 import static org.junit.Assert.*;
 
 import org.apache.commons.io.IOUtils;
+import org.apache.commons.io.FileUtils;
+import org.apache.commons.lang.StringUtils;
 
 import java.io.InputStream;
 import java.io.IOException;
 import java.util.Map;
 import java.util.HashMap;
+import java.util.Arrays;
 
 
 public class MobyParserTest {
@@ -39,12 +43,6 @@
     private static final String INPUT_2 = "parser-test-input-2.xml";
     private static final String INPUT_3 = "parser-test-input-3.xml";
     private static final String INPUT_4 = "parser-test-input-4.xml";
-
-    private static final String OUTPUT_1 = "parser-test-output-1.xml";
-    private static final String OUTPUT_2 = "parser-test-output-2.xml";
-    private static final String OUTPUT_3 = "parser-test-output-3.xml";
-    private static final String OUTPUT_4 = "parser-test-output-4.xml";
-
  
     /**************************************************************************
      *
@@ -55,38 +53,55 @@
     @Test
     public void testNormal()
 	throws IOException, MobyException {
-	parse (INPUT_1, OUTPUT_1, null, null);
-    }
-
-    @Test
-    public void testUnknownTopLevel()
-	throws IOException, MobyException {
-	parse (INPUT_2, OUTPUT_2, "DNASequence", null);
-    }
-
-    @Test
-    public void testUnknownTopLevelAndMember()
-	throws IOException, MobyException {
-	parse (INPUT_3, OUTPUT_3, "BasicGFF3MultiFeature", null);
-    }
-
-    @Test
-    public void testMoreUnknownTopLevels()
-	throws IOException, MobyException {
-	Map<String,String> backups = new HashMap<String,String>();
-	backups.put ("mySeq",   "DNASequence");
-	backups.put ("myPairs", "BasicGFF3MultiFeature");
-	parse (INPUT_4, OUTPUT_4, null, backups);
-    }
+	MobyPackage moby = parse (INPUT_1, null, null);
+	assertEquals (moby.getServiceNotes(), "freetext notes here");
+	assertEquals (moby.getAuthority(), "http://\"me\".<org>&");
+	MobyJob[] jobs = moby.getJobs();
+	assertEquals (jobs.length, 4);
+	assertEquals (jobs[0].getId(), "a1");
+	MobyObject data = jobs[0].getData();
+	assertEquals (data.getMobyTypeName(), "NucleotideSequence");
+	assertEquals (data.getName(), "");
+	assertEquals (data.getNamespace(), "DragonDB_Allele");
+	assertEquals (data.getId(), "chlorae");
+	assertFalse (data.isPrimitiveType());
+	assertEquals (data.getClass().getName(), "org.biomoby.shared.datatypes.NucleotideSequence");
+	NucleotideSequence typedData = (NucleotideSequence)jobs[0].getData();
+	assertEquals (typedData.get_SequenceString(), ">tata\ntatata");
+	assertEquals (typedData.getMoby_SequenceString().getValue(), ">tata\ntatata");
+	assertEquals (typedData.getMoby_Length().getIntValue(), 10);
+    }
+
+//     @Test
+//     public void testUnknownTopLevel()
+// 	throws IOException, MobyException {
+// 	parse (INPUT_2, "DNASequence", null);
+//     }
+
+//     @Test
+//     public void testUnknownTopLevelAndMember()
+// 	throws IOException, MobyException {
+// 	parse (INPUT_3, "BasicGFF3MultiFeature", null);
+//     }
+
+//     @Test
+//     public void testMoreUnknownTopLevels()
+// 	throws IOException, MobyException {
+// 	Map<String,String> backups = new HashMap<String,String>();
+// 	backups.put ("mySeq",   "DNASequence");
+// 	backups.put ("myPairs", "BasicGFF3MultiFeature");
+// 	parse (INPUT_4, null, backups);
+//     }
 
 
     /**************************************************************************
-     * Read XML from 'infile', turn it back to XML and compare it with
-     * 'outfile'. Use 'backup' (or 'backups') as the 'latest known
-     * data top-level(s)' data type (any of them may be null).
+     * Create and return a MobyPackage form the XML 'infile'. Use
+     * 'backup' (or 'backups') as the 'latest known data top-level(s)'
+     * data type (any of them may be null).
      **************************************************************************/
-    protected void parse (String infile, String outfile,
-			  String backup, Map<String,String> backups)
+    protected MobyPackage parse (String infile,
+				 String backup,
+				 Map<String,String> backups)
 	throws IOException, MobyException {
 
 	InputStream ins = null;
@@ -95,7 +110,7 @@
 	    ins = this.getClass().getClassLoader().getResourceAsStream (infile);
 	    if (ins == null) {
 		fail ("Could not find test data resource '" + infile + "'.");
-		return;
+		throw new MobyException ("Test parsing failed.");
 	    }
 	    MobyPackage moby = null;
 	    if (backups != null) {
@@ -104,18 +119,7 @@
 		moby = MobyPackage.createFromXML (IOUtils.toByteArray (ins), backup);
 	    }
 	    assertFalse (moby == null);
-	    IOUtils.closeQuietly (ins);
-
-	    // reading expected result
-	    ins = this.getClass().getClassLoader().getResourceAsStream (outfile);
-	    if (ins == null) {
-		fail ("Could not find test data resource '" + outfile + "'.");
-		return;
-	    }
-	    String expected = IOUtils.toString (ins);
-
-	    // comparing
-	    assertEquals (moby.toXML(), expected);
+	    return moby;
 
 	} finally {
 	    IOUtils.closeQuietly (ins);


From senger at dev.open-bio.org  Sun Mar  2 07:45:26 2008
From: senger at dev.open-bio.org (Martin Senger)
Date: Sun, 2 Mar 2008 07:45:26 -0500
Subject: [MOBY-guts] biomoby commit
Message-ID: <200803021245.m22CjQ5c032764@dev.open-bio.org>


senger
Sun Mar  2 07:45:26 EST 2008
Update of /home/repository/moby/moby-live/Java/src/main/org/biomoby/shared/parser
In directory dev.open-bio.org:/tmp/cvs-serv32345/src/main/org/biomoby/shared/parser

Modified Files:
	MobyParser.java 
Log Message:
Too Many Changes - see docs/ChangeLog

moby-live/Java/src/main/org/biomoby/shared/parser MobyParser.java,1.8,1.9
===================================================================
RCS file: /home/repository/moby/moby-live/Java/src/main/org/biomoby/shared/parser/MobyParser.java,v
retrieving revision 1.8
retrieving revision 1.9
diff -u -r1.8 -r1.9
--- /home/repository/moby/moby-live/Java/src/main/org/biomoby/shared/parser/MobyParser.java	2008/02/28 05:21:48	1.8
+++ /home/repository/moby/moby-live/Java/src/main/org/biomoby/shared/parser/MobyParser.java	2008/03/02 12:45:26	1.9
@@ -18,7 +18,6 @@
 
 import org.tulsoft.tools.loaders.ICreator;
 import org.tulsoft.shared.GException;
-import org.tulsoft.tools.debug.DGUtils;
 import org.tulsoft.tools.xml.XMLUtils2;
 import org.tulsoft.tools.xml.XMLErrorHandler;
 
@@ -55,22 +54,24 @@
  * href="http://biomoby.org/moby-live/Java/docs/APIservices/org/biomoby/shared/datatypes/package-summary.html"
  * target="_top"><tt>org.biomoby.shared.datatypes</tt></a>. <p>
  *
- * There is one situation when the parser tries to substitute an
- * unknown data type by a known one. If the parsing encoutered an XML
- * tag depicting a <em>top-level</em> data object (not a member object
- * of some other data object) and if there is no class available for
- * such object, the parser can be instructed (in its {@link
- * #MobyParser(String) non-default constructor} to create a substituted
- * object whose name was given in the parser constructor. This is to
- * prevent situation when a long-time running and deployed service
- * suddenly gets a request from a client that uses more up-to-date
- * list of data types. It would be bad to let such service die (or
- * minimally respond unproperly) just because its classes were
- * generated too long ago. <p>
+ * There is a situation when the parser tries to substitute an unknown
+ * data type by a known one. If the parsing encoutered an XML tag
+ * depicting a <em>top-level</em> data object, or a member object, and
+ * if there is no class available for such object, the parser can be
+ * instructed (in its {@link #MobyParser(String) non-default
+ * constructor} to create a substituted object whose name was given in
+ * the parser constructor (there is also a constructor where you can
+ * get more than one such substitution object, depicted by its article
+ * name). This is to prevent situation when a long-time running and
+ * deployed service suddenly gets a request from a client that uses
+ * more up-to-date list of data types. It would be bad to let such
+ * service die (or minimally respond unproperly) just because its
+ * classes were generated too long ago. <p>
  *
  * Because also skeletons for services can be generated, it is easy to
  * ensure that a service knows its "the most specialized" data type it
- * can still serve, and that it passes it to the parser constructor. <p>
+ * can still serve, and that it passes it to the parser
+ * constructor. <p>
  *
  * If the parser finds an unknown object/tag but no substitute was
  * passed in the parser constructor, it prints a warning and ignores
@@ -81,29 +82,14 @@
  * types should be generated, and services restarted. Fortunately, it
  * does not happen often at all. <p>
  *
- * Be aware, however, that this substitution may do a wrong thing if
- * there are more bad top-level objects - such as in case when a
- * result has more outputs. I think that this insufficiency should be
- * consider a bug in parser design - but make it properly would need
- * much more complicated interface... <p>
- *
  * If the parser finds another problem, usually related to the invalid
  * XML, it raises a {@link org.biomoby.shared.MobyException
  * MobyException} with error message containing line and column close
  * to place where the error happened. <p>
  *
  * One possible problem would be when article names of the member data
- * types in the parsed XML do not correspond what was registered in
- * the Biomoby registry. An example, I know about at the time of
- * writing this, is a service <tt>MIPSBlastXMLClickableImage</tt> that
- * returns object of type <tt>NCBI_Blast_XML_Gif_Map</tt> which has a
- * member object of type <tt>b64_encoded_gif</tt>. This member was
- * registered with the article name "hitGraph" but the service returns
- * an article name "image". Parser spots it and stops parsing (because
- * it does not know where to put this member object). However, if you
- * insist that you still want to get such XML parsed, even without one
- * part, you can set Java property "biomoby.parser.forgiving" to true,
- * and run it again. <p>
+ * types in the parsed XML do not correspond to what was registered in
+ * the Biomoby registry (or to its more specialized childern). <p>
  *
  * You can test parser by using a simple <tt>TestingMobyParser</tt>
  * client. This is how to invoke it and how to get its help:
@@ -153,6 +139,10 @@
  *                                               "GenericSequence");
  * </pre>
  *
+ * For a constructor with more fallbacks, check generated skeletons
+ * (for example the sample skeleton
+ * <tt>net.jmoby.samples.ConcatSequencesSkel</tt>). <p>
+
  * All XML tags and all attribute names that are recognized and
  * processed by this parser are stored as constants in class {@link
  * MobyTags}. <p>
@@ -171,12 +161,6 @@
     private static org.apache.commons.logging.Log log =
 	org.apache.commons.logging.LogFactory.getLog (MobyParser.class);
 
-    /**
-     * A Java property name. See its purpose in the main description
-     * above.
-     */
-    public static final String BIOMOBY_PARSER_FORGIVING = "biomoby.parser.forgiving";
-
     Locator locator;
     XMLReader parser = null;
     String lowestKnownDataType = null;
@@ -361,9 +345,9 @@
      * all its descendants (with a warning message).
      *
      *    The same mode is also entered when an unknown member object
-     * was found (a member object is never substituted). But here we
-     * issue a warning message only if we are NOT in substitution mode
-     * (in a substitution mode it is normal to found unknown objects).
+     * was found. But here we issue a warning message only if we are
+     * NOT in substitution mode (in a substitution mode it is normal
+     * to found unknown objects).
      *
      *    'inSubstitution' is a mode when a top-level object (not a
      * member object) was not found AND a substitutee was provided in
@@ -402,8 +386,7 @@
 
 	} catch (Error e) {
 	    throw new MobyException ("Serious or unexpected error!\n" +
-				     e.toString() + "\n" +
-				     DGUtils.stackTraceToString (e));
+				     e.toString(), e);
 	}
     }
 
@@ -554,6 +537,20 @@
 				    lowestKnownDataTypes.containsKey (articleName)) {
 				    theClass =
 					mapDataTypes.getClass (lowestKnownDataTypes.get (articleName));
+				} else {
+				    // ...if we are in a collection,
+				    // we need to use the article name
+				    // of that collection
+				    MobyCollection collObj = peekCollection();
+				    if (collObj != null) {
+					articleName = collObj.getName();
+					if (articleName != null &&
+					    lowestKnownDataTypes.containsKey (articleName)) {
+					    theClass =
+						mapDataTypes.getClass
+						(lowestKnownDataTypes.get (articleName));
+					}
+				    }
 				}
 			    }
 
@@ -916,6 +913,21 @@
     }
 
     /*********************************************************************
+     * Return the second last object from the 'objectStack' if it is a
+     * MobyCollectin, otherwise it returns null.
+     ********************************************************************/
+    protected MobyCollection peekCollection() {
+	if (objectStack.size() < 2)
+	    return null;
+	Object obj = objectStack.get (objectStack.size() - 2);
+	if (obj instanceof MobyCollection) {
+	    return (MobyCollection)obj;
+	} else {
+	    return null;
+	}
+    }
+
+    /*********************************************************************
      * Call a method (named 'methodName') on object 'actor', using
      * 'parameter'.
      ********************************************************************/


From senger at dev.open-bio.org  Sun Mar  2 07:45:26 2008
From: senger at dev.open-bio.org (Martin Senger)
Date: Sun, 2 Mar 2008 07:45:26 -0500
Subject: [MOBY-guts] biomoby commit
Message-ID: <200803021245.m22CjQL1032696@dev.open-bio.org>


senger
Sun Mar  2 07:45:26 EST 2008
Update of /home/repository/moby/moby-live/Java/src/main/org/biomoby/service/generator
In directory dev.open-bio.org:/tmp/cvs-serv32345/src/main/org/biomoby/service/generator

Modified Files:
	DataTypesGenerator.java Generator.java ServicesGenerator.java 
Log Message:
Too Many Changes - see docs/ChangeLog

moby-live/Java/src/main/org/biomoby/service/generator DataTypesGenerator.java,1.5,1.6 Generator.java,1.4,1.5 ServicesGenerator.java,1.6,1.7
===================================================================
RCS file: /home/repository/moby/moby-live/Java/src/main/org/biomoby/service/generator/DataTypesGenerator.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/service/generator/DataTypesGenerator.java	2008/02/23 13:58:32	1.5
+++ /home/repository/moby/moby-live/Java/src/main/org/biomoby/service/generator/DataTypesGenerator.java	2008/03/02 12:45:26	1.6
@@ -19,6 +19,7 @@
 import org.biomoby.client.Graphviz;
 
 import java.util.Properties;
+import java.util.Map;
 import java.util.HashMap;
 import java.util.Date;
 import java.util.regex.Pattern;
@@ -105,8 +106,8 @@
     /*************************************************************************
      *
      *************************************************************************/
-    public HashMap getTemplateNames() {
-	HashMap tNames = new HashMap();
+    public Map<String,File> getTemplateNames() {
+	Map<String,File> tNames = new HashMap<String,File>();
 	File dir = new File ("templates");
 	tNames.put (TN_DATA_TYPE,            new File (dir, "DataTypeTemplate.java"));
 	tNames.put (TN_MEMBERS_HAS,          new File (dir, "MembersHASTemplate.java"));
@@ -178,7 +179,7 @@
 	    pattern = Pattern.compile (filter);
 
 	// load all templates (from files)
-	HashMap templates = getTemplateNames();
+	Map<String,File> templates = getTemplateNames();
 	dataTypeTemplate     = loadTemplate (templates.get (TN_DATA_TYPE));
 	membersHASTemplate   = loadTemplate (templates.get (TN_MEMBERS_HAS));
 	membersHASATemplate  = loadTemplate (templates.get (TN_MEMBERS_HASA));

===================================================================
RCS file: /home/repository/moby/moby-live/Java/src/main/org/biomoby/service/generator/Generator.java,v
retrieving revision 1.4
retrieving revision 1.5
diff -u -r1.4 -r1.5
--- /home/repository/moby/moby-live/Java/src/main/org/biomoby/service/generator/Generator.java	2008/02/23 13:58:32	1.4
+++ /home/repository/moby/moby-live/Java/src/main/org/biomoby/service/generator/Generator.java	2008/03/02 12:45:26	1.5
@@ -18,7 +18,7 @@
 import org.biomoby.client.CentralDigestCachedImpl;
 
 import java.util.Properties;
-import java.util.HashMap;
+import java.util.Map;
 import java.util.regex.Pattern;
 import java.io.File;
 
@@ -415,14 +415,14 @@
      * patterns as the original template - so it is not too flexible,
      * anyway). <p>
      *
-     * The values of returned HashMap are filenames. It their names
-     * are relative (which is the best way) then they are looked for
-     * in the CLASSPATH (including all jar files there). <p>
+     * The values of returned Map are files. It their names are
+     * relative (which is the best way) then they are looked for in
+     * the CLASSPATH (including all jar files there). <p>
      *
      * Make sure that the returned path is correct for the system
      * where JVM is running.
      *************************************************************************/
-    abstract public HashMap getTemplateNames();
+    abstract public Map<String,File> getTemplateNames();
 
     /**************************************************************************
      * Generate "things" from a given Biomoby registry. This is the

===================================================================
RCS file: /home/repository/moby/moby-live/Java/src/main/org/biomoby/service/generator/ServicesGenerator.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/service/generator/ServicesGenerator.java	2008/02/28 05:21:48	1.6
+++ /home/repository/moby/moby-live/Java/src/main/org/biomoby/service/generator/ServicesGenerator.java	2008/03/02 12:45:26	1.7
@@ -26,10 +26,13 @@
 import org.biomoby.client.Graphviz;
 
 import org.tulsoft.tools.servlets.Html;
+import org.apache.commons.lang.StringUtils;
 
 import java.util.Properties;
 import java.util.Iterator;
+import java.util.Map;
 import java.util.HashMap;
+import java.util.Set;
 import java.util.HashSet;
 import java.util.Map;
 import java.util.Vector;
@@ -130,8 +133,8 @@
     /*************************************************************************
      *
      *************************************************************************/
-    public HashMap getTemplateNames() {
-	HashMap tNames = new HashMap();
+    public Map<String,File> getTemplateNames() {
+	Map<String,File> tNames = new HashMap<String,File>();
 	File dir = new File ("templates");
 	tNames.put (TN_SERVICE, new File (dir, "ServiceSkeletonTemplate.java"));
 	tNames.put (TN_PARAMETER, new File (dir, "ServiceParameterTemplate.java"));
@@ -162,7 +165,7 @@
     static final Pattern P_SERVICE_URL   = Pattern.compile ("@SERVICE_URL@");
     static final Pattern P_SERVICE_RDF   = Pattern.compile ("@SERVICE_RDF@");
     static final Pattern P_IOTABLE       = Pattern.compile ("@IOTABLE@");
-    static final Pattern P_FALLBACK_TYPE = Pattern.compile ("@FALLBACK_TYPE@");
+    static final Pattern P_FALLBACK_CODE = Pattern.compile ("@FALLBACK_CODE@");
 
     // dynamically created (org.biomoby.shared.datatypes.MapDataTypes)
     // (we need it for generating set/get methods for input/output
@@ -194,15 +197,15 @@
 	// compile patterns for filtering by service and authority names
 	Pattern wantedService = null;
 	String filter = props.getProperty (GPROP_SERVICE);
-	if (filter != null && ! "".equals (filter))
+	if (StringUtils.isNotBlank (filter))
 	    wantedService = Pattern.compile (filter);
 	Pattern wantedAuthority = null;
 	filter = props.getProperty (GPROP_AUTH);
-	if (filter != null && ! "".equals (filter))
+	if (StringUtils.isNotBlank (filter))
 	    wantedAuthority = Pattern.compile (filter);
 
 	// load all templates (from files)
-	HashMap templates = getTemplateNames();
+	Map<String,File> templates = getTemplateNames();
 	serviceTemplate          = loadTemplate (templates.get (TN_SERVICE));
 	serviceParameterTemplate = loadTemplate (templates.get (TN_PARAMETER));
 	servicePISetTemplate     = loadTemplate (templates.get (TN_PISET));
@@ -291,14 +294,38 @@
 	// graphs?
 	boolean graphCreated = createGraph (serviceName, outputDir, props, allServices, allDataTypes);
 
-	// fallback type - just for services with a single primary input
-	String fallbackType = "";
+	// fallback type - its type depends on the number of primary inputs
+	StringBuilder fallbackCode = new StringBuilder();
 	MobyData[] pis = service.getPrimaryInputs();
-	if (pis.length == 1) {
+	if (pis.length == 0) {
+	    fallbackCode.append ("String fallback = null;");
+	} else if (pis.length == 1) {
 	    String dataTypeName = mapDataType2class (pis[0]);
-	    if (dataTypeName != null)
-		fallbackType = dataTypeName;
+	    if (dataTypeName != null) {
+		fallbackCode.append ("String fallback = \"");
+		fallbackCode.append (dataTypeName);
+		fallbackCode.append ("\";");
+	    } else {
+		fallbackCode.append ("String fallback = null;");
+	    }
+	} else if (pis.length > 1) {
+	    fallbackCode.append
+		("java.util.Map<String,String> fallback = new java.util.HashMap<String,String>(); ");
+	    for (MobyData p: pis) {
+		String dataTypeName = mapDataType2class (p);
+		if (dataTypeName != null) {
+		    String articleName = p.getName();
+		    if (StringUtils.isNotBlank (articleName)) {
+			fallbackCode.append ("fallback.put (\"");
+			fallbackCode.append (articleName);
+			fallbackCode.append ("\",\"");
+			fallbackCode.append (dataTypeName);
+			fallbackCode.append ("\"); ");
+		    }
+		}
+	    }
 	}
+	fallbackCode.append ("\n");
 
 	// replace tokens in templates
 	String result = P_SERVICE_NAME.matcher (serviceTemplate).replaceAll (serviceName);
@@ -313,7 +340,7 @@
 	result = P_EMAIL_CONTACT.matcher (result).replaceAll (htmlEscape (service.getEmailContact()));
 	result = P_IMAGESTART.matcher (result).replaceAll (graphCreated ? "" : "<!-- ");
 	result = P_IMAGEEND.matcher (result).replaceAll (graphCreated ? "" : " -->");
-	result = P_FALLBACK_TYPE.matcher (result).replaceAll (fallbackType);
+	result = P_FALLBACK_CODE.matcher (result).replaceAll (fallbackCode.toString());
 
 	// 
  	// now apply templates for set/get methods (put the result in
@@ -359,7 +386,7 @@
 	    String methods = serviceParameterTemplate;
 
 	    String articleName = sis[i].getName();
-	    if (articleName == null || "".equals (articleName.trim())) {
+	    if (StringUtils.isBlank (articleName)) {
 		System.err.println (MSG_SECONDARY_PBL (serviceName, sis[i]));
 		continue;
 	    }
@@ -437,7 +464,7 @@
      * (that's why it gets a 'serviceName') and returns false.
      *************************************************************************/
     protected boolean verifyNames (MobyData[] data, String serviceName) {
-	HashSet names = new HashSet();
+	Set<String> names = new HashSet<String>();
 	for (int i = 0; i < data.length; i++) {
 	    String name = getOrCreateArticleName (data[i]);
 
@@ -468,7 +495,7 @@
      * ignore them or replace them.
      *************************************************************************/
     protected String authority2package (String authority) {
-	if (authority == null || "".equals (authority.trim()))
+	if (StringUtils.isBlank (authority))
 	    return DEFAULT_PACKAGE;
  	StringBuffer buf = new StringBuffer (100);
 	String[] parts = authority.split ("\\.");
@@ -515,7 +542,7 @@
      *************************************************************************/
     protected String getOrCreateArticleName (MobyData data) {
 	String name = data.getName();
-	if (name != null && ! "".equals (name.trim()))
+	if (StringUtils.isNotBlank (name))
 	    return name;
 	return mapDataType2class (data);
     }
@@ -556,7 +583,7 @@
 	throws MobyException {
 	if (allServices == null)
 	    return worker.findService (patternService);
-	Vector v = new Vector();
+	Vector<MobyService> v = new Vector<MobyService>();
 	String name = patternService.getName();
 	String auth = patternService.getAuthority();
 	for (int i = 0; i < allServices.length; i++) {
@@ -641,7 +668,7 @@
 
 	static final String NBSP = "&nbsp;";
 	String nbsp (String value) {
-	    if (value == null || "".equals (value.trim())) return NBSP;
+	    if (StringUtils.isBlank (value)) return NBSP;
 	    else return value;
 	}
 	MobyPrimaryDataSimple getOneSimple (MobyData data) {


From senger at dev.open-bio.org  Sun Mar  2 07:45:27 2008
From: senger at dev.open-bio.org (Martin Senger)
Date: Sun, 2 Mar 2008 07:45:27 -0500
Subject: [MOBY-guts] biomoby commit
Message-ID: <200803021245.m22CjR4h000428@dev.open-bio.org>


senger
Sun Mar  2 07:45:27 EST 2008
Update of /home/repository/moby/moby-live/Java/xmls
In directory dev.open-bio.org:/tmp/cvs-serv32345/xmls

Modified Files:
	dashboardBuild.xml install.xml junit.xml mosesBuild.xml 
	project.pom samplesBuild.xml servletsBuild.xml 
Log Message:
Too Many Changes - see docs/ChangeLog

moby-live/Java/xmls dashboardBuild.xml,1.4,1.5 install.xml,1.1,1.2 junit.xml,1.2,1.3 mosesBuild.xml,1.4,1.5 project.pom,1.5,1.6 samplesBuild.xml,1.4,1.5 servletsBuild.xml,1.1,1.2
===================================================================
RCS file: /home/repository/moby/moby-live/Java/xmls/dashboardBuild.xml,v
retrieving revision 1.4
retrieving revision 1.5
diff -u -r1.4 -r1.5
--- /home/repository/moby/moby-live/Java/xmls/dashboardBuild.xml	2008/02/22 00:54:30	1.4
+++ /home/repository/moby/moby-live/Java/xmls/dashboardBuild.xml	2008/03/02 12:45:27	1.5
@@ -42,8 +42,12 @@
     <not><isset property="log4j.configuration.valid"/></not>
   </condition>
   
-  <java classname="org.biomoby.service.dashboard.Dashboard" taskname="Dashboard"
-    classpathref="dashboard.build.classpath" fork="true" failonerror="true">
+  <java
+    classname="org.biomoby.service.dashboard.Dashboard"
+    taskname="Dashboard"
+    classpathref="dashboard.build.classpath"
+    fork="true"
+    failonerror="true">
     <jvmarg value="-Xms32m"/>
     <jvmarg value="-Xmx256m"/>
     <arg value="${dashboard.arg.1}"/>

===================================================================
RCS file: /home/repository/moby/moby-live/Java/xmls/install.xml,v
retrieving revision 1.1
retrieving revision 1.2
diff -u -r1.1 -r1.2
--- /home/repository/moby/moby-live/Java/xmls/install.xml	2008/02/14 06:13:37	1.1
+++ /home/repository/moby/moby-live/Java/xmls/install.xml	2008/03/02 12:45:27	1.2
@@ -9,15 +9,18 @@
 <!-- ====================================================== -->
 
 <target name="install"
-  description="Install and build jMoby">
+  description="Install and build jMoby"
+  depends="pre-compile,compile,post-compile"/>
+
+<target name="pre-compile">
   <echo taskname="welcome">
 ------------------------------------------
-Welcome to the jMoby world.              |
-Project documentation is available from: |
-http://biomoby.org/                      |
+| Welcome to the jMoby world.            |
+| Project documentation is available at: |
+| http://biomoby.org/                    |
 ------------------------------------------
   </echo>
-  <echo/>
+
   <echo taskname="version">
 ${ant.version}
 Java: ${java.version}
@@ -32,25 +35,103 @@
   <available file="${lib.dir}/alltools2.jar" property="old.jar.present"/>
   <antcall target="libcheck"/>
 
-  <echo/>
-  <echo taskname="build">
-The jMoby is going to build itself. It will need to fetch a lot of
-libraries from the Internet (using the Maven technology for resolving
-project dependencies). Just be patient, please...
+  <!-- Give name of the local cache -->
 
-Thanks for any comments and suggestions.
+  <touch file="build.properties"/>
+  <input taskname="Give Cache Name"
+    addproperty="registry.cache.dir"
+    defaultvalue="${project.home}/myCache">
+During the installation, jMoby is going to fetch data
+from the BioMoby central registry and store them in a
+local file system to allow much faster access to it.
+
+In order to do it, it needs to know a directory where
+you wish to store the local cache. For now, you can
+type it here - but for future the best is to add this
+line to your build.properties file:
+
+   registry.cache.dir = /full/name/of/cache/directory
+
+Default value (just pres ENTER to accept it) is:
+  </input>
+  <echo taskname="Give Cache Name">
+Local cache: ${registry.cache.dir}
+  </echo>
+
+  <echo file="build.properties" append="true">
+registry.cache.dir = ${registry.cache.dir}
+</echo>
+
+  <!-- build itself -->
+
+  <echo taskname="build">
+The jMoby is going to build itself. It will need to
+fetch a lot of libraries from the Internet (using the
+Maven technology for resolving project dependencies).
+Just be patient, please...
   </echo>
   <input taskname=" Attention ">Press Return key to continue...</input>
+  <antcall target="clean"/>
+
+</target>
+
+
 
-  <echo/>
-  <antcall target="compile"/>
+
+<target name="post-compile">
+  <antcall target="dashboard-config"/>
+
+
+  <!-- fill local cache -->
+
+  <echo taskname="Local cache">
+The jMoby is going to create local cache. Depending
+on the network speed, it may take several minutes
+(usually it should be done within about a minute).
+
+[You can check the progress in the jMoby.log file.]
+  </echo>
+
+  <java
+    taskname="Local cache"
+    classname="CacheRegistryClient"
+    fork="no"
+    failonerror="true">
+    <classpath refid="build.classpath"/>
+    <classpath refid="dependency.classpath"/>
+    <sysproperty key="log4j.configuration" value="file:${log4j.configuration}"/>
+    <arg value="-cachedir"/>
+    <arg file="${registry.cache.dir}"/>
+    <arg value="-v"/>
+    <arg value="-fill"/>
+  </java>
+
+
+  <!-- footnote message -->
 
   <echo taskname="Success">
 Installation completed.
+
+Thanks for any comments and suggestions
+(moby-l at biomoby.org or moby-dev at biomoby.org)
   </echo>
 
+
+  <!-- start Dashboard -->
+
+  <input taskname=" Attention ">Press Return key to start Dashboard...</input>
+  <!--
+(or press Ctrl-C and start Dashboard later
+ by typing 'ant dashboard')
+</input>
+-->
+  <antcall target="dashboard"/>
+
 </target>
 
+<!-- ====================================================== -->
+<!--                                                        -->
+<!-- ====================================================== -->
 <target name="check-ant-version">
   <fail
     taskname="check"

===================================================================
RCS file: /home/repository/moby/moby-live/Java/xmls/junit.xml,v
retrieving revision 1.2
retrieving revision 1.3
diff -u -r1.2 -r1.3
--- /home/repository/moby/moby-live/Java/xmls/junit.xml	2008/02/28 05:21:48	1.2
+++ /home/repository/moby/moby-live/Java/xmls/junit.xml	2008/03/02 12:45:27	1.3
@@ -90,7 +90,10 @@
     <jvmarg value="-Dlog4j.configuration=file:${log4j.configuration}"/>
     <formatter type="plain"/>
     <batchtest todir="${test.report.dir}">
-      <fileset dir="${build.test}" includes="**/*Test.*" />
+      <fileset dir="${build.test}">
+        <include name="**/MobyParserTest.*"/>
+      </fileset>
+      <!--      <fileset dir="${build.test}" includes="**/*Test.*" /> -->
     </batchtest>
   </junit>
 
@@ -103,16 +106,25 @@
 <target name="compile-tests" if="junit.is.present" depends="compile,junit-present">
   
   <!-- compilation options -->    
-  <property name="compile.test.debug"       value="${compile.debugtrue}" />
-  <property name="compile.test.verbose"     value="${compile.verbosefalse}" />
-  <property name="compile.test.deprecation" value="${compile.deprecationfalse}" />
-  <property name="compile.test.optimize"    value="${compile.optimizefalse}" />
-  <property name="compile.test.warnings"    value="${compile.warningsfalse}" />
+  <property name="compile.test.debug"       value="${compile.debug}" />
+  <property name="compile.test.verbose"     value="${compile.verbose}" />
+  <property name="compile.test.deprecation" value="${compile.deprecation}" />
+  <property name="compile.test.optimize"    value="${compile.optimize}" />
+  <property name="compile.test.warnings"    value="${compile.warnings}" />
     
   <condition property="xlint.test.param" value="-Xlint:unchecked" else="-Xlint:none">
     <istrue value="${compile.test.warnings}"/>
   </condition>
 
+  <path id="tests.classpath">
+    <pathelement location="${build.classes}"/>
+    <pathelement path="${classes.datatypes}"/>
+    <pathelement path="${classes.skeletons}"/>
+    <fileset dir="${lib.dir}">
+      <include name="*.jar"/>
+    </fileset>
+  </path>
+
   <javac
     srcdir="${src.test}"
     destdir="${build.test}"
@@ -122,7 +134,7 @@
     deprecation="${compile.test.deprecation}"
     optimize="${compile.test.optimize}"
     excludes="${project.excludes}">
-    <classpath refid="build.classpath"/>
+    <classpath refid="tests.classpath"/>
     <classpath refid="dependency.classpath"/>
     <compilerarg value="${xlint.test.param}"/>
   </javac>

===================================================================
RCS file: /home/repository/moby/moby-live/Java/xmls/mosesBuild.xml,v
retrieving revision 1.4
retrieving revision 1.5
diff -u -r1.4 -r1.5
--- /home/repository/moby/moby-live/Java/xmls/mosesBuild.xml	2008/02/28 05:21:49	1.4
+++ /home/repository/moby/moby-live/Java/xmls/mosesBuild.xml	2008/03/02 12:45:27	1.5
@@ -21,6 +21,7 @@
 
            generate-datatypes     generate-services
            clean-datatypes        clean-services
+           compile-datatypes      compile-services
            jar-datatypes          jar-services
            moses-datatypes        moses-services
 
@@ -107,6 +108,10 @@
     </or>
   </condition>
   
+  <condition property="xlint.param" value="-Xlint:unchecked" else="-Xlint:none">
+    <istrue value="${compile.warnings}"/>
+  </condition>
+
 </target>
 
 <!-- ================================================================== -->
@@ -125,6 +130,7 @@
   
   <property name="moses.filter.dt" value="&quot;&quot;"/>
   <property name="dot.location" value="&quot;&quot;"/>
+  <property name="registry.cache.dir" value=""/>
   
   <java classname="MosesGenerators" taskname="Data Types"
     classpathref="moses.build.classpath" fork="true" failonerror="true">
@@ -189,9 +195,6 @@
   <delete includeemptydirs="true" quiet="true">
     <fileset dir="${src.skeletons}" includes="**/*"/>
   </delete>
-  <delete includeemptydirs="true">
-    <fileset dir="${classes.skeletons}" includes="**/*"/>
-  </delete>
 </target>
 
 <target name="generate-services" depends="moses-init,service-check"
@@ -200,6 +203,7 @@
   <property name="moses.service" value="&quot;&quot;"/>
   <property name="moses.authority" value="&quot;&quot;"/>
   <property name="dot.location" value="&quot;&quot;"/>
+  <property name="registry.cache.dir" value=""/>
   
   <java classname="MosesGenerators" taskname="Service(s)"
     classpathref="moses.build.classpath" fork="true" failonerror="true">
@@ -267,21 +271,36 @@
 <!-- ================================================================== -->
 <!-- Moses generally: Compile generated datatypes and skeletons         -->
 <!-- ================================================================== -->
-<target name="moses-compile" depends="moses-init,compile"
-  description="Compile all generated sources.">
-  <javac srcdir="${src.datatypes}"
+<target name="moses-compile" depends="compile-datatypes,compile-services"
+  description="Compile all generated sources."/>
+
+<target name="compile-datatypes" depends="moses-init,compile">
+  <javac
+    srcdir="${src.datatypes}"
     destdir="${classes.datatypes}"
-    debug="true"
+    verbose="${compile.verbose}"
+    debug="${compile.debug}"
     debuglevel="lines,vars,source"
+    deprecation="${compile.deprecation}"
+    optimize="${compile.optimize}"
     excludes="${project.excludes}">
     <classpath refid="moses.build.classpath"/>
+    <compilerarg value="${xlint.param}"/>
   </javac>
-  <javac srcdir="${src.skeletons}"
-    debug="true"
-    debuglevel="lines,vars,source"
+</target>
+
+<target name="compile-services" depends="moses-init,compile">
+  <javac
+    srcdir="${src.skeletons}"
     destdir="${classes.skeletons}"
+    verbose="${compile.verbose}"
+    debug="${compile.debug}"
+    debuglevel="lines,vars,source"
+    deprecation="${compile.deprecation}"
+    optimize="${compile.optimize}"
     excludes="${project.excludes}">
     <classpath refid="moses.build.classpath"/>
+    <compilerarg value="${xlint.param}"/>
   </javac>
 </target>
 
@@ -349,3 +368,14 @@
 <target name="moses-jars" depends="jar-datatypes,jar-services"
   description="Create jar files with generated data types and skeletons.">
 </target>
+
+<!-- ================================================================== -->
+<!-- Moses generally: do it all                                         -->
+<!-- ================================================================== -->
+<target name="moses"
+  depends="compile,moses-clean,clean-services,generate-datatypes,compile-datatypes,generate-services,compile-services,moses-jars"
+  description="Clean/enerate/compile/pack data types and skeletons.">
+</target>
+
+<target name="moses-test" depends="generate-datatypes,moses-compile">
+</target>

===================================================================
RCS file: /home/repository/moby/moby-live/Java/xmls/project.pom,v
retrieving revision 1.5
retrieving revision 1.6
diff -u -r1.5 -r1.6
--- /home/repository/moby/moby-live/Java/xmls/project.pom	2008/02/28 05:21:49	1.5
+++ /home/repository/moby/moby-live/Java/xmls/project.pom	2008/03/02 12:45:27	1.6
@@ -167,6 +167,21 @@
     </dependency>
 
     <dependency>
+      <groupId>commons-configuration</groupId>
+      <artifactId>commons-configuration</artifactId>
+      <version>1.5</version>
+      <!-- we need to exclude this in order to get Java 1.5. XML parser
+           (otherwise axis will complain about the lexical-handler
+           feature not supported -->
+      <exclusions>
+        <exclusion>
+          <groupId>xerces</groupId>
+          <artifactId>xerces</artifactId>
+        </exclusion>
+      </exclusions>  
+    </dependency>
+
+    <dependency>
       <groupId>castor</groupId>
       <artifactId>castor</artifactId>
       <version>0.9.5</version>
@@ -366,6 +381,12 @@
     </dependency>
 
     <dependency>
+      <groupId>org.apache.ant</groupId>
+      <artifactId>ant-nodeps</artifactId>
+      <version>1.7.0</version>
+    </dependency>
+
+    <dependency>
       <groupId>ant-contrib</groupId>
       <artifactId>ant-contrib</artifactId>
       <version>1.0b2</version>

===================================================================
RCS file: /home/repository/moby/moby-live/Java/xmls/samplesBuild.xml,v
retrieving revision 1.4
retrieving revision 1.5
diff -u -r1.4 -r1.5
--- /home/repository/moby/moby-live/Java/xmls/samplesBuild.xml	2008/02/22 00:54:30	1.4
+++ /home/repository/moby/moby-live/Java/xmls/samplesBuild.xml	2008/03/02 12:45:27	1.5
@@ -57,6 +57,10 @@
     <pathelement location="${classes.samples}"/>
   </path>
    
+  <condition property="xlint.param" value="-Xlint:unchecked" else="-Xlint:none">
+    <istrue value="${compile.warnings}"/>
+  </condition>
+
 </target>
 
 <!-- ================================================================== -->
@@ -64,15 +68,22 @@
 <!-- ================================================================== -->
 <target name="samples-compile" depends="samples-init,moses-compile"
   description="Compile samples and tutorial.">
+
   <copy todir="${classes.samples}/resources">
     <fileset dir="${samples.resources}"/>
   </copy>
-  <javac srcdir="${src.samples}"
-    debug="true"
-    debuglevel="lines,vars,source"
+
+  <javac
+    srcdir="${src.samples}"
     destdir="${classes.samples}"
+    verbose="${compile.verbose}"
+    debug="${compile.debug}"
+    debuglevel="lines,vars,source"
+    deprecation="${compile.deprecation}"
+    optimize="${compile.optimize}"
     excludes="${project.excludes}">
     <classpath refid="samples.build.classpath"/>
+    <compilerarg value="${xlint.param}"/>
   </javac>
 </target>
 
@@ -154,13 +165,14 @@
   <antcall target="generate-services">
     <param name="moses.authority" value="samples.jmoby.net"/>
   </antcall>
+  <antcall target="generate-services">
+    <param name="moses.service" value="getFeatureList|TrimSequenceVector"/>
+  </antcall>
 
 </target>
 
 <!-- ================================================================== -->
 <!-- Samples: All in one                                                -->
 <!-- ================================================================== -->
-<!-- <target name="samples" depends="samples-generate,samples-compile,samples-jar,samples-docs,deploy-services" -->
-<!-- <target name="samples" depends="samples-compile,samples-jar,deploy-services" -->
-<target name="samples" depends="samples-compile,samples-jar"
+<target name="samples" depends="moses,samples-compile,samples-jar"
   description="Do (almost) everything for samples."/>

===================================================================
RCS file: /home/repository/moby/moby-live/Java/xmls/servletsBuild.xml,v
retrieving revision 1.1
retrieving revision 1.2
diff -u -r1.1 -r1.2
--- /home/repository/moby/moby-live/Java/xmls/servletsBuild.xml	2006/04/28 00:13:41	1.1
+++ /home/repository/moby/moby-live/Java/xmls/servletsBuild.xml	2008/03/02 12:45:27	1.2
@@ -25,6 +25,9 @@
   description="Create a war file with jMoby servlets.">
   <mkdir dir="${build.webapps}"/>
   <mkdir dir="${build.webapps}/cache"/>
+
+  <property name="registry.cache.dir" value=""/>
+
   <copy file="${src.webapps}/web.xml.template"
     tofile="${build.webapps}/web.xml"
     overwrite="yes">


From senger at dev.open-bio.org  Sun Mar  2 10:36:25 2008
From: senger at dev.open-bio.org (Martin Senger)
Date: Sun, 2 Mar 2008 10:36:25 -0500
Subject: [MOBY-guts] biomoby commit
Message-ID: <200803021536.m22FaPbJ000970@dev.open-bio.org>


senger
Sun Mar  2 10:36:24 EST 2008
Update of /home/repository/moby/moby-live/Java/xmls
In directory dev.open-bio.org:/tmp/cvs-serv951/xmls

Modified Files:
	install.xml 
Log Message:
few details added to the installation task
moby-live/Java/xmls install.xml,1.2,1.3
===================================================================
RCS file: /home/repository/moby/moby-live/Java/xmls/install.xml,v
retrieving revision 1.2
retrieving revision 1.3
diff -u -r1.2 -r1.3
--- /home/repository/moby/moby-live/Java/xmls/install.xml	2008/03/02 12:45:27	1.2
+++ /home/repository/moby/moby-live/Java/xmls/install.xml	2008/03/02 15:36:24	1.3
@@ -85,7 +85,7 @@
   <!-- fill local cache -->
 
   <echo taskname="Local cache">
-The jMoby is going to create local cache. Depending
+The jMoby is now creating a local cache. Depending
 on the network speed, it may take several minutes
 (usually it should be done within about a minute).
 
@@ -107,6 +107,13 @@
   </java>
 
 
+  <!-- generate datatypes and samples -->
+
+  <property name="moses.nographs" value="true"/>
+  <antcall target="samples"/>
+
+
+
   <!-- footnote message -->
 
   <echo taskname="Success">
@@ -125,6 +132,7 @@
  by typing 'ant dashboard')
 </input>
 -->
+
   <antcall target="dashboard"/>
 
 </target>


From senger at dev.open-bio.org  Sun Mar  2 10:43:28 2008
From: senger at dev.open-bio.org (Martin Senger)
Date: Sun, 2 Mar 2008 10:43:28 -0500
Subject: [MOBY-guts] biomoby commit
Message-ID: <200803021543.m22FhS2I001023@dev.open-bio.org>


senger
Sun Mar  2 10:43:28 EST 2008
Update of /home/repository/moby/moby-live/Java/xmls
In directory dev.open-bio.org:/tmp/cvs-serv1004/xmls

Modified Files:
	install.xml 
Log Message:
few details added to the installation task
moby-live/Java/xmls install.xml,1.3,1.4
===================================================================
RCS file: /home/repository/moby/moby-live/Java/xmls/install.xml,v
retrieving revision 1.3
retrieving revision 1.4
diff -u -r1.3 -r1.4
--- /home/repository/moby/moby-live/Java/xmls/install.xml	2008/03/02 15:36:24	1.3
+++ /home/repository/moby/moby-live/Java/xmls/install.xml	2008/03/02 15:43:28	1.4
@@ -109,6 +109,7 @@
 
   <!-- generate datatypes and samples -->
 
+  <property name="moses.authority" value="samples.jmoby.net"/>
   <property name="moses.nographs" value="true"/>
   <antcall target="samples"/>
 


From senger at dev.open-bio.org  Sun Mar  2 11:05:01 2008
From: senger at dev.open-bio.org (Martin Senger)
Date: Sun, 2 Mar 2008 11:05:01 -0500
Subject: [MOBY-guts] biomoby commit
Message-ID: <200803021605.m22G51UB001077@dev.open-bio.org>


senger
Sun Mar  2 11:05:01 EST 2008
Update of /home/repository/moby/moby-live/Java/xmls
In directory dev.open-bio.org:/tmp/cvs-serv1058/xmls

Modified Files:
	install.xml 
Log Message:
few details added to the installation task
moby-live/Java/xmls install.xml,1.4,1.5
===================================================================
RCS file: /home/repository/moby/moby-live/Java/xmls/install.xml,v
retrieving revision 1.4
retrieving revision 1.5
diff -u -r1.4 -r1.5
--- /home/repository/moby/moby-live/Java/xmls/install.xml	2008/03/02 15:43:28	1.4
+++ /home/repository/moby/moby-live/Java/xmls/install.xml	2008/03/02 16:05:01	1.5
@@ -40,7 +40,7 @@
   <touch file="build.properties"/>
   <input taskname="Give Cache Name"
     addproperty="registry.cache.dir"
-    defaultvalue="${project.home}/myCache">
+    defaultvalue="${basedir.unix}/myCache">
 During the installation, jMoby is going to fetch data
 from the BioMoby central registry and store them in a
 local file system to allow much faster access to it.
@@ -52,7 +52,7 @@
 
    registry.cache.dir = /full/name/of/cache/directory
 
-Default value (just pres ENTER to accept it) is:
+Default value (just press ENTER to accept it) is:
   </input>
   <echo taskname="Give Cache Name">
 Local cache: ${registry.cache.dir}
@@ -70,7 +70,7 @@
 Maven technology for resolving project dependencies).
 Just be patient, please...
   </echo>
-  <input taskname=" Attention ">Press Return key to continue...</input>
+  <!--  <input taskname=" Attention ">Press Return key to continue...</input> -->
   <antcall target="clean"/>
 
 </target>
@@ -127,7 +127,7 @@
 
   <!-- start Dashboard -->
 
-  <input taskname=" Attention ">Press Return key to start Dashboard...</input>
+  <input taskname=" Attention ">Press (twice) Return key to start Dashboard...</input>
   <!--
 (or press Ctrl-C and start Dashboard later
  by typing 'ant dashboard')


From senger at dev.open-bio.org  Sun Mar  2 11:19:15 2008
From: senger at dev.open-bio.org (Martin Senger)
Date: Sun, 2 Mar 2008 11:19:15 -0500
Subject: [MOBY-guts] biomoby commit
Message-ID: <200803021619.m22GJFEj001149@dev.open-bio.org>


senger
Sun Mar  2 11:19:15 EST 2008
Update of /home/repository/moby/moby-live/Java/src/main/org/biomoby/service/dashboard
In directory dev.open-bio.org:/tmp/cvs-serv1130/src/main/org/biomoby/service/dashboard

Modified Files:
	RegistryPanel.java 
Log Message:
problem with Windows vs. Unix filenames
moby-live/Java/src/main/org/biomoby/service/dashboard RegistryPanel.java,1.29,1.30
===================================================================
RCS file: /home/repository/moby/moby-live/Java/src/main/org/biomoby/service/dashboard/RegistryPanel.java,v
retrieving revision 1.29
retrieving revision 1.30
diff -u -r1.29 -r1.30
--- /home/repository/moby/moby-live/Java/src/main/org/biomoby/service/dashboard/RegistryPanel.java	2008/03/02 12:45:26	1.29
+++ /home/repository/moby/moby-live/Java/src/main/org/biomoby/service/dashboard/RegistryPanel.java	2008/03/02 16:19:15	1.30
@@ -17,6 +17,8 @@
 import org.biomoby.registry.meta.RegistriesList;
 import org.biomoby.registry.meta.Registry;
 
+import org.apache.commons.io.FilenameUtils;
+
 import javax.swing.JPanel;
 import javax.swing.JLabel;
 import javax.swing.Icon;
@@ -515,8 +517,9 @@
    	labelCacheDir = new JLabel("Cache directory");
 	cacheDir = createFileSelector ("Select directory for/with local cache",
 				       "Select",
-				       DashboardConfig.getString (DP_REGISTRY_CACHE_DIR,
-								  getUserTmpDir()),
+				       FilenameUtils.separatorsToSystem
+				       (DashboardConfig.getString (DP_REGISTRY_CACHE_DIR,
+								   getUserTmpDir())),
 				       "cacheDirectory",
 				       DP_CACHE_DIR);
 	cacheDir.getFileChooser().setFileSelectionMode (JFileChooser.DIRECTORIES_ONLY);


From senger at dev.open-bio.org  Sun Mar  2 11:20:49 2008
From: senger at dev.open-bio.org (Martin Senger)
Date: Sun, 2 Mar 2008 11:20:49 -0500
Subject: [MOBY-guts] biomoby commit
Message-ID: <200803021620.m22GKnvR001201@dev.open-bio.org>


senger
Sun Mar  2 11:20:49 EST 2008
Update of /home/repository/moby/moby-live/Java
In directory dev.open-bio.org:/tmp/cvs-serv1182

Modified Files:
	.cvsignore.template 
Log Message:

moby-live/Java .cvsignore.template,1.6,1.7
===================================================================
RCS file: /home/repository/moby/moby-live/Java/.cvsignore.template,v
retrieving revision 1.6
retrieving revision 1.7
diff -u -r1.6 -r1.7
--- /home/repository/moby/moby-live/Java/.cvsignore.template	2008/02/14 06:13:34	1.6
+++ /home/repository/moby/moby-live/Java/.cvsignore.template	2008/03/02 16:20:49	1.7
@@ -6,3 +6,4 @@
 *.log
 *.log.?
 testout
+myCache


From senger at dev.open-bio.org  Sun Mar  2 11:59:54 2008
From: senger at dev.open-bio.org (Martin Senger)
Date: Sun, 2 Mar 2008 11:59:54 -0500
Subject: [MOBY-guts] biomoby commit
Message-ID: <200803021659.m22GxsAQ001291@dev.open-bio.org>


senger
Sun Mar  2 11:59:54 EST 2008
Update of /home/repository/moby/moby-live/Java/src/main/org/biomoby/service/dashboard
In directory dev.open-bio.org:/tmp/cvs-serv1272/src/main/org/biomoby/service/dashboard

Modified Files:
	GeneratorPanel.java 
Log Message:

moby-live/Java/src/main/org/biomoby/service/dashboard GeneratorPanel.java,1.17,1.18
===================================================================
RCS file: /home/repository/moby/moby-live/Java/src/main/org/biomoby/service/dashboard/GeneratorPanel.java,v
retrieving revision 1.17
retrieving revision 1.18
diff -u -r1.17 -r1.18
--- /home/repository/moby/moby-live/Java/src/main/org/biomoby/service/dashboard/GeneratorPanel.java	2008/03/02 12:45:26	1.17
+++ /home/repository/moby/moby-live/Java/src/main/org/biomoby/service/dashboard/GeneratorPanel.java	2008/03/02 16:59:54	1.18
@@ -189,7 +189,7 @@
 	// split it into resizable panels
 	JSplitPane split = hSplit (vSplit (hSplit (selection,
 						   generators, 0.9),
-					   console, 0.1),
+					   console, 0.2),
 				   deployment, 0.9);
   	SwingUtils.addComponent (pComponent, split,  0, 0, 1, 1, BOTH, NWEST,  1.0, 1.0);
 	return pComponent;


From senger at dev.open-bio.org  Sun Mar  2 13:47:35 2008
From: senger at dev.open-bio.org (Martin Senger)
Date: Sun, 2 Mar 2008 13:47:35 -0500
Subject: [MOBY-guts] biomoby commit
Message-ID: <200803021847.m22IlZYk001434@dev.open-bio.org>


senger
Sun Mar  2 13:47:35 EST 2008
Update of /home/repository/moby/moby-live/Java/src/main/org/biomoby/shared/datatypes
In directory dev.open-bio.org:/tmp/cvs-serv1415/src/main/org/biomoby/shared/datatypes

Modified Files:
	MobyObject.java 
Log Message:
Fixed cross references by primitive types

moby-live/Java/src/main/org/biomoby/shared/datatypes MobyObject.java,1.7,1.8
===================================================================
RCS file: /home/repository/moby/moby-live/Java/src/main/org/biomoby/shared/datatypes/MobyObject.java,v
retrieving revision 1.7
retrieving revision 1.8
diff -u -r1.7 -r1.8
--- /home/repository/moby/moby-live/Java/src/main/org/biomoby/shared/datatypes/MobyObject.java	2008/03/02 12:45:26	1.7
+++ /home/repository/moby/moby-live/Java/src/main/org/biomoby/shared/datatypes/MobyObject.java	2008/03/02 18:47:35	1.8
@@ -62,7 +62,7 @@
     protected String name = "";   // articleName
     protected String value = "";
     protected MobyProvisionInfo provision;
-    protected Vector xrefs = new Vector();   // of type MobyXref
+    protected Vector<MobyXref> xrefs = new Vector<MobyXref>();
     protected boolean isValueCDATA = false;
 
     // is this a primitive type?
@@ -153,7 +153,6 @@
 
 	if (provision != null)
 	    elem.addContent (JDOMUtils.toXMLElement(provision));
-
 	if (xrefs.size() > 0) {
 	    Element crElem = MobyPackage.getXMLElement (MobyTags.CROSSREFERENCE);
 	    for (Enumeration en = xrefs.elements(); en.hasMoreElements(); )
@@ -165,7 +164,7 @@
 	    if (isValueCDATA)
 		elem.addContent (new CDATA (value));
 	    else
-		elem.setText (value);
+		elem.addContent (value);
 	}
 
 	return elem;
@@ -286,7 +285,7 @@
      *************************************************************************/
     public void setXrefs (MobyXref[] xrefs) {
 	if (xrefs != null) {
-	    this.xrefs = new Vector();
+	    this.xrefs = new Vector<MobyXref>();
 	    for (int i = 0; i < xrefs.length; i++)
 		this.xrefs.addElement (xrefs[i]);
 	}


From senger at dev.open-bio.org  Sun Mar  2 22:11:28 2008
From: senger at dev.open-bio.org (Martin Senger)
Date: Sun, 2 Mar 2008 22:11:28 -0500
Subject: [MOBY-guts] biomoby commit
Message-ID: <200803030311.m233BShE002177@dev.open-bio.org>


senger
Sun Mar  2 22:11:27 EST 2008
Update of /home/repository/moby/moby-live/Java/src/test/junit-resources
In directory dev.open-bio.org:/tmp/cvs-serv2132/src/test/junit-resources

Modified Files:
	parser-test-input-2.xml parser-test-input-3.xml 
	parser-test-input-4.xml 
Added Files:
	parser-test-input-set.xml parser-test-input-xrefs.xml 
Log Message:
More junit tests for XML parser

moby-live/Java/src/test/junit-resources parser-test-input-set.xml,NONE,1.1 parser-test-input-xrefs.xml,NONE,1.1 parser-test-input-2.xml,1.1,1.2 parser-test-input-3.xml,1.1,1.2 parser-test-input-4.xml,1.1,1.2
===================================================================
RCS file: /home/repository/moby/moby-live/Java/src/test/junit-resources/parser-test-input-2.xml,v
retrieving revision 1.1
retrieving revision 1.2
diff -u -r1.1 -r1.2
--- /home/repository/moby/moby-live/Java/src/test/junit-resources/parser-test-input-2.xml	2008/02/28 05:21:48	1.1
+++ /home/repository/moby/moby-live/Java/src/test/junit-resources/parser-test-input-2.xml	2008/03/03 03:11:27	1.2
@@ -6,8 +6,8 @@
     <moby:mobyData moby:queryID="a1">
       <moby:Simple moby:articleName="myDNA">
         <moby:MyDNASequence xmlns:moby="http://www.biomoby.org/moby" moby:id="ir" moby:namespace="">
-          <moby:Integer moby:id="3" moby:namespace="a" moby:articleName="Length">12</moby:Integer>
-          <moby:String moby:id="3" moby:namespace="b" moby:articleName="SequenceString">abcd</moby:String>
+          <moby:Integer moby:id="1" moby:namespace="a" moby:articleName="Length">12</moby:Integer>
+          <moby:String moby:id="2" moby:namespace="b" moby:articleName="SequenceString">abcd</moby:String>
           <moby:Boolean moby:id="3" moby:namespace="c" moby:articleName="Flag">true</moby:Boolean>
         </moby:MyDNASequence>
       </moby:Simple>

===================================================================
RCS file: /home/repository/moby/moby-live/Java/src/test/junit-resources/parser-test-input-3.xml,v
retrieving revision 1.1
retrieving revision 1.2
diff -u -r1.1 -r1.2
--- /home/repository/moby/moby-live/Java/src/test/junit-resources/parser-test-input-3.xml	2008/02/28 05:21:48	1.1
+++ /home/repository/moby/moby-live/Java/src/test/junit-resources/parser-test-input-3.xml	2008/03/03 03:11:27	1.2
@@ -10,9 +10,16 @@
             <Integer id="" namespace="" articleName="start">1</Integer>
             <String id="" namespace="" articleName="phase">b</String>
             <Float id="" namespace="" articleName="score">12.34</Float>
-            <MY_multi_key_value_pair id="" namespace="" articleName="column9_tag_value">
+            <MY_multi_key_value_pair id="1" namespace="" articleName="column9_tag_value">
               <String id="" namespace="" articleName="key">key1</String>
               <String id="" namespace="" articleName="value">value1</String>
+              <String id="" namespace="" articleName="value">value2</String>
+              <String id="" namespace="" articleName="value">value3</String>
+              <String id="" namespace="" articleName="mode">mode1</String>
+            </MY_multi_key_value_pair>
+            <MY_multi_key_value_pair id="2" namespace="" articleName="column9_tag_value">
+              <String id="" namespace="" articleName="key">key2</String>
+              <String id="" namespace="" articleName="value">valueA</String>
               <String id="" namespace="" articleName="mode">mode1</String>
             </MY_multi_key_value_pair>
           </BasicGFF3SequenceFeature>

===================================================================
RCS file: /home/repository/moby/moby-live/Java/src/test/junit-resources/parser-test-input-4.xml,v
retrieving revision 1.1
retrieving revision 1.2
diff -u -r1.1 -r1.2
--- /home/repository/moby/moby-live/Java/src/test/junit-resources/parser-test-input-4.xml	2008/02/28 05:21:48	1.1
+++ /home/repository/moby/moby-live/Java/src/test/junit-resources/parser-test-input-4.xml	2008/03/03 03:11:27	1.2
@@ -1,10 +1,5 @@
 <?xml version="1.0" encoding="UTF-8"?>
 
-<!-- ========================================== -->
-<!-- A testing data for MobyParser.             -->
-<!-- Use: build/run/run-moby-parser "this-file" -->
-<!-- ========================================== -->
-
 <moby:MOBY xmlns:moby="http://www.biomoby.org/moby">
   <moby:mobyContent moby:authority="http://&quot;me&quot;.&lt;org&gt;&amp;">
     <moby:serviceNotes><Notes>freetext notes here the notes</Notes></moby:serviceNotes>
@@ -24,8 +19,8 @@
       </moby:Simple>
       <moby:Simple moby:articleName="mySeq">
         <moby:MyDNASequence xmlns:moby="http://www.biomoby.org/moby" moby:id="ir" moby:namespace="">
-          <moby:Integer moby:id="3" moby:namespace="a" moby:articleName="Length">12</moby:Integer>
-          <moby:String moby:id="3" moby:namespace="b" moby:articleName="SequenceString">abcd</moby:String>
+          <moby:Integer moby:id="3" moby:namespace="c" moby:articleName="Length">123</moby:Integer>
+          <moby:String moby:id="4" moby:namespace="d" moby:articleName="SequenceString">xyz</moby:String>
         </moby:MyDNASequence>
       </moby:Simple>
     </moby:mobyData>


From senger at dev.open-bio.org  Sun Mar  2 22:11:28 2008
From: senger at dev.open-bio.org (Martin Senger)
Date: Sun, 2 Mar 2008 22:11:28 -0500
Subject: [MOBY-guts] biomoby commit
Message-ID: <200803030311.m233BSPU002151@dev.open-bio.org>


senger
Sun Mar  2 22:11:27 EST 2008
Update of /home/repository/moby/moby-live/Java/src/test/java/org/biomoby/shared/parser
In directory dev.open-bio.org:/tmp/cvs-serv2132/src/test/java/org/biomoby/shared/parser

Modified Files:
	MobyParserTest.java 
Log Message:
More junit tests for XML parser

moby-live/Java/src/test/java/org/biomoby/shared/parser MobyParserTest.java,1.2,1.3
===================================================================
RCS file: /home/repository/moby/moby-live/Java/src/test/java/org/biomoby/shared/parser/MobyParserTest.java,v
retrieving revision 1.2
retrieving revision 1.3
diff -u -r1.2 -r1.3
--- /home/repository/moby/moby-live/Java/src/test/java/org/biomoby/shared/parser/MobyParserTest.java	2008/03/02 12:45:27	1.2
+++ /home/repository/moby/moby-live/Java/src/test/java/org/biomoby/shared/parser/MobyParserTest.java	2008/03/03 03:11:27	1.3
@@ -20,6 +20,7 @@
 package org.biomoby.shared.parser;
 
 import org.biomoby.shared.MobyException;
+import org.biomoby.shared.data.MobyProvisionInfo;
 import org.biomoby.shared.datatypes.*;
 
 import org.junit.Before;
@@ -39,10 +40,12 @@
 
 public class MobyParserTest {
 
-    private static final String INPUT_1 = "parser-test-input-1.xml";
-    private static final String INPUT_2 = "parser-test-input-2.xml";
-    private static final String INPUT_3 = "parser-test-input-3.xml";
-    private static final String INPUT_4 = "parser-test-input-4.xml";
+    private static final String INPUT_1     = "parser-test-input-1.xml";
+    private static final String INPUT_2     = "parser-test-input-2.xml";
+    private static final String INPUT_3     = "parser-test-input-3.xml";
+    private static final String INPUT_4     = "parser-test-input-4.xml";
+    private static final String INPUT_XREFS = "parser-test-input-xrefs.xml";
+    private static final String INPUT_SET   = "parser-test-input-set.xml";
  
     /**************************************************************************
      *
@@ -72,26 +75,101 @@
 	assertEquals (typedData.getMoby_Length().getIntValue(), 10);
     }
 
-//     @Test
-//     public void testUnknownTopLevel()
-// 	throws IOException, MobyException {
-// 	parse (INPUT_2, "DNASequence", null);
-//     }
-
-//     @Test
-//     public void testUnknownTopLevelAndMember()
-// 	throws IOException, MobyException {
-// 	parse (INPUT_3, "BasicGFF3MultiFeature", null);
-//     }
-
-//     @Test
-//     public void testMoreUnknownTopLevels()
-// 	throws IOException, MobyException {
-// 	Map<String,String> backups = new HashMap<String,String>();
-// 	backups.put ("mySeq",   "DNASequence");
-// 	backups.put ("myPairs", "BasicGFF3MultiFeature");
-// 	parse (INPUT_4, null, backups);
-//     }
+     @Test
+     public void testUnknownTopLevel()
+ 	throws IOException, MobyException {
+	MobyPackage moby = parse (INPUT_2, "DNASequence", null);
+	DNASequence typedData = (DNASequence)moby.getJob(0).getData ("myDNA");
+	assertEquals (typedData.get_SequenceString(), "abcd");
+	assertEquals (typedData.getMoby_Length().getIntValue(), 12);
+     }
+
+    @Test
+    public void testUnknownTopLevelAndMember()
+	throws IOException, MobyException {
+	MobyPackage moby = parse (INPUT_3, "BasicGFF3MultiFeature", null);
+	BasicGFF3MultiFeature typedData = (BasicGFF3MultiFeature)moby.getJob(0).getData ("myPairs");
+	BasicGFF3SequenceFeature[] data = typedData.getMoby_BasicGFF3SequenceFeature();
+	assertEquals (data.length, 1);
+	assertEquals (data[0].getMoby_start().getIntValue(), 1);
+	assertEquals (data[0].getMoby_score().getFloatValue(), 12.34, 0);
+	assertEquals (data[0].get_phase(), "b");
+	multi_key_value_pair[] pairs = data[0].getMoby_column9_tag_value();
+	assertEquals (pairs.length, 2);
+	assertEquals (pairs[0].get_key(), "key1");
+	assertEquals (pairs[0].get_the_value().length, 3);
+	assertEquals (pairs[0].get_the_value()[0], "value1");
+	assertEquals (pairs[1].get_key(), "key2");
+	assertEquals (pairs[1].get_the_value().length, 1);
+	assertEquals (pairs[1].get_the_value()[0], "valueA");
+    }
+
+    @Test
+    public void testMoreUnknownTopLevels()
+	throws IOException, MobyException {
+	Map<String,String> backups = new HashMap<String,String>();
+	backups.put ("mySeq",   "DNASequence");
+	backups.put ("myPairs", "BasicGFF3MultiFeature");
+	MobyPackage moby = parse (INPUT_4, null, backups);
+	BasicGFF3MultiFeature typedData = (BasicGFF3MultiFeature)moby.getJob(0).getData ("myPairs");
+	BasicGFF3SequenceFeature[] data = typedData.getMoby_BasicGFF3SequenceFeature();
+	assertEquals (data.length, 1);
+	assertEquals (data[0].getMoby_start().getIntValue(), 1);
+	assertEquals (data[0].getMoby_score().getFloatValue(), 12.34, 0);
+	assertEquals (data[0].get_phase(), "b");
+	multi_key_value_pair[] pairs = data[0].getMoby_column9_tag_value();
+	assertEquals (pairs.length, 1);
+	assertEquals (pairs[0].get_key(), "key1");
+	assertEquals (pairs[0].get_the_value().length, 1);
+	assertEquals (pairs[0].get_the_value()[0], "value1");
+	DNASequence seqData = (DNASequence)moby.getJob(0).getData ("mySeq");
+	assertEquals (seqData.get_SequenceString(), "xyz");
+	assertEquals (seqData.getMoby_Length().getIntValue(), 123);
+    }
+
+    @Test
+    public void testSetWithSubstitution()
+	throws IOException, MobyException {
+ 	Map<String,String> backups = new HashMap<String,String>();
+ 	backups.put ("mySequenceCollection", "GenericSequence");
+	MobyPackage moby = parse (INPUT_SET, null, backups);
+	MobyObject[] data = moby.getJob(0).getDataSet ("mySequenceCollection");
+	assertEquals (data[0].getMobyTypeName(), "DNASequence");
+	assertEquals (data[1].getMobyTypeName(), "GenericSequence");
+	GenericSequence typedData = (GenericSequence)data[0];
+	assertEquals (typedData.get_SequenceString(), "tatatatata");
+	assertEquals (typedData.getMoby_Length().getIntValue(), 10);
+	typedData = (GenericSequence)data[1];
+	assertEquals (typedData.get_SequenceString(), "");
+	assertEquals (typedData.getMoby_Length().getIntValue(), 5);
+    }
+
+    @Test
+    public void testXref()
+	throws IOException, MobyException {
+	MobyPackage moby = parse (INPUT_XREFS, null, null);
+	assertEquals (moby.getJob(0).getData().getValue().trim(),
+		      "This is a value");
+	MobyXref[] xrefs = moby.getJob(0).getData().getXrefs();
+	assertEquals (xrefs.length, 3);
+	assertTrue  (xrefs[0].isSimpleXref());
+	assertTrue  (xrefs[1].isSimpleXref());
+	assertFalse (xrefs[2].isSimpleXref());
+	assertEquals (xrefs[0].getId(), "At263644");
+	assertEquals (xrefs[0].getNamespace(), "TIGR");
+	assertEquals (xrefs[2].getId(), "yes");
+	assertEquals (xrefs[2].getNamespace(), "LION");
+	assertEquals (xrefs[2].getEvidenceCode(), "IEA");
+
+	MobyProvisionInfo pi = moby.getJob(0).getData().getProvision();
+	assertEquals (pi.getSoftwareName(),    "InterPro");
+	assertEquals (pi.getSoftwareVersion(), "1.2");
+	assertEquals (pi.getSoftwareComment(), "HMMER's not run");
+	assertEquals (pi.getDBName(),    "Genbank/nt");
+	assertEquals (pi.getDBVersion(), "April 8, 2003");
+	assertEquals (pi.getDBComment(), "DBver");
+	assertEquals (pi.getComment(), "this <&>\"<&>\" is a software comment");
+    }
 
 
     /**************************************************************************


From senger at dev.open-bio.org  Mon Mar  3 06:34:17 2008
From: senger at dev.open-bio.org (Martin Senger)
Date: Mon, 3 Mar 2008 06:34:17 -0500
Subject: [MOBY-guts] biomoby commit
Message-ID: <200803031134.m23BYHBX003189@dev.open-bio.org>


senger
Mon Mar  3 06:34:16 EST 2008
Update of /home/repository/moby/moby-live/Java
In directory dev.open-bio.org:/tmp/cvs-serv3170

Modified Files:
	build.xml 
Log Message:
* more work on junit testing and its infrastructure
* removing some compiler warnings from generated data types
* better use of caching in skeleton generator

moby-live/Java build.xml,1.70,1.71
===================================================================
RCS file: /home/repository/moby/moby-live/Java/build.xml,v
retrieving revision 1.70
retrieving revision 1.71
diff -u -r1.70 -r1.71
--- /home/repository/moby/moby-live/Java/build.xml	2008/03/02 12:45:24	1.70
+++ /home/repository/moby/moby-live/Java/build.xml	2008/03/03 11:34:16	1.71
@@ -237,7 +237,7 @@
   <!-- Builds config files and run-time scripts                           -->
   <!-- ================================================================== -->
   <target name="config" depends="init"
-    description="Create all run-time scripts and configuration files.">
+    description="Create all run-time scripts and configuration files">
 
     <property name="my.log4j.properties"
       location="${src.config}/log4j.properties.template"/>
@@ -313,7 +313,7 @@
   <!-- Compiles everything                                                -->
   <!-- ================================================================== -->
   <target name="compile" depends="config"
-    description="Compile all source code (default).">
+    description="Compile all source code (default)">
 
     <condition property="xlint.param" value="-Xlint:unchecked" else="-Xlint:none">
       <istrue value="${compile.warnings}"/>
@@ -361,7 +361,7 @@
   <!-- Copy help files of the Dashboard panels to the docs directory       -->
   <!-- =================================================================== -->
   <target name="docs" depends="compile,cleanapi"
-    description="Generate API documentation.">
+    description="Generate API documentation">
     
     <javadoc
       additionalparam="-quiet"
@@ -417,7 +417,12 @@
   <!-- Clean-up                                                           -->
   <!-- ================================================================== -->
   <target name="clean" depends="cleanapi"
-    description="Remove all generated files.">
+    description="Remove compiled classes and built files">
+    <delete dir="${build.dir}"/>
+  </target>
+  
+  <target name="cleanall" depends="clean,clean-services,clean-datatypes"
+    description="Remove all generated files">
     <delete dir="${build.dir}"/>
   </target>
   
@@ -431,7 +436,7 @@
   <!-- Builds a jar file with jMoby classes                               -->
   <!-- ================================================================== -->
   <target name="jars" depends="compile"
-    description="Create jar files with jMoby classes.">
+    description="Create jar files with jMoby classes">
     
     <property name="released.date" value="${TODAY_SHORT}"/>
     <property name="project.jar"
@@ -462,7 +467,7 @@
    <!-- ================================================================== -->
    <target name="all"
      depends="clean,compile,docs,jars,jar-rdfagent,wardist,bindist-rdfagent"
-     description="Clean, compile, generate docs, then build the rest."/>
+     description="Clean, compile, generate docs, then build the rest"/>
 
    <!-- ================================================================== -->
    <!-- Just for testing...                                                -->


From senger at dev.open-bio.org  Mon Mar  3 06:34:17 2008
From: senger at dev.open-bio.org (Martin Senger)
Date: Mon, 3 Mar 2008 06:34:17 -0500
Subject: [MOBY-guts] biomoby commit
Message-ID: <200803031134.m23BYH5n003255@dev.open-bio.org>


senger
Mon Mar  3 06:34:17 EST 2008
Update of /home/repository/moby/moby-live/Java/src/config/templates
In directory dev.open-bio.org:/tmp/cvs-serv3170/src/config/templates

Modified Files:
	DataTypeTemplate.java MembersHASTemplate.java 
	MethodsHASTemplate.java MethodsHAS_string_Template.java 
Log Message:
* more work on junit testing and its infrastructure
* removing some compiler warnings from generated data types
* better use of caching in skeleton generator

moby-live/Java/src/config/templates DataTypeTemplate.java,1.2,1.3 MembersHASTemplate.java,1.2,1.3 MethodsHASTemplate.java,1.2,1.3 MethodsHAS_string_Template.java,1.2,1.3
===================================================================
RCS file: /home/repository/moby/moby-live/Java/src/config/templates/DataTypeTemplate.java,v
retrieving revision 1.2
retrieving revision 1.3
diff -u -r1.2 -r1.3
--- /home/repository/moby/moby-live/Java/src/config/templates/DataTypeTemplate.java	2005/09/19 08:08:32	1.2
+++ /home/repository/moby/moby-live/Java/src/config/templates/DataTypeTemplate.java	2008/03/03 11:34:16	1.3
@@ -43,10 +43,10 @@
      *
      *************************************************************************/
     public String toString() {
-	StringBuffer buf_I_am_sorry_that_this_produces_a_warning = new StringBuffer();
+	StringBuilder buf_I_am_sorry_that_this_produces_a_warning = new StringBuilder();
 	buf_I_am_sorry_that_this_produces_a_warning.append (super.toString());
 @TO_STRING@
-	return new String (buf_I_am_sorry_that_this_produces_a_warning);
+	return new String (buf_I_am_sorry_that_this_produces_a_warning.toString());
     }
 
     /**************************************************************************

===================================================================
RCS file: /home/repository/moby/moby-live/Java/src/config/templates/MembersHASTemplate.java,v
retrieving revision 1.2
retrieving revision 1.3
diff -u -r1.2 -r1.3
--- /home/repository/moby/moby-live/Java/src/config/templates/MembersHASTemplate.java	2005/09/19 08:08:32	1.2
+++ /home/repository/moby/moby-live/Java/src/config/templates/MembersHASTemplate.java	2008/03/03 11:34:17	1.3
@@ -1,5 +1,5 @@
     /** An article name for a member of this object. */
     public static final String ARTICLE_NAME_ at ESC_UPPER_ARTICLE_NAME@ = "@ARTICLE_NAME@";
     // elements are of type @CHILDTYPE_NAME@
-    protected java.util.Vector @ESC_ARTICLE_NAME@ = new java.util.Vector();
+    protected java.util.Vector<Object> @ESC_ARTICLE_NAME@ = new java.util.Vector<Object>();
 

===================================================================
RCS file: /home/repository/moby/moby-live/Java/src/config/templates/MethodsHASTemplate.java,v
retrieving revision 1.2
retrieving revision 1.3
diff -u -r1.2 -r1.3
--- /home/repository/moby/moby-live/Java/src/config/templates/MethodsHASTemplate.java	2005/09/19 08:08:32	1.2
+++ /home/repository/moby/moby-live/Java/src/config/templates/MethodsHASTemplate.java	2008/03/03 11:34:17	1.3
@@ -19,7 +19,7 @@
      * only one value
      *************************************************************************/
     public void set_ at ESC_ARTICLE_NAME@ (@CHILDTYPE_NAME@[] value) {
-	this. at ESC_ARTICLE_NAME@ = new java.util.Vector();
+	this. at ESC_ARTICLE_NAME@ = new java.util.Vector<Object>();
 	for (int i = 0; i < value.length; i++)
 	    set_ at ESC_ARTICLE_NAME@ (value[i]);
     }

===================================================================
RCS file: /home/repository/moby/moby-live/Java/src/config/templates/MethodsHAS_string_Template.java,v
retrieving revision 1.2
retrieving revision 1.3
diff -u -r1.2 -r1.3
--- /home/repository/moby/moby-live/Java/src/config/templates/MethodsHAS_string_Template.java	2005/09/19 08:08:32	1.2
+++ /home/repository/moby/moby-live/Java/src/config/templates/MethodsHAS_string_Template.java	2008/03/03 11:34:17	1.3
@@ -21,7 +21,7 @@
      * only one value
      *************************************************************************/
     public void set_ at ESC_ARTICLE_NAME@ (String[] value) {
-	this. at ESC_ARTICLE_NAME@ = new java.util.Vector();
+	this. at ESC_ARTICLE_NAME@ = new java.util.Vector<Object>();
 	for (int i = 0; i < value.length; i++)
 	    set_ at ESC_ARTICLE_NAME@ (value[i]);
     }


From senger at dev.open-bio.org  Mon Mar  3 06:34:17 2008
From: senger at dev.open-bio.org (Martin Senger)
Date: Mon, 3 Mar 2008 06:34:17 -0500
Subject: [MOBY-guts] biomoby commit
Message-ID: <200803031134.m23BYHaD003347@dev.open-bio.org>


senger
Mon Mar  3 06:34:17 EST 2008
Update of /home/repository/moby/moby-live/Java/src/main/org/biomoby/shared
In directory dev.open-bio.org:/tmp/cvs-serv3170/src/main/org/biomoby/shared

Modified Files:
	CentralCached.java Utils.java 
Log Message:
* more work on junit testing and its infrastructure
* removing some compiler warnings from generated data types
* better use of caching in skeleton generator

moby-live/Java/src/main/org/biomoby/shared CentralCached.java,1.1,1.2 Utils.java,1.19,1.20
===================================================================
RCS file: /home/repository/moby/moby-live/Java/src/main/org/biomoby/shared/CentralCached.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/CentralCached.java	2008/02/23 13:58:32	1.1
+++ /home/repository/moby/moby-live/Java/src/main/org/biomoby/shared/CentralCached.java	2008/03/03 11:34:17	1.2
@@ -131,4 +131,11 @@
      **************************************************************************/
     String getCacheInfoFormatted (String id);
 
+    /***************************************************************************
+     * Indicate whether the implementtaion really is using a local cache. <p>
+     * 
+     * @return true if a local cache is used
+     **************************************************************************/
+    boolean isUsingCache();
+
 }

===================================================================
RCS file: /home/repository/moby/moby-live/Java/src/main/org/biomoby/shared/Utils.java,v
retrieving revision 1.19
retrieving revision 1.20
diff -u -r1.19 -r1.20
--- /home/repository/moby/moby-live/Java/src/main/org/biomoby/shared/Utils.java	2008/02/28 16:59:47	1.19
+++ /home/repository/moby/moby-live/Java/src/main/org/biomoby/shared/Utils.java	2008/03/03 11:34:17	1.20
@@ -546,8 +546,7 @@
 	    }
 	    
 	} catch (IOException e) {
-	    throw new MobyException("Error creating input stream:", e
-		    .getCause());
+	    throw new MobyException ("Error creating input stream: " + e.toString());
 	}
     }
     


From senger at dev.open-bio.org  Mon Mar  3 06:34:17 2008
From: senger at dev.open-bio.org (Martin Senger)
Date: Mon, 3 Mar 2008 06:34:17 -0500
Subject: [MOBY-guts] biomoby commit
Message-ID: <200803031134.m23BYHPd003207@dev.open-bio.org>


senger
Mon Mar  3 06:34:16 EST 2008
Update of /home/repository/moby/moby-live/Java/docs
In directory dev.open-bio.org:/tmp/cvs-serv3170/docs

Modified Files:
	ChangeLog 
Log Message:
* more work on junit testing and its infrastructure
* removing some compiler warnings from generated data types
* better use of caching in skeleton generator

moby-live/Java/docs ChangeLog,1.85,1.86
===================================================================
RCS file: /home/repository/moby/moby-live/Java/docs/ChangeLog,v
retrieving revision 1.85
retrieving revision 1.86
diff -u -r1.85 -r1.86
--- /home/repository/moby/moby-live/Java/docs/ChangeLog	2008/03/02 12:45:24	1.85
+++ /home/repository/moby/moby-live/Java/docs/ChangeLog	2008/03/03 11:34:16	1.86
@@ -1,3 +1,15 @@
+2008-03-03  Martin Senger  <martin.senger&#64;gmail.com>
+
+	* Added a new method isUsingCache() to the CentralCached
+	interface.
+
+	* Fixed access to the local cache in the MoSeS service generator
+	(the cache was not used in all circumstances).
+
+	* Fixed compilation warnings for MoSeS generated data types.
+
+	* Added constructors to the ExtendedServiceLocator.
+
 2008-03-02  Martin Senger  <martin.senger&#64;gmail.com>
 
 	* Added: new installation task (type: ant install) - it downloads


From senger at dev.open-bio.org  Mon Mar  3 06:34:17 2008
From: senger at dev.open-bio.org (Martin Senger)
Date: Mon, 3 Mar 2008 06:34:17 -0500
Subject: [MOBY-guts] biomoby commit
Message-ID: <200803031134.m23BYH0E003285@dev.open-bio.org>


senger
Mon Mar  3 06:34:17 EST 2008
Update of /home/repository/moby/moby-live/Java/src/main/org/biomoby/client
In directory dev.open-bio.org:/tmp/cvs-serv3170/src/main/org/biomoby/client

Modified Files:
	CentralDigestCachedSimpleImpl.java ExtendedServiceLocator.java 
Log Message:
* more work on junit testing and its infrastructure
* removing some compiler warnings from generated data types
* better use of caching in skeleton generator

moby-live/Java/src/main/org/biomoby/client CentralDigestCachedSimpleImpl.java,1.2,1.3 ExtendedServiceLocator.java,1.2,1.3
===================================================================
RCS file: /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/CentralDigestCachedSimpleImpl.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/CentralDigestCachedSimpleImpl.java	2008/02/23 13:58:32	1.2
+++ /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/CentralDigestCachedSimpleImpl.java	2008/03/03 11:34:17	1.3
@@ -117,6 +117,15 @@
 	return cacheDir;
     }
 
+    /***************************************************************************
+     * Indicate whether the implementtaion really is using a local cache. <p>
+     * 
+     * @return true if a local cache is used
+     **************************************************************************/
+    public boolean isUsingCache() {
+	return getCacheDir() != null;
+    }
+
     /**************************************************************************
      * Removes object groups from the cache. If 'id' is null it
      * removes the whole cache (for that Moby registry this instance

===================================================================
RCS file: /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/ExtendedServiceLocator.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/ExtendedServiceLocator.java	2006/02/20 05:51:09	1.2
+++ /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/ExtendedServiceLocator.java	2008/03/03 11:34:17	1.3
@@ -8,6 +8,8 @@
 
 package org.biomoby.client;
 
+import org.biomoby.shared.MobyService;
+
 /**
  * An extended container allowing to store information how to call a
  * biomoby service using non-biomoby protocols. A typical example
@@ -33,6 +35,20 @@
     boolean loop = false;
 
     /**************************************************************************
+     * Default constructor.
+     *************************************************************************/
+    public ExtendedServiceLocator() {
+	super();
+    }
+
+    /**************************************************************************
+     * Another constructor, seeting also a service.
+     *************************************************************************/
+    public ExtendedServiceLocator (MobyService service) {
+	super (service);
+    }
+
+    /**************************************************************************
      * Set name of a local class that represents (implements) a
      * service. <p>
      *


From senger at dev.open-bio.org  Mon Mar  3 06:34:17 2008
From: senger at dev.open-bio.org (Martin Senger)
Date: Mon, 3 Mar 2008 06:34:17 -0500
Subject: [MOBY-guts] biomoby commit
Message-ID: <200803031134.m23BYHnm003225@dev.open-bio.org>


senger
Mon Mar  3 06:34:16 EST 2008
Update of /home/repository/moby/moby-live/Java/src/Clients
In directory dev.open-bio.org:/tmp/cvs-serv3170/src/Clients

Modified Files:
	MosesGenerators.java 
Log Message:
* more work on junit testing and its infrastructure
* removing some compiler warnings from generated data types
* better use of caching in skeleton generator

moby-live/Java/src/Clients MosesGenerators.java,1.4,1.5
===================================================================
RCS file: /home/repository/moby/moby-live/Java/src/Clients/MosesGenerators.java,v
retrieving revision 1.4
retrieving revision 1.5
diff -u -r1.4 -r1.5
--- /home/repository/moby/moby-live/Java/src/Clients/MosesGenerators.java	2008/02/23 13:58:32	1.4
+++ /home/repository/moby/moby-live/Java/src/Clients/MosesGenerators.java	2008/03/03 11:34:16	1.5
@@ -56,7 +56,6 @@
 	    boolean generateServices = cmd.hasOption ("-s");
 	    boolean nogenerate = cmd.hasOption ("-n");
 	    boolean nographs = cmd.hasOption ("-ng");
-	    String cacheDir = cmd.getParam ("-cacheDir");
 	    String filter = cmd.getParam ("-filter");
 	    String outdir = cmd.getParam ("-outdir");
 	    String dotLocation = cmd.getParam ("-dot");


From senger at dev.open-bio.org  Mon Mar  3 06:34:17 2008
From: senger at dev.open-bio.org (Martin Senger)
Date: Mon, 3 Mar 2008 06:34:17 -0500
Subject: [MOBY-guts] biomoby commit
Message-ID: <200803031134.m23BYHOv003369@dev.open-bio.org>


senger
Mon Mar  3 06:34:17 EST 2008
Update of /home/repository/moby/moby-live/Java/src/main/org/biomoby/shared/datatypes
In directory dev.open-bio.org:/tmp/cvs-serv3170/src/main/org/biomoby/shared/datatypes

Modified Files:
	MapPrimitiveDataTypes.java 
Log Message:
* more work on junit testing and its infrastructure
* removing some compiler warnings from generated data types
* better use of caching in skeleton generator

moby-live/Java/src/main/org/biomoby/shared/datatypes MapPrimitiveDataTypes.java,1.4,1.5
===================================================================
RCS file: /home/repository/moby/moby-live/Java/src/main/org/biomoby/shared/datatypes/MapPrimitiveDataTypes.java,v
retrieving revision 1.4
retrieving revision 1.5
diff -u -r1.4 -r1.5
--- /home/repository/moby/moby-live/Java/src/main/org/biomoby/shared/datatypes/MapPrimitiveDataTypes.java	2008/02/28 05:21:48	1.4
+++ /home/repository/moby/moby-live/Java/src/main/org/biomoby/shared/datatypes/MapPrimitiveDataTypes.java	2008/03/03 11:34:17	1.5
@@ -9,6 +9,7 @@
 package org.biomoby.shared.datatypes;
 
 import org.biomoby.shared.MobyException;
+import java.util.Map;
 import java.util.HashMap;
 import java.util.Iterator;
 import java.util.Map;
@@ -29,7 +30,7 @@
  */
 abstract public class MapPrimitiveDataTypes {
 
-    protected static HashMap type2class = new HashMap();
+    protected static Map<String,String> type2class = new HashMap<String,String>();
     static {
         type2class.put ("Object", "org.biomoby.shared.datatypes.MobyObject");
 
@@ -52,7 +53,7 @@
      *************************************************************************/
     public Class getClass (String dataTypeName)
 	throws MobyException {
-	String className = (String)type2class.get (dataTypeName);
+	String className = type2class.get (dataTypeName);
 	if (className == null) {
 
 	    // a hack: sometimes the 'dataTypeName' is wrong - it is


From senger at dev.open-bio.org  Mon Mar  3 06:34:42 2008
From: senger at dev.open-bio.org (Martin Senger)
Date: Mon, 3 Mar 2008 06:34:42 -0500
Subject: [MOBY-guts] biomoby commit
Message-ID: <200803031134.m23BYg1e003496@dev.open-bio.org>


senger
Mon Mar  3 06:34:42 EST 2008
Update of /home/repository/moby/moby-live/Java/src/test/java/org/biomoby/service
In directory dev.open-bio.org:/tmp/cvs-serv3478/src/test/java/org/biomoby/service

Log Message:
Directory /home/repository/moby/moby-live/Java/src/test/java/org/biomoby/service added to the repository

moby-live/Java/src/test/java/org/biomoby/service - New directory
rcsdiff: /home/repository/moby/moby-live/Java/src/test/java/org/biomoby/service/RCS/-,v: No such file or directory

rcsdiff: /home/repository/moby/moby-live/Java/src/test/java/org/biomoby/service/RCS/New,v: No such file or directory

rcsdiff: /home/repository/moby/moby-live/Java/src/test/java/org/biomoby/service/RCS/directory,v: No such file or directory


From senger at dev.open-bio.org  Mon Mar  3 06:34:17 2008
From: senger at dev.open-bio.org (Martin Senger)
Date: Mon, 3 Mar 2008 06:34:17 -0500
Subject: [MOBY-guts] biomoby commit
Message-ID: <200803031134.m23BYH2Q003417@dev.open-bio.org>


senger
Mon Mar  3 06:34:17 EST 2008
Update of /home/repository/moby/moby-live/Java/src/test/java/org/biomoby/shared/parser
In directory dev.open-bio.org:/tmp/cvs-serv3170/src/test/java/org/biomoby/shared/parser

Modified Files:
	MobyParserTest.java 
Log Message:
* more work on junit testing and its infrastructure
* removing some compiler warnings from generated data types
* better use of caching in skeleton generator

moby-live/Java/src/test/java/org/biomoby/shared/parser MobyParserTest.java,1.3,1.4
===================================================================
RCS file: /home/repository/moby/moby-live/Java/src/test/java/org/biomoby/shared/parser/MobyParserTest.java,v
retrieving revision 1.3
retrieving revision 1.4
diff -u -r1.3 -r1.4
--- /home/repository/moby/moby-live/Java/src/test/java/org/biomoby/shared/parser/MobyParserTest.java	2008/03/03 03:11:27	1.3
+++ /home/repository/moby/moby-live/Java/src/test/java/org/biomoby/shared/parser/MobyParserTest.java	2008/03/03 11:34:17	1.4
@@ -57,22 +57,22 @@
     public void testNormal()
 	throws IOException, MobyException {
 	MobyPackage moby = parse (INPUT_1, null, null);
-	assertEquals (moby.getServiceNotes(), "freetext notes here");
-	assertEquals (moby.getAuthority(), "http://\"me\".<org>&");
+	assertEquals ("freetext notes here", moby.getServiceNotes());
+	assertEquals ("http://\"me\".<org>&", moby.getAuthority());
 	MobyJob[] jobs = moby.getJobs();
-	assertEquals (jobs.length, 4);
-	assertEquals (jobs[0].getId(), "a1");
+	assertEquals (4, jobs.length);
+	assertEquals ("a1", jobs[0].getId());
 	MobyObject data = jobs[0].getData();
-	assertEquals (data.getMobyTypeName(), "NucleotideSequence");
-	assertEquals (data.getName(), "");
-	assertEquals (data.getNamespace(), "DragonDB_Allele");
-	assertEquals (data.getId(), "chlorae");
+	assertEquals ("NucleotideSequence", data.getMobyTypeName());
+	assertEquals ("", data.getName());
+	assertEquals ("DragonDB_Allele", data.getNamespace());
+	assertEquals ("chlorae", data.getId());
 	assertFalse (data.isPrimitiveType());
-	assertEquals (data.getClass().getName(), "org.biomoby.shared.datatypes.NucleotideSequence");
+	assertEquals ("org.biomoby.shared.datatypes.NucleotideSequence", data.getClass().getName());
 	NucleotideSequence typedData = (NucleotideSequence)jobs[0].getData();
-	assertEquals (typedData.get_SequenceString(), ">tata\ntatata");
-	assertEquals (typedData.getMoby_SequenceString().getValue(), ">tata\ntatata");
-	assertEquals (typedData.getMoby_Length().getIntValue(), 10);
+	assertEquals (">tata\ntatata", typedData.get_SequenceString());
+	assertEquals (">tata\ntatata", typedData.getMoby_SequenceString().getValue());
+	assertEquals (10, typedData.getMoby_Length().getIntValue());
     }
 
      @Test
@@ -80,8 +80,8 @@
  	throws IOException, MobyException {
 	MobyPackage moby = parse (INPUT_2, "DNASequence", null);
 	DNASequence typedData = (DNASequence)moby.getJob(0).getData ("myDNA");
-	assertEquals (typedData.get_SequenceString(), "abcd");
-	assertEquals (typedData.getMoby_Length().getIntValue(), 12);
+	assertEquals ("abcd", typedData.get_SequenceString());
+	assertEquals (12, typedData.getMoby_Length().getIntValue());
      }
 
     @Test
@@ -90,18 +90,18 @@
 	MobyPackage moby = parse (INPUT_3, "BasicGFF3MultiFeature", null);
 	BasicGFF3MultiFeature typedData = (BasicGFF3MultiFeature)moby.getJob(0).getData ("myPairs");
 	BasicGFF3SequenceFeature[] data = typedData.getMoby_BasicGFF3SequenceFeature();
-	assertEquals (data.length, 1);
-	assertEquals (data[0].getMoby_start().getIntValue(), 1);
-	assertEquals (data[0].getMoby_score().getFloatValue(), 12.34, 0);
-	assertEquals (data[0].get_phase(), "b");
+	assertEquals (1, data.length);
+	assertEquals (1, data[0].getMoby_start().getIntValue());
+	assertEquals (12.34, data[0].getMoby_score().getFloatValue(), 0.01);
+	assertEquals ("b", data[0].get_phase());
 	multi_key_value_pair[] pairs = data[0].getMoby_column9_tag_value();
-	assertEquals (pairs.length, 2);
-	assertEquals (pairs[0].get_key(), "key1");
-	assertEquals (pairs[0].get_the_value().length, 3);
-	assertEquals (pairs[0].get_the_value()[0], "value1");
-	assertEquals (pairs[1].get_key(), "key2");
-	assertEquals (pairs[1].get_the_value().length, 1);
-	assertEquals (pairs[1].get_the_value()[0], "valueA");
+	assertEquals (2, pairs.length);
+	assertEquals ("key1", pairs[0].get_key());
+	assertEquals (3, pairs[0].get_the_value().length);
+	assertEquals ("value1", pairs[0].get_the_value()[0]);
+	assertEquals ("key2", pairs[1].get_key());
+	assertEquals (1, pairs[1].get_the_value().length);
+	assertEquals ("valueA", pairs[1].get_the_value()[0]);
     }
 
