Moby Service Definition Error

"+answer.replaceAll("<", "<")+"
"+stringResult.toString().replaceAll("<", "<")+"
"+markup+"
"+newMarkup+"
context-param
dataRecorder
param-value
WEB-INF/classes
");
 	    e.printStackTrace(out);
 	    out.print("
");
 	    e.printStackTrace(out);
@@ -200,7 +247,9 @@
 					      Source.class,
 					      Service.Mode.PAYLOAD);
 	} catch(Exception e){
-	    out.print("Error" +
+	    out.print("Error\n"+
+		      "\n"+
+		      "" +
 		      e.getClass().getName() + " while using JAX-WS to create a dispatch for a port on " +
 		      "the service " + serviceQName + ", either the WSDL or the WSDLConfig's " +
 		      "portQName parsed (" + portQName + ") is wrong:");	    
@@ -250,22 +299,30 @@
 		if(delimiter.equals(DQUOTE_OPTION) || delimiter.equals(SQUOTE_OPTION)){
 		    value = value.trim();
 		    if(delimiter.equals(DQUOTE_OPTION) && !value.startsWith("\"")){
-			out.print("Error" +
+			out.print("Error\n"+
+				  "\n"+
+				  "" +
 				  "The delimiter for field " + paramName + " was double quotes" +
 				  " but the value does not start with a double quote");
 		    }
 		    if(delimiter.equals(SQUOTE_OPTION) && !value.startsWith("'")){
-			out.print("Error" +
+			out.print("Error\n"+
+				  "\n"+
+				  "" +
 				  "The delimiter for field " + paramName + " was single quotes" +
 				  " but the value does not start with a single quote");
 		    }
 		    if(delimiter.equals(DQUOTE_OPTION) && !value.endsWith("\"")){
-			out.print("Error" +
+			out.print("Error\n"+
+				  "\n"+
+				  "" +
 				  "The delimiter for field " + paramName + " was double quotes" +
 				  " but the value does not end with a double quote");
 		    }
 		    if(delimiter.equals(SQUOTE_OPTION) && !value.endsWith("'")){
-			out.print("Error" +
+			out.print("Error\n"+
+				  "\n"+
+				  "" +
 				  "The delimiter for field " + paramName + " was single quotes" +
 				  " but the value does not end with a single quote");
 		    }		    
@@ -358,7 +415,9 @@
 						     new javax.xml.transform.stream.StreamResult(stringResult));
 		}
 	    } catch(Exception e){
-		out.print("Error" +
+		out.print("Error\n"+
+			  "\n"+
+			  "" +
 			  e.getClass().getName() + " while transforming response from " +
 			  "the service " + serviceQName + " (probably an internal error):");	    
 		e.printStackTrace(out);
@@ -370,7 +429,9 @@
 	    answer = ""+stringResult.toString().replaceAll("<", "<")+"";
 	}
 
-	out.print("Service Response"+answer+"");
+	out.print("Service Response\n"+
+		  "\n" +
+		  ""+answer+"");
     }
 
     // Asks for the WSDL file
@@ -387,7 +448,7 @@
 	}
 
 	try{
-	    out.write("Generic SOAP Client\n".getBytes());
+	    out.write("Generic SOAP Client\n".getBytes());
 	    out.write("Enter the URL of the WSDL file below: ").getBytes());
 	    out.write("".getBytes());
@@ -416,7 +477,9 @@
 	try{
 	    url = new URL(endpoint);
 	} catch(Exception e){
-	    out.print("The URL specified (" + endpoint + ") could not be parsed

");
+	    out.print("Parsing Error\n"+
+		      "\n" +
+		      "The URL specified (" + endpoint + ") could not be parsed

");
 	    e.printStackTrace(out);
 	    out.print("\n");
 	    return;
@@ -424,7 +487,7 @@
 
 	try{
 	    out.print("Input interface for WSDL Services at " + url + 
-		      "");
+		      "\n");
 	    if(recorder != null){
 		out.print(recorder.getHead(request));
 	    }