     @Test
@@ -113,18 +113,18 @@
 	MobyPackage moby = parse (INPUT_4, null, backups);
 	BasicGFF3MultiFeature typedData = (BasicGFF3MultiFeature)moby.getJob(0).getData ("myPairs");
 	BasicGFF3SequenceFeature[] data = typedData.getMoby_BasicGFF3SequenceFeature();
-	assertEquals (data.length, 1);
-	assertEquals (data[0].getMoby_start().getIntValue(), 1);
-	assertEquals (data[0].getMoby_score().getFloatValue(), 12.34, 0);
-	assertEquals (data[0].get_phase(), "b");
+	assertEquals (1, data.length);
+	assertEquals (1, data[0].getMoby_start().getIntValue());
+	assertEquals (12.34, data[0].getMoby_score().getFloatValue(), 0.01);
+	assertEquals ("b", data[0].get_phase());
 	multi_key_value_pair[] pairs = data[0].getMoby_column9_tag_value();
-	assertEquals (pairs.length, 1);
-	assertEquals (pairs[0].get_key(), "key1");
-	assertEquals (pairs[0].get_the_value().length, 1);
-	assertEquals (pairs[0].get_the_value()[0], "value1");
+	assertEquals (1, pairs.length);
+	assertEquals ("key1", pairs[0].get_key());
+	assertEquals (1, pairs[0].get_the_value().length);
+	assertEquals ("value1", pairs[0].get_the_value()[0]);
 	DNASequence seqData = (DNASequence)moby.getJob(0).getData ("mySeq");
-	assertEquals (seqData.get_SequenceString(), "xyz");
-	assertEquals (seqData.getMoby_Length().getIntValue(), 123);
+	assertEquals ("xyz", seqData.get_SequenceString());
+	assertEquals (123, seqData.getMoby_Length().getIntValue());
     }
 
     @Test
@@ -134,41 +134,40 @@
  	backups.put ("mySequenceCollection", "GenericSequence");
 	MobyPackage moby = parse (INPUT_SET, null, backups);
 	MobyObject[] data = moby.getJob(0).getDataSet ("mySequenceCollection");
-	assertEquals (data[0].getMobyTypeName(), "DNASequence");
-	assertEquals (data[1].getMobyTypeName(), "GenericSequence");
+	assertEquals ("DNASequence", data[0].getMobyTypeName());
+	assertEquals ("GenericSequence", data[1].getMobyTypeName());
 	GenericSequence typedData = (GenericSequence)data[0];
-	assertEquals (typedData.get_SequenceString(), "tatatatata");
-	assertEquals (typedData.getMoby_Length().getIntValue(), 10);
+	assertEquals ("tatatatata", typedData.get_SequenceString());
+	assertEquals (10, typedData.getMoby_Length().getIntValue());
 	typedData = (GenericSequence)data[1];
-	assertEquals (typedData.get_SequenceString(), "");
-	assertEquals (typedData.getMoby_Length().getIntValue(), 5);
+	assertEquals ("", typedData.get_SequenceString());
+	assertEquals (5, typedData.getMoby_Length().getIntValue());
     }
 
     @Test
     public void testXref()
 	throws IOException, MobyException {
 	MobyPackage moby = parse (INPUT_XREFS, null, null);
-	assertEquals (moby.getJob(0).getData().getValue().trim(),
-		      "This is a value");
+	assertEquals ("This is a value", moby.getJob(0).getData().getValue().trim());
 	MobyXref[] xrefs = moby.getJob(0).getData().getXrefs();
-	assertEquals (xrefs.length, 3);
+	assertEquals (3, xrefs.length);
 	assertTrue  (xrefs[0].isSimpleXref());
 	assertTrue  (xrefs[1].isSimpleXref());
 	assertFalse (xrefs[2].isSimpleXref());
-	assertEquals (xrefs[0].getId(), "At263644");
-	assertEquals (xrefs[0].getNamespace(), "TIGR");
-	assertEquals (xrefs[2].getId(), "yes");
-	assertEquals (xrefs[2].getNamespace(), "LION");
-	assertEquals (xrefs[2].getEvidenceCode(), "IEA");
+	assertEquals ("At263644", xrefs[0].getId());
+	assertEquals ("TIGR", xrefs[0].getNamespace());
+	assertEquals ("yes", xrefs[2].getId());
+	assertEquals ("LION", xrefs[2].getNamespace());
+	assertEquals ("IEA", xrefs[2].getEvidenceCode());
 
 	MobyProvisionInfo pi = moby.getJob(0).getData().getProvision();
-	assertEquals (pi.getSoftwareName(),    "InterPro");
-	assertEquals (pi.getSoftwareVersion(), "1.2");
-	assertEquals (pi.getSoftwareComment(), "HMMER's not run");
-	assertEquals (pi.getDBName(),    "Genbank/nt");
-	assertEquals (pi.getDBVersion(), "April 8, 2003");
-	assertEquals (pi.getDBComment(), "DBver");
-	assertEquals (pi.getComment(), "this <&>\"<&>\" is a software comment");
+	assertEquals ("InterPro", pi.getSoftwareName());
+	assertEquals ("1.2", pi.getSoftwareVersion());
+	assertEquals ("HMMER's not run", pi.getSoftwareComment());
+	assertEquals ("Genbank/nt", pi.getDBName());
+	assertEquals ("April 8, 2003", pi.getDBVersion());
+	assertEquals ("DBver", pi.getDBComment());
+	assertEquals ("this <&>\"<&>\" is a software comment", pi.getComment());
     }
 
 


From senger at dev.open-bio.org  Mon Mar  3 06:34:17 2008
From: senger at dev.open-bio.org (Martin Senger)
Date: Mon, 3 Mar 2008 06:34:17 -0500
Subject: [MOBY-guts] biomoby commit
Message-ID: <200803031134.m23BYHrX003395@dev.open-bio.org>


senger
Mon Mar  3 06:34:17 EST 2008
Update of /home/repository/moby/moby-live/Java/src/samples/org/jmoby/tutorial/service
In directory dev.open-bio.org:/tmp/cvs-serv3170/src/samples/org/jmoby/tutorial/service

Modified Files:
	ConcatSequenceSetImpl.java ConcatSequencesImpl.java 
Log Message:
* more work on junit testing and its infrastructure
* removing some compiler warnings from generated data types
* better use of caching in skeleton generator

moby-live/Java/src/samples/org/jmoby/tutorial/service ConcatSequenceSetImpl.java,1.1,1.2 ConcatSequencesImpl.java,1.1,1.2
===================================================================
RCS file: /home/repository/moby/moby-live/Java/src/samples/org/jmoby/tutorial/service/ConcatSequenceSetImpl.java,v
retrieving revision 1.1
retrieving revision 1.2
diff -u -r1.1 -r1.2
--- /home/repository/moby/moby-live/Java/src/samples/org/jmoby/tutorial/service/ConcatSequenceSetImpl.java	2008/03/02 12:49:33	1.1
+++ /home/repository/moby/moby-live/Java/src/samples/org/jmoby/tutorial/service/ConcatSequenceSetImpl.java	2008/03/03 11:34:17	1.2
@@ -72,7 +72,7 @@
 	result.set_SequenceString (onlyLength ? "" : buf.toString());
 	result.set_Length (new MobyInteger (totalLength));
 
-	response.setData (result);
+	set_result (response, result);
     }
 
 }

===================================================================
RCS file: /home/repository/moby/moby-live/Java/src/samples/org/jmoby/tutorial/service/ConcatSequencesImpl.java,v
retrieving revision 1.1
retrieving revision 1.2
diff -u -r1.1 -r1.2
--- /home/repository/moby/moby-live/Java/src/samples/org/jmoby/tutorial/service/ConcatSequencesImpl.java	2008/03/02 12:49:33	1.1
+++ /home/repository/moby/moby-live/Java/src/samples/org/jmoby/tutorial/service/ConcatSequencesImpl.java	2008/03/03 11:34:17	1.2
@@ -69,7 +69,7 @@
 	result.set_SequenceString (onlyLength ? "" : buf.toString());
 	result.set_Length (new MobyInteger (totalLength));
 
-	response.setData (result);
+	set_result (response, result);
     }
 
     /**************************************************************************


From senger at dev.open-bio.org  Mon Mar  3 06:34:17 2008
From: senger at dev.open-bio.org (Martin Senger)
Date: Mon, 3 Mar 2008 06:34:17 -0500
Subject: [MOBY-guts] biomoby commit
Message-ID: <200803031134.m23BYHoc003431@dev.open-bio.org>


senger
Mon Mar  3 06:34:17 EST 2008
Update of /home/repository/moby/moby-live/Java/src/test/junit-resources
In directory dev.open-bio.org:/tmp/cvs-serv3170/src/test/junit-resources

Added Files:
	ConcatSequenceSet-input.xml 
Log Message:
* more work on junit testing and its infrastructure
* removing some compiler warnings from generated data types
* better use of caching in skeleton generator

moby-live/Java/src/test/junit-resources ConcatSequenceSet-input.xml,NONE,1.1

From senger at dev.open-bio.org  Mon Mar  3 06:34:17 2008
From: senger at dev.open-bio.org (Martin Senger)
Date: Mon, 3 Mar 2008 06:34:17 -0500
Subject: [MOBY-guts] biomoby commit
Message-ID: <200803031134.m23BYHjA003321@dev.open-bio.org>


senger
Mon Mar  3 06:34:17 EST 2008
Update of /home/repository/moby/moby-live/Java/src/main/org/biomoby/service/generator
In directory dev.open-bio.org:/tmp/cvs-serv3170/src/main/org/biomoby/service/generator

Modified Files:
	DataTypesGenerator.java Generator.java ServicesGenerator.java 
Log Message:
* more work on junit testing and its infrastructure
* removing some compiler warnings from generated data types
* better use of caching in skeleton generator

moby-live/Java/src/main/org/biomoby/service/generator DataTypesGenerator.java,1.6,1.7 Generator.java,1.5,1.6 ServicesGenerator.java,1.7,1.8
===================================================================
RCS file: /home/repository/moby/moby-live/Java/src/main/org/biomoby/service/generator/DataTypesGenerator.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/service/generator/DataTypesGenerator.java	2008/03/02 12:45:26	1.6
+++ /home/repository/moby/moby-live/Java/src/main/org/biomoby/service/generator/DataTypesGenerator.java	2008/03/03 11:34:17	1.7
@@ -18,6 +18,8 @@
 import org.biomoby.client.FilterDataTypes;
 import org.biomoby.client.Graphviz;
 
+import org.apache.commons.lang.BooleanUtils;
+
 import java.util.Properties;
 import java.util.Map;
 import java.util.HashMap;
@@ -171,7 +173,7 @@
     public void generate (Properties props)
 	throws MobyException {
 
-	verbose = isTrue (props.get (GPROP_VERBOSE));
+	verbose = BooleanUtils.toBoolean (props.getProperty (GPROP_VERBOSE));
 
 	Pattern pattern = null;
 	String filter = props.getProperty (GPROP_FILTER);
@@ -245,7 +247,7 @@
 	throws MobyException {
 
 	String dataTypeName = Utils.pureName (dataType.getName());
-	if (isTrue (props.get (GPROP_NOGEN))) {
+	if (BooleanUtils.toBoolean (props.getProperty (GPROP_NOGEN))) {
 	    System.out.println (dataTypeName);
 	    return;
 	}
@@ -459,7 +461,8 @@
 				   MobyDataType[] allDataTypes,
 				   StringBuffer spaceForImageMap) {
 
-	if (isTrue (props.get (GPROP_NOGRAPHS))) return false;
+	if (BooleanUtils.toBoolean (props.getProperty (GPROP_NOGRAPHS)))
+	    return false;
 
 	MobyDataType[] subTree = FilterDataTypes.getSubTree (dataType,
 							     allDataTypes);

===================================================================
RCS file: /home/repository/moby/moby-live/Java/src/main/org/biomoby/service/generator/Generator.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/service/generator/Generator.java	2008/03/02 12:45:26	1.5
+++ /home/repository/moby/moby-live/Java/src/main/org/biomoby/service/generator/Generator.java	2008/03/03 11:34:17	1.6
@@ -17,6 +17,8 @@
 import org.biomoby.shared.Utils;
 import org.biomoby.client.CentralDigestCachedImpl;
 
+import org.apache.commons.lang.BooleanUtils;
+
 import java.util.Properties;
 import java.util.Map;
 import java.util.regex.Pattern;
@@ -220,13 +222,6 @@
     }
 
     /*************************************************************************
-     * Read a boolean property...
-     *************************************************************************/
-    protected static boolean isTrue (Object value) {
-	return new Boolean ((String)value).booleanValue();
-    }
-
-    /*************************************************************************
      * Format who generated this...
      *************************************************************************/
     protected static String getSignature() {
@@ -293,7 +288,8 @@
      *************************************************************************/
     protected void makeDirForGraphs (File outputDir, Properties props) {
 
-	if (isTrue (props.get (GPROP_NOGRAPHS))) return;
+	if (BooleanUtils.toBoolean (props.getProperty (GPROP_NOGRAPHS)))
+	    return;
 
 	File graphDir = new File (outputDir, "doc-files");
 	if (! graphDir.exists()) {

===================================================================
RCS file: /home/repository/moby/moby-live/Java/src/main/org/biomoby/service/generator/ServicesGenerator.java,v
retrieving revision 1.7
retrieving revision 1.8
diff -u -r1.7 -r1.8
--- /home/repository/moby/moby-live/Java/src/main/org/biomoby/service/generator/ServicesGenerator.java	2008/03/02 12:45:26	1.7
+++ /home/repository/moby/moby-live/Java/src/main/org/biomoby/service/generator/ServicesGenerator.java	2008/03/03 11:34:17	1.8
@@ -27,6 +27,7 @@
 
 import org.tulsoft.tools.servlets.Html;
 import org.apache.commons.lang.StringUtils;
+import org.apache.commons.lang.BooleanUtils;
 
 import java.util.Properties;
 import java.util.Iterator;
@@ -192,7 +193,7 @@
     public void generate (Properties props)
 	throws MobyException {
 
-	verbose = isTrue (props.get (GPROP_VERBOSE));
+	verbose = BooleanUtils.toBoolean (props.getProperty (GPROP_VERBOSE));
 
 	// compile patterns for filtering by service and authority names
 	Pattern wantedService = null;
@@ -225,7 +226,8 @@
 	// conditionally, read all data types (also from a registry)
 	MobyDataType[] allDataTypes = null;
 	MobyService[] allServices = null;
-	if (! isTrue (props.get (GPROP_NOGRAPHS))) {
+	if (worker.isUsingCache() ||
+	    ! BooleanUtils.toBoolean (props.getProperty (GPROP_NOGRAPHS))) {
 	    if (verbose)
 		System.out.println ("Reading data type definitions...");
 	    allDataTypes = worker.getDataTypes();
@@ -277,7 +279,7 @@
 	    return;
 	}
 
-	if (isTrue (props.get (GPROP_NOGEN))) {
+	if (BooleanUtils.toBoolean (props.getProperty (GPROP_NOGEN))) {
 	    System.out.println (service.toShortString());
 	    return;
 	}
@@ -569,9 +571,9 @@
     /**************************************************************************
      * Return services that match 'patternService'. You can take an
      * advantage of already collected all services in 'allServices' if
-     * it is not null (it is null if graphs are not required,
-     * BTW). If it is null, however, do a normal way: go to a registry
-     * using given 'worker'.
+     * it is not null (it is null if a local cache is not used, or if
+     * graphs are not required). If it is null, however, do a normal
+     * way: go to a registry using given 'worker'.
      *
      * Note that 'patternService' has filled only service and
      * authority name (and both are guaranteed not to be null), so
@@ -581,8 +583,8 @@
 					 CentralCached worker,
 					 MobyService[] allServices)
 	throws MobyException {
-	if (allServices == null)
-	    return worker.findService (patternService);
+ 	if (allServices == null)
+ 	    return worker.findService (patternService);
 	Vector<MobyService> v = new Vector<MobyService>();
 	String name = patternService.getName();
 	String auth = patternService.getAuthority();
@@ -612,7 +614,10 @@
 				   MobyService[] allServices,
 				   MobyDataType[] allDataTypes) {
 
-	if (isTrue (props.get (GPROP_NOGRAPHS))) return false;
+	if (BooleanUtils.toBoolean (props.getProperty (GPROP_NOGRAPHS)))
+	    return false;
+	if (allServices == null || allDataTypes == null)
+	    return false;
 
 	ServicesEdge[] edges
 	    = ServiceConnections.build (allDataTypes, allServices);


From senger at dev.open-bio.org  Mon Mar  3 06:34:17 2008
From: senger at dev.open-bio.org (Martin Senger)
Date: Mon, 3 Mar 2008 06:34:17 -0500
Subject: [MOBY-guts] biomoby commit
Message-ID: <200803031134.m23BYHf2003455@dev.open-bio.org>


senger
Mon Mar  3 06:34:17 EST 2008
Update of /home/repository/moby/moby-live/Java/xmls
In directory dev.open-bio.org:/tmp/cvs-serv3170/xmls

Modified Files:
	junit.xml 
Log Message:
* more work on junit testing and its infrastructure
* removing some compiler warnings from generated data types
* better use of caching in skeleton generator

moby-live/Java/xmls junit.xml,1.3,1.4
===================================================================
RCS file: /home/repository/moby/moby-live/Java/xmls/junit.xml,v
retrieving revision 1.3
retrieving revision 1.4
diff -u -r1.3 -r1.4
--- /home/repository/moby/moby-live/Java/xmls/junit.xml	2008/03/02 12:45:27	1.3
+++ /home/repository/moby/moby-live/Java/xmls/junit.xml	2008/03/03 11:34:17	1.4
@@ -15,7 +15,8 @@
 <!-- The main entry point to junit testing. If tests are successful,    -->
 <!-- it does nothing. It only reports when a failure occured.           -->
 <!-- ================================================================== -->
-<target name="test-junit" if="test.failure" depends="do-junit,do-junit-2"
+<target name="test-junit" if="test.failure"
+  depends="samples,compile-tests,do-junit,do-junit-2"
   description="Run the junit test cases">
   <fail message="There were test failures." />
 </target>
@@ -34,6 +35,7 @@
 </target>
   
 <!-- this is the core: here is the testing done -->
+<!-- [ maintained by Paul Gordon ]              -->
 <target name="do-junit" if="junit.is.present" depends="junit-present">
 
   <junit
@@ -73,7 +75,11 @@
 
 <!-- this is the core: here is the testing done -->
 <!-- (put here only relatively fast tests)      -->
-<target name="do-junit-2" if="junit.is.present" depends="junit-present,compile-tests">
+<!-- [ maintained by Martin Senger ]            -->
+<target name="do-junit-2" if="junit.is.present" depends="junit-present,samples,dojunit2">
+</target>
+
+<target name="dojunit2"  if="junit.is.present" depends="compile-tests">
 
   <junit
     printsummary="yes"
@@ -85,6 +91,9 @@
       <path refid="dependency.classpath"/>
       <pathelement path="${classes.datatypes}"/>
       <pathelement path="${build.test}"/>
+      <pathelement path="${classes.datatypes}"/>
+      <pathelement path="${classes.skeletons}"/>
+      <pathelement path="${classes.samples}"/>
       <pathelement path="${junit.resources}"/>
     </classpath>
     <jvmarg value="-Dlog4j.configuration=file:${log4j.configuration}"/>
@@ -92,6 +101,7 @@
     <batchtest todir="${test.report.dir}">
       <fileset dir="${build.test}">
         <include name="**/MobyParserTest.*"/>
+        <include name="**/ServicesTest.*"/>
       </fileset>
       <!--      <fileset dir="${build.test}" includes="**/*Test.*" /> -->
     </batchtest>


From senger at dev.open-bio.org  Mon Mar  3 06:35:07 2008
From: senger at dev.open-bio.org (Martin Senger)
Date: Mon, 3 Mar 2008 06:35:07 -0500
Subject: [MOBY-guts] biomoby commit
Message-ID: <200803031135.m23BZ7qc003550@dev.open-bio.org>


senger
Mon Mar  3 06:35:07 EST 2008
Update of /home/repository/moby/moby-live/Java/src/test/java/org/biomoby/service
In directory dev.open-bio.org:/tmp/cvs-serv3535/src/test/java/org/biomoby/service

Added Files:
	ServicesTest.java 
Log Message:

moby-live/Java/src/test/java/org/biomoby/service ServicesTest.java,NONE,1.1

From senger at dev.open-bio.org  Mon Mar  3 06:54:28 2008
From: senger at dev.open-bio.org (Martin Senger)
Date: Mon, 3 Mar 2008 06:54:28 -0500
Subject: [MOBY-guts] biomoby commit
Message-ID: <200803031154.m23BsS3q003591@dev.open-bio.org>


senger
Mon Mar  3 06:54:28 EST 2008
Update of /home/repository/moby/moby-live/Java/src/main/org/biomoby/client
In directory dev.open-bio.org:/tmp/cvs-serv3572/src/main/org/biomoby/client

Modified Files:
	CentralImpl.java 
Log Message:
Fixing deprecation warnings

moby-live/Java/src/main/org/biomoby/client CentralImpl.java,1.54,1.55
===================================================================
RCS file: /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/CentralImpl.java,v
retrieving revision 1.54
retrieving revision 1.55
diff -u -r1.54 -r1.55
--- /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/CentralImpl.java	2008/03/02 12:45:25	1.54
+++ /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/CentralImpl.java	2008/03/03 11:54:28	1.55
@@ -952,6 +952,8 @@
 
     /**************************************************************************
      *
+     * @deprecated Replaced by {@link #getFullNamespaces} that gives
+     * more information for the same price. <p>
      *************************************************************************/
     public Map getNamespaces()
 	throws MobyException {


From senger at dev.open-bio.org  Mon Mar  3 06:54:28 2008
From: senger at dev.open-bio.org (Martin Senger)
Date: Mon, 3 Mar 2008 06:54:28 -0500
Subject: [MOBY-guts] biomoby commit
Message-ID: <200803031154.m23BsSYK003611@dev.open-bio.org>


senger
Mon Mar  3 06:54:28 EST 2008
Update of /home/repository/moby/moby-live/Java/src/main/org/biomoby/registry/Central
In directory dev.open-bio.org:/tmp/cvs-serv3572/src/main/org/biomoby/registry/Central

Modified Files:
	RegistryImpl.java 
Log Message:
Fixing deprecation warnings

moby-live/Java/src/main/org/biomoby/registry/Central RegistryImpl.java,1.3,1.4
===================================================================
RCS file: /home/repository/moby/moby-live/Java/src/main/org/biomoby/registry/Central/RegistryImpl.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/registry/Central/RegistryImpl.java	2006/04/20 15:17:43	1.3
+++ /home/repository/moby/moby-live/Java/src/main/org/biomoby/registry/Central/RegistryImpl.java	2008/03/03 11:54:28	1.4
@@ -83,8 +83,9 @@
 		return null;
 	}
 
-	/* (non-Javadoc)
+         /**
 	 * @see org.biomoby.registry.Central.Registry#deregisterService(java.lang.String)
+	 * @deprecated
 	 */
 	public String deregisterService(String deregistrationObject) {
 		Document doc = null;


From senger at dev.open-bio.org  Mon Mar  3 06:54:28 2008
From: senger at dev.open-bio.org (Martin Senger)
Date: Mon, 3 Mar 2008 06:54:28 -0500
Subject: [MOBY-guts] biomoby commit
Message-ID: <200803031154.m23BsSCw003631@dev.open-bio.org>


senger
Mon Mar  3 06:54:28 EST 2008
Update of /home/repository/moby/moby-live/Java/src/main/org/biomoby/shared
In directory dev.open-bio.org:/tmp/cvs-serv3572/src/main/org/biomoby/shared

Modified Files:
	MobySecondaryData.java 
Log Message:
Fixing deprecation warnings

moby-live/Java/src/main/org/biomoby/shared MobySecondaryData.java,1.11,1.12
===================================================================
RCS file: /home/repository/moby/moby-live/Java/src/main/org/biomoby/shared/MobySecondaryData.java,v
retrieving revision 1.11
retrieving revision 1.12
diff -u -r1.11 -r1.12
--- /home/repository/moby/moby-live/Java/src/main/org/biomoby/shared/MobySecondaryData.java	2008/01/07 22:11:36	1.11
+++ /home/repository/moby/moby-live/Java/src/main/org/biomoby/shared/MobySecondaryData.java	2008/03/03 11:54:28	1.12
@@ -136,9 +136,6 @@
 	defaultValue = (value == null ? "" : value);
     }
 
-    /**
-     * @deprecated Use {@link #getMinValue} instead.
-     */
     public int getMinimumValue() {
 	try {
 	    return Integer.valueOf (minimumValue).intValue();
@@ -162,9 +159,6 @@
 	minimumValue = (value == null ? "" : value);
     }
 
-    /**
-     * @deprecated Use {@link #getMaxValue} instead.
-     */
     public int getMaximumValue() {
 	try {
 	    return Integer.valueOf (maximumValue).intValue();


From senger at dev.open-bio.org  Mon Mar  3 06:54:28 2008
From: senger at dev.open-bio.org (Martin Senger)
Date: Mon, 3 Mar 2008 06:54:28 -0500
Subject: [MOBY-guts] biomoby commit
Message-ID: <200803031154.m23BsS4k003655@dev.open-bio.org>


senger
Mon Mar  3 06:54:28 EST 2008
Update of /home/repository/moby/moby-live/Java/src/main/org/biomoby/shared/schema
In directory dev.open-bio.org:/tmp/cvs-serv3572/src/main/org/biomoby/shared/schema

Modified Files:
	MainGUI.java 
Log Message:
Fixing deprecation warnings

moby-live/Java/src/main/org/biomoby/shared/schema MainGUI.java,1.2,1.3
===================================================================
RCS file: /home/repository/moby/moby-live/Java/src/main/org/biomoby/shared/schema/MainGUI.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/schema/MainGUI.java	2005/09/06 21:29:50	1.2
+++ /home/repository/moby/moby-live/Java/src/main/org/biomoby/shared/schema/MainGUI.java	2008/03/03 11:54:28	1.3
@@ -26,7 +26,7 @@
 		
 		
 		frame.addWindowListener(new GenericWindowListener());
-		frame.show();
+		frame.setVisible (true);
 	}
 
 }


From senger at dev.open-bio.org  Mon Mar  3 09:11:08 2008
From: senger at dev.open-bio.org (Martin Senger)
Date: Mon, 3 Mar 2008 09:11:08 -0500
Subject: [MOBY-guts] biomoby commit
Message-ID: <200803031411.m23EB8nL004089@dev.open-bio.org>


senger
Mon Mar  3 09:11:08 EST 2008
Update of /home/repository/moby/moby-live/Java/src/webapps
In directory dev.open-bio.org:/tmp/cvs-serv4034/src/webapps

Modified Files:
	remote.deploy.build.xml.template 
Log Message:
Remote deployment scripts fixed.

moby-live/Java/src/webapps remote.deploy.build.xml.template,1.4,1.5
===================================================================
RCS file: /home/repository/moby/moby-live/Java/src/webapps/remote.deploy.build.xml.template,v
retrieving revision 1.4
retrieving revision 1.5
diff -u -r1.4 -r1.5
--- /home/repository/moby/moby-live/Java/src/webapps/remote.deploy.build.xml.template	2008/02/21 13:19:34	1.4
+++ /home/repository/moby/moby-live/Java/src/webapps/remote.deploy.build.xml.template	2008/03/03 14:11:08	1.5
@@ -18,6 +18,7 @@
    <property name="wsdd.undeploy.dir"  location="${project.home}/undeploy-wsdd"/>
    <property name="lib.dir"            location="${project.home}/lib"/>
    <property name="lib.dir.2"          location="${project.home}/lib2"/>
+   <property name="classes"            location="${project.home}/classes"/>
 
    <!-- Tomcat/Axis/servlets related properties -->
    <property name="tomcat.home"        value="@TOMCAT_HOME@"/>
@@ -153,12 +154,17 @@
        <fileset dir="${lib.dir.2}" includes="*.jar"/>
      </foreach>
 
-     <!-- copy jar files to Tomcat/Axis -->
+     <!-- copy jar files to Tomcat/Axis - lib directory -->
      <copy todir="${deploy.axis.dir}/lib">
        <fileset dir="${lib.dir}"/>
        <fileset dir="${lib.dir.2}"/>
      </copy>
 
+     <!-- copy other files to Tomcat/Axis - classes directory -->
+     <copy todir="${deploy.axis.dir}/classes">
+       <fileset dir="${classes}"/>
+     </copy>
+
    </target>
 
    <!-- parameter: ${jarfile.name} -->


From senger at dev.open-bio.org  Mon Mar  3 09:11:08 2008
From: senger at dev.open-bio.org (Martin Senger)
Date: Mon, 3 Mar 2008 09:11:08 -0500
Subject: [MOBY-guts] biomoby commit
Message-ID: <200803031411.m23EB8fG004071@dev.open-bio.org>


senger
Mon Mar  3 09:11:08 EST 2008
Update of /home/repository/moby/moby-live/Java/src/samples/org/jmoby/tutorial/service
In directory dev.open-bio.org:/tmp/cvs-serv4034/src/samples/org/jmoby/tutorial/service

Modified Files:
	TestServiceNotesImpl.java 
Log Message:
Remote deployment scripts fixed.

moby-live/Java/src/samples/org/jmoby/tutorial/service TestServiceNotesImpl.java,1.3,1.4
===================================================================
RCS file: /home/repository/moby/moby-live/Java/src/samples/org/jmoby/tutorial/service/TestServiceNotesImpl.java,v
retrieving revision 1.3
retrieving revision 1.4
diff -u -r1.3 -r1.4
--- /home/repository/moby/moby-live/Java/src/samples/org/jmoby/tutorial/service/TestServiceNotesImpl.java	2007/05/29 03:51:46	1.3
+++ /home/repository/moby/moby-live/Java/src/samples/org/jmoby/tutorial/service/TestServiceNotesImpl.java	2008/03/03 14:11:08	1.4
@@ -36,9 +36,11 @@
 			   MobyPackage outputContext)
 	throws MobyException {
 	MobyDateTime input = get_input_date (request);
-	String date = input.getValue();
-	outputContext.addException (ServiceException.info ("Input date was " + date),
-				    request);
+	if (input != null) {
+	    String date = input.getValue();
+	    outputContext.addException (ServiceException.info ("Input date was " + date),
+					request);
+	}
 
 	StringBuilder buf = new StringBuilder();
 	buf.append ("This is a general service note.\n");


From senger at dev.open-bio.org  Mon Mar  3 09:11:08 2008
From: senger at dev.open-bio.org (Martin Senger)
Date: Mon, 3 Mar 2008 09:11:08 -0500
Subject: [MOBY-guts] biomoby commit
Message-ID: <200803031411.m23EB8cb004111@dev.open-bio.org>


senger
Mon Mar  3 09:11:08 EST 2008
Update of /home/repository/moby/moby-live/Java/xmls
In directory dev.open-bio.org:/tmp/cvs-serv4034/xmls

Modified Files:
	deployBuild.xml tomcat.xml 
Log Message:
Remote deployment scripts fixed.

moby-live/Java/xmls deployBuild.xml,1.5,1.6 tomcat.xml,1.1,1.2
===================================================================
RCS file: /home/repository/moby/moby-live/Java/xmls/deployBuild.xml,v
retrieving revision 1.5
retrieving revision 1.6
diff -u -r1.5 -r1.6
--- /home/repository/moby/moby-live/Java/xmls/deployBuild.xml	2008/02/21 13:19:35	1.5
+++ /home/repository/moby/moby-live/Java/xmls/deployBuild.xml	2008/03/03 14:11:08	1.6
@@ -97,7 +97,8 @@
   
   <!-- copy user-defined and remaining jar files to Tomcat/Axis -->
   <antcall target="-populate">
-    <param name="destination.axis.dir" location="${deploy.axis.dir}/lib"/>
+    <param name="destination.axis.lib.dir"     location="${deploy.axis.dir}/lib"/>
+    <param name="destination.axis.classes.dir" location="${deploy.axis.dir}/classes"/>
   </antcall>
   
 </target>
@@ -131,14 +132,15 @@
 <!-- Sub-target of tomcat-populate                                      -->
 <!-- (used both for local and remote deployment)                        -->
 <!-- ================================================================== -->
-<!-- parameter: ${destination.axis.dir} -->
+<!-- parameter: ${destination.axis.lib.dir} -->
+<!-- parameter: ${destination.axis.classes.dir} -->
 <target name="-populate" depends="initmaven">
   
   <!-- copy user-defined jar files to Tomcat/Axis -->
   <if>
     <isset property="users.lib.dir"/>
     <then>
-      <copy todir="${destination.axis.dir}">
+      <copy todir="${destination.axis.lib.dir}">
         <fileset dir="${users.lib.dir}" includes="*.jar"/>
       </copy>
     </then>
@@ -146,13 +148,13 @@
   <if>
     <isset property="users.lib.file"/>
     <then>
-      <copy todir="${destination.axis.dir}" file="${users.lib.file}"/>
+      <copy todir="${destination.axis.lib.dir}" file="${users.lib.file}"/>
     </then>
   </if>
   
   <!-- copy remaining jar files to Tomcat/Axis -->
   <copy
-    todir="${destination.axis.dir}"
+    todir="${destination.axis.lib.dir}"
     flatten="true">
     <fileset refid="runtime.dependency.fileset"/>
   </copy>
@@ -160,12 +162,12 @@
   <!--
   <delete>
     <fileset
-      dir="${destination.axis.dir}"
+      dir="${destination.axis.lib.dir}"
       excludes="alltools2*,jdom*,commons-lang*,*xerces*"/>
   </delete>
   -->
   <copy
-    todir="${destination.axis.dir}">
+    todir="${destination.axis.lib.dir}">
     <fileset dir="${build.lib}" includes="*.jar"/>
   </copy>
   
@@ -176,7 +178,7 @@
     location="${src.config}/log4j.properties.template"/>
   <copy
     file="${server.log4j.configuration}"
-    tofile="${deploy.axis.dir}/classes/log4j.properties">
+    tofile="${destination.axis.classes.dir}/log4j.properties">
     <filterset>
       <filter token="LOGDIR" value="${server.log.dir}"/>
     </filterset>
@@ -318,7 +320,8 @@
   
   <!-- add user-defined and other jar files (but not those already in lib2) -->
   <antcall target="-populate">
-    <param name="destination.axis.dir" location="${result.dir}/lib"/>
+    <param name="destination.axis.lib.dir"     location="${result.dir}/lib"/>
+    <param name="destination.axis.classes.dir" location="${result.dir}/classes"/>
   </antcall>
   <delete quiet="true">
     <fileset dir="${result.dir}/lib" includes="${datatypes.jar},${skeletons.jar}"/>

===================================================================
RCS file: /home/repository/moby/moby-live/Java/xmls/tomcat.xml,v
retrieving revision 1.1
retrieving revision 1.2
diff -u -r1.1 -r1.2
--- /home/repository/moby/moby-live/Java/xmls/tomcat.xml	2008/02/14 06:13:37	1.1
+++ /home/repository/moby/moby-live/Java/xmls/tomcat.xml	2008/03/03 14:11:08	1.2
@@ -28,6 +28,10 @@
     <isset property="tomcat.home"/>
   </condition>
 
+  <!-- properties set from other properties that were set in conditions above -->
+  <property name="deploy.axis.dir"
+    location="${real.catalina.home}/${tomcat.webapps}/${axis.relative.path}/WEB-INF"/>
+    
   <!-- check that we know about Tomcat -->
   <fail unless="real.catalina.home">
 '


From senger at dev.open-bio.org  Mon Mar  3 09:11:08 2008
From: senger at dev.open-bio.org (Martin Senger)
Date: Mon, 3 Mar 2008 09:11:08 -0500
Subject: [MOBY-guts] biomoby commit
Message-ID: <200803031411.m23EB8J6004053@dev.open-bio.org>


senger
Mon Mar  3 09:11:08 EST 2008
Update of /home/repository/moby/moby-live/Java
In directory dev.open-bio.org:/tmp/cvs-serv4034

Modified Files:
	build.xml 
Log Message:
Remote deployment scripts fixed.

moby-live/Java build.xml,1.71,1.72
===================================================================
RCS file: /home/repository/moby/moby-live/Java/build.xml,v
retrieving revision 1.71
retrieving revision 1.72
diff -u -r1.71 -r1.72
--- /home/repository/moby/moby-live/Java/build.xml	2008/03/03 11:34:16	1.71
+++ /home/repository/moby/moby-live/Java/build.xml	2008/03/03 14:11:08	1.72
@@ -222,10 +222,6 @@
       <filter token="LOG4J" value="${log4j.value}"/>
     </filterset>
     
-    <!-- properties set from other properties that were set in conditions above -->
-    <property name="deploy.axis.dir"
-      location="${real.catalina.home}/${tomcat.webapps}/${axis.relative.path}/WEB-INF"/>
-    
     <!-- contributed tasks -->
     <taskdef resource="net/sf/antcontrib/antlib.xml">
       <classpath refid="dependency.classpath"/>


From kawas at dev.open-bio.org  Wed Mar  5 12:29:18 2008
From: kawas at dev.open-bio.org (Eddie Kawas)
Date: Wed, 5 Mar 2008 12:29:18 -0500
Subject: [MOBY-guts] biomoby commit
Message-ID: <200803051729.m25HTIFd016018@dev.open-bio.org>


kawas
Wed Mar  5 12:29:17 EST 2008
Update of /home/repository/moby/moby-live/Perl/MOBY-Client/t
In directory dev.open-bio.org:/tmp/cvs-serv15985/Perl/MOBY-Client/t

Removed Files:
	pod.t pod-coverage.t 
Log Message:
removed the pod tests because they cause fails on cpan
moby-live/Perl/MOBY-Client/t pod.t,1.1,NONE pod-coverage.t,1.1,NONE
rcsdiff: /home/repository/moby/moby-live/Perl/MOBY-Client/t/RCS/pod.t,v: No such file or directory

rcsdiff: /home/repository/moby/moby-live/Perl/MOBY-Client/t/RCS/pod-coverage.t,v: No such file or directory


From kawas at dev.open-bio.org  Wed Mar  5 12:30:00 2008
From: kawas at dev.open-bio.org (Eddie Kawas)
Date: Wed, 5 Mar 2008 12:30:00 -0500
Subject: [MOBY-guts] biomoby commit
Message-ID: <200803051730.m25HU0S9016058@dev.open-bio.org>


kawas
Wed Mar  5 12:29:59 EST 2008
Update of /home/repository/moby/moby-live/Perl/MOBY-Client
In directory dev.open-bio.org:/tmp/cvs-serv16023/Perl/MOBY-Client

Modified Files:
	MANIFEST 
Log Message:
removed the pod tests because they cause fails on cpan
moby-live/Perl/MOBY-Client MANIFEST,1.2,1.3
===================================================================
RCS file: /home/repository/moby/moby-live/Perl/MOBY-Client/MANIFEST,v
retrieving revision 1.2
retrieving revision 1.3
diff -u -r1.2 -r1.3
--- /home/repository/moby/moby-live/Perl/MOBY-Client/MANIFEST	2008/02/22 16:42:05	1.2
+++ /home/repository/moby/moby-live/Perl/MOBY-Client/MANIFEST	2008/03/05 17:29:59	1.3
@@ -54,5 +54,4 @@
 t/Client-Service.t
 t/Client-ServiceInstance.t
 t/Client-SimpleArticle.t
-t/pod-coverage.t
-t/pod.t
+


From kawas at dev.open-bio.org  Wed Mar  5 12:38:19 2008
From: kawas at dev.open-bio.org (Eddie Kawas)
Date: Wed, 5 Mar 2008 12:38:19 -0500
Subject: [MOBY-guts] biomoby commit
Message-ID: <200803051738.m25HcJlJ016245@dev.open-bio.org>


kawas
Wed Mar  5 12:38:19 EST 2008
Update of /home/repository/moby/moby-live/Perl/MOBY-Server/lib/MOBY/RDF
In directory dev.open-bio.org:/tmp/cvs-serv16210/Perl/MOBY-Server/lib/MOBY/RDF

Modified Files:
	Utils.pm 
Log Message:
helper method for downloading from a url
moby-live/Perl/MOBY-Server/lib/MOBY/RDF Utils.pm,1.2,1.3
===================================================================
RCS file: /home/repository/moby/moby-live/Perl/MOBY-Server/lib/MOBY/RDF/Utils.pm,v
retrieving revision 1.2
retrieving revision 1.3
diff -u -r1.2 -r1.3
--- /home/repository/moby/moby-live/Perl/MOBY-Server/lib/MOBY/RDF/Utils.pm	2008/02/21 17:15:41	1.2
+++ /home/repository/moby/moby-live/Perl/MOBY-Server/lib/MOBY/RDF/Utils.pm	2008/03/05 17:38:19	1.3
@@ -91,19 +91,19 @@
 
 sub prettyPrintXML {
 	my ( $self, $hash ) = @_;
-	my $xml        = $hash->{xml};
-	unless ( $xml ) {
+	my $xml = $hash->{xml};
+	unless ($xml) {
 		$xml = <<END;
 	<rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"></rdf:RDF>
 END
 	}
-	
+
 	eval "require XML::LibXSLT";
 	if ($@) {
-		my $parser     = XML::LibXML->new();
-		my $source     = $parser->parse_string($xml);
+		my $parser = XML::LibXML->new();
+		my $source = $parser->parse_string($xml);
 		$xml = $source->toString(0);
-		return $xml;    
+		return $xml;
 	} else {
 		my $parser     = XML::LibXML->new();
 		my $xslt       = XML::LibXSLT->new();
@@ -112,9 +112,42 @@
 		my $stylesheet = $xslt->parse_stylesheet($style_doc);
 		my $results    = $stylesheet->transform($source);
 		$xml = $stylesheet->output_string($results);
-		return  "<?xml version=\"1.0\" encoding=\"UTF-8\"?>". $xml;
+		return "<?xml version=\"1.0\" encoding=\"UTF-8\"?>" . $xml;
 	}
 }
 
+=head2 getHttpRequestByURL
+
+returns a scalar of text obtained from the url or dies if there was no success
+
+=cut
+
+sub getHttpRequestByURL {
+	my ( $self, $url ) = @_;
+	my $ua = LWP::UserAgent->new;
+	$ua->agent( "pMOBY/Central/1.0");
+
+	my $req =
+	  HTTP::Request->new( GET =>
+		  $url );
+
+	# accept gzip encoding
+	$req->header( 'Accept-Encoding' => 'gzip' );
+
+	# send request
+	my $res = $ua->request($req);
+
+	# check the outcome
+	if ( $res->is_success ) {
+		if ( $res->header('content-encoding') and $res->header('content-encoding') eq 'gzip' ) {
+			return $res->decoded_content;
+		} else {
+			return $res->content;
+		}
+	} else {
+		die "Error getting data from URL:\n\t" . $res->status_line;
+	}    
+}
+
 1;
 __END__


From kawas at dev.open-bio.org  Wed Mar  5 12:39:44 2008
From: kawas at dev.open-bio.org (Eddie Kawas)
Date: Wed, 5 Mar 2008 12:39:44 -0500
Subject: [MOBY-guts] biomoby commit
Message-ID: <200803051739.m25HdiB9016322@dev.open-bio.org>


kawas
Wed Mar  5 12:39:43 EST 2008
Update of /home/repository/moby/moby-live/Perl/MOBY-Server/lib/MOBY/RDF
In directory dev.open-bio.org:/tmp/cvs-serv16286/Perl/MOBY-Server/lib/MOBY/RDF

Modified Files:
	Utils.pm 
Log Message:
added some 'use' statements, but i am not so sure that they are necessary
moby-live/Perl/MOBY-Server/lib/MOBY/RDF Utils.pm,1.3,1.4
===================================================================
RCS file: /home/repository/moby/moby-live/Perl/MOBY-Server/lib/MOBY/RDF/Utils.pm,v
retrieving revision 1.3
retrieving revision 1.4
diff -u -r1.3 -r1.4
--- /home/repository/moby/moby-live/Perl/MOBY-Server/lib/MOBY/RDF/Utils.pm	2008/03/05 17:38:19	1.3
+++ /home/repository/moby/moby-live/Perl/MOBY-Server/lib/MOBY/RDF/Utils.pm	2008/03/05 17:39:43	1.4
@@ -9,6 +9,8 @@
 package MOBY::RDF::Utils;
 
 use XML::LibXML;
+use LWP::UserAgent;
+use HTTP::Request;
 
 use strict;
 


From kawas at dev.open-bio.org  Wed Mar  5 12:42:06 2008
From: kawas at dev.open-bio.org (Eddie Kawas)
Date: Wed, 5 Mar 2008 12:42:06 -0500
Subject: [MOBY-guts] biomoby commit
Message-ID: <200803051742.m25Hg6X2016421@dev.open-bio.org>


kawas
Wed Mar  5 12:42:06 EST 2008
Update of /home/repository/moby/moby-live/Perl/MOBY-Server/lib/MOBY/RDF/Parsers
In directory dev.open-bio.org:/tmp/cvs-serv16386/Perl/MOBY-Server/lib/MOBY/RDF/Parsers

Log Message:
Directory /home/repository/moby/moby-live/Perl/MOBY-Server/lib/MOBY/RDF/Parsers added to the repository

moby-live/Perl/MOBY-Server/lib/MOBY/RDF/Parsers - New directory
rcsdiff: /home/repository/moby/moby-live/Perl/MOBY-Server/lib/MOBY/RDF/Parsers/RCS/-,v: No such file or directory

rcsdiff: /home/repository/moby/moby-live/Perl/MOBY-Server/lib/MOBY/RDF/Parsers/RCS/New,v: No such file or directory

rcsdiff: /home/repository/moby/moby-live/Perl/MOBY-Server/lib/MOBY/RDF/Parsers/RCS/directory,v: No such file or directory


From kawas at dev.open-bio.org  Wed Mar  5 12:42:09 2008
From: kawas at dev.open-bio.org (Eddie Kawas)
Date: Wed, 5 Mar 2008 12:42:09 -0500
Subject: [MOBY-guts] biomoby commit
Message-ID: <200803051742.m25Hg9RZ016475@dev.open-bio.org>


kawas
Wed Mar  5 12:42:08 EST 2008
Update of /home/repository/moby/moby-live/Perl/MOBY-Server/lib/MOBY/RDF/Parsers
In directory dev.open-bio.org:/tmp/cvs-serv16444/Perl/MOBY-Server/lib/MOBY/RDF/Parsers

Added Files:
	ServiceTypeParser.pm NamespaceParser.pm 
Log Message:
module converts the RDF representation of the ontology into a perl representation. These can be used in the following manner:

1. getResourceRefs
2. create namespaces/servicetypes from the resource ref

Items returned are very similar to those returned by MOBY::Client::Central
moby-live/Perl/MOBY-Server/lib/MOBY/RDF/Parsers ServiceTypeParser.pm,NONE,1.1 NamespaceParser.pm,NONE,1.1

From kawas at dev.open-bio.org  Wed Mar  5 12:43:11 2008
From: kawas at dev.open-bio.org (Eddie Kawas)
Date: Wed, 5 Mar 2008 12:43:11 -0500
Subject: [MOBY-guts] biomoby commit
Message-ID: <200803051743.m25HhBdG016547@dev.open-bio.org>


kawas
Wed Mar  5 12:43:11 EST 2008
Update of /home/repository/moby/moby-live/Perl/MOBY-Server/lib/MOBY/RDF/Parsers
In directory dev.open-bio.org:/tmp/cvs-serv16508/Perl/MOBY-Server/lib/MOBY/RDF/Parsers

Modified Files:
	ServiceTypeParser.pm NamespaceParser.pm 
Log Message:
removed unused 'use' statement.
moby-live/Perl/MOBY-Server/lib/MOBY/RDF/Parsers ServiceTypeParser.pm,1.1,1.2 NamespaceParser.pm,1.1,1.2
===================================================================
RCS file: /home/repository/moby/moby-live/Perl/MOBY-Server/lib/MOBY/RDF/Parsers/ServiceTypeParser.pm,v
retrieving revision 1.1
retrieving revision 1.2
diff -u -r1.1 -r1.2
--- /home/repository/moby/moby-live/Perl/MOBY-Server/lib/MOBY/RDF/Parsers/ServiceTypeParser.pm	2008/03/05 17:42:08	1.1
+++ /home/repository/moby/moby-live/Perl/MOBY-Server/lib/MOBY/RDF/Parsers/ServiceTypeParser.pm	2008/03/05 17:43:11	1.2
@@ -14,8 +14,6 @@
 use RDF::Core::Storage::Memory;
 use RDF::Core::Resource;
 
-use LWP::UserAgent;
-
 use MOBY::RDF::Utils;
 use MOBY::RDF::Predicates::DC_PROTEGE;
 use MOBY::RDF::Predicates::MOBY_PREDICATES;

===================================================================
RCS file: /home/repository/moby/moby-live/Perl/MOBY-Server/lib/MOBY/RDF/Parsers/NamespaceParser.pm,v
retrieving revision 1.1
retrieving revision 1.2
diff -u -r1.1 -r1.2
--- /home/repository/moby/moby-live/Perl/MOBY-Server/lib/MOBY/RDF/Parsers/NamespaceParser.pm	2008/03/05 17:42:08	1.1
+++ /home/repository/moby/moby-live/Perl/MOBY-Server/lib/MOBY/RDF/Parsers/NamespaceParser.pm	2008/03/05 17:43:11	1.2
@@ -14,8 +14,6 @@
 use RDF::Core::Storage::Memory;
 use RDF::Core::Resource;
 
-use LWP::UserAgent;
-
 use MOBY::RDF::Utils;
 use MOBY::RDF::Predicates::DC_PROTEGE;
 use MOBY::RDF::Predicates::MOBY_PREDICATES;


From kawas at dev.open-bio.org  Wed Mar  5 12:44:02 2008
From: kawas at dev.open-bio.org (Eddie Kawas)
Date: Wed, 5 Mar 2008 12:44:02 -0500
Subject: [MOBY-guts] biomoby commit
Message-ID: <200803051744.m25Hi20P016609@dev.open-bio.org>


kawas
Wed Mar  5 12:44:02 EST 2008
Update of /home/repository/moby/moby-live/Perl/MOBY-Client
In directory dev.open-bio.org:/tmp/cvs-serv16574/Perl/MOBY-Client

Modified Files:
	MANIFEST 
Log Message:
updated the manifest to include 2 new files
moby-live/Perl/MOBY-Client MANIFEST,1.3,1.4
===================================================================
RCS file: /home/repository/moby/moby-live/Perl/MOBY-Client/MANIFEST,v
retrieving revision 1.3
retrieving revision 1.4
diff -u -r1.3 -r1.4
--- /home/repository/moby/moby-live/Perl/MOBY-Client/MANIFEST	2008/03/05 17:29:59	1.3
+++ /home/repository/moby/moby-live/Perl/MOBY-Client/MANIFEST	2008/03/05 17:44:02	1.4
@@ -28,6 +28,8 @@
 lib/MOBY/Client/ServiceInstance.pm
 lib/MOBY/Client/SimpleArticle.pm
 lib/MOBY/Client/SimpleInput.pm
+lib/MOBY/RDF/Ontologies/Parsers/NamespaceParser.pm
+lib/MOBY/RDF/Ontologies/Parsers/ServiceTypeParser.pm
 lib/MOBY/CommonSubs.pm
 lib/MOBY/CrossReference.pm
 lib/MOBY/MobyXMLConstants.pm


From kawas at dev.open-bio.org  Wed Mar  5 12:44:40 2008
From: kawas at dev.open-bio.org (Eddie Kawas)
Date: Wed, 5 Mar 2008 12:44:40 -0500
Subject: [MOBY-guts] biomoby commit
Message-ID: <200803051744.m25HiecU016665@dev.open-bio.org>


kawas
Wed Mar  5 12:44:40 EST 2008
Update of /home/repository/moby/moby-live/Perl/MOBY-Client
In directory dev.open-bio.org:/tmp/cvs-serv16630/Perl/MOBY-Client

Modified Files:
	MANIFEST 
Log Message:

moby-live/Perl/MOBY-Client MANIFEST,1.4,1.5
===================================================================
RCS file: /home/repository/moby/moby-live/Perl/MOBY-Client/MANIFEST,v
retrieving revision 1.4
retrieving revision 1.5
diff -u -r1.4 -r1.5
--- /home/repository/moby/moby-live/Perl/MOBY-Client/MANIFEST	2008/03/05 17:44:02	1.4
+++ /home/repository/moby/moby-live/Perl/MOBY-Client/MANIFEST	2008/03/05 17:44:40	1.5
@@ -33,6 +33,7 @@
 lib/MOBY/CommonSubs.pm
 lib/MOBY/CrossReference.pm
 lib/MOBY/MobyXMLConstants.pm
+lib/MOBY/RDF/Utils.pm
 License
 Makefile.PL
 MANIFEST			This list of files


From kawas at dev.open-bio.org  Wed Mar  5 12:52:46 2008
From: kawas at dev.open-bio.org (Eddie Kawas)
Date: Wed, 5 Mar 2008 12:52:46 -0500
Subject: [MOBY-guts] biomoby commit
Message-ID: <200803051752.m25Hqkw3016907@dev.open-bio.org>


kawas
Wed Mar  5 12:52:46 EST 2008
Update of /home/repository/moby/moby-live/Perl/MOBY-Client
In directory dev.open-bio.org:/tmp/cvs-serv16872/Perl/MOBY-Client

Modified Files:
	populate_libs.pl 
Log Message:
added the new modules 'NamespaceParser, ServiceTypeParser, Utils'
moby-live/Perl/MOBY-Client populate_libs.pl,1.1,1.2
===================================================================
RCS file: /home/repository/moby/moby-live/Perl/MOBY-Client/populate_libs.pl,v
retrieving revision 1.1
retrieving revision 1.2
diff -u -r1.1 -r1.2
--- /home/repository/moby/moby-live/Perl/MOBY-Client/populate_libs.pl	2008/02/21 00:14:33	1.1
+++ /home/repository/moby/moby-live/Perl/MOBY-Client/populate_libs.pl	2008/03/05 17:52:46	1.2
@@ -12,6 +12,8 @@
 my @Async 		= qw ( LSAE.pm Service.pm SimpleServer.pm WSRF.pm );
 my @Client		= qw ( Central.pm CollectionArticle.pm OntologyServer.pm Registration.pm SecondaryArticle.pm Service.pm ServiceInstance.pm SimpleArticle.pm SimpleInput.pm );
 my @Exception 	= qw ( MobyException.pm MobyExceptionCodes.pm );
+my @RDF 		= qw ( Utils.pm );
+my @Parsers 	= qw ( ServiceTypeParser.pm NamespaceParser.pm );
 
 # current working directory ...
 my $dir = getcwd;
@@ -55,6 +57,18 @@
 	warn "couldn't copy file $file: $!\n" unless copy("$origin_directory/$subpath/$file","$destination_directory/$subpath/$file") == 1;
 }
 
+# copy the RDF files
+foreach my $file (@RDF) {
+	my $subpath = "MOBY/RDF";
+	warn "couldn't copy file $file: $!\n" unless copy("$origin_directory/$subpath/$file","$destination_directory/$subpath/$file") == 1;
+}
+
+# copy the Parsers files
+foreach my $file (@Parsers) {
+	my $subpath = "MOBY/RDF/Parsers";
+	warn "couldn't copy file $file: $!\n" unless copy("$origin_directory/$subpath/$file","$destination_directory/$subpath/$file") == 1;
+}
+
 
 # Directory Structure is:
 #
@@ -71,16 +85,23 @@
 #    ?       WSRF.pm
 #    ?
 #    +---Client
-#        ?   Central.pm
-#        ?   CollectionArticle.pm
-#        ?   OntologyServer.pm
-#        ?   Registration.pm
-#        ?   SecondaryArticle.pm
-#        ?   Service.pm
-#        ?   ServiceInstance.pm
-#        ?   SimpleArticle.pm
-#        ?   SimpleInput.pm
-#        ?
-#        +---Exception
-#                MobyException.pm
-#                MobyExceptionCodes.pm
+#    ?   ?   Central.pm
+#    ?   ?   CollectionArticle.pm
+#    ?   ?   OntologyServer.pm
+#    ?   ?   Registration.pm
+#    ?   ?   SecondaryArticle.pm
+#    ?   ?   Service.pm
+#    ?   ?   ServiceInstance.pm
+#    ?   ?   SimpleArticle.pm
+#    ?   ?   SimpleInput.pm
+#    ?   ?
+#    ?   +---Exception
+#    ?           MobyException.pm
+#    ?           MobyExceptionCodes.pm
+#    ?
+#    +---RDF
+#    ?   ?   Utils.pm
+#    ?   ?   
+#    ?   +---Parsers
+#    ?           ServiceTypeParser.pm
+#    ?           NamespaceParser.pm


From kawas at dev.open-bio.org  Wed Mar  5 12:59:58 2008
From: kawas at dev.open-bio.org (Eddie Kawas)
Date: Wed, 5 Mar 2008 12:59:58 -0500
Subject: [MOBY-guts] biomoby commit
Message-ID: <200803051759.m25Hxw3A017139@dev.open-bio.org>


kawas
Wed Mar  5 12:59:58 EST 2008
Update of /home/repository/moby/moby-live/Perl/MOBY-Client
In directory dev.open-bio.org:/tmp/cvs-serv17095/Perl/MOBY-Client

Modified Files:
	populate_libs.pl MANIFEST Makefile.PL 
Log Message:
added rdf::core to the makefile, updated the Manifest to include the predicate vocabs and added the vocabs to the populate libs script
moby-live/Perl/MOBY-Client populate_libs.pl,1.2,1.3 MANIFEST,1.5,1.6 Makefile.PL,1.3,1.4
===================================================================
RCS file: /home/repository/moby/moby-live/Perl/MOBY-Client/populate_libs.pl,v
retrieving revision 1.2
retrieving revision 1.3
diff -u -r1.2 -r1.3
--- /home/repository/moby/moby-live/Perl/MOBY-Client/populate_libs.pl	2008/03/05 17:52:46	1.2
+++ /home/repository/moby/moby-live/Perl/MOBY-Client/populate_libs.pl	2008/03/05 17:59:58	1.3
@@ -14,6 +14,7 @@
 my @Exception 	= qw ( MobyException.pm MobyExceptionCodes.pm );
 my @RDF 		= qw ( Utils.pm );
 my @Parsers 	= qw ( ServiceTypeParser.pm NamespaceParser.pm );
+my @predicates  = qw ( DC_PROTEGE.pm MOBY_PREDICATES.pm OMG_LSID.pm RDF.pm RDFS.pm FETA.pm OWL.pm );
 
 # current working directory ...
 my $dir = getcwd;
@@ -69,6 +70,11 @@
 	warn "couldn't copy file $file: $!\n" unless copy("$origin_directory/$subpath/$file","$destination_directory/$subpath/$file") == 1;
 }
 
+# copy the Predicates files
+foreach my $file (@predicates) {
+	my $subpath = "MOBY/RDF/Predicates";
+	warn "couldn't copy file $file: $!\n" unless copy("$origin_directory/$subpath/$file","$destination_directory/$subpath/$file") == 1;
+}
 
 # Directory Structure is:
 #
@@ -103,5 +109,14 @@
 #    ?   ?   Utils.pm
 #    ?   ?   
 #    ?   +---Parsers
-#    ?           ServiceTypeParser.pm
-#    ?           NamespaceParser.pm
+#    ?   ?       ServiceTypeParser.pm
+#    ?   ?       NamespaceParser.pm
+#    ?   ?
+#    ?   +---Predicates
+#    ?           DC_PROTEGE.pm
+#    ?           FETA.pm
+#    ?           MOBY_PREDICATES.pm
+#    ?           OMG_LSID.pm
+#    ?           OWL.pm
+#    ?           RDF.pm
+#    ?           RDFS.pm

===================================================================
RCS file: /home/repository/moby/moby-live/Perl/MOBY-Client/MANIFEST,v
retrieving revision 1.5
retrieving revision 1.6
diff -u -r1.5 -r1.6
--- /home/repository/moby/moby-live/Perl/MOBY-Client/MANIFEST	2008/03/05 17:44:40	1.5
+++ /home/repository/moby/moby-live/Perl/MOBY-Client/MANIFEST	2008/03/05 17:59:58	1.6
@@ -30,6 +30,13 @@
 lib/MOBY/Client/SimpleInput.pm
 lib/MOBY/RDF/Ontologies/Parsers/NamespaceParser.pm
 lib/MOBY/RDF/Ontologies/Parsers/ServiceTypeParser.pm
+lib/MOBY/RDF/Predicates/DC_PROTEGE.pm
+lib/MOBY/RDF/Predicates/FETA.pm
+lib/MOBY/RDF/Predicates/MOBY_PREDICATES.pm
+lib/MOBY/RDF/Predicates/OMG_LSID.pm
+lib/MOBY/RDF/Predicates/OWL.pm
+lib/MOBY/RDF/Predicates/RDF.pm
+lib/MOBY/RDF/Predicates/RDFS.pm
 lib/MOBY/CommonSubs.pm
 lib/MOBY/CrossReference.pm
 lib/MOBY/MobyXMLConstants.pm

===================================================================
RCS file: /home/repository/moby/moby-live/Perl/MOBY-Client/Makefile.PL,v
retrieving revision 1.3
retrieving revision 1.4
diff -u -r1.3 -r1.4
--- /home/repository/moby/moby-live/Perl/MOBY-Client/Makefile.PL	2008/02/22 17:38:24	1.3
+++ /home/repository/moby/moby-live/Perl/MOBY-Client/Makefile.PL	2008/03/05 17:59:58	1.4
@@ -19,6 +19,7 @@
 requires 'CGI'                   => 0;
 requires 'HTTP::Request::Common' => 0;
 requires 'URI::Escape'           => 0;
+requires 'RDF::Core'             => '0.51';
 
 # MOBY::CommonSubs depends
 requires 'HTML::Entities' => 0;


From kawas at dev.open-bio.org  Wed Mar  5 13:00:48 2008
From: kawas at dev.open-bio.org (Eddie Kawas)
Date: Wed, 5 Mar 2008 13:00:48 -0500
Subject: [MOBY-guts] biomoby commit
Message-ID: <200803051800.m25I0mbJ017253@dev.open-bio.org>


kawas
Wed Mar  5 13:00:48 EST 2008
Update of /home/repository/moby/moby-live/Perl/MOBY-Server
In directory dev.open-bio.org:/tmp/cvs-serv17218/Perl/MOBY-Server

Modified Files:
	MANIFEST 
Log Message:
updated the manifest to include 2 new files
moby-live/Perl/MOBY-Server MANIFEST,1.1,1.2
===================================================================
RCS file: /home/repository/moby/moby-live/Perl/MOBY-Server/MANIFEST,v
retrieving revision 1.1
retrieving revision 1.2
diff -u -r1.1 -r1.2
--- /home/repository/moby/moby-live/Perl/MOBY-Server/MANIFEST	2008/02/21 00:21:28	1.1
+++ /home/repository/moby/moby-live/Perl/MOBY-Server/MANIFEST	2008/03/05 18:00:48	1.2
@@ -55,6 +55,8 @@
 lib/MOBY/MOBYXSLT.pm
 lib/MOBY/mysql.pm
 lib/MOBY/OntologyServer.pm
+lib/MOBY/RDF/Ontologies/Parsers/NamespaceParser.pm
+lib/MOBY/RDF/Ontologies/Parsers/ServiceTypeParser.pm
 lib/MOBY/RDF/Ontologies/Cache/CacheUtils.pm
 lib/MOBY/RDF/Ontologies/Cache/NamespaceCache.pm
 lib/MOBY/RDF/Ontologies/Cache/ObjectCache.pm


From kawas at dev.open-bio.org  Wed Mar  5 13:22:00 2008
From: kawas at dev.open-bio.org (Eddie Kawas)
Date: Wed, 5 Mar 2008 13:22:00 -0500
Subject: [MOBY-guts] biomoby commit
Message-ID: <200803051822.m25IM0Tj017663@dev.open-bio.org>


kawas
Wed Mar  5 13:22:00 EST 2008
Update of /home/repository/moby/moby-live/Perl/MOBY-Client
In directory dev.open-bio.org:/tmp/cvs-serv17628/Perl/MOBY-Client

Modified Files:
	populate_libs.pl 
Log Message:
added the new directories to the script
moby-live/Perl/MOBY-Client populate_libs.pl,1.3,1.4
===================================================================
RCS file: /home/repository/moby/moby-live/Perl/MOBY-Client/populate_libs.pl,v
retrieving revision 1.3
retrieving revision 1.4
diff -u -r1.3 -r1.4
--- /home/repository/moby/moby-live/Perl/MOBY-Client/populate_libs.pl	2008/03/05 17:59:58	1.3
+++ /home/repository/moby/moby-live/Perl/MOBY-Client/populate_libs.pl	2008/03/05 18:22:00	1.4
@@ -25,7 +25,7 @@
 my $destination_directory 	= "$dir/lib";
 
 # directory structure for ../lib/
-my @main_dirs = qw( MOBY MOBY/Async MOBY/Client MOBY/Client/Exception);
+my @main_dirs = qw( MOBY MOBY/Async MOBY/Client MOBY/Client/Exception MOBY/RDF MOBY/RDF/Predicates MOBY/RDF/Parsers );
 
 #create main directories as needed ...
 foreach my $dir (@main_dirs) {


From kawas at dev.open-bio.org  Wed Mar  5 13:24:22 2008
From: kawas at dev.open-bio.org (Eddie Kawas)
Date: Wed, 5 Mar 2008 13:24:22 -0500
Subject: [MOBY-guts] biomoby commit
Message-ID: <200803051824.m25IOMdi017703@dev.open-bio.org>


kawas
Wed Mar  5 13:24:22 EST 2008
Update of /home/repository/moby/moby-live/Perl/MOBY-Client
In directory dev.open-bio.org:/tmp/cvs-serv17668/Perl/MOBY-Client

Modified Files:
	MANIFEST 
Log Message:

moby-live/Perl/MOBY-Client MANIFEST,1.6,1.7
===================================================================
RCS file: /home/repository/moby/moby-live/Perl/MOBY-Client/MANIFEST,v
retrieving revision 1.6
retrieving revision 1.7
diff -u -r1.6 -r1.7
--- /home/repository/moby/moby-live/Perl/MOBY-Client/MANIFEST	2008/03/05 17:59:58	1.6
+++ /home/repository/moby/moby-live/Perl/MOBY-Client/MANIFEST	2008/03/05 18:24:22	1.7
@@ -28,8 +28,8 @@
 lib/MOBY/Client/ServiceInstance.pm
 lib/MOBY/Client/SimpleArticle.pm
 lib/MOBY/Client/SimpleInput.pm
-lib/MOBY/RDF/Ontologies/Parsers/NamespaceParser.pm
-lib/MOBY/RDF/Ontologies/Parsers/ServiceTypeParser.pm
+lib/MOBY/RDF/Parsers/NamespaceParser.pm
+lib/MOBY/RDF/Parsers/ServiceTypeParser.pm
 lib/MOBY/RDF/Predicates/DC_PROTEGE.pm
 lib/MOBY/RDF/Predicates/FETA.pm
 lib/MOBY/RDF/Predicates/MOBY_PREDICATES.pm


From kawas at dev.open-bio.org  Wed Mar  5 13:25:01 2008
From: kawas at dev.open-bio.org (Eddie Kawas)
Date: Wed, 5 Mar 2008 13:25:01 -0500
Subject: [MOBY-guts] biomoby commit
Message-ID: <200803051825.m25IP1dq017743@dev.open-bio.org>


kawas
Wed Mar  5 13:25:01 EST 2008
Update of /home/repository/moby/moby-live/Perl/MOBY-Server
In directory dev.open-bio.org:/tmp/cvs-serv17708/Perl/MOBY-Server

Modified Files:
	MANIFEST 
Log Message:

moby-live/Perl/MOBY-Server MANIFEST,1.2,1.3
===================================================================
RCS file: /home/repository/moby/moby-live/Perl/MOBY-Server/MANIFEST,v
retrieving revision 1.2
retrieving revision 1.3
diff -u -r1.2 -r1.3
--- /home/repository/moby/moby-live/Perl/MOBY-Server/MANIFEST	2008/03/05 18:00:48	1.2
+++ /home/repository/moby/moby-live/Perl/MOBY-Server/MANIFEST	2008/03/05 18:25:01	1.3
@@ -55,8 +55,8 @@
 lib/MOBY/MOBYXSLT.pm
 lib/MOBY/mysql.pm
 lib/MOBY/OntologyServer.pm
-lib/MOBY/RDF/Ontologies/Parsers/NamespaceParser.pm
-lib/MOBY/RDF/Ontologies/Parsers/ServiceTypeParser.pm
+lib/MOBY/RDF/Parsers/NamespaceParser.pm
+lib/MOBY/RDF/Parsers/ServiceTypeParser.pm
 lib/MOBY/RDF/Ontologies/Cache/CacheUtils.pm
 lib/MOBY/RDF/Ontologies/Cache/NamespaceCache.pm
 lib/MOBY/RDF/Ontologies/Cache/ObjectCache.pm


From kawas at dev.open-bio.org  Wed Mar  5 13:38:40 2008
From: kawas at dev.open-bio.org (Eddie Kawas)
Date: Wed, 5 Mar 2008 13:38:40 -0500
Subject: [MOBY-guts] biomoby commit
Message-ID: <200803051838.m25IceMc017883@dev.open-bio.org>


kawas
Wed Mar  5 13:38:40 EST 2008
Update of /home/repository/moby/moby-live/Perl/MOBY-Client
In directory dev.open-bio.org:/tmp/cvs-serv17840/Perl/MOBY-Client

Modified Files:
	META.yml Makefile.PL Changes 
Log Message:
updated the Changes file to reflect new items before releasing to cpan
moby-live/Perl/MOBY-Client META.yml,1.1,1.2 Makefile.PL,1.4,1.5 Changes,1.1,1.2
===================================================================
RCS file: /home/repository/moby/moby-live/Perl/MOBY-Client/META.yml,v
retrieving revision 1.1
retrieving revision 1.2
diff -u -r1.1 -r1.2
--- /home/repository/moby/moby-live/Perl/MOBY-Client/META.yml	2008/02/21 00:14:33	1.1
+++ /home/repository/moby/moby-live/Perl/MOBY-Client/META.yml	2008/03/05 18:38:40	1.2
@@ -24,4 +24,5 @@
   URI::Escape: 0
   XML::LibXML: 0
   WSRF::Lite: 0
-version: 1.0
+  RDF::Core: 0.51
+version: 1.01

===================================================================
RCS file: /home/repository/moby/moby-live/Perl/MOBY-Client/Makefile.PL,v
retrieving revision 1.4
retrieving revision 1.5
diff -u -r1.4 -r1.5
--- /home/repository/moby/moby-live/Perl/MOBY-Client/Makefile.PL	2008/03/05 17:59:58	1.4
+++ /home/repository/moby/moby-live/Perl/MOBY-Client/Makefile.PL	2008/03/05 18:38:40	1.5
@@ -4,7 +4,7 @@
 
 # all_from 'lib/MOBY/Client/Central.pm';
 author 'Mark Wilkinson <markw at illuminae.com>';
-version '1.0';
+version '1.01';
 license 'perl';
 
 build_requires 'Test::More' => 0;

===================================================================
RCS file: /home/repository/moby/moby-live/Perl/MOBY-Client/Changes,v
retrieving revision 1.1
retrieving revision 1.2
diff -u -r1.1 -r1.2
--- /home/repository/moby/moby-live/Perl/MOBY-Client/Changes	2008/02/21 00:14:33	1.1
+++ /home/repository/moby/moby-live/Perl/MOBY-Client/Changes	2008/03/05 18:38:40	1.2
@@ -1,5 +1,9 @@
 Revision history for Moby-Client
 
+1.01    5 March 2008
+        * removed some failing pod tests
+        * added some preliminary modules for parsing RDF (Namespaces/ServiceTypes). Others will follow
+
 1.00    12 Feb 2008
         MOBY::Client released to CPAN
 


From kawas at dev.open-bio.org  Wed Mar  5 15:27:12 2008
From: kawas at dev.open-bio.org (Eddie Kawas)
Date: Wed, 5 Mar 2008 15:27:12 -0500
Subject: [MOBY-guts] biomoby commit
Message-ID: <200803052027.m25KRC1r018033@dev.open-bio.org>


kawas
Wed Mar  5 15:27:11 EST 2008
Update of /home/repository/moby/moby-live/Perl/MOBY-Server/lib/MOBY
In directory dev.open-bio.org:/tmp/cvs-serv17998/Perl/MOBY-Server/lib/MOBY

Modified Files:
	CommonSubs.pm 
Log Message:
fixed a bug where an unqualified articlename failed to get found when calling getNodeContentWithArticle
moby-live/Perl/MOBY-Server/lib/MOBY CommonSubs.pm,1.2,1.3
===================================================================
RCS file: /home/repository/moby/moby-live/Perl/MOBY-Server/lib/MOBY/CommonSubs.pm,v
retrieving revision 1.2
retrieving revision 1.3
diff -u -r1.2 -r1.3
--- /home/repository/moby/moby-live/Perl/MOBY-Server/lib/MOBY/CommonSubs.pm	2008/02/21 17:15:40	1.2
+++ /home/repository/moby/moby-live/Perl/MOBY-Server/lib/MOBY/CommonSubs.pm	2008/03/05 20:27:11	1.3
@@ -1042,7 +1042,7 @@
   for ( 1 .. $nodes->size() ) {
     my $child = $nodes->get_node( $_ );
     if ( _moby_getAttribute($child, "articleName")
-	 && ( $child->getAttribute("articleName") eq $articleName )
+	 && ( _moby_getAttribute($child, "articleName") eq $articleName )
        )
       {
 	# now we have a valid child, get the content... stringified... regardless of what it is


From kawas at dev.open-bio.org  Thu Mar  6 11:44:55 2008
From: kawas at dev.open-bio.org (Eddie Kawas)
Date: Thu, 6 Mar 2008 11:44:55 -0500
Subject: [MOBY-guts] biomoby commit
Message-ID: <200803061644.m26GitGc024846@dev.open-bio.org>


kawas
Thu Mar  6 11:44:55 EST 2008
Update of /home/repository/moby/moby-live/Perl/MOBY-Server/bin/scripts
In directory dev.open-bio.org:/tmp/cvs-serv24808/Perl/MOBY-Server/bin/scripts

Modified Files:
	moby-s-install.pl 
Log Message:
*updated the script to make the cgi files copied executable
*fixed some of the messages that came out of the script

moby-live/Perl/MOBY-Server/bin/scripts moby-s-install.pl,1.1,1.2
===================================================================
RCS file: /home/repository/moby/moby-live/Perl/MOBY-Server/bin/scripts/moby-s-install.pl,v
retrieving revision 1.1
retrieving revision 1.2
diff -u -r1.1 -r1.2
--- /home/repository/moby/moby-live/Perl/MOBY-Server/bin/scripts/moby-s-install.pl	2008/02/21 00:21:28	1.1
+++ /home/repository/moby/moby-live/Perl/MOBY-Server/bin/scripts/moby-s-install.pl	2008/03/06 16:44:55	1.2
@@ -188,6 +188,10 @@
 	} else {
 		say "\n$file_desc created: '$file'\n\tPlease ensure that the file is executable!\n";
 	}
+	# try to make file executable
+	eval {
+		my $mode = 0655;   chmod $mode, "$file";
+	};
 }
 
 # create a config file from a template
@@ -1253,7 +1257,7 @@
 
 #
 
-say 'Please remember to set up the RDF agent! Just restart apache and your registry has been set up!\n\nDone.';
+say "Please remember to set up the RDF agent! Just restart apache and your registry has been set up!\n\nDone.";
 
 package SimplePrompt;
 


From kawas at dev.open-bio.org  Thu Mar  6 11:58:42 2008
From: kawas at dev.open-bio.org (Eddie Kawas)
Date: Thu, 6 Mar 2008 11:58:42 -0500
Subject: [MOBY-guts] biomoby commit
Message-ID: <200803061658.m26Gwgmo025246@dev.open-bio.org>


kawas
Thu Mar  6 11:58:42 EST 2008
Update of /home/repository/moby/moby-live/Java/docs
In directory dev.open-bio.org:/tmp/cvs-serv25211/Java/docs

Modified Files:
	ConfigureRDFAgent.html 
Log Message:
added a more detail for building the agent.
moby-live/Java/docs ConfigureRDFAgent.html,1.6,1.7
===================================================================
RCS file: /home/repository/moby/moby-live/Java/docs/ConfigureRDFAgent.html,v
retrieving revision 1.6
retrieving revision 1.7
diff -u -r1.6 -r1.7
--- /home/repository/moby/moby-live/Java/docs/ConfigureRDFAgent.html	2008/02/20 19:59:56	1.6
+++ /home/repository/moby/moby-live/Java/docs/ConfigureRDFAgent.html	2008/03/06 16:58:42	1.7
@@ -49,7 +49,10 @@
     </li>
     <li class="dcount"> You can build the latest RDFAgent from the cvs.
     <blockquote>
-    <p>ant bindist-rdfagent </p>
+    <pre class="script">
+    cd /path/to/moby-live/Java
+    ant bindist-rdfagent</pre>
+    <p><strong>Need to check out the code from the cvs? Click</strong> <a href="CVS.html" target="_blank">Here!</a></p>
     </blockquote>
     </li>
     <blockquote>


From mwilkinson at dev.open-bio.org  Thu Mar  6 12:02:56 2008
From: mwilkinson at dev.open-bio.org (Mark Wilkinson)
Date: Thu, 6 Mar 2008 12:02:56 -0500
Subject: [MOBY-guts] biomoby commit
Message-ID: <200803061702.m26H2uDj025425@dev.open-bio.org>


mwilkinson
Thu Mar  6 12:02:55 EST 2008
Update of /home/repository/moby/moby-live/Docs/ProjectDocs
In directory dev.open-bio.org:/tmp/cvs-serv25406/ProjectDocs

Modified Files:
	index.html 
Log Message:
fixing docs
moby-live/Docs/ProjectDocs index.html,1.8,1.9
===================================================================
RCS file: /home/repository/moby/moby-live/Docs/ProjectDocs/index.html,v
retrieving revision 1.8
retrieving revision 1.9
diff -u -r1.8 -r1.9
--- /home/repository/moby/moby-live/Docs/ProjectDocs/index.html	2007/06/21 22:12:52	1.8
+++ /home/repository/moby/moby-live/Docs/ProjectDocs/index.html	2008/03/06 17:02:55	1.9
@@ -23,8 +23,8 @@
             <td>Location</td><td>Endpoint</td><td>Public?</td><td>Description</td><td>Policy</td>
         </tr>
         <tr>
-            <td>iCAPTURE Centre</td><td>Endpoint: http://mobycentral.icapture.ubc.ca/cgi-bin/MOBY05/mobycentral.pl
-                                        <br>URI: http://mobycentral.icapture.ubc.ca/MOBY/Central</td><td>YES</td><td>A curated public registry hosted at the iCAPTURE Centre, Vancouver</td><td><a href="http://mobycentral.icapture.ubc.ca/MOBYCentral_Policy.html">Policy</a></td>
+            <td>SUN Centre of Excellence</td><td>Endpoint: http://moby.ucalgary.ca/moby/MOBY-Central.pl
+                                        <br>URI: http://moby.ucalgary.ca/MOBY/Central</td><td>YES</td><td>A curated public registry hosted at the SUN Centre of Excellence, Calgary</td><td><a href="http://mobycentral.icapture.ubc.ca/MOBYCentral_Policy.html">Policy: open, non-test registry.  Test services may be deleted at any time.</a></td>
         </tr>
         <tr>
             <td>Open TEST registry</td><td>Endpoint: http://bioinfo.icapture.ubc.ca/cgi-bin/mobycentral/MOBY-Central.pl


From kawas at dev.open-bio.org  Thu Mar  6 12:05:09 2008
From: kawas at dev.open-bio.org (Eddie Kawas)
Date: Thu, 6 Mar 2008 12:05:09 -0500
Subject: [MOBY-guts] biomoby commit
Message-ID: <200803061705.m26H593M025575@dev.open-bio.org>


kawas
Thu Mar  6 12:05:09 EST 2008
Update of /home/repository/moby/moby-live/Perl/MOBY-Server/lib
In directory dev.open-bio.org:/tmp/cvs-serv25540/Perl/MOBY-Server/lib

Modified Files:
	MOBY.pm 
Log Message:

moby-live/Perl/MOBY-Server/lib MOBY.pm,1.1,1.2
===================================================================
RCS file: /home/repository/moby/moby-live/Perl/MOBY-Server/lib/MOBY.pm,v
retrieving revision 1.1
retrieving revision 1.2
diff -u -r1.1 -r1.2
--- /home/repository/moby/moby-live/Perl/MOBY-Server/lib/MOBY.pm	2008/02/21 00:21:28	1.1
+++ /home/repository/moby/moby-live/Perl/MOBY-Server/lib/MOBY.pm	2008/03/06 17:05:09	1.2
@@ -102,7 +102,7 @@
 
 =back
 
-Once you are sure that you satisfy the above items, go ahead and run the B<moby-s-install.pl> script, by typing C<moby-s-install.pl> at the command line.
+Once you are sure that you satisfy the above items, go ahead and run the B<moby-s-install.pl> script, by typing C<moby-s-install.pl> at the command line. This file was installed onto your machine when you did your 'make install'!
 
 =head3 What Exactly does moby-s-install.pl do?
 
@@ -208,10 +208,22 @@
 
 =cut
 
+=head3 How do I set up the RDF Agent?
+
+Detailed instructions for building, installing and configuring the agent can be found at http://biomoby.open-bio.org/CVS_CONTENT/moby-live/Java/docs/ConfigureRDFAgent.html
+
+=cut
+
 =cut
 
 =head2 Missing Features
 
+=over
+
+=item * automatic installation of the RDF Agent
+
+=back
+
 =cut
 
 =head2 Acknowledgement


From mwilkinson at dev.open-bio.org  Thu Mar  6 13:04:35 2008
From: mwilkinson at dev.open-bio.org (Mark Wilkinson)
Date: Thu, 6 Mar 2008 13:04:35 -0500
Subject: [MOBY-guts] biomoby commit
Message-ID: <200803061804.m26I4ZYQ028481@dev.open-bio.org>


mwilkinson
Thu Mar  6 13:04:35 EST 2008
Update of /home/repository/moby/moby-live/Perl/MOBY-Server/lib/MOBY/Client
In directory dev.open-bio.org:/tmp/cvs-serv28462

Modified Files:
	Central.pm 
Log Message:
updating docs
moby-live/Perl/MOBY-Server/lib/MOBY/Client Central.pm,1.2,1.3
===================================================================
RCS file: /home/repository/moby/moby-live/Perl/MOBY-Server/lib/MOBY/Client/Central.pm,v
retrieving revision 1.2
retrieving revision 1.3
diff -u -r1.2 -r1.3
--- /home/repository/moby/moby-live/Perl/MOBY-Server/lib/MOBY/Client/Central.pm	2008/02/21 17:15:40	1.2
+++ /home/repository/moby/moby-live/Perl/MOBY-Server/lib/MOBY/Client/Central.pm	2008/03/06 18:04:35	1.3
@@ -80,14 +80,15 @@
 
  ENV & PROXY : you can set environment variables to change the defaults.
              By default, a call to 'new' will initialize MOBY::Client::Central
-             to connect to the MOBY Central registry at:
-             http://mobycentral.cbr.nrc.ca/cgi-bin/MOBY05/mobycentral.pl
+             to connect to the default MOBY Central registry.  The location of
+             this registry can be determined by examining the redirect from:
+                http://biomoby.org/mobycentral
              If you wish to chose another registry by default, or if you need
              to set up additional connection details (e.g. PROXY) then you may
              set the following environment variables to whatever you
              require:
-             MOBY_SERVER  (default http://mobycentral.cbr.nrc.ca/cgi-bin/MOBY05/mobycentral.pl)
-             MOBY_URI     (default http://mobycentral.cbr.nrc.ca/MOBY/Central)
+             MOBY_SERVER  (default http://moby.ucalgary.ca/moby/MOBY-Central.pl)
+             MOBY_URI     (default http://moby.ucalgary.ca/MOBY/Central)
              MOBY_PROXY   (no default)
 
  Args      :    user_agent - optional.  The name of your software application
@@ -104,8 +105,8 @@
                                 }
                             - by default this becomes
                             {mobycentral => {
-                                 URL => 'http://mobycentral.cbr.nrc.ca/cgi-bin/MOBY05/mobycentral.pl',
-                                 URI => 'http://mobycentral.cbr.nrc.ca/MOBY/Central'}
+                                 URL => 'http://moby.ucalgary.ca/moby/MOBY-Central.pl',
+                                 URI => 'http://moby.ucalgary.ca/MOBY/Central'}
                              }
  Discussion:    Each registry must have a different
                 NAME.  If you have more than one


From kawas at dev.open-bio.org  Thu Mar  6 13:45:58 2008
From: kawas at dev.open-bio.org (Eddie Kawas)
Date: Thu, 6 Mar 2008 13:45:58 -0500
Subject: [MOBY-guts] biomoby commit
Message-ID: <200803061845.m26IjwBt029614@dev.open-bio.org>


kawas
Thu Mar  6 13:45:57 EST 2008
Update of /home/repository/moby/moby-live/Perl/MOBY-Client/share
In directory dev.open-bio.org:/tmp/cvs-serv29579/Perl/MOBY-Client/share

Modified Files:
	HelloWorldService.pm 
Log Message:
added a missing semi-colon
moby-live/Perl/MOBY-Client/share HelloWorldService.pm,1.1,1.2
===================================================================
RCS file: /home/repository/moby/moby-live/Perl/MOBY-Client/share/HelloWorldService.pm,v
retrieving revision 1.1
retrieving revision 1.2
diff -u -r1.1 -r1.2
--- /home/repository/moby/moby-live/Perl/MOBY-Client/share/HelloWorldService.pm	2008/02/22 16:32:43	1.1
+++ /home/repository/moby/moby-live/Perl/MOBY-Client/share/HelloWorldService.pm	2008/03/06 18:45:57	1.2
@@ -4,7 +4,7 @@
 # to you what you send it... in proper MOBY
 # message format of course :-)
 
-use MOBY::CommonSubs qw(:all)
+use MOBY::CommonSubs qw(:all);
 
 sub helloWorld {
 	my ($caller, $message) = @_;  # get the incoming MOBY query XML


From kawas at dev.open-bio.org  Thu Mar  6 18:18:32 2008
From: kawas at dev.open-bio.org (Eddie Kawas)
Date: Thu, 6 Mar 2008 18:18:32 -0500
Subject: [MOBY-guts] biomoby commit
Message-ID: <200803062318.m26NIWZS029915@dev.open-bio.org>


kawas
Thu Mar  6 18:18:32 EST 2008
Update of /home/repository/moby/moby-live/Perl/MOBY-Server/share/cgi
In directory dev.open-bio.org:/tmp/cvs-serv29880/Perl/MOBY-Server/share/cgi

Modified Files:
	RESOURCES 
Log Message:
added support for FULL
moby-live/Perl/MOBY-Server/share/cgi RESOURCES,1.1,1.2
===================================================================
RCS file: /home/repository/moby/moby-live/Perl/MOBY-Server/share/cgi/RESOURCES,v
retrieving revision 1.1
retrieving revision 1.2
diff -u -r1.1 -r1.2
--- /home/repository/moby/moby-live/Perl/MOBY-Server/share/cgi/RESOURCES	2008/02/21 00:21:27	1.1
+++ /home/repository/moby/moby-live/Perl/MOBY-Server/share/cgi/RESOURCES	2008/03/06 23:18:32	1.2
@@ -35,6 +35,8 @@
 use MOBY::RDF::Ontologies::Cache::ServiceTypeCache;
 use MOBY::Config;
 
+use XML::LibXML;
+
 # your cache dir
 my $dir = MOBY::Config->new->{mobycentral}->{rdf_cache} || "/tmp/";
 
@@ -119,15 +121,16 @@
 		} unless $x;
 	} unless $string;
 	do {
-		my $x = MOBY::RDF::Ontologies::Services->new;    
-		my $sname = substr ($string, index($string, ',')+1);
-        my $prov  = substr ($string, 1, index($string, ',')-1);
+		my $x     = MOBY::RDF::Ontologies::Services->new;
+		my $sname = substr( $string, index( $string, ',' ) + 1 );
+		my $prov  = substr( $string, 1, index( $string, ',' ) - 1 );
+
 		# get pretty printed RDF/XML for one service
 		$x = $x->findService(
-						   {
-							 serviceName => $sname,
-							 authURI     =>  $prov,
-						   }
+							  {
+								serviceName => $sname,
+								authURI     => $prov,
+							  }
 		);
 		print $form->header('text/xml'), $x if $x;
 	} if $string;
@@ -152,11 +155,86 @@
 		print $form->header('text/xml'), $rdf if $rdf;
 	} if $1;
 } elsif ( $url =~ m/^RESOURCES\/MOBY\-S\/FULL$/ ) {
+	my $dom    = undef;
+	my $parser = XML::LibXML->new();
 
-	print $form->header('text/html');
-	$form->start_html( -title => 'unavailable', );
-	print h2( "not", "implemented" );
-	print end_html;
+	# print this right away, because this might take a long time ...
+	print $form->header('text/xml');
+	if ($useCache) {
+		my $x =
+		  MOBY::RDF::Ontologies::Cache::NamespaceCache->new( cache => "$dir", );
+		$x = $x->get_rdf();
+		do {
+			my $doc = $parser->parse_string($x);
+			$dom = $doc;
+
+		} if $x;
+		$x =
+		  MOBY::RDF::Ontologies::Cache::ServiceTypeCache->new( cache => "$dir",
+		  );
+		$x = $x->get_rdf();
+		do {
+			my $doc = $parser->parse_string($x);
+			_appendChildrenOfDOMToOtherDOM( $doc, \$dom ) if $dom;
+			$dom = $doc unless $dom;
+		} if $x;
+		$x = MOBY::RDF::Ontologies::Cache::ObjectCache->new( cache => "$dir", );
+		$x = $x->get_rdf();
+		do {
+			my $doc = $parser->parse_string($x);
+			_appendChildrenOfDOMToOtherDOM( $doc, \$dom ) if $dom;
+			$dom = $doc unless $dom;
+
+		} if $x;
+		$x =
+		  MOBY::RDF::Ontologies::Cache::ServiceCache->new( cache => "$dir", );
+		$x = $x->get_rdf();
+		do {
+			my $doc = $parser->parse_string($x);
+			_appendChildrenOfDOMToOtherDOM( $doc, \$dom ) if $dom;
+			$dom = $doc unless $dom;
+
+		} if $x;
+
+		# TODO append ServiceDescription too when complete
+		print $dom->toString if $dom;
+
+	} else {
+		my $x = MOBY::RDF::Ontologies::Namespaces->new;
+		$x = $x->createAll();
+		do {
+			my $doc = $parser->parse_string($x);
+			_appendChildrenOfDOMToOtherDOM( $doc, \$dom ) if $dom;
+			$dom = $doc unless $dom;
+		} if $x;
+		
+		$x = MOBY::RDF::Ontologies::Objects->new;
+		$x = $x->createAll();
+		do {
+			my $doc = $parser->parse_string($x);
+			_appendChildrenOfDOMToOtherDOM( $doc, \$dom ) if $dom;
+			$dom = $doc unless $dom;
+		} if $x;
+		
+		$x = MOBY::RDF::Ontologies::ServiceTypes->new;
+		$x = $x->createAll();
+		do {
+			my $doc = $parser->parse_string($x);
+			_appendChildrenOfDOMToOtherDOM( $doc, \$dom ) if $dom;
+			$dom = $doc unless $dom;
+		} if $x;
+		
+		$x = MOBY::RDF::Ontologies::Services->new;
+		$x = $x->findService();
+		do {
+			my $doc = $parser->parse_string($x);
+			_appendChildrenOfDOMToOtherDOM( $doc, \$dom ) if $dom;
+			$dom = $doc unless $dom;
+		} if $x;
+
+		# TODO append ServiceDescription too when complete
+		print $dom->toString if $dom;
+	}
 
 } elsif ( $url =~ m/^RESOURCES\/MOBY\-S\/ServiceDescription$/ ) {
 	print $form->header('text/html');
@@ -172,3 +250,10 @@
 	print end_html;
 }
 
+sub _appendChildrenOfDOMToOtherDOM {
+	my ( $dom, $other_dom ) = @_;
+	foreach my $service ( $dom->findnodes('/rdf:RDF/rdf:Description') ) {
+		$$other_dom->documentElement->appendChild($service);
+	}
+	return $other_dom;
+}


From gordonp at dev.open-bio.org  Fri Mar  7 17:42:04 2008
From: gordonp at dev.open-bio.org (Paul Gordon)
Date: Fri, 7 Mar 2008 17:42:04 -0500
Subject: [MOBY-guts] biomoby commit
Message-ID: <200803072242.m27Mg4kb001004@dev.open-bio.org>


gordonp
Fri Mar  7 17:42:03 EST 2008
Update of /home/repository/moby/moby-live/Java/src/main/org/biomoby/shared
In directory dev.open-bio.org:/tmp/cvs-serv968/src/main/org/biomoby/shared

Modified Files:
	MobyPrefixResolver.java 
Log Message:
Fixed unchecked operation warning, added SAWSDL support for semantic WSDL wrapping servlet to come shortly
moby-live/Java/src/main/org/biomoby/shared MobyPrefixResolver.java,1.11,1.12
===================================================================
RCS file: /home/repository/moby/moby-live/Java/src/main/org/biomoby/shared/MobyPrefixResolver.java,v
retrieving revision 1.11
retrieving revision 1.12
diff -u -r1.11 -r1.12
--- /home/repository/moby/moby-live/Java/src/main/org/biomoby/shared/MobyPrefixResolver.java	2008/02/13 01:28:06	1.11
+++ /home/repository/moby/moby-live/Java/src/main/org/biomoby/shared/MobyPrefixResolver.java	2008/03/07 22:42:03	1.12
@@ -44,6 +44,8 @@
     public static final String XHTML_NAMESPACE = "http://www.w3.org/1999/xhtml";
     public static final String XLINK_PREFIX = "xlink";
     public static final String XLINK_NAMESPACE = "http://www.w3.org/1999/xlink";
+    public static final String SAWSDL_PREFIX = "sawsdl";
+    public static final String SAWSDL_NAMESPACE = "http://www.w3.org/ns/sawsdl";
 
     /**
      * We don't really implement this as it can be extremely complicated.
@@ -121,10 +123,10 @@
     }
 
     public static class MobyNodeList implements NodeList{
-	private Vector nodes;
-	public MobyNodeList(){nodes = new Vector();}
+	private Vector<Node> nodes;
+	public MobyNodeList(){nodes = new Vector<Node>();}
 	public int getLength(){return nodes.size();}
-	public Node item(int index){return (Node) nodes.elementAt(index);}
+	public Node item(int index){return nodes.elementAt(index);}
 	public void add(Node n){nodes.add(n);}
     };
 


From gordonp at dev.open-bio.org  Fri Mar  7 17:42:32 2008
From: gordonp at dev.open-bio.org (Paul Gordon)
Date: Fri, 7 Mar 2008 17:42:32 -0500
Subject: [MOBY-guts] biomoby commit
Message-ID: <200803072242.m27MgWhc001048@dev.open-bio.org>


gordonp
Fri Mar  7 17:42:31 EST 2008
Update of /home/repository/moby/moby-live/Java/src/main/org/biomoby/shared
In directory dev.open-bio.org:/tmp/cvs-serv1012/src/main/org/biomoby/shared

Modified Files:
	NamespaceContextImpl.java 
Log Message:
Added SAWSDL support for semantic WSDL wrapping servlet to come shortly
moby-live/Java/src/main/org/biomoby/shared NamespaceContextImpl.java,1.3,1.4
===================================================================
RCS file: /home/repository/moby/moby-live/Java/src/main/org/biomoby/shared/NamespaceContextImpl.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/NamespaceContextImpl.java	2008/02/13 01:28:06	1.3
+++ /home/repository/moby/moby-live/Java/src/main/org/biomoby/shared/NamespaceContextImpl.java	2008/03/07 22:42:31	1.4
@@ -31,6 +31,7 @@
 	prefixes.put(MobyPrefixResolver.WSRP_NAMESPACE, MobyPrefixResolver.WSRP_PREFIX);	
 	prefixes.put(MobyPrefixResolver.XHTML_NAMESPACE, MobyPrefixResolver.XHTML_PREFIX);
 	prefixes.put(MobyPrefixResolver.XLINK_NAMESPACE, MobyPrefixResolver.XLINK_PREFIX);
+	prefixes.put(MobyPrefixResolver.SAWSDL_NAMESPACE, MobyPrefixResolver.SAWSDL_PREFIX);
 
 	// Reverse map prefix -> nsURI
 	nsURIs.put(MobyPrefixResolver.XSI_PREFIX, MobyPrefixResolver.XSI_NAMESPACE2001);


From senger at dev.open-bio.org  Sat Mar  8 07:34:08 2008
From: senger at dev.open-bio.org (Martin Senger)
Date: Sat, 8 Mar 2008 07:34:08 -0500
Subject: [MOBY-guts] biomoby commit
Message-ID: <200803081234.m28CY8wY002469@dev.open-bio.org>


senger
Sat Mar  8 07:34:07 EST 2008
Update of /home/repository/moby/moby-live/Java/docs
In directory dev.open-bio.org:/tmp/cvs-serv2450/docs

Modified Files:
	index.html 
Log Message:
Broken link updated

moby-live/Java/docs index.html,1.31,1.32
===================================================================
RCS file: /home/repository/moby/moby-live/Java/docs/index.html,v
retrieving revision 1.31
retrieving revision 1.32
diff -u -r1.31 -r1.32
--- /home/repository/moby/moby-live/Java/docs/index.html	2008/02/22 03:07:20	1.31
+++ /home/repository/moby/moby-live/Java/docs/index.html	2008/03/08 12:34:07	1.32
@@ -57,7 +57,7 @@
        The main issue is that jMoby uses now the 3rd-party libraries
 form the various Maven repositories. It fetches them when you compile
 jMoby, or when you use the new Ant's task <tt>install</tt>. There is
-<a href="http://pantheon.generationcp.org/UsingMaven.html">an
+<a href="http://pantheon.generationcp.org/index.php?option=com_content&task=view&id=379&Itemid=197">an
 article</a> about how it is done (coming from a different project but
 using the same principles as in jMoby). <p>
 
@@ -225,7 +225,7 @@
 <div align=right class="address">
 <address><A HREF="mailto:martin.senger at gmail.com">Martin Senger</A><BR></address>
 <!-- hhmts start -->
-Last modified: Fri Feb 22 11:00:53 2008
+Last modified: Sat Mar  8 20:32:22 2008
 <!-- hhmts end -->
 </div>
 </body> </html>


From jmrc at dev.open-bio.org  Mon Mar 10 08:14:19 2008
From: jmrc at dev.open-bio.org (José Manuel Rodríguez Carrasco)
Date: Mon, 10 Mar 2008 08:14:19 -0400
Subject: [MOBY-guts] biomoby commit
Message-ID: <200803101214.m2ACEJ6K008798@dev.open-bio.org>


jmrc
Mon Mar 10 08:14:18 EDT 2008
Update of /home/repository/moby/moby-live/Docs/asyncDocs
In directory dev.open-bio.org:/tmp/cvs-serv8763/asyncDocs

Log Message:
Directory /home/repository/moby/moby-live/Docs/asyncDocs added to the repository

moby-live/Docs/asyncDocs - New directory
rcsdiff: /home/repository/moby/moby-live/Docs/asyncDocs/RCS/-,v: No such file or directory

rcsdiff: /home/repository/moby/moby-live/Docs/asyncDocs/RCS/New,v: No such file or directory

rcsdiff: /home/repository/moby/moby-live/Docs/asyncDocs/RCS/directory,v: No such file or directory


From jmrc at dev.open-bio.org  Mon Mar 10 08:25:34 2008
From: jmrc at dev.open-bio.org (José Manuel Rodríguez Carrasco)
Date: Mon, 10 Mar 2008 08:25:34 -0400
Subject: [MOBY-guts] biomoby commit
Message-ID: <200803101225.m2ACPYBx008995@dev.open-bio.org>


jmrc
Mon Mar 10 08:25:34 EDT 2008
Update of /home/repository/moby/moby-live/Docs/asyncDocs/async-MOBY-test
In directory dev.open-bio.org:/tmp/cvs-serv8960/async-MOBY-test

Log Message:
Directory /home/repository/moby/moby-live/Docs/asyncDocs/async-MOBY-test added to the repository

moby-live/Docs/asyncDocs/async-MOBY-test - New directory
rcsdiff: /home/repository/moby/moby-live/Docs/asyncDocs/async-MOBY-test/RCS/-,v: No such file or directory

rcsdiff: /home/repository/moby/moby-live/Docs/asyncDocs/async-MOBY-test/RCS/New,v: No such file or directory

rcsdiff: /home/repository/moby/moby-live/Docs/asyncDocs/async-MOBY-test/RCS/directory,v: No such file or directory


From jmrc at dev.open-bio.org  Mon Mar 10 08:31:31 2008
From: jmrc at dev.open-bio.org (José Manuel Rodríguez Carrasco)
Date: Mon, 10 Mar 2008 08:31:31 -0400
Subject: [MOBY-guts] biomoby commit
Message-ID: <200803101231.m2ACVVrR009108@dev.open-bio.org>


jmrc
Mon Mar 10 08:31:31 EDT 2008
Update of /home/repository/moby/moby-live/Docs/asyncDocs
In directory dev.open-bio.org:/tmp/cvs-serv9073/asyncDocs

Added Files:
	BioMOBY Asynchronous Service Specification_v2.4.1.pdf 
Log Message:
user: jmrc
date: 10-March-2008

Specification document of asynchronous proposal with examples.



moby-live/Docs/asyncDocs BioMOBY Asynchronous Service Specification_v2.4.1.pdf,NONE,1.1
rcsdiff: /home/repository/moby/moby-live/Docs/asyncDocs/RCS/BioMOBY,v: No such file or directory

rcsdiff: /home/repository/moby/moby-live/Docs/asyncDocs/RCS/Asynchronous,v: No such file or directory

rcsdiff: /home/repository/moby/moby-live/Docs/asyncDocs/RCS/Service,v: No such file or directory


From jmrc at dev.open-bio.org  Mon Mar 10 08:31:31 2008
From: jmrc at dev.open-bio.org (José Manuel Rodríguez Carrasco)
Date: Mon, 10 Mar 2008 08:31:31 -0400
Subject: [MOBY-guts] biomoby commit
Message-ID: <200803101231.m2ACVVKJ009124@dev.open-bio.org>


jmrc
Mon Mar 10 08:31:31 EDT 2008
Update of /home/repository/moby/moby-live/Docs/asyncDocs/async-MOBY-test
In directory dev.open-bio.org:/tmp/cvs-serv9073/asyncDocs/async-MOBY-test

Added Files:
	AsyncService.pm async-MOBY-test.cgi async-MOBY-test.cgi.pl 
	deregister-runAsyncMOBYService.pl 
	register-runAsyncMOBYService.pl 
	running_runAsyncMOBYservice-StepByStep.pl 
	running_runAsyncMOBYservice.pl sayHello-description.xml 
	sayHello.wsdl 
Log Message:
user: jmrc
date: 10-March-2008

Specification document of asynchronous proposal with examples.



moby-live/Docs/asyncDocs/async-MOBY-test AsyncService.pm,NONE,1.1 async-MOBY-test.cgi,NONE,1.1 async-MOBY-test.cgi.pl,NONE,1.1 deregister-runAsyncMOBYService.pl,NONE,1.1 register-runAsyncMOBYService.pl,NONE,1.1 running_runAsyncMOBYservice-StepByStep.pl,NONE,1.1 running_runAsyncMOBYservice.pl,NONE,1.1 sayHello-description.xml,NONE,1.1 sayHello.wsdl,NONE,1.1

From jmrc at dev.open-bio.org  Mon Mar 10 09:13:02 2008
From: jmrc at dev.open-bio.org (José Manuel Rodríguez Carrasco)
Date: Mon, 10 Mar 2008 09:13:02 -0400
Subject: [MOBY-guts] biomoby commit
Message-ID: <200803101313.m2ADD2GN009389@dev.open-bio.org>


jmrc
Mon Mar 10 09:13:01 EDT 2008
Update of /home/repository/moby/moby-live/Docs/asyncDocs
In directory dev.open-bio.org:/tmp/cvs-serv9357

Added Files:
	README.txt 
Log Message:
user: jmrc
date: 10-March-2008

README file that details the documents of asynchronous proposal.



moby-live/Docs/asyncDocs README.txt,NONE,1.1

From kawas at dev.open-bio.org  Tue Mar 11 10:44:19 2008
From: kawas at dev.open-bio.org (Eddie Kawas)
Date: Tue, 11 Mar 2008 10:44:19 -0400
Subject: [MOBY-guts] biomoby commit
Message-ID: <200803111444.m2BEiJfa019295@dev.open-bio.org>


kawas
Tue Mar 11 10:44:18 EDT 2008
Update of /home/repository/moby/moby-live/Perl/MOBY-Server/share/cgi
In directory dev.open-bio.org:/tmp/cvs-serv19260/Perl/MOBY-Server/share/cgi

Modified Files:
	authority.pl 
Log Message:
added code that returns wsdl documents (declared via import statements) requested whenever you try to use parse the wsdl obtained from the lsid server.
the code loops through the INC paths looking for files. if they are found, they are printed out to stdout. otherwise, the default behaviour is done.
moby-live/Perl/MOBY-Server/share/cgi authority.pl,1.1,1.2
===================================================================
RCS file: /home/repository/moby/moby-live/Perl/MOBY-Server/share/cgi/authority.pl,v
retrieving revision 1.1
retrieving revision 1.2
diff -u -r1.1 -r1.2
--- /home/repository/moby/moby-live/Perl/MOBY-Server/share/cgi/authority.pl	2008/02/21 00:21:27	1.1
+++ /home/repository/moby/moby-live/Perl/MOBY-Server/share/cgi/authority.pl	2008/03/11 14:44:18	1.2
@@ -37,6 +37,25 @@
 
 ##############
 
+# serve wsdl documents on request if they exist and are readable ...
+# obtain them from the INC
+if($ENV{'REQUEST_URI'} && ($ENV{'REQUEST_URI'} =~ /^\/authority\/(\w+)\.wsdl/)) {
+  my $wsdl_location = undef;
+  for my $dir (@INC) {
+    my $ls_module = "LS/Authority/WSDL/$1.wsdl";
+    $wsdl_location = "$dir/$ls_module" if -e "$dir/$ls_module";
+  }
+  if ($wsdl_location and -e $wsdl_location and -r $wsdl_location) {
+    my $parser = XML::LibXML->new();
+    my $doc = undef;
+    eval {
+      $doc    = $parser->parse_file( "$wsdl_location" );
+      my $doc = $doc->toString();
+      print "Content-type: text/xml\n\n$doc" if $doc;
+    }
+  }
+}
+
 my $location = 'http://';
 
 # TODO get this from the mobyconfig file


From gordonp at dev.open-bio.org  Wed Mar 12 13:32:08 2008
From: gordonp at dev.open-bio.org (Paul Gordon)
Date: Wed, 12 Mar 2008 13:32:08 -0400
Subject: [MOBY-guts] biomoby commit
Message-ID: <200803121732.m2CHW8kn021799@dev.open-bio.org>


gordonp
Wed Mar 12 13:32:07 EDT 2008
Update of /home/repository/moby/moby-live/Java/src/main/org/biomoby/shared/test
In directory dev.open-bio.org:/tmp/cvs-serv21764/src/main/org/biomoby/shared/test

Log Message:
Directory /home/repository/moby/moby-live/Java/src/main/org/biomoby/shared/test added to the repository

moby-live/Java/src/main/org/biomoby/shared/test - New directory
rcsdiff: /home/repository/moby/moby-live/Java/src/main/org/biomoby/shared/test/RCS/-,v: No such file or directory

rcsdiff: /home/repository/moby/moby-live/Java/src/main/org/biomoby/shared/test/RCS/New,v: No such file or directory

rcsdiff: /home/repository/moby/moby-live/Java/src/main/org/biomoby/shared/test/RCS/directory,v: No such file or directory


From gordonp at dev.open-bio.org  Wed Mar 12 13:47:18 2008
From: gordonp at dev.open-bio.org (Paul Gordon)
Date: Wed, 12 Mar 2008 13:47:18 -0400
Subject: [MOBY-guts] biomoby commit
Message-ID: <200803121747.m2CHlIc8021974@dev.open-bio.org>


gordonp
Wed Mar 12 13:47:18 EDT 2008
Update of /home/repository/moby/moby-live/Java/src/main/org/biomoby/shared/test
In directory dev.open-bio.org:/tmp/cvs-serv21918/src/main/org/biomoby/shared/test

Added Files:
	LSIDResolverTestCase.java 
Log Message:
Initial commit of lightweight LSID resolver
moby-live/Java/src/main/org/biomoby/shared/test LSIDResolverTestCase.java,NONE,1.1

From gordonp at dev.open-bio.org  Wed Mar 12 13:47:18 2008
From: gordonp at dev.open-bio.org (Paul Gordon)
Date: Wed, 12 Mar 2008 13:47:18 -0400
Subject: [MOBY-guts] biomoby commit
Message-ID: <200803121747.m2CHlIn1021958@dev.open-bio.org>


gordonp
Wed Mar 12 13:47:18 EDT 2008
Update of /home/repository/moby/moby-live/Java/src/main/org/biomoby/shared
In directory dev.open-bio.org:/tmp/cvs-serv21918/src/main/org/biomoby/shared

Modified Files:
	MobyPrefixResolver.java NamespaceContextImpl.java 
Added Files:
	LSIDResolver.java 
Log Message:
Initial commit of lightweight LSID resolver
moby-live/Java/src/main/org/biomoby/shared LSIDResolver.java,NONE,1.1 MobyPrefixResolver.java,1.12,1.13 NamespaceContextImpl.java,1.4,1.5
===================================================================
RCS file: /home/repository/moby/moby-live/Java/src/main/org/biomoby/shared/MobyPrefixResolver.java,v
retrieving revision 1.12
retrieving revision 1.13
diff -u -r1.12 -r1.13
--- /home/repository/moby/moby-live/Java/src/main/org/biomoby/shared/MobyPrefixResolver.java	2008/03/07 22:42:03	1.12
+++ /home/repository/moby/moby-live/Java/src/main/org/biomoby/shared/MobyPrefixResolver.java	2008/03/12 17:47:18	1.13
@@ -44,8 +44,14 @@
     public static final String XHTML_NAMESPACE = "http://www.w3.org/1999/xhtml";
     public static final String XLINK_PREFIX = "xlink";
     public static final String XLINK_NAMESPACE = "http://www.w3.org/1999/xlink";
+    public static final String WSDL_PREFIX = "wsdl";
+    public static final String WSDL_NAMESPACE = "http://schemas.xmlsoap.org/wsdl/";
+    public static final String HTTP_PREFIX = "http";
+    public static final String HTTP_NAMESPACE = "http://schemas.xmlsoap.org/wsdl/http/";
     public static final String SAWSDL_PREFIX = "sawsdl";
     public static final String SAWSDL_NAMESPACE = "http://www.w3.org/ns/sawsdl";
+    public static final String LSID_PREFIX = "lsid";
+    public static final String LSID_NAMESPACE = "http://lsid.omg.org/predicates#";
 
     /**
      * We don't really implement this as it can be extremely complicated.

===================================================================
RCS file: /home/repository/moby/moby-live/Java/src/main/org/biomoby/shared/NamespaceContextImpl.java,v
retrieving revision 1.4
retrieving revision 1.5
diff -u -r1.4 -r1.5
--- /home/repository/moby/moby-live/Java/src/main/org/biomoby/shared/NamespaceContextImpl.java	2008/03/07 22:42:31	1.4
+++ /home/repository/moby/moby-live/Java/src/main/org/biomoby/shared/NamespaceContextImpl.java	2008/03/12 17:47:18	1.5
@@ -31,7 +31,10 @@
 	prefixes.put(MobyPrefixResolver.WSRP_NAMESPACE, MobyPrefixResolver.WSRP_PREFIX);	
 	prefixes.put(MobyPrefixResolver.XHTML_NAMESPACE, MobyPrefixResolver.XHTML_PREFIX);
 	prefixes.put(MobyPrefixResolver.XLINK_NAMESPACE, MobyPrefixResolver.XLINK_PREFIX);
+	prefixes.put(MobyPrefixResolver.WSDL_NAMESPACE, MobyPrefixResolver.WSDL_PREFIX);
+	prefixes.put(MobyPrefixResolver.HTTP_NAMESPACE, MobyPrefixResolver.HTTP_PREFIX);
 	prefixes.put(MobyPrefixResolver.SAWSDL_NAMESPACE, MobyPrefixResolver.SAWSDL_PREFIX);
+	prefixes.put(MobyPrefixResolver.LSID_NAMESPACE, MobyPrefixResolver.LSID_PREFIX);
 
 	// Reverse map prefix -> nsURI
 	nsURIs.put(MobyPrefixResolver.XSI_PREFIX, MobyPrefixResolver.XSI_NAMESPACE2001);


From senger at dev.open-bio.org  Wed Mar 12 14:41:26 2008
From: senger at dev.open-bio.org (Martin Senger)
Date: Wed, 12 Mar 2008 14:41:26 -0400
Subject: [MOBY-guts] biomoby commit
Message-ID: <200803121841.m2CIfQKH022077@dev.open-bio.org>


senger
Wed Mar 12 14:41:26 EDT 2008
Update of /home/repository/moby/moby-live/Java/xmls
In directory dev.open-bio.org:/tmp/cvs-serv22058/xmls

Modified Files:
	project.pom 
Log Message:
Excluding xerces parser from dependencies

moby-live/Java/xmls project.pom,1.6,1.7
===================================================================
RCS file: /home/repository/moby/moby-live/Java/xmls/project.pom,v
retrieving revision 1.6
retrieving revision 1.7
diff -u -r1.6 -r1.7
--- /home/repository/moby/moby-live/Java/xmls/project.pom	2008/03/02 12:45:27	1.6
+++ /home/repository/moby/moby-live/Java/xmls/project.pom	2008/03/12 18:41:26	1.7
@@ -164,6 +164,16 @@
       <groupId>commons-dbcp</groupId>
       <artifactId>commons-dbcp</artifactId>
       <version>1.1</version>
+      <!-- we need to exclude this in order to load SAXParserFactory from 
+       default J2SE 1.5, And it will work.If SAXParserFactory is loaded 
+       from any of the older versions of JAXP, exception is thrown.
+       -->
+      <exclusions>
+        <exclusion>
+          <groupId>xerces</groupId>
+          <artifactId>xercesImpl</artifactId>
+        </exclusion>
+      </exclusions> 
     </dependency>
 
     <dependency>
@@ -197,6 +207,16 @@
       <groupId>com.hp.hpl.jena</groupId>
       <artifactId>jena</artifactId>
       <version>2.5.4</version>
+      <!-- we need to exclude this in order to load SAXParserFactory from 
+       default J2SE 1.5, And it will work.If SAXParserFactory is loaded 
+       from any of the older versions of JAXP, exception is thrown.
+       -->
+      <exclusions>
+        <exclusion>
+          <groupId>xerces</groupId>
+          <artifactId>xercesImpl</artifactId>
+        </exclusion>
+      </exclusions> 
     </dependency>
 
     <dependency>
@@ -251,6 +271,16 @@
       <groupId>jaxen</groupId>
       <artifactId>jaxen</artifactId>
       <version>1.1.1</version>
+      <!-- we need to exclude this in order to load SAXParserFactory from 
+       default J2SE 1.5, And it will work.If SAXParserFactory is loaded 
+       from any of the older versions of JAXP, exception is thrown.
+       -->
+      <exclusions>
+        <exclusion>
+          <groupId>xerces</groupId>
+          <artifactId>xercesImpl</artifactId>
+        </exclusion>
+      </exclusions> 
     </dependency>
 
     <dependency>


From kawas at dev.open-bio.org  Thu Mar 13 11:03:58 2008
From: kawas at dev.open-bio.org (Eddie Kawas)
Date: Thu, 13 Mar 2008 11:03:58 -0400
Subject: [MOBY-guts] biomoby commit
Message-ID: <200803131503.m2DF3wk3028670@dev.open-bio.org>


kawas
Thu Mar 13 11:03:58 EDT 2008
Update of /home/repository/moby/moby-live/Perl/MOBY-Server/share/cgi
In directory dev.open-bio.org:/tmp/cvs-serv28634/Perl/MOBY-Server/share/cgi

Modified Files:
	authority.pl 
Log Message:
removed the soap ports. unfortunately, since we have to serve attachments when using soap and soap lite doesnt have attachment support (currently) these ports are now disabled.
moby-live/Perl/MOBY-Server/share/cgi authority.pl,1.2,1.3
===================================================================
RCS file: /home/repository/moby/moby-live/Perl/MOBY-Server/share/cgi/authority.pl,v
retrieving revision 1.2
retrieving revision 1.3
diff -u -r1.2 -r1.3
--- /home/repository/moby/moby-live/Perl/MOBY-Server/share/cgi/authority.pl	2008/03/11 14:44:18	1.2
+++ /home/repository/moby/moby-live/Perl/MOBY-Server/share/cgi/authority.pl	2008/03/13 15:03:58	1.3
@@ -91,12 +91,12 @@
 
 my $port;
 
-$port = LS::Authority::WSDL::Simple::MetadataPort->newMetadata(
-	portName=> 'BioMOBYSoapPort',
-	endpoint=> "$location/authority/metadata",
-	protocol=> $LS::Authority::WSDL::Constants::Protocols::SOAP,
-  );
-$authority->addPort(serviceName=> 'BioMOBYSoapMeta', port=> $port);
+#$port = LS::Authority::WSDL::Simple::MetadataPort->newMetadata(
+#	portName=> 'BioMOBYSoapPort',
+#	endpoint=> "$location/authority/metadata",
+#	protocol=> $LS::Authority::WSDL::Constants::Protocols::SOAP,
+#  );
+#$authority->addPort(serviceName=> 'BioMOBYSoapMeta', port=> $port);
 
 $port = LS::Authority::WSDL::Simple::MetadataPort->newMetadata(
 	portName=> 'BioMOBYHttpPort',
@@ -112,13 +112,13 @@
         protocol=> $LS::Authority::WSDL::Constants::Protocols::HTTP,
   );
 
-$authority->addPort(serviceName=> 'BioMOBYHttpData', port=> $port);
-$port = LS::Authority::WSDL::Simple::DataPort->newData(
-        portName=> 'BioMOBYSoapPort',
-        endpoint=> "$location/authority/data",
-        protocol=> $LS::Authority::WSDL::Constants::Protocols::SOAP,
-  );
-$authority->addPort(serviceName=> 'BioMOBYSoapData', port=> $port);
+#$authority->addPort(serviceName=> 'BioMOBYSoapData', port=> $port);
+#$port = LS::Authority::WSDL::Simple::DataPort->newData(
+#        portName=> 'BioMOBYSoapPort',
+#        endpoint=> "$location/authority/data",
+#        protocol=> $LS::Authority::WSDL::Constants::Protocols::SOAP,
+#  );
+#$authority->addPort(serviceName=> 'BioMOBYSoapData', port=> $port);
 
 
 # Add the metadata service with namespaces


From senger at dev.open-bio.org  Thu Mar 13 11:09:14 2008
From: senger at dev.open-bio.org (Martin Senger)
Date: Thu, 13 Mar 2008 11:09:14 -0400
Subject: [MOBY-guts] biomoby commit
Message-ID: <200803131509.m2DF9Ecm028742@dev.open-bio.org>


senger
Thu Mar 13 11:09:14 EDT 2008
Update of /home/repository/moby/moby-live/Java/src/main/org/biomoby/service/dashboard/help
In directory dev.open-bio.org:/tmp/cvs-serv28723/src/main/org/biomoby/service/dashboard/help

Modified Files:
	GeneratorPanel.html 
Log Message:
Dashboard help about the (remote) deployment improved.

moby-live/Java/src/main/org/biomoby/service/dashboard/help GeneratorPanel.html,1.3,1.4
===================================================================
RCS file: /home/repository/moby/moby-live/Java/src/main/org/biomoby/service/dashboard/help/GeneratorPanel.html,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/service/dashboard/help/GeneratorPanel.html	2006/06/01 15:20:08	1.3
+++ /home/repository/moby/moby-live/Java/src/main/org/biomoby/service/dashboard/help/GeneratorPanel.html	2008/03/13 15:09:14	1.4
@@ -80,7 +80,14 @@
 
 Usually, only <em>Tomcat home directory</em> needs to be changed
 (unless you have installed Axis in Tomcat in a non-standard
-place). The <em>WSDD template file</em> is an advanced feature - see
+place). <p>
+
+Be aware, however, that the deployment also uses properties defined in
+your <tt>build.properties</tt> file, and the value of the environment
+variable <tt>CATALINA_HOME</tt> (if defined). These properties take
+precedence over the values specified in the Dasboard's fields! <p>
+
+The <em>WSDD template file</em> is an advanced feature - see
 the deployment documentation. <p>
 
 Very important is the <em>Directory with user's jar files</em>. Here


From senger at dev.open-bio.org  Thu Mar 13 12:49:35 2008
From: senger at dev.open-bio.org (Martin Senger)
Date: Thu, 13 Mar 2008 12:49:35 -0400
Subject: [MOBY-guts] biomoby commit
Message-ID: <200803131649.m2DGnZnq028855@dev.open-bio.org>


senger
Thu Mar 13 12:49:35 EDT 2008
Update of /home/repository/moby/moby-live/Java/xmls
In directory dev.open-bio.org:/tmp/cvs-serv28832/xmls

Modified Files:
	project.pom upload2maven.xml 
Log Message:
Last few typos before uploading jMoby, version 1.0.0, to Maven

moby-live/Java/xmls project.pom,1.7,1.8 upload2maven.xml,1.1,1.2
===================================================================
RCS file: /home/repository/moby/moby-live/Java/xmls/project.pom,v
retrieving revision 1.7
retrieving revision 1.8
diff -u -r1.7 -r1.8
--- /home/repository/moby/moby-live/Java/xmls/project.pom	2008/03/12 18:41:26	1.7
+++ /home/repository/moby/moby-live/Java/xmls/project.pom	2008/03/13 16:49:35	1.8
@@ -4,7 +4,9 @@
   <artifactId>jmoby</artifactId>
   <version>1.0.0</version>
   <name>jMoby</name>
-  <description>A sub-project of the BioMoby project. It aims to develop tools in Java for BioMoby.</description>
+  <description>
+A sub-project of the BioMoby project. It aims to develop tools in Java for BioMoby.
+</description>
   <url>http://biomoby.open-bio.org/CVS_CONTENT/moby-live/Java/docs/</url>
 
   <developers>

===================================================================
RCS file: /home/repository/moby/moby-live/Java/xmls/upload2maven.xml,v
retrieving revision 1.1
retrieving revision 1.2
diff -u -r1.1 -r1.2
--- /home/repository/moby/moby-live/Java/xmls/upload2maven.xml	2008/02/14 06:13:37	1.1
+++ /home/repository/moby/moby-live/Java/xmls/upload2maven.xml	2008/03/13 16:49:35	1.2
@@ -23,7 +23,6 @@
 <!-- Deploy all parts of this project to a remote Maven repository -->
 <target name="mdeploy" depends="mdeploy-core"/>
 
-<!-- deploying soaplab.jar -->
 <target name="mdeploy-core" depends="initmaven,jars">
   <artifact:install-provider artifactId="${bio.maven.install.provider}" version="1.0-alpha-5"/>
 


From kawas at dev.open-bio.org  Thu Mar 13 15:12:08 2008
From: kawas at dev.open-bio.org (Eddie Kawas)
Date: Thu, 13 Mar 2008 15:12:08 -0400
Subject: [MOBY-guts] biomoby commit
Message-ID: <200803131912.m2DJC8nb029085@dev.open-bio.org>


kawas
Thu Mar 13 15:12:07 EDT 2008
Update of /home/repository/moby/moby-live/Perl/MOBY-Server/lib/MOBY/RDF/Parsers
In directory dev.open-bio.org:/tmp/cvs-serv29054/Perl/MOBY-Server/lib/MOBY/RDF/Parsers

Added Files:
	DatatypeParser.pm 
Log Message:
an rdf parser for datatypes
moby-live/Perl/MOBY-Server/lib/MOBY/RDF/Parsers DatatypeParser.pm,NONE,1.1

From kawas at dev.open-bio.org  Thu Mar 13 15:12:29 2008
From: kawas at dev.open-bio.org (Eddie Kawas)
Date: Thu, 13 Mar 2008 15:12:29 -0400
Subject: [MOBY-guts] biomoby commit
Message-ID: <200803131912.m2DJCTCM029125@dev.open-bio.org>


kawas
Thu Mar 13 15:12:29 EDT 2008
Update of /home/repository/moby/moby-live/Perl/MOBY-Server
In directory dev.open-bio.org:/tmp/cvs-serv29090/Perl/MOBY-Server

Modified Files:
	MANIFEST 
Log Message:
added the DatatypeParser.pm module
moby-live/Perl/MOBY-Server MANIFEST,1.3,1.4
===================================================================
RCS file: /home/repository/moby/moby-live/Perl/MOBY-Server/MANIFEST,v
retrieving revision 1.3
retrieving revision 1.4
diff -u -r1.3 -r1.4
--- /home/repository/moby/moby-live/Perl/MOBY-Server/MANIFEST	2008/03/05 18:25:01	1.3
+++ /home/repository/moby/moby-live/Perl/MOBY-Server/MANIFEST	2008/03/13 19:12:29	1.4
@@ -57,6 +57,7 @@
 lib/MOBY/OntologyServer.pm
 lib/MOBY/RDF/Parsers/NamespaceParser.pm
 lib/MOBY/RDF/Parsers/ServiceTypeParser.pm
+lib/MOBY/RDF/Parsers/DatatypeParser.pm
 lib/MOBY/RDF/Ontologies/Cache/CacheUtils.pm
 lib/MOBY/RDF/Ontologies/Cache/NamespaceCache.pm
 lib/MOBY/RDF/Ontologies/Cache/ObjectCache.pm


From kawas at dev.open-bio.org  Thu Mar 13 15:12:45 2008
From: kawas at dev.open-bio.org (Eddie Kawas)
Date: Thu, 13 Mar 2008 15:12:45 -0400
Subject: [MOBY-guts] biomoby commit
Message-ID: <200803131912.m2DJCjP7029165@dev.open-bio.org>


kawas
Thu Mar 13 15:12:44 EDT 2008
Update of /home/repository/moby/moby-live/Perl/MOBY-Client
In directory dev.open-bio.org:/tmp/cvs-serv29130/Perl/MOBY-Client

Modified Files:
	populate_libs.pl 
Log Message:
added the DatatypeParser.pm module
moby-live/Perl/MOBY-Client populate_libs.pl,1.4,1.5
===================================================================
RCS file: /home/repository/moby/moby-live/Perl/MOBY-Client/populate_libs.pl,v
retrieving revision 1.4
retrieving revision 1.5
diff -u -r1.4 -r1.5
--- /home/repository/moby/moby-live/Perl/MOBY-Client/populate_libs.pl	2008/03/05 18:22:00	1.4
+++ /home/repository/moby/moby-live/Perl/MOBY-Client/populate_libs.pl	2008/03/13 19:12:44	1.5
@@ -13,7 +13,7 @@
 my @Client		= qw ( Central.pm CollectionArticle.pm OntologyServer.pm Registration.pm SecondaryArticle.pm Service.pm ServiceInstance.pm SimpleArticle.pm SimpleInput.pm );
 my @Exception 	= qw ( MobyException.pm MobyExceptionCodes.pm );
 my @RDF 		= qw ( Utils.pm );
-my @Parsers 	= qw ( ServiceTypeParser.pm NamespaceParser.pm );
+my @Parsers 	= qw ( ServiceTypeParser.pm NamespaceParser.pm DatatypeParser.pm);
 my @predicates  = qw ( DC_PROTEGE.pm MOBY_PREDICATES.pm OMG_LSID.pm RDF.pm RDFS.pm FETA.pm OWL.pm );
 
 # current working directory ...


From kawas at dev.open-bio.org  Thu Mar 13 15:13:00 2008
From: kawas at dev.open-bio.org (Eddie Kawas)
Date: Thu, 13 Mar 2008 15:13:00 -0400
Subject: [MOBY-guts] biomoby commit
Message-ID: <200803131913.m2DJD06I029205@dev.open-bio.org>


kawas
Thu Mar 13 15:12:59 EDT 2008
Update of /home/repository/moby/moby-live/Perl/MOBY-Client
In directory dev.open-bio.org:/tmp/cvs-serv29170/Perl/MOBY-Client

Modified Files:
	MANIFEST 
Log Message:
added the DatatypeParser.pm module
moby-live/Perl/MOBY-Client MANIFEST,1.7,1.8
===================================================================
RCS file: /home/repository/moby/moby-live/Perl/MOBY-Client/MANIFEST,v
retrieving revision 1.7
retrieving revision 1.8
diff -u -r1.7 -r1.8
--- /home/repository/moby/moby-live/Perl/MOBY-Client/MANIFEST	2008/03/05 18:24:22	1.7
+++ /home/repository/moby/moby-live/Perl/MOBY-Client/MANIFEST	2008/03/13 19:12:59	1.8
@@ -30,6 +30,7 @@
 lib/MOBY/Client/SimpleInput.pm
 lib/MOBY/RDF/Parsers/NamespaceParser.pm
 lib/MOBY/RDF/Parsers/ServiceTypeParser.pm
+lib/MOBY/RDF/Parsers/DatatypeParser.pm
 lib/MOBY/RDF/Predicates/DC_PROTEGE.pm
 lib/MOBY/RDF/Predicates/FETA.pm
 lib/MOBY/RDF/Predicates/MOBY_PREDICATES.pm


From gordonp at dev.open-bio.org  Thu Mar 13 18:56:53 2008
From: gordonp at dev.open-bio.org (Paul Gordon)
Date: Thu, 13 Mar 2008 18:56:53 -0400
Subject: [MOBY-guts] biomoby commit
Message-ID: <200803132256.m2DMur3r031157@dev.open-bio.org>


gordonp
Thu Mar 13 18:56:53 EDT 2008
Update of /home/repository/moby/moby-live/Java/src/main/org/biomoby/shared
In directory dev.open-bio.org:/tmp/cvs-serv31121/src/main/org/biomoby/shared

Modified Files:
	MobyPrefixResolver.java 
Log Message:
Added WSDL 2.0 support
moby-live/Java/src/main/org/biomoby/shared MobyPrefixResolver.java,1.13,1.14
===================================================================
RCS file: /home/repository/moby/moby-live/Java/src/main/org/biomoby/shared/MobyPrefixResolver.java,v
retrieving revision 1.13
retrieving revision 1.14
diff -u -r1.13 -r1.14
--- /home/repository/moby/moby-live/Java/src/main/org/biomoby/shared/MobyPrefixResolver.java	2008/03/12 17:47:18	1.13
+++ /home/repository/moby/moby-live/Java/src/main/org/biomoby/shared/MobyPrefixResolver.java	2008/03/13 22:56:52	1.14
@@ -46,6 +46,8 @@
     public static final String XLINK_NAMESPACE = "http://www.w3.org/1999/xlink";
     public static final String WSDL_PREFIX = "wsdl";
     public static final String WSDL_NAMESPACE = "http://schemas.xmlsoap.org/wsdl/";
+    public static final String WSDL20_PREFIX = "wsdl20";
+    public static final String WSDL20_NAMESPACE = "http://www.w3.org/2006/01/wsdl";
     public static final String HTTP_PREFIX = "http";
     public static final String HTTP_NAMESPACE = "http://schemas.xmlsoap.org/wsdl/http/";
     public static final String SAWSDL_PREFIX = "sawsdl";


From gordonp at dev.open-bio.org  Thu Mar 13 18:58:11 2008
From: gordonp at dev.open-bio.org (Paul Gordon)
Date: Thu, 13 Mar 2008 18:58:11 -0400
Subject: [MOBY-guts] biomoby commit
Message-ID: <200803132258.m2DMwBFO031259@dev.open-bio.org>


gordonp
Thu Mar 13 18:58:10 EDT 2008
Update of /home/repository/moby/moby-live/Java/src/main/org/biomoby/service/test
In directory dev.open-bio.org:/tmp/cvs-serv31223/src/main/org/biomoby/service/test

Modified Files:
	MobyServletTestCase.java 
Log Message:
Better servlet initialization
moby-live/Java/src/main/org/biomoby/service/test MobyServletTestCase.java,1.8,1.9
===================================================================
RCS file: /home/repository/moby/moby-live/Java/src/main/org/biomoby/service/test/MobyServletTestCase.java,v
retrieving revision 1.8
retrieving revision 1.9
diff -u -r1.8 -r1.9
--- /home/repository/moby/moby-live/Java/src/main/org/biomoby/service/test/MobyServletTestCase.java	2007/12/14 16:26:00	1.8
+++ /home/repository/moby/moby-live/Java/src/main/org/biomoby/service/test/MobyServletTestCase.java	2008/03/13 22:58:10	1.9
@@ -224,6 +224,15 @@
 	}
 	resultContents.clear();  // so we don't build up junk from multiple responses
 
+	// Sets up hashtables, etc. we'll use implicitly below for error checking
+	try{
+	    fasta_na2dna.init(getMobyServlet().getServletConfig()); 
+	} catch(Exception e){
+	    e.printStackTrace();
+	    fail("Exception while configuring FromFastaToDNASequence servlet for testing: " + e);
+	}
+
+	System.err.println("Don't worry, an exception warning about INPUT_INCORRECT_SIMPLE should appear next...it's expected");
 	// Call second service on output of previous service, the input is actually AA, not DNA as expected
 	try{
 	    fasta_na2dna.processRequests(MobyDataUtils.fromXMLDocument(new java.io.ByteArrayInputStream(outBuffer.getBuffer().toString().getBytes())), 
@@ -295,6 +304,7 @@
 	testRequest.setInputStream(testDataURL.openStream());
 
 	MobyServlet servlet = getMobyServlet();
+	servlet.createServiceFromConfig(null);  // initialized required settings
 	MobyContentInstance mobyContents = servlet.getMobyContents(testRequest);
 	assertNotNull("Could not retrieve the MOBY data payload from the test HTTP request", mobyContents);
     }
@@ -310,7 +320,8 @@
      * @return a test suite for all the test methods of this test case.
      */
     public static Test suite() {
-
+	System.setProperty("javax.xml.parsers.DocumentBuilderFactory", 
+			   "com.sun.org.apache.xerces.internal.jaxp.DocumentBuilderFactoryImpl"); 
 	TestSuite suite = new TestSuite();
       	suite.addTest(new MobyServletTestCase("testRDF"));
  	suite.addTest(new MobyServletTestCase("testSoapParsing"));


From gordonp at dev.open-bio.org  Thu Mar 13 19:02:22 2008
From: gordonp at dev.open-bio.org (Paul Gordon)
Date: Thu, 13 Mar 2008 19:02:22 -0400
Subject: [MOBY-guts] biomoby commit
Message-ID: <200803132302.m2DN2MiM031465@dev.open-bio.org>


gordonp
Thu Mar 13 19:02:22 EDT 2008
Update of /home/repository/moby/moby-live/Java/src/main/org/biomoby/service
In directory dev.open-bio.org:/tmp/cvs-serv31429/src/main/org/biomoby/service

Modified Files:
	MobyServlet.java 
Log Message:
Extra parameter override configuration, and moby annotation parsing improved
moby-live/Java/src/main/org/biomoby/service MobyServlet.java,1.14,1.15
===================================================================
RCS file: /home/repository/moby/moby-live/Java/src/main/org/biomoby/service/MobyServlet.java,v
retrieving revision 1.14
retrieving revision 1.15
diff -u -r1.14 -r1.15
--- /home/repository/moby/moby-live/Java/src/main/org/biomoby/service/MobyServlet.java	2008/02/14 06:08:31	1.14
+++ /home/repository/moby/moby-live/Java/src/main/org/biomoby/service/MobyServlet.java	2008/03/13 23:02:22	1.15
@@ -82,6 +82,7 @@
     // Only use for keep track of MobyServices if they have template values that are filled in at service invocation
     protected Map<Thread,MobyService> templatedServicesMap; 
     protected Map<Thread,MobyContentInstance> responseContentInstanceMap; 
+    protected Map<String,String> extraConfig;
 
     public void doGet(HttpServletRequest request,
 		      HttpServletResponse response)
@@ -308,6 +309,9 @@
 	    MobyPrimaryData param = template[i];
 	    MobyDataInstance nameMatch = job.get(param.getName());
 	    if(nameMatch == null){
+                MobyContentInstance mci = new MobyContentInstance();
+                mci.put(job);
+                MobyDataUtils.toXMLDocument(System.err, mci);
 		throw new IllegalArgumentException(errMessagePrefix + 
 					       ": required primary value \"" + param.getName() + 
 					       "\" in job " + job.getID() + " is missing");
@@ -738,6 +742,9 @@
     }
 
     protected String getCoCInitParameter(String paramName){
+        if(extraConfig != null && extraConfig.containsKey(paramName)){
+            return extraConfig.get(paramName);
+        }
 	javax.servlet.ServletConfig config = getServletConfig();
 	if(config != null){
 	    if(config.getInitParameter(paramName) != null){
@@ -753,6 +760,13 @@
 	return getInitParameter(paramName);
     }
 
+    public synchronized void setCoCInitParameter(String param, String value){
+        if(extraConfig == null){
+          extraConfig = new HashMap<String,String>();
+        }
+        extraConfig.put(param, value);
+    }
+
     public synchronized MobyService createServiceFromConfig(HttpServletRequest request) throws Exception{
 	MobyService service = new MobyService(getServiceName());
 
@@ -909,7 +923,7 @@
 	   param.indexOf(".") < 2 || param.indexOf(".") > param.length()-2 ||
 	   param.lastIndexOf("@") > param.lastIndexOf(".")){
 	    throw new Exception("Required " + MOBY_CONTACT_PARAM + 
-				" parameter in servlet config did not have the form \"name at mail.domain\")");
+				" parameter in servlet config did not have the form \"name at mail.domain\" (found "+param+")");
 	}
 	
 	service.setEmailContact(param);
@@ -985,7 +999,7 @@
      * e.g. <code>hits:Integer:100:[0,]</code>
      */
     public static MobySecondaryData stringToSecondaryDataTemplate(String template) throws Exception{
-	String[] fields = template.split(":");
+	String[] fields = template.split(":", -2); // -2 == don't strip trailing blank fields
 	if(fields.length < 3){
 	    throw new Exception("The parameter specification (" + 
 				template + ") must have the minimal form " +
@@ -1023,16 +1037,16 @@
 
 	// Ensure the [] are there, and strip them
 	if(spec.length() > 0){
-	    if(spec.indexOf('[') != 1 || spec.lastIndexOf(']') != spec.length()){
+	    if(spec.length() < 3 || spec.indexOf('[') != 0 || spec.lastIndexOf(']') != spec.length()-1){
 		throw new Exception("Parameter options specification (4th field of '" + 
 				    template + "') " +
 				    "does not have the required form '[...]', but rather: " + spec);
 	    }
-	    spec = spec.substring(1, spec.length());
+	    spec = spec.substring(1, spec.length()-1);
 	}
 	String[] specValues = new String[0];
 	if(spec.length() > 0){
-	    specValues = spec.split(",");
+	    specValues = spec.split(",", -2); // -2 == keep trailing blank values
 	}
 
 	if(dataType.equals(MobySecondaryData.INTEGER_TYPE) ||
@@ -1063,7 +1077,7 @@
 					    "is less than the minimum value specified");
 		    }
 		}
-		if(min != null){
+		if(max != null){
 		    if(max.compareTo(defaultNumber) < 0){
 			throw new Exception("Numeric parameter default (3rd field of " + template + "') " +
 					    "is greater than the maximum value specified");
@@ -1307,6 +1321,7 @@
             return;
 	}
 
+        
         MobyServlet servlet = new MobyServlet();
 	ClassLoader classLoader = servlet.getClass().getClassLoader();
         try{


From gordonp at dev.open-bio.org  Thu Mar 13 19:05:48 2008
From: gordonp at dev.open-bio.org (Paul Gordon)
Date: Thu, 13 Mar 2008 19:05:48 -0400
Subject: [MOBY-guts] biomoby commit
Message-ID: <200803132305.m2DN5mEE031735@dev.open-bio.org>


gordonp
Thu Mar 13 19:05:47 EDT 2008
Update of /home/repository/moby/moby-live/Java/src/main/ca/ucalgary/services/util
In directory dev.open-bio.org:/tmp/cvs-serv31699/src/main/ca/ucalgary/services/util

Modified Files:
	XHTMLForm.java 
Added Files:
	MobySpecWrapper.java 
Log Message:
Moved a bunch of code common to all legacy wrapping configs to MobySpecWrapper
moby-live/Java/src/main/ca/ucalgary/services/util MobySpecWrapper.java,NONE,1.1 XHTMLForm.java,1.6,1.7
===================================================================
RCS file: /home/repository/moby/moby-live/Java/src/main/ca/ucalgary/services/util/XHTMLForm.java,v
retrieving revision 1.6
retrieving revision 1.7
diff -u -r1.6 -r1.7
--- /home/repository/moby/moby-live/Java/src/main/ca/ucalgary/services/util/XHTMLForm.java	2008/02/12 09:00:16	1.6
+++ /home/repository/moby/moby-live/Java/src/main/ca/ucalgary/services/util/XHTMLForm.java	2008/03/13 23:05:47	1.7
@@ -21,27 +21,13 @@
  * This allows us to wrap Web pages as Moby services using a similar mechanism to that
  * which wraps ACD-described command line tools such as EMBOSS programs.
  */
-public class XHTMLForm{
+public class XHTMLForm extends MobySpecWrapper{
 
     private static XPath xPath;
     private static DocumentBuilder docBuilder;
     private Document xhtmlDoc;
     private URL formURL;
     
-    private Map<String,String> serviceNames;
-    private String currentService;
-    private Map<String,String> serviceTypes;
-    private Map<String,String> serviceDescs;
-    private Map<String,String> providerURIs;
-    private Map<String,String> centralEndpoints;
-    private String contactEmail;
-
-    private Map<String,Map<String,String>> serviceInputs;
-    private Map<String,Map<String,String>> serviceInputFormats;
-    private Map<String,Map<String,String>> serviceSecondaries;
-    private Map<String,String[]> serviceOutputs;
-    private Map<String,Map<String,String>> fixedParams;
-
     private Map<String,List<String>> formFiles;
     private Map<String,String> formEncType;
     private Map<String,String> formAction;
@@ -102,17 +88,6 @@
     public XHTMLForm(URL url) throws Exception{
 	formURL = url;
 
-	serviceNames = new HashMap<String,String>();
-	currentService = "";
-	serviceTypes = new HashMap<String,String>();
-	serviceDescs = new HashMap<String,String>();
-	providerURIs = new HashMap<String,String>();
-	centralEndpoints = new HashMap<String,String>();
-	fixedParams = new HashMap<String,Map<String,String>>();
-	serviceInputs = new HashMap<String,Map<String,String>>();
-	serviceInputFormats = new HashMap<String,Map<String,String>>();
-	serviceSecondaries = new HashMap<String,Map<String,String>>();
-	serviceOutputs = new HashMap<String,String[]>();
 	formFiles = new HashMap<String,List<String>>();
 	formEncType = new HashMap<String,String>();
 	formAction = new HashMap<String,String>();
@@ -677,7 +652,7 @@
 
 	// The output datatype of the service is also declared in the form tag
 	List<String> outputSpecs = parseMobySpecs(serviceFormElement, mobyPrefix);
-	String[] cleanOutputSpecs = new String[outputSpecs.size()];
+	Map<String,String> cleanOutputSpecs = new HashMap<String,String>();
 	for(int i = 0; i < outputSpecs.size(); i++){
 	    String spec = outputSpecs.get(i);
 	    if(!outputSpecs.get(i).startsWith(serviceName+":")){
@@ -693,7 +668,17 @@
 				    ") not of the required form '"+mobyPrefix+":"+
 				    serviceName+":paramName:DataType'");
 	    }
-	    cleanOutputSpecs[i] = spec.substring(serviceName.length()+1);
+	    // The outputs have no existing names in the HTML/text/etc. output, 
+	    // so enforce that they be the same as the Moby param names 
+	    // (i.e. the stuff before the first colon in the moby param spec)
+	    String outParam = spec.substring(serviceName.length()+1);
+	    if(!outParam.contains(":")){
+		throw new Exception("The form for service '" + serviceName +
+				    "' contains moby specs (" + spec + 
+				    ") not of the required form '"+mobyPrefix+":"+
+				    serviceName+":paramName:DataType' (last colon missing)");
+	    }
+	    cleanOutputSpecs.put(outParam.substring(0, outParam.indexOf(":")), outParam);
 	}
 
 	setPrimaryOutputs(cleanOutputSpecs);
@@ -966,105 +951,6 @@
 	return optionsMap;
     }
 
-    public String[] getServiceNames(){
-	return providerURIs.keySet().toArray(new String[providerURIs.size()]);
-    }
-
-    public void setCurrentService(String serviceToReport) throws IllegalArgumentException{
-	currentService = serviceToReport;
-    }
-
-    public String getServiceName(){
-	return currentService;
-    }
-
-    public void setServiceType(String type){
-	serviceTypes.put(currentService, type);
-    }
-
-    public String getServiceType(){
-	return serviceTypes.get(currentService);
-    }
-
-    public void setServiceDesc(String desc){
-	serviceDescs.put(currentService, desc);
-    }
-
-    public String getServiceDesc(){
-	return serviceDescs.get(currentService);
-    }
-
-    public void setProviderURI(String uri){
-	providerURIs.put(currentService, uri);
-    }
-
-    public String getProviderURI(){
-	return providerURIs.get(currentService);
-    }
-
-    public void setCentralEndpoint(String ep){
-	centralEndpoints.put(currentService, ep);
-    }
-
-    public String getCentralEndpoint(){
-	return centralEndpoints.get(currentService);
-    }
-
-    public void setContactEmail(String email){
-	contactEmail = email;
-    }
-
-    public String getContactEmail(){
-	return contactEmail;
-    }
-
-    /**
-     * @param specs Map<cgi_param_name,mobyservlet_param_spec>, where mobyservlet_param_spec has an extra field at the end describing the text-type
-     */
-    public void setPrimaryInputs(Map<String,String> specs){
-	serviceInputs.put(currentService, specs);
-    }
-
-    public Map<String,String> getPrimaryInputs(){
-	return serviceInputs.get(currentService);
-    }
-
-    public void setPrimaryInputFormats(Map<String,String> specs){
-	serviceInputFormats.put(currentService, specs);
-    }
-
-    public Map<String,String> getPrimaryInputFormats(){
-	return serviceInputFormats.get(currentService);
-    }
-
-    public void setPrimaryOutputs(String[] specs){
-	serviceOutputs.put(currentService, specs);
-    }
-
-    public String[] getPrimaryOutputs(){
-	return serviceOutputs.get(currentService);
-    }
-
-    /**
-     * @param specs Map<cgi_param_name,mobyservlet_secondary_param_spec>
-     */
-    public void setSecondaryInputs(Map<String,String> specs){
-	serviceSecondaries.put(currentService, specs);
-    }
-
-    public Map<String,String> getSecondaryInputs(){
-	return serviceSecondaries.get(currentService);
-    }
-
-    // Note that the map is not cloned...
-    public void setFixedParams(Map<String,String> params){
-	fixedParams.put(currentService, params);
-    }
-
-    public Map<String,String> getFixedParams(){
-	return fixedParams.get(currentService);
-    }
-   
     // Note that the map is not cloned...
     public void setSubmitOptions(Map<String,String> options){
 	formSubmitOptions.put(currentService, options);


From gordonp at dev.open-bio.org  Thu Mar 13 19:06:48 2008
From: gordonp at dev.open-bio.org (Paul Gordon)
Date: Thu, 13 Mar 2008 19:06:48 -0400
Subject: [MOBY-guts] biomoby commit
Message-ID: <200803132306.m2DN6mUR031807@dev.open-bio.org>


gordonp
Thu Mar 13 19:06:48 EDT 2008
Update of /home/repository/moby/moby-live/Java/src/main/ca/ucalgary/services/util/test
In directory dev.open-bio.org:/tmp/cvs-serv31771/src/main/ca/ucalgary/services/util/test

Modified Files:
	XHTMLFormTestCase.java 
Log Message:
Changes made to reflect refactoring for XHTMLForm/MobySpecWrapper
moby-live/Java/src/main/ca/ucalgary/services/util/test XHTMLFormTestCase.java,1.5,1.6
===================================================================
RCS file: /home/repository/moby/moby-live/Java/src/main/ca/ucalgary/services/util/test/XHTMLFormTestCase.java,v
retrieving revision 1.5
retrieving revision 1.6
diff -u -r1.5 -r1.6
--- /home/repository/moby/moby-live/Java/src/main/ca/ucalgary/services/util/test/XHTMLFormTestCase.java	2008/02/27 15:26:12	1.5
+++ /home/repository/moby/moby-live/Java/src/main/ca/ucalgary/services/util/test/XHTMLFormTestCase.java	2008/03/13 23:06:48	1.6
@@ -120,10 +120,10 @@
 		   ") was not as expected (" + NUM_SECONDARY_INPUTS + ")",
 		   NUM_SECONDARY_INPUTS == secondaryInputs.size());
 
-	String[] outputs = form.getPrimaryOutputs();
-	assertTrue("The number of primary output parameters defined (" + outputs.length +
+	Map<String,String> outputs = form.getPrimaryOutputs();
+	assertTrue("The number of primary output parameters defined (" + outputs.size() +
 		   ") was not as expected (" + NUM_OUTPUTS + ")",
-		   NUM_OUTPUTS == outputs.length);
+		   NUM_OUTPUTS == outputs.size());
 	
 	// Check the HTML-specific specs
 	Map<String,String> fixedParams = form.getFixedParams();
@@ -156,9 +156,9 @@
 		   inseqFormat + "'",
 		   inseqFormat.equals(primaryInputFormats.get(inputHTMLParamName)));
 	assertTrue("The value of the output parameter 'primers' (" +
-		   outputs[0] + ") was not the expected value '" + 
+		   outputs.get("primers") + ") was not the expected value '" + 
 		   primers + "'",
-		   primers.equals(outputs[0]));
+		   primers.equals(outputs.get("primers")));
      
 	assertTrue("The value of the secondary parameter 'bias' (" + 
 		   secondaryInputs.get("bias") + ") was not the expected value '" + bias + "'", 


From gordonp at dev.open-bio.org  Thu Mar 13 19:06:48 2008
From: gordonp at dev.open-bio.org (Paul Gordon)
Date: Thu, 13 Mar 2008 19:06:48 -0400
Subject: [MOBY-guts] biomoby commit
Message-ID: <200803132306.m2DN6mok031827@dev.open-bio.org>


gordonp
Thu Mar 13 19:06:48 EDT 2008
Update of /home/repository/moby/moby-live/Java/src/main/ca/ucalgary/services
In directory dev.open-bio.org:/tmp/cvs-serv31771/src/main/ca/ucalgary/services

Modified Files:
	CGIService.java 
Log Message:
Changes made to reflect refactoring for XHTMLForm/MobySpecWrapper
moby-live/Java/src/main/ca/ucalgary/services CGIService.java,1.6,1.7
===================================================================
RCS file: /home/repository/moby/moby-live/Java/src/main/ca/ucalgary/services/CGIService.java,v
retrieving revision 1.6
retrieving revision 1.7
diff -u -r1.6 -r1.7
--- /home/repository/moby/moby-live/Java/src/main/ca/ucalgary/services/CGIService.java	2008/02/27 15:23:56	1.6
+++ /home/repository/moby/moby-live/Java/src/main/ca/ucalgary/services/CGIService.java	2008/03/13 23:06:48	1.7
@@ -22,10 +22,9 @@
  * publishing, etc.  The service description fetching, and the command invocation
  * are overridden.
  */
-public class CGIService extends LegacyService{
+public class CGIService extends WrapperService<XHTMLForm>{
     protected URL remoteFormURL;
     // params that override annoation and servlet context/config params
-    protected Map<String,String> cgiConfig; 
     protected XHTMLForm formConfig;
     // mobyParamName -> form fields that used a transformed version of it
     protected Map<String,String[]> mobyPrimary2FormFields;
@@ -40,7 +39,6 @@
     public void init(){
 	super.init();
 
-	cgiConfig = new HashMap<String,String>();
 	mobyPrimary2FormFields = new HashMap<String,String[]>();
 	mobySecondary2FormFields = new HashMap<String,String[]>();
 
@@ -158,77 +156,18 @@
     public MobyService createServiceFromConfig(javax.servlet.http.HttpServletRequest request)
 	throws Exception{
 	
-	String remoteFormURLString = null;
-	if(getCoCInitParameter(HTML_FORM_URL_PARAM) != null){
-	    remoteFormURLString = getCoCInitParameter(HTML_FORM_URL_PARAM);
-	}
-	else{
-	    throw new Exception("No parameter called " + HTML_FORM_URL_PARAM + 
-				" was found in the servlet configuration");
-	}
-	try{
-	    remoteFormURL = new URL(remoteFormURLString);
-	} catch(Exception e){
-            // Fallback to finding it as a resource
-            remoteFormURL = getClass().getClassLoader().getResource(remoteFormURLString);
-            if(remoteFormURL == null){
-	      throw new Exception("The configuration parameter '" + remoteFormURLString +
-	    			  "' (value '" + remoteFormURLString + 
-				  "') was not parseable as a URL");
-            }
-	}
+        remoteFormURL = getSpecURL(HTML_FORM_URL_PARAM);
 
 	try{
 	    formConfig = new XHTMLForm(remoteFormURL);
 	} catch(Exception e){
             e.printStackTrace();
 	    throw new Exception("Could not determine Moby service configuration from the HTML form (" + 
-				remoteFormURLString + "): " + e);
+				remoteFormURL.toString() + "): " + e);
 	}
-	// Configure meta-data for the Moby service about to be created
-	String[] serviceNames = formConfig.getServiceNames();
-	if(serviceNames.length > 1){
-	    String targetedService = getCoCInitParameter(MOBY_SERVICENAME_PARAM);
-	    String valuesString = "";
-	    for(String value: serviceNames){
-		valuesString += value + " ";
-	    }
-	    if(targetedService == null || targetedService.trim().length() == 0){
-		throw new Exception("The HTML page to wrap contains more than one Moby-annotated " +
-				    "form/service, but no '"+MOBY_SERVICENAME_PARAM+"' parameter was " +
-				    "specified in the servlet configuration.  Please specify this " +
-				    "parameter with one of the following values: " + valuesString);
-	    }
-	    boolean foundService = false;
-	    for(String validName: serviceNames){
-		if(targetedService.equals(validName)){
-		    foundService = true; 
-		    break;
-		}
-	    }
-	    if(!foundService){
-		throw new Exception("The service to wrap (" + targetedService + 
-				    "), named in the servlet configuration parameter '" +
-				    MOBY_SERVICENAME_PARAM + "', was not one of the service names " +
-				    "available from the HTML page.  Valid values are: " + valuesString);
-	    }
-	    formConfig.setCurrentService(targetedService);
-	}
-	setCoCInitParameter(MOBY_SERVICENAME_PARAM, formConfig.getServiceName());
-	setCoCInitParameter(MOBY_SERVICETYPE_PARAM, formConfig.getServiceType());
-	setCoCInitParameter(MOBY_SERVICE_DESC_PARAM, formConfig.getServiceDesc());
-	setCoCInitParameter(MOBY_PROVIDER_URI_PARAM, formConfig.getProviderURI());
-	setCoCInitParameter(MOBY_CENTRAL_URL_PARAM, formConfig.getCentralEndpoint());
-	setCoCInitParameter(MOBY_CONTACT_PARAM, formConfig.getContactEmail());
-
-	// Determine primary I/O parameters
-	setCoCInitParameter(MOBY_INPUT_PARAM, createInputSpecString(formConfig));
-	setCoCInitParameter(MOBY_OUTPUT_PARAM, createOutputSpecString(formConfig));
-	// Determine secondary parameters
-	setCoCInitParameter(MOBY_SECONDARYINPUT_PARAM, createSecondarySpecString(formConfig));
 
-	// Set up reusable http client objects
-	return super.createServiceFromConfig(request);
+        //Call to parent, which handles spec-wrapper-to-MobyServlet-config conversion
+	return createServiceFromConfig(request, formConfig);
     }
 
     protected MultipartRequestEntity getMultipartRequest(Map<String,byte[]> dataInstances, 
@@ -270,18 +209,6 @@
 	return XHTMLForm.join("+", queryItems);
     }
 
-    protected String getCoCInitParameter(String paramName){
-	javax.servlet.ServletConfig config = getServletConfig();
-	if(cgiConfig != null && cgiConfig.containsKey(paramName)){
-	    return cgiConfig.get(paramName);
-	}
-	return super.getCoCInitParameter(paramName);
-    }
-
-    public void setCoCInitParameter(String param, String value){
-	cgiConfig.put(param, value);
-    }
-
     public String createInputSpecString(XHTMLForm form){
 	Map<String,String> ins = form.getPrimaryInputs();
 	// Create a reverse map so we can look up where a moby param 
@@ -319,10 +246,16 @@
     }
 
     public String createOutputSpecString(XHTMLForm form){
-	return XHTMLForm.join(",", form.getPrimaryOutputs());
+	Map<String,String> outs = form.getPrimaryOutputs();
+	String[] outSpec = new String[outs.size()];
+	int i = 0;
+	for(String key: outs.keySet()){
+	    outSpec[i++] = key;
+	}
+	return XHTMLForm.join(",", outSpec);
     }
 
-    protected String createSecondarySpecString(XHTMLForm form){
+    public String createSecondarySpecString(XHTMLForm form){
 	Map<String,String> secondaries = form.getSecondaryInputs();
 	// Create a reverse map so we can look up where a moby param 
 	// slots into in the form.


From gordonp at dev.open-bio.org  Thu Mar 13 19:08:26 2008
From: gordonp at dev.open-bio.org (Paul Gordon)
Date: Thu, 13 Mar 2008 19:08:26 -0400
Subject: [MOBY-guts] biomoby commit
Message-ID: <200803132308.m2DN8QNp031937@dev.open-bio.org>


gordonp
Thu Mar 13 19:08:26 EDT 2008
Update of /home/repository/moby/moby-live/Java/src/main/ca/ucalgary/services/util
In directory dev.open-bio.org:/tmp/cvs-serv31905/src/main/ca/ucalgary/services/util

Added Files:
	WSDLConfig.java 
Log Message:
Initial commit of Semantic Annotations for WSDL-based Web Service wrapping code
moby-live/Java/src/main/ca/ucalgary/services/util WSDLConfig.java,NONE,1.1

From gordonp at dev.open-bio.org  Thu Mar 13 19:08:26 2008
From: gordonp at dev.open-bio.org (Paul Gordon)
Date: Thu, 13 Mar 2008 19:08:26 -0400
Subject: [MOBY-guts] biomoby commit
Message-ID: <200803132308.m2DN8Qg1031953@dev.open-bio.org>


gordonp
Thu Mar 13 19:08:26 EDT 2008
Update of /home/repository/moby/moby-live/Java/src/main/ca/ucalgary/services/util/test
In directory dev.open-bio.org:/tmp/cvs-serv31905/src/main/ca/ucalgary/services/util/test

Added Files:
	WSDLConfigTestCase.java KEGG.wsdl 
Log Message:
Initial commit of Semantic Annotations for WSDL-based Web Service wrapping code
moby-live/Java/src/main/ca/ucalgary/services/util/test WSDLConfigTestCase.java,NONE,1.1 KEGG.wsdl,NONE,1.1

From gordonp at dev.open-bio.org  Thu Mar 13 19:10:11 2008
From: gordonp at dev.open-bio.org (Paul Gordon)
Date: Thu, 13 Mar 2008 19:10:11 -0400
Subject: [MOBY-guts] biomoby commit
Message-ID: <200803132310.m2DNABsm032065@dev.open-bio.org>


gordonp
Thu Mar 13 19:10:11 EDT 2008
Update of /home/repository/moby/moby-live/Java/src/main/ca/ucalgary/services
In directory dev.open-bio.org:/tmp/cvs-serv32033/src/main/ca/ucalgary/services

Added Files:
	WrapperService.java 
Log Message:
Code from various wrapper classes in this package was refactored into this common class
moby-live/Java/src/main/ca/ucalgary/services WrapperService.java,NONE,1.1

From groscurt at dev.open-bio.org  Fri Mar 14 07:50:03 2008
From: groscurt at dev.open-bio.org (Andreas Groscurth)
Date: Fri, 14 Mar 2008 07:50:03 -0400
Subject: [MOBY-guts] biomoby commit
Message-ID: <200803141150.m2EBo30D004957@dev.open-bio.org>


groscurt
Fri Mar 14 07:50:02 EDT 2008
Update of /home/repository/moby/moby-live/Java
In directory dev.open-bio.org:/tmp/cvs-serv4926

Added Files:
	.classpath.template 
Log Message:
Added .classpath.template which eclipse users can use to integrate jmoby with eclipse

moby-live/Java .classpath.template,NONE,1.1

From groscurt at dev.open-bio.org  Fri Mar 14 10:01:01 2008
From: groscurt at dev.open-bio.org (Andreas Groscurth)
Date: Fri, 14 Mar 2008 10:01:01 -0400
Subject: [MOBY-guts] biomoby commit
Message-ID: <200803141401.m2EE11UC005125@dev.open-bio.org>


groscurt
Fri Mar 14 10:01:01 EDT 2008
Update of /home/repository/moby/moby-live/Java/docs
In directory dev.open-bio.org:/tmp/cvs-serv5088/docs

Modified Files:
	EclipseAndJMoby.html 
Added Files:
	ErrorsInEclipse.html 
Log Message:
changes in the documentation about the integration of JMoby in Eclipse and how to solve known errors
moby-live/Java/docs ErrorsInEclipse.html,NONE,1.1 EclipseAndJMoby.html,1.8,1.9
===================================================================
RCS file: /home/repository/moby/moby-live/Java/docs/EclipseAndJMoby.html,v
retrieving revision 1.8
retrieving revision 1.9
diff -u -r1.8 -r1.9
--- /home/repository/moby/moby-live/Java/docs/EclipseAndJMoby.html	2008/02/21 11:44:46	1.8
+++ /home/repository/moby/moby-live/Java/docs/EclipseAndJMoby.html	2008/03/14 14:01:01	1.9
@@ -123,6 +123,22 @@
 <tt>-showlocation</tt> - then the path of the current workspace is
 shown in the window title. <p>
 
+<h3>Integrate Maven plugin</h3>
+
+<p>As JMoby uses Maven we need to enable Maven in Eclipse. The Maven plugin requires two other plugins which we need to load.<br>
+<b class="step">Help -&gt; Software Updates -&gt; Find and Install -&gt; Search for new features and install</b> will open a dialog
+which shows all existing update sites your Eclipse already know.</p>
+
+<p>For each of the plugins please open <b class="step">New Remote Update Site</b> and add the following sites and install them 
+(make sure that you unselect optional components of the plugins if they produce errors):
+<ol>
+	<li>Name: Buckminster<br>URL: http://download.eclipse.org/tools/buckminster/updates</li>
+	<li>Name: Subversion<br>URL: http://subclipse.tigris.org/update_1.2.x</li>
+	<li>Name: Maven<br>URL: http://m2eclipse.sonatype.org/update/</li>
+</ol>
+After install the plugins please restart Eclipse to enable the Maven plugin.
+</p>
+
 <h3>Create a new CVS repository location</h3>
 
 <b class="step">Window -&gt; Open Perspective -&gt; Other -&gt; CVS
@@ -162,6 +178,13 @@
 about where jMoby has things and how it uses them. But before we fix
 that let's do one more thing... <p>
 
+<h3>Telling Eclipse the classpath</h3>
+We need to tell Eclipse now the building structure of JMoby, so that it knows where which source files are and to where it has to compile what.<br>
+For that (and only for the first time you set up Eclipse and JMoby) rename the <tt>.classpath.template</tt> from the checkout to <tt>.classpath</tt> 
+(and by that overwrite the .classpath file generated by Eclipse) and refresh your project either by right-click on the project and selecting <b class="step">Refresh</b> or by just hitting F5.<br>
+You will now see the new source folder structure. In the case you dont have a <tt>generated/skeletons</tt> and <tt>generated/datatypes</tt> folder shown
+up as source folder please add this two folders. Eclipse will then automatically recognize them as source folders.
+
 <!--
 <h3>Change location of Ant</h3>
 
@@ -184,20 +207,7 @@
 <tt>&lt;jMoby&gt;/lib/ant_home</tt>. <p>
 -->
 
-<!--
-<h3>Gather 3rd-party libraries</h3>
-
-This is done only the first time (and occasionally, time to time when
-the libraries change). If you are putting into Eclipse a copy of jMoby
-that you were already been working with, you probably already have the
-libraries fetched (but it does not harm if you go through this step,
-as well). <p>
-
-We are doing this step now, before telling Eclipse where the libraries
-are (because we first need to have them in order to show them to
-Eclipse, don't we?). Eclipse already found some 3rd-party libraries in
-jMoby and listed them in our project. These are from the included Ant
-(they were not needed for jMoby programs until recently). <p>
+<h3>Gather 3rd-party libraries and set up JMoby</h3>
 
 Now it's time for our real libraries. Open an Ant view by <b
 class="step">Window -&gt; Show View -&gt; Ant</b>. Then right-click
@@ -205,7 +215,7 @@
 class="step">build.xml</b> from jMoby. You can <b class="step">Hide
 internal targets</b> by clicking on the stroke green target icon. <p>
 
-Double-click on <b class="step">gather</b>. It shows progress in the
+Double-click on <b class="step">install</b>. It shows progress in the
 bottom of the screen in a console window. After that you may <b
 class="step">Refresh</b> your workspace. <p>
 
@@ -217,15 +227,20 @@
 jMoby documentation (e.g. about <a
 href="Download.html#targets">general targets</a>, or about <a
 href="Moses.html">Moses</a>).
-
 </blockquote>
 
+When the task is finished, double-click on <b class="step">initeclipse</b>, which will generate the file <tt>pom.xml</tt> 
+which the Maven plugin requires to work correctly. After the task refresh your workspace and right-click on the project 
+<b class="step">Maven -&gt; Enable Dependency Management</b>. This will now tell Eclipse to use the maven repository for the build path.<br>
+By now all your erros should be erazed and you only see several warnings (if you still got errors check <a href="ErrorsInEclipse.html">here</a>)
+
+<!--
 Again, right-click on the project name <b class="step">(jMoby) -&gt;
 Properties -&gt; Java Build Path</b>, select again tab <b
 class="step">Libraries</b>, and <b class="step">Add External
 JARS...</b>. Select all JAR files from &lt;jMoby&gt;/lib
 directory. <p>
--->
+
 
 <h3>Set source files</h3>
 
@@ -311,7 +326,7 @@
 you are an annoyed jMoby user, change warning preferences in <b
 class="step">Window -&gt; Preferences -&gt; Java -&gt; Compiler -&gt;
 Errors/Warnings</b> not to see them. <p>
-
+-->
 <h3>Fix <tt>javadoc</tt> location</h3>
 
 Ant's targets using <tt>javadoc</tt> (such as <tt>docs</tt> or


From senger at dev.open-bio.org  Fri Mar 14 19:27:41 2008
From: senger at dev.open-bio.org (Martin Senger)
Date: Fri, 14 Mar 2008 19:27:41 -0400
Subject: [MOBY-guts] biomoby commit
Message-ID: <200803142327.m2ENRfVP010464@dev.open-bio.org>


senger
Fri Mar 14 19:27:41 EDT 2008
Update of /home/repository/moby/moby-live/Java/docs
In directory dev.open-bio.org:/tmp/cvs-serv10444/docs

Modified Files:
	ChangeLog 
Log Message:
Putting back xercesImpl - but its newer version

moby-live/Java/docs ChangeLog,1.86,1.87
===================================================================
RCS file: /home/repository/moby/moby-live/Java/docs/ChangeLog,v
retrieving revision 1.86
retrieving revision 1.87
diff -u -r1.86 -r1.87
--- /home/repository/moby/moby-live/Java/docs/ChangeLog	2008/03/03 11:34:16	1.86
+++ /home/repository/moby/moby-live/Java/docs/ChangeLog	2008/03/14 23:27:41	1.87
@@ -1,3 +1,12 @@
+2008-03-14  Martin Senger  <martin.senger&#64;gmail.com>
+
+	* Fixed a bug with missing xercesImpl classes. Putting back
+	xercesImpl - but now with a newer version (2.7.1)
+
+2008-03-12  Martin Senger  <martin.senger&#64;gmail.com>
+
+	* Version 1.0.0 released
+
 2008-03-03  Martin Senger  <martin.senger&#64;gmail.com>
 
 	* Added a new method isUsingCache() to the CentralCached


From senger at dev.open-bio.org  Fri Mar 14 19:27:41 2008
From: senger at dev.open-bio.org (Martin Senger)
Date: Fri, 14 Mar 2008 19:27:41 -0400
Subject: [MOBY-guts] biomoby commit
Message-ID: <200803142327.m2ENRff6010484@dev.open-bio.org>


senger
Fri Mar 14 19:27:41 EDT 2008
Update of /home/repository/moby/moby-live/Java/xmls
In directory dev.open-bio.org:/tmp/cvs-serv10444/xmls

Modified Files:
	project.pom 
Log Message:
Putting back xercesImpl - but its newer version

moby-live/Java/xmls project.pom,1.8,1.9
===================================================================
RCS file: /home/repository/moby/moby-live/Java/xmls/project.pom,v
retrieving revision 1.8
retrieving revision 1.9
diff -u -r1.8 -r1.9
--- /home/repository/moby/moby-live/Java/xmls/project.pom	2008/03/13 16:49:35	1.8
+++ /home/repository/moby/moby-live/Java/xmls/project.pom	2008/03/14 23:27:41	1.9
@@ -222,6 +222,12 @@
     </dependency>
 
     <dependency>
+      <groupId>xerces</groupId>
+      <artifactId>xercesImpl</artifactId>
+      <version>2.7.1</version>
+    </dependency>
+
+    <dependency>
       <groupId>com.ibm.lsid</groupId>
       <artifactId>lsid-server</artifactId>
       <version>1.1.2</version>


From senger at dev.open-bio.org  Sat Mar 15 09:10:55 2008
From: senger at dev.open-bio.org (Martin Senger)
Date: Sat, 15 Mar 2008 09:10:55 -0400
Subject: [MOBY-guts] biomoby commit
Message-ID: <200803151310.m2FDAtmI011966@dev.open-bio.org>


senger
Sat Mar 15 09:10:54 EDT 2008
Update of /home/repository/moby/moby-live/Java/src/test/java/org/biomoby/service
In directory dev.open-bio.org:/tmp/cvs-serv11933/src/test/java/org/biomoby/service

Modified Files:
	ServicesTest.java 
Log Message:

moby-live/Java/src/test/java/org/biomoby/service ServicesTest.java,1.1,1.2
===================================================================
RCS file: /home/repository/moby/moby-live/Java/src/test/java/org/biomoby/service/ServicesTest.java,v
retrieving revision 1.1
retrieving revision 1.2
diff -u -r1.1 -r1.2
--- /home/repository/moby/moby-live/Java/src/test/java/org/biomoby/service/ServicesTest.java	2008/03/03 11:35:07	1.1
+++ /home/repository/moby/moby-live/Java/src/test/java/org/biomoby/service/ServicesTest.java	2008/03/15 13:10:54	1.2
@@ -190,14 +190,36 @@
      * This is to be able to run this JUnit 4 tests with a JUnit 3.x runner.
      **************************************************************************/
     public static junit.framework.Test suite() {
-        return new junit.framework.JUnit4TestAdapter (ServicesTest.class);
+        return new junit.framework.JUnit4TestAdapter (getThisClass());
     }
 
     /**************************************************************************
      * Run tests from the command line.
      **************************************************************************/
     public static void main (String args[]) {
-	org.junit.runner.JUnitCore.main ("org.biomoby.service.ServicesTest");
+	org.junit.runner.JUnitCore.main (getThisClassName());
+    }
+
+    /**************************************************************************
+     * Get the class (name) of this class (note that this is a static
+     * method). This madness is here just because I do not want to
+     * change the class name in the optional methods above when I copy
+     * and paste this into a new test file.
+     **************************************************************************/
+    private static String getThisClassName() {
+	Exception e = new Exception();
+	StackTraceElement[] sTrace = e.getStackTrace();
+	// sTrace[0] will be always there
+	return sTrace[0].getClassName();
+    }
+
+    private static Class getThisClass() {
+	try {
+	    return org.apache.commons.lang.ClassUtils.getClass (getThisClassName());
+	} catch (ClassNotFoundException e) {
+	    System.err.println ("Cannot get class name.");
+	    return java.lang.Object.class;
+	}
     }
 
 }


From senger at dev.open-bio.org  Sat Mar 15 09:10:55 2008
From: senger at dev.open-bio.org (Martin Senger)
Date: Sat, 15 Mar 2008 09:10:55 -0400
Subject: [MOBY-guts] biomoby commit
Message-ID: <200803151310.m2FDAtdH011984@dev.open-bio.org>


senger
Sat Mar 15 09:10:55 EDT 2008
Update of /home/repository/moby/moby-live/Java/src/test/java/org/biomoby/shared/parser
In directory dev.open-bio.org:/tmp/cvs-serv11933/src/test/java/org/biomoby/shared/parser

Modified Files:
	MobyParserTest.java 
Log Message:

moby-live/Java/src/test/java/org/biomoby/shared/parser MobyParserTest.java,1.4,1.5
===================================================================
RCS file: /home/repository/moby/moby-live/Java/src/test/java/org/biomoby/shared/parser/MobyParserTest.java,v
retrieving revision 1.4
retrieving revision 1.5
diff -u -r1.4 -r1.5
--- /home/repository/moby/moby-live/Java/src/test/java/org/biomoby/shared/parser/MobyParserTest.java	2008/03/03 11:34:17	1.4
+++ /home/repository/moby/moby-live/Java/src/test/java/org/biomoby/shared/parser/MobyParserTest.java	2008/03/15 13:10:55	1.5
@@ -216,14 +216,36 @@
      * This is to be able to run this JUnit 4 tests with a JUnit 3.x runner.
      **************************************************************************/
     public static junit.framework.Test suite() {
-        return new junit.framework.JUnit4TestAdapter (MobyParserTest.class);
+        return new junit.framework.JUnit4TestAdapter (getThisClass());
     }
 
     /**************************************************************************
      * Run tests from the command line.
      **************************************************************************/
     public static void main (String args[]) {
-	org.junit.runner.JUnitCore.main ("org.biomoby.shared.parser.MobyParserTest");
+	org.junit.runner.JUnitCore.main (getThisClassName());
+    }
+
+    /**************************************************************************
+     * Get the class (name) of this class (note that this is a static
+     * method). This madness is here just because I do not want to
+     * change the class name in the optional methods above when I copy
+     * and paste this into a new test file.
+     **************************************************************************/
+    private static String getThisClassName() {
+	Exception e = new Exception();
+	StackTraceElement[] sTrace = e.getStackTrace();
+	// sTrace[0] will be always there
+	return sTrace[0].getClassName();
+    }
+
+    private static Class getThisClass() {
+	try {
+	    return org.apache.commons.lang.ClassUtils.getClass (getThisClassName());
+	} catch (ClassNotFoundException e) {
+	    System.err.println ("Cannot get class name.");
+	    return java.lang.Object.class;
+	}
     }
 
 }


From senger at dev.open-bio.org  Sat Mar 15 09:10:55 2008
From: senger at dev.open-bio.org (Martin Senger)
Date: Sat, 15 Mar 2008 09:10:55 -0400
Subject: [MOBY-guts] biomoby commit
Message-ID: <200803151310.m2FDAtxi011948@dev.open-bio.org>


senger
Sat Mar 15 09:10:54 EDT 2008
Update of /home/repository/moby/moby-live/Java/src/config
In directory dev.open-bio.org:/tmp/cvs-serv11933/src/config

Added Files:
	run-junit-test run-junit-test.bat 
Log Message:

moby-live/Java/src/config run-junit-test,NONE,1.1 run-junit-test.bat,NONE,1.1

From kawas at dev.open-bio.org  Mon Mar 17 10:29:53 2008
From: kawas at dev.open-bio.org (Eddie Kawas)
Date: Mon, 17 Mar 2008 10:29:53 -0400
Subject: [MOBY-guts] biomoby commit
Message-ID: <200803171429.m2HETrSV019194@dev.open-bio.org>


kawas
Mon Mar 17 10:29:53 EDT 2008
Update of /home/repository/moby/moby-live/Java/src/main/org/biomoby/shared
In directory dev.open-bio.org:/tmp/cvs-serv19159/src/main/org/biomoby/shared

Modified Files:
	Utils.java 
Log Message:
modified getInputStream() such that it can resolve any url and not just HTTP urls.
moby-live/Java/src/main/org/biomoby/shared Utils.java,1.20,1.21
===================================================================
RCS file: /home/repository/moby/moby-live/Java/src/main/org/biomoby/shared/Utils.java,v
retrieving revision 1.20
retrieving revision 1.21
diff -u -r1.20 -r1.21
--- /home/repository/moby/moby-live/Java/src/main/org/biomoby/shared/Utils.java	2008/03/03 11:34:17	1.20
+++ /home/repository/moby/moby-live/Java/src/main/org/biomoby/shared/Utils.java	2008/03/17 14:29:53	1.21
@@ -19,6 +19,7 @@
 import java.net.HttpURLConnection;
 import java.net.MalformedURLException;
 import java.net.URL;
+import java.net.URLConnection;
 import java.nio.charset.Charset;
 import java.util.HashSet;
 import java.util.zip.GZIPInputStream;
@@ -529,24 +530,32 @@
 	if (url == null)
 	    throw new MobyException("Can't get RESOURCE from a null URL!");
 	try {
-	    HttpURLConnection urlConnection = null;
-	    urlConnection = (HttpURLConnection) url.openConnection();
-	    urlConnection
-		    .setRequestProperty("User-Agent", "jmoby-central/1.0");
-	    urlConnection
-		    .setRequestProperty("Accept-Encoding", "gzip, deflate");
-	    urlConnection.setDefaultUseCaches(false);
-	    urlConnection.setUseCaches(false);
-
-	    if (("gzip").equalsIgnoreCase(urlConnection.getContentEncoding())) {
-		// handle gzip encoded content
-		return new GZIPInputStream(urlConnection.getInputStream());
+	    URLConnection connection = url.openConnection();
+	    // try gzip content encoding iff we have a HTTP url
+	    if (connection instanceof HttpURLConnection) {
+		HttpURLConnection urlConnection = null;
+		urlConnection = (HttpURLConnection) connection;
+		urlConnection.setRequestProperty("User-Agent",
+			"jmoby-central/1.0");
+		urlConnection.setRequestProperty("Accept-Encoding",
+			"gzip, deflate");
+		urlConnection.setDefaultUseCaches(false);
+		urlConnection.setUseCaches(false);
+
+		if (("gzip").equalsIgnoreCase(urlConnection
+			.getContentEncoding())) {
+		    // handle gzip encoded content
+		    return new GZIPInputStream(urlConnection.getInputStream());
+		} else {
+		    return urlConnection.getInputStream();
+		}
 	    } else {
-		return urlConnection.getInputStream();
+		return connection.getInputStream();
 	    }
-	    
+
 	} catch (IOException e) {
-	    throw new MobyException ("Error creating input stream: " + e.toString());
+	    throw new MobyException("Error creating input stream: "
+		    + e.toString());
 	}
     }
     


From senger at dev.open-bio.org  Mon Mar 17 19:46:35 2008
From: senger at dev.open-bio.org (Martin Senger)
Date: Mon, 17 Mar 2008 19:46:35 -0400
Subject: [MOBY-guts] biomoby commit
Message-ID: <200803172346.m2HNkZdZ019861@dev.open-bio.org>


senger
Mon Mar 17 19:46:35 EDT 2008
Update of /home/repository/moby/moby-live/Java/src/test/java/org/biomoby/shared/extended
In directory dev.open-bio.org:/tmp/cvs-serv19843/src/test/java/org/biomoby/shared/extended

Log Message:
Directory /home/repository/moby/moby-live/Java/src/test/java/org/biomoby/shared/extended added to the repository

moby-live/Java/src/test/java/org/biomoby/shared/extended - New directory
rcsdiff: /home/repository/moby/moby-live/Java/src/test/java/org/biomoby/shared/extended/RCS/-,v: No such file or directory

rcsdiff: /home/repository/moby/moby-live/Java/src/test/java/org/biomoby/shared/extended/RCS/New,v: No such file or directory

rcsdiff: /home/repository/moby/moby-live/Java/src/test/java/org/biomoby/shared/extended/RCS/directory,v: No such file or directory


From senger at dev.open-bio.org  Mon Mar 17 19:48:01 2008
From: senger at dev.open-bio.org (Martin Senger)
Date: Mon, 17 Mar 2008 19:48:01 -0400
Subject: [MOBY-guts] biomoby commit
Message-ID: <200803172348.m2HNm1qm019894@dev.open-bio.org>


senger
Mon Mar 17 19:48:01 EDT 2008
Update of /home/repository/moby/moby-live/Java/src/test/java/org/biomoby/shared/extended
In directory dev.open-bio.org:/tmp/cvs-serv19879/src/test/java/org/biomoby/shared/extended

Added Files:
	FromRDFTest.java 
Log Message:
Added (few) junit tests for RDF parsing

moby-live/Java/src/test/java/org/biomoby/shared/extended FromRDFTest.java,NONE,1.1

From senger at dev.open-bio.org  Mon Mar 17 19:48:01 2008
From: senger at dev.open-bio.org (Martin Senger)
Date: Mon, 17 Mar 2008 19:48:01 -0400
Subject: [MOBY-guts] biomoby commit
Message-ID: <200803172348.m2HNm1Dx019910@dev.open-bio.org>


senger
Mon Mar 17 19:48:01 EDT 2008
Update of /home/repository/moby/moby-live/Java/src/test/junit-resources
In directory dev.open-bio.org:/tmp/cvs-serv19879/src/test/junit-resources

Added Files:
	dtypes.rdf namespaces.rdf services.rdf stypes.rdf 
Log Message:
Added (few) junit tests for RDF parsing

moby-live/Java/src/test/junit-resources dtypes.rdf,NONE,1.1 namespaces.rdf,NONE,1.1 services.rdf,NONE,1.1 stypes.rdf,NONE,1.1

From senger at dev.open-bio.org  Mon Mar 17 19:48:01 2008
From: senger at dev.open-bio.org (Martin Senger)
Date: Mon, 17 Mar 2008 19:48:01 -0400
Subject: [MOBY-guts] biomoby commit
Message-ID: <200803172348.m2HNm1AO019932@dev.open-bio.org>


senger
Mon Mar 17 19:48:01 EDT 2008
Update of /home/repository/moby/moby-live/Java/xmls
In directory dev.open-bio.org:/tmp/cvs-serv19879/xmls

Modified Files:
	junit.xml 
Log Message:
Added (few) junit tests for RDF parsing

moby-live/Java/xmls junit.xml,1.4,1.5
===================================================================
RCS file: /home/repository/moby/moby-live/Java/xmls/junit.xml,v
retrieving revision 1.4
retrieving revision 1.5
diff -u -r1.4 -r1.5
--- /home/repository/moby/moby-live/Java/xmls/junit.xml	2008/03/03 11:34:17	1.4
+++ /home/repository/moby/moby-live/Java/xmls/junit.xml	2008/03/17 23:48:01	1.5
@@ -102,6 +102,7 @@
       <fileset dir="${build.test}">
         <include name="**/MobyParserTest.*"/>
         <include name="**/ServicesTest.*"/>
+        <include name="**/FromRDFTest.*"/>
       </fileset>
       <!--      <fileset dir="${build.test}" includes="**/*Test.*" /> -->
     </batchtest>


From kawas at dev.open-bio.org  Wed Mar 19 12:55:35 2008
From: kawas at dev.open-bio.org (Eddie Kawas)
Date: Wed, 19 Mar 2008 12:55:35 -0400
Subject: [MOBY-guts] biomoby commit
Message-ID: <200803191655.m2JGtZ1x028491@dev.open-bio.org>


kawas
Wed Mar 19 12:55:35 EDT 2008
Update of /home/repository/moby/moby-live/Perl/MOBY-Server/bin/scripts
In directory dev.open-bio.org:/tmp/cvs-serv28455/Perl/MOBY-Server/bin/scripts

Modified Files:
	moby-s-install.pl 
Log Message:
fixed bug where authority script wasnt being installed by script
moby-live/Perl/MOBY-Server/bin/scripts moby-s-install.pl,1.2,1.3
===================================================================
RCS file: /home/repository/moby/moby-live/Perl/MOBY-Server/bin/scripts/moby-s-install.pl,v
retrieving revision 1.2
retrieving revision 1.3
diff -u -r1.2 -r1.3
--- /home/repository/moby/moby-live/Perl/MOBY-Server/bin/scripts/moby-s-install.pl	2008/03/06 16:44:55	1.2
+++ /home/repository/moby/moby-live/Perl/MOBY-Server/bin/scripts/moby-s-install.pl	2008/03/19 16:55:35	1.3
@@ -90,7 +90,7 @@
 		check_module('WSRF::Lite');
 		check_module('Crypt::OpenSSL::X509');
 		check_module('IPC::Shareable');
-	}    
+	}
 
 	if ($errors_found) {
 		say "\nSorry, some needed modules were not found.";
@@ -131,20 +131,24 @@
 }
 
 sub prompt_for_directory_expand {
-    my ($prompt, $prompted_dir) = @_;
-    while (1) {
-	my $dir = pprompt ("$prompt [$prompted_dir] ");
-	$dir =~ s/^\s*//; $dir =~ s/\s*$//;
-	$dir = $prompted_dir unless $dir;
-	return $dir if -d $dir and -w $dir;  # okay: writable directory
-	$prompted_dir = $dir;
-	next if -e $dir and say "'$dir' is not a writable directory. Try again please.";
-	next unless pprompt ("Directory '$dir' does not exists. Create? ", -yn);
-
-	# okay, we agreed to create it
-	mkdir ($dir, 0755 )and return $dir;
-	say "'$dir' not created: $!";
-    }
+	my ( $prompt, $prompted_dir ) = @_;
+	while (1) {
+		my $dir = pprompt("$prompt [$prompted_dir] ");
+		$dir =~ s/^\s*//;
+		$dir =~ s/\s*$//;
+		$dir = $prompted_dir unless $dir;
+		return $dir if -d $dir and -w $dir;    # okay: writable directory
+		$prompted_dir = $dir;
+		next
+		  if -e $dir
+		  and say "'$dir' is not a writable directory. Try again please.";
+		next
+		  unless pprompt( "Directory '$dir' does not exists. Create? ", -yn );
+
+		# okay, we agreed to create it
+		mkdir( $dir, 0755 ) and return $dir;
+		say "'$dir' not created: $!";
+	}
 }
 
 sub prompt_user_input {
@@ -186,11 +190,14 @@
 	if ($@) {
 		say "ERROR: $file_desc was (probably) not created.\n$@";
 	} else {
-		say "\n$file_desc created: '$file'\n\tPlease ensure that the file is executable!\n";
+		say
+"\n$file_desc created: '$file'\n\tPlease ensure that the file is executable!\n";
 	}
+
 	# try to make file executable
 	eval {
-		my $mode = 0655;   chmod $mode, "$file";
+		my $mode = 0655;
+		chmod $mode, "$file";
 	};
 }
 
@@ -472,8 +479,7 @@
   prompt_for_directory( "What is the path of the apache 'cgi-bin' directory?",
 						"$apache_base/cgi-bin" );
 $perl_exec =
-  prompt_user_input( "What is the path to your perl executable?", 
-  						$perl_exec );
+  prompt_user_input( "What is the path to your perl executable?", $perl_exec );
 $perl_exec = "$perl_exec -w";
 
 say "\nusing $apache_base as base directory ...";
@@ -540,7 +546,7 @@
 												   'MOBY', 'cgi/MOBY-Central.pl'
 						),
 						'MOBY-Central Dispatch file',
-						{'#!/usr/bin/perl -w'    => "#!$perl_exec",}
+						{ '#!/usr/bin/perl -w' => "#!$perl_exec", }
 	);
 	file_from_template(
 						"$apache_cgi/OntologyServer.cgi",
@@ -548,8 +554,9 @@
 												'MOBY', 'cgi/OntologyServer.cgi'
 						),
 						'MOBY-Central Ontology Server file',
-						{'#!/usr/bin/perl -w'    => "#!$perl_exec",}
+						{ '#!/usr/bin/perl -w' => "#!$perl_exec", }
 	);
+
 	#install the moby-admin module
 	file_from_template(
 						"$apache_cgi/MOBY-Admin.pl",
@@ -557,7 +564,7 @@
 												   'MOBY', 'cgi/MOBY-Admin.pl'
 						),
 						'MOBY-Admin Dispatch file',
-						{'#!/usr/bin/perl -w'    => "#!$perl_exec",}
+						{ '#!/usr/bin/perl -w' => "#!$perl_exec", }
 	);
 
 	# configure httpd.conf
@@ -662,12 +669,18 @@
 
 do {
 	my $ready_to_go = 0;
-	my $sql_error = 0;
+	my $sql_error   = 0;
+
 	#check to see if we can call mysql ... if not, then die!
-	print "mysql is installed ...\n" if `mysql --version 2>&1` =~ m/^mysql\s+Ver\s+.*$/;
-	print "mysql is started ...\n" unless `mysql 2>&1` =~ m/^ERROR 200.*Can't connect to .*$/ ;
+	print "mysql is installed ...\n"
+	  if `mysql --version 2>&1` =~ m/^mysql\s+Ver\s+.*$/;
+	print "mysql is started ...\n"
+	  unless `mysql 2>&1` =~ m/^ERROR 200.*Can't connect to .*$/;
 
-	unless ( `mysql --version 2>&1`  =~ m/^mysql\s+Ver\s+.*$/ and not (`mysql 2>&1` =~ m/^ERROR .*Can't connect to local MySQL .*$/) ) {
+	unless ( `mysql --version 2>&1` =~ m/^mysql\s+Ver\s+.*$/
+		 and not( `mysql 2>&1` =~ m/^ERROR .*Can't connect to local MySQL .*$/ )
+	  )
+	{
 		say
 "\nmysql doesn't seem to be accessible ... please ensure that it is on the path, started and try again.\n";
 		$sql_error = 1;
@@ -675,274 +688,278 @@
 
 	# proceed if mysql check was good
 	do {
-	# have the values been set already?
-	$ready_to_go = 1
-	  if $username
-	  and $url
-	  and $port
-	  and $m_object
-	  and $m_relationship
-	  and $m_service
-	  and $m_namespace
-	  and $m_central;
+
+		# have the values been set already?
+		$ready_to_go = 1
+		  if $username
+		  and $url
+		  and $port
+		  and $m_object
+		  and $m_relationship
+		  and $m_service
+		  and $m_namespace
+		  and $m_central;
 
 #check to see if mobycentral.config has been created in the conf directory first -> if so, parse it
-	if (    -e "$apache_conf/mobycentral.config"
-		 && !( -d "$apache_conf/mobycentral.config" )
-		 && !$ready_to_go )
-	{
-		my %db_sections = ();
-		open IN, "$apache_conf/mobycentral.config"
-		  or die
+		if (    -e "$apache_conf/mobycentral.config"
+			 && !( -d "$apache_conf/mobycentral.config" )
+			 && !$ready_to_go )
+		{
+			my %db_sections = ();
+			open IN, "$apache_conf/mobycentral.config"
+			  or die
 "can't open MOBY Configuration file '$apache_conf/mobycentral.config' for unknown reasons: $!\n";
-		my @sections = split /(\[\s*\S+\s*\][^\[]*)/s, join "", <IN>;
-		foreach my $section (@sections) {
-			my $dbConfig = MOBY::dbConfig->new( section => $section );
-			next unless $dbConfig;
-			my $dbname = $dbConfig->section_title;
-			next unless $dbname;
-			$db_sections{$dbname} = $dbConfig;
-		}
+			my @sections = split /(\[\s*\S+\s*\][^\[]*)/s, join "", <IN>;
+			foreach my $section (@sections) {
+				my $dbConfig = MOBY::dbConfig->new( section => $section );
+				next unless $dbConfig;
+				my $dbname = $dbConfig->section_title;
+				next unless $dbname;
+				$db_sections{$dbname} = $dbConfig;
+			}
 
-		$username       = $db_sections{mobycentral}->{username};
-		$password       = $db_sections{mobycentral}->{password} || "";
-		$url            = $db_sections{mobycentral}->{url};
-		$port           = $db_sections{mobycentral}->{port};
-		$m_object       = $db_sections{mobyobject}->{dbname};
-		$m_relationship = $db_sections{mobyrelationship}->{dbname};
-		$m_service      = $db_sections{mobyservice}->{dbname};
-		$m_namespace    = $db_sections{mobynamespace}->{dbname};
-		$m_central      = $db_sections{mobycentral}->{dbname};
+			$username       = $db_sections{mobycentral}->{username};
+			$password       = $db_sections{mobycentral}->{password} || "";
+			$url            = $db_sections{mobycentral}->{url};
+			$port           = $db_sections{mobycentral}->{port};
+			$m_object       = $db_sections{mobyobject}->{dbname};
+			$m_relationship = $db_sections{mobyrelationship}->{dbname};
+			$m_service      = $db_sections{mobyservice}->{dbname};
+			$m_namespace    = $db_sections{mobynamespace}->{dbname};
+			$m_central      = $db_sections{mobycentral}->{dbname};
 
-		$ready_to_go = 1;
-	}
+			$ready_to_go = 1;
+		}
 
-	# if the values havent been set, then prompt for them
-	do {
+		# if the values havent been set, then prompt for them
+		do {
 
-		say "  Installing the file '$apache_conf/mobycentral.config' ...";
+			say "  Installing the file '$apache_conf/mobycentral.config' ...";
 
-		# fill out mobycentral.config
-		(
-		   $username,  $password,    $url,
-		   $port,      $m_object,    $m_relationship,
-		   $m_service, $m_namespace, $m_central
-		  )
-		  = prompt_moby_config_info;
-		fill_out_moby_conf(
-							"$apache_conf/mobycentral.config",
-							$username,  $password,    $url,
-							$port,      $m_object,    $m_relationship,
-							$m_service, $m_namespace, $m_central
-		);
+			# fill out mobycentral.config
+			(
+			   $username,  $password,    $url,
+			   $port,      $m_object,    $m_relationship,
+			   $m_service, $m_namespace, $m_central
+			  )
+			  = prompt_moby_config_info;
+			fill_out_moby_conf(
+								"$apache_conf/mobycentral.config",
+								$username,  $password,    $url,
+								$port,      $m_object,    $m_relationship,
+								$m_service, $m_namespace, $m_central
+			);
 
-	} unless $ready_to_go;
+		} unless $ready_to_go;
 
-	# now start creating the tables
-	say "   creating the tables to use for the registry ...";
-	my %dbsections = (
-					   'mobycentral'      => $m_central,
-					   'mobyobject'       => $m_object,
-					   'mobyservice'      => $m_service,
-					   'mobynamespace'    => $m_namespace,
-					   'mobyrelationship' => $m_relationship
-	);
+		# now start creating the tables
+		say "   creating the tables to use for the registry ...";
+		my %dbsections = (
+						   'mobycentral'      => $m_central,
+						   'mobyobject'       => $m_object,
+						   'mobyservice'      => $m_service,
+						   'mobynamespace'    => $m_namespace,
+						   'mobyrelationship' => $m_relationship
+		);
 
-	my $clone = 0;
-	my $central;
-	do {
-		$clone = 1;
-		my %registries = (
-			default => {
-				url =>
-"http://moby.ucalgary.ca/moby/MOBY-Central.pl",
-				uri => "http://moby.ucalgary.ca/MOBY/Central"
-			},
-			testing => {
-				url =>
+		my $clone = 0;
+		my $central;
+		do {
+			$clone = 1;
+			my %registries = (
+				default => {
+						  url => "http://moby.ucalgary.ca/moby/MOBY-Central.pl",
+						  uri => "http://moby.ucalgary.ca/MOBY/Central"
+				},
+				testing => {
+					url =>
 "http://bioinfo.icapture.ubc.ca/cgi-bin/mobycentral/MOBY-Central.pl",
-				uri => "http://bioinfo.icapture.ubc.ca/MOBY/Central"
-			},
-			IRRI => {
+					uri => "http://bioinfo.icapture.ubc.ca/MOBY/Central"
+				},
+				IRRI => {
 					  url => "http://cropwiki.irri.org/cgi-bin/MOBY-Central.pl",
 					  uri => "http://cropwiki.irri.org/MOBY/Central"
-			},
+				},
 
-			#			localhost => {
-			#					url=>"http://localhost/cgi-bin/MOBY-Central.pl",
-			#					uri=>"http://localhost/MOBY/Central"
-			#			},
-		);
-		my $registry = pprompt( "What registry to use? [b] ",
-								-m => [ sort keys %registries ] );
+				#			localhost => {
+				#					url=>"http://localhost/cgi-bin/MOBY-Central.pl",
+				#					uri=>"http://localhost/MOBY/Central"
+				#			},
+			);
+			my $registry = pprompt( "What registry to use? [b] ",
+									-m => [ sort keys %registries ] );
 
-		$central = MOBY::Client::Central->new(
+			$central = MOBY::Client::Central->new(
 									 Registries => {
 										 mobycentral => {
 											 URL => $registries{$registry}{url},
 											 URI => $registries{$registry}{uri}
 										 }
 									 }
-		);
-	  }
-	  if pprompt( "Would you like to clone a mobycentral registry? [n] ",
-				  -ynd => 'n' ) eq 'y';
-	my $error = 0;
-	if ($clone) {
-		say "Getting db dumps ...";
-		my (
-			 $mobycentral,   $mobyobject, $mobyservice,
-			 $mobynamespace, $mobyrelationship
-		  )
-		  = $central->MOBY::Client::Central::DUMP();
-		my $drh = DBI->install_driver("mysql");
-
-		my ( $fh, $filename ) = tempfile( UNLINK => 1 );
-		say "Processing dump for service instances ...";
-		print $fh $mobycentral;
-		eval {
-			$drh->func( 'dropdb', $dbsections{mobycentral},
-						$url, $username, $password, 'admin' );
-		};
-		eval {
-			$drh->func( 'createdb', $dbsections{mobycentral},
-						$url, $username, $password, 'admin' );
-		};
-		system(   "mysql -h $url -P $port -u $username --password=$password "
-				. $dbsections{mobycentral}
-				. "<$filename" ) == 0
-		  or ( say "Error populating service instance ontology ...\n$!"
-			   and $error++ );
-
-		( $fh, $filename ) = tempfile( UNLINK => 1 );
-		say "Processing dump for the objects ontology ...";
-		print $fh $mobyobject;
-		eval {
-			$drh->func( 'dropdb', $dbsections{mobyobject}, $url, $username,
-						$password, 'admin' );
-		};
-		eval {
-			$drh->func( 'createdb', $dbsections{mobyobject}, $url, $username,
-						$password, 'admin' );
-		};
-		system(   "mysql -h $url -P $port -u $username --password=$password "
-				. $dbsections{mobyobject}
-				. "<$filename" ) == 0
-		  or ( say "Error populating objects ontology ...\n$!" and $error++ );
-
-		( $fh, $filename ) = tempfile( UNLINK => 1 );
-		say "Processing dump for service types ...";
-		print $fh $mobyservice;
-		eval {
-			$drh->func( 'dropdb', $dbsections{mobyservice},
-						$url, $username, $password, 'admin' );
-		};
-		eval {
-			$drh->func( 'createdb', $dbsections{mobyservice},
-						$url, $username, $password, 'admin' );
-		};
-		system(   "mysql -h $url -P $port -u $username --password=$password "
-				. $dbsections{mobyservice}
-				. "<$filename" ) == 0
-		  or ( say "Error populating service types ontology ...\n$!"
-			   and $error++ );
-
-		( $fh, $filename ) = tempfile( UNLINK => 1 );
-		say "Processing dump for the namespace ontology ...";
-		print $fh $mobynamespace;
-		eval {
-			$drh->func( 'dropdb', $dbsections{mobynamespace},
-						$url, $username, $password, 'admin' );
-		};
-		eval {
-			$drh->func( 'createdb', $dbsections{mobynamespace},
-						$url, $username, $password, 'admin' );
-		};
-		system(   "mysql -h $url -P $port -u $username --password=$password "
-				. $dbsections{mobynamespace}
-				. "<$filename" ) == 0
-		  or ( say "Error populating namespace ontology ...\n$!" and $error++ );
-
-		( $fh, $filename ) = tempfile( UNLINK => 1 );
-		say "Processing dump for the relationships ontology ...";
-		print $fh $mobyrelationship;
-		eval {
-			$drh->func( 'dropdb', $dbsections{mobyrelationship},
-						$url, $username, $password, 'admin' );
-		};
-		eval {
-			$drh->func( 'createdb', $dbsections{mobyrelationship},
-						$url, $username, $password, 'admin' );
-		};
-		system(   "mysql -h $url -P $port -u $username --password=$password "
-				. $dbsections{mobyrelationship}
-				. "<$filename" ) == 0
-		  or ( say "Error populating relationships ontology ...\n$!"
-			   and $error++ );
-
-	} else {
-
-		# no clone, so create minimalist databases
-		my $drop_db = 0;
-
-		#ask for permission on dropping data from db ...
-		do {
-			$drop_db = 1;
+			);
 		  }
-		  if pprompt(
-				"Shall I drop all pre-existing databases used by BioMOBY? [n] ",
-				-ynd => 'n' ) eq 'y';
-
-		#process each db
-		foreach my $section ( keys %dbsections ) {
-			my $sqlfilepath =
-			  File::ShareDir::dist_file( 'MOBY', "db/schema/$section.mysql" );
+		  if pprompt( "Would you like to clone a mobycentral registry? [n] ",
+					  -ynd => 'n' ) eq 'y';
+		my $error = 0;
+		if ($clone) {
+			say "Getting db dumps ...";
+			my (
+				 $mobycentral,   $mobyobject, $mobyservice,
+				 $mobynamespace, $mobyrelationship
+			  )
+			  = $central->MOBY::Client::Central::DUMP();
 			my $drh = DBI->install_driver("mysql");
 
-			# drop the db
+			my ( $fh, $filename ) = tempfile( UNLINK => 1 );
+			say "Processing dump for service instances ...";
+			print $fh $mobycentral;
 			eval {
-				$drh->func( 'dropdb', $dbsections{$section}, $url, $username,
-							$password, 'admin' );
-			} if $drop_db;
-
-			# create the db
+				$drh->func( 'dropdb', $dbsections{mobycentral},
+							$url, $username, $password, 'admin' );
+			};
 			eval {
-				$drh->func( 'createdb', $dbsections{$section}, $url, $username,
+				$drh->func( 'createdb', $dbsections{mobycentral},
+							$url, $username, $password, 'admin' );
+			};
+			system( "mysql -h $url -P $port -u $username --password=$password "
+					. $dbsections{mobycentral}
+					. "<$filename" ) == 0
+			  or ( say "Error populating service instance ontology ...\n$!"
+				   and $error++ );
+
+			( $fh, $filename ) = tempfile( UNLINK => 1 );
+			say "Processing dump for the objects ontology ...";
+			print $fh $mobyobject;
+			eval {
+				$drh->func( 'dropdb', $dbsections{mobyobject}, $url, $username,
 							$password, 'admin' );
 			};
+			eval {
+				$drh->func( 'createdb', $dbsections{mobyobject}, $url,
+							$username, $password, 'admin' );
+			};
+			system( "mysql -h $url -P $port -u $username --password=$password "
+					. $dbsections{mobyobject}
+					. "<$filename" ) == 0
+			  or
+			  ( say "Error populating objects ontology ...\n$!" and $error++ );
+
+			( $fh, $filename ) = tempfile( UNLINK => 1 );
+			say "Processing dump for service types ...";
+			print $fh $mobyservice;
+			eval {
+				$drh->func( 'dropdb', $dbsections{mobyservice},
+							$url, $username, $password, 'admin' );
+			};
+			eval {
+				$drh->func( 'createdb', $dbsections{mobyservice},
+							$url, $username, $password, 'admin' );
+			};
+			system( "mysql -h $url -P $port -u $username --password=$password "
+					. $dbsections{mobyservice}
+					. "<$filename" ) == 0
+			  or ( say "Error populating service types ontology ...\n$!"
+				   and $error++ );
+
+			( $fh, $filename ) = tempfile( UNLINK => 1 );
+			say "Processing dump for the namespace ontology ...";
+			print $fh $mobynamespace;
+			eval {
+				$drh->func( 'dropdb', $dbsections{mobynamespace},
+							$url, $username, $password, 'admin' );
+			};
+			eval {
+				$drh->func( 'createdb', $dbsections{mobynamespace},
+							$url, $username, $password, 'admin' );
+			};
+			system( "mysql -h $url -P $port -u $username --password=$password "
+					. $dbsections{mobynamespace}
+					. "<$filename" ) == 0
+			  or ( say "Error populating namespace ontology ...\n$!"
+				   and $error++ );
+
+			( $fh, $filename ) = tempfile( UNLINK => 1 );
+			say "Processing dump for the relationships ontology ...";
+			print $fh $mobyrelationship;
+			eval {
+				$drh->func( 'dropdb', $dbsections{mobyrelationship},
+							$url, $username, $password, 'admin' );
+			};
+			eval {
+				$drh->func( 'createdb', $dbsections{mobyrelationship},
+							$url, $username, $password, 'admin' );
+			};
+			system( "mysql -h $url -P $port -u $username --password=$password "
+					. $dbsections{mobyrelationship}
+					. "<$filename" ) == 0
+			  or ( say "Error populating relationships ontology ...\n$!"
+				   and $error++ );
+
+		} else {
+
+			# no clone, so create minimalist databases
+			my $drop_db = 0;
 
-			#create the tables in the db
+			#ask for permission on dropping data from db ...
 			do {
-				say "\n\tProblem creating tables in the db: $section: $!";
+				$drop_db = 1;
 			  }
-			  unless system(
+			  if pprompt(
+				"Shall I drop all pre-existing databases used by BioMOBY? [n] ",
+				-ynd => 'n'
+			  ) eq 'y';
+
+			#process each db
+			foreach my $section ( keys %dbsections ) {
+				my $sqlfilepath = File::ShareDir::dist_file( 'MOBY',
+												   "db/schema/$section.mysql" );
+				my $drh = DBI->install_driver("mysql");
+
+				# drop the db
+				eval {
+					$drh->func( 'dropdb', $dbsections{$section}, $url,
+								$username, $password, 'admin' );
+				} if $drop_db;
+
+				# create the db
+				eval {
+					$drh->func( 'createdb', $dbsections{$section}, $url,
+								$username, $password, 'admin' );
+				};
+
+				#create the tables in the db
+				do {
+					say "\n\tProblem creating tables in the db: $section: $!";
+				  }
+				  unless system(
 					 "mysql -h $url -P $port -u $username --password=$password "
 					   . $dbsections{$section}
 					   . "<$sqlfilepath" ) == 0;
-			say "\tProcessing of $section completed ... ";
-		}
-		say "populating the tables with basic data ...";
-		%dbsections = (
-						'mobyobject'       => $m_object,
-						'mobyservice'      => $m_service,
-						'mobyrelationship' => $m_relationship
-		);
-		foreach my $section ( keys %dbsections ) {
-			my $sqlfilepath =
-			  File::ShareDir::dist_file( 'MOBY', "db/data/$section.data" );
-			system( "mysql -h $url -P $port -u $username --password=$password "
-					. $dbsections{$section}
-					. "<$sqlfilepath" ) == 0
-			  or say "\n\tProblem populating the db: $section: $!";
-			say "\tPopulation processing for db $section completed ...";
+				say "\tProcessing of $section completed ... ";
+			}
+			say "populating the tables with basic data ...";
+			%dbsections = (
+							'mobyobject'       => $m_object,
+							'mobyservice'      => $m_service,
+							'mobyrelationship' => $m_relationship
+			);
+			foreach my $section ( keys %dbsections ) {
+				my $sqlfilepath =
+				  File::ShareDir::dist_file( 'MOBY', "db/data/$section.data" );
+				system(
+					 "mysql -h $url -P $port -u $username --password=$password "
+					   . $dbsections{$section}
+					   . "<$sqlfilepath" ) == 0
+				  or say "\n\tProblem populating the db: $section: $!";
+				say "\tPopulation processing for db $section completed ...";
+			}
 		}
-	}
 
-	say "Set up of mySQL complete!" if $error == 0;
-	say
+		say "Set up of mySQL complete!" if $error == 0;
+		say
 "There were some problems encountered. Please correct the errors and re-run this script!"
-	  if $error > 0;
-} unless $sql_error;
+		  if $error > 0;
+	} unless $sql_error;
 } if pprompt( "Would you like to set up mySQL? [n] ", -ynd => 'n' ) eq 'y';
 
 do {
@@ -957,15 +974,22 @@
 		  if pprompt( "The RESOURCES script already exists, overwrite? [n] ",
 					  -ynd => 'n' ) eq 'y';
 	} if -e "$apache_cgi/RESOURCES";
-	
-	my $rdf_cache_location =  prompt_for_directory_expand( "Where would you like to store the RDF cache?", "$apache_base/moby_cache" );
-	
-	say 'Please make sure that you make that directory read/writable by your web server!\n';
-	
+
+	my $rdf_cache_location =
+	  prompt_for_directory_expand(
+								 "Where would you like to store the RDF cache?",
+								 "$apache_base/moby_cache" );
+
+	say
+"Please make sure that you make that directory read/writable by your web server!\n";
+
 	# copy the file
-	file_from_template( "$apache_cgi/RESOURCES",
+	file_from_template(
+						"$apache_cgi/RESOURCES",
 						File::ShareDir::dist_file( 'MOBY', 'cgi/RESOURCES' ),
-						'RESOURCES script', {'#!/usr/bin/perl -w'    => "#!$perl_exec",} )
+						'RESOURCES script',
+						{ '#!/usr/bin/perl -w' => "#!$perl_exec", }
+	  )
 	  if $exists == 0;
 
 	# update mobycentral.config file to reflect the location of the script
@@ -985,7 +1009,7 @@
 									 'mobycentral' => {
 														'resourceURL'  => 0,
 														'allResources' => 0,
-														'rdf_cache' => 0
+														'rdf_cache'    => 0
 									 },
 									 'mobyobject'    => { 'resourceURL' => 0 },
 									 'mobyservice'   => { 'resourceURL' => 0 },
@@ -1002,7 +1026,7 @@
 			'MOBY/SQL Configuration file',
 
 			# mysql settings
-			{'rdf_cache'		=> "$rdf_cache_location"},
+			{ 'rdf_cache' => "$rdf_cache_location" },
 
 			# db section mappings
 			{},
@@ -1039,16 +1063,16 @@
 		  }
 		  if pprompt( "The authority script already exists, overwrite? [n] ",
 					  -ynd => 'n' ) eq 'y';
-		file_from_template(
-						"$apache_cgi/authority.pl",
-						File::ShareDir::dist_file(
-												'MOBY', 'cgi/authority.pl'
-						),
-						'MOBY-Central LSID authority server file',
-						{'#!/usr/bin/perl -w'    => "#!$perl_exec",}
-		) if $exists == 0;
 	} if -e "$apache_cgi/authority.pl";
 
+	file_from_template(
+		"$apache_cgi/authority.pl",    
+		File::ShareDir::dist_file( 'MOBY', 'cgi/authority.pl' ),
+		'MOBY-Central LSID authority server file',
+		{ '#!/usr/bin/perl -w' => "#!$perl_exec", }
+	  )
+	  if $exists == 0;
+
 	# update mobycentral.config file to reflect the particulars of the script
 	do {
 
@@ -1167,97 +1191,99 @@
 
 do {
 
-		# prompt for a location for the service_tester_path
-		my $service_tester_path =  prompt_for_directory_expand( "Where would you like to place the service pinger script?", "$apache_base/moby_tester" );
-		say 'Please make sure that you make that directory read/writable by your web server!\n';
-		# make sure that the key service_tester_path exists for the config file
-		my $search = search_config_file(
-								   "$apache_conf/mobycentral.config",
-								   {
-									 'mobycentral' => {
-														'service_tester_path'  => 0,
-									 }
-								   }
-		);
-		add_missing_keys_to_config_file( "$apache_conf/mobycentral.config", $search );
+	# prompt for a location for the service_tester_path
+	my $service_tester_path =
+	  prompt_for_directory_expand(
+					 "Where would you like to place the service pinger script?",
+					 "$apache_base/moby_tester" );
+	say
+'Please make sure that you make that directory read/writable by your web server!\n';
 
-		# copy the information
-		config_file_from_template(
-			"$apache_conf/mobycentral.config",
-			"$apache_conf/mobycentral.config",
-			'MOBY/SQL Configuration file',
+	# make sure that the key service_tester_path exists for the config file
+	my $search = search_config_file( "$apache_conf/mobycentral.config",
+						 { 'mobycentral' => { 'service_tester_path' => 0, } } );
+	add_missing_keys_to_config_file( "$apache_conf/mobycentral.config",
+									 $search );
 
-			# mysql settings
-			{'service_tester_path'	=> "$service_tester_path"},
+	# copy the information
+	config_file_from_template(
+		"$apache_conf/mobycentral.config",
+		"$apache_conf/mobycentral.config",
+		'MOBY/SQL Configuration file',
 
-			# db section mappings
-			{},
+		# mysql settings
+		{ 'service_tester_path' => "$service_tester_path" },
 
-			# resource urls
-			{},
+		# db section mappings
+		{},
 
-			# lsid info
-			{}
-		);
-		
-		file_from_template(
+		# resource urls
+		{},
+
+		# lsid info
+		{}
+	);
+
+	file_from_template(
 						"$service_tester_path/service_tester.pl",
 						File::ShareDir::dist_file(
-												'MOBY', 'cgi/service_tester.pl'
+												 'MOBY', 'cgi/service_tester.pl'
 						),
 						'MOBY-Central service tester script',
-						{'#!/usr/bin/perl -w'    => "#!$perl_exec",}
-		);
-		say 'Please don\'t forget to place the service pinger on a cron! TODO - explain how to do that!';
-		
-		#copy the other scripts now
-		file_from_template(
+						{ '#!/usr/bin/perl -w' => "#!$perl_exec", }
+	);
+	say
+'Please don\'t forget to place the service pinger on a cron! TODO - explain how to do that!';
+
+	#copy the other scripts now
+	file_from_template(
 						"$apache_cgi/AgentRDFValidator",
 						File::ShareDir::dist_file(
-												'MOBY', 'cgi/AgentRDFValidator'
+												 'MOBY', 'cgi/AgentRDFValidator'
 						),
 						'The RDF agent validator page',
-						{'#!/usr/bin/perl -w'    => "#!$perl_exec",}
-		);
-		file_from_template(
+						{ '#!/usr/bin/perl -w' => "#!$perl_exec", }
+	);
+	file_from_template(
 						"$apache_cgi/GenerateRDF.cgi",
 						File::ShareDir::dist_file(
-												'MOBY', 'cgi/GenerateRDF.cgi'
+												   'MOBY', 'cgi/GenerateRDF.cgi'
 						),
 						'MOBY-Central service instance RDF generating form',
-						{'#!/usr/bin/perl -w'    => "#!$perl_exec",}
-		);
-		file_from_template(
+						{ '#!/usr/bin/perl -w' => "#!$perl_exec", }
+	);
+	file_from_template(
 						"$apache_cgi/Moby",
-						File::ShareDir::dist_file(
-												'MOBY', 'cgi/Moby'
-						),
+						File::ShareDir::dist_file( 'MOBY', 'cgi/Moby' ),
 						'MOBY-Central test page for auxillary scripts',
-						{'#!/usr/bin/perl -w'    => "#!$perl_exec",}
-		);
-		file_from_template(
+						{ '#!/usr/bin/perl -w' => "#!$perl_exec", }
+	);
+	file_from_template(
 						"$apache_cgi/ServicePingerValidator",
 						File::ShareDir::dist_file(
-												'MOBY', 'cgi/ServicePingerValidator'
+											'MOBY', 'cgi/ServicePingerValidator'
 						),
 						'MOBY-Central service invocation test form',
-						{'#!/usr/bin/perl -w'    => "#!$perl_exec",}
-		);
-		file_from_template(
+						{ '#!/usr/bin/perl -w' => "#!$perl_exec", }
+	);
+	file_from_template(
 						"$apache_cgi/ValidateService",
 						File::ShareDir::dist_file(
-												'MOBY', 'cgi/ValidateService'
+												   'MOBY', 'cgi/ValidateService'
 						),
 						'MOBY-Central service tester information page',
-						{'#!/usr/bin/perl -w'    => "#!$perl_exec",}
-		);
+						{ '#!/usr/bin/perl -w' => "#!$perl_exec", }
+	);
   }
-	  if pprompt( "Would you like to auxillary scripts? These include the service pinger, a test page for the rdf agent, an RDF generator page, etc? [y] ",
-			  -ynd => 'y' ) eq 'y';
+  if pprompt(
+"Would you like to auxillary scripts? These include the service pinger, a test page for the rdf agent, an RDF generator page, etc? [y] ",
+	-ynd => 'y'
+  ) eq 'y';
 
 #
 
-say "Please remember to set up the RDF agent! Just restart apache and your registry has been set up!\n\nDone.";
+say
+"Please remember to set up the RDF agent! Just restart apache and your registry has been set up!\n\nDone.";
 
 package SimplePrompt;
 


From walexander at dev.open-bio.org  Wed Mar 19 18:49:47 2008
From: walexander at dev.open-bio.org (Wendy Alexander)
Date: Wed, 19 Mar 2008 18:49:47 -0400
Subject: [MOBY-guts] biomoby commit
Message-ID: <200803192249.m2JMnlC4028988@dev.open-bio.org>


walexander
Wed Mar 19 18:49:47 EDT 2008
Update of /home/repository/moby/moby-live/Java/src/main/org/biomoby/service/dashboard
In directory dev.open-bio.org:/tmp/cvs-serv28953

Modified Files:
	SimpleClientPanel.java 
Log Message:
Added pinger button.
moby-live/Java/src/main/org/biomoby/service/dashboard SimpleClientPanel.java,1.9,1.10
===================================================================
RCS file: /home/repository/moby/moby-live/Java/src/main/org/biomoby/service/dashboard/SimpleClientPanel.java,v
retrieving revision 1.9
retrieving revision 1.10
diff -u -r1.9 -r1.10
--- /home/repository/moby/moby-live/Java/src/main/org/biomoby/service/dashboard/SimpleClientPanel.java	2008/03/02 12:45:26	1.9
+++ /home/repository/moby/moby-live/Java/src/main/org/biomoby/service/dashboard/SimpleClientPanel.java	2008/03/19 22:49:47	1.10
@@ -248,12 +248,16 @@
 	className = createText (null, DP_IMPL_CLASS, DP_IMPL_CLASS);
 
 	ButtonGroup group = new ButtonGroup();
-	JRadioButton htNone, htRegistry, htEndpoint, htLocal, htNewURL;
+	JRadioButton htNone, htRegistry, htEndpoint, htLocal, htNewURL, htPing;
 	group.add (htEndpoint = createHowToButton ("Use service's usual endpoint", DP_CS_URL));
 	group.add (htNone     = createHowToButton ("No real call, just show/echo input", DP_CS_NONE));
 	group.add (htRegistry = createHowToButton ("Ask registry where service is, and call it", DP_CS_REGISTRY));
 	group.add (htNewURL   = createHowToButton ("Use this endpoint", DP_CS_NEWURL));
 	group.add (htLocal    = createHowToButton ("Use this local class", DP_CS_CLASS));
+	group.add (htPing	  = createHowToButton ("'Ping' this service", DP_CS_PING));
+	htPing.setToolTipText("A Moby 'Ping' is used to determine if the service is responsive, " +
+			"and if it responds in an API-compliant manner");
+	
 
 	boolean usingAsBytes = getPrefValue (DP_INP_ASBYTES, false);
 	JCheckBox asBytes = createCheckBox
@@ -280,7 +284,8 @@
  	SwingUtils.addComponent (howTo, htLocal,    0, 3, 1, 1, NONE, NWEST,  0.0, 0.0);
  	SwingUtils.addComponent (howTo, className,  1, 3, 1, 1, HORI, NWEST,  1.0, 0.0);
  	SwingUtils.addComponent (howTo, htNone,     0, 4, 2, 1, NONE, NWEST,  0.0, 0.0);
- 	SwingUtils.addComponent (howTo, asBytes,    0, 5, 2, 1, NONE, NWEST,  0.0, 0.0, BREATH_TOP);
+ 	SwingUtils.addComponent (howTo, htPing,		0, 5, 2, 1, NONE, NWEST,  0.0, 0.0);	
+ 	SwingUtils.addComponent (howTo, asBytes,    0, 6, 2, 1, NONE, NWEST,  0.0, 0.0, BREATH_TOP);
 
 	// run the service
 	runButton =
@@ -534,6 +539,16 @@
 		if ( DP_CS_NONE.equals (propertyChannel.getString (DP_CALL_SERVICE)) ||
 		     (propertyChannel.getBoolean (DP_INP_SHOWXML, false)) ) {
 		    input.setText ((String)data.getData());
+		} 
+		
+		// If we are only pinging the service, set the data object to an empty message
+		if (DP_CS_PING.equals(propertyChannel.getString(DP_CALL_SERVICE))) {
+			String emptyMsg = "<?xml version=\"1.0\" encoding=\"UTF-8\"?>\n" +
+			"<moby:MOBY xmlns:moby=\"http://www.biomoby.org/moby\">\n" +
+			"  <moby:mobyContent />\n" +
+			"</moby:MOBY>";
+			data.setData(emptyMsg);
+			input.setText(emptyMsg);
 		}
 
 		// finally, call the service
@@ -559,15 +574,27 @@
 	    }
 
 	    if (exception == null) {
-		propertyChannel.fire (DP_STATUS_MSG, "Service invocation finished.");
-
-		// handle results here (using renderers...)
-		if (! DP_CS_NONE.equals (propertyChannel.getString (DP_CALL_SERVICE)) )
-		    results.updateComponent (data);
+	    	
+			// handle results here (using renderers...)
+			if (DP_CS_PING.equals(propertyChannel.getString(DP_CALL_SERVICE))) {
+				propertyChannel.fire (DP_STATUS_MSG, service.getName()+" isAlive.");
+			} else {
+				propertyChannel.fire (DP_STATUS_MSG, "Service invocation finished.");
+			}
+			
+			if (! DP_CS_NONE.equals (propertyChannel.getString (DP_CALL_SERVICE))) {
+			    results.updateComponent (data);			
+			}
 
 	    } else {
-		propertyChannel.fire (DP_STATUS_MSG, "Service invocation failed.");
-		error (CALLER_ERROR, exception);
+			if (DP_CS_PING.equals(propertyChannel.getString(DP_CALL_SERVICE))) {
+		    	propertyChannel.fire (DP_STATUS_MSG, service.getName()+" is dead.");
+				results.removeResults();
+			} else {
+		    	propertyChannel.fire (DP_STATUS_MSG, "Service invocation failed.");
+				error (CALLER_ERROR, exception);
+			}
+			exception.printStackTrace();
 	    }
 	    serviceFinished();
 	}


From walexander at dev.open-bio.org  Wed Mar 19 18:50:14 2008
From: walexander at dev.open-bio.org (Wendy Alexander)
Date: Wed, 19 Mar 2008 18:50:14 -0400
Subject: [MOBY-guts] biomoby commit
Message-ID: <200803192250.m2JMoEXc029031@dev.open-bio.org>


walexander
Wed Mar 19 18:50:14 EDT 2008
Update of /home/repository/moby/moby-live/Java/src/main/org/biomoby/service/dashboard
In directory dev.open-bio.org:/tmp/cvs-serv28996

Modified Files:
	ServiceCallerModel.java 
Log Message:
Added pinger button.
moby-live/Java/src/main/org/biomoby/service/dashboard ServiceCallerModel.java,1.4,1.5
===================================================================
RCS file: /home/repository/moby/moby-live/Java/src/main/org/biomoby/service/dashboard/ServiceCallerModel.java,v
retrieving revision 1.4
retrieving revision 1.5
diff -u -r1.4 -r1.5
--- /home/repository/moby/moby-live/Java/src/main/org/biomoby/service/dashboard/ServiceCallerModel.java	2007/04/05 14:24:57	1.4
+++ /home/repository/moby/moby-live/Java/src/main/org/biomoby/service/dashboard/ServiceCallerModel.java	2008/03/19 22:50:14	1.5
@@ -145,7 +145,7 @@
 		if (! UUtils.isEmpty (sEndpoint))
 		    clonedService.setURL (sEndpoint);
 
-	    } else if (DP_CS_REGISTRY.equals (howToCall)) {
+	    } else if (DP_CS_REGISTRY.equals (howToCall) || DP_CS_PING.equals(howToCall)) {
 		clonedService.setURL (null);
 		setRegistryEndpoint (propertyChannel.getString (DP_REGISTRY_ENDPOINT));
 		setRegistryNamespace (propertyChannel.getString (DP_REGISTRY_NAMESPACE));
@@ -158,7 +158,7 @@
 
 	    } else if (DP_CS_NONE.equals (howToCall)) {
 		setLoop (true);
-	    }
+	    } 
 
 	    setAsBytes (propertyChannel.getBoolean (DP_INP_ASBYTES, false));
 


From walexander at dev.open-bio.org  Wed Mar 19 18:50:46 2008
From: walexander at dev.open-bio.org (Wendy Alexander)
Date: Wed, 19 Mar 2008 18:50:46 -0400
Subject: [MOBY-guts] biomoby commit
Message-ID: <200803192250.m2JMokh8029076@dev.open-bio.org>


walexander
Wed Mar 19 18:50:46 EDT 2008
Update of /home/repository/moby/moby-live/Java/src/main/org/biomoby/service/dashboard
In directory dev.open-bio.org:/tmp/cvs-serv29041

Modified Files:
	DashboardProperties.java 
Log Message:
Added pinger button.
moby-live/Java/src/main/org/biomoby/service/dashboard DashboardProperties.java,1.26,1.27
===================================================================
RCS file: /home/repository/moby/moby-live/Java/src/main/org/biomoby/service/dashboard/DashboardProperties.java,v
retrieving revision 1.26
retrieving revision 1.27
diff -u -r1.26 -r1.27
--- /home/repository/moby/moby-live/Java/src/main/org/biomoby/service/dashboard/DashboardProperties.java	2008/03/02 12:45:26	1.26
+++ /home/repository/moby/moby-live/Java/src/main/org/biomoby/service/dashboard/DashboardProperties.java	2008/03/19 22:50:46	1.27
@@ -65,6 +65,7 @@
     static final String DP_CS_URL = "service-endpoint";
     static final String DP_CS_NEWURL = "service-new-endpoint";
     static final String DP_CS_REGISTRY = "as-registered";
+    static final String DP_CS_PING = "ping";
 
     static final String DP_ENDPOINT = "serviceEndpoint";
     static final String DP_IMPL_CLASS = "serviceImplClass";


From kawas at dev.open-bio.org  Wed Mar 19 19:36:02 2008
From: kawas at dev.open-bio.org (Eddie Kawas)
Date: Wed, 19 Mar 2008 19:36:02 -0400
Subject: [MOBY-guts] biomoby commit
Message-ID: <200803192336.m2JNa27G029203@dev.open-bio.org>


kawas
Wed Mar 19 19:36:02 EDT 2008
Update of /home/repository/moby/moby-live/Perl/MOBY-Server
In directory dev.open-bio.org:/tmp/cvs-serv29168/Perl/MOBY-Server

Modified Files:
	Makefile.PL 
Log Message:
hmm, turns out the cpan release had very old documentation ... not sure how it snuck in ...
moby-live/Perl/MOBY-Server Makefile.PL,1.2,1.3
===================================================================
RCS file: /home/repository/moby/moby-live/Perl/MOBY-Server/Makefile.PL,v
retrieving revision 1.2
retrieving revision 1.3
diff -u -r1.2 -r1.3
--- /home/repository/moby/moby-live/Perl/MOBY-Server/Makefile.PL	2008/02/22 17:52:06	1.2
+++ /home/repository/moby/moby-live/Perl/MOBY-Server/Makefile.PL	2008/03/19 23:36:02	1.3
@@ -3,7 +3,7 @@
 
 	# Define metadata
 	name 'MOBY';
-	version '1.00';
+	version '1.01';
 	license 'perl';
 	abstract
 'This distribution is for communicating with or creating your own MOBY Central registry';


From kawas at dev.open-bio.org  Thu Mar 20 13:35:43 2008
From: kawas at dev.open-bio.org (Eddie Kawas)
Date: Thu, 20 Mar 2008 13:35:43 -0400
Subject: [MOBY-guts] biomoby commit
Message-ID: <200803201735.m2KHZh4b030890@dev.open-bio.org>


kawas
Thu Mar 20 13:35:42 EDT 2008
Update of /home/repository/moby/moby-live/Perl/MOBY-Server/lib/MOBY
In directory dev.open-bio.org:/tmp/cvs-serv30839/Perl/MOBY-Server/lib/MOBY

Modified Files:
	MOBY.pm 
Log Message:
found 2 MOBY.pm modules. cpan ignored the correct one and indexed the wrong one ...
moby-live/Perl/MOBY-Server/lib/MOBY MOBY.pm,1.1,1.2
===================================================================
RCS file: /home/repository/moby/moby-live/Perl/MOBY-Server/lib/MOBY/MOBY.pm,v
retrieving revision 1.1
retrieving revision 1.2
diff -u -r1.1 -r1.2
--- /home/repository/moby/moby-live/Perl/MOBY-Server/lib/MOBY/MOBY.pm	2008/02/21 00:21:27	1.1
+++ /home/repository/moby/moby-live/Perl/MOBY-Server/lib/MOBY/MOBY.pm	2008/03/20 17:35:42	1.2
@@ -1,84 +1,270 @@
 package MOBY;
 
-use 5.008008;
 use strict;
 use warnings;
 
-require Exporter;
 
-our @ISA = qw(Exporter);
 
-# Items to export into callers namespace by default. Note: do not export
-# names by default without a very good reason. Use EXPORT_OK instead.
-# Do not simply export all your public functions/methods/constants.
+use vars qw{$VERSION @ISA @EXPORT @EXPORT_OK};
+BEGIN {
+	$VERSION = '0.85';
+	@ISA       = qw{ Exporter };
+	@EXPORT    = qw{};
+	@EXPORT_OK = qw{};
+}
 
-# This allows declaration	use MOBY ':all';
-# If you do not need this, moving things directly into @EXPORT or @EXPORT_OK
-# will save memory.
-our %EXPORT_TAGS = ( 'all' => [ qw(
-	
-) ] );
-
-our @EXPORT_OK = ( @{ $EXPORT_TAGS{'all'} } );
-
-our @EXPORT = qw(
-	
-);
-
-our $VERSION = '0.01';
 
 
 # Preloaded methods go here.
 
 1;
 __END__
-# Below is stub documentation for your module. You'd better edit it!
 
 =head1 NAME
 
-MOBY - Perl extension for blah blah blah
+MOBY - API for hosting and/or communicating with a MOBY Central registry
+
+=head1 DESCRIPTION
 
-=head1 SYNOPSIS
+This module serves 2 purposes:
 
-  use MOBY;
-  blah blah blah
+=over 4
 
-=head1 DESCRIPTION
+=item * Used to do various transactions with MOBY-Central registry, including registering new Object and Service types, querying for these types, registering new Servers/Services, or queryiong for available services given certain input/output or service type constraints.
+
+=item * Aid in the installation of a custom local MOBY-Central registry.
+
+=back
+
+=head2 Package Installation
+
+Installation of this perl package is straightforward!
+
+On *nix machines, install as follows:
+
+=over 4
+
+=item * C<perl Makefile.PL>
+
+=item * C<make test>
+
+=item * C<make install>
+
+=back
+
+On Window machines, substitute C<nmake> for C<make>!
+
+B<Important> if you are upgrading to newer versions, please make sure to remove any files that may be cached by this module!
+
+=cut
+
+=head2 Installing A Custom MOBY-Central Registry
+
+Assuming that you have already installed this package, the very first thing that you should do is run the script B<moby-s-install.pl>.
+
+This script will do the following:
+
+=over 4
+
+=item * Check for prerequisite modules and warn you if they are missing
+
+=item * Run you through some configuration details
+
+=item * Optionally help you mirror an already existing registry
+
+=item * Optionally install various scripts used by the registry or its' clients
+
+=back
+
+=cut
+
+=head2 BioMOBY Client Installation
+
+Once the module has been installed using the command B<make install>, there is nothing further left for you to do. You are free to start using the BioMOBY API.
+
+=cut
+
+=head2 BioMOBY Server Installation
+
+To set up your own custom registry, you have to ensure that a few things are ready before hand!
+
+=over 4
+
+=item * You have an apache webserver installed/started on your machine
+
+=item * You have mysql installed/started on your machine
+
+=item * You are aware of the full path to the apache cgi-bin directory
+
+=item * You have a mysql username/password with read/write access available to use
+
+=item * You have root priviledges on your machine!
+
+=back
+
+Once you are sure that you satisfy the above items, go ahead and run the B<moby-s-install.pl> script, by typing C<moby-s-install.pl> at the command line. This file was installed onto your machine when you did your 'make install'!
+
+=head3 What Exactly does moby-s-install.pl do?
+
+Like we said before, the install script helps you install/configure your custom MOBY-Central registry.
+
+First of all, the script ensure that you have all of the proper libraries installed.
+
+The very next thing that the script does is prompt you for some information:
+
+=over 4
+
+=item * What is your base installation path for apache?
+
+=item * Where is the conf/cgi-bin directory for apache located?
+
+=item * What is the path to your Perl executable?
+
+=back
+
+Once that information is entered, the script prompts you to set up apache. 
+
+=head4 Apache setup
+
+The following is done when the installation script sets up apache:
+
+=over 4
+
+=item * A mobycentral configuration file is added to your apache conf directory
+
+=item * mySQL connection information is obtained from you and inserted into the the configuration file
+
+=item * mySQL table names for the registry are chosen
+
+=item * Optionally, httpd.conf is edited adding various environment variables necessary for the registry
 
-Stub documentation for MOBY, created by h2xs. It looks like the
-author of the extension was negligent enough to leave the stub
-unedited.
+=back
 
-Blah blah blah.
+=cut
+
+Once apache has been set up, the installation script prompts you to set up mySQL. 
+
+During mySQL setup, you will be prompted to either create a complete clone of an existing registry or to simply add the base tables required for a registry to your database.
+
+The very next thing that will happen, is that you will be prompted to install the RESOURCES script. This script is mandatory for those hosting a registry.
+
+During the installation of the RESOURCES script, you will be prompted for a place to store the RDF cache. This directory needs to read/writable by apache.
+
+After installation of the RESOURCES script, you will be prompted to install the LSID authority script. 
+
+The very last thing that the script does is to prompt you install other auxillary scripts. While they are not required, it is recommended to install them.
+
+Please make sure that any file installed into your cgi-bin directory is executable and that you restart apache so that all changes are reflected!
+
+Assuming that you installed the auxillary scripts, from a web browser, browse to the url:
+
+C<http://localhost/cgi-bin/Moby> 
+
+B<Note:> Of course, we are assuming that your localhost is your valid hostname and that the cgi-bin directory location is correct. 
+
+A helper page with various links should be visible. Go ahead and try them out!
+
+=cut
+
+=cut
+
+=head2 FAQ
+
+=head3 When I run the install script, IO::Prompt complains ...
+
+This could mean that the package C<IO::Prompt> is not installed properly.
+
+What version do you have?
+
+C<perl -MIO::Prompt -e'print "$IO::Prompt::VERSION\n";'>
+
+We have tested version 0.99.2 on both *nix machines and windows. Please make sure that you have  that version. If you do not, please remove the one that you have (the cpan module B<CPAN Plus> is very useful here) and install version 0.99.2! Version 0.99.4 doesn't seem to work too well and produces numerous warnings in our module. Other versions have yet to be tested.
+
+=cut
+
+=head3 How can I make the service tester run every hour?
+
+First of all, the service tester only works on *NIX machines and will not work on Windows. The reason is due to a the module IPC::Shareable which doesn't port to windows.
+
+To set up the service tester simply create a cron job. The following is an illustration of how to do this!
+
+=over 4
+
+=item * Edit your crontab (as root): 
+
+C<crontab -e>
+
+=item * Add the following to the top of the crontab 
+
+C<MOBY_CENTRAL_CONFIG=/etc/apache2/mobycentral.config>
+
+=item * Add the actual job:
+
+C<00 * * * * perl /path/to/the/service_tester.pl>
+
+=back
+
+This will set up a cron job to run every start of the hour!
+
+=cut
+
+=head3 How do I set up the RDF Agent?
+
+Detailed instructions for building, installing and configuring the agent can be found at http://biomoby.open-bio.org/CVS_CONTENT/moby-live/Java/docs/ConfigureRDFAgent.html
+
+=cut
+
+=cut
+
+=head2 Missing Features
+
+=over
+
+=item * automatic installation of the RDF Agent
+
+=back
+
+=cut
+
+=head2 Acknowledgement
+
+
+=cut
 
 =head2 EXPORT
 
 None by default.
 
 
-
 =head1 SEE ALSO
 
-Mention other useful documentation such as the documentation of
-related modules or operating system documentation (such as man pages
-in UNIX), or any relevant external documentation such as RFCs or
-standards.
+For the most up-to-date documentation, visit the BioMOBY website at L<http://biomoby.org>!
 
-If you have a mailing list set up for your module, mention it here.
+If you have questions or comments, please feel free to message us on the following mailing lists:
 
-If you have a web site set up for your module, mention it here.
+=over
 
-=head1 AUTHOR
+=item MOBY discussion list L<http://www.biomoby.org/mailman/listinfo/moby-l>
 
-A. U. Thor, E<lt>a.u.thor at a.galaxy.far.far.awayE<gt>
+=item MOBY Developers List L<http://www.biomoby.org/mailman/listinfo/moby-dev>
 
-=head1 COPYRIGHT AND LICENSE
+=item MOBY bugs discussion list L<http://www.biomoby.org/mailman/listinfo/moby-bugs>
 
-Copyright (C) 2007 by A. U. Thor
+=back
 
-This library is free software; you can redistribute it and/or modify
-it under the same terms as Perl itself, either Perl version 5.8.8 or,
-at your option, any later version of Perl 5 you may have available.
+=head1 AUTHORS
 
 
 =cut
+
+=head1 COPYRIGHT
+
+Copyright (c) 2007 The Biomoby Consortium.
+
+This module is free software; you can redistribute it and/or modify
+it under the same terms as Perl itself.
+
+This software is provided "as is" without warranty of any kind.
+
+=cut
+


From kawas at dev.open-bio.org  Thu Mar 20 13:35:43 2008
From: kawas at dev.open-bio.org (Eddie Kawas)
Date: Thu, 20 Mar 2008 13:35:43 -0400
Subject: [MOBY-guts] biomoby commit
Message-ID: <200803201735.m2KHZh2T030872@dev.open-bio.org>


kawas
Thu Mar 20 13:35:42 EDT 2008
Update of /home/repository/moby/moby-live/Perl/MOBY-Server/lib
In directory dev.open-bio.org:/tmp/cvs-serv30839/Perl/MOBY-Server/lib

Removed Files:
	MOBY.pm 
Log Message:
found 2 MOBY.pm modules. cpan ignored the correct one and indexed the wrong one ...
moby-live/Perl/MOBY-Server/lib MOBY.pm,1.2,NONE
rcsdiff: /home/repository/moby/moby-live/Perl/MOBY-Server/lib/RCS/MOBY.pm,v: No such file or directory


From kawas at dev.open-bio.org  Thu Mar 20 13:36:33 2008
From: kawas at dev.open-bio.org (Eddie Kawas)
Date: Thu, 20 Mar 2008 13:36:33 -0400
Subject: [MOBY-guts] biomoby commit
Message-ID: <200803201736.m2KHaXvL030942@dev.open-bio.org>


kawas
Thu Mar 20 13:36:33 EDT 2008
Update of /home/repository/moby/moby-live/Perl/MOBY-Server
In directory dev.open-bio.org:/tmp/cvs-serv30899/Perl/MOBY-Server

Modified Files:
	META.yml MANIFEST Makefile.PL 
Log Message:
changed the version numbers
moby-live/Perl/MOBY-Server META.yml,1.1,1.2 MANIFEST,1.4,1.5 Makefile.PL,1.3,1.4
===================================================================
RCS file: /home/repository/moby/moby-live/Perl/MOBY-Server/META.yml,v
retrieving revision 1.1
retrieving revision 1.2
diff -u -r1.1 -r1.2
--- /home/repository/moby/moby-live/Perl/MOBY-Server/META.yml	2008/02/21 00:21:28	1.1
+++ /home/repository/moby/moby-live/Perl/MOBY-Server/META.yml	2008/03/20 17:36:33	1.2
@@ -41,4 +41,4 @@
   XML::DOM: 0
   XML::LibXML: 1.62
   XML::XPath: 1.12
-version: 1.00
+version: 1.03

===================================================================
RCS file: /home/repository/moby/moby-live/Perl/MOBY-Server/MANIFEST,v
retrieving revision 1.4
retrieving revision 1.5
diff -u -r1.4 -r1.5
--- /home/repository/moby/moby-live/Perl/MOBY-Server/MANIFEST	2008/03/13 19:12:29	1.4
+++ /home/repository/moby/moby-live/Perl/MOBY-Server/MANIFEST	2008/03/20 17:36:33	1.5
@@ -13,7 +13,6 @@
 inc/Module/Install/Share.pm
 inc/Module/Install/Win32.pm
 inc/Module/Install/WriteAll.pm
-lib/MOBY.pm
 lib/MOBY/Adaptor/moby/DataAccessI.pm
 lib/MOBY/Adaptor/moby/DataAdapterI.pm
 lib/MOBY/Adaptor/moby/Impl/FetaQueryAdaptor.pm

===================================================================
RCS file: /home/repository/moby/moby-live/Perl/MOBY-Server/Makefile.PL,v
retrieving revision 1.3
retrieving revision 1.4
diff -u -r1.3 -r1.4
--- /home/repository/moby/moby-live/Perl/MOBY-Server/Makefile.PL	2008/03/19 23:36:02	1.3
+++ /home/repository/moby/moby-live/Perl/MOBY-Server/Makefile.PL	2008/03/20 17:36:33	1.4
@@ -3,7 +3,7 @@
 
 	# Define metadata
 	name 'MOBY';
-	version '1.01';
+	version '1.03';
 	license 'perl';
 	abstract
 'This distribution is for communicating with or creating your own MOBY Central registry';


From kawas at dev.open-bio.org  Thu Mar 20 14:45:11 2008
From: kawas at dev.open-bio.org (Eddie Kawas)
Date: Thu, 20 Mar 2008 14:45:11 -0400
Subject: [MOBY-guts] biomoby commit
Message-ID: <200803201845.m2KIjBgM031113@dev.open-bio.org>


kawas
Thu Mar 20 14:45:10 EDT 2008
Update of /home/repository/moby/moby-live/Perl
In directory dev.open-bio.org:/tmp/cvs-serv31078/Perl

Modified Files:
	README 
Log Message:
added explanations for installing the client side of moby and added some more lines to the 'creating cpan releases'
moby-live/Perl README,1.4,1.5
===================================================================
RCS file: /home/repository/moby/moby-live/Perl/README,v
retrieving revision 1.4
retrieving revision 1.5
diff -u -r1.4 -r1.5
--- /home/repository/moby/moby-live/Perl/README	2008/02/22 20:22:15	1.4
+++ /home/repository/moby/moby-live/Perl/README	2008/03/20 18:45:10	1.5
@@ -44,6 +44,18 @@
    make
    make test
    make install
+   
+To install just the *client* Perl MOBY libraries on your system, 
+type the following (from within MOBY-Client/):
+
+   perl populate_libs.pl
+   perl Makefile.PL
+   make
+   make test
+   make install
+
+The script populate_libs.pl goes through the MOBY-Server directory
+and extracts those modules required just for Client side MOBY.
 
 DEPENDENCIES
 
@@ -69,6 +81,7 @@
 			moby-live/Perl/MOBY-Client>rm -rf ./lib
 			moby-live/Perl/MOBY-Client>perl populate_libs.pl
 			moby-live/Perl/MOBY-Client>perl Makefile.PL
+			moby-live/Perl/MOBY-Client>make test
 			moby-live/Perl/MOBY-Client>make dist
 	
 		Once you are done, you should have a MOBY-Client*.tar.gz 
@@ -82,6 +95,8 @@
 		
 			moby-live/Perl>cd MOBY-Server
 			moby-live/Perl/MOBY-Server>perl Makefile.PL
+			moby-live/Perl/MOBY-Server>make
+			moby-live/Perl/MOBY-Server>make test
 			moby-live/Perl/MOBY-Server>make dist
 	
 		Once you are done, you should have a MOBY-Server*.tar.gz 
@@ -95,6 +110,8 @@
 		
 			moby-live/Perl>cd MOSES-MOBY
 			moby-live/Perl/MOSES-MOBY>perl Makefile.PL
+			moby-live/Perl/MOSES-MOBY>make 
+			moby-live/Perl/MOSES-MOBY>make test
 			moby-live/Perl/MOSES-MOBY>make dist
 	
 		Once you are done, you should have a MOSES-MOBY*.tar.gz 


From senger at dev.open-bio.org  Fri Mar 28 07:19:02 2008
From: senger at dev.open-bio.org (Martin Senger)
Date: Fri, 28 Mar 2008 07:19:02 -0400
Subject: [MOBY-guts] biomoby commit
Message-ID: <200803281119.m2SBJ2Hd024200@dev.open-bio.org>


senger
Fri Mar 28 07:19:02 EDT 2008
Update of /home/repository/moby/moby-live/Java/xmls
In directory dev.open-bio.org:/tmp/cvs-serv24163/xmls

Modified Files:
	project.pom 
Log Message:
dependency for more recent commons-collections
moby-live/Java/xmls project.pom,1.9,1.10
===================================================================
RCS file: /home/repository/moby/moby-live/Java/xmls/project.pom,v
retrieving revision 1.9
retrieving revision 1.10
diff -u -r1.9 -r1.10
--- /home/repository/moby/moby-live/Java/xmls/project.pom	2008/03/14 23:27:41	1.9
+++ /home/repository/moby/moby-live/Java/xmls/project.pom	2008/03/28 11:19:02	1.10
@@ -175,6 +175,10 @@
           <groupId>xerces</groupId>
           <artifactId>xercesImpl</artifactId>
         </exclusion>
+        <exclusion>
+          <groupId>commons-collections</groupId>
+          <artifactId>commons-collections</artifactId>
+        </exclusion>
       </exclusions> 
     </dependency>
 


From senger at dev.open-bio.org  Fri Mar 28 07:19:02 2008
From: senger at dev.open-bio.org (Martin Senger)
Date: Fri, 28 Mar 2008 07:19:02 -0400
Subject: [MOBY-guts] biomoby commit
Message-ID: <200803281119.m2SBJ2T7024182@dev.open-bio.org>


senger
Fri Mar 28 07:19:02 EDT 2008
Update of /home/repository/moby/moby-live/Java/docs
In directory dev.open-bio.org:/tmp/cvs-serv24163/docs

Modified Files:
	ChangeLog 
Log Message:
dependency for more recent commons-collections
moby-live/Java/docs ChangeLog,1.87,1.88
===================================================================
RCS file: /home/repository/moby/moby-live/Java/docs/ChangeLog,v
retrieving revision 1.87
retrieving revision 1.88
diff -u -r1.87 -r1.88
--- /home/repository/moby/moby-live/Java/docs/ChangeLog	2008/03/14 23:27:41	1.87
+++ /home/repository/moby/moby-live/Java/docs/ChangeLog	2008/03/28 11:19:02	1.88
@@ -1,3 +1,7 @@
+2008-03-28  Martin Senger  <martin.senger&#64;gmail.com>
+
+	* Fixed a dependency for commons-collection in the project.pom.
+
 2008-03-14  Martin Senger  <martin.senger&#64;gmail.com>
 
 	* Fixed a bug with missing xercesImpl classes. Putting back


From kawas at dev.open-bio.org  Mon Mar 31 14:04:47 2008
From: kawas at dev.open-bio.org (Eddie Kawas)
Date: Mon, 31 Mar 2008 14:04:47 -0400
Subject: [MOBY-guts] biomoby commit
Message-ID: <200803311804.m2VI4l2q001190@dev.open-bio.org>


kawas
Mon Mar 31 14:04:47 EDT 2008
Update of /home/repository/moby/moby-live/Perl/MOSES-MOBY/lib/MOSES/MOBY/Generators
In directory dev.open-bio.org:/tmp/cvs-serv1155

Modified Files:
	GenServices.pm 
Log Message:
added initial support for namespace checking.
moby-live/Perl/MOSES-MOBY/lib/MOSES/MOBY/Generators GenServices.pm,1.3,1.4
===================================================================
RCS file: /home/repository/moby/moby-live/Perl/MOSES-MOBY/lib/MOSES/MOBY/Generators/GenServices.pm,v
retrieving revision 1.3
retrieving revision 1.4
diff -u -r1.3 -r1.4
--- /home/repository/moby/moby-live/Perl/MOSES-MOBY/lib/MOSES/MOBY/Generators/GenServices.pm	2008/02/21 00:12:56	1.3
+++ /home/repository/moby/moby-live/Perl/MOSES-MOBY/lib/MOSES/MOBY/Generators/GenServices.pm	2008/03/31 18:04:47	1.4
@@ -212,11 +212,25 @@
 	    $input_paths{$main_name} = $self->_tree2paths ($tree);
 	}
 #	print MOSES::MOBY::Base->toString (\%input_paths);
-
 	# create implementation specific object
 	my $impl = {
 	    package => ($args{impl_prefix} || 'Service') . '::' . $name,
 	};
+	my @input_ns = ();
+        foreach my $in (@{ $obj->inputs }) {
+
+	    if (ref ($in) eq 'MOSES::MOBY::Def::PrimaryDataSimple') {
+                foreach my $ns ( @{$in->namespaces} ) {
+                    push @input_ns, $ns->name;
+                }
+            } else {
+                foreach my $sim (@{ $in->elements }) {
+                    foreach my $ns ( @{$sim->namespaces} ) {
+                        push @input_ns, $ns->name;
+                    }
+                }
+            }
+        }
 	if ($args{outcode}) {
 	    $tt->process ( $input, { base         => $obj,
 				     impl         => $impl,
@@ -224,6 +238,7 @@
 				     get_children => $ref_sub_get_children,
 				     ref          => $ref_sub_ref,
                                      input_paths  => \%input_paths,
+				     input_ns     =>,\@input_ns,
 				 },
 			   $args{outcode} ) || $LOG->logdie ($tt->error());
 	} else {
@@ -244,6 +259,7 @@
 				     get_children => $ref_sub_get_children,
 				     ref          => $ref_sub_ref,
                                      input_paths  => \%input_paths,
+                                     input_ns     => \@input_ns,
 				 },
 			   $outfile ) || $LOG->logdie ($tt->error());
 	    $LOG->info ("Created $outfile\n");


From kawas at dev.open-bio.org  Mon Mar 31 14:05:18 2008
From: kawas at dev.open-bio.org (Eddie Kawas)
Date: Mon, 31 Mar 2008 14:05:18 -0400
Subject: [MOBY-guts] biomoby commit
Message-ID: <200803311805.m2VI5IeA001274@dev.open-bio.org>


kawas
Mon Mar 31 14:05:17 EDT 2008
Update of /home/repository/moby/moby-live/Perl/MOSES-MOBY/lib/MOSES/MOBY/Generators/templates
In directory dev.open-bio.org:/tmp/cvs-serv1239

Modified Files:
	service.tt 
Log Message:
added initial support for namespace checking.
moby-live/Perl/MOSES-MOBY/lib/MOSES/MOBY/Generators/templates service.tt,1.3,1.4
===================================================================
RCS file: /home/repository/moby/moby-live/Perl/MOSES-MOBY/lib/MOSES/MOBY/Generators/templates/service.tt,v
retrieving revision 1.3
retrieving revision 1.4
diff -u -r1.3 -r1.4
--- /home/repository/moby/moby-live/Perl/MOSES-MOBY/lib/MOSES/MOBY/Generators/templates/service.tt	2008/02/21 00:12:55	1.3
+++ /home/repository/moby/moby-live/Perl/MOSES-MOBY/lib/MOSES/MOBY/Generators/templates/service.tt	2008/03/31 18:05:17	1.4
@@ -143,6 +143,7 @@
 use MOSES::MOBY::ServiceException;
 use strict;
 
+my %valid_namespaces = ( [% FOREACH ns IN input_ns %] '[%ns%]'=>1,  [% END %]);
 #-----------------------------------------------------------------
 # process_it
 #    This method is called for every job in the client request.
@@ -169,11 +170,23 @@
 	
     [%- IF is_simple (input) %]
 [% get_members (input_paths.${input.name}, 4) %]
+    # perform namespace checking for inputs to this service
+#   do {
+#       $response->record_error ( { code => INPUT_INCORRECT_NAMESPACE,
+#                                   msg  => 'This service requires inputs under the namespaces: {"' . join(',', keys %valid_namespaces) . '"}' } );
+#       return;
+#   } unless $valid_namespaces{$namespace};
     [%- ELSE %]
     if (defined $[% input.name %]_collection) {
         foreach my $[% input.name %]_element (@{ $[% input.name %]_collection }) {
             my $[% input.name %] = $[% input.name %]_element->data;
 [% get_members (input_paths.${input.name}, 12) %]
+            # perform namespace checking for inputs to this service
+        #   do {
+        #       $response->record_error ( { code => INPUT_INCORRECT_NAMESPACE,
+        #                                   msg  => 'This service requires inputs under the namespaces: { "' . join(',', keys %valid_namespaces) . '"}' } );
+        #       return;
+        #   } unless $valid_namespaces{$namespace};
         }
     }
     [%- END %]


From senger at dev.open-bio.org  Sun Mar  2 12:45:25 2008
From: senger at dev.open-bio.org (Martin Senger)
Date: Sun, 2 Mar 2008 07:45:25 -0500
Subject: [MOBY-guts] biomoby commit
Message-ID: <200803021245.m22CjPI4032364@dev.open-bio.org>


senger
Sun Mar  2 07:45:24 EST 2008
Update of /home/repository/moby/moby-live/Java
In directory dev.open-bio.org:/tmp/cvs-serv32345

Modified Files:
	build.xml 
Log Message:
Too Many Changes - see docs/ChangeLog

moby-live/Java build.xml,1.69,1.70
===================================================================
RCS file: /home/repository/moby/moby-live/Java/build.xml,v
retrieving revision 1.69
retrieving revision 1.70
diff -u -r1.69 -r1.70
--- /home/repository/moby/moby-live/Java/build.xml	2008/02/28 05:21:48	1.69
+++ /home/repository/moby/moby-live/Java/build.xml	2008/03/02 12:45:24	1.70
@@ -97,7 +97,6 @@
   <property name="proxySet" value=""/>
   
   <property name="dot.location" value=""/>
-  <property name="registry.cache.dir" value=""/>
   
   <!-- Classpath -->
   <path id="build.classpath">
@@ -106,12 +105,9 @@
     <fileset dir="${lib.dir}">
       <include name="*.jar"/>
     </fileset>
-    <!-- it should not be necessary anymore because
-         tools.jar are now defined in xmls/project.pom
     <fileset dir="${java.home}/../lib">
       <include name="tools.jar"/>
     </fileset>
-    -->
   </path>
           
   <!-- this differs from the ${build.classpath} by not including



From senger at dev.open-bio.org  Sun Mar  2 12:45:25 2008
From: senger at dev.open-bio.org (Martin Senger)
Date: Sun, 2 Mar 2008 07:45:25 -0500
Subject: [MOBY-guts] biomoby commit
Message-ID: <200803021245.m22CjPFH032415@dev.open-bio.org>


senger
Sun Mar  2 07:45:24 EST 2008
Update of /home/repository/moby/moby-live/Java/docs
In directory dev.open-bio.org:/tmp/cvs-serv32345/docs

Modified Files:
	ChangeLog Dashboard-NOTES.txt 
Log Message:
Too Many Changes - see docs/ChangeLog

moby-live/Java/docs ChangeLog,1.84,1.85 Dashboard-NOTES.txt,1.14,1.15
===================================================================
RCS file: /home/repository/moby/moby-live/Java/docs/ChangeLog,v
retrieving revision 1.84
retrieving revision 1.85
diff -u -r1.84 -r1.85
--- /home/repository/moby/moby-live/Java/docs/ChangeLog	2008/02/28 05:21:48	1.84
+++ /home/repository/moby/moby-live/Java/docs/ChangeLog	2008/03/02 12:45:24	1.85
@@ -1,3 +1,43 @@
+2008-03-02  Martin Senger  <martin.senger&#64;gmail.com>
+
+	* Added: new installation task (type: ant install) - it downloads
+	all needed librraies, builds the jMoby, fills the local cache and
+	starts Dashboard.
+
+	* Added: method MobyException.formatAndLog()
+
+	* Changes in Dashboard:
+	
+	  - Better support for configuration; it uses now also properties
+	  from the 'build.properties' file (which helps, for example, in
+	  finding the same registry local cache as the one used during the
+	  jMoby installation (ant install).
+
+	  - Allowing to select category when registering a new service.
+
+	  - The component layout in the MoSeS generators panel was
+	  slightly changed (the never-implemented flavours removed; more
+	  space for the console).
+
+	  - The console panels, in the append mode, now scroll better to
+	  their ends (in order to better follow what is being written
+	  there).
+
+	  - Fix the local class selector in the SimpleClient panel (before
+	  it suggested a file to select but in fact it was a class name
+	  that should be entered there).
+
+	
+2008-02-29  Martin Senger  <martin.senger&#64;gmail.com>
+
+	* Fixed: Calling various tasks from Dashboard sometimes caused a
+	mysterious NullPointerException in the SimpleAnt task. This was
+	because of a (still mysterious) bug in Ant itself. But I at least
+	found a workaround so the bug should not occur again.
+
+	* Added: New method getResource(URL url) in CentralImp class,
+	dealing with gzipped RDF resources.
+
 2008-02-28  Martin Senger  <martin.senger&#64;gmail.com>
 
 	* Fixed: the jMoby XML message parser can accept now more

===================================================================
RCS file: /home/repository/moby/moby-live/Java/docs/Dashboard-NOTES.txt,v
retrieving revision 1.14
retrieving revision 1.15
diff -u -r1.14 -r1.15
--- /home/repository/moby/moby-live/Java/docs/Dashboard-NOTES.txt	2006/10/14 20:46:55	1.14
+++ /home/repository/moby/moby-live/Java/docs/Dashboard-NOTES.txt	2008/03/02 12:45:24	1.15
@@ -15,20 +15,9 @@
 Should be done:
 ---------------
 
-* jMoby.jar for service providers should be smaller (no need for many
-  classes there - like ui...)
-
 * Dashborad should have a way to create/show XML data representing a
   data type *before* there is a service registered that uses such data
 
-* when moses panel generates datatypes they are not immediately
-  recognized by the same dashbord (e.g. in the SimpleClient panel);
-  one must restart the dashboard; it should be better to dynamically
-  extend the dashboard's classpath
-
-* add a cache action button: "show me what's would be updated if I
-  update my cache"
-
 * right-click
   - if nothing selected, it should take what is under the
     mouse (selected first), otherwise it is annoying
@@ -82,9 +71,6 @@
 
 ? move help system to Java Help; more contextual help
 
-? cache: start to work on/think of the RDF-based cache 
-? cache: remove memory-caching from CentralImpl
-
 ? Possible new panels:
   - verify registry
   - browsing in graphs



From senger at dev.open-bio.org  Sun Mar  2 12:45:25 2008
From: senger at dev.open-bio.org (Martin Senger)
Date: Sun, 2 Mar 2008 07:45:25 -0500
Subject: [MOBY-guts] biomoby commit
Message-ID: <200803021245.m22CjP3e032468@dev.open-bio.org>


senger
Sun Mar  2 07:45:25 EST 2008
Update of /home/repository/moby/moby-live/Java/src/Clients/help
In directory dev.open-bio.org:/tmp/cvs-serv32345/src/Clients/help

Added Files:
	MobyDigestClient_usage.txt 
Removed Files:
	MobyDigest_usage.txt 
Log Message:
Too Many Changes - see docs/ChangeLog

moby-live/Java/src/Clients/help MobyDigestClient_usage.txt,NONE,1.1 MobyDigest_usage.txt,1.7,NONE
rcsdiff: /home/repository/moby/moby-live/Java/src/Clients/help/RCS/MobyDigest_usage.txt,v: No such file or directory



From senger at dev.open-bio.org  Sun Mar  2 12:45:25 2008
From: senger at dev.open-bio.org (Martin Senger)
Date: Sun, 2 Mar 2008 07:45:25 -0500
Subject: [MOBY-guts] biomoby commit
Message-ID: <200803021245.m22CjPYM032393@dev.open-bio.org>


senger
Sun Mar  2 07:45:24 EST 2008
Update of /home/repository/moby/moby-live/Java/data/registrations
In directory dev.open-bio.org:/tmp/cvs-serv32345/data/registrations

Added Files:
	ConcatSequenceSet-registration.xml 
	ConcatSequences-registration.xml 
	HelloBiomobyWorld-registration.xml Mabuhay-registration.xml 
	README Regex.datatype.xml TestServiceNotes-registration.xml 
	TextExtract-registration.xml 
Log Message:
Too Many Changes - see docs/ChangeLog

moby-live/Java/data/registrations ConcatSequenceSet-registration.xml,NONE,1.1 ConcatSequences-registration.xml,NONE,1.1 HelloBiomobyWorld-registration.xml,NONE,1.1 Mabuhay-registration.xml,NONE,1.1 README,NONE,1.1 Regex.datatype.xml,NONE,1.1 TestServiceNotes-registration.xml,NONE,1.1 TextExtract-registration.xml,NONE,1.1


From senger at dev.open-bio.org  Sun Mar  2 12:45:25 2008
From: senger at dev.open-bio.org (Martin Senger)
Date: Sun, 2 Mar 2008 07:45:25 -0500
Subject: [MOBY-guts] biomoby commit
Message-ID: <200803021245.m22CjPJk032379@dev.open-bio.org>


senger
Sun Mar  2 07:45:24 EST 2008
Update of /home/repository/moby/moby-live/Java/data
In directory dev.open-bio.org:/tmp/cvs-serv32345/data

Removed Files:
	parser-test-input2.xml 
Log Message:
Too Many Changes - see docs/ChangeLog

moby-live/Java/data parser-test-input2.xml,1.2,NONE
rcsdiff: /home/repository/moby/moby-live/Java/data/RCS/parser-test-input2.xml,v: No such file or directory



From senger at dev.open-bio.org  Sun Mar  2 12:45:25 2008
From: senger at dev.open-bio.org (Martin Senger)
Date: Sun, 2 Mar 2008 07:45:25 -0500
Subject: [MOBY-guts] biomoby commit
Message-ID: <200803021245.m22CjPju032526@dev.open-bio.org>


senger
Sun Mar  2 07:45:25 EST 2008
Update of /home/repository/moby/moby-live/Java/src/config/dashboard/META-INF/services
In directory dev.open-bio.org:/tmp/cvs-serv32345/src/config/dashboard/META-INF/services

Modified Files:
	org.biomoby.service.dashboard.renderers.Renderer 
Log Message:
Too Many Changes - see docs/ChangeLog

moby-live/Java/src/config/dashboard/META-INF/services org.biomoby.service.dashboard.renderers.Renderer,1.3,1.4
===================================================================
RCS file: /home/repository/moby/moby-live/Java/src/config/dashboard/META-INF/services/org.biomoby.service.dashboard.renderers.Renderer,v
retrieving revision 1.3
retrieving revision 1.4
diff -u -r1.3 -r1.4
--- /home/repository/moby/moby-live/Java/src/config/dashboard/META-INF/services/org.biomoby.service.dashboard.renderers.Renderer	2006/02/19 18:42:55	1.3
+++ /home/repository/moby/moby-live/Java/src/config/dashboard/META-INF/services/org.biomoby.service.dashboard.renderers.Renderer	2008/03/02 12:45:25	1.4
@@ -2,4 +2,4 @@
 org.biomoby.service.dashboard.renderers.PlainMobyText
 org.biomoby.service.dashboard.renderers.Base64Image
 org.biomoby.service.dashboard.renderers.XMLTreeRenderer
-org.biomoby.service.dashboard.renderers.ICISPedigreeTree
+#org.biomoby.service.dashboard.renderers.ICISPedigreeTree



From senger at dev.open-bio.org  Sun Mar  2 12:45:25 2008
From: senger at dev.open-bio.org (Martin Senger)
Date: Sun, 2 Mar 2008 07:45:25 -0500
Subject: [MOBY-guts] biomoby commit
Message-ID: <200803021245.m22CjPGj032441@dev.open-bio.org>


senger
Sun Mar  2 07:45:25 EST 2008
Update of /home/repository/moby/moby-live/Java/src/Clients
In directory dev.open-bio.org:/tmp/cvs-serv32345/src/Clients

Modified Files:
	CacheRegistryClient.java MobyDigestClient.java 
	TestingCentral.java 
Log Message:
Too Many Changes - see docs/ChangeLog

moby-live/Java/src/Clients CacheRegistryClient.java,1.9,1.10 MobyDigestClient.java,1.8,1.9 TestingCentral.java,1.10,1.11
===================================================================
RCS file: /home/repository/moby/moby-live/Java/src/Clients/CacheRegistryClient.java,v
retrieving revision 1.9
retrieving revision 1.10
diff -u -r1.9 -r1.10
--- /home/repository/moby/moby-live/Java/src/Clients/CacheRegistryClient.java	2008/02/23 13:58:32	1.9
+++ /home/repository/moby/moby-live/Java/src/Clients/CacheRegistryClient.java	2008/03/02 12:45:25	1.10
@@ -16,8 +16,7 @@
 import org.biomoby.shared.event.Notifier;
 
 import org.tulsoft.tools.BaseCmdLine;
-import org.tulsoft.shared.FileUtils;
-import org.tulsoft.shared.GException;
+import org.apache.commons.lang.time.DurationFormatUtils;
 
 /**
  * This is a command-line client creating (and removing) a cache of a
@@ -65,53 +64,91 @@
 	    if (! cmd.hasOption ("-q"))
 		worker.addNotificationListener (new LogListener());
 
+	    long started, elapsed, total = 0;
+
 	    //
 	    // [re-]fill the cache
 	    //
+	    if (cmd.hasOption ("-fill") || cmd.hasOption ("-fill-n")) {
+		worker.removeFromCache (CentralCached.CACHE_PART_NAMESPACES);
+		decoration ("Retrieving namespaces...    ");
+		started = System.currentTimeMillis();
+		worker.getFullNamespaces();
+		elapsed = System.currentTimeMillis() - started;
+		total += elapsed;
+		decorationLn (DurationFormatUtils.formatDurationHMS (elapsed));
+	    }
 	    if (cmd.hasOption ("-fill") || cmd.hasOption ("-fill-d")) {
 		worker.removeFromCache (CentralCached.CACHE_PART_DATATYPES);
-		decorationLn ("Retrieving data types...");
+		decoration ("Retrieving data types...    ");
+		started = System.currentTimeMillis();
 		worker.getDataTypes();
+		elapsed = System.currentTimeMillis() - started;
+		total += elapsed;
+		decorationLn (DurationFormatUtils.formatDurationHMS (elapsed));
 	    }
 	    if (cmd.hasOption ("-fill") || cmd.hasOption ("-fill-s")) {
 		worker.removeFromCache (CentralCached.CACHE_PART_SERVICES);
-		decorationLn ("Retrieving services...");
+		decoration ("Retrieving services...      ");
+		started = System.currentTimeMillis();
 		worker.getServices();
+		elapsed = System.currentTimeMillis() - started;
+		total += elapsed;
+		decorationLn (DurationFormatUtils.formatDurationHMS (elapsed));
 	    }
 	    if (cmd.hasOption ("-fill") || cmd.hasOption ("-fill-t")) {
 		worker.removeFromCache (CentralCached.CACHE_PART_SERVICETYPES);
-		decorationLn ("Retrieving service types...");
+		decoration ("Retrieving service types... ");
+		started = System.currentTimeMillis();
 		worker.getFullServiceTypes();
-	    }
-	    if (cmd.hasOption ("-fill") || cmd.hasOption ("-fill-n")) {
-		worker.removeFromCache (CentralCached.CACHE_PART_NAMESPACES);
-		decorationLn ("Retrieving namespaces...");
-		worker.getFullNamespaces();
+		elapsed = System.currentTimeMillis() - started;
+		total += elapsed;
+		decorationLn (DurationFormatUtils.formatDurationHMS (elapsed));
 	    }
 
 	    //
 	    // update the cache
 	    //
+	    if (cmd.hasOption ("-update") || cmd.hasOption ("-update-n")) {
+		decoration ("Updating namespaces...      ");
+		started = System.currentTimeMillis();
+		worker.updateCache (CentralCached.CACHE_PART_NAMESPACES);
+		elapsed = System.currentTimeMillis() - started;
+		total += elapsed;
+		decorationLn (DurationFormatUtils.formatDurationHMS (elapsed));
+	    }
 	    if (cmd.hasOption ("-update") || cmd.hasOption ("-update-d")) {
-		decorationLn ("Updating data types...");
+		decoration ("Updating data types...      ");
+		started = System.currentTimeMillis();
 		worker.updateCache (CentralCached.CACHE_PART_DATATYPES);
+		elapsed = System.currentTimeMillis() - started;
+		total += elapsed;
+		decorationLn (DurationFormatUtils.formatDurationHMS (elapsed));
 	    }
 	    if (cmd.hasOption ("-update") || cmd.hasOption ("-update-s")) {
-		decorationLn ("Updating services...");
+		decoration ("Updating services...        ");
+		started = System.currentTimeMillis();
 		worker.updateCache (CentralCached.CACHE_PART_SERVICES);
+		elapsed = System.currentTimeMillis() - started;
+		total += elapsed;
+		decorationLn (DurationFormatUtils.formatDurationHMS (elapsed));
 	    }
 	    if (cmd.hasOption ("-update") || cmd.hasOption ("-update-t")) {
-		decorationLn ("Updating service types...");
+		decoration ("Updating service types...   ");
+		started = System.currentTimeMillis();
 		worker.updateCache (CentralCached.CACHE_PART_SERVICETYPES);
-	    }
-	    if (cmd.hasOption ("-update") || cmd.hasOption ("-update-n")) {
-		decorationLn ("Updating namespaces...");
-		worker.updateCache (CentralCached.CACHE_PART_NAMESPACES);
+		elapsed = System.currentTimeMillis() - started;
+		total += elapsed;
+		decorationLn (DurationFormatUtils.formatDurationHMS (elapsed));
 	    }
 
 	    //
 	    // remove the cache
 	    //
+	    if (cmd.hasOption ("-remove") || cmd.hasOption ("-remove-n")) {
+		worker.removeFromCache (CentralCached.CACHE_PART_NAMESPACES);
+		decorationLn ("Cache for namespaces removed.");
+	    }
 	    if (cmd.hasOption ("-remove") || cmd.hasOption ("-remove-d")) {
 		worker.removeFromCache (CentralCached.CACHE_PART_DATATYPES);
 		decorationLn ("Cache for data types removed.");
@@ -124,14 +161,15 @@
 		worker.removeFromCache (CentralCached.CACHE_PART_SERVICETYPES);
 		decorationLn ("Cache for service types removed.");
 	    }
-	    if (cmd.hasOption ("-remove") || cmd.hasOption ("-remove-n")) {
-		worker.removeFromCache (CentralCached.CACHE_PART_NAMESPACES);
-		decorationLn ("Cache for namespaces removed.");
-	    }
 
 	    //
 	    // cache info
 	    //
+	    if (cmd.hasOption ("-info") || cmd.hasOption ("-info-n")) {
+		decorationLn ("Cache for namespaces...");
+		msgln
+		    (worker.getCacheInfoFormatted (CentralCached.CACHE_PART_NAMESPACES));
+	    }
 	    if (cmd.hasOption ("-info") || cmd.hasOption ("-info-d")) {
 		decorationLn ("Cache for data types...");
 		msgln
@@ -147,11 +185,11 @@
 		msgln
 		    (worker.getCacheInfoFormatted (CentralCached.CACHE_PART_SERVICETYPES));
 	    }
-	    if (cmd.hasOption ("-info") || cmd.hasOption ("-info-n")) {
-		decorationLn ("Cache for namespaces...");
-		msgln
-		    (worker.getCacheInfoFormatted (CentralCached.CACHE_PART_NAMESPACES));
-	    }
+
+
+	    decorationLn ("Total spent time:           " +
+			  DurationFormatUtils.formatDurationHMS (total));
+
 
 	} catch (Throwable e) {
 	    processErrorAndExit (e);

===================================================================
RCS file: /home/repository/moby/moby-live/Java/src/Clients/MobyDigestClient.java,v
retrieving revision 1.8
retrieving revision 1.9
diff -u -r1.8 -r1.9
--- /home/repository/moby/moby-live/Java/src/Clients/MobyDigestClient.java	2006/02/08 17:24:13	1.8
+++ /home/repository/moby/moby-live/Java/src/Clients/MobyDigestClient.java	2008/03/02 12:45:25	1.9
@@ -6,16 +6,21 @@
 // Copyright Martin Senger (martin.senger at gmail.com).
 //
 
-import org.biomoby.shared.*;
+import org.biomoby.client.CmdLineHelper;
+import org.biomoby.shared.CentralCached;
+import org.biomoby.shared.MobyDataType;
+import org.biomoby.shared.MobyNamespace;
+import org.biomoby.shared.MobyService;
+import org.biomoby.shared.MobyServiceType;
+import org.biomoby.shared.MobyData;
+import org.biomoby.shared.MobySecondaryData;
+import org.biomoby.shared.MobyPrimaryDataSet;
 import org.biomoby.shared.event.SimpleListener;
-import org.biomoby.shared.event.Notifier;
-import org.biomoby.client.*;
 
 import org.tulsoft.tools.BaseCmdLine;
-import org.tulsoft.shared.FileUtils;
-import org.tulsoft.shared.GException;
 
 import java.util.Map;
+import java.util.Set;
 import java.util.HashSet;
 import java.util.Iterator;
 
@@ -28,22 +33,8 @@
  * @version $Id$
  */
 
-public class MobyDigestClient {
-
-    /*************************************************************************
-     * Return a help text how to use this client.
-     *************************************************************************/
-    public static String getUsage() {
-	String helpFile = "help/MobyDigest_usage.txt";
-	try {
-	    return new String (FileUtils.findAndGetBinaryFile (helpFile));
-	} catch (GException e) {
-	    return
-		"Sorry but an error occured.\n" +
-		"I cannot find the help file '" + helpFile + "'.\n" +
-		e.getMessage();
-	}
-    }
+public class MobyDigestClient
+    extends CmdLineHelper {
 
     /*************************************************************************
      *
@@ -53,38 +44,31 @@
     public static void main (String [] args) {
 	try {
 
-	    BaseCmdLine cmd = new BaseCmdLine (args, true);
-	    if (cmd.hasParam ("-help") || cmd.hasParam ("-h")) {
-		System.out.print (MobyDigestClient.getUsage());
-		System.exit (0);
-	    }
+	    BaseCmdLine cmd = getCmdLine (args, MobyDigestClient.class);
 
 	    // where is a Moby registry
-	    CentralAll worker =
-		new CentralDigestCachedImpl (cmd.getParam ("-e"),
-					     cmd.getParam ("-uri"),
-					     cmd.getParam ("-cachedir"));
+	    CentralCached worker = getCachableRegistryWorker (cmd);
 
 	    // how much to show
 	    boolean details = cmd.hasOption ("-details");
 	    boolean summary = cmd.hasOption ("-summary");
 	    boolean verbose = (cmd.hasOption ("-v") || cmd.hasOption ("-verbose"));
 	    if (verbose)
-		((Notifier)worker).addNotificationListener (new SimpleListener());
+		worker.addNotificationListener (new SimpleListener());
 
 	    // read (sometimes all) data types and their relationships
 	    if (cmd.hasOption ("-d")) {
 		if (details) {
 		    MobyDataType[] dataTypes = worker.getDataTypes();
 		    for (int i = 0; i < dataTypes.length; i++) {
-			System.out.println (dataTypes[i].toString());
-			System.out.println ("---");
+			msgln (dataTypes[i].toString());
+			msgln ("---");
 		    }
 		} else {
 		    Map dataTypeNames = worker.getDataTypeNames();
 		    for (Iterator it = dataTypeNames.entrySet().iterator(); it.hasNext(); ) {
 			Map.Entry entry = (Map.Entry)it.next();
-			System.out.println (entry.getKey());
+			msgln (entry.getKey());
 		    }
 		}
 	    }
@@ -94,9 +78,9 @@
 		MobyServiceType[] serviceTypes = worker.getFullServiceTypes();
 		for (int i = 0; i < serviceTypes.length; i++) {
 		    if (details)
-			System.out.println (serviceTypes[i]);
+			msgln (serviceTypes[i]);
 		    else
-			System.out.println (serviceTypes[i].getName());
+			msgln (serviceTypes[i].getName());
 		}
 	    }
 
@@ -106,21 +90,21 @@
 		    MobyService[] services = worker.getServices();
 		    if (details) {
 			for (int i = 0; i < services.length; i++) {
-			    System.out.println (services[i]);
-			    System.out.println ("---");
+			    msgln (services[i]);
+			    msgln ("---");
 			}
 		    } else {  // summary
-			System.out.println
+			msgln
 			    ("#Prim\t#Sec\tSType\t#Out\tInColl\tOutColl\tService\tAuthority");
 			for (int i = 0; i < services.length; i++) {
 			    MobyService service = services[i];
 			    MobyData[] pInputs = service.getPrimaryInputs();
 			    MobyData[] sInputs = service.getSecondaryInputs();
 			    MobyData[] outputs = service.getPrimaryOutputs();
-			    System.out.print (pInputs.length + "\t");
-			    System.out.print (sInputs.length + "\t");
+			    msg (pInputs.length + "\t");
+			    msg (sInputs.length + "\t");
 			    StringBuffer buf = new StringBuffer();
-			    HashSet set = new HashSet();
+			    Set<String> set = new HashSet<String>();
 			    for (int j = 0; j < sInputs.length; j++) {
 				String abbrev =
 				    ( ((MobySecondaryData)sInputs[j]).getDataType()
@@ -130,8 +114,8 @@
 				    set.add (abbrev);
 				}
 			    }
-			    System.out.print (buf + "\t");
-			    System.out.print (outputs.length + "\t");
+			    msg (buf + "\t");
+			    msg (outputs.length + "\t");
 			    boolean found = false;
 			    for (int j = 0; j < pInputs.length; j++) {
 				if (pInputs[j] instanceof MobyPrimaryDataSet) {
@@ -139,7 +123,7 @@
 				    break;
 				}
 			    }
-			    System.out.print (found + "\t");
+			    msg (found + "\t");
 			    found = false;
 			    for (int j = 0; j < outputs.length; j++) {
 				if (outputs[j] instanceof MobyPrimaryDataSet) {
@@ -147,10 +131,9 @@
 				    break;
 				}
 			    }
-			    System.out.print (found + "\t");
-			    System.out.print (service.getName() + "\t");
- 			    System.out.print (service.getAuthority());
-			    System.out.println();
+			    msg (found + "\t");
+			    msg (service.getName() + "\t");
+ 			    msgln (service.getAuthority());
 			}
 		    }
 		} else {
@@ -160,7 +143,7 @@
 			String authority = (String)entry.getKey();
 			String[] names = (String[])entry.getValue();
 			for (int i = 0; i < names.length; i++) {
-			    System.out.println (names[i] + " (" + authority + ")");
+			    msgln (names[i] + " (" + authority + ")");
 			}
 		    }
 		}
@@ -171,16 +154,14 @@
 		MobyNamespace[] namespaces = worker.getFullNamespaces();
 		for (int i = 0; i < namespaces.length; i++) {
 		    if (details)
-			System.out.println (namespaces[i]);
+			msgln (namespaces[i]);
 		    else
-			System.out.println (namespaces[i].getName());
+			msgln (namespaces[i].getName());
 		}
 	    }
 
-	} catch (Exception e) {
-	    System.err.println ("===ERROR===");
-	    e.printStackTrace();
-	    System.err.println ("===========");
+	} catch (Throwable e) {
+	    processErrorAndExit (e);
 	}
     }
 }

===================================================================
RCS file: /home/repository/moby/moby-live/Java/src/Clients/TestingCentral.java,v
retrieving revision 1.10
retrieving revision 1.11
diff -u -r1.10 -r1.11
--- /home/repository/moby/moby-live/Java/src/Clients/TestingCentral.java	2006/12/07 18:41:00	1.10
+++ /home/repository/moby/moby-live/Java/src/Clients/TestingCentral.java	2008/03/02 12:45:25	1.11
@@ -94,8 +94,8 @@
         }
 	if (type.equalsIgnoreCase ("Integer")) {
 	    data.setDefaultValue ("123");
-	    data.setMaximumValue (234);
-	    data.setMinimumValue (23);
+	    data.setMaxValue     ("234");
+	    data.setMinValue     ("23");
 	    data.addAllowedValue ("30");
 	    data.addAllowedValue ("40");
 	    data.addAllowedValue ("50");



From senger at dev.open-bio.org  Sun Mar  2 12:45:26 2008
From: senger at dev.open-bio.org (Martin Senger)
Date: Sun, 2 Mar 2008 07:45:26 -0500
Subject: [MOBY-guts] biomoby commit
Message-ID: <200803021245.m22CjQGl032570@dev.open-bio.org>


senger
Sun Mar  2 07:45:25 EST 2008
Update of /home/repository/moby/moby-live/Java/src/main/org/biomoby/client
In directory dev.open-bio.org:/tmp/cvs-serv32345/src/main/org/biomoby/client

Modified Files:
	CentralImpl.java 
Log Message:
Too Many Changes - see docs/ChangeLog

moby-live/Java/src/main/org/biomoby/client CentralImpl.java,1.53,1.54
===================================================================
RCS file: /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/CentralImpl.java,v
retrieving revision 1.53
retrieving revision 1.54
diff -u -r1.53 -r1.54
--- /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/CentralImpl.java	2008/02/28 16:58:56	1.53
+++ /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/CentralImpl.java	2008/03/02 12:45:25	1.54
@@ -21,6 +21,7 @@
 import org.biomoby.shared.NoSuccessException;
 import org.biomoby.shared.PendingCurationException;
 import org.biomoby.shared.MobyResourceRef;
+import org.biomoby.shared.Utils;
 
 import javax.xml.parsers.DocumentBuilderFactory;
 import javax.xml.parsers.DocumentBuilder;
@@ -772,7 +773,8 @@
 	    Element elem = (Element)list.item (i);
 	    String name = elem.getAttribute ("name");
 	    String auth = elem.getAttribute ("authURI");
-	    Vector v = (results.containsKey (auth) ? (Vector)results.get (auth) : new Vector());
+	    Vector<Object> v =
+		(results.containsKey (auth) ? (Vector)results.get (auth) : new Vector<Object>());
 	    if (onlyNames) {
 		v.addElement (name);
 	    } else {
@@ -1597,7 +1599,7 @@
 	throws MobyException {
 
 	// parse returned XML
-	Vector v = new Vector();
+	Vector<String> v = new Vector<String>();
 	Document document = loadDocument (new ByteArrayInputStream (result.getBytes()));
 	NodeList list = document.getElementsByTagName ("Relationship");
 	for (int i = 0; i < list.getLength(); i++) {
@@ -1661,7 +1663,7 @@
 	    Element elem = (Element)list.item (i);
 	    String relType = elem.getAttribute ("relationshipType");
 	    NodeList children = elem.getChildNodes();
-	    Vector v = new Vector();
+	    Vector<String> v = new Vector<String>();
 	    for (int j = 0; j < children.getLength(); j++) {
 		if (children.item (j).getNodeName().equals ("objectType")) {
 		    v.addElement (getFirstValue (children.item (j)));
@@ -1707,7 +1709,7 @@
 			    });
 
 	// parse returned XML
-	Vector v = new Vector();
+	Vector<String> v = new Vector<String>();
 	Document document = loadDocument (new ByteArrayInputStream (result.getBytes()));
 	NodeList list = document.getElementsByTagName ("Relationship");
 
@@ -1755,11 +1757,11 @@
      * Parses and imports the following XML.
      * <pre>
      * &lt;resourceURLs&gt;
-     *   &lt;Resource name="Service"         url="..." type="..."/&gt;
-     *   &lt;Resource name="Object"          url="..." type="..."/&gt;
-     *   &lt;Resource name="Namespace"       url="..." type="..."/&gt;
-     *   &lt;Resource name="ServiceInstance" url="..." type="..."/&gt;
-     *   &lt;Resource name="Full"            url="..." type="..."/&gt;
+     *   &lt;Resource name="Service"         url="..." /&gt;
+     *   &lt;Resource name="Object"          url="..." /&gt;
+     *   &lt;Resource name="Namespace"       url="..." /&gt;
+     *   &lt;Resource name="ServiceInstance" url="..." /&gt;
+     *   &lt;Resource name="Full"            url="..." /&gt;
      * &lt;/resourceURLs&gt;
      * </pre>
      *************************************************************************/
@@ -1775,7 +1777,7 @@
 					new Object[] {});
 
 	// parse returned XML
-	Vector v = new Vector();
+	Vector<MobyResourceRef> v = new Vector<MobyResourceRef>();
 	Document document = loadDocument (new ByteArrayInputStream (result.getBytes()));
 	NodeList list = document.getElementsByTagName ("Resource");
 	for (int i = 0; i < list.getLength(); i++) {
@@ -1809,12 +1811,7 @@
 	MobyResourceRef[] resourceRefs = getResourceRefs();
 	for (int i = 0; i < resourceRefs.length; i++) {
 	    if (resourceName.equalsIgnoreCase (resourceRefs[i].getResourceName())) {
-		URL url = resourceRefs[i].getResourceLocation();
-		try {
-		    return url.openStream();
-		} catch (java.io.IOException e2) {
-		    throw new MobyException (e2.toString(), e2);
-		}
+		return Utils.getInputStream (resourceRefs[i].getResourceLocation());
 	    }
 	}
 	throw new MobyException ("No resource found for '" + resourceName + "'.");



From senger at dev.open-bio.org  Sun Mar  2 12:45:25 2008
From: senger at dev.open-bio.org (Martin Senger)
Date: Sun, 2 Mar 2008 07:45:25 -0500
Subject: [MOBY-guts] biomoby commit
Message-ID: <200803021245.m22CjPEW032550@dev.open-bio.org>


senger
Sun Mar  2 07:45:25 EST 2008
Update of /home/repository/moby/moby-live/Java/src/config/templates
In directory dev.open-bio.org:/tmp/cvs-serv32345/src/config/templates

Modified Files:
	ServiceSkeletonTemplate.java 
Log Message:
Too Many Changes - see docs/ChangeLog

moby-live/Java/src/config/templates ServiceSkeletonTemplate.java,1.3,1.4
===================================================================
RCS file: /home/repository/moby/moby-live/Java/src/config/templates/ServiceSkeletonTemplate.java,v
retrieving revision 1.3
retrieving revision 1.4
diff -u -r1.3 -r1.4
--- /home/repository/moby/moby-live/Java/src/config/templates/ServiceSkeletonTemplate.java	2005/11/15 03:25:51	1.3
+++ /home/repository/moby/moby-live/Java/src/config/templates/ServiceSkeletonTemplate.java	2008/03/02 12:45:25	1.4
@@ -47,8 +47,10 @@
 
 	MobyPackage mobyOutput = null;
 	try {
+
+            @FALLBACK_CODE@
 	    // reading the whole input
-	    MobyPackage mobyInput = MobyPackage.createFromXML (data, "@FALLBACK_TYPE@");
+	    MobyPackage mobyInput = MobyPackage.createFromXML (data, fallback);
 
 	    // prepare an output object
 	    mobyOutput = prepareOutput (mobyInput);



From senger at dev.open-bio.org  Sun Mar  2 12:45:25 2008
From: senger at dev.open-bio.org (Martin Senger)
Date: Sun, 2 Mar 2008 07:45:25 -0500
Subject: [MOBY-guts] biomoby commit
Message-ID: <200803021245.m22CjPDc032504@dev.open-bio.org>


senger
Sun Mar  2 07:45:25 EST 2008
Update of /home/repository/moby/moby-live/Java/src/config
In directory dev.open-bio.org:/tmp/cvs-serv32345/src/config

Modified Files:
	run-any-client run-dashboard run-dashboard.bat 
Log Message:
Too Many Changes - see docs/ChangeLog

moby-live/Java/src/config run-any-client,1.9,1.10 run-dashboard,1.8,1.9 run-dashboard.bat,1.7,1.8
===================================================================
RCS file: /home/repository/moby/moby-live/Java/src/config/run-any-client,v
retrieving revision 1.9
retrieving revision 1.10
diff -u -r1.9 -r1.10
--- /home/repository/moby/moby-live/Java/src/config/run-any-client	2008/02/14 06:13:36	1.9
+++ /home/repository/moby/moby-live/Java/src/config/run-any-client	2008/03/02 12:45:25	1.10
@@ -7,14 +7,29 @@
 #  $Id$
 # ----------------------------------------------------
 
+# --- setup JAVA_HOME (needed to get to the tools.jar)
+if [ -z "$JAVA_HOME" ] ; then
+  JAVA=`which java`
+  if [ -z "$JAVA" ] ; then
+    echo "Cannot find JAVA. Please set your PATH."
+    exit 1
+  else
+      JAVA_BIN=`dirname $JAVA`
+      JAVA_HOME=$JAVA_BIN/..
+      export JAVA_HOME
+  fi
+fi
+
 PROJECT_HOME=@PROJECT_HOME@
 LIBS_PATH=@PROJECT_DEPS@
 
 CLASSPATH=$LIBS_PATH
+CLASSPATH=${JAVA_HOME}/lib/tools.jar:$CLASSPATH
 CLASSPATH=${PROJECT_HOME}/build/others/datatypes:$CLASSPATH
 CLASSPATH=${PROJECT_HOME}/build/others/skeletons:$CLASSPATH
 CLASSPATH=${PROJECT_HOME}/build/others/samples:$CLASSPATH
 CLASSPATH=${PROJECT_HOME}/build/classes:$CLASSPATH
 CLASSPATH=${PROJECT_HOME}/build/Clients:$CLASSPATH
 
-exec java -cp $CLASSPATH @LOG4J@ "$@"
+JAVA=$JAVA_HOME/bin/java
+exec $JAVA -cp $CLASSPATH @LOG4J@ "$@"

===================================================================
RCS file: /home/repository/moby/moby-live/Java/src/config/run-dashboard,v
retrieving revision 1.8
retrieving revision 1.9
diff -u -r1.8 -r1.9
--- /home/repository/moby/moby-live/Java/src/config/run-dashboard	2008/02/22 00:54:30	1.8
+++ /home/repository/moby/moby-live/Java/src/config/run-dashboard	2008/03/02 12:45:25	1.9
@@ -4,10 +4,25 @@
 #
 #  $Id$
 # ----------------------------------------------------
+
+# --- setup JAVA_HOME (needed to get to the tools.jar for compilation)
+if [ -z "$JAVA_HOME" ] ; then
+  JAVA=`which java`
+  if [ -z "$JAVA" ] ; then
+    echo "Cannot find JAVA. Please set your PATH."
+    exit 1
+  else
+      JAVA_BIN=`dirname $JAVA`
+      JAVA_HOME=$JAVA_BIN/..
+      export JAVA_HOME
+  fi
+fi
+
 PROJECT_HOME=@PROJECT_HOME@
 LIBS_PATH=@PROJECT_DEPS@
 
 CLASSPATH=$LIBS_PATH
+CLASSPATH=${JAVA_HOME}/lib/tools.jar:$CLASSPATH
 CLASSPATH=${PROJECT_HOME}/build/others/datatypes:$CLASSPATH
 CLASSPATH=${PROJECT_HOME}/build/others/skeletons:$CLASSPATH
 CLASSPATH=${PROJECT_HOME}/build/others/samples:$CLASSPATH
@@ -15,4 +30,5 @@
 CLASSPATH=${PROJECT_HOME}/build/classes:$CLASSPATH
 CLASSPATH=${PROJECT_HOME}/build/Clients:$CLASSPATH
 
-exec java -Xms32m -Xmx256m -cp $CLASSPATH @LOG4J@ org.biomoby.service.dashboard.Dashboard "$@"
+JAVA=$JAVA_HOME/bin/java
+exec $JAVA -Xms32m -Xmx256m -cp $CLASSPATH @LOG4J@ org.biomoby.service.dashboard.Dashboard "$@"

===================================================================
RCS file: /home/repository/moby/moby-live/Java/src/config/run-dashboard.bat,v
retrieving revision 1.7
retrieving revision 1.8
diff -u -r1.7 -r1.8
--- /home/repository/moby/moby-live/Java/src/config/run-dashboard.bat	2008/02/14 06:13:36	1.7
+++ /home/repository/moby/moby-live/Java/src/config/run-dashboard.bat	2008/03/02 12:45:25	1.8
@@ -1,10 +1,20 @@
 @echo off
 
+if NOT "%JAVA_HOME%"=="" goto javadone
+echo =======================================================
+echo Setup the JAVA_HOME environment variable.
+echo Hint (for XP): Click Start -- Control Panel -- System.
+echo Then click Advanced, then click "Environment Variables".
+echo ========================================================
+goto end
+:javadone
+
 set "PROJECT_HOME=@PROJECT_HOME@"
 set "PROJECT_DEPS=@PROJECT_DEPS@"
 cd "%PROJECT_HOME%"
 set CP=
 set CP=%PROJECT_DEPS%;%CP%
+set "CP=%JAVA_HOME%\lib\tools.jar;%CP%"
 set CP=build\classes;%CP%
 set CP=build\Clients;%CP%
 set CP=build\others\datatypes;%CP%
@@ -12,4 +22,7 @@
 set CP=build\others\samples;%CP%
 set CP=build\lib\dashboard-config.jar;%CP%
 
-java -classpath "%CP%" @LOG4J@ org.biomoby.service.dashboard.Dashboard  %*
+set "JAVA=%JAVA_HOME%\bin\java"
+"%JAVA%" -classpath "%CP%" @LOG4J@ org.biomoby.service.dashboard.Dashboard  %*
+
+java -Xms32m -Xmx256m -classpath "%CP%" @LOG4J@ org.biomoby.service.dashboard.Dashboard  %*



From senger at dev.open-bio.org  Sun Mar  2 12:49:33 2008
From: senger at dev.open-bio.org (Martin Senger)
Date: Sun, 2 Mar 2008 07:49:33 -0500
Subject: [MOBY-guts] biomoby commit
Message-ID: <200803021249.m22CnXpT000482@dev.open-bio.org>


senger
Sun Mar  2 07:49:33 EST 2008
Update of /home/repository/moby/moby-live/Java/src/Clients
In directory dev.open-bio.org:/tmp/cvs-serv467/src/Clients

Added Files:
	TestAntWorker2.java 
Log Message:

moby-live/Java/src/Clients TestAntWorker2.java,NONE,1.1


From senger at dev.open-bio.org  Sun Mar  2 12:49:33 2008
From: senger at dev.open-bio.org (Martin Senger)
Date: Sun, 2 Mar 2008 07:49:33 -0500
Subject: [MOBY-guts] biomoby commit
Message-ID: <200803021249.m22CnXSd000498@dev.open-bio.org>


senger
Sun Mar  2 07:49:33 EST 2008
Update of /home/repository/moby/moby-live/Java/src/samples/org/jmoby/tutorial/service
In directory dev.open-bio.org:/tmp/cvs-serv467/src/samples/org/jmoby/tutorial/service

Added Files:
	ConcatSequenceSetImpl.java ConcatSequencesImpl.java 
Log Message:

moby-live/Java/src/samples/org/jmoby/tutorial/service ConcatSequenceSetImpl.java,NONE,1.1 ConcatSequencesImpl.java,NONE,1.1


From senger at dev.open-bio.org  Sun Mar  2 12:49:33 2008
From: senger at dev.open-bio.org (Martin Senger)
Date: Sun, 2 Mar 2008 07:49:33 -0500
Subject: [MOBY-guts] biomoby commit
Message-ID: <200803021249.m22CnXYd000512@dev.open-bio.org>


senger
Sun Mar  2 07:49:33 EST 2008
Update of /home/repository/moby/moby-live/Java/src/test/junit-resources
In directory dev.open-bio.org:/tmp/cvs-serv467/src/test/junit-resources

Added Files:
	ConcatSequences-input.xml 
Log Message:

moby-live/Java/src/test/junit-resources ConcatSequences-input.xml,NONE,1.1


From senger at dev.open-bio.org  Sun Mar  2 12:45:27 2008
From: senger at dev.open-bio.org (Martin Senger)
Date: Sun, 2 Mar 2008 07:45:27 -0500
Subject: [MOBY-guts] biomoby commit
Message-ID: <200803021245.m22CjROo000382@dev.open-bio.org>


senger
Sun Mar  2 07:45:27 EST 2008
Update of /home/repository/moby/moby-live/Java/src/test/junit-resources
In directory dev.open-bio.org:/tmp/cvs-serv32345/src/test/junit-resources

Removed Files:
	parser-test-output-1.xml parser-test-output-2.xml 
	parser-test-output-3.xml parser-test-output-4.xml 
Log Message:
Too Many Changes - see docs/ChangeLog

moby-live/Java/src/test/junit-resources parser-test-output-1.xml,1.1,NONE parser-test-output-2.xml,1.1,NONE parser-test-output-3.xml,1.1,NONE parser-test-output-4.xml,1.1,NONE
rcsdiff: /home/repository/moby/moby-live/Java/src/test/junit-resources/RCS/parser-test-output-1.xml,v: No such file or directory

rcsdiff: /home/repository/moby/moby-live/Java/src/test/junit-resources/RCS/parser-test-output-2.xml,v: No such file or directory

rcsdiff: /home/repository/moby/moby-live/Java/src/test/junit-resources/RCS/parser-test-output-3.xml,v: No such file or directory

rcsdiff: /home/repository/moby/moby-live/Java/src/test/junit-resources/RCS/parser-test-output-4.xml,v: No such file or directory



From senger at dev.open-bio.org  Sun Mar  2 12:45:26 2008
From: senger at dev.open-bio.org (Martin Senger)
Date: Sun, 2 Mar 2008 07:45:26 -0500
Subject: [MOBY-guts] biomoby commit
Message-ID: <200803021245.m22CjQpT032592@dev.open-bio.org>


senger
Sun Mar  2 07:45:26 EST 2008
Update of /home/repository/moby/moby-live/Java/src/main/org/biomoby/service
In directory dev.open-bio.org:/tmp/cvs-serv32345/src/main/org/biomoby/service

Modified Files:
	BaseService.java 
Log Message:
Too Many Changes - see docs/ChangeLog

moby-live/Java/src/main/org/biomoby/service BaseService.java,1.8,1.9
===================================================================
RCS file: /home/repository/moby/moby-live/Java/src/main/org/biomoby/service/BaseService.java,v
retrieving revision 1.8
retrieving revision 1.9
diff -u -r1.8 -r1.9
--- /home/repository/moby/moby-live/Java/src/main/org/biomoby/service/BaseService.java	2007/05/27 19:18:17	1.8
+++ /home/repository/moby/moby-live/Java/src/main/org/biomoby/service/BaseService.java	2008/03/02 12:45:26	1.9
@@ -85,9 +85,9 @@
 <pre> public class AServiceImpl
     extends A_ServiceSkel {
 
-    public boolean processIt (MobyJob request,
-			      MobyJob response,
-			      MobyPackage outputContext)
+    public void processIt (MobyJob request,
+		           MobyJob response,
+			   MobyPackage outputContext)
 	throws MobyException {
 
         // this is how to get input data
@@ -96,7 +96,6 @@
 
         // this is an example of a trivial "business logic"
 	response.setData (new MobyInteger (seq.length()));
-	return true;
     }
 }</pre>
  * </td></tr></table><p>



From senger at dev.open-bio.org  Sun Mar  2 12:45:27 2008
From: senger at dev.open-bio.org (Martin Senger)
Date: Sun, 2 Mar 2008 07:45:27 -0500
Subject: [MOBY-guts] biomoby commit
Message-ID: <200803021245.m22CjRFn000314@dev.open-bio.org>


senger
Sun Mar  2 07:45:26 EST 2008
Update of /home/repository/moby/moby-live/Java/src/samples/org/jmoby/tutorial/service
In directory dev.open-bio.org:/tmp/cvs-serv32345/src/samples/org/jmoby/tutorial/service

Modified Files:
	MabuhayImpl.java 
Log Message:
Too Many Changes - see docs/ChangeLog

moby-live/Java/src/samples/org/jmoby/tutorial/service MabuhayImpl.java,1.1,1.2
===================================================================
RCS file: /home/repository/moby/moby-live/Java/src/samples/org/jmoby/tutorial/service/MabuhayImpl.java,v
retrieving revision 1.1
retrieving revision 1.2
diff -u -r1.1 -r1.2
--- /home/repository/moby/moby-live/Java/src/samples/org/jmoby/tutorial/service/MabuhayImpl.java	2005/08/26 06:27:05	1.1
+++ /home/repository/moby/moby-live/Java/src/samples/org/jmoby/tutorial/service/MabuhayImpl.java	2008/03/02 12:45:26	1.2
@@ -93,7 +93,7 @@
 	}
 
 	// match pattern against all possible values we have
-	Vector v = new Vector();
+	Vector<simple_key_value_pair> v = new Vector<simple_key_value_pair>();
 	Matcher matcher = pattern.matcher ("");
 	for (int i = 0; i < languages.length; i++) {
  	    matcher.reset (languages[i]);
@@ -124,8 +124,8 @@
 	    ("resources/mabuhay.file");
 	if (ins != null) {
 	    try {
-		Vector l = new Vector (3000);
-		Vector h = new Vector (3000);
+		Vector<String> l = new Vector<String> (3000);
+		Vector<String> h = new Vector<String> (3000);
 		BufferedReader data = new BufferedReader (new InputStreamReader (ins));
 		String line;
 		while ((line = data.readLine()) != null) {



From senger at dev.open-bio.org  Sun Mar  2 12:45:26 2008
From: senger at dev.open-bio.org (Martin Senger)
Date: Sun, 2 Mar 2008 07:45:26 -0500
Subject: [MOBY-guts] biomoby commit
Message-ID: <200803021245.m22CjQJW032742@dev.open-bio.org>


senger
Sun Mar  2 07:45:26 EST 2008
Update of /home/repository/moby/moby-live/Java/src/main/org/biomoby/shared/datatypes
In directory dev.open-bio.org:/tmp/cvs-serv32345/src/main/org/biomoby/shared/datatypes

Modified Files:
	MobyObject.java 
Log Message:
Too Many Changes - see docs/ChangeLog

moby-live/Java/src/main/org/biomoby/shared/datatypes MobyObject.java,1.6,1.7
===================================================================
RCS file: /home/repository/moby/moby-live/Java/src/main/org/biomoby/shared/datatypes/MobyObject.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/shared/datatypes/MobyObject.java	2006/07/07 04:12:40	1.6
+++ /home/repository/moby/moby-live/Java/src/main/org/biomoby/shared/datatypes/MobyObject.java	2008/03/02 12:45:26	1.7
@@ -100,8 +100,7 @@
      * @return a formatted string
      *************************************************************************/
     public String toString() {
-	StringBuffer buf = new StringBuffer();
-// 	buf.append (Utils.simpleClassName (this.getClass().getName()));
+	StringBuilder buf = new StringBuilder();
 	buf.append (getMobyTypeName());
 	if (! name.equals (""))      buf.append (", Article name: " + name);
 	if (! id.equals (""))        buf.append (", Id: " + id);
@@ -112,7 +111,7 @@
 	    buf.append (((MobyXref)en.nextElement()).format (1));
 	}
 	if (! value.equals (""))     buf.append ("   Value: " + value + "\n");
-	return new String (buf);
+	return new String (buf.toString());
     }
 
     /**************************************************************************



From senger at dev.open-bio.org  Sun Mar  2 12:45:27 2008
From: senger at dev.open-bio.org (Martin Senger)
Date: Sun, 2 Mar 2008 07:45:27 -0500
Subject: [MOBY-guts] biomoby commit
Message-ID: <200803021245.m22CjReI000346@dev.open-bio.org>


senger
Sun Mar  2 07:45:27 EST 2008
Update of /home/repository/moby/moby-live/Java/src/support
In directory dev.open-bio.org:/tmp/cvs-serv32345/src/support

Removed Files:
	README _README.FIRST_ run-any-client run-any-client.bat 
	run-cache-client run-cache-client.bat run-cmdline-client 
	run-cmdline-client.bat run-digest-client run-digest-client.bat 
	run-graphs-client run-graphs-client.bat run-testing-central 
	run-testing-central.bat 
Log Message:
Too Many Changes - see docs/ChangeLog

moby-live/Java/src/support README,1.5,NONE _README.FIRST_,1.2,NONE run-any-client,1.1,NONE run-any-client.bat,1.2,NONE run-cache-client,1.1,NONE run-cache-client.bat,1.2,NONE run-cmdline-client,1.1,NONE run-cmdline-client.bat,1.2,NONE run-digest-client,1.1,NONE run-digest-client.bat,1.2,NONE run-graphs-client,1.1,NONE run-graphs-client.bat,1.2,NONE run-testing-central,1.1,NONE run-testing-central.bat,1.2,NONE
rcsdiff: /home/repository/moby/moby-live/Java/src/support/RCS/README,v: No such file or directory

rcsdiff: /home/repository/moby/moby-live/Java/src/support/RCS/_README.FIRST_,v: No such file or directory

rcsdiff: /home/repository/moby/moby-live/Java/src/support/RCS/run-any-client,v: No such file or directory

rcsdiff: /home/repository/moby/moby-live/Java/src/support/RCS/run-any-client.bat,v: No such file or directory

rcsdiff: /home/repository/moby/moby-live/Java/src/support/RCS/run-cache-client,v: No such file or directory

rcsdiff: /home/repository/moby/moby-live/Java/src/support/RCS/run-cache-client.bat,v: No such file or directory

rcsdiff: /home/repository/moby/moby-live/Java/src/support/RCS/run-cmdline-client,v: No such file or directory

rcsdiff: /home/repository/moby/moby-live/Java/src/support/RCS/run-cmdline-client.bat,v: No such file or directory

rcsdiff: /home/repository/moby/moby-live/Java/src/support/RCS/run-digest-client,v: No such file or directory

rcsdiff: /home/repository/moby/moby-live/Java/src/support/RCS/run-digest-client.bat,v: No such file or directory

rcsdiff: /home/repository/moby/moby-live/Java/src/support/RCS/run-graphs-client,v: No such file or directory

rcsdiff: /home/repository/moby/moby-live/Java/src/support/RCS/run-graphs-client.bat,v: No such file or directory

rcsdiff: /home/repository/moby/moby-live/Java/src/support/RCS/run-testing-central,v: No such file or directory

rcsdiff: /home/repository/moby/moby-live/Java/src/support/RCS/run-testing-central.bat,v: No such file or directory



From senger at dev.open-bio.org  Sun Mar  2 12:45:26 2008
From: senger at dev.open-bio.org (Martin Senger)
Date: Sun, 2 Mar 2008 07:45:26 -0500
Subject: [MOBY-guts] biomoby commit
Message-ID: <200803021245.m22CjQUS032722@dev.open-bio.org>


senger
Sun Mar  2 07:45:26 EST 2008
Update of /home/repository/moby/moby-live/Java/src/main/org/biomoby/shared
In directory dev.open-bio.org:/tmp/cvs-serv32345/src/main/org/biomoby/shared

Modified Files:
	MobyException.java MobyResourceRef.java MobyService.java 
Log Message:
Too Many Changes - see docs/ChangeLog

moby-live/Java/src/main/org/biomoby/shared MobyException.java,1.4,1.5 MobyResourceRef.java,1.4,1.5 MobyService.java,1.23,1.24
===================================================================
RCS file: /home/repository/moby/moby-live/Java/src/main/org/biomoby/shared/MobyException.java,v
retrieving revision 1.4
retrieving revision 1.5
diff -u -r1.4 -r1.5
--- /home/repository/moby/moby-live/Java/src/main/org/biomoby/shared/MobyException.java	2005/11/15 03:25:51	1.4
+++ /home/repository/moby/moby-live/Java/src/main/org/biomoby/shared/MobyException.java	2008/03/02 12:45:26	1.5
@@ -47,20 +47,8 @@
     public MobyException (String s, Throwable e) {
 	super (s, e);
 	if (e != null) {
-	    boolean seriousError =
-		( (e instanceof java.lang.NullPointerException)              ||
-		  (e instanceof java.lang.ClassCastException)                ||
-		  (e instanceof java.lang.reflect.InvocationTargetException) ||
-		  (e instanceof java.lang.ClassNotFoundException) );
-	    if (seriousError || log.isDebugEnabled()) {
-		StringWriter sw = new StringWriter (500);
-		e.printStackTrace (new PrintWriter (sw));
-		if (seriousError)
-		    log.error (sw.toString());
-		else
-		    log.debug (sw.toString());
-	    }
-	}
+ 	    formatAndLog (e, log);
+ 	}
     }
 
     /******************************************************************************
@@ -75,4 +63,28 @@
 	return getCause();
     }
 
+    /******************************************************************************
+     * Format given exception 'e' depending on how serious it it. In
+     * same cases add stack trace. Log the result in the given
+     * 'log'. <p>
+     *
+     * @param e an exception to be formatted and logged
+     * @param log where to log it
+     ******************************************************************************/
+    public static void formatAndLog (Throwable e,
+				     org.apache.commons.logging.Log log) {
+	boolean seriousError =
+	    (e instanceof java.lang.RuntimeException);
+	if (seriousError || log.isDebugEnabled()) {
+	    StringWriter sw = new StringWriter (500);
+	    e.printStackTrace (new PrintWriter (sw));
+	    if (seriousError)
+		log.error (sw.toString());
+	    else
+		log.debug (sw.toString());
+	} else {
+	    log.error (e.getMessage());
+	}
+    }
+    
 }

===================================================================
RCS file: /home/repository/moby/moby-live/Java/src/main/org/biomoby/shared/MobyResourceRef.java,v
retrieving revision 1.4
retrieving revision 1.5
diff -u -r1.4 -r1.5
--- /home/repository/moby/moby-live/Java/src/main/org/biomoby/shared/MobyResourceRef.java	2006/07/07 23:27:27	1.4
+++ /home/repository/moby/moby-live/Java/src/main/org/biomoby/shared/MobyResourceRef.java	2008/03/02 12:45:26	1.5
@@ -65,7 +65,11 @@
     }
 
     /**
-     * Return resource content type.
+     * Return resource content type. 
+     *
+     * @deprecated Biomoby registry never gives the content type
+     * back. Therefore, this method does not have anything reasonable
+     * to return.
      */
     public String getResourceContentType() {
 	return contentType;

===================================================================
RCS file: /home/repository/moby/moby-live/Java/src/main/org/biomoby/shared/MobyService.java,v
retrieving revision 1.23
retrieving revision 1.24
diff -u -r1.23 -r1.24
--- /home/repository/moby/moby-live/Java/src/main/org/biomoby/shared/MobyService.java	2008/01/07 22:01:09	1.23
+++ /home/repository/moby/moby-live/Java/src/main/org/biomoby/shared/MobyService.java	2008/03/02 12:45:26	1.24
@@ -67,6 +67,13 @@
     /** Name of a category for asynchornous BioMoby services. */
     public static final String CATEGORY_MOBY_ASYNC = "moby-async";
 
+    /** Name of a category for document/literal BioMoby services. */
+    public static final String CATEGORY_MOBY_DOCLIT = "doc-literal";
+
+    /** Name of a category for asynchronous document/literal BioMoby
+     * services. */
+    public static final String CATEGORY_MOBY_DOCLIT_ASYNC = "doc-literal-async";
+
     /** A suffix added to a service name in order to make a method
      * name that submits input to an asynchronous service.
      */
@@ -601,6 +608,8 @@
     }
 
     public boolean isAsynchronous(){
-	return category.equals (CATEGORY_MOBY_ASYNC);
+	return
+	    category.equals (CATEGORY_MOBY_ASYNC) ||
+	    category.equals (CATEGORY_MOBY_DOCLIT_ASYNC);
     }
 }



From senger at dev.open-bio.org  Sun Mar  2 12:45:27 2008
From: senger at dev.open-bio.org (Martin Senger)
Date: Sun, 2 Mar 2008 07:45:27 -0500
Subject: [MOBY-guts] biomoby commit
Message-ID: <200803021245.m22CjRA5000364@dev.open-bio.org>


senger
Sun Mar  2 07:45:27 EST 2008
Update of /home/repository/moby/moby-live/Java/src/test/java/org/biomoby/shared/parser
In directory dev.open-bio.org:/tmp/cvs-serv32345/src/test/java/org/biomoby/shared/parser

Modified Files:
	MobyParserTest.java 
Log Message:
Too Many Changes - see docs/ChangeLog

moby-live/Java/src/test/java/org/biomoby/shared/parser MobyParserTest.java,1.1,1.2
===================================================================
RCS file: /home/repository/moby/moby-live/Java/src/test/java/org/biomoby/shared/parser/MobyParserTest.java,v
retrieving revision 1.1
retrieving revision 1.2
diff -u -r1.1 -r1.2
--- /home/repository/moby/moby-live/Java/src/test/java/org/biomoby/shared/parser/MobyParserTest.java	2008/02/28 05:21:48	1.1
+++ /home/repository/moby/moby-live/Java/src/test/java/org/biomoby/shared/parser/MobyParserTest.java	2008/03/02 12:45:27	1.2
@@ -1,4 +1,4 @@
-// MobyParserTestCase.java
+// MobyParserTest.java
 //
 // Created: February 2008
 //
@@ -20,17 +20,21 @@
 package org.biomoby.shared.parser;
 
 import org.biomoby.shared.MobyException;
+import org.biomoby.shared.datatypes.*;
 
 import org.junit.Before;
 import org.junit.Test;
 import static org.junit.Assert.*;
 
 import org.apache.commons.io.IOUtils;
+import org.apache.commons.io.FileUtils;
+import org.apache.commons.lang.StringUtils;
 
 import java.io.InputStream;
 import java.io.IOException;
 import java.util.Map;
 import java.util.HashMap;
+import java.util.Arrays;
 
 
 public class MobyParserTest {
@@ -39,12 +43,6 @@
     private static final String INPUT_2 = "parser-test-input-2.xml";
     private static final String INPUT_3 = "parser-test-input-3.xml";
     private static final String INPUT_4 = "parser-test-input-4.xml";
-
-    private static final String OUTPUT_1 = "parser-test-output-1.xml";
-    private static final String OUTPUT_2 = "parser-test-output-2.xml";
-    private static final String OUTPUT_3 = "parser-test-output-3.xml";
-    private static final String OUTPUT_4 = "parser-test-output-4.xml";
-
  
     /**************************************************************************
      *
@@ -55,38 +53,55 @@
     @Test
     public void testNormal()
 	throws IOException, MobyException {
-	parse (INPUT_1, OUTPUT_1, null, null);
-    }
-
-    @Test
-    public void testUnknownTopLevel()
-	throws IOException, MobyException {
-	parse (INPUT_2, OUTPUT_2, "DNASequence", null);
-    }
-
-    @Test
-    public void testUnknownTopLevelAndMember()
-	throws IOException, MobyException {
-	parse (INPUT_3, OUTPUT_3, "BasicGFF3MultiFeature", null);
-    }
-
-    @Test
-    public void testMoreUnknownTopLevels()
-	throws IOException, MobyException {
-	Map<String,String> backups = new HashMap<String,String>();
-	backups.put ("mySeq",   "DNASequence");
-	backups.put ("myPairs", "BasicGFF3MultiFeature");
-	parse (INPUT_4, OUTPUT_4, null, backups);
-    }
+	MobyPackage moby = parse (INPUT_1, null, null);
+	assertEquals (moby.getServiceNotes(), "freetext notes here");
+	assertEquals (moby.getAuthority(), "http://\"me\".<org>&");
+	MobyJob[] jobs = moby.getJobs();
+	assertEquals (jobs.length, 4);
+	assertEquals (jobs[0].getId(), "a1");
+	MobyObject data = jobs[0].getData();
+	assertEquals (data.getMobyTypeName(), "NucleotideSequence");
+	assertEquals (data.getName(), "");
+	assertEquals (data.getNamespace(), "DragonDB_Allele");
+	assertEquals (data.getId(), "chlorae");
+	assertFalse (data.isPrimitiveType());
+	assertEquals (data.getClass().getName(), "org.biomoby.shared.datatypes.NucleotideSequence");
+	NucleotideSequence typedData = (NucleotideSequence)jobs[0].getData();
+	assertEquals (typedData.get_SequenceString(), ">tata\ntatata");
+	assertEquals (typedData.getMoby_SequenceString().getValue(), ">tata\ntatata");
+	assertEquals (typedData.getMoby_Length().getIntValue(), 10);
+    }
+
+//     @Test
+//     public void testUnknownTopLevel()
+// 	throws IOException, MobyException {
+// 	parse (INPUT_2, "DNASequence", null);
+//     }
+
+//     @Test
+//     public void testUnknownTopLevelAndMember()
+// 	throws IOException, MobyException {
+// 	parse (INPUT_3, "BasicGFF3MultiFeature", null);
+//     }
+
+//     @Test
+//     public void testMoreUnknownTopLevels()
+// 	throws IOException, MobyException {
+// 	Map<String,String> backups = new HashMap<String,String>();
+// 	backups.put ("mySeq",   "DNASequence");
+// 	backups.put ("myPairs", "BasicGFF3MultiFeature");
+// 	parse (INPUT_4, null, backups);
+//     }
 
 
     /**************************************************************************
-     * Read XML from 'infile', turn it back to XML and compare it with
-     * 'outfile'. Use 'backup' (or 'backups') as the 'latest known
-     * data top-level(s)' data type (any of them may be null).
+     * Create and return a MobyPackage form the XML 'infile'. Use
+     * 'backup' (or 'backups') as the 'latest known data top-level(s)'
+     * data type (any of them may be null).
      **************************************************************************/
-    protected void parse (String infile, String outfile,
-			  String backup, Map<String,String> backups)
+    protected MobyPackage parse (String infile,
+				 String backup,
+				 Map<String,String> backups)
 	throws IOException, MobyException {
 
 	InputStream ins = null;
@@ -95,7 +110,7 @@
 	    ins = this.getClass().getClassLoader().getResourceAsStream (infile);
 	    if (ins == null) {
 		fail ("Could not find test data resource '" + infile + "'.");
-		return;
+		throw new MobyException ("Test parsing failed.");
 	    }
 	    MobyPackage moby = null;
 	    if (backups != null) {
@@ -104,18 +119,7 @@
 		moby = MobyPackage.createFromXML (IOUtils.toByteArray (ins), backup);
 	    }
 	    assertFalse (moby == null);
-	    IOUtils.closeQuietly (ins);
-
-	    // reading expected result
-	    ins = this.getClass().getClassLoader().getResourceAsStream (outfile);
-	    if (ins == null) {
-		fail ("Could not find test data resource '" + outfile + "'.");
-		return;
-	    }
-	    String expected = IOUtils.toString (ins);
-
-	    // comparing
-	    assertEquals (moby.toXML(), expected);
+	    return moby;
 
 	} finally {
 	    IOUtils.closeQuietly (ins);



From senger at dev.open-bio.org  Sun Mar  2 12:45:26 2008
From: senger at dev.open-bio.org (Martin Senger)
Date: Sun, 2 Mar 2008 07:45:26 -0500
Subject: [MOBY-guts] biomoby commit
Message-ID: <200803021245.m22CjQ5c032764@dev.open-bio.org>


senger
Sun Mar  2 07:45:26 EST 2008
Update of /home/repository/moby/moby-live/Java/src/main/org/biomoby/shared/parser
In directory dev.open-bio.org:/tmp/cvs-serv32345/src/main/org/biomoby/shared/parser

Modified Files:
	MobyParser.java 
Log Message:
Too Many Changes - see docs/ChangeLog

moby-live/Java/src/main/org/biomoby/shared/parser MobyParser.java,1.8,1.9
===================================================================
RCS file: /home/repository/moby/moby-live/Java/src/main/org/biomoby/shared/parser/MobyParser.java,v
retrieving revision 1.8
retrieving revision 1.9
diff -u -r1.8 -r1.9
--- /home/repository/moby/moby-live/Java/src/main/org/biomoby/shared/parser/MobyParser.java	2008/02/28 05:21:48	1.8
+++ /home/repository/moby/moby-live/Java/src/main/org/biomoby/shared/parser/MobyParser.java	2008/03/02 12:45:26	1.9
@@ -18,7 +18,6 @@
 
 import org.tulsoft.tools.loaders.ICreator;
 import org.tulsoft.shared.GException;
-import org.tulsoft.tools.debug.DGUtils;
 import org.tulsoft.tools.xml.XMLUtils2;
 import org.tulsoft.tools.xml.XMLErrorHandler;
 
@@ -55,22 +54,24 @@
  * href="http://biomoby.org/moby-live/Java/docs/APIservices/org/biomoby/shared/datatypes/package-summary.html"
  * target="_top"><tt>org.biomoby.shared.datatypes</tt></a>. <p>
  *
- * There is one situation when the parser tries to substitute an
- * unknown data type by a known one. If the parsing encoutered an XML
- * tag depicting a <em>top-level</em> data object (not a member object
- * of some other data object) and if there is no class available for
- * such object, the parser can be instructed (in its {@link
- * #MobyParser(String) non-default constructor} to create a substituted
- * object whose name was given in the parser constructor. This is to
- * prevent situation when a long-time running and deployed service
- * suddenly gets a request from a client that uses more up-to-date
- * list of data types. It would be bad to let such service die (or
- * minimally respond unproperly) just because its classes were
- * generated too long ago. <p>
+ * There is a situation when the parser tries to substitute an unknown
+ * data type by a known one. If the parsing encoutered an XML tag
+ * depicting a <em>top-level</em> data object, or a member object, and
+ * if there is no class available for such object, the parser can be
+ * instructed (in its {@link #MobyParser(String) non-default
+ * constructor} to create a substituted object whose name was given in
+ * the parser constructor (there is also a constructor where you can
+ * get more than one such substitution object, depicted by its article
+ * name). This is to prevent situation when a long-time running and
+ * deployed service suddenly gets a request from a client that uses
+ * more up-to-date list of data types. It would be bad to let such
+ * service die (or minimally respond unproperly) just because its
+ * classes were generated too long ago. <p>
  *
  * Because also skeletons for services can be generated, it is easy to
  * ensure that a service knows its "the most specialized" data type it
- * can still serve, and that it passes it to the parser constructor. <p>
+ * can still serve, and that it passes it to the parser
+ * constructor. <p>
  *
  * If the parser finds an unknown object/tag but no substitute was
  * passed in the parser constructor, it prints a warning and ignores
@@ -81,29 +82,14 @@
  * types should be generated, and services restarted. Fortunately, it
  * does not happen often at all. <p>
  *
- * Be aware, however, that this substitution may do a wrong thing if
- * there are more bad top-level objects - such as in case when a
- * result has more outputs. I think that this insufficiency should be
- * consider a bug in parser design - but make it properly would need
- * much more complicated interface... <p>
- *
  * If the parser finds another problem, usually related to the invalid
  * XML, it raises a {@link org.biomoby.shared.MobyException
  * MobyException} with error message containing line and column close
  * to place where the error happened. <p>
  *
  * One possible problem would be when article names of the member data
- * types in the parsed XML do not correspond what was registered in
- * the Biomoby registry. An example, I know about at the time of
- * writing this, is a service <tt>MIPSBlastXMLClickableImage</tt> that
- * returns object of type <tt>NCBI_Blast_XML_Gif_Map</tt> which has a
- * member object of type <tt>b64_encoded_gif</tt>. This member was
- * registered with the article name "hitGraph" but the service returns
- * an article name "image". Parser spots it and stops parsing (because
- * it does not know where to put this member object). However, if you
- * insist that you still want to get such XML parsed, even without one
- * part, you can set Java property "biomoby.parser.forgiving" to true,
- * and run it again. <p>
+ * types in the parsed XML do not correspond to what was registered in
+ * the Biomoby registry (or to its more specialized childern). <p>
  *
  * You can test parser by using a simple <tt>TestingMobyParser</tt>
  * client. This is how to invoke it and how to get its help:
@@ -153,6 +139,10 @@
  *                                               "GenericSequence");
  * </pre>
  *
+ * For a constructor with more fallbacks, check generated skeletons
+ * (for example the sample skeleton
+ * <tt>net.jmoby.samples.ConcatSequencesSkel</tt>). <p>
+
  * All XML tags and all attribute names that are recognized and
  * processed by this parser are stored as constants in class {@link
  * MobyTags}. <p>
@@ -171,12 +161,6 @@
     private static org.apache.commons.logging.Log log =
 	org.apache.commons.logging.LogFactory.getLog (MobyParser.class);
 
-    /**
-     * A Java property name. See its purpose in the main description
-     * above.
-     */
-    public static final String BIOMOBY_PARSER_FORGIVING = "biomoby.parser.forgiving";
-
     Locator locator;
     XMLReader parser = null;
     String lowestKnownDataType = null;
@@ -361,9 +345,9 @@
      * all its descendants (with a warning message).
      *
      *    The same mode is also entered when an unknown member object
-     * was found (a member object is never substituted). But here we
-     * issue a warning message only if we are NOT in substitution mode
-     * (in a substitution mode it is normal to found unknown objects).
+     * was found. But here we issue a warning message only if we are
+     * NOT in substitution mode (in a substitution mode it is normal
+     * to found unknown objects).
      *
      *    'inSubstitution' is a mode when a top-level object (not a
      * member object) was not found AND a substitutee was provided in
@@ -402,8 +386,7 @@
 
 	} catch (Error e) {
 	    throw new MobyException ("Serious or unexpected error!\n" +
-				     e.toString() + "\n" +
-				     DGUtils.stackTraceToString (e));
+				     e.toString(), e);
 	}
     }
 
@@ -554,6 +537,20 @@
 				    lowestKnownDataTypes.containsKey (articleName)) {
 				    theClass =
 					mapDataTypes.getClass (lowestKnownDataTypes.get (articleName));
+				} else {
+				    // ...if we are in a collection,
+				    // we need to use the article name
+				    // of that collection
+				    MobyCollection collObj = peekCollection();
+				    if (collObj != null) {
+					articleName = collObj.getName();
+					if (articleName != null &&
+					    lowestKnownDataTypes.containsKey (articleName)) {
+					    theClass =
+						mapDataTypes.getClass
+						(lowestKnownDataTypes.get (articleName));
+					}
+				    }
 				}
 			    }
 
@@ -916,6 +913,21 @@
     }
 
     /*********************************************************************
+     * Return the second last object from the 'objectStack' if it is a
+     * MobyCollectin, otherwise it returns null.
+     ********************************************************************/
+    protected MobyCollection peekCollection() {
+	if (objectStack.size() < 2)
+	    return null;
+	Object obj = objectStack.get (objectStack.size() - 2);
+	if (obj instanceof MobyCollection) {
+	    return (MobyCollection)obj;
+	} else {
+	    return null;
+	}
+    }
+
+    /*********************************************************************
      * Call a method (named 'methodName') on object 'actor', using
      * 'parameter'.
      ********************************************************************/



From senger at dev.open-bio.org  Sun Mar  2 12:45:26 2008
From: senger at dev.open-bio.org (Martin Senger)
Date: Sun, 2 Mar 2008 07:45:26 -0500
Subject: [MOBY-guts] biomoby commit
Message-ID: <200803021245.m22CjQL1032696@dev.open-bio.org>


senger
Sun Mar  2 07:45:26 EST 2008
Update of /home/repository/moby/moby-live/Java/src/main/org/biomoby/service/generator
In directory dev.open-bio.org:/tmp/cvs-serv32345/src/main/org/biomoby/service/generator

Modified Files:
	DataTypesGenerator.java Generator.java ServicesGenerator.java 
Log Message:
Too Many Changes - see docs/ChangeLog

moby-live/Java/src/main/org/biomoby/service/generator DataTypesGenerator.java,1.5,1.6 Generator.java,1.4,1.5 ServicesGenerator.java,1.6,1.7
===================================================================
RCS file: /home/repository/moby/moby-live/Java/src/main/org/biomoby/service/generator/DataTypesGenerator.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/service/generator/DataTypesGenerator.java	2008/02/23 13:58:32	1.5
+++ /home/repository/moby/moby-live/Java/src/main/org/biomoby/service/generator/DataTypesGenerator.java	2008/03/02 12:45:26	1.6
@@ -19,6 +19,7 @@
 import org.biomoby.client.Graphviz;
 
 import java.util.Properties;
+import java.util.Map;
 import java.util.HashMap;
 import java.util.Date;
 import java.util.regex.Pattern;
@@ -105,8 +106,8 @@
     /*************************************************************************
      *
      *************************************************************************/
-    public HashMap getTemplateNames() {
-	HashMap tNames = new HashMap();
+    public Map<String,File> getTemplateNames() {
+	Map<String,File> tNames = new HashMap<String,File>();
 	File dir = new File ("templates");
 	tNames.put (TN_DATA_TYPE,            new File (dir, "DataTypeTemplate.java"));
 	tNames.put (TN_MEMBERS_HAS,          new File (dir, "MembersHASTemplate.java"));
@@ -178,7 +179,7 @@
 	    pattern = Pattern.compile (filter);
 
 	// load all templates (from files)
-	HashMap templates = getTemplateNames();
+	Map<String,File> templates = getTemplateNames();
 	dataTypeTemplate     = loadTemplate (templates.get (TN_DATA_TYPE));
 	membersHASTemplate   = loadTemplate (templates.get (TN_MEMBERS_HAS));
 	membersHASATemplate  = loadTemplate (templates.get (TN_MEMBERS_HASA));

===================================================================
RCS file: /home/repository/moby/moby-live/Java/src/main/org/biomoby/service/generator/Generator.java,v
retrieving revision 1.4
retrieving revision 1.5
diff -u -r1.4 -r1.5
--- /home/repository/moby/moby-live/Java/src/main/org/biomoby/service/generator/Generator.java	2008/02/23 13:58:32	1.4
+++ /home/repository/moby/moby-live/Java/src/main/org/biomoby/service/generator/Generator.java	2008/03/02 12:45:26	1.5
@@ -18,7 +18,7 @@
 import org.biomoby.client.CentralDigestCachedImpl;
 
 import java.util.Properties;
-import java.util.HashMap;
+import java.util.Map;
 import java.util.regex.Pattern;
 import java.io.File;
 
@@ -415,14 +415,14 @@
      * patterns as the original template - so it is not too flexible,
      * anyway). <p>
      *
-     * The values of returned HashMap are filenames. It their names
-     * are relative (which is the best way) then they are looked for
-     * in the CLASSPATH (including all jar files there). <p>
+     * The values of returned Map are files. It their names are
+     * relative (which is the best way) then they are looked for in
+     * the CLASSPATH (including all jar files there). <p>
      *
      * Make sure that the returned path is correct for the system
      * where JVM is running.
      *************************************************************************/
-    abstract public HashMap getTemplateNames();
+    abstract public Map<String,File> getTemplateNames();
 
     /**************************************************************************
      * Generate "things" from a given Biomoby registry. This is the

===================================================================
RCS file: /home/repository/moby/moby-live/Java/src/main/org/biomoby/service/generator/ServicesGenerator.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/service/generator/ServicesGenerator.java	2008/02/28 05:21:48	1.6
+++ /home/repository/moby/moby-live/Java/src/main/org/biomoby/service/generator/ServicesGenerator.java	2008/03/02 12:45:26	1.7
@@ -26,10 +26,13 @@
 import org.biomoby.client.Graphviz;
 
 import org.tulsoft.tools.servlets.Html;
+import org.apache.commons.lang.StringUtils;
 
 import java.util.Properties;
 import java.util.Iterator;
+import java.util.Map;
 import java.util.HashMap;
+import java.util.Set;
 import java.util.HashSet;
 import java.util.Map;
 import java.util.Vector;
@@ -130,8 +133,8 @@
     /*************************************************************************
      *
      *************************************************************************/
-    public HashMap getTemplateNames() {
-	HashMap tNames = new HashMap();
+    public Map<String,File> getTemplateNames() {
+	Map<String,File> tNames = new HashMap<String,File>();
 	File dir = new File ("templates");
 	tNames.put (TN_SERVICE, new File (dir, "ServiceSkeletonTemplate.java"));
 	tNames.put (TN_PARAMETER, new File (dir, "ServiceParameterTemplate.java"));
@@ -162,7 +165,7 @@
     static final Pattern P_SERVICE_URL   = Pattern.compile ("@SERVICE_URL@");
     static final Pattern P_SERVICE_RDF   = Pattern.compile ("@SERVICE_RDF@");
     static final Pattern P_IOTABLE       = Pattern.compile ("@IOTABLE@");
-    static final Pattern P_FALLBACK_TYPE = Pattern.compile ("@FALLBACK_TYPE@");
+    static final Pattern P_FALLBACK_CODE = Pattern.compile ("@FALLBACK_CODE@");
 
     // dynamically created (org.biomoby.shared.datatypes.MapDataTypes)
     // (we need it for generating set/get methods for input/output
@@ -194,15 +197,15 @@
 	// compile patterns for filtering by service and authority names
 	Pattern wantedService = null;
 	String filter = props.getProperty (GPROP_SERVICE);
-	if (filter != null && ! "".equals (filter))
+	if (StringUtils.isNotBlank (filter))
 	    wantedService = Pattern.compile (filter);
 	Pattern wantedAuthority = null;
 	filter = props.getProperty (GPROP_AUTH);
-	if (filter != null && ! "".equals (filter))
+	if (StringUtils.isNotBlank (filter))
 	    wantedAuthority = Pattern.compile (filter);
 
 	// load all templates (from files)
-	HashMap templates = getTemplateNames();
+	Map<String,File> templates = getTemplateNames();
 	serviceTemplate          = loadTemplate (templates.get (TN_SERVICE));
 	serviceParameterTemplate = loadTemplate (templates.get (TN_PARAMETER));
 	servicePISetTemplate     = loadTemplate (templates.get (TN_PISET));
@@ -291,14 +294,38 @@
 	// graphs?
 	boolean graphCreated = createGraph (serviceName, outputDir, props, allServices, allDataTypes);
 
-	// fallback type - just for services with a single primary input
-	String fallbackType = "";
+	// fallback type - its type depends on the number of primary inputs
+	StringBuilder fallbackCode = new StringBuilder();
 	MobyData[] pis = service.getPrimaryInputs();
-	if (pis.length == 1) {
+	if (pis.length == 0) {
+	    fallbackCode.append ("String fallback = null;");
+	} else if (pis.length == 1) {
 	    String dataTypeName = mapDataType2class (pis[0]);
-	    if (dataTypeName != null)
-		fallbackType = dataTypeName;
+	    if (dataTypeName != null) {
+		fallbackCode.append ("String fallback = \"");
+		fallbackCode.append (dataTypeName);
+		fallbackCode.append ("\";");
+	    } else {
+		fallbackCode.append ("String fallback = null;");
+	    }
+	} else if (pis.length > 1) {
+	    fallbackCode.append
+		("java.util.Map<String,String> fallback = new java.util.HashMap<String,String>(); ");
+	    for (MobyData p: pis) {
+		String dataTypeName = mapDataType2class (p);
+		if (dataTypeName != null) {
+		    String articleName = p.getName();
+		    if (StringUtils.isNotBlank (articleName)) {
+			fallbackCode.append ("fallback.put (\"");
+			fallbackCode.append (articleName);
+			fallbackCode.append ("\",\"");
+			fallbackCode.append (dataTypeName);
+			fallbackCode.append ("\"); ");
+		    }
+		}
+	    }
 	}
+	fallbackCode.append ("\n");
 
 	// replace tokens in templates
 	String result = P_SERVICE_NAME.matcher (serviceTemplate).replaceAll (serviceName);
@@ -313,7 +340,7 @@
 	result = P_EMAIL_CONTACT.matcher (result).replaceAll (htmlEscape (service.getEmailContact()));
 	result = P_IMAGESTART.matcher (result).replaceAll (graphCreated ? "" : "<!-- ");
 	result = P_IMAGEEND.matcher (result).replaceAll (graphCreated ? "" : " -->");
-	result = P_FALLBACK_TYPE.matcher (result).replaceAll (fallbackType);
+	result = P_FALLBACK_CODE.matcher (result).replaceAll (fallbackCode.toString());
 
 	// 
  	// now apply templates for set/get methods (put the result in
@@ -359,7 +386,7 @@
 	    String methods = serviceParameterTemplate;
 
 	    String articleName = sis[i].getName();
-	    if (articleName == null || "".equals (articleName.trim())) {
+	    if (StringUtils.isBlank (articleName)) {
 		System.err.println (MSG_SECONDARY_PBL (serviceName, sis[i]));
 		continue;
 	    }
@@ -437,7 +464,7 @@
      * (that's why it gets a 'serviceName') and returns false.
      *************************************************************************/
     protected boolean verifyNames (MobyData[] data, String serviceName) {
-	HashSet names = new HashSet();
+	Set<String> names = new HashSet<String>();
 	for (int i = 0; i < data.length; i++) {
 	    String name = getOrCreateArticleName (data[i]);
 
@@ -468,7 +495,7 @@
      * ignore them or replace them.
      *************************************************************************/
     protected String authority2package (String authority) {
-	if (authority == null || "".equals (authority.trim()))
+	if (StringUtils.isBlank (authority))
 	    return DEFAULT_PACKAGE;
  	StringBuffer buf = new StringBuffer (100);
 	String[] parts = authority.split ("\\.");
@@ -515,7 +542,7 @@
      *************************************************************************/
     protected String getOrCreateArticleName (MobyData data) {
 	String name = data.getName();
-	if (name != null && ! "".equals (name.trim()))
+	if (StringUtils.isNotBlank (name))
 	    return name;
 	return mapDataType2class (data);
     }
@@ -556,7 +583,7 @@
 	throws MobyException {
 	if (allServices == null)
 	    return worker.findService (patternService);
-	Vector v = new Vector();
+	Vector<MobyService> v = new Vector<MobyService>();
 	String name = patternService.getName();
 	String auth = patternService.getAuthority();
 	for (int i = 0; i < allServices.length; i++) {
@@ -641,7 +668,7 @@
 
 	static final String NBSP = "&nbsp;";
 	String nbsp (String value) {
-	    if (value == null || "".equals (value.trim())) return NBSP;
+	    if (StringUtils.isBlank (value)) return NBSP;
 	    else return value;
 	}
 	MobyPrimaryDataSimple getOneSimple (MobyData data) {



From senger at dev.open-bio.org  Sun Mar  2 12:45:27 2008
From: senger at dev.open-bio.org (Martin Senger)
Date: Sun, 2 Mar 2008 07:45:27 -0500
Subject: [MOBY-guts] biomoby commit
Message-ID: <200803021245.m22CjR4h000428@dev.open-bio.org>


senger
Sun Mar  2 07:45:27 EST 2008
Update of /home/repository/moby/moby-live/Java/xmls
In directory dev.open-bio.org:/tmp/cvs-serv32345/xmls

Modified Files:
	dashboardBuild.xml install.xml junit.xml mosesBuild.xml 
	project.pom samplesBuild.xml servletsBuild.xml 
Log Message:
Too Many Changes - see docs/ChangeLog

moby-live/Java/xmls dashboardBuild.xml,1.4,1.5 install.xml,1.1,1.2 junit.xml,1.2,1.3 mosesBuild.xml,1.4,1.5 project.pom,1.5,1.6 samplesBuild.xml,1.4,1.5 servletsBuild.xml,1.1,1.2
===================================================================
RCS file: /home/repository/moby/moby-live/Java/xmls/dashboardBuild.xml,v
retrieving revision 1.4
retrieving revision 1.5
diff -u -r1.4 -r1.5
--- /home/repository/moby/moby-live/Java/xmls/dashboardBuild.xml	2008/02/22 00:54:30	1.4
+++ /home/repository/moby/moby-live/Java/xmls/dashboardBuild.xml	2008/03/02 12:45:27	1.5
@@ -42,8 +42,12 @@
     <not><isset property="log4j.configuration.valid"/></not>
   </condition>
   
-  <java classname="org.biomoby.service.dashboard.Dashboard" taskname="Dashboard"
-    classpathref="dashboard.build.classpath" fork="true" failonerror="true">
+  <java
+    classname="org.biomoby.service.dashboard.Dashboard"
+    taskname="Dashboard"
+    classpathref="dashboard.build.classpath"
+    fork="true"
+    failonerror="true">
     <jvmarg value="-Xms32m"/>
     <jvmarg value="-Xmx256m"/>
     <arg value="${dashboard.arg.1}"/>

===================================================================
RCS file: /home/repository/moby/moby-live/Java/xmls/install.xml,v
retrieving revision 1.1
retrieving revision 1.2
diff -u -r1.1 -r1.2
--- /home/repository/moby/moby-live/Java/xmls/install.xml	2008/02/14 06:13:37	1.1
+++ /home/repository/moby/moby-live/Java/xmls/install.xml	2008/03/02 12:45:27	1.2
@@ -9,15 +9,18 @@
 <!-- ====================================================== -->
 
 <target name="install"
-  description="Install and build jMoby">
+  description="Install and build jMoby"
+  depends="pre-compile,compile,post-compile"/>
+
+<target name="pre-compile">
   <echo taskname="welcome">
 ------------------------------------------
-Welcome to the jMoby world.              |
-Project documentation is available from: |
-http://biomoby.org/                      |
+| Welcome to the jMoby world.            |
+| Project documentation is available at: |
+| http://biomoby.org/                    |
 ------------------------------------------
   </echo>
-  <echo/>
+
   <echo taskname="version">
 ${ant.version}
 Java: ${java.version}
@@ -32,25 +35,103 @@
   <available file="${lib.dir}/alltools2.jar" property="old.jar.present"/>
   <antcall target="libcheck"/>
 
-  <echo/>
-  <echo taskname="build">
-The jMoby is going to build itself. It will need to fetch a lot of
-libraries from the Internet (using the Maven technology for resolving
-project dependencies). Just be patient, please...
+  <!-- Give name of the local cache -->
 
-Thanks for any comments and suggestions.
+  <touch file="build.properties"/>
+  <input taskname="Give Cache Name"
+    addproperty="registry.cache.dir"
+    defaultvalue="${project.home}/myCache">
+During the installation, jMoby is going to fetch data
+from the BioMoby central registry and store them in a
+local file system to allow much faster access to it.
+
+In order to do it, it needs to know a directory where
+you wish to store the local cache. For now, you can
+type it here - but for future the best is to add this
+line to your build.properties file:
+
+   registry.cache.dir = /full/name/of/cache/directory
+
+Default value (just pres ENTER to accept it) is:
+  </input>
+  <echo taskname="Give Cache Name">
+Local cache: ${registry.cache.dir}
+  </echo>
+
+  <echo file="build.properties" append="true">
+registry.cache.dir = ${registry.cache.dir}
+</echo>
+
+  <!-- build itself -->
+
+  <echo taskname="build">
+The jMoby is going to build itself. It will need to
+fetch a lot of libraries from the Internet (using the
+Maven technology for resolving project dependencies).
+Just be patient, please...
   </echo>
   <input taskname=" Attention ">Press Return key to continue...</input>
+  <antcall target="clean"/>
+
+</target>
+
+
 
-  <echo/>
-  <antcall target="compile"/>
+
+<target name="post-compile">
+  <antcall target="dashboard-config"/>
+
+
+  <!-- fill local cache -->
+
+  <echo taskname="Local cache">
+The jMoby is going to create local cache. Depending
+on the network speed, it may take several minutes
+(usually it should be done within about a minute).
+
+[You can check the progress in the jMoby.log file.]
+  </echo>
+
+  <java
+    taskname="Local cache"
+    classname="CacheRegistryClient"
+    fork="no"
+    failonerror="true">
+    <classpath refid="build.classpath"/>
+    <classpath refid="dependency.classpath"/>
+    <sysproperty key="log4j.configuration" value="file:${log4j.configuration}"/>
+    <arg value="-cachedir"/>
+    <arg file="${registry.cache.dir}"/>
+    <arg value="-v"/>
+    <arg value="-fill"/>
+  </java>
+
+
+  <!-- footnote message -->
 
   <echo taskname="Success">
 Installation completed.
+
+Thanks for any comments and suggestions
+(moby-l at biomoby.org or moby-dev at biomoby.org)
   </echo>
 
+
+  <!-- start Dashboard -->
+
+  <input taskname=" Attention ">Press Return key to start Dashboard...</input>
+  <!--
+(or press Ctrl-C and start Dashboard later
+ by typing 'ant dashboard')
+</input>
+-->
+  <antcall target="dashboard"/>
+
 </target>
 
+<!-- ====================================================== -->
+<!--                                                        -->
+<!-- ====================================================== -->
 <target name="check-ant-version">
   <fail
     taskname="check"

===================================================================
RCS file: /home/repository/moby/moby-live/Java/xmls/junit.xml,v
retrieving revision 1.2
retrieving revision 1.3
diff -u -r1.2 -r1.3
--- /home/repository/moby/moby-live/Java/xmls/junit.xml	2008/02/28 05:21:48	1.2
+++ /home/repository/moby/moby-live/Java/xmls/junit.xml	2008/03/02 12:45:27	1.3
@@ -90,7 +90,10 @@
     <jvmarg value="-Dlog4j.configuration=file:${log4j.configuration}"/>
     <formatter type="plain"/>
     <batchtest todir="${test.report.dir}">
-      <fileset dir="${build.test}" includes="**/*Test.*" />
+      <fileset dir="${build.test}">
+        <include name="**/MobyParserTest.*"/>
+      </fileset>
+      <!--      <fileset dir="${build.test}" includes="**/*Test.*" /> -->
     </batchtest>
   </junit>
 
@@ -103,16 +106,25 @@
 <target name="compile-tests" if="junit.is.present" depends="compile,junit-present">
   
   <!-- compilation options -->    
-  <property name="compile.test.debug"       value="${compile.debugtrue}" />
-  <property name="compile.test.verbose"     value="${compile.verbosefalse}" />
-  <property name="compile.test.deprecation" value="${compile.deprecationfalse}" />
-  <property name="compile.test.optimize"    value="${compile.optimizefalse}" />
-  <property name="compile.test.warnings"    value="${compile.warningsfalse}" />
+  <property name="compile.test.debug"       value="${compile.debug}" />
+  <property name="compile.test.verbose"     value="${compile.verbose}" />
+  <property name="compile.test.deprecation" value="${compile.deprecation}" />
+  <property name="compile.test.optimize"    value="${compile.optimize}" />
+  <property name="compile.test.warnings"    value="${compile.warnings}" />
     
   <condition property="xlint.test.param" value="-Xlint:unchecked" else="-Xlint:none">
     <istrue value="${compile.test.warnings}"/>
   </condition>
 
+  <path id="tests.classpath">
+    <pathelement location="${build.classes}"/>
+    <pathelement path="${classes.datatypes}"/>
+    <pathelement path="${classes.skeletons}"/>
+    <fileset dir="${lib.dir}">
+      <include name="*.jar"/>
+    </fileset>
+  </path>
+
   <javac
     srcdir="${src.test}"
     destdir="${build.test}"
@@ -122,7 +134,7 @@
     deprecation="${compile.test.deprecation}"
     optimize="${compile.test.optimize}"
     excludes="${project.excludes}">
-    <classpath refid="build.classpath"/>
+    <classpath refid="tests.classpath"/>
     <classpath refid="dependency.classpath"/>
     <compilerarg value="${xlint.test.param}"/>
   </javac>

===================================================================
RCS file: /home/repository/moby/moby-live/Java/xmls/mosesBuild.xml,v
retrieving revision 1.4
retrieving revision 1.5
diff -u -r1.4 -r1.5
--- /home/repository/moby/moby-live/Java/xmls/mosesBuild.xml	2008/02/28 05:21:49	1.4
+++ /home/repository/moby/moby-live/Java/xmls/mosesBuild.xml	2008/03/02 12:45:27	1.5
@@ -21,6 +21,7 @@
 
            generate-datatypes     generate-services
            clean-datatypes        clean-services
+           compile-datatypes      compile-services
            jar-datatypes          jar-services
            moses-datatypes        moses-services
 
@@ -107,6 +108,10 @@
     </or>
   </condition>
   
+  <condition property="xlint.param" value="-Xlint:unchecked" else="-Xlint:none">
+    <istrue value="${compile.warnings}"/>
+  </condition>
+
 </target>
 
 <!-- ================================================================== -->
@@ -125,6 +130,7 @@
   
   <property name="moses.filter.dt" value="&quot;&quot;"/>
   <property name="dot.location" value="&quot;&quot;"/>
+  <property name="registry.cache.dir" value=""/>
   
   <java classname="MosesGenerators" taskname="Data Types"
     classpathref="moses.build.classpath" fork="true" failonerror="true">
@@ -189,9 +195,6 @@
   <delete includeemptydirs="true" quiet="true">
     <fileset dir="${src.skeletons}" includes="**/*"/>
   </delete>
-  <delete includeemptydirs="true">
-    <fileset dir="${classes.skeletons}" includes="**/*"/>
-  </delete>
 </target>
 
 <target name="generate-services" depends="moses-init,service-check"
@@ -200,6 +203,7 @@
   <property name="moses.service" value="&quot;&quot;"/>
   <property name="moses.authority" value="&quot;&quot;"/>
   <property name="dot.location" value="&quot;&quot;"/>
+  <property name="registry.cache.dir" value=""/>
   
   <java classname="MosesGenerators" taskname="Service(s)"
     classpathref="moses.build.classpath" fork="true" failonerror="true">
@@ -267,21 +271,36 @@
 <!-- ================================================================== -->
 <!-- Moses generally: Compile generated datatypes and skeletons         -->
 <!-- ================================================================== -->
-<target name="moses-compile" depends="moses-init,compile"
-  description="Compile all generated sources.">
-  <javac srcdir="${src.datatypes}"
+<target name="moses-compile" depends="compile-datatypes,compile-services"
+  description="Compile all generated sources."/>
+
+<target name="compile-datatypes" depends="moses-init,compile">
+  <javac
+    srcdir="${src.datatypes}"
     destdir="${classes.datatypes}"
-    debug="true"
+    verbose="${compile.verbose}"
+    debug="${compile.debug}"
     debuglevel="lines,vars,source"
+    deprecation="${compile.deprecation}"
+    optimize="${compile.optimize}"
     excludes="${project.excludes}">
     <classpath refid="moses.build.classpath"/>
+    <compilerarg value="${xlint.param}"/>
   </javac>
-  <javac srcdir="${src.skeletons}"
-    debug="true"
-    debuglevel="lines,vars,source"
+</target>
+
+<target name="compile-services" depends="moses-init,compile">
+  <javac
+    srcdir="${src.skeletons}"
     destdir="${classes.skeletons}"
+    verbose="${compile.verbose}"
+    debug="${compile.debug}"
+    debuglevel="lines,vars,source"
+    deprecation="${compile.deprecation}"
+    optimize="${compile.optimize}"
     excludes="${project.excludes}">
     <classpath refid="moses.build.classpath"/>
+    <compilerarg value="${xlint.param}"/>
   </javac>
 </target>
 
@@ -349,3 +368,14 @@
 <target name="moses-jars" depends="jar-datatypes,jar-services"
   description="Create jar files with generated data types and skeletons.">
 </target>
+
+<!-- ================================================================== -->
+<!-- Moses generally: do it all                                         -->
+<!-- ================================================================== -->
+<target name="moses"
+  depends="compile,moses-clean,clean-services,generate-datatypes,compile-datatypes,generate-services,compile-services,moses-jars"
+  description="Clean/enerate/compile/pack data types and skeletons.">
+</target>
+
+<target name="moses-test" depends="generate-datatypes,moses-compile">
+</target>

===================================================================
RCS file: /home/repository/moby/moby-live/Java/xmls/project.pom,v
retrieving revision 1.5
retrieving revision 1.6
diff -u -r1.5 -r1.6
--- /home/repository/moby/moby-live/Java/xmls/project.pom	2008/02/28 05:21:49	1.5
+++ /home/repository/moby/moby-live/Java/xmls/project.pom	2008/03/02 12:45:27	1.6
@@ -167,6 +167,21 @@
     </dependency>
 
     <dependency>
+      <groupId>commons-configuration</groupId>
+      <artifactId>commons-configuration</artifactId>
+      <version>1.5</version>
+      <!-- we need to exclude this in order to get Java 1.5. XML parser
+           (otherwise axis will complain about the lexical-handler
+           feature not supported -->
+      <exclusions>
+        <exclusion>
+          <groupId>xerces</groupId>
+          <artifactId>xerces</artifactId>
+        </exclusion>
+      </exclusions>  
+    </dependency>
+
+    <dependency>
       <groupId>castor</groupId>
       <artifactId>castor</artifactId>
       <version>0.9.5</version>
@@ -366,6 +381,12 @@
     </dependency>
 
     <dependency>
+      <groupId>org.apache.ant</groupId>
+      <artifactId>ant-nodeps</artifactId>
+      <version>1.7.0</version>
+    </dependency>
+
+    <dependency>
       <groupId>ant-contrib</groupId>
       <artifactId>ant-contrib</artifactId>
       <version>1.0b2</version>

===================================================================
RCS file: /home/repository/moby/moby-live/Java/xmls/samplesBuild.xml,v
retrieving revision 1.4
retrieving revision 1.5
diff -u -r1.4 -r1.5
--- /home/repository/moby/moby-live/Java/xmls/samplesBuild.xml	2008/02/22 00:54:30	1.4
+++ /home/repository/moby/moby-live/Java/xmls/samplesBuild.xml	2008/03/02 12:45:27	1.5
@@ -57,6 +57,10 @@
     <pathelement location="${classes.samples}"/>
   </path>
    
+  <condition property="xlint.param" value="-Xlint:unchecked" else="-Xlint:none">
+    <istrue value="${compile.warnings}"/>
+  </condition>
+
 </target>
 
 <!-- ================================================================== -->
@@ -64,15 +68,22 @@
 <!-- ================================================================== -->
 <target name="samples-compile" depends="samples-init,moses-compile"
   description="Compile samples and tutorial.">
+
   <copy todir="${classes.samples}/resources">
     <fileset dir="${samples.resources}"/>
   </copy>
-  <javac srcdir="${src.samples}"
-    debug="true"
-    debuglevel="lines,vars,source"
+
+  <javac
+    srcdir="${src.samples}"
     destdir="${classes.samples}"
+    verbose="${compile.verbose}"
+    debug="${compile.debug}"
+    debuglevel="lines,vars,source"
+    deprecation="${compile.deprecation}"
+    optimize="${compile.optimize}"
     excludes="${project.excludes}">
     <classpath refid="samples.build.classpath"/>
+    <compilerarg value="${xlint.param}"/>
   </javac>
 </target>
 
@@ -154,13 +165,14 @@
   <antcall target="generate-services">
     <param name="moses.authority" value="samples.jmoby.net"/>
   </antcall>
+  <antcall target="generate-services">
+    <param name="moses.service" value="getFeatureList|TrimSequenceVector"/>
+  </antcall>
 
 </target>
 
 <!-- ================================================================== -->
 <!-- Samples: All in one                                                -->
 <!-- ================================================================== -->
-<!-- <target name="samples" depends="samples-generate,samples-compile,samples-jar,samples-docs,deploy-services" -->
-<!-- <target name="samples" depends="samples-compile,samples-jar,deploy-services" -->
-<target name="samples" depends="samples-compile,samples-jar"
+<target name="samples" depends="moses,samples-compile,samples-jar"
   description="Do (almost) everything for samples."/>

===================================================================
RCS file: /home/repository/moby/moby-live/Java/xmls/servletsBuild.xml,v
retrieving revision 1.1
retrieving revision 1.2
diff -u -r1.1 -r1.2
--- /home/repository/moby/moby-live/Java/xmls/servletsBuild.xml	2006/04/28 00:13:41	1.1
+++ /home/repository/moby/moby-live/Java/xmls/servletsBuild.xml	2008/03/02 12:45:27	1.2
@@ -25,6 +25,9 @@
   description="Create a war file with jMoby servlets.">
   <mkdir dir="${build.webapps}"/>
   <mkdir dir="${build.webapps}/cache"/>
+
+  <property name="registry.cache.dir" value=""/>
+
   <copy file="${src.webapps}/web.xml.template"
     tofile="${build.webapps}/web.xml"
     overwrite="yes">



From senger at dev.open-bio.org  Sun Mar  2 15:36:25 2008
From: senger at dev.open-bio.org (Martin Senger)
Date: Sun, 2 Mar 2008 10:36:25 -0500
Subject: [MOBY-guts] biomoby commit
Message-ID: <200803021536.m22FaPbJ000970@dev.open-bio.org>


senger
Sun Mar  2 10:36:24 EST 2008
Update of /home/repository/moby/moby-live/Java/xmls
In directory dev.open-bio.org:/tmp/cvs-serv951/xmls

Modified Files:
	install.xml 
Log Message:
few details added to the installation task
moby-live/Java/xmls install.xml,1.2,1.3
===================================================================
RCS file: /home/repository/moby/moby-live/Java/xmls/install.xml,v
retrieving revision 1.2
retrieving revision 1.3
diff -u -r1.2 -r1.3
--- /home/repository/moby/moby-live/Java/xmls/install.xml	2008/03/02 12:45:27	1.2
+++ /home/repository/moby/moby-live/Java/xmls/install.xml	2008/03/02 15:36:24	1.3
@@ -85,7 +85,7 @@
   <!-- fill local cache -->
 
   <echo taskname="Local cache">
-The jMoby is going to create local cache. Depending
+The jMoby is now creating a local cache. Depending
 on the network speed, it may take several minutes
 (usually it should be done within about a minute).
 
@@ -107,6 +107,13 @@
   </java>
 
 
+  <!-- generate datatypes and samples -->
+
+  <property name="moses.nographs" value="true"/>
+  <antcall target="samples"/>
+
+
+
   <!-- footnote message -->
 
   <echo taskname="Success">
@@ -125,6 +132,7 @@
  by typing 'ant dashboard')
 </input>
 -->
+
   <antcall target="dashboard"/>
 
 </target>



From senger at dev.open-bio.org  Sun Mar  2 15:43:28 2008
From: senger at dev.open-bio.org (Martin Senger)
Date: Sun, 2 Mar 2008 10:43:28 -0500
Subject: [MOBY-guts] biomoby commit
Message-ID: <200803021543.m22FhS2I001023@dev.open-bio.org>


senger
Sun Mar  2 10:43:28 EST 2008
Update of /home/repository/moby/moby-live/Java/xmls
In directory dev.open-bio.org:/tmp/cvs-serv1004/xmls

Modified Files:
	install.xml 
Log Message:
few details added to the installation task
moby-live/Java/xmls install.xml,1.3,1.4
===================================================================
RCS file: /home/repository/moby/moby-live/Java/xmls/install.xml,v
retrieving revision 1.3
retrieving revision 1.4
diff -u -r1.3 -r1.4
--- /home/repository/moby/moby-live/Java/xmls/install.xml	2008/03/02 15:36:24	1.3
+++ /home/repository/moby/moby-live/Java/xmls/install.xml	2008/03/02 15:43:28	1.4
@@ -109,6 +109,7 @@
 
   <!-- generate datatypes and samples -->
 
+  <property name="moses.authority" value="samples.jmoby.net"/>
   <property name="moses.nographs" value="true"/>
   <antcall target="samples"/>
 



From senger at dev.open-bio.org  Sun Mar  2 16:05:01 2008
From: senger at dev.open-bio.org (Martin Senger)
Date: Sun, 2 Mar 2008 11:05:01 -0500
Subject: [MOBY-guts] biomoby commit
Message-ID: <200803021605.m22G51UB001077@dev.open-bio.org>


senger
Sun Mar  2 11:05:01 EST 2008
Update of /home/repository/moby/moby-live/Java/xmls
In directory dev.open-bio.org:/tmp/cvs-serv1058/xmls

Modified Files:
	install.xml 
Log Message:
few details added to the installation task
moby-live/Java/xmls install.xml,1.4,1.5
===================================================================
RCS file: /home/repository/moby/moby-live/Java/xmls/install.xml,v
retrieving revision 1.4
retrieving revision 1.5
diff -u -r1.4 -r1.5
--- /home/repository/moby/moby-live/Java/xmls/install.xml	2008/03/02 15:43:28	1.4
+++ /home/repository/moby/moby-live/Java/xmls/install.xml	2008/03/02 16:05:01	1.5
@@ -40,7 +40,7 @@
   <touch file="build.properties"/>
   <input taskname="Give Cache Name"
     addproperty="registry.cache.dir"
-    defaultvalue="${project.home}/myCache">
+    defaultvalue="${basedir.unix}/myCache">
 During the installation, jMoby is going to fetch data
 from the BioMoby central registry and store them in a
 local file system to allow much faster access to it.
@@ -52,7 +52,7 @@
 
    registry.cache.dir = /full/name/of/cache/directory
 
-Default value (just pres ENTER to accept it) is:
+Default value (just press ENTER to accept it) is:
   </input>
   <echo taskname="Give Cache Name">
 Local cache: ${registry.cache.dir}
@@ -70,7 +70,7 @@
 Maven technology for resolving project dependencies).
 Just be patient, please...
   </echo>
-  <input taskname=" Attention ">Press Return key to continue...</input>
+  <!--  <input taskname=" Attention ">Press Return key to continue...</input> -->
   <antcall target="clean"/>
 
 </target>
@@ -127,7 +127,7 @@
 
   <!-- start Dashboard -->
 
-  <input taskname=" Attention ">Press Return key to start Dashboard...</input>
+  <input taskname=" Attention ">Press (twice) Return key to start Dashboard...</input>
   <!--
 (or press Ctrl-C and start Dashboard later
  by typing 'ant dashboard')



From senger at dev.open-bio.org  Sun Mar  2 16:19:15 2008
From: senger at dev.open-bio.org (Martin Senger)
Date: Sun, 2 Mar 2008 11:19:15 -0500
Subject: [MOBY-guts] biomoby commit
Message-ID: <200803021619.m22GJFEj001149@dev.open-bio.org>


senger
Sun Mar  2 11:19:15 EST 2008
Update of /home/repository/moby/moby-live/Java/src/main/org/biomoby/service/dashboard
In directory dev.open-bio.org:/tmp/cvs-serv1130/src/main/org/biomoby/service/dashboard

Modified Files:
	RegistryPanel.java 
Log Message:
problem with Windows vs. Unix filenames
moby-live/Java/src/main/org/biomoby/service/dashboard RegistryPanel.java,1.29,1.30
===================================================================
RCS file: /home/repository/moby/moby-live/Java/src/main/org/biomoby/service/dashboard/RegistryPanel.java,v
retrieving revision 1.29
retrieving revision 1.30
diff -u -r1.29 -r1.30
--- /home/repository/moby/moby-live/Java/src/main/org/biomoby/service/dashboard/RegistryPanel.java	2008/03/02 12:45:26	1.29
+++ /home/repository/moby/moby-live/Java/src/main/org/biomoby/service/dashboard/RegistryPanel.java	2008/03/02 16:19:15	1.30
@@ -17,6 +17,8 @@
 import org.biomoby.registry.meta.RegistriesList;
 import org.biomoby.registry.meta.Registry;
 
+import org.apache.commons.io.FilenameUtils;
+
 import javax.swing.JPanel;
 import javax.swing.JLabel;
 import javax.swing.Icon;
@@ -515,8 +517,9 @@
    	labelCacheDir = new JLabel("Cache directory");
 	cacheDir = createFileSelector ("Select directory for/with local cache",
 				       "Select",
-				       DashboardConfig.getString (DP_REGISTRY_CACHE_DIR,
-								  getUserTmpDir()),
+				       FilenameUtils.separatorsToSystem
+				       (DashboardConfig.getString (DP_REGISTRY_CACHE_DIR,
+								   getUserTmpDir())),
 				       "cacheDirectory",
 				       DP_CACHE_DIR);
 	cacheDir.getFileChooser().setFileSelectionMode (JFileChooser.DIRECTORIES_ONLY);



From senger at dev.open-bio.org  Sun Mar  2 16:20:49 2008
From: senger at dev.open-bio.org (Martin Senger)
Date: Sun, 2 Mar 2008 11:20:49 -0500
Subject: [MOBY-guts] biomoby commit
Message-ID: <200803021620.m22GKnvR001201@dev.open-bio.org>


senger
Sun Mar  2 11:20:49 EST 2008
Update of /home/repository/moby/moby-live/Java
In directory dev.open-bio.org:/tmp/cvs-serv1182

Modified Files:
	.cvsignore.template 
Log Message:

moby-live/Java .cvsignore.template,1.6,1.7
===================================================================
RCS file: /home/repository/moby/moby-live/Java/.cvsignore.template,v
retrieving revision 1.6
retrieving revision 1.7
diff -u -r1.6 -r1.7
--- /home/repository/moby/moby-live/Java/.cvsignore.template	2008/02/14 06:13:34	1.6
+++ /home/repository/moby/moby-live/Java/.cvsignore.template	2008/03/02 16:20:49	1.7
@@ -6,3 +6,4 @@
 *.log
 *.log.?
 testout
+myCache



From senger at dev.open-bio.org  Sun Mar  2 16:59:54 2008
From: senger at dev.open-bio.org (Martin Senger)
Date: Sun, 2 Mar 2008 11:59:54 -0500
Subject: [MOBY-guts] biomoby commit
Message-ID: <200803021659.m22GxsAQ001291@dev.open-bio.org>


senger
Sun Mar  2 11:59:54 EST 2008
Update of /home/repository/moby/moby-live/Java/src/main/org/biomoby/service/dashboard
In directory dev.open-bio.org:/tmp/cvs-serv1272/src/main/org/biomoby/service/dashboard

Modified Files:
	GeneratorPanel.java 
Log Message:

moby-live/Java/src/main/org/biomoby/service/dashboard GeneratorPanel.java,1.17,1.18
===================================================================
RCS file: /home/repository/moby/moby-live/Java/src/main/org/biomoby/service/dashboard/GeneratorPanel.java,v
retrieving revision 1.17
retrieving revision 1.18
diff -u -r1.17 -r1.18
--- /home/repository/moby/moby-live/Java/src/main/org/biomoby/service/dashboard/GeneratorPanel.java	2008/03/02 12:45:26	1.17
+++ /home/repository/moby/moby-live/Java/src/main/org/biomoby/service/dashboard/GeneratorPanel.java	2008/03/02 16:59:54	1.18
@@ -189,7 +189,7 @@
 	// split it into resizable panels
 	JSplitPane split = hSplit (vSplit (hSplit (selection,
 						   generators, 0.9),
-					   console, 0.1),
+					   console, 0.2),
 				   deployment, 0.9);
   	SwingUtils.addComponent (pComponent, split,  0, 0, 1, 1, BOTH, NWEST,  1.0, 1.0);
 	return pComponent;



From senger at dev.open-bio.org  Sun Mar  2 18:47:35 2008
From: senger at dev.open-bio.org (Martin Senger)
Date: Sun, 2 Mar 2008 13:47:35 -0500
Subject: [MOBY-guts] biomoby commit
Message-ID: <200803021847.m22IlZYk001434@dev.open-bio.org>


senger
Sun Mar  2 13:47:35 EST 2008
Update of /home/repository/moby/moby-live/Java/src/main/org/biomoby/shared/datatypes
In directory dev.open-bio.org:/tmp/cvs-serv1415/src/main/org/biomoby/shared/datatypes

Modified Files:
	MobyObject.java 
Log Message:
Fixed cross references by primitive types

moby-live/Java/src/main/org/biomoby/shared/datatypes MobyObject.java,1.7,1.8
===================================================================
RCS file: /home/repository/moby/moby-live/Java/src/main/org/biomoby/shared/datatypes/MobyObject.java,v
retrieving revision 1.7
retrieving revision 1.8
diff -u -r1.7 -r1.8
--- /home/repository/moby/moby-live/Java/src/main/org/biomoby/shared/datatypes/MobyObject.java	2008/03/02 12:45:26	1.7
+++ /home/repository/moby/moby-live/Java/src/main/org/biomoby/shared/datatypes/MobyObject.java	2008/03/02 18:47:35	1.8
@@ -62,7 +62,7 @@
     protected String name = "";   // articleName
     protected String value = "";
     protected MobyProvisionInfo provision;
-    protected Vector xrefs = new Vector();   // of type MobyXref
+    protected Vector<MobyXref> xrefs = new Vector<MobyXref>();
     protected boolean isValueCDATA = false;
 
     // is this a primitive type?
@@ -153,7 +153,6 @@
 
 	if (provision != null)
 	    elem.addContent (JDOMUtils.toXMLElement(provision));
-
 	if (xrefs.size() > 0) {
 	    Element crElem = MobyPackage.getXMLElement (MobyTags.CROSSREFERENCE);
 	    for (Enumeration en = xrefs.elements(); en.hasMoreElements(); )
@@ -165,7 +164,7 @@
 	    if (isValueCDATA)
 		elem.addContent (new CDATA (value));
 	    else
-		elem.setText (value);
+		elem.addContent (value);
 	}
 
 	return elem;
@@ -286,7 +285,7 @@
      *************************************************************************/
     public void setXrefs (MobyXref[] xrefs) {
 	if (xrefs != null) {
-	    this.xrefs = new Vector();
+	    this.xrefs = new Vector<MobyXref>();
 	    for (int i = 0; i < xrefs.length; i++)
 		this.xrefs.addElement (xrefs[i]);
 	}



From senger at dev.open-bio.org  Mon Mar  3 03:11:28 2008
From: senger at dev.open-bio.org (Martin Senger)
Date: Sun, 2 Mar 2008 22:11:28 -0500
Subject: [MOBY-guts] biomoby commit
Message-ID: <200803030311.m233BShE002177@dev.open-bio.org>


senger
Sun Mar  2 22:11:27 EST 2008
Update of /home/repository/moby/moby-live/Java/src/test/junit-resources
In directory dev.open-bio.org:/tmp/cvs-serv2132/src/test/junit-resources

Modified Files:
	parser-test-input-2.xml parser-test-input-3.xml 
	parser-test-input-4.xml 
Added Files:
	parser-test-input-set.xml parser-test-input-xrefs.xml 
Log Message:
More junit tests for XML parser

moby-live/Java/src/test/junit-resources parser-test-input-set.xml,NONE,1.1 parser-test-input-xrefs.xml,NONE,1.1 parser-test-input-2.xml,1.1,1.2 parser-test-input-3.xml,1.1,1.2 parser-test-input-4.xml,1.1,1.2
===================================================================
RCS file: /home/repository/moby/moby-live/Java/src/test/junit-resources/parser-test-input-2.xml,v
retrieving revision 1.1
retrieving revision 1.2
diff -u -r1.1 -r1.2
--- /home/repository/moby/moby-live/Java/src/test/junit-resources/parser-test-input-2.xml	2008/02/28 05:21:48	1.1
+++ /home/repository/moby/moby-live/Java/src/test/junit-resources/parser-test-input-2.xml	2008/03/03 03:11:27	1.2
@@ -6,8 +6,8 @@
     <moby:mobyData moby:queryID="a1">
       <moby:Simple moby:articleName="myDNA">
         <moby:MyDNASequence xmlns:moby="http://www.biomoby.org/moby" moby:id="ir" moby:namespace="">
-          <moby:Integer moby:id="3" moby:namespace="a" moby:articleName="Length">12</moby:Integer>
-          <moby:String moby:id="3" moby:namespace="b" moby:articleName="SequenceString">abcd</moby:String>
+          <moby:Integer moby:id="1" moby:namespace="a" moby:articleName="Length">12</moby:Integer>
+          <moby:String moby:id="2" moby:namespace="b" moby:articleName="SequenceString">abcd</moby:String>
           <moby:Boolean moby:id="3" moby:namespace="c" moby:articleName="Flag">true</moby:Boolean>
         </moby:MyDNASequence>
       </moby:Simple>

===================================================================
RCS file: /home/repository/moby/moby-live/Java/src/test/junit-resources/parser-test-input-3.xml,v
retrieving revision 1.1
retrieving revision 1.2
diff -u -r1.1 -r1.2
--- /home/repository/moby/moby-live/Java/src/test/junit-resources/parser-test-input-3.xml	2008/02/28 05:21:48	1.1
+++ /home/repository/moby/moby-live/Java/src/test/junit-resources/parser-test-input-3.xml	2008/03/03 03:11:27	1.2
@@ -10,9 +10,16 @@
             <Integer id="" namespace="" articleName="start">1</Integer>
             <String id="" namespace="" articleName="phase">b</String>
             <Float id="" namespace="" articleName="score">12.34</Float>
-            <MY_multi_key_value_pair id="" namespace="" articleName="column9_tag_value">
+            <MY_multi_key_value_pair id="1" namespace="" articleName="column9_tag_value">
               <String id="" namespace="" articleName="key">key1</String>
               <String id="" namespace="" articleName="value">value1</String>
+              <String id="" namespace="" articleName="value">value2</String>
+              <String id="" namespace="" articleName="value">value3</String>
+              <String id="" namespace="" articleName="mode">mode1</String>
+            </MY_multi_key_value_pair>
+            <MY_multi_key_value_pair id="2" namespace="" articleName="column9_tag_value">
+              <String id="" namespace="" articleName="key">key2</String>
+              <String id="" namespace="" articleName="value">valueA</String>
               <String id="" namespace="" articleName="mode">mode1</String>
             </MY_multi_key_value_pair>
           </BasicGFF3SequenceFeature>

===================================================================
RCS file: /home/repository/moby/moby-live/Java/src/test/junit-resources/parser-test-input-4.xml,v
retrieving revision 1.1
retrieving revision 1.2
diff -u -r1.1 -r1.2
--- /home/repository/moby/moby-live/Java/src/test/junit-resources/parser-test-input-4.xml	2008/02/28 05:21:48	1.1
+++ /home/repository/moby/moby-live/Java/src/test/junit-resources/parser-test-input-4.xml	2008/03/03 03:11:27	1.2
@@ -1,10 +1,5 @@
 <?xml version="1.0" encoding="UTF-8"?>
 
-<!-- ========================================== -->
-<!-- A testing data for MobyParser.             -->
-<!-- Use: build/run/run-moby-parser "this-file" -->
-<!-- ========================================== -->
-
 <moby:MOBY xmlns:moby="http://www.biomoby.org/moby">
   <moby:mobyContent moby:authority="http://&quot;me&quot;.&lt;org&gt;&amp;">
     <moby:serviceNotes><Notes>freetext notes here the notes</Notes></moby:serviceNotes>
@@ -24,8 +19,8 @@
       </moby:Simple>
       <moby:Simple moby:articleName="mySeq">
         <moby:MyDNASequence xmlns:moby="http://www.biomoby.org/moby" moby:id="ir" moby:namespace="">
-          <moby:Integer moby:id="3" moby:namespace="a" moby:articleName="Length">12</moby:Integer>
-          <moby:String moby:id="3" moby:namespace="b" moby:articleName="SequenceString">abcd</moby:String>
+          <moby:Integer moby:id="3" moby:namespace="c" moby:articleName="Length">123</moby:Integer>
+          <moby:String moby:id="4" moby:namespace="d" moby:articleName="SequenceString">xyz</moby:String>
         </moby:MyDNASequence>
       </moby:Simple>
     </moby:mobyData>



From senger at dev.open-bio.org  Mon Mar  3 03:11:28 2008
From: senger at dev.open-bio.org (Martin Senger)
Date: Sun, 2 Mar 2008 22:11:28 -0500
Subject: [MOBY-guts] biomoby commit
Message-ID: <200803030311.m233BSPU002151@dev.open-bio.org>


senger
Sun Mar  2 22:11:27 EST 2008
Update of /home/repository/moby/moby-live/Java/src/test/java/org/biomoby/shared/parser
In directory dev.open-bio.org:/tmp/cvs-serv2132/src/test/java/org/biomoby/shared/parser

Modified Files:
	MobyParserTest.java 
Log Message:
More junit tests for XML parser

moby-live/Java/src/test/java/org/biomoby/shared/parser MobyParserTest.java,1.2,1.3
===================================================================
RCS file: /home/repository/moby/moby-live/Java/src/test/java/org/biomoby/shared/parser/MobyParserTest.java,v
retrieving revision 1.2
retrieving revision 1.3
diff -u -r1.2 -r1.3
--- /home/repository/moby/moby-live/Java/src/test/java/org/biomoby/shared/parser/MobyParserTest.java	2008/03/02 12:45:27	1.2
+++ /home/repository/moby/moby-live/Java/src/test/java/org/biomoby/shared/parser/MobyParserTest.java	2008/03/03 03:11:27	1.3
@@ -20,6 +20,7 @@
 package org.biomoby.shared.parser;
 
 import org.biomoby.shared.MobyException;
+import org.biomoby.shared.data.MobyProvisionInfo;
 import org.biomoby.shared.datatypes.*;
 
 import org.junit.Before;
@@ -39,10 +40,12 @@
 
 public class MobyParserTest {
 
-    private static final String INPUT_1 = "parser-test-input-1.xml";
-    private static final String INPUT_2 = "parser-test-input-2.xml";
-    private static final String INPUT_3 = "parser-test-input-3.xml";
-    private static final String INPUT_4 = "parser-test-input-4.xml";
+    private static final String INPUT_1     = "parser-test-input-1.xml";
+    private static final String INPUT_2     = "parser-test-input-2.xml";
+    private static final String INPUT_3     = "parser-test-input-3.xml";
+    private static final String INPUT_4     = "parser-test-input-4.xml";
+    private static final String INPUT_XREFS = "parser-test-input-xrefs.xml";
+    private static final String INPUT_SET   = "parser-test-input-set.xml";
  
     /**************************************************************************
      *
@@ -72,26 +75,101 @@
 	assertEquals (typedData.getMoby_Length().getIntValue(), 10);
     }
 
-//     @Test
-//     public void testUnknownTopLevel()
-// 	throws IOException, MobyException {
-// 	parse (INPUT_2, "DNASequence", null);
-//     }
-
-//     @Test
-//     public void testUnknownTopLevelAndMember()
-// 	throws IOException, MobyException {
-// 	parse (INPUT_3, "BasicGFF3MultiFeature", null);
-//     }
-
-//     @Test
-//     public void testMoreUnknownTopLevels()
-// 	throws IOException, MobyException {
-// 	Map<String,String> backups = new HashMap<String,String>();
-// 	backups.put ("mySeq",   "DNASequence");
-// 	backups.put ("myPairs", "BasicGFF3MultiFeature");
-// 	parse (INPUT_4, null, backups);
-//     }
+     @Test
+     public void testUnknownTopLevel()
+ 	throws IOException, MobyException {
+	MobyPackage moby = parse (INPUT_2, "DNASequence", null);
+	DNASequence typedData = (DNASequence)moby.getJob(0).getData ("myDNA");
+	assertEquals (typedData.get_SequenceString(), "abcd");
+	assertEquals (typedData.getMoby_Length().getIntValue(), 12);
+     }
+
+    @Test
+    public void testUnknownTopLevelAndMember()
+	throws IOException, MobyException {
+	MobyPackage moby = parse (INPUT_3, "BasicGFF3MultiFeature", null);
+	BasicGFF3MultiFeature typedData = (BasicGFF3MultiFeature)moby.getJob(0).getData ("myPairs");
+	BasicGFF3SequenceFeature[] data = typedData.getMoby_BasicGFF3SequenceFeature();
+	assertEquals (data.length, 1);
+	assertEquals (data[0].getMoby_start().getIntValue(), 1);
+	assertEquals (data[0].getMoby_score().getFloatValue(), 12.34, 0);
+	assertEquals (data[0].get_phase(), "b");
+	multi_key_value_pair[] pairs = data[0].getMoby_column9_tag_value();
+	assertEquals (pairs.length, 2);
+	assertEquals (pairs[0].get_key(), "key1");
+	assertEquals (pairs[0].get_the_value().length, 3);
+	assertEquals (pairs[0].get_the_value()[0], "value1");
+	assertEquals (pairs[1].get_key(), "key2");
+	assertEquals (pairs[1].get_the_value().length, 1);
+	assertEquals (pairs[1].get_the_value()[0], "valueA");
+    }
+
+    @Test
+    public void testMoreUnknownTopLevels()
+	throws IOException, MobyException {
+	Map<String,String> backups = new HashMap<String,String>();
+	backups.put ("mySeq",   "DNASequence");
+	backups.put ("myPairs", "BasicGFF3MultiFeature");
+	MobyPackage moby = parse (INPUT_4, null, backups);
+	BasicGFF3MultiFeature typedData = (BasicGFF3MultiFeature)moby.getJob(0).getData ("myPairs");
+	BasicGFF3SequenceFeature[] data = typedData.getMoby_BasicGFF3SequenceFeature();
+	assertEquals (data.length, 1);
+	assertEquals (data[0].getMoby_start().getIntValue(), 1);
+	assertEquals (data[0].getMoby_score().getFloatValue(), 12.34, 0);
+	assertEquals (data[0].get_phase(), "b");
+	multi_key_value_pair[] pairs = data[0].getMoby_column9_tag_value();
+	assertEquals (pairs.length, 1);
+	assertEquals (pairs[0].get_key(), "key1");
+	assertEquals (pairs[0].get_the_value().length, 1);
+	assertEquals (pairs[0].get_the_value()[0], "value1");
+	DNASequence seqData = (DNASequence)moby.getJob(0).getData ("mySeq");
+	assertEquals (seqData.get_SequenceString(), "xyz");
+	assertEquals (seqData.getMoby_Length().getIntValue(), 123);
+    }
+
+    @Test
+    public void testSetWithSubstitution()
+	throws IOException, MobyException {
+ 	Map<String,String> backups = new HashMap<String,String>();
+ 	backups.put ("mySequenceCollection", "GenericSequence");
+	MobyPackage moby = parse (INPUT_SET, null, backups);
+	MobyObject[] data = moby.getJob(0).getDataSet ("mySequenceCollection");
+	assertEquals (data[0].getMobyTypeName(), "DNASequence");
+	assertEquals (data[1].getMobyTypeName(), "GenericSequence");
+	GenericSequence typedData = (GenericSequence)data[0];
+	assertEquals (typedData.get_SequenceString(), "tatatatata");
+	assertEquals (typedData.getMoby_Length().getIntValue(), 10);
+	typedData = (GenericSequence)data[1];
+	assertEquals (typedData.get_SequenceString(), "");
+	assertEquals (typedData.getMoby_Length().getIntValue(), 5);
+    }
+
+    @Test
+    public void testXref()
+	throws IOException, MobyException {
+	MobyPackage moby = parse (INPUT_XREFS, null, null);
+	assertEquals (moby.getJob(0).getData().getValue().trim(),
+		      "This is a value");
+	MobyXref[] xrefs = moby.getJob(0).getData().getXrefs();
+	assertEquals (xrefs.length, 3);
+	assertTrue  (xrefs[0].isSimpleXref());
+	assertTrue  (xrefs[1].isSimpleXref());
+	assertFalse (xrefs[2].isSimpleXref());
+	assertEquals (xrefs[0].getId(), "At263644");
+	assertEquals (xrefs[0].getNamespace(), "TIGR");
+	assertEquals (xrefs[2].getId(), "yes");
+	assertEquals (xrefs[2].getNamespace(), "LION");
+	assertEquals (xrefs[2].getEvidenceCode(), "IEA");
+
+	MobyProvisionInfo pi = moby.getJob(0).getData().getProvision();
+	assertEquals (pi.getSoftwareName(),    "InterPro");
+	assertEquals (pi.getSoftwareVersion(), "1.2");
+	assertEquals (pi.getSoftwareComment(), "HMMER's not run");
+	assertEquals (pi.getDBName(),    "Genbank/nt");
+	assertEquals (pi.getDBVersion(), "April 8, 2003");
+	assertEquals (pi.getDBComment(), "DBver");
+	assertEquals (pi.getComment(), "this <&>\"<&>\" is a software comment");
+    }
 
 
     /**************************************************************************



From senger at dev.open-bio.org  Mon Mar  3 11:34:17 2008
From: senger at dev.open-bio.org (Martin Senger)
Date: Mon, 3 Mar 2008 06:34:17 -0500
Subject: [MOBY-guts] biomoby commit
Message-ID: <200803031134.m23BYHBX003189@dev.open-bio.org>


senger
Mon Mar  3 06:34:16 EST 2008
Update of /home/repository/moby/moby-live/Java
In directory dev.open-bio.org:/tmp/cvs-serv3170

Modified Files:
	build.xml 
Log Message:
* more work on junit testing and its infrastructure
* removing some compiler warnings from generated data types
* better use of caching in skeleton generator

moby-live/Java build.xml,1.70,1.71
===================================================================
RCS file: /home/repository/moby/moby-live/Java/build.xml,v
retrieving revision 1.70
retrieving revision 1.71
diff -u -r1.70 -r1.71
--- /home/repository/moby/moby-live/Java/build.xml	2008/03/02 12:45:24	1.70
+++ /home/repository/moby/moby-live/Java/build.xml	2008/03/03 11:34:16	1.71
@@ -237,7 +237,7 @@
   <!-- Builds config files and run-time scripts                           -->
   <!-- ================================================================== -->
   <target name="config" depends="init"
-    description="Create all run-time scripts and configuration files.">
+    description="Create all run-time scripts and configuration files">
 
     <property name="my.log4j.properties"
       location="${src.config}/log4j.properties.template"/>
@@ -313,7 +313,7 @@
   <!-- Compiles everything                                                -->
   <!-- ================================================================== -->
   <target name="compile" depends="config"
-    description="Compile all source code (default).">
+    description="Compile all source code (default)">
 
     <condition property="xlint.param" value="-Xlint:unchecked" else="-Xlint:none">
       <istrue value="${compile.warnings}"/>
@@ -361,7 +361,7 @@
   <!-- Copy help files of the Dashboard panels to the docs directory       -->
   <!-- =================================================================== -->
   <target name="docs" depends="compile,cleanapi"
-    description="Generate API documentation.">
+    description="Generate API documentation">
     
     <javadoc
       additionalparam="-quiet"
@@ -417,7 +417,12 @@
   <!-- Clean-up                                                           -->
   <!-- ================================================================== -->
   <target name="clean" depends="cleanapi"
-    description="Remove all generated files.">
+    description="Remove compiled classes and built files">
+    <delete dir="${build.dir}"/>
+  </target>
+  
+  <target name="cleanall" depends="clean,clean-services,clean-datatypes"
+    description="Remove all generated files">
     <delete dir="${build.dir}"/>
   </target>
   
@@ -431,7 +436,7 @@
   <!-- Builds a jar file with jMoby classes                               -->
   <!-- ================================================================== -->
   <target name="jars" depends="compile"
-    description="Create jar files with jMoby classes.">
+    description="Create jar files with jMoby classes">
     
     <property name="released.date" value="${TODAY_SHORT}"/>
     <property name="project.jar"
@@ -462,7 +467,7 @@
    <!-- ================================================================== -->
    <target name="all"
      depends="clean,compile,docs,jars,jar-rdfagent,wardist,bindist-rdfagent"
-     description="Clean, compile, generate docs, then build the rest."/>
+     description="Clean, compile, generate docs, then build the rest"/>
 
    <!-- ================================================================== -->
    <!-- Just for testing...                                                -->



From senger at dev.open-bio.org  Mon Mar  3 11:34:17 2008
From: senger at dev.open-bio.org (Martin Senger)
Date: Mon, 3 Mar 2008 06:34:17 -0500
Subject: [MOBY-guts] biomoby commit
Message-ID: <200803031134.m23BYH5n003255@dev.open-bio.org>


senger
Mon Mar  3 06:34:17 EST 2008
Update of /home/repository/moby/moby-live/Java/src/config/templates
In directory dev.open-bio.org:/tmp/cvs-serv3170/src/config/templates

Modified Files:
	DataTypeTemplate.java MembersHASTemplate.java 
	MethodsHASTemplate.java MethodsHAS_string_Template.java 
Log Message:
* more work on junit testing and its infrastructure
* removing some compiler warnings from generated data types
* better use of caching in skeleton generator

moby-live/Java/src/config/templates DataTypeTemplate.java,1.2,1.3 MembersHASTemplate.java,1.2,1.3 MethodsHASTemplate.java,1.2,1.3 MethodsHAS_string_Template.java,1.2,1.3
===================================================================
RCS file: /home/repository/moby/moby-live/Java/src/config/templates/DataTypeTemplate.java,v
retrieving revision 1.2
retrieving revision 1.3
diff -u -r1.2 -r1.3
--- /home/repository/moby/moby-live/Java/src/config/templates/DataTypeTemplate.java	2005/09/19 08:08:32	1.2
+++ /home/repository/moby/moby-live/Java/src/config/templates/DataTypeTemplate.java	2008/03/03 11:34:16	1.3
@@ -43,10 +43,10 @@
      *
      *************************************************************************/
     public String toString() {
-	StringBuffer buf_I_am_sorry_that_this_produces_a_warning = new StringBuffer();
+	StringBuilder buf_I_am_sorry_that_this_produces_a_warning = new StringBuilder();
 	buf_I_am_sorry_that_this_produces_a_warning.append (super.toString());
 @TO_STRING@
-	return new String (buf_I_am_sorry_that_this_produces_a_warning);
+	return new String (buf_I_am_sorry_that_this_produces_a_warning.toString());
     }
 
     /**************************************************************************

===================================================================
RCS file: /home/repository/moby/moby-live/Java/src/config/templates/MembersHASTemplate.java,v
retrieving revision 1.2
retrieving revision 1.3
diff -u -r1.2 -r1.3
--- /home/repository/moby/moby-live/Java/src/config/templates/MembersHASTemplate.java	2005/09/19 08:08:32	1.2
+++ /home/repository/moby/moby-live/Java/src/config/templates/MembersHASTemplate.java	2008/03/03 11:34:17	1.3
@@ -1,5 +1,5 @@
     /** An article name for a member of this object. */
     public static final String ARTICLE_NAME_ at ESC_UPPER_ARTICLE_NAME@ = "@ARTICLE_NAME@";
     // elements are of type @CHILDTYPE_NAME@
-    protected java.util.Vector @ESC_ARTICLE_NAME@ = new java.util.Vector();
+    protected java.util.Vector<Object> @ESC_ARTICLE_NAME@ = new java.util.Vector<Object>();
 

===================================================================
RCS file: /home/repository/moby/moby-live/Java/src/config/templates/MethodsHASTemplate.java,v
retrieving revision 1.2
retrieving revision 1.3
diff -u -r1.2 -r1.3
--- /home/repository/moby/moby-live/Java/src/config/templates/MethodsHASTemplate.java	2005/09/19 08:08:32	1.2
+++ /home/repository/moby/moby-live/Java/src/config/templates/MethodsHASTemplate.java	2008/03/03 11:34:17	1.3
@@ -19,7 +19,7 @@
      * only one value
      *************************************************************************/
     public void set_ at ESC_ARTICLE_NAME@ (@CHILDTYPE_NAME@[] value) {
-	this. at ESC_ARTICLE_NAME@ = new java.util.Vector();
+	this. at ESC_ARTICLE_NAME@ = new java.util.Vector<Object>();
 	for (int i = 0; i < value.length; i++)
 	    set_ at ESC_ARTICLE_NAME@ (value[i]);
     }

===================================================================
RCS file: /home/repository/moby/moby-live/Java/src/config/templates/MethodsHAS_string_Template.java,v
retrieving revision 1.2
retrieving revision 1.3
diff -u -r1.2 -r1.3
--- /home/repository/moby/moby-live/Java/src/config/templates/MethodsHAS_string_Template.java	2005/09/19 08:08:32	1.2
+++ /home/repository/moby/moby-live/Java/src/config/templates/MethodsHAS_string_Template.java	2008/03/03 11:34:17	1.3
@@ -21,7 +21,7 @@
      * only one value
      *************************************************************************/
     public void set_ at ESC_ARTICLE_NAME@ (String[] value) {
-	this. at ESC_ARTICLE_NAME@ = new java.util.Vector();
+	this. at ESC_ARTICLE_NAME@ = new java.util.Vector<Object>();
 	for (int i = 0; i < value.length; i++)
 	    set_ at ESC_ARTICLE_NAME@ (value[i]);
     }



From senger at dev.open-bio.org  Mon Mar  3 11:34:17 2008
From: senger at dev.open-bio.org (Martin Senger)
Date: Mon, 3 Mar 2008 06:34:17 -0500
Subject: [MOBY-guts] biomoby commit
Message-ID: <200803031134.m23BYHaD003347@dev.open-bio.org>


senger
Mon Mar  3 06:34:17 EST 2008
Update of /home/repository/moby/moby-live/Java/src/main/org/biomoby/shared
In directory dev.open-bio.org:/tmp/cvs-serv3170/src/main/org/biomoby/shared

Modified Files:
	CentralCached.java Utils.java 
Log Message:
* more work on junit testing and its infrastructure
* removing some compiler warnings from generated data types
* better use of caching in skeleton generator

moby-live/Java/src/main/org/biomoby/shared CentralCached.java,1.1,1.2 Utils.java,1.19,1.20
===================================================================
RCS file: /home/repository/moby/moby-live/Java/src/main/org/biomoby/shared/CentralCached.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/CentralCached.java	2008/02/23 13:58:32	1.1
+++ /home/repository/moby/moby-live/Java/src/main/org/biomoby/shared/CentralCached.java	2008/03/03 11:34:17	1.2
@@ -131,4 +131,11 @@
      **************************************************************************/
     String getCacheInfoFormatted (String id);
 
+    /***************************************************************************
+     * Indicate whether the implementtaion really is using a local cache. <p>
+     * 
+     * @return true if a local cache is used
+     **************************************************************************/
+    boolean isUsingCache();
+
 }

===================================================================
RCS file: /home/repository/moby/moby-live/Java/src/main/org/biomoby/shared/Utils.java,v
retrieving revision 1.19
retrieving revision 1.20
diff -u -r1.19 -r1.20
--- /home/repository/moby/moby-live/Java/src/main/org/biomoby/shared/Utils.java	2008/02/28 16:59:47	1.19
+++ /home/repository/moby/moby-live/Java/src/main/org/biomoby/shared/Utils.java	2008/03/03 11:34:17	1.20
@@ -546,8 +546,7 @@
 	    }
 	    
 	} catch (IOException e) {
-	    throw new MobyException("Error creating input stream:", e
-		    .getCause());
+	    throw new MobyException ("Error creating input stream: " + e.toString());
 	}
     }
     



From senger at dev.open-bio.org  Mon Mar  3 11:34:17 2008
From: senger at dev.open-bio.org (Martin Senger)
Date: Mon, 3 Mar 2008 06:34:17 -0500
Subject: [MOBY-guts] biomoby commit
Message-ID: <200803031134.m23BYHPd003207@dev.open-bio.org>


senger
Mon Mar  3 06:34:16 EST 2008
Update of /home/repository/moby/moby-live/Java/docs
In directory dev.open-bio.org:/tmp/cvs-serv3170/docs

Modified Files:
	ChangeLog 
Log Message:
* more work on junit testing and its infrastructure
* removing some compiler warnings from generated data types
* better use of caching in skeleton generator

moby-live/Java/docs ChangeLog,1.85,1.86
===================================================================
RCS file: /home/repository/moby/moby-live/Java/docs/ChangeLog,v
retrieving revision 1.85
retrieving revision 1.86
diff -u -r1.85 -r1.86
--- /home/repository/moby/moby-live/Java/docs/ChangeLog	2008/03/02 12:45:24	1.85
+++ /home/repository/moby/moby-live/Java/docs/ChangeLog	2008/03/03 11:34:16	1.86
@@ -1,3 +1,15 @@
+2008-03-03  Martin Senger  <martin.senger&#64;gmail.com>
+
+	* Added a new method isUsingCache() to the CentralCached
+	interface.
+
+	* Fixed access to the local cache in the MoSeS service generator
+	(the cache was not used in all circumstances).
+
+	* Fixed compilation warnings for MoSeS generated data types.
+
+	* Added constructors to the ExtendedServiceLocator.
+
 2008-03-02  Martin Senger  <martin.senger&#64;gmail.com>
 
 	* Added: new installation task (type: ant install) - it downloads



From senger at dev.open-bio.org  Mon Mar  3 11:34:17 2008
From: senger at dev.open-bio.org (Martin Senger)
Date: Mon, 3 Mar 2008 06:34:17 -0500
Subject: [MOBY-guts] biomoby commit
Message-ID: <200803031134.m23BYH0E003285@dev.open-bio.org>


senger
Mon Mar  3 06:34:17 EST 2008
Update of /home/repository/moby/moby-live/Java/src/main/org/biomoby/client
In directory dev.open-bio.org:/tmp/cvs-serv3170/src/main/org/biomoby/client

Modified Files:
	CentralDigestCachedSimpleImpl.java ExtendedServiceLocator.java 
Log Message:
* more work on junit testing and its infrastructure
* removing some compiler warnings from generated data types
* better use of caching in skeleton generator

moby-live/Java/src/main/org/biomoby/client CentralDigestCachedSimpleImpl.java,1.2,1.3 ExtendedServiceLocator.java,1.2,1.3
===================================================================
RCS file: /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/CentralDigestCachedSimpleImpl.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/CentralDigestCachedSimpleImpl.java	2008/02/23 13:58:32	1.2
+++ /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/CentralDigestCachedSimpleImpl.java	2008/03/03 11:34:17	1.3
@@ -117,6 +117,15 @@
 	return cacheDir;
     }
 
+    /***************************************************************************
+     * Indicate whether the implementtaion really is using a local cache. <p>
+     * 
+     * @return true if a local cache is used
+     **************************************************************************/
+    public boolean isUsingCache() {
+	return getCacheDir() != null;
+    }
+
     /**************************************************************************
      * Removes object groups from the cache. If 'id' is null it
      * removes the whole cache (for that Moby registry this instance

===================================================================
RCS file: /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/ExtendedServiceLocator.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/ExtendedServiceLocator.java	2006/02/20 05:51:09	1.2
+++ /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/ExtendedServiceLocator.java	2008/03/03 11:34:17	1.3
@@ -8,6 +8,8 @@
 
 package org.biomoby.client;
 
+import org.biomoby.shared.MobyService;
+
 /**
  * An extended container allowing to store information how to call a
  * biomoby service using non-biomoby protocols. A typical example
@@ -33,6 +35,20 @@
     boolean loop = false;
 
     /**************************************************************************
+     * Default constructor.
+     *************************************************************************/
+    public ExtendedServiceLocator() {
+	super();
+    }
+
+    /**************************************************************************
+     * Another constructor, seeting also a service.
+     *************************************************************************/
+    public ExtendedServiceLocator (MobyService service) {
+	super (service);
+    }
+
+    /**************************************************************************
      * Set name of a local class that represents (implements) a
      * service. <p>
      *



From senger at dev.open-bio.org  Mon Mar  3 11:34:17 2008
From: senger at dev.open-bio.org (Martin Senger)
Date: Mon, 3 Mar 2008 06:34:17 -0500
Subject: [MOBY-guts] biomoby commit
Message-ID: <200803031134.m23BYHnm003225@dev.open-bio.org>


senger
Mon Mar  3 06:34:16 EST 2008
Update of /home/repository/moby/moby-live/Java/src/Clients
In directory dev.open-bio.org:/tmp/cvs-serv3170/src/Clients

Modified Files:
	MosesGenerators.java 
Log Message:
* more work on junit testing and its infrastructure
* removing some compiler warnings from generated data types
* better use of caching in skeleton generator

moby-live/Java/src/Clients MosesGenerators.java,1.4,1.5
===================================================================
RCS file: /home/repository/moby/moby-live/Java/src/Clients/MosesGenerators.java,v
retrieving revision 1.4
retrieving revision 1.5
diff -u -r1.4 -r1.5
--- /home/repository/moby/moby-live/Java/src/Clients/MosesGenerators.java	2008/02/23 13:58:32	1.4
+++ /home/repository/moby/moby-live/Java/src/Clients/MosesGenerators.java	2008/03/03 11:34:16	1.5
@@ -56,7 +56,6 @@
 	    boolean generateServices = cmd.hasOption ("-s");
 	    boolean nogenerate = cmd.hasOption ("-n");
 	    boolean nographs = cmd.hasOption ("-ng");
-	    String cacheDir = cmd.getParam ("-cacheDir");
 	    String filter = cmd.getParam ("-filter");
 	    String outdir = cmd.getParam ("-outdir");
 	    String dotLocation = cmd.getParam ("-dot");



From senger at dev.open-bio.org  Mon Mar  3 11:34:17 2008
From: senger at dev.open-bio.org (Martin Senger)
Date: Mon, 3 Mar 2008 06:34:17 -0500
Subject: [MOBY-guts] biomoby commit
Message-ID: <200803031134.m23BYHOv003369@dev.open-bio.org>


senger
Mon Mar  3 06:34:17 EST 2008
Update of /home/repository/moby/moby-live/Java/src/main/org/biomoby/shared/datatypes
In directory dev.open-bio.org:/tmp/cvs-serv3170/src/main/org/biomoby/shared/datatypes

Modified Files:
	MapPrimitiveDataTypes.java 
Log Message:
* more work on junit testing and its infrastructure
* removing some compiler warnings from generated data types
* better use of caching in skeleton generator

moby-live/Java/src/main/org/biomoby/shared/datatypes MapPrimitiveDataTypes.java,1.4,1.5
===================================================================
RCS file: /home/repository/moby/moby-live/Java/src/main/org/biomoby/shared/datatypes/MapPrimitiveDataTypes.java,v
retrieving revision 1.4
retrieving revision 1.5
diff -u -r1.4 -r1.5
--- /home/repository/moby/moby-live/Java/src/main/org/biomoby/shared/datatypes/MapPrimitiveDataTypes.java	2008/02/28 05:21:48	1.4
+++ /home/repository/moby/moby-live/Java/src/main/org/biomoby/shared/datatypes/MapPrimitiveDataTypes.java	2008/03/03 11:34:17	1.5
@@ -9,6 +9,7 @@
 package org.biomoby.shared.datatypes;
 
 import org.biomoby.shared.MobyException;
+import java.util.Map;
 import java.util.HashMap;
 import java.util.Iterator;
 import java.util.Map;
@@ -29,7 +30,7 @@
  */
 abstract public class MapPrimitiveDataTypes {
 
-    protected static HashMap type2class = new HashMap();
+    protected static Map<String,String> type2class = new HashMap<String,String>();
     static {
         type2class.put ("Object", "org.biomoby.shared.datatypes.MobyObject");
 
@@ -52,7 +53,7 @@
      *************************************************************************/
     public Class getClass (String dataTypeName)
 	throws MobyException {
-	String className = (String)type2class.get (dataTypeName);
+	String className = type2class.get (dataTypeName);
 	if (className == null) {
 
 	    // a hack: sometimes the 'dataTypeName' is wrong - it is



From senger at dev.open-bio.org  Mon Mar  3 11:34:42 2008
From: senger at dev.open-bio.org (Martin Senger)
Date: Mon, 3 Mar 2008 06:34:42 -0500
Subject: [MOBY-guts] biomoby commit
Message-ID: <200803031134.m23BYg1e003496@dev.open-bio.org>


senger
Mon Mar  3 06:34:42 EST 2008
Update of /home/repository/moby/moby-live/Java/src/test/java/org/biomoby/service
In directory dev.open-bio.org:/tmp/cvs-serv3478/src/test/java/org/biomoby/service

Log Message:
Directory /home/repository/moby/moby-live/Java/src/test/java/org/biomoby/service added to the repository

moby-live/Java/src/test/java/org/biomoby/service - New directory
rcsdiff: /home/repository/moby/moby-live/Java/src/test/java/org/biomoby/service/RCS/-,v: No such file or directory

rcsdiff: /home/repository/moby/moby-live/Java/src/test/java/org/biomoby/service/RCS/New,v: No such file or directory

rcsdiff: /home/repository/moby/moby-live/Java/src/test/java/org/biomoby/service/RCS/directory,v: No such file or directory



From senger at dev.open-bio.org  Mon Mar  3 11:34:17 2008
From: senger at dev.open-bio.org (Martin Senger)
Date: Mon, 3 Mar 2008 06:34:17 -0500
Subject: [MOBY-guts] biomoby commit
Message-ID: <200803031134.m23BYH2Q003417@dev.open-bio.org>


senger
Mon Mar  3 06:34:17 EST 2008
Update of /home/repository/moby/moby-live/Java/src/test/java/org/biomoby/shared/parser
In directory dev.open-bio.org:/tmp/cvs-serv3170/src/test/java/org/biomoby/shared/parser

Modified Files:
	MobyParserTest.java 
Log Message:
* more work on junit testing and its infrastructure
* removing some compiler warnings from generated data types
* better use of caching in skeleton generator

moby-live/Java/src/test/java/org/biomoby/shared/parser MobyParserTest.java,1.3,1.4
===================================================================
RCS file: /home/repository/moby/moby-live/Java/src/test/java/org/biomoby/shared/parser/MobyParserTest.java,v
retrieving revision 1.3
retrieving revision 1.4
diff -u -r1.3 -r1.4
--- /home/repository/moby/moby-live/Java/src/test/java/org/biomoby/shared/parser/MobyParserTest.java	2008/03/03 03:11:27	1.3
+++ /home/repository/moby/moby-live/Java/src/test/java/org/biomoby/shared/parser/MobyParserTest.java	2008/03/03 11:34:17	1.4
@@ -57,22 +57,22 @@
     public void testNormal()
 	throws IOException, MobyException {
 	MobyPackage moby = parse (INPUT_1, null, null);
-	assertEquals (moby.getServiceNotes(), "freetext notes here");
-	assertEquals (moby.getAuthority(), "http://\"me\".<org>&");
+	assertEquals ("freetext notes here", moby.getServiceNotes());
+	assertEquals ("http://\"me\".<org>&", moby.getAuthority());
 	MobyJob[] jobs = moby.getJobs();
-	assertEquals (jobs.length, 4);
-	assertEquals (jobs[0].getId(), "a1");
+	assertEquals (4, jobs.length);
+	assertEquals ("a1", jobs[0].getId());
 	MobyObject data = jobs[0].getData();
-	assertEquals (data.getMobyTypeName(), "NucleotideSequence");
-	assertEquals (data.getName(), "");
-	assertEquals (data.getNamespace(), "DragonDB_Allele");
-	assertEquals (data.getId(), "chlorae");
+	assertEquals ("NucleotideSequence", data.getMobyTypeName());
+	assertEquals ("", data.getName());
+	assertEquals ("DragonDB_Allele", data.getNamespace());
+	assertEquals ("chlorae", data.getId());
 	assertFalse (data.isPrimitiveType());
-	assertEquals (data.getClass().getName(), "org.biomoby.shared.datatypes.NucleotideSequence");
+	assertEquals ("org.biomoby.shared.datatypes.NucleotideSequence", data.getClass().getName());
 	NucleotideSequence typedData = (NucleotideSequence)jobs[0].getData();
-	assertEquals (typedData.get_SequenceString(), ">tata\ntatata");
-	assertEquals (typedData.getMoby_SequenceString().getValue(), ">tata\ntatata");
-	assertEquals (typedData.getMoby_Length().getIntValue(), 10);
+	assertEquals (">tata\ntatata", typedData.get_SequenceString());
+	assertEquals (">tata\ntatata", typedData.getMoby_SequenceString().getValue());
+	assertEquals (10, typedData.getMoby_Length().getIntValue());
     }
 
      @Test
@@ -80,8 +80,8 @@
  	throws IOException, MobyException {
 	MobyPackage moby = parse (INPUT_2, "DNASequence", null);
 	DNASequence typedData = (DNASequence)moby.getJob(0).getData ("myDNA");
-	assertEquals (typedData.get_SequenceString(), "abcd");
-	assertEquals (typedData.getMoby_Length().getIntValue(), 12);
+	assertEquals ("abcd", typedData.get_SequenceString());
+	assertEquals (12, typedData.getMoby_Length().getIntValue());
      }
 
     @Test
@@ -90,18 +90,18 @@
 	MobyPackage moby = parse (INPUT_3, "BasicGFF3MultiFeature", null);
 	BasicGFF3MultiFeature typedData = (BasicGFF3MultiFeature)moby.getJob(0).getData ("myPairs");
 	BasicGFF3SequenceFeature[] data = typedData.getMoby_BasicGFF3SequenceFeature();
-	assertEquals (data.length, 1);
-	assertEquals (data[0].getMoby_start().getIntValue(), 1);
-	assertEquals (data[0].getMoby_score().getFloatValue(), 12.34, 0);
-	assertEquals (data[0].get_phase(), "b");
+	assertEquals (1, data.length);
+	assertEquals (1, data[0].getMoby_start().getIntValue());
+	assertEquals (12.34, data[0].getMoby_score().getFloatValue(), 0.01);
+	assertEquals ("b", data[0].get_phase());
 	multi_key_value_pair[] pairs = data[0].getMoby_column9_tag_value();
-	assertEquals (pairs.length, 2);
-	assertEquals (pairs[0].get_key(), "key1");
-	assertEquals (pairs[0].get_the_value().length, 3);
-	assertEquals (pairs[0].get_the_value()[0], "value1");
-	assertEquals (pairs[1].get_key(), "key2");
-	assertEquals (pairs[1].get_the_value().length, 1);
-	assertEquals (pairs[1].get_the_value()[0], "valueA");
+	assertEquals (2, pairs.length);
+	assertEquals ("key1", pairs[0].get_key());
+	assertEquals (3, pairs[0].get_the_value().length);
+	assertEquals ("value1", pairs[0].get_the_value()[0]);
+	assertEquals ("key2", pairs[1].get_key());
+	assertEquals (1, pairs[1].get_the_value().length);
+	assertEquals ("valueA", pairs[1].get_the_value()[0]);
     }
 
     @Test
@@ -113,18 +113,18 @@
 	MobyPackage moby = parse (INPUT_4, null, backups);
 	BasicGFF3MultiFeature typedData = (BasicGFF3MultiFeature)moby.getJob(0).getData ("myPairs");
 	BasicGFF3SequenceFeature[] data = typedData.getMoby_BasicGFF3SequenceFeature();
-	assertEquals (data.length, 1);
-	assertEquals (data[0].getMoby_start().getIntValue(), 1);
-	assertEquals (data[0].getMoby_score().getFloatValue(), 12.34, 0);
-	assertEquals (data[0].get_phase(), "b");
+	assertEquals (1, data.length);
+	assertEquals (1, data[0].getMoby_start().getIntValue());
+	assertEquals (12.34, data[0].getMoby_score().getFloatValue(), 0.01);
+	assertEquals ("b", data[0].get_phase());
 	multi_key_value_pair[] pairs = data[0].getMoby_column9_tag_value();
-	assertEquals (pairs.length, 1);
-	assertEquals (pairs[0].get_key(), "key1");
-	assertEquals (pairs[0].get_the_value().length, 1);
-	assertEquals (pairs[0].get_the_value()[0], "value1");
+	assertEquals (1, pairs.length);
+	assertEquals ("key1", pairs[0].get_key());
+	assertEquals (1, pairs[0].get_the_value().length);
+	assertEquals ("value1", pairs[0].get_the_value()[0]);
 	DNASequence seqData = (DNASequence)moby.getJob(0).getData ("mySeq");
-	assertEquals (seqData.get_SequenceString(), "xyz");
-	assertEquals (seqData.getMoby_Length().getIntValue(), 123);
+	assertEquals ("xyz", seqData.get_SequenceString());
+	assertEquals (123, seqData.getMoby_Length().getIntValue());
     }
 
     @Test
@@ -134,41 +134,40 @@
  	backups.put ("mySequenceCollection", "GenericSequence");
 	MobyPackage moby = parse (INPUT_SET, null, backups);
 	MobyObject[] data = moby.getJob(0).getDataSet ("mySequenceCollection");
-	assertEquals (data[0].getMobyTypeName(), "DNASequence");
-	assertEquals (data[1].getMobyTypeName(), "GenericSequence");
+	assertEquals ("DNASequence", data[0].getMobyTypeName());
+	assertEquals ("GenericSequence", data[1].getMobyTypeName());
 	GenericSequence typedData = (GenericSequence)data[0];
-	assertEquals (typedData.get_SequenceString(), "tatatatata");
-	assertEquals (typedData.getMoby_Length().getIntValue(), 10);
+	assertEquals ("tatatatata", typedData.get_SequenceString());
+	assertEquals (10, typedData.getMoby_Length().getIntValue());
 	typedData = (GenericSequence)data[1];
-	assertEquals (typedData.get_SequenceString(), "");
-	assertEquals (typedData.getMoby_Length().getIntValue(), 5);
+	assertEquals ("", typedData.get_SequenceString());
+	assertEquals (5, typedData.getMoby_Length().getIntValue());
     }
 
     @Test
     public void testXref()
 	throws IOException, MobyException {
 	MobyPackage moby = parse (INPUT_XREFS, null, null);
-	assertEquals (moby.getJob(0).getData().getValue().trim(),
-		      "This is a value");
+	assertEquals ("This is a value", moby.getJob(0).getData().getValue().trim());
 	MobyXref[] xrefs = moby.getJob(0).getData().getXrefs();
-	assertEquals (xrefs.length, 3);
+	assertEquals (3, xrefs.length);
 	assertTrue  (xrefs[0].isSimpleXref());
 	assertTrue  (xrefs[1].isSimpleXref());
 	assertFalse (xrefs[2].isSimpleXref());
-	assertEquals (xrefs[0].getId(), "At263644");
-	assertEquals (xrefs[0].getNamespace(), "TIGR");
-	assertEquals (xrefs[2].getId(), "yes");
-	assertEquals (xrefs[2].getNamespace(), "LION");
-	assertEquals (xrefs[2].getEvidenceCode(), "IEA");
+	assertEquals ("At263644", xrefs[0].getId());
+	assertEquals ("TIGR", xrefs[0].getNamespace());
+	assertEquals ("yes", xrefs[2].getId());
+	assertEquals ("LION", xrefs[2].getNamespace());
+	assertEquals ("IEA", xrefs[2].getEvidenceCode());
 
 	MobyProvisionInfo pi = moby.getJob(0).getData().getProvision();
-	assertEquals (pi.getSoftwareName(),    "InterPro");
-	assertEquals (pi.getSoftwareVersion(), "1.2");
-	assertEquals (pi.getSoftwareComment(), "HMMER's not run");
-	assertEquals (pi.getDBName(),    "Genbank/nt");
-	assertEquals (pi.getDBVersion(), "April 8, 2003");
-	assertEquals (pi.getDBComment(), "DBver");
-	assertEquals (pi.getComment(), "this <&>\"<&>\" is a software comment");
+	assertEquals ("InterPro", pi.getSoftwareName());
+	assertEquals ("1.2", pi.getSoftwareVersion());
+	assertEquals ("HMMER's not run", pi.getSoftwareComment());
+	assertEquals ("Genbank/nt", pi.getDBName());
+	assertEquals ("April 8, 2003", pi.getDBVersion());
+	assertEquals ("DBver", pi.getDBComment());
+	assertEquals ("this <&>\"<&>\" is a software comment", pi.getComment());
     }
 
 



From senger at dev.open-bio.org  Mon Mar  3 11:34:17 2008
From: senger at dev.open-bio.org (Martin Senger)
Date: Mon, 3 Mar 2008 06:34:17 -0500
Subject: [MOBY-guts] biomoby commit
Message-ID: <200803031134.m23BYHrX003395@dev.open-bio.org>


senger
Mon Mar  3 06:34:17 EST 2008
Update of /home/repository/moby/moby-live/Java/src/samples/org/jmoby/tutorial/service
In directory dev.open-bio.org:/tmp/cvs-serv3170/src/samples/org/jmoby/tutorial/service

Modified Files:
	ConcatSequenceSetImpl.java ConcatSequencesImpl.java 
Log Message:
* more work on junit testing and its infrastructure
* removing some compiler warnings from generated data types
* better use of caching in skeleton generator

moby-live/Java/src/samples/org/jmoby/tutorial/service ConcatSequenceSetImpl.java,1.1,1.2 ConcatSequencesImpl.java,1.1,1.2
===================================================================
RCS file: /home/repository/moby/moby-live/Java/src/samples/org/jmoby/tutorial/service/ConcatSequenceSetImpl.java,v
retrieving revision 1.1
retrieving revision 1.2
diff -u -r1.1 -r1.2
--- /home/repository/moby/moby-live/Java/src/samples/org/jmoby/tutorial/service/ConcatSequenceSetImpl.java	2008/03/02 12:49:33	1.1
+++ /home/repository/moby/moby-live/Java/src/samples/org/jmoby/tutorial/service/ConcatSequenceSetImpl.java	2008/03/03 11:34:17	1.2
@@ -72,7 +72,7 @@
 	result.set_SequenceString (onlyLength ? "" : buf.toString());
 	result.set_Length (new MobyInteger (totalLength));
 
-	response.setData (result);
+	set_result (response, result);
     }
 
 }

===================================================================
RCS file: /home/repository/moby/moby-live/Java/src/samples/org/jmoby/tutorial/service/ConcatSequencesImpl.java,v
retrieving revision 1.1
retrieving revision 1.2
diff -u -r1.1 -r1.2
--- /home/repository/moby/moby-live/Java/src/samples/org/jmoby/tutorial/service/ConcatSequencesImpl.java	2008/03/02 12:49:33	1.1
+++ /home/repository/moby/moby-live/Java/src/samples/org/jmoby/tutorial/service/ConcatSequencesImpl.java	2008/03/03 11:34:17	1.2
@@ -69,7 +69,7 @@
 	result.set_SequenceString (onlyLength ? "" : buf.toString());
 	result.set_Length (new MobyInteger (totalLength));
 
-	response.setData (result);
+	set_result (response, result);
     }
 
     /**************************************************************************



From senger at dev.open-bio.org  Mon Mar  3 11:34:17 2008
From: senger at dev.open-bio.org (Martin Senger)
Date: Mon, 3 Mar 2008 06:34:17 -0500
Subject: [MOBY-guts] biomoby commit
Message-ID: <200803031134.m23BYHoc003431@dev.open-bio.org>


senger
Mon Mar  3 06:34:17 EST 2008
Update of /home/repository/moby/moby-live/Java/src/test/junit-resources
In directory dev.open-bio.org:/tmp/cvs-serv3170/src/test/junit-resources

Added Files:
	ConcatSequenceSet-input.xml 
Log Message:
* more work on junit testing and its infrastructure
* removing some compiler warnings from generated data types
* better use of caching in skeleton generator

moby-live/Java/src/test/junit-resources ConcatSequenceSet-input.xml,NONE,1.1


From senger at dev.open-bio.org  Mon Mar  3 11:34:17 2008
From: senger at dev.open-bio.org (Martin Senger)
Date: Mon, 3 Mar 2008 06:34:17 -0500
Subject: [MOBY-guts] biomoby commit
Message-ID: <200803031134.m23BYHjA003321@dev.open-bio.org>


senger
Mon Mar  3 06:34:17 EST 2008
Update of /home/repository/moby/moby-live/Java/src/main/org/biomoby/service/generator
In directory dev.open-bio.org:/tmp/cvs-serv3170/src/main/org/biomoby/service/generator

Modified Files:
	DataTypesGenerator.java Generator.java ServicesGenerator.java 
Log Message:
* more work on junit testing and its infrastructure
* removing some compiler warnings from generated data types
* better use of caching in skeleton generator

moby-live/Java/src/main/org/biomoby/service/generator DataTypesGenerator.java,1.6,1.7 Generator.java,1.5,1.6 ServicesGenerator.java,1.7,1.8
===================================================================
RCS file: /home/repository/moby/moby-live/Java/src/main/org/biomoby/service/generator/DataTypesGenerator.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/service/generator/DataTypesGenerator.java	2008/03/02 12:45:26	1.6
+++ /home/repository/moby/moby-live/Java/src/main/org/biomoby/service/generator/DataTypesGenerator.java	2008/03/03 11:34:17	1.7
@@ -18,6 +18,8 @@
 import org.biomoby.client.FilterDataTypes;
 import org.biomoby.client.Graphviz;
 
+import org.apache.commons.lang.BooleanUtils;
+
 import java.util.Properties;
 import java.util.Map;
 import java.util.HashMap;
@@ -171,7 +173,7 @@
     public void generate (Properties props)
 	throws MobyException {
 
-	verbose = isTrue (props.get (GPROP_VERBOSE));
+	verbose = BooleanUtils.toBoolean (props.getProperty (GPROP_VERBOSE));
 
 	Pattern pattern = null;
 	String filter = props.getProperty (GPROP_FILTER);
@@ -245,7 +247,7 @@
 	throws MobyException {
 
 	String dataTypeName = Utils.pureName (dataType.getName());
-	if (isTrue (props.get (GPROP_NOGEN))) {
+	if (BooleanUtils.toBoolean (props.getProperty (GPROP_NOGEN))) {
 	    System.out.println (dataTypeName);
 	    return;
 	}
@@ -459,7 +461,8 @@
 				   MobyDataType[] allDataTypes,
 				   StringBuffer spaceForImageMap) {
 
-	if (isTrue (props.get (GPROP_NOGRAPHS))) return false;
+	if (BooleanUtils.toBoolean (props.getProperty (GPROP_NOGRAPHS)))
+	    return false;
 
 	MobyDataType[] subTree = FilterDataTypes.getSubTree (dataType,
 							     allDataTypes);

===================================================================
RCS file: /home/repository/moby/moby-live/Java/src/main/org/biomoby/service/generator/Generator.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/service/generator/Generator.java	2008/03/02 12:45:26	1.5
+++ /home/repository/moby/moby-live/Java/src/main/org/biomoby/service/generator/Generator.java	2008/03/03 11:34:17	1.6
@@ -17,6 +17,8 @@
 import org.biomoby.shared.Utils;
 import org.biomoby.client.CentralDigestCachedImpl;
 
+import org.apache.commons.lang.BooleanUtils;
+
 import java.util.Properties;
 import java.util.Map;
 import java.util.regex.Pattern;
@@ -220,13 +222,6 @@
     }
 
     /*************************************************************************
-     * Read a boolean property...
-     *************************************************************************/
-    protected static boolean isTrue (Object value) {
-	return new Boolean ((String)value).booleanValue();
-    }
-
-    /*************************************************************************
      * Format who generated this...
      *************************************************************************/
     protected static String getSignature() {
@@ -293,7 +288,8 @@
      *************************************************************************/
     protected void makeDirForGraphs (File outputDir, Properties props) {
 
-	if (isTrue (props.get (GPROP_NOGRAPHS))) return;
+	if (BooleanUtils.toBoolean (props.getProperty (GPROP_NOGRAPHS)))
+	    return;
 
 	File graphDir = new File (outputDir, "doc-files");
 	if (! graphDir.exists()) {

===================================================================
RCS file: /home/repository/moby/moby-live/Java/src/main/org/biomoby/service/generator/ServicesGenerator.java,v
retrieving revision 1.7
retrieving revision 1.8
diff -u -r1.7 -r1.8
--- /home/repository/moby/moby-live/Java/src/main/org/biomoby/service/generator/ServicesGenerator.java	2008/03/02 12:45:26	1.7
+++ /home/repository/moby/moby-live/Java/src/main/org/biomoby/service/generator/ServicesGenerator.java	2008/03/03 11:34:17	1.8
@@ -27,6 +27,7 @@
 
 import org.tulsoft.tools.servlets.Html;
 import org.apache.commons.lang.StringUtils;
+import org.apache.commons.lang.BooleanUtils;
 
 import java.util.Properties;
 import java.util.Iterator;
@@ -192,7 +193,7 @@
     public void generate (Properties props)
 	throws MobyException {
 
-	verbose = isTrue (props.get (GPROP_VERBOSE));
+	verbose = BooleanUtils.toBoolean (props.getProperty (GPROP_VERBOSE));
 
 	// compile patterns for filtering by service and authority names
 	Pattern wantedService = null;
@@ -225,7 +226,8 @@
 	// conditionally, read all data types (also from a registry)
 	MobyDataType[] allDataTypes = null;
 	MobyService[] allServices = null;
-	if (! isTrue (props.get (GPROP_NOGRAPHS))) {
+	if (worker.isUsingCache() ||
+	    ! BooleanUtils.toBoolean (props.getProperty (GPROP_NOGRAPHS))) {
 	    if (verbose)
 		System.out.println ("Reading data type definitions...");
 	    allDataTypes = worker.getDataTypes();
@@ -277,7 +279,7 @@
 	    return;
 	}
 
-	if (isTrue (props.get (GPROP_NOGEN))) {
+	if (BooleanUtils.toBoolean (props.getProperty (GPROP_NOGEN))) {
 	    System.out.println (service.toShortString());
 	    return;
 	}
@@ -569,9 +571,9 @@
     /**************************************************************************
      * Return services that match 'patternService'. You can take an
      * advantage of already collected all services in 'allServices' if
-     * it is not null (it is null if graphs are not required,
-     * BTW). If it is null, however, do a normal way: go to a registry
-     * using given 'worker'.
+     * it is not null (it is null if a local cache is not used, or if
+     * graphs are not required). If it is null, however, do a normal
+     * way: go to a registry using given 'worker'.
      *
      * Note that 'patternService' has filled only service and
      * authority name (and both are guaranteed not to be null), so
@@ -581,8 +583,8 @@
 					 CentralCached worker,
 					 MobyService[] allServices)
 	throws MobyException {
-	if (allServices == null)
-	    return worker.findService (patternService);
+ 	if (allServices == null)
+ 	    return worker.findService (patternService);
 	Vector<MobyService> v = new Vector<MobyService>();
 	String name = patternService.getName();
 	String auth = patternService.getAuthority();
@@ -612,7 +614,10 @@
 				   MobyService[] allServices,
 				   MobyDataType[] allDataTypes) {
 
-	if (isTrue (props.get (GPROP_NOGRAPHS))) return false;
+	if (BooleanUtils.toBoolean (props.getProperty (GPROP_NOGRAPHS)))
+	    return false;
+	if (allServices == null || allDataTypes == null)
+	    return false;
 
 	ServicesEdge[] edges
 	    = ServiceConnections.build (allDataTypes, allServices);



From senger at dev.open-bio.org  Mon Mar  3 11:34:17 2008
From: senger at dev.open-bio.org (Martin Senger)
Date: Mon, 3 Mar 2008 06:34:17 -0500
Subject: [MOBY-guts] biomoby commit
Message-ID: <200803031134.m23BYHf2003455@dev.open-bio.org>


senger
Mon Mar  3 06:34:17 EST 2008
Update of /home/repository/moby/moby-live/Java/xmls
In directory dev.open-bio.org:/tmp/cvs-serv3170/xmls

Modified Files:
	junit.xml 
Log Message:
* more work on junit testing and its infrastructure
* removing some compiler warnings from generated data types
* better use of caching in skeleton generator

moby-live/Java/xmls junit.xml,1.3,1.4
===================================================================
RCS file: /home/repository/moby/moby-live/Java/xmls/junit.xml,v
retrieving revision 1.3
retrieving revision 1.4
diff -u -r1.3 -r1.4
--- /home/repository/moby/moby-live/Java/xmls/junit.xml	2008/03/02 12:45:27	1.3
+++ /home/repository/moby/moby-live/Java/xmls/junit.xml	2008/03/03 11:34:17	1.4
@@ -15,7 +15,8 @@
 <!-- The main entry point to junit testing. If tests are successful,    -->
 <!-- it does nothing. It only reports when a failure occured.           -->
 <!-- ================================================================== -->
-<target name="test-junit" if="test.failure" depends="do-junit,do-junit-2"
+<target name="test-junit" if="test.failure"
+  depends="samples,compile-tests,do-junit,do-junit-2"
   description="Run the junit test cases">
   <fail message="There were test failures." />
 </target>
@@ -34,6 +35,7 @@
 </target>
   
 <!-- this is the core: here is the testing done -->
+<!-- [ maintained by Paul Gordon ]              -->
 <target name="do-junit" if="junit.is.present" depends="junit-present">
 
   <junit
@@ -73,7 +75,11 @@
 
 <!-- this is the core: here is the testing done -->
 <!-- (put here only relatively fast tests)      -->
-<target name="do-junit-2" if="junit.is.present" depends="junit-present,compile-tests">
+<!-- [ maintained by Martin Senger ]            -->
+<target name="do-junit-2" if="junit.is.present" depends="junit-present,samples,dojunit2">
+</target>
+
+<target name="dojunit2"  if="junit.is.present" depends="compile-tests">
 
   <junit
     printsummary="yes"
@@ -85,6 +91,9 @@
       <path refid="dependency.classpath"/>
       <pathelement path="${classes.datatypes}"/>
       <pathelement path="${build.test}"/>
+      <pathelement path="${classes.datatypes}"/>
+      <pathelement path="${classes.skeletons}"/>
+      <pathelement path="${classes.samples}"/>
       <pathelement path="${junit.resources}"/>
     </classpath>
     <jvmarg value="-Dlog4j.configuration=file:${log4j.configuration}"/>
@@ -92,6 +101,7 @@
     <batchtest todir="${test.report.dir}">
       <fileset dir="${build.test}">
         <include name="**/MobyParserTest.*"/>
+        <include name="**/ServicesTest.*"/>
       </fileset>
       <!--      <fileset dir="${build.test}" includes="**/*Test.*" /> -->
     </batchtest>



From senger at dev.open-bio.org  Mon Mar  3 11:35:07 2008
From: senger at dev.open-bio.org (Martin Senger)
Date: Mon, 3 Mar 2008 06:35:07 -0500
Subject: [MOBY-guts] biomoby commit
Message-ID: <200803031135.m23BZ7qc003550@dev.open-bio.org>


senger
Mon Mar  3 06:35:07 EST 2008
Update of /home/repository/moby/moby-live/Java/src/test/java/org/biomoby/service
In directory dev.open-bio.org:/tmp/cvs-serv3535/src/test/java/org/biomoby/service

Added Files:
	ServicesTest.java 
Log Message:

moby-live/Java/src/test/java/org/biomoby/service ServicesTest.java,NONE,1.1


From senger at dev.open-bio.org  Mon Mar  3 11:54:28 2008
From: senger at dev.open-bio.org (Martin Senger)
Date: Mon, 3 Mar 2008 06:54:28 -0500
Subject: [MOBY-guts] biomoby commit
Message-ID: <200803031154.m23BsS3q003591@dev.open-bio.org>


senger
Mon Mar  3 06:54:28 EST 2008
Update of /home/repository/moby/moby-live/Java/src/main/org/biomoby/client
In directory dev.open-bio.org:/tmp/cvs-serv3572/src/main/org/biomoby/client

Modified Files:
	CentralImpl.java 
Log Message:
Fixing deprecation warnings

moby-live/Java/src/main/org/biomoby/client CentralImpl.java,1.54,1.55
===================================================================
RCS file: /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/CentralImpl.java,v
retrieving revision 1.54
retrieving revision 1.55
diff -u -r1.54 -r1.55
--- /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/CentralImpl.java	2008/03/02 12:45:25	1.54
+++ /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/CentralImpl.java	2008/03/03 11:54:28	1.55
@@ -952,6 +952,8 @@
 
     /**************************************************************************
      *
+     * @deprecated Replaced by {@link #getFullNamespaces} that gives
+     * more information for the same price. <p>
      *************************************************************************/
     public Map getNamespaces()
 	throws MobyException {



From senger at dev.open-bio.org  Mon Mar  3 11:54:28 2008
From: senger at dev.open-bio.org (Martin Senger)
Date: Mon, 3 Mar 2008 06:54:28 -0500
Subject: [MOBY-guts] biomoby commit
Message-ID: <200803031154.m23BsSYK003611@dev.open-bio.org>


senger
Mon Mar  3 06:54:28 EST 2008
Update of /home/repository/moby/moby-live/Java/src/main/org/biomoby/registry/Central
In directory dev.open-bio.org:/tmp/cvs-serv3572/src/main/org/biomoby/registry/Central

Modified Files:
	RegistryImpl.java 
Log Message:
Fixing deprecation warnings

moby-live/Java/src/main/org/biomoby/registry/Central RegistryImpl.java,1.3,1.4
===================================================================
RCS file: /home/repository/moby/moby-live/Java/src/main/org/biomoby/registry/Central/RegistryImpl.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/registry/Central/RegistryImpl.java	2006/04/20 15:17:43	1.3
+++ /home/repository/moby/moby-live/Java/src/main/org/biomoby/registry/Central/RegistryImpl.java	2008/03/03 11:54:28	1.4
@@ -83,8 +83,9 @@
 		return null;
 	}
 
-	/* (non-Javadoc)
+         /**
 	 * @see org.biomoby.registry.Central.Registry#deregisterService(java.lang.String)
+	 * @deprecated
 	 */
 	public String deregisterService(String deregistrationObject) {
 		Document doc = null;



From senger at dev.open-bio.org  Mon Mar  3 11:54:28 2008
From: senger at dev.open-bio.org (Martin Senger)
Date: Mon, 3 Mar 2008 06:54:28 -0500
Subject: [MOBY-guts] biomoby commit
Message-ID: <200803031154.m23BsSCw003631@dev.open-bio.org>


senger
Mon Mar  3 06:54:28 EST 2008
Update of /home/repository/moby/moby-live/Java/src/main/org/biomoby/shared
In directory dev.open-bio.org:/tmp/cvs-serv3572/src/main/org/biomoby/shared

Modified Files:
	MobySecondaryData.java 
Log Message:
Fixing deprecation warnings

moby-live/Java/src/main/org/biomoby/shared MobySecondaryData.java,1.11,1.12
===================================================================
RCS file: /home/repository/moby/moby-live/Java/src/main/org/biomoby/shared/MobySecondaryData.java,v
retrieving revision 1.11
retrieving revision 1.12
diff -u -r1.11 -r1.12
--- /home/repository/moby/moby-live/Java/src/main/org/biomoby/shared/MobySecondaryData.java	2008/01/07 22:11:36	1.11
+++ /home/repository/moby/moby-live/Java/src/main/org/biomoby/shared/MobySecondaryData.java	2008/03/03 11:54:28	1.12
@@ -136,9 +136,6 @@
 	defaultValue = (value == null ? "" : value);
     }
 
-    /**
-     * @deprecated Use {@link #getMinValue} instead.
-     */
     public int getMinimumValue() {
 	try {
 	    return Integer.valueOf (minimumValue).intValue();
@@ -162,9 +159,6 @@
 	minimumValue = (value == null ? "" : value);
     }
 
-    /**
-     * @deprecated Use {@link #getMaxValue} instead.
-     */
     public int getMaximumValue() {
 	try {
 	    return Integer.valueOf (maximumValue).intValue();



From senger at dev.open-bio.org  Mon Mar  3 11:54:28 2008
From: senger at dev.open-bio.org (Martin Senger)
Date: Mon, 3 Mar 2008 06:54:28 -0500
Subject: [MOBY-guts] biomoby commit
Message-ID: <200803031154.m23BsS4k003655@dev.open-bio.org>


senger
Mon Mar  3 06:54:28 EST 2008
Update of /home/repository/moby/moby-live/Java/src/main/org/biomoby/shared/schema
In directory dev.open-bio.org:/tmp/cvs-serv3572/src/main/org/biomoby/shared/schema

Modified Files:
	MainGUI.java 
Log Message:
Fixing deprecation warnings

moby-live/Java/src/main/org/biomoby/shared/schema MainGUI.java,1.2,1.3
===================================================================
RCS file: /home/repository/moby/moby-live/Java/src/main/org/biomoby/shared/schema/MainGUI.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/schema/MainGUI.java	2005/09/06 21:29:50	1.2
+++ /home/repository/moby/moby-live/Java/src/main/org/biomoby/shared/schema/MainGUI.java	2008/03/03 11:54:28	1.3
@@ -26,7 +26,7 @@
 		
 		
 		frame.addWindowListener(new GenericWindowListener());
-		frame.show();
+		frame.setVisible (true);
 	}
 
 }



From senger at dev.open-bio.org  Mon Mar  3 14:11:08 2008
From: senger at dev.open-bio.org (Martin Senger)
Date: Mon, 3 Mar 2008 09:11:08 -0500
Subject: [MOBY-guts] biomoby commit
Message-ID: <200803031411.m23EB8nL004089@dev.open-bio.org>


senger
Mon Mar  3 09:11:08 EST 2008
Update of /home/repository/moby/moby-live/Java/src/webapps
In directory dev.open-bio.org:/tmp/cvs-serv4034/src/webapps

Modified Files:
	remote.deploy.build.xml.template 
Log Message:
Remote deployment scripts fixed.

moby-live/Java/src/webapps remote.deploy.build.xml.template,1.4,1.5
===================================================================
RCS file: /home/repository/moby/moby-live/Java/src/webapps/remote.deploy.build.xml.template,v
retrieving revision 1.4
retrieving revision 1.5
diff -u -r1.4 -r1.5
--- /home/repository/moby/moby-live/Java/src/webapps/remote.deploy.build.xml.template	2008/02/21 13:19:34	1.4
+++ /home/repository/moby/moby-live/Java/src/webapps/remote.deploy.build.xml.template	2008/03/03 14:11:08	1.5
@@ -18,6 +18,7 @@
    <property name="wsdd.undeploy.dir"  location="${project.home}/undeploy-wsdd"/>
    <property name="lib.dir"            location="${project.home}/lib"/>
    <property name="lib.dir.2"          location="${project.home}/lib2"/>
+   <property name="classes"            location="${project.home}/classes"/>
 
    <!-- Tomcat/Axis/servlets related properties -->
    <property name="tomcat.home"        value="@TOMCAT_HOME@"/>
@@ -153,12 +154,17 @@
        <fileset dir="${lib.dir.2}" includes="*.jar"/>
      </foreach>
 
-     <!-- copy jar files to Tomcat/Axis -->
+     <!-- copy jar files to Tomcat/Axis - lib directory -->
      <copy todir="${deploy.axis.dir}/lib">
        <fileset dir="${lib.dir}"/>
        <fileset dir="${lib.dir.2}"/>
      </copy>
 
+     <!-- copy other files to Tomcat/Axis - classes directory -->
+     <copy todir="${deploy.axis.dir}/classes">
+       <fileset dir="${classes}"/>
+     </copy>
+
    </target>
 
    <!-- parameter: ${jarfile.name} -->



From senger at dev.open-bio.org  Mon Mar  3 14:11:08 2008
From: senger at dev.open-bio.org (Martin Senger)
Date: Mon, 3 Mar 2008 09:11:08 -0500
Subject: [MOBY-guts] biomoby commit
Message-ID: <200803031411.m23EB8fG004071@dev.open-bio.org>


senger
Mon Mar  3 09:11:08 EST 2008
Update of /home/repository/moby/moby-live/Java/src/samples/org/jmoby/tutorial/service
In directory dev.open-bio.org:/tmp/cvs-serv4034/src/samples/org/jmoby/tutorial/service

Modified Files:
	TestServiceNotesImpl.java 
Log Message:
Remote deployment scripts fixed.

moby-live/Java/src/samples/org/jmoby/tutorial/service TestServiceNotesImpl.java,1.3,1.4
===================================================================
RCS file: /home/repository/moby/moby-live/Java/src/samples/org/jmoby/tutorial/service/TestServiceNotesImpl.java,v
retrieving revision 1.3
retrieving revision 1.4
diff -u -r1.3 -r1.4
--- /home/repository/moby/moby-live/Java/src/samples/org/jmoby/tutorial/service/TestServiceNotesImpl.java	2007/05/29 03:51:46	1.3
+++ /home/repository/moby/moby-live/Java/src/samples/org/jmoby/tutorial/service/TestServiceNotesImpl.java	2008/03/03 14:11:08	1.4
@@ -36,9 +36,11 @@
 			   MobyPackage outputContext)
 	throws MobyException {
 	MobyDateTime input = get_input_date (request);
-	String date = input.getValue();
-	outputContext.addException (ServiceException.info ("Input date was " + date),
-				    request);
+	if (input != null) {
+	    String date = input.getValue();
+	    outputContext.addException (ServiceException.info ("Input date was " + date),
+					request);
+	}
 
 	StringBuilder buf = new StringBuilder();
 	buf.append ("This is a general service note.\n");



From senger at dev.open-bio.org  Mon Mar  3 14:11:08 2008
From: senger at dev.open-bio.org (Martin Senger)
Date: Mon, 3 Mar 2008 09:11:08 -0500
Subject: [MOBY-guts] biomoby commit
Message-ID: <200803031411.m23EB8cb004111@dev.open-bio.org>


senger
Mon Mar  3 09:11:08 EST 2008
Update of /home/repository/moby/moby-live/Java/xmls
In directory dev.open-bio.org:/tmp/cvs-serv4034/xmls

Modified Files:
	deployBuild.xml tomcat.xml 
Log Message:
Remote deployment scripts fixed.

moby-live/Java/xmls deployBuild.xml,1.5,1.6 tomcat.xml,1.1,1.2
===================================================================
RCS file: /home/repository/moby/moby-live/Java/xmls/deployBuild.xml,v
retrieving revision 1.5
retrieving revision 1.6
diff -u -r1.5 -r1.6
--- /home/repository/moby/moby-live/Java/xmls/deployBuild.xml	2008/02/21 13:19:35	1.5
+++ /home/repository/moby/moby-live/Java/xmls/deployBuild.xml	2008/03/03 14:11:08	1.6
@@ -97,7 +97,8 @@
   
   <!-- copy user-defined and remaining jar files to Tomcat/Axis -->
   <antcall target="-populate">
-    <param name="destination.axis.dir" location="${deploy.axis.dir}/lib"/>
+    <param name="destination.axis.lib.dir"     location="${deploy.axis.dir}/lib"/>
+    <param name="destination.axis.classes.dir" location="${deploy.axis.dir}/classes"/>
   </antcall>
   
 </target>
@@ -131,14 +132,15 @@
 <!-- Sub-target of tomcat-populate                                      -->
 <!-- (used both for local and remote deployment)                        -->
 <!-- ================================================================== -->
-<!-- parameter: ${destination.axis.dir} -->
+<!-- parameter: ${destination.axis.lib.dir} -->
+<!-- parameter: ${destination.axis.classes.dir} -->
 <target name="-populate" depends="initmaven">
   
   <!-- copy user-defined jar files to Tomcat/Axis -->
   <if>
     <isset property="users.lib.dir"/>
     <then>
-      <copy todir="${destination.axis.dir}">
+      <copy todir="${destination.axis.lib.dir}">
         <fileset dir="${users.lib.dir}" includes="*.jar"/>
       </copy>
     </then>
@@ -146,13 +148,13 @@
   <if>
     <isset property="users.lib.file"/>
     <then>
-      <copy todir="${destination.axis.dir}" file="${users.lib.file}"/>
+      <copy todir="${destination.axis.lib.dir}" file="${users.lib.file}"/>
     </then>
   </if>
   
   <!-- copy remaining jar files to Tomcat/Axis -->
   <copy
-    todir="${destination.axis.dir}"
+    todir="${destination.axis.lib.dir}"
     flatten="true">
     <fileset refid="runtime.dependency.fileset"/>
   </copy>
@@ -160,12 +162,12 @@
   <!--
   <delete>
     <fileset
-      dir="${destination.axis.dir}"
+      dir="${destination.axis.lib.dir}"
       excludes="alltools2*,jdom*,commons-lang*,*xerces*"/>
   </delete>
   -->
   <copy
-    todir="${destination.axis.dir}">
+    todir="${destination.axis.lib.dir}">
     <fileset dir="${build.lib}" includes="*.jar"/>
   </copy>
   
@@ -176,7 +178,7 @@
     location="${src.config}/log4j.properties.template"/>
   <copy
     file="${server.log4j.configuration}"
-    tofile="${deploy.axis.dir}/classes/log4j.properties">
+    tofile="${destination.axis.classes.dir}/log4j.properties">
     <filterset>
       <filter token="LOGDIR" value="${server.log.dir}"/>
     </filterset>
@@ -318,7 +320,8 @@
   
   <!-- add user-defined and other jar files (but not those already in lib2) -->
   <antcall target="-populate">
-    <param name="destination.axis.dir" location="${result.dir}/lib"/>
+    <param name="destination.axis.lib.dir"     location="${result.dir}/lib"/>
+    <param name="destination.axis.classes.dir" location="${result.dir}/classes"/>
   </antcall>
   <delete quiet="true">
     <fileset dir="${result.dir}/lib" includes="${datatypes.jar},${skeletons.jar}"/>

===================================================================
RCS file: /home/repository/moby/moby-live/Java/xmls/tomcat.xml,v
retrieving revision 1.1
retrieving revision 1.2
diff -u -r1.1 -r1.2
--- /home/repository/moby/moby-live/Java/xmls/tomcat.xml	2008/02/14 06:13:37	1.1
+++ /home/repository/moby/moby-live/Java/xmls/tomcat.xml	2008/03/03 14:11:08	1.2
@@ -28,6 +28,10 @@
     <isset property="tomcat.home"/>
   </condition>
 
+  <!-- properties set from other properties that were set in conditions above -->
+  <property name="deploy.axis.dir"
+    location="${real.catalina.home}/${tomcat.webapps}/${axis.relative.path}/WEB-INF"/>
+    
   <!-- check that we know about Tomcat -->
   <fail unless="real.catalina.home">
 '



From senger at dev.open-bio.org  Mon Mar  3 14:11:08 2008
From: senger at dev.open-bio.org (Martin Senger)
Date: Mon, 3 Mar 2008 09:11:08 -0500
Subject: [MOBY-guts] biomoby commit
Message-ID: <200803031411.m23EB8J6004053@dev.open-bio.org>


senger
Mon Mar  3 09:11:08 EST 2008
Update of /home/repository/moby/moby-live/Java
In directory dev.open-bio.org:/tmp/cvs-serv4034

Modified Files:
	build.xml 
Log Message:
Remote deployment scripts fixed.

moby-live/Java build.xml,1.71,1.72
===================================================================
RCS file: /home/repository/moby/moby-live/Java/build.xml,v
retrieving revision 1.71
retrieving revision 1.72
diff -u -r1.71 -r1.72
--- /home/repository/moby/moby-live/Java/build.xml	2008/03/03 11:34:16	1.71
+++ /home/repository/moby/moby-live/Java/build.xml	2008/03/03 14:11:08	1.72
@@ -222,10 +222,6 @@
       <filter token="LOG4J" value="${log4j.value}"/>
     </filterset>
     
-    <!-- properties set from other properties that were set in conditions above -->
-    <property name="deploy.axis.dir"
-      location="${real.catalina.home}/${tomcat.webapps}/${axis.relative.path}/WEB-INF"/>
-    
     <!-- contributed tasks -->
     <taskdef resource="net/sf/antcontrib/antlib.xml">
       <classpath refid="dependency.classpath"/>



From kawas at dev.open-bio.org  Wed Mar  5 17:29:18 2008
From: kawas at dev.open-bio.org (Eddie Kawas)
Date: Wed, 5 Mar 2008 12:29:18 -0500
Subject: [MOBY-guts] biomoby commit
Message-ID: <200803051729.m25HTIFd016018@dev.open-bio.org>


kawas
Wed Mar  5 12:29:17 EST 2008
Update of /home/repository/moby/moby-live/Perl/MOBY-Client/t
In directory dev.open-bio.org:/tmp/cvs-serv15985/Perl/MOBY-Client/t

Removed Files:
	pod.t pod-coverage.t 
Log Message:
removed the pod tests because they cause fails on cpan
moby-live/Perl/MOBY-Client/t pod.t,1.1,NONE pod-coverage.t,1.1,NONE
rcsdiff: /home/repository/moby/moby-live/Perl/MOBY-Client/t/RCS/pod.t,v: No such file or directory

rcsdiff: /home/repository/moby/moby-live/Perl/MOBY-Client/t/RCS/pod-coverage.t,v: No such file or directory



From kawas at dev.open-bio.org  Wed Mar  5 17:30:00 2008
From: kawas at dev.open-bio.org (Eddie Kawas)
Date: Wed, 5 Mar 2008 12:30:00 -0500
Subject: [MOBY-guts] biomoby commit
Message-ID: <200803051730.m25HU0S9016058@dev.open-bio.org>


kawas
Wed Mar  5 12:29:59 EST 2008
Update of /home/repository/moby/moby-live/Perl/MOBY-Client
In directory dev.open-bio.org:/tmp/cvs-serv16023/Perl/MOBY-Client

Modified Files:
	MANIFEST 
Log Message:
removed the pod tests because they cause fails on cpan
moby-live/Perl/MOBY-Client MANIFEST,1.2,1.3
===================================================================
RCS file: /home/repository/moby/moby-live/Perl/MOBY-Client/MANIFEST,v
retrieving revision 1.2
retrieving revision 1.3
diff -u -r1.2 -r1.3
--- /home/repository/moby/moby-live/Perl/MOBY-Client/MANIFEST	2008/02/22 16:42:05	1.2
+++ /home/repository/moby/moby-live/Perl/MOBY-Client/MANIFEST	2008/03/05 17:29:59	1.3
@@ -54,5 +54,4 @@
 t/Client-Service.t
 t/Client-ServiceInstance.t
 t/Client-SimpleArticle.t
-t/pod-coverage.t
-t/pod.t
+



From kawas at dev.open-bio.org  Wed Mar  5 17:38:19 2008
From: kawas at dev.open-bio.org (Eddie Kawas)
Date: Wed, 5 Mar 2008 12:38:19 -0500
Subject: [MOBY-guts] biomoby commit
Message-ID: <200803051738.m25HcJlJ016245@dev.open-bio.org>


kawas
Wed Mar  5 12:38:19 EST 2008
Update of /home/repository/moby/moby-live/Perl/MOBY-Server/lib/MOBY/RDF
In directory dev.open-bio.org:/tmp/cvs-serv16210/Perl/MOBY-Server/lib/MOBY/RDF

Modified Files:
	Utils.pm 
Log Message:
helper method for downloading from a url
moby-live/Perl/MOBY-Server/lib/MOBY/RDF Utils.pm,1.2,1.3
===================================================================
RCS file: /home/repository/moby/moby-live/Perl/MOBY-Server/lib/MOBY/RDF/Utils.pm,v
retrieving revision 1.2
retrieving revision 1.3
diff -u -r1.2 -r1.3
--- /home/repository/moby/moby-live/Perl/MOBY-Server/lib/MOBY/RDF/Utils.pm	2008/02/21 17:15:41	1.2
+++ /home/repository/moby/moby-live/Perl/MOBY-Server/lib/MOBY/RDF/Utils.pm	2008/03/05 17:38:19	1.3
@@ -91,19 +91,19 @@
 
 sub prettyPrintXML {
 	my ( $self, $hash ) = @_;
-	my $xml        = $hash->{xml};
-	unless ( $xml ) {
+	my $xml = $hash->{xml};
+	unless ($xml) {
 		$xml = <<END;
 	<rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"></rdf:RDF>
 END
 	}
-	
+
 	eval "require XML::LibXSLT";
 	if ($@) {
-		my $parser     = XML::LibXML->new();
-		my $source     = $parser->parse_string($xml);
+		my $parser = XML::LibXML->new();
+		my $source = $parser->parse_string($xml);
 		$xml = $source->toString(0);
-		return $xml;    
+		return $xml;
 	} else {
 		my $parser     = XML::LibXML->new();
 		my $xslt       = XML::LibXSLT->new();
@@ -112,9 +112,42 @@
 		my $stylesheet = $xslt->parse_stylesheet($style_doc);
 		my $results    = $stylesheet->transform($source);
 		$xml = $stylesheet->output_string($results);
-		return  "<?xml version=\"1.0\" encoding=\"UTF-8\"?>". $xml;
+		return "<?xml version=\"1.0\" encoding=\"UTF-8\"?>" . $xml;
 	}
 }
 
+=head2 getHttpRequestByURL
+
+returns a scalar of text obtained from the url or dies if there was no success
+
+=cut
+
+sub getHttpRequestByURL {
+	my ( $self, $url ) = @_;
+	my $ua = LWP::UserAgent->new;
+	$ua->agent( "pMOBY/Central/1.0");
+
+	my $req =
+	  HTTP::Request->new( GET =>
+		  $url );
+
+	# accept gzip encoding
+	$req->header( 'Accept-Encoding' => 'gzip' );
+
+	# send request
+	my $res = $ua->request($req);
+
+	# check the outcome
+	if ( $res->is_success ) {
+		if ( $res->header('content-encoding') and $res->header('content-encoding') eq 'gzip' ) {
+			return $res->decoded_content;
+		} else {
+			return $res->content;
+		}
+	} else {
+		die "Error getting data from URL:\n\t" . $res->status_line;
+	}    
+}
+
 1;
 __END__



From kawas at dev.open-bio.org  Wed Mar  5 17:39:44 2008
From: kawas at dev.open-bio.org (Eddie Kawas)
Date: Wed, 5 Mar 2008 12:39:44 -0500
Subject: [MOBY-guts] biomoby commit
Message-ID: <200803051739.m25HdiB9016322@dev.open-bio.org>


kawas
Wed Mar  5 12:39:43 EST 2008
Update of /home/repository/moby/moby-live/Perl/MOBY-Server/lib/MOBY/RDF
In directory dev.open-bio.org:/tmp/cvs-serv16286/Perl/MOBY-Server/lib/MOBY/RDF

Modified Files:
	Utils.pm 
Log Message:
added some 'use' statements, but i am not so sure that they are necessary
moby-live/Perl/MOBY-Server/lib/MOBY/RDF Utils.pm,1.3,1.4
===================================================================
RCS file: /home/repository/moby/moby-live/Perl/MOBY-Server/lib/MOBY/RDF/Utils.pm,v
retrieving revision 1.3
retrieving revision 1.4
diff -u -r1.3 -r1.4
--- /home/repository/moby/moby-live/Perl/MOBY-Server/lib/MOBY/RDF/Utils.pm	2008/03/05 17:38:19	1.3
+++ /home/repository/moby/moby-live/Perl/MOBY-Server/lib/MOBY/RDF/Utils.pm	2008/03/05 17:39:43	1.4
@@ -9,6 +9,8 @@
 package MOBY::RDF::Utils;
 
 use XML::LibXML;
+use LWP::UserAgent;
+use HTTP::Request;
 
 use strict;
 



From kawas at dev.open-bio.org  Wed Mar  5 17:42:06 2008
From: kawas at dev.open-bio.org (Eddie Kawas)
Date: Wed, 5 Mar 2008 12:42:06 -0500
Subject: [MOBY-guts] biomoby commit
Message-ID: <200803051742.m25Hg6X2016421@dev.open-bio.org>


kawas
Wed Mar  5 12:42:06 EST 2008
Update of /home/repository/moby/moby-live/Perl/MOBY-Server/lib/MOBY/RDF/Parsers
In directory dev.open-bio.org:/tmp/cvs-serv16386/Perl/MOBY-Server/lib/MOBY/RDF/Parsers

Log Message:
Directory /home/repository/moby/moby-live/Perl/MOBY-Server/lib/MOBY/RDF/Parsers added to the repository

moby-live/Perl/MOBY-Server/lib/MOBY/RDF/Parsers - New directory
rcsdiff: /home/repository/moby/moby-live/Perl/MOBY-Server/lib/MOBY/RDF/Parsers/RCS/-,v: No such file or directory

rcsdiff: /home/repository/moby/moby-live/Perl/MOBY-Server/lib/MOBY/RDF/Parsers/RCS/New,v: No such file or directory

rcsdiff: /home/repository/moby/moby-live/Perl/MOBY-Server/lib/MOBY/RDF/Parsers/RCS/directory,v: No such file or directory



From kawas at dev.open-bio.org  Wed Mar  5 17:42:09 2008
From: kawas at dev.open-bio.org (Eddie Kawas)
Date: Wed, 5 Mar 2008 12:42:09 -0500
Subject: [MOBY-guts] biomoby commit
Message-ID: <200803051742.m25Hg9RZ016475@dev.open-bio.org>


kawas
Wed Mar  5 12:42:08 EST 2008
Update of /home/repository/moby/moby-live/Perl/MOBY-Server/lib/MOBY/RDF/Parsers
In directory dev.open-bio.org:/tmp/cvs-serv16444/Perl/MOBY-Server/lib/MOBY/RDF/Parsers

Added Files:
	ServiceTypeParser.pm NamespaceParser.pm 
Log Message:
module converts the RDF representation of the ontology into a perl representation. These can be used in the following manner:

1. getResourceRefs
2. create namespaces/servicetypes from the resource ref

Items returned are very similar to those returned by MOBY::Client::Central
moby-live/Perl/MOBY-Server/lib/MOBY/RDF/Parsers ServiceTypeParser.pm,NONE,1.1 NamespaceParser.pm,NONE,1.1


From kawas at dev.open-bio.org  Wed Mar  5 17:43:11 2008
From: kawas at dev.open-bio.org (Eddie Kawas)
Date: Wed, 5 Mar 2008 12:43:11 -0500
Subject: [MOBY-guts] biomoby commit
Message-ID: <200803051743.m25HhBdG016547@dev.open-bio.org>


kawas
Wed Mar  5 12:43:11 EST 2008
Update of /home/repository/moby/moby-live/Perl/MOBY-Server/lib/MOBY/RDF/Parsers
In directory dev.open-bio.org:/tmp/cvs-serv16508/Perl/MOBY-Server/lib/MOBY/RDF/Parsers

Modified Files:
	ServiceTypeParser.pm NamespaceParser.pm 
Log Message:
removed unused 'use' statement.
moby-live/Perl/MOBY-Server/lib/MOBY/RDF/Parsers ServiceTypeParser.pm,1.1,1.2 NamespaceParser.pm,1.1,1.2
===================================================================
RCS file: /home/repository/moby/moby-live/Perl/MOBY-Server/lib/MOBY/RDF/Parsers/ServiceTypeParser.pm,v
retrieving revision 1.1
retrieving revision 1.2
diff -u -r1.1 -r1.2
--- /home/repository/moby/moby-live/Perl/MOBY-Server/lib/MOBY/RDF/Parsers/ServiceTypeParser.pm	2008/03/05 17:42:08	1.1
+++ /home/repository/moby/moby-live/Perl/MOBY-Server/lib/MOBY/RDF/Parsers/ServiceTypeParser.pm	2008/03/05 17:43:11	1.2
@@ -14,8 +14,6 @@
 use RDF::Core::Storage::Memory;
 use RDF::Core::Resource;
 
-use LWP::UserAgent;
-
 use MOBY::RDF::Utils;
 use MOBY::RDF::Predicates::DC_PROTEGE;
 use MOBY::RDF::Predicates::MOBY_PREDICATES;

===================================================================
RCS file: /home/repository/moby/moby-live/Perl/MOBY-Server/lib/MOBY/RDF/Parsers/NamespaceParser.pm,v
retrieving revision 1.1
retrieving revision 1.2
diff -u -r1.1 -r1.2
--- /home/repository/moby/moby-live/Perl/MOBY-Server/lib/MOBY/RDF/Parsers/NamespaceParser.pm	2008/03/05 17:42:08	1.1
+++ /home/repository/moby/moby-live/Perl/MOBY-Server/lib/MOBY/RDF/Parsers/NamespaceParser.pm	2008/03/05 17:43:11	1.2
@@ -14,8 +14,6 @@
 use RDF::Core::Storage::Memory;
 use RDF::Core::Resource;
 
-use LWP::UserAgent;
-
 use MOBY::RDF::Utils;
 use MOBY::RDF::Predicates::DC_PROTEGE;
 use MOBY::RDF::Predicates::MOBY_PREDICATES;



From kawas at dev.open-bio.org  Wed Mar  5 17:44:02 2008
From: kawas at dev.open-bio.org (Eddie Kawas)
Date: Wed, 5 Mar 2008 12:44:02 -0500
Subject: [MOBY-guts] biomoby commit
Message-ID: <200803051744.m25Hi20P016609@dev.open-bio.org>


kawas
Wed Mar  5 12:44:02 EST 2008
Update of /home/repository/moby/moby-live/Perl/MOBY-Client
In directory dev.open-bio.org:/tmp/cvs-serv16574/Perl/MOBY-Client

Modified Files:
	MANIFEST 
Log Message:
updated the manifest to include 2 new files
moby-live/Perl/MOBY-Client MANIFEST,1.3,1.4
===================================================================
RCS file: /home/repository/moby/moby-live/Perl/MOBY-Client/MANIFEST,v
retrieving revision 1.3
retrieving revision 1.4
diff -u -r1.3 -r1.4
--- /home/repository/moby/moby-live/Perl/MOBY-Client/MANIFEST	2008/03/05 17:29:59	1.3
+++ /home/repository/moby/moby-live/Perl/MOBY-Client/MANIFEST	2008/03/05 17:44:02	1.4
@@ -28,6 +28,8 @@
 lib/MOBY/Client/ServiceInstance.pm
 lib/MOBY/Client/SimpleArticle.pm
 lib/MOBY/Client/SimpleInput.pm
+lib/MOBY/RDF/Ontologies/Parsers/NamespaceParser.pm
+lib/MOBY/RDF/Ontologies/Parsers/ServiceTypeParser.pm
 lib/MOBY/CommonSubs.pm
 lib/MOBY/CrossReference.pm
 lib/MOBY/MobyXMLConstants.pm



From kawas at dev.open-bio.org  Wed Mar  5 17:44:40 2008
From: kawas at dev.open-bio.org (Eddie Kawas)
Date: Wed, 5 Mar 2008 12:44:40 -0500
Subject: [MOBY-guts] biomoby commit
Message-ID: <200803051744.m25HiecU016665@dev.open-bio.org>


kawas
Wed Mar  5 12:44:40 EST 2008
Update of /home/repository/moby/moby-live/Perl/MOBY-Client
In directory dev.open-bio.org:/tmp/cvs-serv16630/Perl/MOBY-Client

Modified Files:
	MANIFEST 
Log Message:

moby-live/Perl/MOBY-Client MANIFEST,1.4,1.5
===================================================================
RCS file: /home/repository/moby/moby-live/Perl/MOBY-Client/MANIFEST,v
retrieving revision 1.4
retrieving revision 1.5
diff -u -r1.4 -r1.5
--- /home/repository/moby/moby-live/Perl/MOBY-Client/MANIFEST	2008/03/05 17:44:02	1.4
+++ /home/repository/moby/moby-live/Perl/MOBY-Client/MANIFEST	2008/03/05 17:44:40	1.5
@@ -33,6 +33,7 @@
 lib/MOBY/CommonSubs.pm
 lib/MOBY/CrossReference.pm
 lib/MOBY/MobyXMLConstants.pm
+lib/MOBY/RDF/Utils.pm
 License
 Makefile.PL
 MANIFEST			This list of files



From kawas at dev.open-bio.org  Wed Mar  5 17:52:46 2008
From: kawas at dev.open-bio.org (Eddie Kawas)
Date: Wed, 5 Mar 2008 12:52:46 -0500
Subject: [MOBY-guts] biomoby commit
Message-ID: <200803051752.m25Hqkw3016907@dev.open-bio.org>


kawas
Wed Mar  5 12:52:46 EST 2008
Update of /home/repository/moby/moby-live/Perl/MOBY-Client
In directory dev.open-bio.org:/tmp/cvs-serv16872/Perl/MOBY-Client

Modified Files:
	populate_libs.pl 
Log Message:
added the new modules 'NamespaceParser, ServiceTypeParser, Utils'
moby-live/Perl/MOBY-Client populate_libs.pl,1.1,1.2
===================================================================
RCS file: /home/repository/moby/moby-live/Perl/MOBY-Client/populate_libs.pl,v
retrieving revision 1.1
retrieving revision 1.2
diff -u -r1.1 -r1.2
--- /home/repository/moby/moby-live/Perl/MOBY-Client/populate_libs.pl	2008/02/21 00:14:33	1.1
+++ /home/repository/moby/moby-live/Perl/MOBY-Client/populate_libs.pl	2008/03/05 17:52:46	1.2
@@ -12,6 +12,8 @@
 my @Async 		= qw ( LSAE.pm Service.pm SimpleServer.pm WSRF.pm );
 my @Client		= qw ( Central.pm CollectionArticle.pm OntologyServer.pm Registration.pm SecondaryArticle.pm Service.pm ServiceInstance.pm SimpleArticle.pm SimpleInput.pm );
 my @Exception 	= qw ( MobyException.pm MobyExceptionCodes.pm );
+my @RDF 		= qw ( Utils.pm );
+my @Parsers 	= qw ( ServiceTypeParser.pm NamespaceParser.pm );
 
 # current working directory ...
 my $dir = getcwd;
@@ -55,6 +57,18 @@
 	warn "couldn't copy file $file: $!\n" unless copy("$origin_directory/$subpath/$file","$destination_directory/$subpath/$file") == 1;
 }
 
+# copy the RDF files
+foreach my $file (@RDF) {
+	my $subpath = "MOBY/RDF";
+	warn "couldn't copy file $file: $!\n" unless copy("$origin_directory/$subpath/$file","$destination_directory/$subpath/$file") == 1;
+}
+
+# copy the Parsers files
+foreach my $file (@Parsers) {
+	my $subpath = "MOBY/RDF/Parsers";
+	warn "couldn't copy file $file: $!\n" unless copy("$origin_directory/$subpath/$file","$destination_directory/$subpath/$file") == 1;
+}
+
 
 # Directory Structure is:
 #
@@ -71,16 +85,23 @@
 #    ?       WSRF.pm
 #    ?
 #    +---Client
-#        ?   Central.pm
-#        ?   CollectionArticle.pm
-#        ?   OntologyServer.pm
-#        ?   Registration.pm
-#        ?   SecondaryArticle.pm
-#        ?   Service.pm
-#        ?   ServiceInstance.pm
-#        ?   SimpleArticle.pm
-#        ?   SimpleInput.pm
-#        ?
-#        +---Exception
-#                MobyException.pm
-#                MobyExceptionCodes.pm
+#    ?   ?   Central.pm
+#    ?   ?   CollectionArticle.pm
+#    ?   ?   OntologyServer.pm
+#    ?   ?   Registration.pm
+#    ?   ?   SecondaryArticle.pm
+#    ?   ?   Service.pm
+#    ?   ?   ServiceInstance.pm
+#    ?   ?   SimpleArticle.pm
+#    ?   ?   SimpleInput.pm
+#    ?   ?
+#    ?   +---Exception
+#    ?           MobyException.pm
+#    ?           MobyExceptionCodes.pm
+#    ?
+#    +---RDF
+#    ?   ?   Utils.pm
+#    ?   ?   
+#    ?   +---Parsers
+#    ?           ServiceTypeParser.pm
+#    ?           NamespaceParser.pm



From kawas at dev.open-bio.org  Wed Mar  5 17:59:58 2008
From: kawas at dev.open-bio.org (Eddie Kawas)
Date: Wed, 5 Mar 2008 12:59:58 -0500
Subject: [MOBY-guts] biomoby commit
Message-ID: <200803051759.m25Hxw3A017139@dev.open-bio.org>


kawas
Wed Mar  5 12:59:58 EST 2008
Update of /home/repository/moby/moby-live/Perl/MOBY-Client
In directory dev.open-bio.org:/tmp/cvs-serv17095/Perl/MOBY-Client

Modified Files:
	populate_libs.pl MANIFEST Makefile.PL 
Log Message:
added rdf::core to the makefile, updated the Manifest to include the predicate vocabs and added the vocabs to the populate libs script
moby-live/Perl/MOBY-Client populate_libs.pl,1.2,1.3 MANIFEST,1.5,1.6 Makefile.PL,1.3,1.4
===================================================================
RCS file: /home/repository/moby/moby-live/Perl/MOBY-Client/populate_libs.pl,v
retrieving revision 1.2
retrieving revision 1.3
diff -u -r1.2 -r1.3
--- /home/repository/moby/moby-live/Perl/MOBY-Client/populate_libs.pl	2008/03/05 17:52:46	1.2
+++ /home/repository/moby/moby-live/Perl/MOBY-Client/populate_libs.pl	2008/03/05 17:59:58	1.3
@@ -14,6 +14,7 @@
 my @Exception 	= qw ( MobyException.pm MobyExceptionCodes.pm );
 my @RDF 		= qw ( Utils.pm );
 my @Parsers 	= qw ( ServiceTypeParser.pm NamespaceParser.pm );
+my @predicates  = qw ( DC_PROTEGE.pm MOBY_PREDICATES.pm OMG_LSID.pm RDF.pm RDFS.pm FETA.pm OWL.pm );
 
 # current working directory ...
 my $dir = getcwd;
@@ -69,6 +70,11 @@
 	warn "couldn't copy file $file: $!\n" unless copy("$origin_directory/$subpath/$file","$destination_directory/$subpath/$file") == 1;
 }
 
+# copy the Predicates files
+foreach my $file (@predicates) {
+	my $subpath = "MOBY/RDF/Predicates";
+	warn "couldn't copy file $file: $!\n" unless copy("$origin_directory/$subpath/$file","$destination_directory/$subpath/$file") == 1;
+}
 
 # Directory Structure is:
 #
@@ -103,5 +109,14 @@
 #    ?   ?   Utils.pm
 #    ?   ?   
 #    ?   +---Parsers
-#    ?           ServiceTypeParser.pm
-#    ?           NamespaceParser.pm
+#    ?   ?       ServiceTypeParser.pm
+#    ?   ?       NamespaceParser.pm
+#    ?   ?
+#    ?   +---Predicates
+#    ?           DC_PROTEGE.pm
+#    ?           FETA.pm
+#    ?           MOBY_PREDICATES.pm
+#    ?           OMG_LSID.pm
+#    ?           OWL.pm
+#    ?           RDF.pm
+#    ?           RDFS.pm

===================================================================
RCS file: /home/repository/moby/moby-live/Perl/MOBY-Client/MANIFEST,v
retrieving revision 1.5
retrieving revision 1.6
diff -u -r1.5 -r1.6
--- /home/repository/moby/moby-live/Perl/MOBY-Client/MANIFEST	2008/03/05 17:44:40	1.5
+++ /home/repository/moby/moby-live/Perl/MOBY-Client/MANIFEST	2008/03/05 17:59:58	1.6
@@ -30,6 +30,13 @@
 lib/MOBY/Client/SimpleInput.pm
 lib/MOBY/RDF/Ontologies/Parsers/NamespaceParser.pm
 lib/MOBY/RDF/Ontologies/Parsers/ServiceTypeParser.pm
+lib/MOBY/RDF/Predicates/DC_PROTEGE.pm
+lib/MOBY/RDF/Predicates/FETA.pm
+lib/MOBY/RDF/Predicates/MOBY_PREDICATES.pm
+lib/MOBY/RDF/Predicates/OMG_LSID.pm
+lib/MOBY/RDF/Predicates/OWL.pm
+lib/MOBY/RDF/Predicates/RDF.pm
+lib/MOBY/RDF/Predicates/RDFS.pm
 lib/MOBY/CommonSubs.pm
 lib/MOBY/CrossReference.pm
 lib/MOBY/MobyXMLConstants.pm

===================================================================
RCS file: /home/repository/moby/moby-live/Perl/MOBY-Client/Makefile.PL,v
retrieving revision 1.3
retrieving revision 1.4
diff -u -r1.3 -r1.4
--- /home/repository/moby/moby-live/Perl/MOBY-Client/Makefile.PL	2008/02/22 17:38:24	1.3
+++ /home/repository/moby/moby-live/Perl/MOBY-Client/Makefile.PL	2008/03/05 17:59:58	1.4
@@ -19,6 +19,7 @@
 requires 'CGI'                   => 0;
 requires 'HTTP::Request::Common' => 0;
 requires 'URI::Escape'           => 0;
+requires 'RDF::Core'             => '0.51';
 
 # MOBY::CommonSubs depends
 requires 'HTML::Entities' => 0;



From kawas at dev.open-bio.org  Wed Mar  5 18:00:48 2008
From: kawas at dev.open-bio.org (Eddie Kawas)
Date: Wed, 5 Mar 2008 13:00:48 -0500
Subject: [MOBY-guts] biomoby commit
Message-ID: <200803051800.m25I0mbJ017253@dev.open-bio.org>


kawas
Wed Mar  5 13:00:48 EST 2008
Update of /home/repository/moby/moby-live/Perl/MOBY-Server
In directory dev.open-bio.org:/tmp/cvs-serv17218/Perl/MOBY-Server

Modified Files:
	MANIFEST 
Log Message:
updated the manifest to include 2 new files
moby-live/Perl/MOBY-Server MANIFEST,1.1,1.2
===================================================================
RCS file: /home/repository/moby/moby-live/Perl/MOBY-Server/MANIFEST,v
retrieving revision 1.1
retrieving revision 1.2
diff -u -r1.1 -r1.2
--- /home/repository/moby/moby-live/Perl/MOBY-Server/MANIFEST	2008/02/21 00:21:28	1.1
+++ /home/repository/moby/moby-live/Perl/MOBY-Server/MANIFEST	2008/03/05 18:00:48	1.2
@@ -55,6 +55,8 @@
 lib/MOBY/MOBYXSLT.pm
 lib/MOBY/mysql.pm
 lib/MOBY/OntologyServer.pm
+lib/MOBY/RDF/Ontologies/Parsers/NamespaceParser.pm
+lib/MOBY/RDF/Ontologies/Parsers/ServiceTypeParser.pm
 lib/MOBY/RDF/Ontologies/Cache/CacheUtils.pm
 lib/MOBY/RDF/Ontologies/Cache/NamespaceCache.pm
 lib/MOBY/RDF/Ontologies/Cache/ObjectCache.pm



From kawas at dev.open-bio.org  Wed Mar  5 18:22:00 2008
From: kawas at dev.open-bio.org (Eddie Kawas)
Date: Wed, 5 Mar 2008 13:22:00 -0500
Subject: [MOBY-guts] biomoby commit
Message-ID: <200803051822.m25IM0Tj017663@dev.open-bio.org>


kawas
Wed Mar  5 13:22:00 EST 2008
Update of /home/repository/moby/moby-live/Perl/MOBY-Client
In directory dev.open-bio.org:/tmp/cvs-serv17628/Perl/MOBY-Client

Modified Files:
	populate_libs.pl 
Log Message:
added the new directories to the script
moby-live/Perl/MOBY-Client populate_libs.pl,1.3,1.4
===================================================================
RCS file: /home/repository/moby/moby-live/Perl/MOBY-Client/populate_libs.pl,v
retrieving revision 1.3
retrieving revision 1.4
diff -u -r1.3 -r1.4
--- /home/repository/moby/moby-live/Perl/MOBY-Client/populate_libs.pl	2008/03/05 17:59:58	1.3
+++ /home/repository/moby/moby-live/Perl/MOBY-Client/populate_libs.pl	2008/03/05 18:22:00	1.4
@@ -25,7 +25,7 @@
 my $destination_directory 	= "$dir/lib";
 
 # directory structure for ../lib/
-my @main_dirs = qw( MOBY MOBY/Async MOBY/Client MOBY/Client/Exception);
+my @main_dirs = qw( MOBY MOBY/Async MOBY/Client MOBY/Client/Exception MOBY/RDF MOBY/RDF/Predicates MOBY/RDF/Parsers );
 
 #create main directories as needed ...
 foreach my $dir (@main_dirs) {



From kawas at dev.open-bio.org  Wed Mar  5 18:24:22 2008
From: kawas at dev.open-bio.org (Eddie Kawas)
Date: Wed, 5 Mar 2008 13:24:22 -0500
Subject: [MOBY-guts] biomoby commit
Message-ID: <200803051824.m25IOMdi017703@dev.open-bio.org>


kawas
Wed Mar  5 13:24:22 EST 2008
Update of /home/repository/moby/moby-live/Perl/MOBY-Client
In directory dev.open-bio.org:/tmp/cvs-serv17668/Perl/MOBY-Client

Modified Files:
	MANIFEST 
Log Message:

moby-live/Perl/MOBY-Client MANIFEST,1.6,1.7
===================================================================
RCS file: /home/repository/moby/moby-live/Perl/MOBY-Client/MANIFEST,v
retrieving revision 1.6
retrieving revision 1.7
diff -u -r1.6 -r1.7
--- /home/repository/moby/moby-live/Perl/MOBY-Client/MANIFEST	2008/03/05 17:59:58	1.6
+++ /home/repository/moby/moby-live/Perl/MOBY-Client/MANIFEST	2008/03/05 18:24:22	1.7
@@ -28,8 +28,8 @@
 lib/MOBY/Client/ServiceInstance.pm
 lib/MOBY/Client/SimpleArticle.pm
 lib/MOBY/Client/SimpleInput.pm
-lib/MOBY/RDF/Ontologies/Parsers/NamespaceParser.pm
-lib/MOBY/RDF/Ontologies/Parsers/ServiceTypeParser.pm
+lib/MOBY/RDF/Parsers/NamespaceParser.pm
+lib/MOBY/RDF/Parsers/ServiceTypeParser.pm
 lib/MOBY/RDF/Predicates/DC_PROTEGE.pm
 lib/MOBY/RDF/Predicates/FETA.pm
 lib/MOBY/RDF/Predicates/MOBY_PREDICATES.pm



From kawas at dev.open-bio.org  Wed Mar  5 18:25:01 2008
From: kawas at dev.open-bio.org (Eddie Kawas)
Date: Wed, 5 Mar 2008 13:25:01 -0500
Subject: [MOBY-guts] biomoby commit
Message-ID: <200803051825.m25IP1dq017743@dev.open-bio.org>


kawas
Wed Mar  5 13:25:01 EST 2008
Update of /home/repository/moby/moby-live/Perl/MOBY-Server
In directory dev.open-bio.org:/tmp/cvs-serv17708/Perl/MOBY-Server

Modified Files:
	MANIFEST 
Log Message:

moby-live/Perl/MOBY-Server MANIFEST,1.2,1.3
===================================================================
RCS file: /home/repository/moby/moby-live/Perl/MOBY-Server/MANIFEST,v
retrieving revision 1.2
retrieving revision 1.3
diff -u -r1.2 -r1.3
--- /home/repository/moby/moby-live/Perl/MOBY-Server/MANIFEST	2008/03/05 18:00:48	1.2
+++ /home/repository/moby/moby-live/Perl/MOBY-Server/MANIFEST	2008/03/05 18:25:01	1.3
@@ -55,8 +55,8 @@
 lib/MOBY/MOBYXSLT.pm
 lib/MOBY/mysql.pm
 lib/MOBY/OntologyServer.pm
-lib/MOBY/RDF/Ontologies/Parsers/NamespaceParser.pm
-lib/MOBY/RDF/Ontologies/Parsers/ServiceTypeParser.pm
+lib/MOBY/RDF/Parsers/NamespaceParser.pm
+lib/MOBY/RDF/Parsers/ServiceTypeParser.pm
 lib/MOBY/RDF/Ontologies/Cache/CacheUtils.pm
 lib/MOBY/RDF/Ontologies/Cache/NamespaceCache.pm
 lib/MOBY/RDF/Ontologies/Cache/ObjectCache.pm



From kawas at dev.open-bio.org  Wed Mar  5 18:38:40 2008
From: kawas at dev.open-bio.org (Eddie Kawas)
Date: Wed, 5 Mar 2008 13:38:40 -0500
Subject: [MOBY-guts] biomoby commit
Message-ID: <200803051838.m25IceMc017883@dev.open-bio.org>


kawas
Wed Mar  5 13:38:40 EST 2008
Update of /home/repository/moby/moby-live/Perl/MOBY-Client
In directory dev.open-bio.org:/tmp/cvs-serv17840/Perl/MOBY-Client

Modified Files:
	META.yml Makefile.PL Changes 
Log Message:
updated the Changes file to reflect new items before releasing to cpan
moby-live/Perl/MOBY-Client META.yml,1.1,1.2 Makefile.PL,1.4,1.5 Changes,1.1,1.2
===================================================================
RCS file: /home/repository/moby/moby-live/Perl/MOBY-Client/META.yml,v
retrieving revision 1.1
retrieving revision 1.2
diff -u -r1.1 -r1.2
--- /home/repository/moby/moby-live/Perl/MOBY-Client/META.yml	2008/02/21 00:14:33	1.1
+++ /home/repository/moby/moby-live/Perl/MOBY-Client/META.yml	2008/03/05 18:38:40	1.2
@@ -24,4 +24,5 @@
   URI::Escape: 0
   XML::LibXML: 0
   WSRF::Lite: 0
-version: 1.0
+  RDF::Core: 0.51
+version: 1.01

===================================================================
RCS file: /home/repository/moby/moby-live/Perl/MOBY-Client/Makefile.PL,v
retrieving revision 1.4
retrieving revision 1.5
diff -u -r1.4 -r1.5
--- /home/repository/moby/moby-live/Perl/MOBY-Client/Makefile.PL	2008/03/05 17:59:58	1.4
+++ /home/repository/moby/moby-live/Perl/MOBY-Client/Makefile.PL	2008/03/05 18:38:40	1.5
@@ -4,7 +4,7 @@
 
 # all_from 'lib/MOBY/Client/Central.pm';
 author 'Mark Wilkinson <markw at illuminae.com>';
-version '1.0';
+version '1.01';
 license 'perl';
 
 build_requires 'Test::More' => 0;

===================================================================
RCS file: /home/repository/moby/moby-live/Perl/MOBY-Client/Changes,v
retrieving revision 1.1
retrieving revision 1.2
diff -u -r1.1 -r1.2
--- /home/repository/moby/moby-live/Perl/MOBY-Client/Changes	2008/02/21 00:14:33	1.1
+++ /home/repository/moby/moby-live/Perl/MOBY-Client/Changes	2008/03/05 18:38:40	1.2
@@ -1,5 +1,9 @@
 Revision history for Moby-Client
 
+1.01    5 March 2008
+        * removed some failing pod tests
+        * added some preliminary modules for parsing RDF (Namespaces/ServiceTypes). Others will follow
+
 1.00    12 Feb 2008
         MOBY::Client released to CPAN
 



From kawas at dev.open-bio.org  Wed Mar  5 20:27:12 2008
From: kawas at dev.open-bio.org (Eddie Kawas)
Date: Wed, 5 Mar 2008 15:27:12 -0500
Subject: [MOBY-guts] biomoby commit
Message-ID: <200803052027.m25KRC1r018033@dev.open-bio.org>


kawas
Wed Mar  5 15:27:11 EST 2008
Update of /home/repository/moby/moby-live/Perl/MOBY-Server/lib/MOBY
In directory dev.open-bio.org:/tmp/cvs-serv17998/Perl/MOBY-Server/lib/MOBY

Modified Files:
	CommonSubs.pm 
Log Message:
fixed a bug where an unqualified articlename failed to get found when calling getNodeContentWithArticle
moby-live/Perl/MOBY-Server/lib/MOBY CommonSubs.pm,1.2,1.3
===================================================================
RCS file: /home/repository/moby/moby-live/Perl/MOBY-Server/lib/MOBY/CommonSubs.pm,v
retrieving revision 1.2
retrieving revision 1.3
diff -u -r1.2 -r1.3
--- /home/repository/moby/moby-live/Perl/MOBY-Server/lib/MOBY/CommonSubs.pm	2008/02/21 17:15:40	1.2
+++ /home/repository/moby/moby-live/Perl/MOBY-Server/lib/MOBY/CommonSubs.pm	2008/03/05 20:27:11	1.3
@@ -1042,7 +1042,7 @@
   for ( 1 .. $nodes->size() ) {
     my $child = $nodes->get_node( $_ );
     if ( _moby_getAttribute($child, "articleName")
-	 && ( $child->getAttribute("articleName") eq $articleName )
+	 && ( _moby_getAttribute($child, "articleName") eq $articleName )
        )
       {
 	# now we have a valid child, get the content... stringified... regardless of what it is



From kawas at dev.open-bio.org  Thu Mar  6 16:44:55 2008
From: kawas at dev.open-bio.org (Eddie Kawas)
Date: Thu, 6 Mar 2008 11:44:55 -0500
Subject: [MOBY-guts] biomoby commit
Message-ID: <200803061644.m26GitGc024846@dev.open-bio.org>


kawas
Thu Mar  6 11:44:55 EST 2008
Update of /home/repository/moby/moby-live/Perl/MOBY-Server/bin/scripts
In directory dev.open-bio.org:/tmp/cvs-serv24808/Perl/MOBY-Server/bin/scripts

Modified Files:
	moby-s-install.pl 
Log Message:
*updated the script to make the cgi files copied executable
*fixed some of the messages that came out of the script

moby-live/Perl/MOBY-Server/bin/scripts moby-s-install.pl,1.1,1.2
===================================================================
RCS file: /home/repository/moby/moby-live/Perl/MOBY-Server/bin/scripts/moby-s-install.pl,v
retrieving revision 1.1
retrieving revision 1.2
diff -u -r1.1 -r1.2
--- /home/repository/moby/moby-live/Perl/MOBY-Server/bin/scripts/moby-s-install.pl	2008/02/21 00:21:28	1.1
+++ /home/repository/moby/moby-live/Perl/MOBY-Server/bin/scripts/moby-s-install.pl	2008/03/06 16:44:55	1.2
@@ -188,6 +188,10 @@
 	} else {
 		say "\n$file_desc created: '$file'\n\tPlease ensure that the file is executable!\n";
 	}
+	# try to make file executable
+	eval {
+		my $mode = 0655;   chmod $mode, "$file";
+	};
 }
 
 # create a config file from a template
@@ -1253,7 +1257,7 @@
 
 #
 
-say 'Please remember to set up the RDF agent! Just restart apache and your registry has been set up!\n\nDone.';
+say "Please remember to set up the RDF agent! Just restart apache and your registry has been set up!\n\nDone.";
 
 package SimplePrompt;
 



From kawas at dev.open-bio.org  Thu Mar  6 16:58:42 2008
From: kawas at dev.open-bio.org (Eddie Kawas)
Date: Thu, 6 Mar 2008 11:58:42 -0500
Subject: [MOBY-guts] biomoby commit
Message-ID: <200803061658.m26Gwgmo025246@dev.open-bio.org>


kawas
Thu Mar  6 11:58:42 EST 2008
Update of /home/repository/moby/moby-live/Java/docs
In directory dev.open-bio.org:/tmp/cvs-serv25211/Java/docs

Modified Files:
	ConfigureRDFAgent.html 
Log Message:
added a more detail for building the agent.
moby-live/Java/docs ConfigureRDFAgent.html,1.6,1.7
===================================================================
RCS file: /home/repository/moby/moby-live/Java/docs/ConfigureRDFAgent.html,v
retrieving revision 1.6
retrieving revision 1.7
diff -u -r1.6 -r1.7
--- /home/repository/moby/moby-live/Java/docs/ConfigureRDFAgent.html	2008/02/20 19:59:56	1.6
+++ /home/repository/moby/moby-live/Java/docs/ConfigureRDFAgent.html	2008/03/06 16:58:42	1.7
@@ -49,7 +49,10 @@
     </li>
     <li class="dcount"> You can build the latest RDFAgent from the cvs.
     <blockquote>
-    <p>ant bindist-rdfagent </p>
+    <pre class="script">
+    cd /path/to/moby-live/Java
+    ant bindist-rdfagent</pre>
+    <p><strong>Need to check out the code from the cvs? Click</strong> <a href="CVS.html" target="_blank">Here!</a></p>
     </blockquote>
     </li>
     <blockquote>



From mwilkinson at dev.open-bio.org  Thu Mar  6 17:02:56 2008
From: mwilkinson at dev.open-bio.org (Mark Wilkinson)
Date: Thu, 6 Mar 2008 12:02:56 -0500
Subject: [MOBY-guts] biomoby commit
Message-ID: <200803061702.m26H2uDj025425@dev.open-bio.org>


mwilkinson
Thu Mar  6 12:02:55 EST 2008
Update of /home/repository/moby/moby-live/Docs/ProjectDocs
In directory dev.open-bio.org:/tmp/cvs-serv25406/ProjectDocs

Modified Files:
	index.html 
Log Message:
fixing docs
moby-live/Docs/ProjectDocs index.html,1.8,1.9
===================================================================
RCS file: /home/repository/moby/moby-live/Docs/ProjectDocs/index.html,v
retrieving revision 1.8
retrieving revision 1.9
diff -u -r1.8 -r1.9
--- /home/repository/moby/moby-live/Docs/ProjectDocs/index.html	2007/06/21 22:12:52	1.8
+++ /home/repository/moby/moby-live/Docs/ProjectDocs/index.html	2008/03/06 17:02:55	1.9
@@ -23,8 +23,8 @@
             <td>Location</td><td>Endpoint</td><td>Public?</td><td>Description</td><td>Policy</td>
         </tr>
         <tr>
-            <td>iCAPTURE Centre</td><td>Endpoint: http://mobycentral.icapture.ubc.ca/cgi-bin/MOBY05/mobycentral.pl
-                                        <br>URI: http://mobycentral.icapture.ubc.ca/MOBY/Central</td><td>YES</td><td>A curated public registry hosted at the iCAPTURE Centre, Vancouver</td><td><a href="http://mobycentral.icapture.ubc.ca/MOBYCentral_Policy.html">Policy</a></td>
+            <td>SUN Centre of Excellence</td><td>Endpoint: http://moby.ucalgary.ca/moby/MOBY-Central.pl
+                                        <br>URI: http://moby.ucalgary.ca/MOBY/Central</td><td>YES</td><td>A curated public registry hosted at the SUN Centre of Excellence, Calgary</td><td><a href="http://mobycentral.icapture.ubc.ca/MOBYCentral_Policy.html">Policy: open, non-test registry.  Test services may be deleted at any time.</a></td>
         </tr>
         <tr>
             <td>Open TEST registry</td><td>Endpoint: http://bioinfo.icapture.ubc.ca/cgi-bin/mobycentral/MOBY-Central.pl



From kawas at dev.open-bio.org  Thu Mar  6 17:05:09 2008
From: kawas at dev.open-bio.org (Eddie Kawas)
Date: Thu, 6 Mar 2008 12:05:09 -0500
Subject: [MOBY-guts] biomoby commit
Message-ID: <200803061705.m26H593M025575@dev.open-bio.org>


kawas
Thu Mar  6 12:05:09 EST 2008
Update of /home/repository/moby/moby-live/Perl/MOBY-Server/lib
In directory dev.open-bio.org:/tmp/cvs-serv25540/Perl/MOBY-Server/lib

Modified Files:
	MOBY.pm 
Log Message:

moby-live/Perl/MOBY-Server/lib MOBY.pm,1.1,1.2
===================================================================
RCS file: /home/repository/moby/moby-live/Perl/MOBY-Server/lib/MOBY.pm,v
retrieving revision 1.1
retrieving revision 1.2
diff -u -r1.1 -r1.2
--- /home/repository/moby/moby-live/Perl/MOBY-Server/lib/MOBY.pm	2008/02/21 00:21:28	1.1
+++ /home/repository/moby/moby-live/Perl/MOBY-Server/lib/MOBY.pm	2008/03/06 17:05:09	1.2
@@ -102,7 +102,7 @@
 
 =back
 
-Once you are sure that you satisfy the above items, go ahead and run the B<moby-s-install.pl> script, by typing C<moby-s-install.pl> at the command line.
+Once you are sure that you satisfy the above items, go ahead and run the B<moby-s-install.pl> script, by typing C<moby-s-install.pl> at the command line. This file was installed onto your machine when you did your 'make install'!
 
 =head3 What Exactly does moby-s-install.pl do?
 
@@ -208,10 +208,22 @@
 
 =cut
 
+=head3 How do I set up the RDF Agent?
+
+Detailed instructions for building, installing and configuring the agent can be found at http://biomoby.open-bio.org/CVS_CONTENT/moby-live/Java/docs/ConfigureRDFAgent.html
+
+=cut
+
 =cut
 
 =head2 Missing Features
 
+=over
+
+=item * automatic installation of the RDF Agent
+
+=back
+
 =cut
 
 =head2 Acknowledgement



From mwilkinson at dev.open-bio.org  Thu Mar  6 18:04:35 2008
From: mwilkinson at dev.open-bio.org (Mark Wilkinson)
Date: Thu, 6 Mar 2008 13:04:35 -0500
Subject: [MOBY-guts] biomoby commit
Message-ID: <200803061804.m26I4ZYQ028481@dev.open-bio.org>


mwilkinson
Thu Mar  6 13:04:35 EST 2008
Update of /home/repository/moby/moby-live/Perl/MOBY-Server/lib/MOBY/Client
In directory dev.open-bio.org:/tmp/cvs-serv28462

Modified Files:
	Central.pm 
Log Message:
updating docs
moby-live/Perl/MOBY-Server/lib/MOBY/Client Central.pm,1.2,1.3
===================================================================
RCS file: /home/repository/moby/moby-live/Perl/MOBY-Server/lib/MOBY/Client/Central.pm,v
retrieving revision 1.2
retrieving revision 1.3
diff -u -r1.2 -r1.3
--- /home/repository/moby/moby-live/Perl/MOBY-Server/lib/MOBY/Client/Central.pm	2008/02/21 17:15:40	1.2
+++ /home/repository/moby/moby-live/Perl/MOBY-Server/lib/MOBY/Client/Central.pm	2008/03/06 18:04:35	1.3
@@ -80,14 +80,15 @@
 
  ENV & PROXY : you can set environment variables to change the defaults.
              By default, a call to 'new' will initialize MOBY::Client::Central
-             to connect to the MOBY Central registry at:
-             http://mobycentral.cbr.nrc.ca/cgi-bin/MOBY05/mobycentral.pl
+             to connect to the default MOBY Central registry.  The location of
+             this registry can be determined by examining the redirect from:
+                http://biomoby.org/mobycentral
              If you wish to chose another registry by default, or if you need
              to set up additional connection details (e.g. PROXY) then you may
              set the following environment variables to whatever you
              require:
-             MOBY_SERVER  (default http://mobycentral.cbr.nrc.ca/cgi-bin/MOBY05/mobycentral.pl)
-             MOBY_URI     (default http://mobycentral.cbr.nrc.ca/MOBY/Central)
+             MOBY_SERVER  (default http://moby.ucalgary.ca/moby/MOBY-Central.pl)
+             MOBY_URI     (default http://moby.ucalgary.ca/MOBY/Central)
              MOBY_PROXY   (no default)
 
  Args      :    user_agent - optional.  The name of your software application
@@ -104,8 +105,8 @@
                                 }
                             - by default this becomes
                             {mobycentral => {
-                                 URL => 'http://mobycentral.cbr.nrc.ca/cgi-bin/MOBY05/mobycentral.pl',
-                                 URI => 'http://mobycentral.cbr.nrc.ca/MOBY/Central'}
+                                 URL => 'http://moby.ucalgary.ca/moby/MOBY-Central.pl',
+                                 URI => 'http://moby.ucalgary.ca/MOBY/Central'}
                              }
  Discussion:    Each registry must have a different
                 NAME.  If you have more than one



From kawas at dev.open-bio.org  Thu Mar  6 18:45:58 2008
From: kawas at dev.open-bio.org (Eddie Kawas)
Date: Thu, 6 Mar 2008 13:45:58 -0500
Subject: [MOBY-guts] biomoby commit
Message-ID: <200803061845.m26IjwBt029614@dev.open-bio.org>


kawas
Thu Mar  6 13:45:57 EST 2008
Update of /home/repository/moby/moby-live/Perl/MOBY-Client/share
In directory dev.open-bio.org:/tmp/cvs-serv29579/Perl/MOBY-Client/share

Modified Files:
	HelloWorldService.pm 
Log Message:
added a missing semi-colon
moby-live/Perl/MOBY-Client/share HelloWorldService.pm,1.1,1.2
===================================================================
RCS file: /home/repository/moby/moby-live/Perl/MOBY-Client/share/HelloWorldService.pm,v
retrieving revision 1.1
retrieving revision 1.2
diff -u -r1.1 -r1.2
--- /home/repository/moby/moby-live/Perl/MOBY-Client/share/HelloWorldService.pm	2008/02/22 16:32:43	1.1
+++ /home/repository/moby/moby-live/Perl/MOBY-Client/share/HelloWorldService.pm	2008/03/06 18:45:57	1.2
@@ -4,7 +4,7 @@
 # to you what you send it... in proper MOBY
 # message format of course :-)
 
-use MOBY::CommonSubs qw(:all)
+use MOBY::CommonSubs qw(:all);
 
 sub helloWorld {
 	my ($caller, $message) = @_;  # get the incoming MOBY query XML



From kawas at dev.open-bio.org  Thu Mar  6 23:18:32 2008
From: kawas at dev.open-bio.org (Eddie Kawas)
Date: Thu, 6 Mar 2008 18:18:32 -0500
Subject: [MOBY-guts] biomoby commit
Message-ID: <200803062318.m26NIWZS029915@dev.open-bio.org>


kawas
Thu Mar  6 18:18:32 EST 2008
Update of /home/repository/moby/moby-live/Perl/MOBY-Server/share/cgi
In directory dev.open-bio.org:/tmp/cvs-serv29880/Perl/MOBY-Server/share/cgi

Modified Files:
	RESOURCES 
Log Message:
added support for FULL
moby-live/Perl/MOBY-Server/share/cgi RESOURCES,1.1,1.2
===================================================================
RCS file: /home/repository/moby/moby-live/Perl/MOBY-Server/share/cgi/RESOURCES,v
retrieving revision 1.1
retrieving revision 1.2
diff -u -r1.1 -r1.2
--- /home/repository/moby/moby-live/Perl/MOBY-Server/share/cgi/RESOURCES	2008/02/21 00:21:27	1.1
+++ /home/repository/moby/moby-live/Perl/MOBY-Server/share/cgi/RESOURCES	2008/03/06 23:18:32	1.2
@@ -35,6 +35,8 @@
 use MOBY::RDF::Ontologies::Cache::ServiceTypeCache;
 use MOBY::Config;
 
+use XML::LibXML;
+
 # your cache dir
 my $dir = MOBY::Config->new->{mobycentral}->{rdf_cache} || "/tmp/";
 
@@ -119,15 +121,16 @@
 		} unless $x;
 	} unless $string;
 	do {
-		my $x = MOBY::RDF::Ontologies::Services->new;    
-		my $sname = substr ($string, index($string, ',')+1);
-        my $prov  = substr ($string, 1, index($string, ',')-1);
+		my $x     = MOBY::RDF::Ontologies::Services->new;
+		my $sname = substr( $string, index( $string, ',' ) + 1 );
+		my $prov  = substr( $string, 1, index( $string, ',' ) - 1 );
+
 		# get pretty printed RDF/XML for one service
 		$x = $x->findService(
-						   {
-							 serviceName => $sname,
-							 authURI     =>  $prov,
-						   }
+							  {
+								serviceName => $sname,
+								authURI     => $prov,
+							  }
 		);
 		print $form->header('text/xml'), $x if $x;
 	} if $string;
@@ -152,11 +155,86 @@
 		print $form->header('text/xml'), $rdf if $rdf;
 	} if $1;
 } elsif ( $url =~ m/^RESOURCES\/MOBY\-S\/FULL$/ ) {
+	my $dom    = undef;
+	my $parser = XML::LibXML->new();
 
-	print $form->header('text/html');
-	$form->start_html( -title => 'unavailable', );
-	print h2( "not", "implemented" );
-	print end_html;
+	# print this right away, because this might take a long time ...
+	print $form->header('text/xml');
+	if ($useCache) {
+		my $x =
+		  MOBY::RDF::Ontologies::Cache::NamespaceCache->new( cache => "$dir", );
+		$x = $x->get_rdf();
+		do {
+			my $doc = $parser->parse_string($x);
+			$dom = $doc;
+
+		} if $x;
+		$x =
+		  MOBY::RDF::Ontologies::Cache::ServiceTypeCache->new( cache => "$dir",
+		  );
+		$x = $x->get_rdf();
+		do {
+			my $doc = $parser->parse_string($x);
+			_appendChildrenOfDOMToOtherDOM( $doc, \$dom ) if $dom;
+			$dom = $doc unless $dom;
+		} if $x;
+		$x = MOBY::RDF::Ontologies::Cache::ObjectCache->new( cache => "$dir", );
+		$x = $x->get_rdf();
+		do {
+			my $doc = $parser->parse_string($x);
+			_appendChildrenOfDOMToOtherDOM( $doc, \$dom ) if $dom;
+			$dom = $doc unless $dom;
+
+		} if $x;
+		$x =
+		  MOBY::RDF::Ontologies::Cache::ServiceCache->new( cache => "$dir", );
+		$x = $x->get_rdf();
+		do {
+			my $doc = $parser->parse_string($x);
+			_appendChildrenOfDOMToOtherDOM( $doc, \$dom ) if $dom;
+			$dom = $doc unless $dom;
+
+		} if $x;
+
+		# TODO append ServiceDescription too when complete
+		print $dom->toString if $dom;
+
+	} else {
+		my $x = MOBY::RDF::Ontologies::Namespaces->new;
+		$x = $x->createAll();
+		do {
+			my $doc = $parser->parse_string($x);
+			_appendChildrenOfDOMToOtherDOM( $doc, \$dom ) if $dom;
+			$dom = $doc unless $dom;
+		} if $x;
+		
+		$x = MOBY::RDF::Ontologies::Objects->new;
+		$x = $x->createAll();
+		do {
+			my $doc = $parser->parse_string($x);
+			_appendChildrenOfDOMToOtherDOM( $doc, \$dom ) if $dom;
+			$dom = $doc unless $dom;
+		} if $x;
+		
+		$x = MOBY::RDF::Ontologies::ServiceTypes->new;
+		$x = $x->createAll();
+		do {
+			my $doc = $parser->parse_string($x);
+			_appendChildrenOfDOMToOtherDOM( $doc, \$dom ) if $dom;
+			$dom = $doc unless $dom;
+		} if $x;
+		
+		$x = MOBY::RDF::Ontologies::Services->new;
+		$x = $x->findService();
+		do {
+			my $doc = $parser->parse_string($x);
+			_appendChildrenOfDOMToOtherDOM( $doc, \$dom ) if $dom;
+			$dom = $doc unless $dom;
+		} if $x;
+
+		# TODO append ServiceDescription too when complete
+		print $dom->toString if $dom;
+	}
 
 } elsif ( $url =~ m/^RESOURCES\/MOBY\-S\/ServiceDescription$/ ) {
 	print $form->header('text/html');
@@ -172,3 +250,10 @@
 	print end_html;
 }
 
+sub _appendChildrenOfDOMToOtherDOM {
+	my ( $dom, $other_dom ) = @_;
+	foreach my $service ( $dom->findnodes('/rdf:RDF/rdf:Description') ) {
+		$$other_dom->documentElement->appendChild($service);
+	}
+	return $other_dom;
+}



From gordonp at dev.open-bio.org  Fri Mar  7 22:42:04 2008
From: gordonp at dev.open-bio.org (Paul Gordon)
Date: Fri, 7 Mar 2008 17:42:04 -0500
Subject: [MOBY-guts] biomoby commit
Message-ID: <200803072242.m27Mg4kb001004@dev.open-bio.org>


gordonp
Fri Mar  7 17:42:03 EST 2008
Update of /home/repository/moby/moby-live/Java/src/main/org/biomoby/shared
In directory dev.open-bio.org:/tmp/cvs-serv968/src/main/org/biomoby/shared

Modified Files:
	MobyPrefixResolver.java 
Log Message:
Fixed unchecked operation warning, added SAWSDL support for semantic WSDL wrapping servlet to come shortly
moby-live/Java/src/main/org/biomoby/shared MobyPrefixResolver.java,1.11,1.12
===================================================================
RCS file: /home/repository/moby/moby-live/Java/src/main/org/biomoby/shared/MobyPrefixResolver.java,v
retrieving revision 1.11
retrieving revision 1.12
diff -u -r1.11 -r1.12
--- /home/repository/moby/moby-live/Java/src/main/org/biomoby/shared/MobyPrefixResolver.java	2008/02/13 01:28:06	1.11
+++ /home/repository/moby/moby-live/Java/src/main/org/biomoby/shared/MobyPrefixResolver.java	2008/03/07 22:42:03	1.12
@@ -44,6 +44,8 @@
     public static final String XHTML_NAMESPACE = "http://www.w3.org/1999/xhtml";
     public static final String XLINK_PREFIX = "xlink";
     public static final String XLINK_NAMESPACE = "http://www.w3.org/1999/xlink";
+    public static final String SAWSDL_PREFIX = "sawsdl";
+    public static final String SAWSDL_NAMESPACE = "http://www.w3.org/ns/sawsdl";
 
     /**
      * We don't really implement this as it can be extremely complicated.
@@ -121,10 +123,10 @@
     }
 
     public static class MobyNodeList implements NodeList{
-	private Vector nodes;
-	public MobyNodeList(){nodes = new Vector();}
+	private Vector<Node> nodes;
+	public MobyNodeList(){nodes = new Vector<Node>();}
 	public int getLength(){return nodes.size();}
-	public Node item(int index){return (Node) nodes.elementAt(index);}
+	public Node item(int index){return nodes.elementAt(index);}
 	public void add(Node n){nodes.add(n);}
     };
 



From gordonp at dev.open-bio.org  Fri Mar  7 22:42:32 2008
From: gordonp at dev.open-bio.org (Paul Gordon)
Date: Fri, 7 Mar 2008 17:42:32 -0500
Subject: [MOBY-guts] biomoby commit
Message-ID: <200803072242.m27MgWhc001048@dev.open-bio.org>


gordonp
Fri Mar  7 17:42:31 EST 2008
Update of /home/repository/moby/moby-live/Java/src/main/org/biomoby/shared
In directory dev.open-bio.org:/tmp/cvs-serv1012/src/main/org/biomoby/shared

Modified Files:
	NamespaceContextImpl.java 
Log Message:
Added SAWSDL support for semantic WSDL wrapping servlet to come shortly
moby-live/Java/src/main/org/biomoby/shared NamespaceContextImpl.java,1.3,1.4
===================================================================
RCS file: /home/repository/moby/moby-live/Java/src/main/org/biomoby/shared/NamespaceContextImpl.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/NamespaceContextImpl.java	2008/02/13 01:28:06	1.3
+++ /home/repository/moby/moby-live/Java/src/main/org/biomoby/shared/NamespaceContextImpl.java	2008/03/07 22:42:31	1.4
@@ -31,6 +31,7 @@
 	prefixes.put(MobyPrefixResolver.WSRP_NAMESPACE, MobyPrefixResolver.WSRP_PREFIX);	
 	prefixes.put(MobyPrefixResolver.XHTML_NAMESPACE, MobyPrefixResolver.XHTML_PREFIX);
 	prefixes.put(MobyPrefixResolver.XLINK_NAMESPACE, MobyPrefixResolver.XLINK_PREFIX);
+	prefixes.put(MobyPrefixResolver.SAWSDL_NAMESPACE, MobyPrefixResolver.SAWSDL_PREFIX);
 
 	// Reverse map prefix -> nsURI
 	nsURIs.put(MobyPrefixResolver.XSI_PREFIX, MobyPrefixResolver.XSI_NAMESPACE2001);



From senger at dev.open-bio.org  Sat Mar  8 12:34:08 2008
From: senger at dev.open-bio.org (Martin Senger)
Date: Sat, 8 Mar 2008 07:34:08 -0500
Subject: [MOBY-guts] biomoby commit
Message-ID: <200803081234.m28CY8wY002469@dev.open-bio.org>


senger
Sat Mar  8 07:34:07 EST 2008
Update of /home/repository/moby/moby-live/Java/docs
In directory dev.open-bio.org:/tmp/cvs-serv2450/docs

Modified Files:
	index.html 
Log Message:
Broken link updated

moby-live/Java/docs index.html,1.31,1.32
===================================================================
RCS file: /home/repository/moby/moby-live/Java/docs/index.html,v
retrieving revision 1.31
retrieving revision 1.32
diff -u -r1.31 -r1.32
--- /home/repository/moby/moby-live/Java/docs/index.html	2008/02/22 03:07:20	1.31
+++ /home/repository/moby/moby-live/Java/docs/index.html	2008/03/08 12:34:07	1.32
@@ -57,7 +57,7 @@
        The main issue is that jMoby uses now the 3rd-party libraries
 form the various Maven repositories. It fetches them when you compile
 jMoby, or when you use the new Ant's task <tt>install</tt>. There is
-<a href="http://pantheon.generationcp.org/UsingMaven.html">an
+<a href="http://pantheon.generationcp.org/index.php?option=com_content&task=view&id=379&Itemid=197">an
 article</a> about how it is done (coming from a different project but
 using the same principles as in jMoby). <p>
 
@@ -225,7 +225,7 @@
 <div align=right class="address">
 <address><A HREF="mailto:martin.senger at gmail.com">Martin Senger</A><BR></address>
 <!-- hhmts start -->
-Last modified: Fri Feb 22 11:00:53 2008
+Last modified: Sat Mar  8 20:32:22 2008
 <!-- hhmts end -->
 </div>
 </body> </html>



From jmrc at dev.open-bio.org  Mon Mar 10 12:14:19 2008
From: jmrc at dev.open-bio.org (José Manuel Rodríguez Carrasco)
Date: Mon, 10 Mar 2008 08:14:19 -0400
Subject: [MOBY-guts] biomoby commit
Message-ID: <200803101214.m2ACEJ6K008798@dev.open-bio.org>


jmrc
Mon Mar 10 08:14:18 EDT 2008
Update of /home/repository/moby/moby-live/Docs/asyncDocs
In directory dev.open-bio.org:/tmp/cvs-serv8763/asyncDocs

Log Message:
Directory /home/repository/moby/moby-live/Docs/asyncDocs added to the repository

moby-live/Docs/asyncDocs - New directory
rcsdiff: /home/repository/moby/moby-live/Docs/asyncDocs/RCS/-,v: No such file or directory

rcsdiff: /home/repository/moby/moby-live/Docs/asyncDocs/RCS/New,v: No such file or directory

rcsdiff: /home/repository/moby/moby-live/Docs/asyncDocs/RCS/directory,v: No such file or directory



From jmrc at dev.open-bio.org  Mon Mar 10 12:25:34 2008
From: jmrc at dev.open-bio.org (José Manuel Rodríguez Carrasco)
Date: Mon, 10 Mar 2008 08:25:34 -0400
Subject: [MOBY-guts] biomoby commit
Message-ID: <200803101225.m2ACPYBx008995@dev.open-bio.org>


jmrc
Mon Mar 10 08:25:34 EDT 2008
Update of /home/repository/moby/moby-live/Docs/asyncDocs/async-MOBY-test
In directory dev.open-bio.org:/tmp/cvs-serv8960/async-MOBY-test

Log Message:
Directory /home/repository/moby/moby-live/Docs/asyncDocs/async-MOBY-test added to the repository

moby-live/Docs/asyncDocs/async-MOBY-test - New directory
rcsdiff: /home/repository/moby/moby-live/Docs/asyncDocs/async-MOBY-test/RCS/-,v: No such file or directory

rcsdiff: /home/repository/moby/moby-live/Docs/asyncDocs/async-MOBY-test/RCS/New,v: No such file or directory

rcsdiff: /home/repository/moby/moby-live/Docs/asyncDocs/async-MOBY-test/RCS/directory,v: No such file or directory



From jmrc at dev.open-bio.org  Mon Mar 10 12:31:31 2008
From: jmrc at dev.open-bio.org (José Manuel Rodríguez Carrasco)
Date: Mon, 10 Mar 2008 08:31:31 -0400
Subject: [MOBY-guts] biomoby commit
Message-ID: <200803101231.m2ACVVrR009108@dev.open-bio.org>


jmrc
Mon Mar 10 08:31:31 EDT 2008
Update of /home/repository/moby/moby-live/Docs/asyncDocs
In directory dev.open-bio.org:/tmp/cvs-serv9073/asyncDocs

Added Files:
	BioMOBY Asynchronous Service Specification_v2.4.1.pdf 
Log Message:
user: jmrc
date: 10-March-2008

Specification document of asynchronous proposal with examples.



moby-live/Docs/asyncDocs BioMOBY Asynchronous Service Specification_v2.4.1.pdf,NONE,1.1
rcsdiff: /home/repository/moby/moby-live/Docs/asyncDocs/RCS/BioMOBY,v: No such file or directory

rcsdiff: /home/repository/moby/moby-live/Docs/asyncDocs/RCS/Asynchronous,v: No such file or directory

rcsdiff: /home/repository/moby/moby-live/Docs/asyncDocs/RCS/Service,v: No such file or directory



From jmrc at dev.open-bio.org  Mon Mar 10 12:31:31 2008
From: jmrc at dev.open-bio.org (José Manuel Rodríguez Carrasco)
Date: Mon, 10 Mar 2008 08:31:31 -0400
Subject: [MOBY-guts] biomoby commit
Message-ID: <200803101231.m2ACVVKJ009124@dev.open-bio.org>


jmrc
Mon Mar 10 08:31:31 EDT 2008
Update of /home/repository/moby/moby-live/Docs/asyncDocs/async-MOBY-test
In directory dev.open-bio.org:/tmp/cvs-serv9073/asyncDocs/async-MOBY-test

Added Files:
	AsyncService.pm async-MOBY-test.cgi async-MOBY-test.cgi.pl 
	deregister-runAsyncMOBYService.pl 
	register-runAsyncMOBYService.pl 
	running_runAsyncMOBYservice-StepByStep.pl 
	running_runAsyncMOBYservice.pl sayHello-description.xml 
	sayHello.wsdl 
Log Message:
user: jmrc
date: 10-March-2008

Specification document of asynchronous proposal with examples.



moby-live/Docs/asyncDocs/async-MOBY-test AsyncService.pm,NONE,1.1 async-MOBY-test.cgi,NONE,1.1 async-MOBY-test.cgi.pl,NONE,1.1 deregister-runAsyncMOBYService.pl,NONE,1.1 register-runAsyncMOBYService.pl,NONE,1.1 running_runAsyncMOBYservice-StepByStep.pl,NONE,1.1 running_runAsyncMOBYservice.pl,NONE,1.1 sayHello-description.xml,NONE,1.1 sayHello.wsdl,NONE,1.1


From jmrc at dev.open-bio.org  Mon Mar 10 13:13:02 2008
From: jmrc at dev.open-bio.org (José Manuel Rodríguez Carrasco)
Date: Mon, 10 Mar 2008 09:13:02 -0400
Subject: [MOBY-guts] biomoby commit
Message-ID: <200803101313.m2ADD2GN009389@dev.open-bio.org>


jmrc
Mon Mar 10 09:13:01 EDT 2008
Update of /home/repository/moby/moby-live/Docs/asyncDocs
In directory dev.open-bio.org:/tmp/cvs-serv9357

Added Files:
	README.txt 
Log Message:
user: jmrc
date: 10-March-2008

README file that details the documents of asynchronous proposal.



moby-live/Docs/asyncDocs README.txt,NONE,1.1


From kawas at dev.open-bio.org  Tue Mar 11 14:44:19 2008
From: kawas at dev.open-bio.org (Eddie Kawas)
Date: Tue, 11 Mar 2008 10:44:19 -0400
Subject: [MOBY-guts] biomoby commit
Message-ID: <200803111444.m2BEiJfa019295@dev.open-bio.org>


kawas
Tue Mar 11 10:44:18 EDT 2008
Update of /home/repository/moby/moby-live/Perl/MOBY-Server/share/cgi
In directory dev.open-bio.org:/tmp/cvs-serv19260/Perl/MOBY-Server/share/cgi

Modified Files:
	authority.pl 
Log Message:
added code that returns wsdl documents (declared via import statements) requested whenever you try to use parse the wsdl obtained from the lsid server.
the code loops through the INC paths looking for files. if they are found, they are printed out to stdout. otherwise, the default behaviour is done.
moby-live/Perl/MOBY-Server/share/cgi authority.pl,1.1,1.2
===================================================================
RCS file: /home/repository/moby/moby-live/Perl/MOBY-Server/share/cgi/authority.pl,v
retrieving revision 1.1
retrieving revision 1.2
diff -u -r1.1 -r1.2
--- /home/repository/moby/moby-live/Perl/MOBY-Server/share/cgi/authority.pl	2008/02/21 00:21:27	1.1
+++ /home/repository/moby/moby-live/Perl/MOBY-Server/share/cgi/authority.pl	2008/03/11 14:44:18	1.2
@@ -37,6 +37,25 @@
 
 ##############
 
+# serve wsdl documents on request if they exist and are readable ...
+# obtain them from the INC
+if($ENV{'REQUEST_URI'} && ($ENV{'REQUEST_URI'} =~ /^\/authority\/(\w+)\.wsdl/)) {
+  my $wsdl_location = undef;
+  for my $dir (@INC) {
+    my $ls_module = "LS/Authority/WSDL/$1.wsdl";
+    $wsdl_location = "$dir/$ls_module" if -e "$dir/$ls_module";
+  }
+  if ($wsdl_location and -e $wsdl_location and -r $wsdl_location) {
+    my $parser = XML::LibXML->new();
+    my $doc = undef;
+    eval {
+      $doc    = $parser->parse_file( "$wsdl_location" );
+      my $doc = $doc->toString();
+      print "Content-type: text/xml\n\n$doc" if $doc;
+    }
+  }
+}
+
 my $location = 'http://';
 
 # TODO get this from the mobyconfig file



From gordonp at dev.open-bio.org  Wed Mar 12 17:32:08 2008
From: gordonp at dev.open-bio.org (Paul Gordon)
Date: Wed, 12 Mar 2008 13:32:08 -0400
Subject: [MOBY-guts] biomoby commit
Message-ID: <200803121732.m2CHW8kn021799@dev.open-bio.org>


gordonp
Wed Mar 12 13:32:07 EDT 2008
Update of /home/repository/moby/moby-live/Java/src/main/org/biomoby/shared/test
In directory dev.open-bio.org:/tmp/cvs-serv21764/src/main/org/biomoby/shared/test

Log Message:
Directory /home/repository/moby/moby-live/Java/src/main/org/biomoby/shared/test added to the repository

moby-live/Java/src/main/org/biomoby/shared/test - New directory
rcsdiff: /home/repository/moby/moby-live/Java/src/main/org/biomoby/shared/test/RCS/-,v: No such file or directory

rcsdiff: /home/repository/moby/moby-live/Java/src/main/org/biomoby/shared/test/RCS/New,v: No such file or directory

rcsdiff: /home/repository/moby/moby-live/Java/src/main/org/biomoby/shared/test/RCS/directory,v: No such file or directory



From gordonp at dev.open-bio.org  Wed Mar 12 17:47:18 2008
From: gordonp at dev.open-bio.org (Paul Gordon)
Date: Wed, 12 Mar 2008 13:47:18 -0400
Subject: [MOBY-guts] biomoby commit
Message-ID: <200803121747.m2CHlIc8021974@dev.open-bio.org>


gordonp
Wed Mar 12 13:47:18 EDT 2008
Update of /home/repository/moby/moby-live/Java/src/main/org/biomoby/shared/test
In directory dev.open-bio.org:/tmp/cvs-serv21918/src/main/org/biomoby/shared/test

Added Files:
	LSIDResolverTestCase.java 
Log Message:
Initial commit of lightweight LSID resolver
moby-live/Java/src/main/org/biomoby/shared/test LSIDResolverTestCase.java,NONE,1.1


From gordonp at dev.open-bio.org  Wed Mar 12 17:47:18 2008
From: gordonp at dev.open-bio.org (Paul Gordon)
Date: Wed, 12 Mar 2008 13:47:18 -0400
Subject: [MOBY-guts] biomoby commit
Message-ID: <200803121747.m2CHlIn1021958@dev.open-bio.org>


gordonp
Wed Mar 12 13:47:18 EDT 2008
Update of /home/repository/moby/moby-live/Java/src/main/org/biomoby/shared
In directory dev.open-bio.org:/tmp/cvs-serv21918/src/main/org/biomoby/shared

Modified Files:
	MobyPrefixResolver.java NamespaceContextImpl.java 
Added Files:
	LSIDResolver.java 
Log Message:
Initial commit of lightweight LSID resolver
moby-live/Java/src/main/org/biomoby/shared LSIDResolver.java,NONE,1.1 MobyPrefixResolver.java,1.12,1.13 NamespaceContextImpl.java,1.4,1.5
===================================================================
RCS file: /home/repository/moby/moby-live/Java/src/main/org/biomoby/shared/MobyPrefixResolver.java,v
retrieving revision 1.12
retrieving revision 1.13
diff -u -r1.12 -r1.13
--- /home/repository/moby/moby-live/Java/src/main/org/biomoby/shared/MobyPrefixResolver.java	2008/03/07 22:42:03	1.12
+++ /home/repository/moby/moby-live/Java/src/main/org/biomoby/shared/MobyPrefixResolver.java	2008/03/12 17:47:18	1.13
@@ -44,8 +44,14 @@
     public static final String XHTML_NAMESPACE = "http://www.w3.org/1999/xhtml";
     public static final String XLINK_PREFIX = "xlink";
     public static final String XLINK_NAMESPACE = "http://www.w3.org/1999/xlink";
+    public static final String WSDL_PREFIX = "wsdl";
+    public static final String WSDL_NAMESPACE = "http://schemas.xmlsoap.org/wsdl/";
+    public static final String HTTP_PREFIX = "http";
+    public static final String HTTP_NAMESPACE = "http://schemas.xmlsoap.org/wsdl/http/";
     public static final String SAWSDL_PREFIX = "sawsdl";
     public static final String SAWSDL_NAMESPACE = "http://www.w3.org/ns/sawsdl";
+    public static final String LSID_PREFIX = "lsid";
+    public static final String LSID_NAMESPACE = "http://lsid.omg.org/predicates#";
 
     /**
      * We don't really implement this as it can be extremely complicated.

===================================================================
RCS file: /home/repository/moby/moby-live/Java/src/main/org/biomoby/shared/NamespaceContextImpl.java,v
retrieving revision 1.4
retrieving revision 1.5
diff -u -r1.4 -r1.5
--- /home/repository/moby/moby-live/Java/src/main/org/biomoby/shared/NamespaceContextImpl.java	2008/03/07 22:42:31	1.4
+++ /home/repository/moby/moby-live/Java/src/main/org/biomoby/shared/NamespaceContextImpl.java	2008/03/12 17:47:18	1.5
@@ -31,7 +31,10 @@
 	prefixes.put(MobyPrefixResolver.WSRP_NAMESPACE, MobyPrefixResolver.WSRP_PREFIX);	
 	prefixes.put(MobyPrefixResolver.XHTML_NAMESPACE, MobyPrefixResolver.XHTML_PREFIX);
 	prefixes.put(MobyPrefixResolver.XLINK_NAMESPACE, MobyPrefixResolver.XLINK_PREFIX);
+	prefixes.put(MobyPrefixResolver.WSDL_NAMESPACE, MobyPrefixResolver.WSDL_PREFIX);
+	prefixes.put(MobyPrefixResolver.HTTP_NAMESPACE, MobyPrefixResolver.HTTP_PREFIX);
 	prefixes.put(MobyPrefixResolver.SAWSDL_NAMESPACE, MobyPrefixResolver.SAWSDL_PREFIX);
+	prefixes.put(MobyPrefixResolver.LSID_NAMESPACE, MobyPrefixResolver.LSID_PREFIX);
 
 	// Reverse map prefix -> nsURI
 	nsURIs.put(MobyPrefixResolver.XSI_PREFIX, MobyPrefixResolver.XSI_NAMESPACE2001);



From senger at dev.open-bio.org  Wed Mar 12 18:41:26 2008
From: senger at dev.open-bio.org (Martin Senger)
Date: Wed, 12 Mar 2008 14:41:26 -0400
Subject: [MOBY-guts] biomoby commit
Message-ID: <200803121841.m2CIfQKH022077@dev.open-bio.org>


senger
Wed Mar 12 14:41:26 EDT 2008
Update of /home/repository/moby/moby-live/Java/xmls
In directory dev.open-bio.org:/tmp/cvs-serv22058/xmls

Modified Files:
	project.pom 
Log Message:
Excluding xerces parser from dependencies

moby-live/Java/xmls project.pom,1.6,1.7
===================================================================
RCS file: /home/repository/moby/moby-live/Java/xmls/project.pom,v
retrieving revision 1.6
retrieving revision 1.7
diff -u -r1.6 -r1.7
--- /home/repository/moby/moby-live/Java/xmls/project.pom	2008/03/02 12:45:27	1.6
+++ /home/repository/moby/moby-live/Java/xmls/project.pom	2008/03/12 18:41:26	1.7
@@ -164,6 +164,16 @@
       <groupId>commons-dbcp</groupId>
       <artifactId>commons-dbcp</artifactId>
       <version>1.1</version>
+      <!-- we need to exclude this in order to load SAXParserFactory from 
+       default J2SE 1.5, And it will work.If SAXParserFactory is loaded 
+       from any of the older versions of JAXP, exception is thrown.
+       -->
+      <exclusions>
+        <exclusion>
+          <groupId>xerces</groupId>
+          <artifactId>xercesImpl</artifactId>
+        </exclusion>
+      </exclusions> 
     </dependency>
 
     <dependency>
@@ -197,6 +207,16 @@
       <groupId>com.hp.hpl.jena</groupId>
       <artifactId>jena</artifactId>
       <version>2.5.4</version>
+      <!-- we need to exclude this in order to load SAXParserFactory from 
+       default J2SE 1.5, And it will work.If SAXParserFactory is loaded 
+       from any of the older versions of JAXP, exception is thrown.
+       -->
+      <exclusions>
+        <exclusion>
+          <groupId>xerces</groupId>
+          <artifactId>xercesImpl</artifactId>
+        </exclusion>
+      </exclusions> 
     </dependency>
 
     <dependency>
@@ -251,6 +271,16 @@
       <groupId>jaxen</groupId>
       <artifactId>jaxen</artifactId>
       <version>1.1.1</version>
+      <!-- we need to exclude this in order to load SAXParserFactory from 
+       default J2SE 1.5, And it will work.If SAXParserFactory is loaded 
+       from any of the older versions of JAXP, exception is thrown.
+       -->
+      <exclusions>
+        <exclusion>
+          <groupId>xerces</groupId>
+          <artifactId>xercesImpl</artifactId>
+        </exclusion>
+      </exclusions> 
     </dependency>
 
     <dependency>



From kawas at dev.open-bio.org  Thu Mar 13 15:03:58 2008
From: kawas at dev.open-bio.org (Eddie Kawas)
Date: Thu, 13 Mar 2008 11:03:58 -0400
Subject: [MOBY-guts] biomoby commit
Message-ID: <200803131503.m2DF3wk3028670@dev.open-bio.org>


kawas
Thu Mar 13 11:03:58 EDT 2008
Update of /home/repository/moby/moby-live/Perl/MOBY-Server/share/cgi
In directory dev.open-bio.org:/tmp/cvs-serv28634/Perl/MOBY-Server/share/cgi

Modified Files:
	authority.pl 
Log Message:
removed the soap ports. unfortunately, since we have to serve attachments when using soap and soap lite doesnt have attachment support (currently) these ports are now disabled.
moby-live/Perl/MOBY-Server/share/cgi authority.pl,1.2,1.3
===================================================================
RCS file: /home/repository/moby/moby-live/Perl/MOBY-Server/share/cgi/authority.pl,v
retrieving revision 1.2
retrieving revision 1.3
diff -u -r1.2 -r1.3
--- /home/repository/moby/moby-live/Perl/MOBY-Server/share/cgi/authority.pl	2008/03/11 14:44:18	1.2
+++ /home/repository/moby/moby-live/Perl/MOBY-Server/share/cgi/authority.pl	2008/03/13 15:03:58	1.3
@@ -91,12 +91,12 @@
 
 my $port;
 
-$port = LS::Authority::WSDL::Simple::MetadataPort->newMetadata(
-	portName=> 'BioMOBYSoapPort',
-	endpoint=> "$location/authority/metadata",
-	protocol=> $LS::Authority::WSDL::Constants::Protocols::SOAP,
-  );
-$authority->addPort(serviceName=> 'BioMOBYSoapMeta', port=> $port);
+#$port = LS::Authority::WSDL::Simple::MetadataPort->newMetadata(
+#	portName=> 'BioMOBYSoapPort',
+#	endpoint=> "$location/authority/metadata",
+#	protocol=> $LS::Authority::WSDL::Constants::Protocols::SOAP,
+#  );
+#$authority->addPort(serviceName=> 'BioMOBYSoapMeta', port=> $port);
 
 $port = LS::Authority::WSDL::Simple::MetadataPort->newMetadata(
 	portName=> 'BioMOBYHttpPort',
@@ -112,13 +112,13 @@
         protocol=> $LS::Authority::WSDL::Constants::Protocols::HTTP,
   );
 
-$authority->addPort(serviceName=> 'BioMOBYHttpData', port=> $port);
-$port = LS::Authority::WSDL::Simple::DataPort->newData(
-        portName=> 'BioMOBYSoapPort',
-        endpoint=> "$location/authority/data",
-        protocol=> $LS::Authority::WSDL::Constants::Protocols::SOAP,
-  );
-$authority->addPort(serviceName=> 'BioMOBYSoapData', port=> $port);
+#$authority->addPort(serviceName=> 'BioMOBYSoapData', port=> $port);
+#$port = LS::Authority::WSDL::Simple::DataPort->newData(
+#        portName=> 'BioMOBYSoapPort',
+#        endpoint=> "$location/authority/data",
+#        protocol=> $LS::Authority::WSDL::Constants::Protocols::SOAP,
+#  );
+#$authority->addPort(serviceName=> 'BioMOBYSoapData', port=> $port);
 
 
 # Add the metadata service with namespaces



From senger at dev.open-bio.org  Thu Mar 13 15:09:14 2008
From: senger at dev.open-bio.org (Martin Senger)
Date: Thu, 13 Mar 2008 11:09:14 -0400
Subject: [MOBY-guts] biomoby commit
Message-ID: <200803131509.m2DF9Ecm028742@dev.open-bio.org>


senger
Thu Mar 13 11:09:14 EDT 2008
Update of /home/repository/moby/moby-live/Java/src/main/org/biomoby/service/dashboard/help
In directory dev.open-bio.org:/tmp/cvs-serv28723/src/main/org/biomoby/service/dashboard/help

Modified Files:
	GeneratorPanel.html 
Log Message:
Dashboard help about the (remote) deployment improved.

moby-live/Java/src/main/org/biomoby/service/dashboard/help GeneratorPanel.html,1.3,1.4
===================================================================
RCS file: /home/repository/moby/moby-live/Java/src/main/org/biomoby/service/dashboard/help/GeneratorPanel.html,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/service/dashboard/help/GeneratorPanel.html	2006/06/01 15:20:08	1.3
+++ /home/repository/moby/moby-live/Java/src/main/org/biomoby/service/dashboard/help/GeneratorPanel.html	2008/03/13 15:09:14	1.4
@@ -80,7 +80,14 @@
 
 Usually, only <em>Tomcat home directory</em> needs to be changed
 (unless you have installed Axis in Tomcat in a non-standard
-place). The <em>WSDD template file</em> is an advanced feature - see
+place). <p>
+
+Be aware, however, that the deployment also uses properties defined in
+your <tt>build.properties</tt> file, and the value of the environment
+variable <tt>CATALINA_HOME</tt> (if defined). These properties take
+precedence over the values specified in the Dasboard's fields! <p>
+
+The <em>WSDD template file</em> is an advanced feature - see
 the deployment documentation. <p>
 
 Very important is the <em>Directory with user's jar files</em>. Here



From senger at dev.open-bio.org  Thu Mar 13 16:49:35 2008
From: senger at dev.open-bio.org (Martin Senger)
Date: Thu, 13 Mar 2008 12:49:35 -0400
Subject: [MOBY-guts] biomoby commit
Message-ID: <200803131649.m2DGnZnq028855@dev.open-bio.org>


senger
Thu Mar 13 12:49:35 EDT 2008
Update of /home/repository/moby/moby-live/Java/xmls
In directory dev.open-bio.org:/tmp/cvs-serv28832/xmls

Modified Files:
	project.pom upload2maven.xml 
Log Message:
Last few typos before uploading jMoby, version 1.0.0, to Maven

moby-live/Java/xmls project.pom,1.7,1.8 upload2maven.xml,1.1,1.2
===================================================================
RCS file: /home/repository/moby/moby-live/Java/xmls/project.pom,v
retrieving revision 1.7
retrieving revision 1.8
diff -u -r1.7 -r1.8
--- /home/repository/moby/moby-live/Java/xmls/project.pom	2008/03/12 18:41:26	1.7
+++ /home/repository/moby/moby-live/Java/xmls/project.pom	2008/03/13 16:49:35	1.8
@@ -4,7 +4,9 @@
   <artifactId>jmoby</artifactId>
   <version>1.0.0</version>
   <name>jMoby</name>
-  <description>A sub-project of the BioMoby project. It aims to develop tools in Java for BioMoby.</description>
+  <description>
+A sub-project of the BioMoby project. It aims to develop tools in Java for BioMoby.
+</description>
   <url>http://biomoby.open-bio.org/CVS_CONTENT/moby-live/Java/docs/</url>
 
   <developers>

===================================================================
RCS file: /home/repository/moby/moby-live/Java/xmls/upload2maven.xml,v
retrieving revision 1.1
retrieving revision 1.2
diff -u -r1.1 -r1.2
--- /home/repository/moby/moby-live/Java/xmls/upload2maven.xml	2008/02/14 06:13:37	1.1
+++ /home/repository/moby/moby-live/Java/xmls/upload2maven.xml	2008/03/13 16:49:35	1.2
@@ -23,7 +23,6 @@
 <!-- Deploy all parts of this project to a remote Maven repository -->
 <target name="mdeploy" depends="mdeploy-core"/>
 
-<!-- deploying soaplab.jar -->
 <target name="mdeploy-core" depends="initmaven,jars">
   <artifact:install-provider artifactId="${bio.maven.install.provider}" version="1.0-alpha-5"/>
 



From kawas at dev.open-bio.org  Thu Mar 13 19:12:08 2008
From: kawas at dev.open-bio.org (Eddie Kawas)
Date: Thu, 13 Mar 2008 15:12:08 -0400
Subject: [MOBY-guts] biomoby commit
Message-ID: <200803131912.m2DJC8nb029085@dev.open-bio.org>


kawas
Thu Mar 13 15:12:07 EDT 2008
Update of /home/repository/moby/moby-live/Perl/MOBY-Server/lib/MOBY/RDF/Parsers
In directory dev.open-bio.org:/tmp/cvs-serv29054/Perl/MOBY-Server/lib/MOBY/RDF/Parsers

Added Files:
	DatatypeParser.pm 
Log Message:
an rdf parser for datatypes
moby-live/Perl/MOBY-Server/lib/MOBY/RDF/Parsers DatatypeParser.pm,NONE,1.1


From kawas at dev.open-bio.org  Thu Mar 13 19:12:29 2008
From: kawas at dev.open-bio.org (Eddie Kawas)
Date: Thu, 13 Mar 2008 15:12:29 -0400
Subject: [MOBY-guts] biomoby commit
Message-ID: <200803131912.m2DJCTCM029125@dev.open-bio.org>


kawas
Thu Mar 13 15:12:29 EDT 2008
Update of /home/repository/moby/moby-live/Perl/MOBY-Server
In directory dev.open-bio.org:/tmp/cvs-serv29090/Perl/MOBY-Server

Modified Files:
	MANIFEST 
Log Message:
added the DatatypeParser.pm module
moby-live/Perl/MOBY-Server MANIFEST,1.3,1.4
===================================================================
RCS file: /home/repository/moby/moby-live/Perl/MOBY-Server/MANIFEST,v
retrieving revision 1.3
retrieving revision 1.4
diff -u -r1.3 -r1.4
--- /home/repository/moby/moby-live/Perl/MOBY-Server/MANIFEST	2008/03/05 18:25:01	1.3
+++ /home/repository/moby/moby-live/Perl/MOBY-Server/MANIFEST	2008/03/13 19:12:29	1.4
@@ -57,6 +57,7 @@
 lib/MOBY/OntologyServer.pm
 lib/MOBY/RDF/Parsers/NamespaceParser.pm
 lib/MOBY/RDF/Parsers/ServiceTypeParser.pm
+lib/MOBY/RDF/Parsers/DatatypeParser.pm
 lib/MOBY/RDF/Ontologies/Cache/CacheUtils.pm
 lib/MOBY/RDF/Ontologies/Cache/NamespaceCache.pm
 lib/MOBY/RDF/Ontologies/Cache/ObjectCache.pm



From kawas at dev.open-bio.org  Thu Mar 13 19:12:45 2008
From: kawas at dev.open-bio.org (Eddie Kawas)
Date: Thu, 13 Mar 2008 15:12:45 -0400
Subject: [MOBY-guts] biomoby commit
Message-ID: <200803131912.m2DJCjP7029165@dev.open-bio.org>


kawas
Thu Mar 13 15:12:44 EDT 2008
Update of /home/repository/moby/moby-live/Perl/MOBY-Client
In directory dev.open-bio.org:/tmp/cvs-serv29130/Perl/MOBY-Client

Modified Files:
	populate_libs.pl 
Log Message:
added the DatatypeParser.pm module
moby-live/Perl/MOBY-Client populate_libs.pl,1.4,1.5
===================================================================
RCS file: /home/repository/moby/moby-live/Perl/MOBY-Client/populate_libs.pl,v
retrieving revision 1.4
retrieving revision 1.5
diff -u -r1.4 -r1.5
--- /home/repository/moby/moby-live/Perl/MOBY-Client/populate_libs.pl	2008/03/05 18:22:00	1.4
+++ /home/repository/moby/moby-live/Perl/MOBY-Client/populate_libs.pl	2008/03/13 19:12:44	1.5
@@ -13,7 +13,7 @@
 my @Client		= qw ( Central.pm CollectionArticle.pm OntologyServer.pm Registration.pm SecondaryArticle.pm Service.pm ServiceInstance.pm SimpleArticle.pm SimpleInput.pm );
 my @Exception 	= qw ( MobyException.pm MobyExceptionCodes.pm );
 my @RDF 		= qw ( Utils.pm );
-my @Parsers 	= qw ( ServiceTypeParser.pm NamespaceParser.pm );
+my @Parsers 	= qw ( ServiceTypeParser.pm NamespaceParser.pm DatatypeParser.pm);
 my @predicates  = qw ( DC_PROTEGE.pm MOBY_PREDICATES.pm OMG_LSID.pm RDF.pm RDFS.pm FETA.pm OWL.pm );
 
 # current working directory ...



From kawas at dev.open-bio.org  Thu Mar 13 19:13:00 2008
From: kawas at dev.open-bio.org (Eddie Kawas)
Date: Thu, 13 Mar 2008 15:13:00 -0400
Subject: [MOBY-guts] biomoby commit
Message-ID: <200803131913.m2DJD06I029205@dev.open-bio.org>


kawas
Thu Mar 13 15:12:59 EDT 2008
Update of /home/repository/moby/moby-live/Perl/MOBY-Client
In directory dev.open-bio.org:/tmp/cvs-serv29170/Perl/MOBY-Client

Modified Files:
	MANIFEST 
Log Message:
added the DatatypeParser.pm module
moby-live/Perl/MOBY-Client MANIFEST,1.7,1.8
===================================================================
RCS file: /home/repository/moby/moby-live/Perl/MOBY-Client/MANIFEST,v
retrieving revision 1.7
retrieving revision 1.8
diff -u -r1.7 -r1.8
--- /home/repository/moby/moby-live/Perl/MOBY-Client/MANIFEST	2008/03/05 18:24:22	1.7
+++ /home/repository/moby/moby-live/Perl/MOBY-Client/MANIFEST	2008/03/13 19:12:59	1.8
@@ -30,6 +30,7 @@
 lib/MOBY/Client/SimpleInput.pm
 lib/MOBY/RDF/Parsers/NamespaceParser.pm
 lib/MOBY/RDF/Parsers/ServiceTypeParser.pm
+lib/MOBY/RDF/Parsers/DatatypeParser.pm
 lib/MOBY/RDF/Predicates/DC_PROTEGE.pm
 lib/MOBY/RDF/Predicates/FETA.pm
 lib/MOBY/RDF/Predicates/MOBY_PREDICATES.pm



From gordonp at dev.open-bio.org  Thu Mar 13 22:56:53 2008
From: gordonp at dev.open-bio.org (Paul Gordon)
Date: Thu, 13 Mar 2008 18:56:53 -0400
Subject: [MOBY-guts] biomoby commit
Message-ID: <200803132256.m2DMur3r031157@dev.open-bio.org>


gordonp
Thu Mar 13 18:56:53 EDT 2008
Update of /home/repository/moby/moby-live/Java/src/main/org/biomoby/shared
In directory dev.open-bio.org:/tmp/cvs-serv31121/src/main/org/biomoby/shared

Modified Files:
	MobyPrefixResolver.java 
Log Message:
Added WSDL 2.0 support
moby-live/Java/src/main/org/biomoby/shared MobyPrefixResolver.java,1.13,1.14
===================================================================
RCS file: /home/repository/moby/moby-live/Java/src/main/org/biomoby/shared/MobyPrefixResolver.java,v
retrieving revision 1.13
retrieving revision 1.14
diff -u -r1.13 -r1.14
--- /home/repository/moby/moby-live/Java/src/main/org/biomoby/shared/MobyPrefixResolver.java	2008/03/12 17:47:18	1.13
+++ /home/repository/moby/moby-live/Java/src/main/org/biomoby/shared/MobyPrefixResolver.java	2008/03/13 22:56:52	1.14
@@ -46,6 +46,8 @@
     public static final String XLINK_NAMESPACE = "http://www.w3.org/1999/xlink";
     public static final String WSDL_PREFIX = "wsdl";
     public static final String WSDL_NAMESPACE = "http://schemas.xmlsoap.org/wsdl/";
+    public static final String WSDL20_PREFIX = "wsdl20";
+    public static final String WSDL20_NAMESPACE = "http://www.w3.org/2006/01/wsdl";
     public static final String HTTP_PREFIX = "http";
     public static final String HTTP_NAMESPACE = "http://schemas.xmlsoap.org/wsdl/http/";
     public static final String SAWSDL_PREFIX = "sawsdl";



From gordonp at dev.open-bio.org  Thu Mar 13 22:58:11 2008
From: gordonp at dev.open-bio.org (Paul Gordon)
Date: Thu, 13 Mar 2008 18:58:11 -0400
Subject: [MOBY-guts] biomoby commit
Message-ID: <200803132258.m2DMwBFO031259@dev.open-bio.org>


gordonp
Thu Mar 13 18:58:10 EDT 2008
Update of /home/repository/moby/moby-live/Java/src/main/org/biomoby/service/test
In directory dev.open-bio.org:/tmp/cvs-serv31223/src/main/org/biomoby/service/test

Modified Files:
	MobyServletTestCase.java 
Log Message:
Better servlet initialization
moby-live/Java/src/main/org/biomoby/service/test MobyServletTestCase.java,1.8,1.9
===================================================================
RCS file: /home/repository/moby/moby-live/Java/src/main/org/biomoby/service/test/MobyServletTestCase.java,v
retrieving revision 1.8
retrieving revision 1.9
diff -u -r1.8 -r1.9
--- /home/repository/moby/moby-live/Java/src/main/org/biomoby/service/test/MobyServletTestCase.java	2007/12/14 16:26:00	1.8
+++ /home/repository/moby/moby-live/Java/src/main/org/biomoby/service/test/MobyServletTestCase.java	2008/03/13 22:58:10	1.9
@@ -224,6 +224,15 @@
 	}
 	resultContents.clear();  // so we don't build up junk from multiple responses
 
+	// Sets up hashtables, etc. we'll use implicitly below for error checking
+	try{
+	    fasta_na2dna.init(getMobyServlet().getServletConfig()); 
+	} catch(Exception e){
+	    e.printStackTrace();
+	    fail("Exception while configuring FromFastaToDNASequence servlet for testing: " + e);
+	}
+
+	System.err.println("Don't worry, an exception warning about INPUT_INCORRECT_SIMPLE should appear next...it's expected");
 	// Call second service on output of previous service, the input is actually AA, not DNA as expected
 	try{
 	    fasta_na2dna.processRequests(MobyDataUtils.fromXMLDocument(new java.io.ByteArrayInputStream(outBuffer.getBuffer().toString().getBytes())), 
@@ -295,6 +304,7 @@
 	testRequest.setInputStream(testDataURL.openStream());
 
 	MobyServlet servlet = getMobyServlet();
+	servlet.createServiceFromConfig(null);  // initialized required settings
 	MobyContentInstance mobyContents = servlet.getMobyContents(testRequest);
 	assertNotNull("Could not retrieve the MOBY data payload from the test HTTP request", mobyContents);
     }
@@ -310,7 +320,8 @@
      * @return a test suite for all the test methods of this test case.
      */
     public static Test suite() {
-
+	System.setProperty("javax.xml.parsers.DocumentBuilderFactory", 
+			   "com.sun.org.apache.xerces.internal.jaxp.DocumentBuilderFactoryImpl"); 
 	TestSuite suite = new TestSuite();
       	suite.addTest(new MobyServletTestCase("testRDF"));
  	suite.addTest(new MobyServletTestCase("testSoapParsing"));



From gordonp at dev.open-bio.org  Thu Mar 13 23:02:22 2008
From: gordonp at dev.open-bio.org (Paul Gordon)
Date: Thu, 13 Mar 2008 19:02:22 -0400
Subject: [MOBY-guts] biomoby commit
Message-ID: <200803132302.m2DN2MiM031465@dev.open-bio.org>


gordonp
Thu Mar 13 19:02:22 EDT 2008
Update of /home/repository/moby/moby-live/Java/src/main/org/biomoby/service
In directory dev.open-bio.org:/tmp/cvs-serv31429/src/main/org/biomoby/service

Modified Files:
	MobyServlet.java 
Log Message:
Extra parameter override configuration, and moby annotation parsing improved
moby-live/Java/src/main/org/biomoby/service MobyServlet.java,1.14,1.15
===================================================================
RCS file: /home/repository/moby/moby-live/Java/src/main/org/biomoby/service/MobyServlet.java,v
retrieving revision 1.14
retrieving revision 1.15
diff -u -r1.14 -r1.15
--- /home/repository/moby/moby-live/Java/src/main/org/biomoby/service/MobyServlet.java	2008/02/14 06:08:31	1.14
+++ /home/repository/moby/moby-live/Java/src/main/org/biomoby/service/MobyServlet.java	2008/03/13 23:02:22	1.15
@@ -82,6 +82,7 @@
     // Only use for keep track of MobyServices if they have template values that are filled in at service invocation
     protected Map<Thread,MobyService> templatedServicesMap; 
     protected Map<Thread,MobyContentInstance> responseContentInstanceMap; 
+    protected Map<String,String> extraConfig;
 
     public void doGet(HttpServletRequest request,
 		      HttpServletResponse response)
@@ -308,6 +309,9 @@
 	    MobyPrimaryData param = template[i];
 	    MobyDataInstance nameMatch = job.get(param.getName());
 	    if(nameMatch == null){
+                MobyContentInstance mci = new MobyContentInstance();
+                mci.put(job);
+                MobyDataUtils.toXMLDocument(System.err, mci);
 		throw new IllegalArgumentException(errMessagePrefix + 
 					       ": required primary value \"" + param.getName() + 
 					       "\" in job " + job.getID() + " is missing");
@@ -738,6 +742,9 @@
     }
 
     protected String getCoCInitParameter(String paramName){
+        if(extraConfig != null && extraConfig.containsKey(paramName)){
+            return extraConfig.get(paramName);
+        }
 	javax.servlet.ServletConfig config = getServletConfig();
 	if(config != null){
 	    if(config.getInitParameter(paramName) != null){
@@ -753,6 +760,13 @@
 	return getInitParameter(paramName);
     }
 
+    public synchronized void setCoCInitParameter(String param, String value){
+        if(extraConfig == null){
+          extraConfig = new HashMap<String,String>();
+        }
+        extraConfig.put(param, value);
+    }
+
     public synchronized MobyService createServiceFromConfig(HttpServletRequest request) throws Exception{
 	MobyService service = new MobyService(getServiceName());
 
@@ -909,7 +923,7 @@
 	   param.indexOf(".") < 2 || param.indexOf(".") > param.length()-2 ||
 	   param.lastIndexOf("@") > param.lastIndexOf(".")){
 	    throw new Exception("Required " + MOBY_CONTACT_PARAM + 
-				" parameter in servlet config did not have the form \"name at mail.domain\")");
+				" parameter in servlet config did not have the form \"name at mail.domain\" (found "+param+")");
 	}
 	
 	service.setEmailContact(param);
@@ -985,7 +999,7 @@
      * e.g. <code>hits:Integer:100:[0,]</code>
      */
     public static MobySecondaryData stringToSecondaryDataTemplate(String template) throws Exception{
-	String[] fields = template.split(":");
+	String[] fields = template.split(":", -2); // -2 == don't strip trailing blank fields
 	if(fields.length < 3){
 	    throw new Exception("The parameter specification (" + 
 				template + ") must have the minimal form " +
@@ -1023,16 +1037,16 @@
 
 	// Ensure the [] are there, and strip them
 	if(spec.length() > 0){
-	    if(spec.indexOf('[') != 1 || spec.lastIndexOf(']') != spec.length()){
+	    if(spec.length() < 3 || spec.indexOf('[') != 0 || spec.lastIndexOf(']') != spec.length()-1){
 		throw new Exception("Parameter options specification (4th field of '" + 
 				    template + "') " +
 				    "does not have the required form '[...]', but rather: " + spec);
 	    }
-	    spec = spec.substring(1, spec.length());
+	    spec = spec.substring(1, spec.length()-1);
 	}
 	String[] specValues = new String[0];
 	if(spec.length() > 0){
-	    specValues = spec.split(",");
+	    specValues = spec.split(",", -2); // -2 == keep trailing blank values
 	}
 
 	if(dataType.equals(MobySecondaryData.INTEGER_TYPE) ||
@@ -1063,7 +1077,7 @@
 					    "is less than the minimum value specified");
 		    }
 		}
-		if(min != null){
+		if(max != null){
 		    if(max.compareTo(defaultNumber) < 0){
 			throw new Exception("Numeric parameter default (3rd field of " + template + "') " +
 					    "is greater than the maximum value specified");
@@ -1307,6 +1321,7 @@
             return;
 	}
 
+        
         MobyServlet servlet = new MobyServlet();
 	ClassLoader classLoader = servlet.getClass().getClassLoader();
         try{



From gordonp at dev.open-bio.org  Thu Mar 13 23:05:48 2008
From: gordonp at dev.open-bio.org (Paul Gordon)
Date: Thu, 13 Mar 2008 19:05:48 -0400
Subject: [MOBY-guts] biomoby commit
Message-ID: <200803132305.m2DN5mEE031735@dev.open-bio.org>


gordonp
Thu Mar 13 19:05:47 EDT 2008
Update of /home/repository/moby/moby-live/Java/src/main/ca/ucalgary/services/util
In directory dev.open-bio.org:/tmp/cvs-serv31699/src/main/ca/ucalgary/services/util

Modified Files:
	XHTMLForm.java 
Added Files:
	MobySpecWrapper.java 
Log Message:
Moved a bunch of code common to all legacy wrapping configs to MobySpecWrapper
moby-live/Java/src/main/ca/ucalgary/services/util MobySpecWrapper.java,NONE,1.1 XHTMLForm.java,1.6,1.7
===================================================================
RCS file: /home/repository/moby/moby-live/Java/src/main/ca/ucalgary/services/util/XHTMLForm.java,v
retrieving revision 1.6
retrieving revision 1.7
diff -u -r1.6 -r1.7
--- /home/repository/moby/moby-live/Java/src/main/ca/ucalgary/services/util/XHTMLForm.java	2008/02/12 09:00:16	1.6
+++ /home/repository/moby/moby-live/Java/src/main/ca/ucalgary/services/util/XHTMLForm.java	2008/03/13 23:05:47	1.7
@@ -21,27 +21,13 @@
  * This allows us to wrap Web pages as Moby services using a similar mechanism to that
  * which wraps ACD-described command line tools such as EMBOSS programs.
  */
-public class XHTMLForm{
+public class XHTMLForm extends MobySpecWrapper{
 
     private static XPath xPath;
     private static DocumentBuilder docBuilder;
     private Document xhtmlDoc;
     private URL formURL;
     
-    private Map<String,String> serviceNames;
-    private String currentService;
-    private Map<String,String> serviceTypes;
-    private Map<String,String> serviceDescs;
-    private Map<String,String> providerURIs;
-    private Map<String,String> centralEndpoints;
-    private String contactEmail;
-
-    private Map<String,Map<String,String>> serviceInputs;
-    private Map<String,Map<String,String>> serviceInputFormats;
-    private Map<String,Map<String,String>> serviceSecondaries;
-    private Map<String,String[]> serviceOutputs;
-    private Map<String,Map<String,String>> fixedParams;
-
     private Map<String,List<String>> formFiles;
     private Map<String,String> formEncType;
     private Map<String,String> formAction;
@@ -102,17 +88,6 @@
     public XHTMLForm(URL url) throws Exception{
 	formURL = url;
 
-	serviceNames = new HashMap<String,String>();
-	currentService = "";
-	serviceTypes = new HashMap<String,String>();
-	serviceDescs = new HashMap<String,String>();
-	providerURIs = new HashMap<String,String>();
-	centralEndpoints = new HashMap<String,String>();
-	fixedParams = new HashMap<String,Map<String,String>>();
-	serviceInputs = new HashMap<String,Map<String,String>>();
-	serviceInputFormats = new HashMap<String,Map<String,String>>();
-	serviceSecondaries = new HashMap<String,Map<String,String>>();
-	serviceOutputs = new HashMap<String,String[]>();
 	formFiles = new HashMap<String,List<String>>();
 	formEncType = new HashMap<String,String>();
 	formAction = new HashMap<String,String>();
@@ -677,7 +652,7 @@
 
 	// The output datatype of the service is also declared in the form tag
 	List<String> outputSpecs = parseMobySpecs(serviceFormElement, mobyPrefix);
-	String[] cleanOutputSpecs = new String[outputSpecs.size()];
+	Map<String,String> cleanOutputSpecs = new HashMap<String,String>();
 	for(int i = 0; i < outputSpecs.size(); i++){
 	    String spec = outputSpecs.get(i);
 	    if(!outputSpecs.get(i).startsWith(serviceName+":")){
@@ -693,7 +668,17 @@
 				    ") not of the required form '"+mobyPrefix+":"+
 				    serviceName+":paramName:DataType'");
 	    }
-	    cleanOutputSpecs[i] = spec.substring(serviceName.length()+1);
+	    // The outputs have no existing names in the HTML/text/etc. output, 
+	    // so enforce that they be the same as the Moby param names 
+	    // (i.e. the stuff before the first colon in the moby param spec)
+	    String outParam = spec.substring(serviceName.length()+1);
+	    if(!outParam.contains(":")){
+		throw new Exception("The form for service '" + serviceName +
+				    "' contains moby specs (" + spec + 
+				    ") not of the required form '"+mobyPrefix+":"+
+				    serviceName+":paramName:DataType' (last colon missing)");
+	    }
+	    cleanOutputSpecs.put(outParam.substring(0, outParam.indexOf(":")), outParam);
 	}
 
 	setPrimaryOutputs(cleanOutputSpecs);
@@ -966,105 +951,6 @@
 	return optionsMap;
     }
 
-    public String[] getServiceNames(){
-	return providerURIs.keySet().toArray(new String[providerURIs.size()]);
-    }
-
-    public void setCurrentService(String serviceToReport) throws IllegalArgumentException{
-	currentService = serviceToReport;
-    }
-
-    public String getServiceName(){
-	return currentService;
-    }
-
-    public void setServiceType(String type){
-	serviceTypes.put(currentService, type);
-    }
-
-    public String getServiceType(){
-	return serviceTypes.get(currentService);
-    }
-
-    public void setServiceDesc(String desc){
-	serviceDescs.put(currentService, desc);
-    }
-
-    public String getServiceDesc(){
-	return serviceDescs.get(currentService);
-    }
-
-    public void setProviderURI(String uri){
-	providerURIs.put(currentService, uri);
-    }
-
-    public String getProviderURI(){
-	return providerURIs.get(currentService);
-    }
-
-    public void setCentralEndpoint(String ep){
-	centralEndpoints.put(currentService, ep);
-    }
-
-    public String getCentralEndpoint(){
-	return centralEndpoints.get(currentService);
-    }
-
-    public void setContactEmail(String email){
-	contactEmail = email;
-    }
-
-    public String getContactEmail(){
-	return contactEmail;
-    }
-
-    /**
-     * @param specs Map<cgi_param_name,mobyservlet_param_spec>, where mobyservlet_param_spec has an extra field at the end describing the text-type
-     */
-    public void setPrimaryInputs(Map<String,String> specs){
-	serviceInputs.put(currentService, specs);
-    }
-
-    public Map<String,String> getPrimaryInputs(){
-	return serviceInputs.get(currentService);
-    }
-
-    public void setPrimaryInputFormats(Map<String,String> specs){
-	serviceInputFormats.put(currentService, specs);
-    }
-
-    public Map<String,String> getPrimaryInputFormats(){
-	return serviceInputFormats.get(currentService);
-    }
-
-    public void setPrimaryOutputs(String[] specs){
-	serviceOutputs.put(currentService, specs);
-    }
-
-    public String[] getPrimaryOutputs(){
-	return serviceOutputs.get(currentService);
-    }
-
-    /**
-     * @param specs Map<cgi_param_name,mobyservlet_secondary_param_spec>
-     */
-    public void setSecondaryInputs(Map<String,String> specs){
-	serviceSecondaries.put(currentService, specs);
-    }
-
-    public Map<String,String> getSecondaryInputs(){
-	return serviceSecondaries.get(currentService);
-    }
-
-    // Note that the map is not cloned...
-    public void setFixedParams(Map<String,String> params){
-	fixedParams.put(currentService, params);
-    }
-
-    public Map<String,String> getFixedParams(){
-	return fixedParams.get(currentService);
-    }
-   
     // Note that the map is not cloned...
     public void setSubmitOptions(Map<String,String> options){
 	formSubmitOptions.put(currentService, options);



From gordonp at dev.open-bio.org  Thu Mar 13 23:06:48 2008
From: gordonp at dev.open-bio.org (Paul Gordon)
Date: Thu, 13 Mar 2008 19:06:48 -0400
Subject: [MOBY-guts] biomoby commit
Message-ID: <200803132306.m2DN6mUR031807@dev.open-bio.org>


gordonp
Thu Mar 13 19:06:48 EDT 2008
Update of /home/repository/moby/moby-live/Java/src/main/ca/ucalgary/services/util/test
In directory dev.open-bio.org:/tmp/cvs-serv31771/src/main/ca/ucalgary/services/util/test

Modified Files:
	XHTMLFormTestCase.java 
Log Message:
Changes made to reflect refactoring for XHTMLForm/MobySpecWrapper
moby-live/Java/src/main/ca/ucalgary/services/util/test XHTMLFormTestCase.java,1.5,1.6
===================================================================
RCS file: /home/repository/moby/moby-live/Java/src/main/ca/ucalgary/services/util/test/XHTMLFormTestCase.java,v
retrieving revision 1.5
retrieving revision 1.6
diff -u -r1.5 -r1.6
--- /home/repository/moby/moby-live/Java/src/main/ca/ucalgary/services/util/test/XHTMLFormTestCase.java	2008/02/27 15:26:12	1.5
+++ /home/repository/moby/moby-live/Java/src/main/ca/ucalgary/services/util/test/XHTMLFormTestCase.java	2008/03/13 23:06:48	1.6
@@ -120,10 +120,10 @@
 		   ") was not as expected (" + NUM_SECONDARY_INPUTS + ")",
 		   NUM_SECONDARY_INPUTS == secondaryInputs.size());
 
-	String[] outputs = form.getPrimaryOutputs();
-	assertTrue("The number of primary output parameters defined (" + outputs.length +
+	Map<String,String> outputs = form.getPrimaryOutputs();
+	assertTrue("The number of primary output parameters defined (" + outputs.size() +
 		   ") was not as expected (" + NUM_OUTPUTS + ")",
-		   NUM_OUTPUTS == outputs.length);
+		   NUM_OUTPUTS == outputs.size());
 	
 	// Check the HTML-specific specs
 	Map<String,String> fixedParams = form.getFixedParams();
@@ -156,9 +156,9 @@
 		   inseqFormat + "'",
 		   inseqFormat.equals(primaryInputFormats.get(inputHTMLParamName)));
 	assertTrue("The value of the output parameter 'primers' (" +
-		   outputs[0] + ") was not the expected value '" + 
+		   outputs.get("primers") + ") was not the expected value '" + 
 		   primers + "'",
-		   primers.equals(outputs[0]));
+		   primers.equals(outputs.get("primers")));
      
 	assertTrue("The value of the secondary parameter 'bias' (" + 
 		   secondaryInputs.get("bias") + ") was not the expected value '" + bias + "'", 



From gordonp at dev.open-bio.org  Thu Mar 13 23:06:48 2008
From: gordonp at dev.open-bio.org (Paul Gordon)
Date: Thu, 13 Mar 2008 19:06:48 -0400
Subject: [MOBY-guts] biomoby commit
Message-ID: <200803132306.m2DN6mok031827@dev.open-bio.org>


gordonp
Thu Mar 13 19:06:48 EDT 2008
Update of /home/repository/moby/moby-live/Java/src/main/ca/ucalgary/services
In directory dev.open-bio.org:/tmp/cvs-serv31771/src/main/ca/ucalgary/services

Modified Files:
	CGIService.java 
Log Message:
Changes made to reflect refactoring for XHTMLForm/MobySpecWrapper
moby-live/Java/src/main/ca/ucalgary/services CGIService.java,1.6,1.7
===================================================================
RCS file: /home/repository/moby/moby-live/Java/src/main/ca/ucalgary/services/CGIService.java,v
retrieving revision 1.6
retrieving revision 1.7
diff -u -r1.6 -r1.7
--- /home/repository/moby/moby-live/Java/src/main/ca/ucalgary/services/CGIService.java	2008/02/27 15:23:56	1.6
+++ /home/repository/moby/moby-live/Java/src/main/ca/ucalgary/services/CGIService.java	2008/03/13 23:06:48	1.7
@@ -22,10 +22,9 @@
  * publishing, etc.  The service description fetching, and the command invocation
  * are overridden.
  */
-public class CGIService extends LegacyService{
+public class CGIService extends WrapperService<XHTMLForm>{
     protected URL remoteFormURL;
     // params that override annoation and servlet context/config params
-    protected Map<String,String> cgiConfig; 
     protected XHTMLForm formConfig;
     // mobyParamName -> form fields that used a transformed version of it
     protected Map<String,String[]> mobyPrimary2FormFields;
@@ -40,7 +39,6 @@
     public void init(){
 	super.init();
 
-	cgiConfig = new HashMap<String,String>();
 	mobyPrimary2FormFields = new HashMap<String,String[]>();
 	mobySecondary2FormFields = new HashMap<String,String[]>();
 
@@ -158,77 +156,18 @@
     public MobyService createServiceFromConfig(javax.servlet.http.HttpServletRequest request)
 	throws Exception{
 	
-	String remoteFormURLString = null;
-	if(getCoCInitParameter(HTML_FORM_URL_PARAM) != null){
-	    remoteFormURLString = getCoCInitParameter(HTML_FORM_URL_PARAM);
-	}
-	else{
-	    throw new Exception("No parameter called " + HTML_FORM_URL_PARAM + 
-				" was found in the servlet configuration");
-	}
-	try{
-	    remoteFormURL = new URL(remoteFormURLString);
-	} catch(Exception e){
-            // Fallback to finding it as a resource
-            remoteFormURL = getClass().getClassLoader().getResource(remoteFormURLString);
-            if(remoteFormURL == null){
-	      throw new Exception("The configuration parameter '" + remoteFormURLString +
-	    			  "' (value '" + remoteFormURLString + 
-				  "') was not parseable as a URL");
-            }
-	}
+        remoteFormURL = getSpecURL(HTML_FORM_URL_PARAM);
 
 	try{
 	    formConfig = new XHTMLForm(remoteFormURL);
 	} catch(Exception e){
             e.printStackTrace();
 	    throw new Exception("Could not determine Moby service configuration from the HTML form (" + 
-				remoteFormURLString + "): " + e);
+				remoteFormURL.toString() + "): " + e);
 	}
-	// Configure meta-data for the Moby service about to be created
-	String[] serviceNames = formConfig.getServiceNames();
-	if(serviceNames.length > 1){
-	    String targetedService = getCoCInitParameter(MOBY_SERVICENAME_PARAM);
-	    String valuesString = "";
-	    for(String value: serviceNames){
-		valuesString += value + " ";
-	    }
-	    if(targetedService == null || targetedService.trim().length() == 0){
-		throw new Exception("The HTML page to wrap contains more than one Moby-annotated " +
-				    "form/service, but no '"+MOBY_SERVICENAME_PARAM+"' parameter was " +
-				    "specified in the servlet configuration.  Please specify this " +
-				    "parameter with one of the following values: " + valuesString);
-	    }
-	    boolean foundService = false;
-	    for(String validName: serviceNames){
-		if(targetedService.equals(validName)){
-		    foundService = true; 
-		    break;
-		}
-	    }
-	    if(!foundService){
-		throw new Exception("The service to wrap (" + targetedService + 
-				    "), named in the servlet configuration parameter '" +
-				    MOBY_SERVICENAME_PARAM + "', was not one of the service names " +
-				    "available from the HTML page.  Valid values are: " + valuesString);
-	    }
-	    formConfig.setCurrentService(targetedService);
-	}
-	setCoCInitParameter(MOBY_SERVICENAME_PARAM, formConfig.getServiceName());
-	setCoCInitParameter(MOBY_SERVICETYPE_PARAM, formConfig.getServiceType());
-	setCoCInitParameter(MOBY_SERVICE_DESC_PARAM, formConfig.getServiceDesc());
-	setCoCInitParameter(MOBY_PROVIDER_URI_PARAM, formConfig.getProviderURI());
-	setCoCInitParameter(MOBY_CENTRAL_URL_PARAM, formConfig.getCentralEndpoint());
-	setCoCInitParameter(MOBY_CONTACT_PARAM, formConfig.getContactEmail());
-
-	// Determine primary I/O parameters
-	setCoCInitParameter(MOBY_INPUT_PARAM, createInputSpecString(formConfig));
-	setCoCInitParameter(MOBY_OUTPUT_PARAM, createOutputSpecString(formConfig));
-	// Determine secondary parameters
-	setCoCInitParameter(MOBY_SECONDARYINPUT_PARAM, createSecondarySpecString(formConfig));
 
-	// Set up reusable http client objects
-	return super.createServiceFromConfig(request);
+        //Call to parent, which handles spec-wrapper-to-MobyServlet-config conversion
+	return createServiceFromConfig(request, formConfig);
     }
 
     protected MultipartRequestEntity getMultipartRequest(Map<String,byte[]> dataInstances, 
@@ -270,18 +209,6 @@
 	return XHTMLForm.join("+", queryItems);
     }
 
-    protected String getCoCInitParameter(String paramName){
-	javax.servlet.ServletConfig config = getServletConfig();
-	if(cgiConfig != null && cgiConfig.containsKey(paramName)){
-	    return cgiConfig.get(paramName);
-	}
-	return super.getCoCInitParameter(paramName);
-    }
-
-    public void setCoCInitParameter(String param, String value){
-	cgiConfig.put(param, value);
-    }
-
     public String createInputSpecString(XHTMLForm form){
 	Map<String,String> ins = form.getPrimaryInputs();
 	// Create a reverse map so we can look up where a moby param 
@@ -319,10 +246,16 @@
     }
 
     public String createOutputSpecString(XHTMLForm form){
-	return XHTMLForm.join(",", form.getPrimaryOutputs());
+	Map<String,String> outs = form.getPrimaryOutputs();
+	String[] outSpec = new String[outs.size()];
+	int i = 0;
+	for(String key: outs.keySet()){
+	    outSpec[i++] = key;
+	}
+	return XHTMLForm.join(",", outSpec);
     }
 
-    protected String createSecondarySpecString(XHTMLForm form){
+    public String createSecondarySpecString(XHTMLForm form){
 	Map<String,String> secondaries = form.getSecondaryInputs();
 	// Create a reverse map so we can look up where a moby param 
 	// slots into in the form.



From gordonp at dev.open-bio.org  Thu Mar 13 23:08:26 2008
From: gordonp at dev.open-bio.org (Paul Gordon)
Date: Thu, 13 Mar 2008 19:08:26 -0400
Subject: [MOBY-guts] biomoby commit
Message-ID: <200803132308.m2DN8QNp031937@dev.open-bio.org>


gordonp
Thu Mar 13 19:08:26 EDT 2008
Update of /home/repository/moby/moby-live/Java/src/main/ca/ucalgary/services/util
In directory dev.open-bio.org:/tmp/cvs-serv31905/src/main/ca/ucalgary/services/util

Added Files:
	WSDLConfig.java 
Log Message:
Initial commit of Semantic Annotations for WSDL-based Web Service wrapping code
moby-live/Java/src/main/ca/ucalgary/services/util WSDLConfig.java,NONE,1.1


From gordonp at dev.open-bio.org  Thu Mar 13 23:08:26 2008
From: gordonp at dev.open-bio.org (Paul Gordon)
Date: Thu, 13 Mar 2008 19:08:26 -0400
Subject: [MOBY-guts] biomoby commit
Message-ID: <200803132308.m2DN8Qg1031953@dev.open-bio.org>


gordonp
Thu Mar 13 19:08:26 EDT 2008
Update of /home/repository/moby/moby-live/Java/src/main/ca/ucalgary/services/util/test
In directory dev.open-bio.org:/tmp/cvs-serv31905/src/main/ca/ucalgary/services/util/test

Added Files:
	WSDLConfigTestCase.java KEGG.wsdl 
Log Message:
Initial commit of Semantic Annotations for WSDL-based Web Service wrapping code
moby-live/Java/src/main/ca/ucalgary/services/util/test WSDLConfigTestCase.java,NONE,1.1 KEGG.wsdl,NONE,1.1


From gordonp at dev.open-bio.org  Thu Mar 13 23:10:11 2008
From: gordonp at dev.open-bio.org (Paul Gordon)
Date: Thu, 13 Mar 2008 19:10:11 -0400
Subject: [MOBY-guts] biomoby commit
Message-ID: <200803132310.m2DNABsm032065@dev.open-bio.org>


gordonp
Thu Mar 13 19:10:11 EDT 2008
Update of /home/repository/moby/moby-live/Java/src/main/ca/ucalgary/services
In directory dev.open-bio.org:/tmp/cvs-serv32033/src/main/ca/ucalgary/services

Added Files:
	WrapperService.java 
Log Message:
Code from various wrapper classes in this package was refactored into this common class
moby-live/Java/src/main/ca/ucalgary/services WrapperService.java,NONE,1.1


From groscurt at dev.open-bio.org  Fri Mar 14 11:50:03 2008
From: groscurt at dev.open-bio.org (Andreas Groscurth)
Date: Fri, 14 Mar 2008 07:50:03 -0400
Subject: [MOBY-guts] biomoby commit
Message-ID: <200803141150.m2EBo30D004957@dev.open-bio.org>


groscurt
Fri Mar 14 07:50:02 EDT 2008
Update of /home/repository/moby/moby-live/Java
In directory dev.open-bio.org:/tmp/cvs-serv4926

Added Files:
	.classpath.template 
Log Message:
Added .classpath.template which eclipse users can use to integrate jmoby with eclipse

moby-live/Java .classpath.template,NONE,1.1


From groscurt at dev.open-bio.org  Fri Mar 14 14:01:01 2008
From: groscurt at dev.open-bio.org (Andreas Groscurth)
Date: Fri, 14 Mar 2008 10:01:01 -0400
Subject: [MOBY-guts] biomoby commit
Message-ID: <200803141401.m2EE11UC005125@dev.open-bio.org>


groscurt
Fri Mar 14 10:01:01 EDT 2008
Update of /home/repository/moby/moby-live/Java/docs
In directory dev.open-bio.org:/tmp/cvs-serv5088/docs

Modified Files:
	EclipseAndJMoby.html 
Added Files:
	ErrorsInEclipse.html 
Log Message:
changes in the documentation about the integration of JMoby in Eclipse and how to solve known errors
moby-live/Java/docs ErrorsInEclipse.html,NONE,1.1 EclipseAndJMoby.html,1.8,1.9
===================================================================
RCS file: /home/repository/moby/moby-live/Java/docs/EclipseAndJMoby.html,v
retrieving revision 1.8
retrieving revision 1.9
diff -u -r1.8 -r1.9
--- /home/repository/moby/moby-live/Java/docs/EclipseAndJMoby.html	2008/02/21 11:44:46	1.8
+++ /home/repository/moby/moby-live/Java/docs/EclipseAndJMoby.html	2008/03/14 14:01:01	1.9
@@ -123,6 +123,22 @@
 <tt>-showlocation</tt> - then the path of the current workspace is
 shown in the window title. <p>
 
+<h3>Integrate Maven plugin</h3>
+
+<p>As JMoby uses Maven we need to enable Maven in Eclipse. The Maven plugin requires two other plugins which we need to load.<br>
+<b class="step">Help -&gt; Software Updates -&gt; Find and Install -&gt; Search for new features and install</b> will open a dialog
+which shows all existing update sites your Eclipse already know.</p>
+
+<p>For each of the plugins please open <b class="step">New Remote Update Site</b> and add the following sites and install them 
+(make sure that you unselect optional components of the plugins if they produce errors):
+<ol>
+	<li>Name: Buckminster<br>URL: http://download.eclipse.org/tools/buckminster/updates</li>
+	<li>Name: Subversion<br>URL: http://subclipse.tigris.org/update_1.2.x</li>
+	<li>Name: Maven<br>URL: http://m2eclipse.sonatype.org/update/</li>
+</ol>
+After install the plugins please restart Eclipse to enable the Maven plugin.
+</p>
+
 <h3>Create a new CVS repository location</h3>
 
 <b class="step">Window -&gt; Open Perspective -&gt; Other -&gt; CVS
@@ -162,6 +178,13 @@
 about where jMoby has things and how it uses them. But before we fix
 that let's do one more thing... <p>
 
+<h3>Telling Eclipse the classpath</h3>
+We need to tell Eclipse now the building structure of JMoby, so that it knows where which source files are and to where it has to compile what.<br>
+For that (and only for the first time you set up Eclipse and JMoby) rename the <tt>.classpath.template</tt> from the checkout to <tt>.classpath</tt> 
+(and by that overwrite the .classpath file generated by Eclipse) and refresh your project either by right-click on the project and selecting <b class="step">Refresh</b> or by just hitting F5.<br>
+You will now see the new source folder structure. In the case you dont have a <tt>generated/skeletons</tt> and <tt>generated/datatypes</tt> folder shown
+up as source folder please add this two folders. Eclipse will then automatically recognize them as source folders.
+
 <!--
 <h3>Change location of Ant</h3>
 
@@ -184,20 +207,7 @@
 <tt>&lt;jMoby&gt;/lib/ant_home</tt>. <p>
 -->
 
-<!--
-<h3>Gather 3rd-party libraries</h3>
-
-This is done only the first time (and occasionally, time to time when
-the libraries change). If you are putting into Eclipse a copy of jMoby
-that you were already been working with, you probably already have the
-libraries fetched (but it does not harm if you go through this step,
-as well). <p>
-
-We are doing this step now, before telling Eclipse where the libraries
-are (because we first need to have them in order to show them to
-Eclipse, don't we?). Eclipse already found some 3rd-party libraries in
-jMoby and listed them in our project. These are from the included Ant
-(they were not needed for jMoby programs until recently). <p>
+<h3>Gather 3rd-party libraries and set up JMoby</h3>
 
 Now it's time for our real libraries. Open an Ant view by <b
 class="step">Window -&gt; Show View -&gt; Ant</b>. Then right-click
@@ -205,7 +215,7 @@
 class="step">build.xml</b> from jMoby. You can <b class="step">Hide
 internal targets</b> by clicking on the stroke green target icon. <p>
 
-Double-click on <b class="step">gather</b>. It shows progress in the
+Double-click on <b class="step">install</b>. It shows progress in the
 bottom of the screen in a console window. After that you may <b
 class="step">Refresh</b> your workspace. <p>
 
@@ -217,15 +227,20 @@
 jMoby documentation (e.g. about <a
 href="Download.html#targets">general targets</a>, or about <a
 href="Moses.html">Moses</a>).
-
 </blockquote>
 
+When the task is finished, double-click on <b class="step">initeclipse</b>, which will generate the file <tt>pom.xml</tt> 
+which the Maven plugin requires to work correctly. After the task refresh your workspace and right-click on the project 
+<b class="step">Maven -&gt; Enable Dependency Management</b>. This will now tell Eclipse to use the maven repository for the build path.<br>
+By now all your erros should be erazed and you only see several warnings (if you still got errors check <a href="ErrorsInEclipse.html">here</a>)
+
+<!--
 Again, right-click on the project name <b class="step">(jMoby) -&gt;
 Properties -&gt; Java Build Path</b>, select again tab <b
 class="step">Libraries</b>, and <b class="step">Add External
 JARS...</b>. Select all JAR files from &lt;jMoby&gt;/lib
 directory. <p>
--->
+
 
 <h3>Set source files</h3>
 
@@ -311,7 +326,7 @@
 you are an annoyed jMoby user, change warning preferences in <b
 class="step">Window -&gt; Preferences -&gt; Java -&gt; Compiler -&gt;
 Errors/Warnings</b> not to see them. <p>
-
+-->
 <h3>Fix <tt>javadoc</tt> location</h3>
 
 Ant's targets using <tt>javadoc</tt> (such as <tt>docs</tt> or



From senger at dev.open-bio.org  Fri Mar 14 23:27:41 2008
From: senger at dev.open-bio.org (Martin Senger)
Date: Fri, 14 Mar 2008 19:27:41 -0400
Subject: [MOBY-guts] biomoby commit
Message-ID: <200803142327.m2ENRfVP010464@dev.open-bio.org>


senger
Fri Mar 14 19:27:41 EDT 2008
Update of /home/repository/moby/moby-live/Java/docs
In directory dev.open-bio.org:/tmp/cvs-serv10444/docs

Modified Files:
	ChangeLog 
Log Message:
Putting back xercesImpl - but its newer version

moby-live/Java/docs ChangeLog,1.86,1.87
===================================================================
RCS file: /home/repository/moby/moby-live/Java/docs/ChangeLog,v
retrieving revision 1.86
retrieving revision 1.87
diff -u -r1.86 -r1.87
--- /home/repository/moby/moby-live/Java/docs/ChangeLog	2008/03/03 11:34:16	1.86
+++ /home/repository/moby/moby-live/Java/docs/ChangeLog	2008/03/14 23:27:41	1.87
@@ -1,3 +1,12 @@
+2008-03-14  Martin Senger  <martin.senger&#64;gmail.com>
+
+	* Fixed a bug with missing xercesImpl classes. Putting back
+	xercesImpl - but now with a newer version (2.7.1)
+
+2008-03-12  Martin Senger  <martin.senger&#64;gmail.com>
+
+	* Version 1.0.0 released
+
 2008-03-03  Martin Senger  <martin.senger&#64;gmail.com>
 
 	* Added a new method isUsingCache() to the CentralCached



From senger at dev.open-bio.org  Fri Mar 14 23:27:41 2008
From: senger at dev.open-bio.org (Martin Senger)
Date: Fri, 14 Mar 2008 19:27:41 -0400
Subject: [MOBY-guts] biomoby commit
Message-ID: <200803142327.m2ENRff6010484@dev.open-bio.org>


senger
Fri Mar 14 19:27:41 EDT 2008
Update of /home/repository/moby/moby-live/Java/xmls
In directory dev.open-bio.org:/tmp/cvs-serv10444/xmls

Modified Files:
	project.pom 
Log Message:
Putting back xercesImpl - but its newer version

moby-live/Java/xmls project.pom,1.8,1.9
===================================================================
RCS file: /home/repository/moby/moby-live/Java/xmls/project.pom,v
retrieving revision 1.8
retrieving revision 1.9
diff -u -r1.8 -r1.9
--- /home/repository/moby/moby-live/Java/xmls/project.pom	2008/03/13 16:49:35	1.8
+++ /home/repository/moby/moby-live/Java/xmls/project.pom	2008/03/14 23:27:41	1.9
@@ -222,6 +222,12 @@
     </dependency>
 
     <dependency>
+      <groupId>xerces</groupId>
+      <artifactId>xercesImpl</artifactId>
+      <version>2.7.1</version>
+    </dependency>
+
+    <dependency>
       <groupId>com.ibm.lsid</groupId>
       <artifactId>lsid-server</artifactId>
       <version>1.1.2</version>



From senger at dev.open-bio.org  Sat Mar 15 13:10:55 2008
From: senger at dev.open-bio.org (Martin Senger)
Date: Sat, 15 Mar 2008 09:10:55 -0400
Subject: [MOBY-guts] biomoby commit
Message-ID: <200803151310.m2FDAtmI011966@dev.open-bio.org>


senger
Sat Mar 15 09:10:54 EDT 2008
Update of /home/repository/moby/moby-live/Java/src/test/java/org/biomoby/service
In directory dev.open-bio.org:/tmp/cvs-serv11933/src/test/java/org/biomoby/service

Modified Files:
	ServicesTest.java 
Log Message:

moby-live/Java/src/test/java/org/biomoby/service ServicesTest.java,1.1,1.2
===================================================================
RCS file: /home/repository/moby/moby-live/Java/src/test/java/org/biomoby/service/ServicesTest.java,v
retrieving revision 1.1
retrieving revision 1.2
diff -u -r1.1 -r1.2
--- /home/repository/moby/moby-live/Java/src/test/java/org/biomoby/service/ServicesTest.java	2008/03/03 11:35:07	1.1
+++ /home/repository/moby/moby-live/Java/src/test/java/org/biomoby/service/ServicesTest.java	2008/03/15 13:10:54	1.2
@@ -190,14 +190,36 @@
      * This is to be able to run this JUnit 4 tests with a JUnit 3.x runner.
      **************************************************************************/
     public static junit.framework.Test suite() {
-        return new junit.framework.JUnit4TestAdapter (ServicesTest.class);
+        return new junit.framework.JUnit4TestAdapter (getThisClass());
     }
 
     /**************************************************************************
      * Run tests from the command line.
      **************************************************************************/
     public static void main (String args[]) {
-	org.junit.runner.JUnitCore.main ("org.biomoby.service.ServicesTest");
+	org.junit.runner.JUnitCore.main (getThisClassName());
+    }
+
+    /**************************************************************************
+     * Get the class (name) of this class (note that this is a static
+     * method). This madness is here just because I do not want to
+     * change the class name in the optional methods above when I copy
+     * and paste this into a new test file.
+     **************************************************************************/
+    private static String getThisClassName() {
+	Exception e = new Exception();
+	StackTraceElement[] sTrace = e.getStackTrace();
+	// sTrace[0] will be always there
+	return sTrace[0].getClassName();
+    }
+
+    private static Class getThisClass() {
+	try {
+	    return org.apache.commons.lang.ClassUtils.getClass (getThisClassName());
+	} catch (ClassNotFoundException e) {
+	    System.err.println ("Cannot get class name.");
+	    return java.lang.Object.class;
+	}
     }
 
 }



From senger at dev.open-bio.org  Sat Mar 15 13:10:55 2008
From: senger at dev.open-bio.org (Martin Senger)
Date: Sat, 15 Mar 2008 09:10:55 -0400
Subject: [MOBY-guts] biomoby commit
Message-ID: <200803151310.m2FDAtdH011984@dev.open-bio.org>


senger
Sat Mar 15 09:10:55 EDT 2008
Update of /home/repository/moby/moby-live/Java/src/test/java/org/biomoby/shared/parser
In directory dev.open-bio.org:/tmp/cvs-serv11933/src/test/java/org/biomoby/shared/parser

Modified Files:
	MobyParserTest.java 
Log Message:

moby-live/Java/src/test/java/org/biomoby/shared/parser MobyParserTest.java,1.4,1.5
===================================================================
RCS file: /home/repository/moby/moby-live/Java/src/test/java/org/biomoby/shared/parser/MobyParserTest.java,v
retrieving revision 1.4
retrieving revision 1.5
diff -u -r1.4 -r1.5
--- /home/repository/moby/moby-live/Java/src/test/java/org/biomoby/shared/parser/MobyParserTest.java	2008/03/03 11:34:17	1.4
+++ /home/repository/moby/moby-live/Java/src/test/java/org/biomoby/shared/parser/MobyParserTest.java	2008/03/15 13:10:55	1.5
@@ -216,14 +216,36 @@
      * This is to be able to run this JUnit 4 tests with a JUnit 3.x runner.
      **************************************************************************/
     public static junit.framework.Test suite() {
-        return new junit.framework.JUnit4TestAdapter (MobyParserTest.class);
+        return new junit.framework.JUnit4TestAdapter (getThisClass());
     }
 
     /**************************************************************************
      * Run tests from the command line.
      **************************************************************************/
     public static void main (String args[]) {
-	org.junit.runner.JUnitCore.main ("org.biomoby.shared.parser.MobyParserTest");
+	org.junit.runner.JUnitCore.main (getThisClassName());
+    }
+
+    /**************************************************************************
+     * Get the class (name) of this class (note that this is a static
+     * method). This madness is here just because I do not want to
+     * change the class name in the optional methods above when I copy
+     * and paste this into a new test file.
+     **************************************************************************/
+    private static String getThisClassName() {
+	Exception e = new Exception();
+	StackTraceElement[] sTrace = e.getStackTrace();
+	// sTrace[0] will be always there
+	return sTrace[0].getClassName();
+    }
+
+    private static Class getThisClass() {
+	try {
+	    return org.apache.commons.lang.ClassUtils.getClass (getThisClassName());
+	} catch (ClassNotFoundException e) {
+	    System.err.println ("Cannot get class name.");
+	    return java.lang.Object.class;
+	}
     }
 
 }



From senger at dev.open-bio.org  Sat Mar 15 13:10:55 2008
From: senger at dev.open-bio.org (Martin Senger)
Date: Sat, 15 Mar 2008 09:10:55 -0400
Subject: [MOBY-guts] biomoby commit
Message-ID: <200803151310.m2FDAtxi011948@dev.open-bio.org>


senger
Sat Mar 15 09:10:54 EDT 2008
Update of /home/repository/moby/moby-live/Java/src/config
In directory dev.open-bio.org:/tmp/cvs-serv11933/src/config

Added Files:
	run-junit-test run-junit-test.bat 
Log Message:

moby-live/Java/src/config run-junit-test,NONE,1.1 run-junit-test.bat,NONE,1.1


From kawas at dev.open-bio.org  Mon Mar 17 14:29:53 2008
From: kawas at dev.open-bio.org (Eddie Kawas)
Date: Mon, 17 Mar 2008 10:29:53 -0400
Subject: [MOBY-guts] biomoby commit
Message-ID: <200803171429.m2HETrSV019194@dev.open-bio.org>


kawas
Mon Mar 17 10:29:53 EDT 2008
Update of /home/repository/moby/moby-live/Java/src/main/org/biomoby/shared
In directory dev.open-bio.org:/tmp/cvs-serv19159/src/main/org/biomoby/shared

Modified Files:
	Utils.java 
Log Message:
modified getInputStream() such that it can resolve any url and not just HTTP urls.
moby-live/Java/src/main/org/biomoby/shared Utils.java,1.20,1.21
===================================================================
RCS file: /home/repository/moby/moby-live/Java/src/main/org/biomoby/shared/Utils.java,v
retrieving revision 1.20
retrieving revision 1.21
diff -u -r1.20 -r1.21
--- /home/repository/moby/moby-live/Java/src/main/org/biomoby/shared/Utils.java	2008/03/03 11:34:17	1.20
+++ /home/repository/moby/moby-live/Java/src/main/org/biomoby/shared/Utils.java	2008/03/17 14:29:53	1.21
@@ -19,6 +19,7 @@
 import java.net.HttpURLConnection;
 import java.net.MalformedURLException;
 import java.net.URL;
+import java.net.URLConnection;
 import java.nio.charset.Charset;
 import java.util.HashSet;
 import java.util.zip.GZIPInputStream;
@@ -529,24 +530,32 @@
 	if (url == null)
 	    throw new MobyException("Can't get RESOURCE from a null URL!");
 	try {
-	    HttpURLConnection urlConnection = null;
-	    urlConnection = (HttpURLConnection) url.openConnection();
-	    urlConnection
-		    .setRequestProperty("User-Agent", "jmoby-central/1.0");
-	    urlConnection
-		    .setRequestProperty("Accept-Encoding", "gzip, deflate");
-	    urlConnection.setDefaultUseCaches(false);
-	    urlConnection.setUseCaches(false);
-
-	    if (("gzip").equalsIgnoreCase(urlConnection.getContentEncoding())) {
-		// handle gzip encoded content
-		return new GZIPInputStream(urlConnection.getInputStream());
+	    URLConnection connection = url.openConnection();
+	    // try gzip content encoding iff we have a HTTP url
+	    if (connection instanceof HttpURLConnection) {
+		HttpURLConnection urlConnection = null;
+		urlConnection = (HttpURLConnection) connection;
+		urlConnection.setRequestProperty("User-Agent",
+			"jmoby-central/1.0");
+		urlConnection.setRequestProperty("Accept-Encoding",
+			"gzip, deflate");
+		urlConnection.setDefaultUseCaches(false);
+		urlConnection.setUseCaches(false);
+
+		if (("gzip").equalsIgnoreCase(urlConnection
+			.getContentEncoding())) {
+		    // handle gzip encoded content
+		    return new GZIPInputStream(urlConnection.getInputStream());
+		} else {
+		    return urlConnection.getInputStream();
+		}
 	    } else {
-		return urlConnection.getInputStream();
+		return connection.getInputStream();
 	    }
-	    
+
 	} catch (IOException e) {
-	    throw new MobyException ("Error creating input stream: " + e.toString());
+	    throw new MobyException("Error creating input stream: "
+		    + e.toString());
 	}
     }
     



From senger at dev.open-bio.org  Mon Mar 17 23:46:35 2008
From: senger at dev.open-bio.org (Martin Senger)
Date: Mon, 17 Mar 2008 19:46:35 -0400
Subject: [MOBY-guts] biomoby commit
Message-ID: <200803172346.m2HNkZdZ019861@dev.open-bio.org>


senger
Mon Mar 17 19:46:35 EDT 2008
Update of /home/repository/moby/moby-live/Java/src/test/java/org/biomoby/shared/extended
In directory dev.open-bio.org:/tmp/cvs-serv19843/src/test/java/org/biomoby/shared/extended

Log Message:
Directory /home/repository/moby/moby-live/Java/src/test/java/org/biomoby/shared/extended added to the repository

moby-live/Java/src/test/java/org/biomoby/shared/extended - New directory
rcsdiff: /home/repository/moby/moby-live/Java/src/test/java/org/biomoby/shared/extended/RCS/-,v: No such file or directory

rcsdiff: /home/repository/moby/moby-live/Java/src/test/java/org/biomoby/shared/extended/RCS/New,v: No such file or directory

rcsdiff: /home/repository/moby/moby-live/Java/src/test/java/org/biomoby/shared/extended/RCS/directory,v: No such file or directory



From senger at dev.open-bio.org  Mon Mar 17 23:48:01 2008
From: senger at dev.open-bio.org (Martin Senger)
Date: Mon, 17 Mar 2008 19:48:01 -0400
Subject: [MOBY-guts] biomoby commit
Message-ID: <200803172348.m2HNm1qm019894@dev.open-bio.org>


senger
Mon Mar 17 19:48:01 EDT 2008
Update of /home/repository/moby/moby-live/Java/src/test/java/org/biomoby/shared/extended
In directory dev.open-bio.org:/tmp/cvs-serv19879/src/test/java/org/biomoby/shared/extended

Added Files:
	FromRDFTest.java 
Log Message:
Added (few) junit tests for RDF parsing

moby-live/Java/src/test/java/org/biomoby/shared/extended FromRDFTest.java,NONE,1.1


From senger at dev.open-bio.org  Mon Mar 17 23:48:01 2008
From: senger at dev.open-bio.org (Martin Senger)
Date: Mon, 17 Mar 2008 19:48:01 -0400
Subject: [MOBY-guts] biomoby commit
Message-ID: <200803172348.m2HNm1Dx019910@dev.open-bio.org>


senger
Mon Mar 17 19:48:01 EDT 2008
Update of /home/repository/moby/moby-live/Java/src/test/junit-resources
In directory dev.open-bio.org:/tmp/cvs-serv19879/src/test/junit-resources

Added Files:
	dtypes.rdf namespaces.rdf services.rdf stypes.rdf 
Log Message:
Added (few) junit tests for RDF parsing

moby-live/Java/src/test/junit-resources dtypes.rdf,NONE,1.1 namespaces.rdf,NONE,1.1 services.rdf,NONE,1.1 stypes.rdf,NONE,1.1


From senger at dev.open-bio.org  Mon Mar 17 23:48:01 2008
From: senger at dev.open-bio.org (Martin Senger)
Date: Mon, 17 Mar 2008 19:48:01 -0400
Subject: [MOBY-guts] biomoby commit
Message-ID: <200803172348.m2HNm1AO019932@dev.open-bio.org>


senger
Mon Mar 17 19:48:01 EDT 2008
Update of /home/repository/moby/moby-live/Java/xmls
In directory dev.open-bio.org:/tmp/cvs-serv19879/xmls

Modified Files:
	junit.xml 
Log Message:
Added (few) junit tests for RDF parsing

moby-live/Java/xmls junit.xml,1.4,1.5
===================================================================
RCS file: /home/repository/moby/moby-live/Java/xmls/junit.xml,v
retrieving revision 1.4
retrieving revision 1.5
diff -u -r1.4 -r1.5
--- /home/repository/moby/moby-live/Java/xmls/junit.xml	2008/03/03 11:34:17	1.4
+++ /home/repository/moby/moby-live/Java/xmls/junit.xml	2008/03/17 23:48:01	1.5
@@ -102,6 +102,7 @@
       <fileset dir="${build.test}">
         <include name="**/MobyParserTest.*"/>
         <include name="**/ServicesTest.*"/>
+        <include name="**/FromRDFTest.*"/>
       </fileset>
       <!--      <fileset dir="${build.test}" includes="**/*Test.*" /> -->
     </batchtest>



From kawas at dev.open-bio.org  Wed Mar 19 16:55:35 2008
From: kawas at dev.open-bio.org (Eddie Kawas)
Date: Wed, 19 Mar 2008 12:55:35 -0400
Subject: [MOBY-guts] biomoby commit
Message-ID: <200803191655.m2JGtZ1x028491@dev.open-bio.org>


kawas
Wed Mar 19 12:55:35 EDT 2008
Update of /home/repository/moby/moby-live/Perl/MOBY-Server/bin/scripts
In directory dev.open-bio.org:/tmp/cvs-serv28455/Perl/MOBY-Server/bin/scripts

Modified Files:
	moby-s-install.pl 
Log Message:
fixed bug where authority script wasnt being installed by script
moby-live/Perl/MOBY-Server/bin/scripts moby-s-install.pl,1.2,1.3
===================================================================
RCS file: /home/repository/moby/moby-live/Perl/MOBY-Server/bin/scripts/moby-s-install.pl,v
retrieving revision 1.2
retrieving revision 1.3
diff -u -r1.2 -r1.3
--- /home/repository/moby/moby-live/Perl/MOBY-Server/bin/scripts/moby-s-install.pl	2008/03/06 16:44:55	1.2
+++ /home/repository/moby/moby-live/Perl/MOBY-Server/bin/scripts/moby-s-install.pl	2008/03/19 16:55:35	1.3
@@ -90,7 +90,7 @@
 		check_module('WSRF::Lite');
 		check_module('Crypt::OpenSSL::X509');
 		check_module('IPC::Shareable');
-	}    
+	}
 
 	if ($errors_found) {
 		say "\nSorry, some needed modules were not found.";
@@ -131,20 +131,24 @@
 }
 
 sub prompt_for_directory_expand {
-    my ($prompt, $prompted_dir) = @_;
-    while (1) {
-	my $dir = pprompt ("$prompt [$prompted_dir] ");
-	$dir =~ s/^\s*//; $dir =~ s/\s*$//;
-	$dir = $prompted_dir unless $dir;
-	return $dir if -d $dir and -w $dir;  # okay: writable directory
-	$prompted_dir = $dir;
-	next if -e $dir and say "'$dir' is not a writable directory. Try again please.";
-	next unless pprompt ("Directory '$dir' does not exists. Create? ", -yn);
-
-	# okay, we agreed to create it
-	mkdir ($dir, 0755 )and return $dir;
-	say "'$dir' not created: $!";
-    }
+	my ( $prompt, $prompted_dir ) = @_;
+	while (1) {
+		my $dir = pprompt("$prompt [$prompted_dir] ");
+		$dir =~ s/^\s*//;
+		$dir =~ s/\s*$//;
+		$dir = $prompted_dir unless $dir;
+		return $dir if -d $dir and -w $dir;    # okay: writable directory
+		$prompted_dir = $dir;
+		next
+		  if -e $dir
+		  and say "'$dir' is not a writable directory. Try again please.";
+		next
+		  unless pprompt( "Directory '$dir' does not exists. Create? ", -yn );
+
+		# okay, we agreed to create it
+		mkdir( $dir, 0755 ) and return $dir;
+		say "'$dir' not created: $!";
+	}
 }
 
 sub prompt_user_input {
@@ -186,11 +190,14 @@
 	if ($@) {
 		say "ERROR: $file_desc was (probably) not created.\n$@";
 	} else {
-		say "\n$file_desc created: '$file'\n\tPlease ensure that the file is executable!\n";
+		say
+"\n$file_desc created: '$file'\n\tPlease ensure that the file is executable!\n";
 	}
+
 	# try to make file executable
 	eval {
-		my $mode = 0655;   chmod $mode, "$file";
+		my $mode = 0655;
+		chmod $mode, "$file";
 	};
 }
 
@@ -472,8 +479,7 @@
   prompt_for_directory( "What is the path of the apache 'cgi-bin' directory?",
 						"$apache_base/cgi-bin" );
 $perl_exec =
-  prompt_user_input( "What is the path to your perl executable?", 
-  						$perl_exec );
+  prompt_user_input( "What is the path to your perl executable?", $perl_exec );
 $perl_exec = "$perl_exec -w";
 
 say "\nusing $apache_base as base directory ...";
@@ -540,7 +546,7 @@
 												   'MOBY', 'cgi/MOBY-Central.pl'
 						),
 						'MOBY-Central Dispatch file',
-						{'#!/usr/bin/perl -w'    => "#!$perl_exec",}
+						{ '#!/usr/bin/perl -w' => "#!$perl_exec", }
 	);
 	file_from_template(
 						"$apache_cgi/OntologyServer.cgi",
@@ -548,8 +554,9 @@
 												'MOBY', 'cgi/OntologyServer.cgi'
 						),
 						'MOBY-Central Ontology Server file',
-						{'#!/usr/bin/perl -w'    => "#!$perl_exec",}
+						{ '#!/usr/bin/perl -w' => "#!$perl_exec", }
 	);
+
 	#install the moby-admin module
 	file_from_template(
 						"$apache_cgi/MOBY-Admin.pl",
@@ -557,7 +564,7 @@
 												   'MOBY', 'cgi/MOBY-Admin.pl'
 						),
 						'MOBY-Admin Dispatch file',
-						{'#!/usr/bin/perl -w'    => "#!$perl_exec",}
+						{ '#!/usr/bin/perl -w' => "#!$perl_exec", }
 	);
 
 	# configure httpd.conf
@@ -662,12 +669,18 @@
 
 do {
 	my $ready_to_go = 0;
-	my $sql_error = 0;
+	my $sql_error   = 0;
+
 	#check to see if we can call mysql ... if not, then die!
-	print "mysql is installed ...\n" if `mysql --version 2>&1` =~ m/^mysql\s+Ver\s+.*$/;
-	print "mysql is started ...\n" unless `mysql 2>&1` =~ m/^ERROR 200.*Can't connect to .*$/ ;
+	print "mysql is installed ...\n"
+	  if `mysql --version 2>&1` =~ m/^mysql\s+Ver\s+.*$/;
+	print "mysql is started ...\n"
+	  unless `mysql 2>&1` =~ m/^ERROR 200.*Can't connect to .*$/;
 
-	unless ( `mysql --version 2>&1`  =~ m/^mysql\s+Ver\s+.*$/ and not (`mysql 2>&1` =~ m/^ERROR .*Can't connect to local MySQL .*$/) ) {
+	unless ( `mysql --version 2>&1` =~ m/^mysql\s+Ver\s+.*$/
+		 and not( `mysql 2>&1` =~ m/^ERROR .*Can't connect to local MySQL .*$/ )
+	  )
+	{
 		say
 "\nmysql doesn't seem to be accessible ... please ensure that it is on the path, started and try again.\n";
 		$sql_error = 1;
@@ -675,274 +688,278 @@
 
 	# proceed if mysql check was good
 	do {
-	# have the values been set already?
-	$ready_to_go = 1
-	  if $username
-	  and $url
-	  and $port
-	  and $m_object
-	  and $m_relationship
-	  and $m_service
-	  and $m_namespace
-	  and $m_central;
+
+		# have the values been set already?
+		$ready_to_go = 1
+		  if $username
+		  and $url
+		  and $port
+		  and $m_object
+		  and $m_relationship
+		  and $m_service
+		  and $m_namespace
+		  and $m_central;
 
 #check to see if mobycentral.config has been created in the conf directory first -> if so, parse it
-	if (    -e "$apache_conf/mobycentral.config"
-		 && !( -d "$apache_conf/mobycentral.config" )
-		 && !$ready_to_go )
-	{
-		my %db_sections = ();
-		open IN, "$apache_conf/mobycentral.config"
-		  or die
+		if (    -e "$apache_conf/mobycentral.config"
+			 && !( -d "$apache_conf/mobycentral.config" )
+			 && !$ready_to_go )
+		{
+			my %db_sections = ();
+			open IN, "$apache_conf/mobycentral.config"
+			  or die
 "can't open MOBY Configuration file '$apache_conf/mobycentral.config' for unknown reasons: $!\n";
-		my @sections = split /(\[\s*\S+\s*\][^\[]*)/s, join "", <IN>;
-		foreach my $section (@sections) {
-			my $dbConfig = MOBY::dbConfig->new( section => $section );
-			next unless $dbConfig;
-			my $dbname = $dbConfig->section_title;
-			next unless $dbname;
-			$db_sections{$dbname} = $dbConfig;
-		}
+			my @sections = split /(\[\s*\S+\s*\][^\[]*)/s, join "", <IN>;
+			foreach my $section (@sections) {
+				my $dbConfig = MOBY::dbConfig->new( section => $section );
+				next unless $dbConfig;
+				my $dbname = $dbConfig->section_title;
+				next unless $dbname;
+				$db_sections{$dbname} = $dbConfig;
+			}
 
-		$username       = $db_sections{mobycentral}->{username};
-		$password       = $db_sections{mobycentral}->{password} || "";
-		$url            = $db_sections{mobycentral}->{url};
-		$port           = $db_sections{mobycentral}->{port};
-		$m_object       = $db_sections{mobyobject}->{dbname};
-		$m_relationship = $db_sections{mobyrelationship}->{dbname};
-		$m_service      = $db_sections{mobyservice}->{dbname};
-		$m_namespace    = $db_sections{mobynamespace}->{dbname};
-		$m_central      = $db_sections{mobycentral}->{dbname};
+			$username       = $db_sections{mobycentral}->{username};
+			$password       = $db_sections{mobycentral}->{password} || "";
+			$url            = $db_sections{mobycentral}->{url};
+			$port           = $db_sections{mobycentral}->{port};
+			$m_object       = $db_sections{mobyobject}->{dbname};
+			$m_relationship = $db_sections{mobyrelationship}->{dbname};
+			$m_service      = $db_sections{mobyservice}->{dbname};
+			$m_namespace    = $db_sections{mobynamespace}->{dbname};
+			$m_central      = $db_sections{mobycentral}->{dbname};
 
-		$ready_to_go = 1;
-	}
+			$ready_to_go = 1;
+		}
 
-	# if the values havent been set, then prompt for them
-	do {
+		# if the values havent been set, then prompt for them
+		do {
 
-		say "  Installing the file '$apache_conf/mobycentral.config' ...";
+			say "  Installing the file '$apache_conf/mobycentral.config' ...";
 
-		# fill out mobycentral.config
-		(
-		   $username,  $password,    $url,
-		   $port,      $m_object,    $m_relationship,
-		   $m_service, $m_namespace, $m_central
-		  )
-		  = prompt_moby_config_info;
-		fill_out_moby_conf(
-							"$apache_conf/mobycentral.config",
-							$username,  $password,    $url,
-							$port,      $m_object,    $m_relationship,
-							$m_service, $m_namespace, $m_central
-		);
+			# fill out mobycentral.config
+			(
+			   $username,  $password,    $url,
+			   $port,      $m_object,    $m_relationship,
+			   $m_service, $m_namespace, $m_central
+			  )
+			  = prompt_moby_config_info;
+			fill_out_moby_conf(
+								"$apache_conf/mobycentral.config",
+								$username,  $password,    $url,
+								$port,      $m_object,    $m_relationship,
+								$m_service, $m_namespace, $m_central
+			);
 
-	} unless $ready_to_go;
+		} unless $ready_to_go;
 
-	# now start creating the tables
-	say "   creating the tables to use for the registry ...";
-	my %dbsections = (
-					   'mobycentral'      => $m_central,
-					   'mobyobject'       => $m_object,
-					   'mobyservice'      => $m_service,
-					   'mobynamespace'    => $m_namespace,
-					   'mobyrelationship' => $m_relationship
-	);
+		# now start creating the tables
+		say "   creating the tables to use for the registry ...";
+		my %dbsections = (
+						   'mobycentral'      => $m_central,
+						   'mobyobject'       => $m_object,
+						   'mobyservice'      => $m_service,
+						   'mobynamespace'    => $m_namespace,
+						   'mobyrelationship' => $m_relationship
+		);
 
-	my $clone = 0;
-	my $central;
-	do {
-		$clone = 1;
-		my %registries = (
-			default => {
-				url =>
-"http://moby.ucalgary.ca/moby/MOBY-Central.pl",
-				uri => "http://moby.ucalgary.ca/MOBY/Central"
-			},
-			testing => {
-				url =>
+		my $clone = 0;
+		my $central;
+		do {
+			$clone = 1;
+			my %registries = (
+				default => {
+						  url => "http://moby.ucalgary.ca/moby/MOBY-Central.pl",
+						  uri => "http://moby.ucalgary.ca/MOBY/Central"
+				},
+				testing => {
+					url =>
 "http://bioinfo.icapture.ubc.ca/cgi-bin/mobycentral/MOBY-Central.pl",
-				uri => "http://bioinfo.icapture.ubc.ca/MOBY/Central"
-			},
-			IRRI => {
+					uri => "http://bioinfo.icapture.ubc.ca/MOBY/Central"
+				},
+				IRRI => {
 					  url => "http://cropwiki.irri.org/cgi-bin/MOBY-Central.pl",
 					  uri => "http://cropwiki.irri.org/MOBY/Central"
-			},
+				},
 
-			#			localhost => {
-			#					url=>"http://localhost/cgi-bin/MOBY-Central.pl",
-			#					uri=>"http://localhost/MOBY/Central"
-			#			},
-		);
-		my $registry = pprompt( "What registry to use? [b] ",
-								-m => [ sort keys %registries ] );
+				#			localhost => {
+				#					url=>"http://localhost/cgi-bin/MOBY-Central.pl",
+				#					uri=>"http://localhost/MOBY/Central"
+				#			},
+			);
+			my $registry = pprompt( "What registry to use? [b] ",
+									-m => [ sort keys %registries ] );
 
-		$central = MOBY::Client::Central->new(
+			$central = MOBY::Client::Central->new(
 									 Registries => {
 										 mobycentral => {
 											 URL => $registries{$registry}{url},
 											 URI => $registries{$registry}{uri}
 										 }
 									 }
-		);
-	  }
-	  if pprompt( "Would you like to clone a mobycentral registry? [n] ",
-				  -ynd => 'n' ) eq 'y';
-	my $error = 0;
-	if ($clone) {
-		say "Getting db dumps ...";
-		my (
-			 $mobycentral,   $mobyobject, $mobyservice,
-			 $mobynamespace, $mobyrelationship
-		  )
-		  = $central->MOBY::Client::Central::DUMP();
-		my $drh = DBI->install_driver("mysql");
-
-		my ( $fh, $filename ) = tempfile( UNLINK => 1 );
-		say "Processing dump for service instances ...";
-		print $fh $mobycentral;
-		eval {
-			$drh->func( 'dropdb', $dbsections{mobycentral},
-						$url, $username, $password, 'admin' );
-		};
-		eval {
-			$drh->func( 'createdb', $dbsections{mobycentral},
-						$url, $username, $password, 'admin' );
-		};
-		system(   "mysql -h $url -P $port -u $username --password=$password "
-				. $dbsections{mobycentral}
-				. "<$filename" ) == 0
-		  or ( say "Error populating service instance ontology ...\n$!"
-			   and $error++ );
-
-		( $fh, $filename ) = tempfile( UNLINK => 1 );
-		say "Processing dump for the objects ontology ...";
-		print $fh $mobyobject;
-		eval {
-			$drh->func( 'dropdb', $dbsections{mobyobject}, $url, $username,
-						$password, 'admin' );
-		};
-		eval {
-			$drh->func( 'createdb', $dbsections{mobyobject}, $url, $username,
-						$password, 'admin' );
-		};
-		system(   "mysql -h $url -P $port -u $username --password=$password "
-				. $dbsections{mobyobject}
-				. "<$filename" ) == 0
-		  or ( say "Error populating objects ontology ...\n$!" and $error++ );
-
-		( $fh, $filename ) = tempfile( UNLINK => 1 );
-		say "Processing dump for service types ...";
-		print $fh $mobyservice;
-		eval {
-			$drh->func( 'dropdb', $dbsections{mobyservice},
-						$url, $username, $password, 'admin' );
-		};
-		eval {
-			$drh->func( 'createdb', $dbsections{mobyservice},
-						$url, $username, $password, 'admin' );
-		};
-		system(   "mysql -h $url -P $port -u $username --password=$password "
-				. $dbsections{mobyservice}
-				. "<$filename" ) == 0
-		  or ( say "Error populating service types ontology ...\n$!"
-			   and $error++ );
-
-		( $fh, $filename ) = tempfile( UNLINK => 1 );
-		say "Processing dump for the namespace ontology ...";
-		print $fh $mobynamespace;
-		eval {
-			$drh->func( 'dropdb', $dbsections{mobynamespace},
-						$url, $username, $password, 'admin' );
-		};
-		eval {
-			$drh->func( 'createdb', $dbsections{mobynamespace},
-						$url, $username, $password, 'admin' );
-		};
-		system(   "mysql -h $url -P $port -u $username --password=$password "
-				. $dbsections{mobynamespace}
-				. "<$filename" ) == 0
-		  or ( say "Error populating namespace ontology ...\n$!" and $error++ );
-
-		( $fh, $filename ) = tempfile( UNLINK => 1 );
-		say "Processing dump for the relationships ontology ...";
-		print $fh $mobyrelationship;
-		eval {
-			$drh->func( 'dropdb', $dbsections{mobyrelationship},
-						$url, $username, $password, 'admin' );
-		};
-		eval {
-			$drh->func( 'createdb', $dbsections{mobyrelationship},
-						$url, $username, $password, 'admin' );
-		};
-		system(   "mysql -h $url -P $port -u $username --password=$password "
-				. $dbsections{mobyrelationship}
-				. "<$filename" ) == 0
-		  or ( say "Error populating relationships ontology ...\n$!"
-			   and $error++ );
-
-	} else {
-
-		# no clone, so create minimalist databases
-		my $drop_db = 0;
-
-		#ask for permission on dropping data from db ...
-		do {
-			$drop_db = 1;
+			);
 		  }
-		  if pprompt(
-				"Shall I drop all pre-existing databases used by BioMOBY? [n] ",
-				-ynd => 'n' ) eq 'y';
-
-		#process each db
-		foreach my $section ( keys %dbsections ) {
-			my $sqlfilepath =
-			  File::ShareDir::dist_file( 'MOBY', "db/schema/$section.mysql" );
+		  if pprompt( "Would you like to clone a mobycentral registry? [n] ",
+					  -ynd => 'n' ) eq 'y';
+		my $error = 0;
+		if ($clone) {
+			say "Getting db dumps ...";
+			my (
+				 $mobycentral,   $mobyobject, $mobyservice,
+				 $mobynamespace, $mobyrelationship
+			  )
+			  = $central->MOBY::Client::Central::DUMP();
 			my $drh = DBI->install_driver("mysql");
 
-			# drop the db
+			my ( $fh, $filename ) = tempfile( UNLINK => 1 );
+			say "Processing dump for service instances ...";
+			print $fh $mobycentral;
 			eval {
-				$drh->func( 'dropdb', $dbsections{$section}, $url, $username,
-							$password, 'admin' );
-			} if $drop_db;
-
-			# create the db
+				$drh->func( 'dropdb', $dbsections{mobycentral},
+							$url, $username, $password, 'admin' );
+			};
 			eval {
-				$drh->func( 'createdb', $dbsections{$section}, $url, $username,
+				$drh->func( 'createdb', $dbsections{mobycentral},
+							$url, $username, $password, 'admin' );
+			};
+			system( "mysql -h $url -P $port -u $username --password=$password "
+					. $dbsections{mobycentral}
+					. "<$filename" ) == 0
+			  or ( say "Error populating service instance ontology ...\n$!"
+				   and $error++ );
+
+			( $fh, $filename ) = tempfile( UNLINK => 1 );
+			say "Processing dump for the objects ontology ...";
+			print $fh $mobyobject;
+			eval {
+				$drh->func( 'dropdb', $dbsections{mobyobject}, $url, $username,
 							$password, 'admin' );
 			};
+			eval {
+				$drh->func( 'createdb', $dbsections{mobyobject}, $url,
+							$username, $password, 'admin' );
+			};
+			system( "mysql -h $url -P $port -u $username --password=$password "
+					. $dbsections{mobyobject}
+					. "<$filename" ) == 0
+			  or
+			  ( say "Error populating objects ontology ...\n$!" and $error++ );
+
+			( $fh, $filename ) = tempfile( UNLINK => 1 );
+			say "Processing dump for service types ...";
+			print $fh $mobyservice;
+			eval {
+				$drh->func( 'dropdb', $dbsections{mobyservice},
+							$url, $username, $password, 'admin' );
+			};
+			eval {
+				$drh->func( 'createdb', $dbsections{mobyservice},
+							$url, $username, $password, 'admin' );
+			};
+			system( "mysql -h $url -P $port -u $username --password=$password "
+					. $dbsections{mobyservice}
+					. "<$filename" ) == 0
+			  or ( say "Error populating service types ontology ...\n$!"
+				   and $error++ );
+
+			( $fh, $filename ) = tempfile( UNLINK => 1 );
+			say "Processing dump for the namespace ontology ...";
+			print $fh $mobynamespace;
+			eval {
+				$drh->func( 'dropdb', $dbsections{mobynamespace},
+							$url, $username, $password, 'admin' );
+			};
+			eval {
+				$drh->func( 'createdb', $dbsections{mobynamespace},
+							$url, $username, $password, 'admin' );
+			};
+			system( "mysql -h $url -P $port -u $username --password=$password "
+					. $dbsections{mobynamespace}
+					. "<$filename" ) == 0
+			  or ( say "Error populating namespace ontology ...\n$!"
+				   and $error++ );
+
+			( $fh, $filename ) = tempfile( UNLINK => 1 );
+			say "Processing dump for the relationships ontology ...";
+			print $fh $mobyrelationship;
+			eval {
+				$drh->func( 'dropdb', $dbsections{mobyrelationship},
+							$url, $username, $password, 'admin' );
+			};
+			eval {
+				$drh->func( 'createdb', $dbsections{mobyrelationship},
+							$url, $username, $password, 'admin' );
+			};
+			system( "mysql -h $url -P $port -u $username --password=$password "
+					. $dbsections{mobyrelationship}
+					. "<$filename" ) == 0
+			  or ( say "Error populating relationships ontology ...\n$!"
+				   and $error++ );
+
+		} else {
+
+			# no clone, so create minimalist databases
+			my $drop_db = 0;
 
-			#create the tables in the db
+			#ask for permission on dropping data from db ...
 			do {
-				say "\n\tProblem creating tables in the db: $section: $!";
+				$drop_db = 1;
 			  }
-			  unless system(
+			  if pprompt(
+				"Shall I drop all pre-existing databases used by BioMOBY? [n] ",
+				-ynd => 'n'
+			  ) eq 'y';
+
+			#process each db
+			foreach my $section ( keys %dbsections ) {
+				my $sqlfilepath = File::ShareDir::dist_file( 'MOBY',
+												   "db/schema/$section.mysql" );
+				my $drh = DBI->install_driver("mysql");
+
+				# drop the db
+				eval {
+					$drh->func( 'dropdb', $dbsections{$section}, $url,
+								$username, $password, 'admin' );
+				} if $drop_db;
+
+				# create the db
+				eval {
+					$drh->func( 'createdb', $dbsections{$section}, $url,
+								$username, $password, 'admin' );
+				};
+
+				#create the tables in the db
+				do {
+					say "\n\tProblem creating tables in the db: $section: $!";
+				  }
+				  unless system(
 					 "mysql -h $url -P $port -u $username --password=$password "
 					   . $dbsections{$section}
 					   . "<$sqlfilepath" ) == 0;
-			say "\tProcessing of $section completed ... ";
-		}
-		say "populating the tables with basic data ...";
-		%dbsections = (
-						'mobyobject'       => $m_object,
-						'mobyservice'      => $m_service,
-						'mobyrelationship' => $m_relationship
-		);
-		foreach my $section ( keys %dbsections ) {
-			my $sqlfilepath =
-			  File::ShareDir::dist_file( 'MOBY', "db/data/$section.data" );
-			system( "mysql -h $url -P $port -u $username --password=$password "
-					. $dbsections{$section}
-					. "<$sqlfilepath" ) == 0
-			  or say "\n\tProblem populating the db: $section: $!";
-			say "\tPopulation processing for db $section completed ...";
+				say "\tProcessing of $section completed ... ";
+			}
+			say "populating the tables with basic data ...";
+			%dbsections = (
+							'mobyobject'       => $m_object,
+							'mobyservice'      => $m_service,
+							'mobyrelationship' => $m_relationship
+			);
+			foreach my $section ( keys %dbsections ) {
+				my $sqlfilepath =
+				  File::ShareDir::dist_file( 'MOBY', "db/data/$section.data" );
+				system(
+					 "mysql -h $url -P $port -u $username --password=$password "
+					   . $dbsections{$section}
+					   . "<$sqlfilepath" ) == 0
+				  or say "\n\tProblem populating the db: $section: $!";
+				say "\tPopulation processing for db $section completed ...";
+			}
 		}
-	}
 
-	say "Set up of mySQL complete!" if $error == 0;
-	say
+		say "Set up of mySQL complete!" if $error == 0;
+		say
 "There were some problems encountered. Please correct the errors and re-run this script!"
-	  if $error > 0;
-} unless $sql_error;
+		  if $error > 0;
+	} unless $sql_error;
 } if pprompt( "Would you like to set up mySQL? [n] ", -ynd => 'n' ) eq 'y';
 
 do {
@@ -957,15 +974,22 @@
 		  if pprompt( "The RESOURCES script already exists, overwrite? [n] ",
 					  -ynd => 'n' ) eq 'y';
 	} if -e "$apache_cgi/RESOURCES";
-	
-	my $rdf_cache_location =  prompt_for_directory_expand( "Where would you like to store the RDF cache?", "$apache_base/moby_cache" );
-	
-	say 'Please make sure that you make that directory read/writable by your web server!\n';
-	
+
+	my $rdf_cache_location =
+	  prompt_for_directory_expand(
+								 "Where would you like to store the RDF cache?",
+								 "$apache_base/moby_cache" );
+
+	say
+"Please make sure that you make that directory read/writable by your web server!\n";
+
 	# copy the file
-	file_from_template( "$apache_cgi/RESOURCES",
+	file_from_template(
+						"$apache_cgi/RESOURCES",
 						File::ShareDir::dist_file( 'MOBY', 'cgi/RESOURCES' ),
-						'RESOURCES script', {'#!/usr/bin/perl -w'    => "#!$perl_exec",} )
+						'RESOURCES script',
+						{ '#!/usr/bin/perl -w' => "#!$perl_exec", }
+	  )
 	  if $exists == 0;
 
 	# update mobycentral.config file to reflect the location of the script
@@ -985,7 +1009,7 @@
 									 'mobycentral' => {
 														'resourceURL'  => 0,
 														'allResources' => 0,
-														'rdf_cache' => 0
+														'rdf_cache'    => 0
 									 },
 									 'mobyobject'    => { 'resourceURL' => 0 },
 									 'mobyservice'   => { 'resourceURL' => 0 },
@@ -1002,7 +1026,7 @@
 			'MOBY/SQL Configuration file',
 
 			# mysql settings
-			{'rdf_cache'		=> "$rdf_cache_location"},
+			{ 'rdf_cache' => "$rdf_cache_location" },
 
 			# db section mappings
 			{},
@@ -1039,16 +1063,16 @@
 		  }
 		  if pprompt( "The authority script already exists, overwrite? [n] ",
 					  -ynd => 'n' ) eq 'y';
-		file_from_template(
-						"$apache_cgi/authority.pl",
-						File::ShareDir::dist_file(
-												'MOBY', 'cgi/authority.pl'
-						),
-						'MOBY-Central LSID authority server file',
-						{'#!/usr/bin/perl -w'    => "#!$perl_exec",}
-		) if $exists == 0;
 	} if -e "$apache_cgi/authority.pl";
 
+	file_from_template(
+		"$apache_cgi/authority.pl",    
+		File::ShareDir::dist_file( 'MOBY', 'cgi/authority.pl' ),
+		'MOBY-Central LSID authority server file',
+		{ '#!/usr/bin/perl -w' => "#!$perl_exec", }
+	  )
+	  if $exists == 0;
+
 	# update mobycentral.config file to reflect the particulars of the script
 	do {
 
@@ -1167,97 +1191,99 @@
 
 do {
 
-		# prompt for a location for the service_tester_path
-		my $service_tester_path =  prompt_for_directory_expand( "Where would you like to place the service pinger script?", "$apache_base/moby_tester" );
-		say 'Please make sure that you make that directory read/writable by your web server!\n';
-		# make sure that the key service_tester_path exists for the config file
-		my $search = search_config_file(
-								   "$apache_conf/mobycentral.config",
-								   {
-									 'mobycentral' => {
-														'service_tester_path'  => 0,
-									 }
-								   }
-		);
-		add_missing_keys_to_config_file( "$apache_conf/mobycentral.config", $search );
+	# prompt for a location for the service_tester_path
+	my $service_tester_path =
+	  prompt_for_directory_expand(
+					 "Where would you like to place the service pinger script?",
+					 "$apache_base/moby_tester" );
+	say
+'Please make sure that you make that directory read/writable by your web server!\n';
 
-		# copy the information
-		config_file_from_template(
-			"$apache_conf/mobycentral.config",
-			"$apache_conf/mobycentral.config",
-			'MOBY/SQL Configuration file',
+	# make sure that the key service_tester_path exists for the config file
+	my $search = search_config_file( "$apache_conf/mobycentral.config",
+						 { 'mobycentral' => { 'service_tester_path' => 0, } } );
+	add_missing_keys_to_config_file( "$apache_conf/mobycentral.config",
+									 $search );
 
-			# mysql settings
-			{'service_tester_path'	=> "$service_tester_path"},
+	# copy the information
+	config_file_from_template(
+		"$apache_conf/mobycentral.config",
+		"$apache_conf/mobycentral.config",
+		'MOBY/SQL Configuration file',
 
-			# db section mappings
-			{},
+		# mysql settings
+		{ 'service_tester_path' => "$service_tester_path" },
 
-			# resource urls
-			{},
+		# db section mappings
+		{},
 
-			# lsid info
-			{}
-		);
-		
-		file_from_template(
+		# resource urls
+		{},
+
+		# lsid info
+		{}
+	);
+
+	file_from_template(
 						"$service_tester_path/service_tester.pl",
 						File::ShareDir::dist_file(
-												'MOBY', 'cgi/service_tester.pl'
+												 'MOBY', 'cgi/service_tester.pl'
 						),
 						'MOBY-Central service tester script',
-						{'#!/usr/bin/perl -w'    => "#!$perl_exec",}
-		);
-		say 'Please don\'t forget to place the service pinger on a cron! TODO - explain how to do that!';
-		
-		#copy the other scripts now
-		file_from_template(
+						{ '#!/usr/bin/perl -w' => "#!$perl_exec", }
+	);
+	say
+'Please don\'t forget to place the service pinger on a cron! TODO - explain how to do that!';
+
+	#copy the other scripts now
+	file_from_template(
 						"$apache_cgi/AgentRDFValidator",
 						File::ShareDir::dist_file(
-												'MOBY', 'cgi/AgentRDFValidator'
+												 'MOBY', 'cgi/AgentRDFValidator'
 						),
 						'The RDF agent validator page',
-						{'#!/usr/bin/perl -w'    => "#!$perl_exec",}
-		);
-		file_from_template(
+						{ '#!/usr/bin/perl -w' => "#!$perl_exec", }
+	);
+	file_from_template(
 						"$apache_cgi/GenerateRDF.cgi",
 						File::ShareDir::dist_file(
-												'MOBY', 'cgi/GenerateRDF.cgi'
+												   'MOBY', 'cgi/GenerateRDF.cgi'
 						),
 						'MOBY-Central service instance RDF generating form',
-						{'#!/usr/bin/perl -w'    => "#!$perl_exec",}
-		);
-		file_from_template(
+						{ '#!/usr/bin/perl -w' => "#!$perl_exec", }
+	);
+	file_from_template(
 						"$apache_cgi/Moby",
-						File::ShareDir::dist_file(
-												'MOBY', 'cgi/Moby'
-						),
+						File::ShareDir::dist_file( 'MOBY', 'cgi/Moby' ),
 						'MOBY-Central test page for auxillary scripts',
-						{'#!/usr/bin/perl -w'    => "#!$perl_exec",}
-		);
-		file_from_template(
+						{ '#!/usr/bin/perl -w' => "#!$perl_exec", }
+	);
+	file_from_template(
 						"$apache_cgi/ServicePingerValidator",
 						File::ShareDir::dist_file(
-												'MOBY', 'cgi/ServicePingerValidator'
+											'MOBY', 'cgi/ServicePingerValidator'
 						),
 						'MOBY-Central service invocation test form',
-						{'#!/usr/bin/perl -w'    => "#!$perl_exec",}
-		);
-		file_from_template(
+						{ '#!/usr/bin/perl -w' => "#!$perl_exec", }
+	);
+	file_from_template(
 						"$apache_cgi/ValidateService",
 						File::ShareDir::dist_file(
-												'MOBY', 'cgi/ValidateService'
+												   'MOBY', 'cgi/ValidateService'
 						),
 						'MOBY-Central service tester information page',
-						{'#!/usr/bin/perl -w'    => "#!$perl_exec",}
-		);
+						{ '#!/usr/bin/perl -w' => "#!$perl_exec", }
+	);
   }
-	  if pprompt( "Would you like to auxillary scripts? These include the service pinger, a test page for the rdf agent, an RDF generator page, etc? [y] ",
-			  -ynd => 'y' ) eq 'y';
+  if pprompt(
+"Would you like to auxillary scripts? These include the service pinger, a test page for the rdf agent, an RDF generator page, etc? [y] ",
+	-ynd => 'y'
+  ) eq 'y';
 
 #
 
-say "Please remember to set up the RDF agent! Just restart apache and your registry has been set up!\n\nDone.";
+say
+"Please remember to set up the RDF agent! Just restart apache and your registry has been set up!\n\nDone.";
 
 package SimplePrompt;
 



From walexander at dev.open-bio.org  Wed Mar 19 22:49:47 2008
From: walexander at dev.open-bio.org (Wendy Alexander)
Date: Wed, 19 Mar 2008 18:49:47 -0400
Subject: [MOBY-guts] biomoby commit
Message-ID: <200803192249.m2JMnlC4028988@dev.open-bio.org>


walexander
Wed Mar 19 18:49:47 EDT 2008
Update of /home/repository/moby/moby-live/Java/src/main/org/biomoby/service/dashboard
In directory dev.open-bio.org:/tmp/cvs-serv28953

Modified Files:
	SimpleClientPanel.java 
Log Message:
Added pinger button.
moby-live/Java/src/main/org/biomoby/service/dashboard SimpleClientPanel.java,1.9,1.10
===================================================================
RCS file: /home/repository/moby/moby-live/Java/src/main/org/biomoby/service/dashboard/SimpleClientPanel.java,v
retrieving revision 1.9
retrieving revision 1.10
diff -u -r1.9 -r1.10
--- /home/repository/moby/moby-live/Java/src/main/org/biomoby/service/dashboard/SimpleClientPanel.java	2008/03/02 12:45:26	1.9
+++ /home/repository/moby/moby-live/Java/src/main/org/biomoby/service/dashboard/SimpleClientPanel.java	2008/03/19 22:49:47	1.10
@@ -248,12 +248,16 @@
 	className = createText (null, DP_IMPL_CLASS, DP_IMPL_CLASS);
 
 	ButtonGroup group = new ButtonGroup();
-	JRadioButton htNone, htRegistry, htEndpoint, htLocal, htNewURL;
+	JRadioButton htNone, htRegistry, htEndpoint, htLocal, htNewURL, htPing;
 	group.add (htEndpoint = createHowToButton ("Use service's usual endpoint", DP_CS_URL));
 	group.add (htNone     = createHowToButton ("No real call, just show/echo input", DP_CS_NONE));
 	group.add (htRegistry = createHowToButton ("Ask registry where service is, and call it", DP_CS_REGISTRY));
 	group.add (htNewURL   = createHowToButton ("Use this endpoint", DP_CS_NEWURL));
 	group.add (htLocal    = createHowToButton ("Use this local class", DP_CS_CLASS));
+	group.add (htPing	  = createHowToButton ("'Ping' this service", DP_CS_PING));
+	htPing.setToolTipText("A Moby 'Ping' is used to determine if the service is responsive, " +
+			"and if it responds in an API-compliant manner");
+	
 
 	boolean usingAsBytes = getPrefValue (DP_INP_ASBYTES, false);
 	JCheckBox asBytes = createCheckBox
@@ -280,7 +284,8 @@
  	SwingUtils.addComponent (howTo, htLocal,    0, 3, 1, 1, NONE, NWEST,  0.0, 0.0);
  	SwingUtils.addComponent (howTo, className,  1, 3, 1, 1, HORI, NWEST,  1.0, 0.0);
  	SwingUtils.addComponent (howTo, htNone,     0, 4, 2, 1, NONE, NWEST,  0.0, 0.0);
- 	SwingUtils.addComponent (howTo, asBytes,    0, 5, 2, 1, NONE, NWEST,  0.0, 0.0, BREATH_TOP);
+ 	SwingUtils.addComponent (howTo, htPing,		0, 5, 2, 1, NONE, NWEST,  0.0, 0.0);	
+ 	SwingUtils.addComponent (howTo, asBytes,    0, 6, 2, 1, NONE, NWEST,  0.0, 0.0, BREATH_TOP);
 
 	// run the service
 	runButton =
@@ -534,6 +539,16 @@
 		if ( DP_CS_NONE.equals (propertyChannel.getString (DP_CALL_SERVICE)) ||
 		     (propertyChannel.getBoolean (DP_INP_SHOWXML, false)) ) {
 		    input.setText ((String)data.getData());
+		} 
+		
+		// If we are only pinging the service, set the data object to an empty message
+		if (DP_CS_PING.equals(propertyChannel.getString(DP_CALL_SERVICE))) {
+			String emptyMsg = "<?xml version=\"1.0\" encoding=\"UTF-8\"?>\n" +
+			"<moby:MOBY xmlns:moby=\"http://www.biomoby.org/moby\">\n" +
+			"  <moby:mobyContent />\n" +
+			"</moby:MOBY>";
+			data.setData(emptyMsg);
+			input.setText(emptyMsg);
 		}
 
 		// finally, call the service
@@ -559,15 +574,27 @@
 	    }
 
 	    if (exception == null) {
-		propertyChannel.fire (DP_STATUS_MSG, "Service invocation finished.");
-
-		// handle results here (using renderers...)
-		if (! DP_CS_NONE.equals (propertyChannel.getString (DP_CALL_SERVICE)) )
-		    results.updateComponent (data);
+	    	
+			// handle results here (using renderers...)
+			if (DP_CS_PING.equals(propertyChannel.getString(DP_CALL_SERVICE))) {
+				propertyChannel.fire (DP_STATUS_MSG, service.getName()+" isAlive.");
+			} else {
+				propertyChannel.fire (DP_STATUS_MSG, "Service invocation finished.");
+			}
+			
+			if (! DP_CS_NONE.equals (propertyChannel.getString (DP_CALL_SERVICE))) {
+			    results.updateComponent (data);			
+			}
 
 	    } else {
-		propertyChannel.fire (DP_STATUS_MSG, "Service invocation failed.");
-		error (CALLER_ERROR, exception);
+			if (DP_CS_PING.equals(propertyChannel.getString(DP_CALL_SERVICE))) {
+		    	propertyChannel.fire (DP_STATUS_MSG, service.getName()+" is dead.");
+				results.removeResults();
+			} else {
+		    	propertyChannel.fire (DP_STATUS_MSG, "Service invocation failed.");
+				error (CALLER_ERROR, exception);
+			}
+			exception.printStackTrace();
 	    }
 	    serviceFinished();
 	}



From walexander at dev.open-bio.org  Wed Mar 19 22:50:14 2008
From: walexander at dev.open-bio.org (Wendy Alexander)
Date: Wed, 19 Mar 2008 18:50:14 -0400
Subject: [MOBY-guts] biomoby commit
Message-ID: <200803192250.m2JMoEXc029031@dev.open-bio.org>


walexander
Wed Mar 19 18:50:14 EDT 2008
Update of /home/repository/moby/moby-live/Java/src/main/org/biomoby/service/dashboard
In directory dev.open-bio.org:/tmp/cvs-serv28996

Modified Files:
	ServiceCallerModel.java 
Log Message:
Added pinger button.
moby-live/Java/src/main/org/biomoby/service/dashboard ServiceCallerModel.java,1.4,1.5
===================================================================
RCS file: /home/repository/moby/moby-live/Java/src/main/org/biomoby/service/dashboard/ServiceCallerModel.java,v
retrieving revision 1.4
retrieving revision 1.5
diff -u -r1.4 -r1.5
--- /home/repository/moby/moby-live/Java/src/main/org/biomoby/service/dashboard/ServiceCallerModel.java	2007/04/05 14:24:57	1.4
+++ /home/repository/moby/moby-live/Java/src/main/org/biomoby/service/dashboard/ServiceCallerModel.java	2008/03/19 22:50:14	1.5
@@ -145,7 +145,7 @@
 		if (! UUtils.isEmpty (sEndpoint))
 		    clonedService.setURL (sEndpoint);
 
-	    } else if (DP_CS_REGISTRY.equals (howToCall)) {
+	    } else if (DP_CS_REGISTRY.equals (howToCall) || DP_CS_PING.equals(howToCall)) {
 		clonedService.setURL (null);
 		setRegistryEndpoint (propertyChannel.getString (DP_REGISTRY_ENDPOINT));
 		setRegistryNamespace (propertyChannel.getString (DP_REGISTRY_NAMESPACE));
@@ -158,7 +158,7 @@
 
 	    } else if (DP_CS_NONE.equals (howToCall)) {
 		setLoop (true);
-	    }
+	    } 
 
 	    setAsBytes (propertyChannel.getBoolean (DP_INP_ASBYTES, false));
 



From walexander at dev.open-bio.org  Wed Mar 19 22:50:46 2008
From: walexander at dev.open-bio.org (Wendy Alexander)
Date: Wed, 19 Mar 2008 18:50:46 -0400
Subject: [MOBY-guts] biomoby commit
Message-ID: <200803192250.m2JMokh8029076@dev.open-bio.org>


walexander
Wed Mar 19 18:50:46 EDT 2008
Update of /home/repository/moby/moby-live/Java/src/main/org/biomoby/service/dashboard
In directory dev.open-bio.org:/tmp/cvs-serv29041

Modified Files:
	DashboardProperties.java 
Log Message:
Added pinger button.
moby-live/Java/src/main/org/biomoby/service/dashboard DashboardProperties.java,1.26,1.27
===================================================================
RCS file: /home/repository/moby/moby-live/Java/src/main/org/biomoby/service/dashboard/DashboardProperties.java,v
retrieving revision 1.26
retrieving revision 1.27
diff -u -r1.26 -r1.27
--- /home/repository/moby/moby-live/Java/src/main/org/biomoby/service/dashboard/DashboardProperties.java	2008/03/02 12:45:26	1.26
+++ /home/repository/moby/moby-live/Java/src/main/org/biomoby/service/dashboard/DashboardProperties.java	2008/03/19 22:50:46	1.27
@@ -65,6 +65,7 @@
     static final String DP_CS_URL = "service-endpoint";
     static final String DP_CS_NEWURL = "service-new-endpoint";
     static final String DP_CS_REGISTRY = "as-registered";
+    static final String DP_CS_PING = "ping";
 
     static final String DP_ENDPOINT = "serviceEndpoint";
     static final String DP_IMPL_CLASS = "serviceImplClass";



From kawas at dev.open-bio.org  Wed Mar 19 23:36:02 2008
From: kawas at dev.open-bio.org (Eddie Kawas)
Date: Wed, 19 Mar 2008 19:36:02 -0400
Subject: [MOBY-guts] biomoby commit
Message-ID: <200803192336.m2JNa27G029203@dev.open-bio.org>


kawas
Wed Mar 19 19:36:02 EDT 2008
Update of /home/repository/moby/moby-live/Perl/MOBY-Server
In directory dev.open-bio.org:/tmp/cvs-serv29168/Perl/MOBY-Server

Modified Files:
	Makefile.PL 
Log Message:
hmm, turns out the cpan release had very old documentation ... not sure how it snuck in ...
moby-live/Perl/MOBY-Server Makefile.PL,1.2,1.3
===================================================================
RCS file: /home/repository/moby/moby-live/Perl/MOBY-Server/Makefile.PL,v
retrieving revision 1.2
retrieving revision 1.3
diff -u -r1.2 -r1.3
--- /home/repository/moby/moby-live/Perl/MOBY-Server/Makefile.PL	2008/02/22 17:52:06	1.2
+++ /home/repository/moby/moby-live/Perl/MOBY-Server/Makefile.PL	2008/03/19 23:36:02	1.3
@@ -3,7 +3,7 @@
 
 	# Define metadata
 	name 'MOBY';
-	version '1.00';
+	version '1.01';
 	license 'perl';
 	abstract
 'This distribution is for communicating with or creating your own MOBY Central registry';



From kawas at dev.open-bio.org  Thu Mar 20 17:35:43 2008
From: kawas at dev.open-bio.org (Eddie Kawas)
Date: Thu, 20 Mar 2008 13:35:43 -0400
Subject: [MOBY-guts] biomoby commit
Message-ID: <200803201735.m2KHZh4b030890@dev.open-bio.org>


kawas
Thu Mar 20 13:35:42 EDT 2008
Update of /home/repository/moby/moby-live/Perl/MOBY-Server/lib/MOBY
In directory dev.open-bio.org:/tmp/cvs-serv30839/Perl/MOBY-Server/lib/MOBY

Modified Files:
	MOBY.pm 
Log Message:
found 2 MOBY.pm modules. cpan ignored the correct one and indexed the wrong one ...
moby-live/Perl/MOBY-Server/lib/MOBY MOBY.pm,1.1,1.2
===================================================================
RCS file: /home/repository/moby/moby-live/Perl/MOBY-Server/lib/MOBY/MOBY.pm,v
retrieving revision 1.1
retrieving revision 1.2
diff -u -r1.1 -r1.2
--- /home/repository/moby/moby-live/Perl/MOBY-Server/lib/MOBY/MOBY.pm	2008/02/21 00:21:27	1.1
+++ /home/repository/moby/moby-live/Perl/MOBY-Server/lib/MOBY/MOBY.pm	2008/03/20 17:35:42	1.2
@@ -1,84 +1,270 @@
 package MOBY;
 
-use 5.008008;
 use strict;
 use warnings;
 
-require Exporter;
 
-our @ISA = qw(Exporter);
 
-# Items to export into callers namespace by default. Note: do not export
-# names by default without a very good reason. Use EXPORT_OK instead.
-# Do not simply export all your public functions/methods/constants.
+use vars qw{$VERSION @ISA @EXPORT @EXPORT_OK};
+BEGIN {
+	$VERSION = '0.85';
+	@ISA       = qw{ Exporter };
+	@EXPORT    = qw{};
+	@EXPORT_OK = qw{};
+}
 
-# This allows declaration	use MOBY ':all';
-# If you do not need this, moving things directly into @EXPORT or @EXPORT_OK
-# will save memory.
-our %EXPORT_TAGS = ( 'all' => [ qw(
-	
-) ] );
-
-our @EXPORT_OK = ( @{ $EXPORT_TAGS{'all'} } );
-
-our @EXPORT = qw(
-	
-);
-
-our $VERSION = '0.01';
 
 
 # Preloaded methods go here.
 
 1;
 __END__
-# Below is stub documentation for your module. You'd better edit it!
 
 =head1 NAME
 
-MOBY - Perl extension for blah blah blah
+MOBY - API for hosting and/or communicating with a MOBY Central registry
+
+=head1 DESCRIPTION
 
-=head1 SYNOPSIS
+This module serves 2 purposes:
 
-  use MOBY;
-  blah blah blah
+=over 4
 
-=head1 DESCRIPTION
+=item * Used to do various transactions with MOBY-Central registry, including registering new Object and Service types, querying for these types, registering new Servers/Services, or queryiong for available services given certain input/output or service type constraints.
+
+=item * Aid in the installation of a custom local MOBY-Central registry.
+
+=back
+
+=head2 Package Installation
+
+Installation of this perl package is straightforward!
+
+On *nix machines, install as follows:
+
+=over 4
+
+=item * C<perl Makefile.PL>
+
+=item * C<make test>
+
+=item * C<make install>
+
+=back
+
+On Window machines, substitute C<nmake> for C<make>!
+
+B<Important> if you are upgrading to newer versions, please make sure to remove any files that may be cached by this module!
+
+=cut
+
+=head2 Installing A Custom MOBY-Central Registry
+
+Assuming that you have already installed this package, the very first thing that you should do is run the script B<moby-s-install.pl>.
+
+This script will do the following:
+
+=over 4
+
+=item * Check for prerequisite modules and warn you if they are missing
+
+=item * Run you through some configuration details
+
+=item * Optionally help you mirror an already existing registry
+
+=item * Optionally install various scripts used by the registry or its' clients
+
+=back
+
+=cut
+
+=head2 BioMOBY Client Installation
+
+Once the module has been installed using the command B<make install>, there is nothing further left for you to do. You are free to start using the BioMOBY API.
+
+=cut
+
+=head2 BioMOBY Server Installation
+
+To set up your own custom registry, you have to ensure that a few things are ready before hand!
+
+=over 4
+
+=item * You have an apache webserver installed/started on your machine
+
+=item * You have mysql installed/started on your machine
+
+=item * You are aware of the full path to the apache cgi-bin directory
+
+=item * You have a mysql username/password with read/write access available to use
+
+=item * You have root priviledges on your machine!
+
+=back
+
+Once you are sure that you satisfy the above items, go ahead and run the B<moby-s-install.pl> script, by typing C<moby-s-install.pl> at the command line. This file was installed onto your machine when you did your 'make install'!
+
+=head3 What Exactly does moby-s-install.pl do?
+
+Like we said before, the install script helps you install/configure your custom MOBY-Central registry.
+
+First of all, the script ensure that you have all of the proper libraries installed.
+
+The very next thing that the script does is prompt you for some information:
+
+=over 4
+
+=item * What is your base installation path for apache?
+
+=item * Where is the conf/cgi-bin directory for apache located?
+
+=item * What is the path to your Perl executable?
+
+=back
+
+Once that information is entered, the script prompts you to set up apache. 
+
+=head4 Apache setup
+
+The following is done when the installation script sets up apache:
+
+=over 4
+
+=item * A mobycentral configuration file is added to your apache conf directory
+
+=item * mySQL connection information is obtained from you and inserted into the the configuration file
+
+=item * mySQL table names for the registry are chosen
+
+=item * Optionally, httpd.conf is edited adding various environment variables necessary for the registry
 
-Stub documentation for MOBY, created by h2xs. It looks like the
-author of the extension was negligent enough to leave the stub
-unedited.
+=back
 
-Blah blah blah.
+=cut
+
+Once apache has been set up, the installation script prompts you to set up mySQL. 
+
+During mySQL setup, you will be prompted to either create a complete clone of an existing registry or to simply add the base tables required for a registry to your database.
+
+The very next thing that will happen, is that you will be prompted to install the RESOURCES script. This script is mandatory for those hosting a registry.
+
+During the installation of the RESOURCES script, you will be prompted for a place to store the RDF cache. This directory needs to read/writable by apache.
+
+After installation of the RESOURCES script, you will be prompted to install the LSID authority script. 
+
+The very last thing that the script does is to prompt you install other auxillary scripts. While they are not required, it is recommended to install them.
+
+Please make sure that any file installed into your cgi-bin directory is executable and that you restart apache so that all changes are reflected!
+
+Assuming that you installed the auxillary scripts, from a web browser, browse to the url:
+
+C<http://localhost/cgi-bin/Moby> 
+
+B<Note:> Of course, we are assuming that your localhost is your valid hostname and that the cgi-bin directory location is correct. 
+
+A helper page with various links should be visible. Go ahead and try them out!
+
+=cut
+
+=cut
+
+=head2 FAQ
+
+=head3 When I run the install script, IO::Prompt complains ...
+
+This could mean that the package C<IO::Prompt> is not installed properly.
+
+What version do you have?
+
+C<perl -MIO::Prompt -e'print "$IO::Prompt::VERSION\n";'>
+
+We have tested version 0.99.2 on both *nix machines and windows. Please make sure that you have  that version. If you do not, please remove the one that you have (the cpan module B<CPAN Plus> is very useful here) and install version 0.99.2! Version 0.99.4 doesn't seem to work too well and produces numerous warnings in our module. Other versions have yet to be tested.
+
+=cut
+
+=head3 How can I make the service tester run every hour?
+
+First of all, the service tester only works on *NIX machines and will not work on Windows. The reason is due to a the module IPC::Shareable which doesn't port to windows.
+
+To set up the service tester simply create a cron job. The following is an illustration of how to do this!
+
+=over 4
+
+=item * Edit your crontab (as root): 
+
+C<crontab -e>
+
+=item * Add the following to the top of the crontab 
+
+C<MOBY_CENTRAL_CONFIG=/etc/apache2/mobycentral.config>
+
+=item * Add the actual job:
+
+C<00 * * * * perl /path/to/the/service_tester.pl>
+
+=back
+
+This will set up a cron job to run every start of the hour!
+
+=cut
+
+=head3 How do I set up the RDF Agent?
+
+Detailed instructions for building, installing and configuring the agent can be found at http://biomoby.open-bio.org/CVS_CONTENT/moby-live/Java/docs/ConfigureRDFAgent.html
+
+=cut
+
+=cut
+
+=head2 Missing Features
+
+=over
+
+=item * automatic installation of the RDF Agent
+
+=back
+
+=cut
+
+=head2 Acknowledgement
+
+
+=cut
 
 =head2 EXPORT
 
 None by default.
 
 
-
 =head1 SEE ALSO
 
-Mention other useful documentation such as the documentation of
-related modules or operating system documentation (such as man pages
-in UNIX), or any relevant external documentation such as RFCs or
-standards.
+For the most up-to-date documentation, visit the BioMOBY website at L<http://biomoby.org>!
 
-If you have a mailing list set up for your module, mention it here.
+If you have questions or comments, please feel free to message us on the following mailing lists:
 
-If you have a web site set up for your module, mention it here.
+=over
 
-=head1 AUTHOR
+=item MOBY discussion list L<http://www.biomoby.org/mailman/listinfo/moby-l>
 
-A. U. Thor, E<lt>a.u.thor at a.galaxy.far.far.awayE<gt>
+=item MOBY Developers List L<http://www.biomoby.org/mailman/listinfo/moby-dev>
 
-=head1 COPYRIGHT AND LICENSE
+=item MOBY bugs discussion list L<http://www.biomoby.org/mailman/listinfo/moby-bugs>
 
-Copyright (C) 2007 by A. U. Thor
+=back
 
-This library is free software; you can redistribute it and/or modify
-it under the same terms as Perl itself, either Perl version 5.8.8 or,
-at your option, any later version of Perl 5 you may have available.
+=head1 AUTHORS
 
 
 =cut
+
+=head1 COPYRIGHT
+
+Copyright (c) 2007 The Biomoby Consortium.
+
+This module is free software; you can redistribute it and/or modify
+it under the same terms as Perl itself.
+
+This software is provided "as is" without warranty of any kind.
+
+=cut
+



From kawas at dev.open-bio.org  Thu Mar 20 17:35:43 2008
From: kawas at dev.open-bio.org (Eddie Kawas)
Date: Thu, 20 Mar 2008 13:35:43 -0400
Subject: [MOBY-guts] biomoby commit
Message-ID: <200803201735.m2KHZh2T030872@dev.open-bio.org>


kawas
Thu Mar 20 13:35:42 EDT 2008
Update of /home/repository/moby/moby-live/Perl/MOBY-Server/lib
In directory dev.open-bio.org:/tmp/cvs-serv30839/Perl/MOBY-Server/lib

Removed Files:
	MOBY.pm 
Log Message:
found 2 MOBY.pm modules. cpan ignored the correct one and indexed the wrong one ...
moby-live/Perl/MOBY-Server/lib MOBY.pm,1.2,NONE
rcsdiff: /home/repository/moby/moby-live/Perl/MOBY-Server/lib/RCS/MOBY.pm,v: No such file or directory



From kawas at dev.open-bio.org  Thu Mar 20 17:36:33 2008
From: kawas at dev.open-bio.org (Eddie Kawas)
Date: Thu, 20 Mar 2008 13:36:33 -0400
Subject: [MOBY-guts] biomoby commit
Message-ID: <200803201736.m2KHaXvL030942@dev.open-bio.org>


kawas
Thu Mar 20 13:36:33 EDT 2008
Update of /home/repository/moby/moby-live/Perl/MOBY-Server
In directory dev.open-bio.org:/tmp/cvs-serv30899/Perl/MOBY-Server

Modified Files:
	META.yml MANIFEST Makefile.PL 
Log Message:
changed the version numbers
moby-live/Perl/MOBY-Server META.yml,1.1,1.2 MANIFEST,1.4,1.5 Makefile.PL,1.3,1.4
===================================================================
RCS file: /home/repository/moby/moby-live/Perl/MOBY-Server/META.yml,v
retrieving revision 1.1
retrieving revision 1.2
diff -u -r1.1 -r1.2
--- /home/repository/moby/moby-live/Perl/MOBY-Server/META.yml	2008/02/21 00:21:28	1.1
+++ /home/repository/moby/moby-live/Perl/MOBY-Server/META.yml	2008/03/20 17:36:33	1.2
@@ -41,4 +41,4 @@
   XML::DOM: 0
   XML::LibXML: 1.62
   XML::XPath: 1.12
-version: 1.00
+version: 1.03

===================================================================
RCS file: /home/repository/moby/moby-live/Perl/MOBY-Server/MANIFEST,v
retrieving revision 1.4
retrieving revision 1.5
diff -u -r1.4 -r1.5
--- /home/repository/moby/moby-live/Perl/MOBY-Server/MANIFEST	2008/03/13 19:12:29	1.4
+++ /home/repository/moby/moby-live/Perl/MOBY-Server/MANIFEST	2008/03/20 17:36:33	1.5
@@ -13,7 +13,6 @@
 inc/Module/Install/Share.pm
 inc/Module/Install/Win32.pm
 inc/Module/Install/WriteAll.pm
-lib/MOBY.pm
 lib/MOBY/Adaptor/moby/DataAccessI.pm
 lib/MOBY/Adaptor/moby/DataAdapterI.pm
 lib/MOBY/Adaptor/moby/Impl/FetaQueryAdaptor.pm

===================================================================
RCS file: /home/repository/moby/moby-live/Perl/MOBY-Server/Makefile.PL,v
retrieving revision 1.3
retrieving revision 1.4
diff -u -r1.3 -r1.4
--- /home/repository/moby/moby-live/Perl/MOBY-Server/Makefile.PL	2008/03/19 23:36:02	1.3
+++ /home/repository/moby/moby-live/Perl/MOBY-Server/Makefile.PL	2008/03/20 17:36:33	1.4
@@ -3,7 +3,7 @@
 
 	# Define metadata
 	name 'MOBY';
-	version '1.01';
+	version '1.03';
 	license 'perl';
 	abstract
 'This distribution is for communicating with or creating your own MOBY Central registry';



From kawas at dev.open-bio.org  Thu Mar 20 18:45:11 2008
From: kawas at dev.open-bio.org (Eddie Kawas)
Date: Thu, 20 Mar 2008 14:45:11 -0400
Subject: [MOBY-guts] biomoby commit
Message-ID: <200803201845.m2KIjBgM031113@dev.open-bio.org>


kawas
Thu Mar 20 14:45:10 EDT 2008
Update of /home/repository/moby/moby-live/Perl
In directory dev.open-bio.org:/tmp/cvs-serv31078/Perl

Modified Files:
	README 
Log Message:
added explanations for installing the client side of moby and added some more lines to the 'creating cpan releases'
moby-live/Perl README,1.4,1.5
===================================================================
RCS file: /home/repository/moby/moby-live/Perl/README,v
retrieving revision 1.4
retrieving revision 1.5
diff -u -r1.4 -r1.5
--- /home/repository/moby/moby-live/Perl/README	2008/02/22 20:22:15	1.4
+++ /home/repository/moby/moby-live/Perl/README	2008/03/20 18:45:10	1.5
@@ -44,6 +44,18 @@
    make
    make test
    make install
+   
+To install just the *client* Perl MOBY libraries on your system, 
+type the following (from within MOBY-Client/):
+
+   perl populate_libs.pl
+   perl Makefile.PL
+   make
+   make test
+   make install
+
+The script populate_libs.pl goes through the MOBY-Server directory
+and extracts those modules required just for Client side MOBY.
 
 DEPENDENCIES
 
@@ -69,6 +81,7 @@
 			moby-live/Perl/MOBY-Client>rm -rf ./lib
 			moby-live/Perl/MOBY-Client>perl populate_libs.pl
 			moby-live/Perl/MOBY-Client>perl Makefile.PL
+			moby-live/Perl/MOBY-Client>make test
 			moby-live/Perl/MOBY-Client>make dist
 	
 		Once you are done, you should have a MOBY-Client*.tar.gz 
@@ -82,6 +95,8 @@
 		
 			moby-live/Perl>cd MOBY-Server
 			moby-live/Perl/MOBY-Server>perl Makefile.PL
+			moby-live/Perl/MOBY-Server>make
+			moby-live/Perl/MOBY-Server>make test
 			moby-live/Perl/MOBY-Server>make dist
 	
 		Once you are done, you should have a MOBY-Server*.tar.gz 
@@ -95,6 +110,8 @@
 		
 			moby-live/Perl>cd MOSES-MOBY
 			moby-live/Perl/MOSES-MOBY>perl Makefile.PL
+			moby-live/Perl/MOSES-MOBY>make 
+			moby-live/Perl/MOSES-MOBY>make test
 			moby-live/Perl/MOSES-MOBY>make dist
 	
 		Once you are done, you should have a MOSES-MOBY*.tar.gz 



From senger at dev.open-bio.org  Fri Mar 28 11:19:02 2008
From: senger at dev.open-bio.org (Martin Senger)
Date: Fri, 28 Mar 2008 07:19:02 -0400
Subject: [MOBY-guts] biomoby commit
Message-ID: <200803281119.m2SBJ2Hd024200@dev.open-bio.org>


senger
Fri Mar 28 07:19:02 EDT 2008
Update of /home/repository/moby/moby-live/Java/xmls
In directory dev.open-bio.org:/tmp/cvs-serv24163/xmls

Modified Files:
	project.pom 
Log Message:
dependency for more recent commons-collections
moby-live/Java/xmls project.pom,1.9,1.10
===================================================================
RCS file: /home/repository/moby/moby-live/Java/xmls/project.pom,v
retrieving revision 1.9
retrieving revision 1.10
diff -u -r1.9 -r1.10
--- /home/repository/moby/moby-live/Java/xmls/project.pom	2008/03/14 23:27:41	1.9
+++ /home/repository/moby/moby-live/Java/xmls/project.pom	2008/03/28 11:19:02	1.10
@@ -175,6 +175,10 @@
           <groupId>xerces</groupId>
           <artifactId>xercesImpl</artifactId>
         </exclusion>
+        <exclusion>
+          <groupId>commons-collections</groupId>
+          <artifactId>commons-collections</artifactId>
+        </exclusion>
       </exclusions> 
     </dependency>
 



From senger at dev.open-bio.org  Fri Mar 28 11:19:02 2008
From: senger at dev.open-bio.org (Martin Senger)
Date: Fri, 28 Mar 2008 07:19:02 -0400
Subject: [MOBY-guts] biomoby commit
Message-ID: <200803281119.m2SBJ2T7024182@dev.open-bio.org>


senger
Fri Mar 28 07:19:02 EDT 2008
Update of /home/repository/moby/moby-live/Java/docs
In directory dev.open-bio.org:/tmp/cvs-serv24163/docs

Modified Files:
	ChangeLog 
Log Message:
dependency for more recent commons-collections
moby-live/Java/docs ChangeLog,1.87,1.88
===================================================================
RCS file: /home/repository/moby/moby-live/Java/docs/ChangeLog,v
retrieving revision 1.87
retrieving revision 1.88
diff -u -r1.87 -r1.88
--- /home/repository/moby/moby-live/Java/docs/ChangeLog	2008/03/14 23:27:41	1.87
+++ /home/repository/moby/moby-live/Java/docs/ChangeLog	2008/03/28 11:19:02	1.88
@@ -1,3 +1,7 @@
+2008-03-28  Martin Senger  <martin.senger&#64;gmail.com>
+
+	* Fixed a dependency for commons-collection in the project.pom.
+
 2008-03-14  Martin Senger  <martin.senger&#64;gmail.com>
 
 	* Fixed a bug with missing xercesImpl classes. Putting back



From kawas at dev.open-bio.org  Mon Mar 31 18:04:47 2008
From: kawas at dev.open-bio.org (Eddie Kawas)
Date: Mon, 31 Mar 2008 14:04:47 -0400
Subject: [MOBY-guts] biomoby commit
Message-ID: <200803311804.m2VI4l2q001190@dev.open-bio.org>


kawas
Mon Mar 31 14:04:47 EDT 2008
Update of /home/repository/moby/moby-live/Perl/MOSES-MOBY/lib/MOSES/MOBY/Generators
In directory dev.open-bio.org:/tmp/cvs-serv1155

Modified Files:
	GenServices.pm 
Log Message:
added initial support for namespace checking.
moby-live/Perl/MOSES-MOBY/lib/MOSES/MOBY/Generators GenServices.pm,1.3,1.4
===================================================================
RCS file: /home/repository/moby/moby-live/Perl/MOSES-MOBY/lib/MOSES/MOBY/Generators/GenServices.pm,v
retrieving revision 1.3
retrieving revision 1.4
diff -u -r1.3 -r1.4
--- /home/repository/moby/moby-live/Perl/MOSES-MOBY/lib/MOSES/MOBY/Generators/GenServices.pm	2008/02/21 00:12:56	1.3
+++ /home/repository/moby/moby-live/Perl/MOSES-MOBY/lib/MOSES/MOBY/Generators/GenServices.pm	2008/03/31 18:04:47	1.4
@@ -212,11 +212,25 @@
 	    $input_paths{$main_name} = $self->_tree2paths ($tree);
 	}
 #	print MOSES::MOBY::Base->toString (\%input_paths);
-
 	# create implementation specific object
 	my $impl = {
 	    package => ($args{impl_prefix} || 'Service') . '::' . $name,
 	};
+	my @input_ns = ();
+        foreach my $in (@{ $obj->inputs }) {
+
+	    if (ref ($in) eq 'MOSES::MOBY::Def::PrimaryDataSimple') {
+                foreach my $ns ( @{$in->namespaces} ) {
+                    push @input_ns, $ns->name;
+                }
+            } else {
+                foreach my $sim (@{ $in->elements }) {
+                    foreach my $ns ( @{$sim->namespaces} ) {
+                        push @input_ns, $ns->name;
+                    }
+                }
+            }
+        }
 	if ($args{outcode}) {
 	    $tt->process ( $input, { base         => $obj,
 				     impl         => $impl,
@@ -224,6 +238,7 @@
 				     get_children => $ref_sub_get_children,
 				     ref          => $ref_sub_ref,
                                      input_paths  => \%input_paths,
+				     input_ns     =>,\@input_ns,
 				 },
 			   $args{outcode} ) || $LOG->logdie ($tt->error());
 	} else {
@@ -244,6 +259,7 @@
 				     get_children => $ref_sub_get_children,
 				     ref          => $ref_sub_ref,
                                      input_paths  => \%input_paths,
+                                     input_ns     => \@input_ns,
 				 },
 			   $outfile ) || $LOG->logdie ($tt->error());
 	    $LOG->info ("Created $outfile\n");



From kawas at dev.open-bio.org  Mon Mar 31 18:05:18 2008
From: kawas at dev.open-bio.org (Eddie Kawas)
Date: Mon, 31 Mar 2008 14:05:18 -0400
Subject: [MOBY-guts] biomoby commit
Message-ID: <200803311805.m2VI5IeA001274@dev.open-bio.org>


kawas
Mon Mar 31 14:05:17 EDT 2008
Update of /home/repository/moby/moby-live/Perl/MOSES-MOBY/lib/MOSES/MOBY/Generators/templates
In directory dev.open-bio.org:/tmp/cvs-serv1239

Modified Files:
	service.tt 
Log Message:
added initial support for namespace checking.
moby-live/Perl/MOSES-MOBY/lib/MOSES/MOBY/Generators/templates service.tt,1.3,1.4
===================================================================
RCS file: /home/repository/moby/moby-live/Perl/MOSES-MOBY/lib/MOSES/MOBY/Generators/templates/service.tt,v
retrieving revision 1.3
retrieving revision 1.4
diff -u -r1.3 -r1.4
--- /home/repository/moby/moby-live/Perl/MOSES-MOBY/lib/MOSES/MOBY/Generators/templates/service.tt	2008/02/21 00:12:55	1.3
+++ /home/repository/moby/moby-live/Perl/MOSES-MOBY/lib/MOSES/MOBY/Generators/templates/service.tt	2008/03/31 18:05:17	1.4
@@ -143,6 +143,7 @@
 use MOSES::MOBY::ServiceException;
 use strict;
 
+my %valid_namespaces = ( [% FOREACH ns IN input_ns %] '[%ns%]'=>1,  [% END %]);
 #-----------------------------------------------------------------
 # process_it
 #    This method is called for every job in the client request.
@@ -169,11 +170,23 @@
 	
     [%- IF is_simple (input) %]
 [% get_members (input_paths.${input.name}, 4) %]
+    # perform namespace checking for inputs to this service
+#   do {
+#       $response->record_error ( { code => INPUT_INCORRECT_NAMESPACE,
+#                                   msg  => 'This service requires inputs under the namespaces: {"' . join(',', keys %valid_namespaces) . '"}' } );
+#       return;
+#   } unless $valid_namespaces{$namespace};
     [%- ELSE %]
     if (defined $[% input.name %]_collection) {
         foreach my $[% input.name %]_element (@{ $[% input.name %]_collection }) {
             my $[% input.name %] = $[% input.name %]_element->data;
 [% get_members (input_paths.${input.name}, 12) %]
+            # perform namespace checking for inputs to this service
+        #   do {
+        #       $response->record_error ( { code => INPUT_INCORRECT_NAMESPACE,
+        #                                   msg  => 'This service requires inputs under the namespaces: { "' . join(',', keys %valid_namespaces) . '"}' } );
+        #       return;
+        #   } unless $valid_namespaces{$namespace};
         }
     }
     [%- END %]