From gordonp at dev.open-bio.org  Thu Aug 20 13:04:36 2009
From: gordonp at dev.open-bio.org (Paul Gordon)
Date: Thu, 20 Aug 2009 13:04:36 -0400
Subject: [MOBY-guts] biomoby commit
Message-ID: <200908201704.n7KH4aq2009746@dev.open-bio.org>


gordonp
Thu Aug 20 13:04:36 EDT 2009
Update of /home/repository/moby/moby-live/Java/docs
In directory dev.open-bio.org:/tmp/cvs-serv9710/docs

Modified Files:
	index.html 
Log Message:
Included link to SoapServlet documentation
moby-live/Java/docs index.html,1.39,1.40
===================================================================
RCS file: /home/repository/moby/moby-live/Java/docs/index.html,v
retrieving revision 1.39
retrieving revision 1.40
diff -u -r1.39 -r1.40

--- /home/repository/moby/moby-live/Java/docs/index.html	2009/01/06 09:41:48	1.39
+++ /home/repository/moby/moby-live/Java/docs/index.html	2009/08/20 17:04:36	1.40
@@ -188,13 +188,14 @@
 Idiots, Dummies, etc. (a.k.a. "MobyServlet")
 		  A note on using secondary articles with MobyServlet
 		  
How to wrap an EMBOSS/ACD program as a Moby service
-		  
How to wrap an existing Web Service as a Moby service (using SAWSDL)
+		  
How to wrap an existing Web Service as a Moby service (using SAWSDL)
+                  
A generic, customizable HTML SOAP Client (used as a base for Daggoo)
+
 		  
The
 org.biomoby.shared.data package "In Anger": creating data
 instances
-		How to setup and create secure BioMoby web services
+		How to setup and create secure BioMoby web services
 
 		
 	      


From gordonp at dev.open-bio.org  Thu Aug 20 15:52:09 2009
From: gordonp at dev.open-bio.org (Paul Gordon)
Date: Thu, 20 Aug 2009 15:52:09 -0400
Subject: [MOBY-guts] biomoby commit
Message-ID: <200908201952.n7KJq9eY010291@dev.open-bio.org>


gordonp
Thu Aug 20 15:52:09 EDT 2009
Update of /home/repository/moby/moby-live/Java/src/main/ca/ucalgary/services
In directory dev.open-bio.org:/tmp/cvs-serv10255/src/main/ca/ucalgary/services

Modified Files:
	SoapServlet.java 
Log Message:
Moved tests from SoapServlet to Test Case class, updated and expanded tests
moby-live/Java/src/main/ca/ucalgary/services SoapServlet.java,1.4,1.5
===================================================================
RCS file: /home/repository/moby/moby-live/Java/src/main/ca/ucalgary/services/SoapServlet.java,v
retrieving revision 1.4
retrieving revision 1.5
diff -u -r1.4 -r1.5
--- /home/repository/moby/moby-live/Java/src/main/ca/ucalgary/services/SoapServlet.java	2009/08/20 16:59:36	1.4
+++ /home/repository/moby/moby-live/Java/src/main/ca/ucalgary/services/SoapServlet.java	2009/08/20 19:52:09	1.5
@@ -3,7 +3,6 @@
 import org.w3c.dom.*;
 
 import ca.ucalgary.services.util.*;
-import org.biomoby.service.test.*;
 
 import javax.servlet.http.*;
 import javax.servlet.ServletException;
@@ -87,7 +86,7 @@
 
 	// See if the user has specified a DataRecorder to be used (customization and/or recording of
 	// user interaction and Web Service response).
-	String dataRecorderClassName = getInitParameter(DATARECORDER_CONTEXTPARAM);
+	String dataRecorderClassName = null;
 	javax.servlet.ServletContext context = getServletContext();
 	if(context != null){
 	    if(context.getInitParameter(DATARECORDER_CONTEXTPARAM) != null){
@@ -1414,73 +1413,6 @@
 	}
     }
 
-    public static void main(String[] args) throws Exception{
-	if(args.length != 1 && args.length != 2){
-	    System.err.println("Usage: java SoapServlet  [run]\n");
-	    System.exit(0);
-	}
-
-	SoapServlet servlet = new SoapServlet();
-
-	if(args.length == 1){
-	    TestHttpServletRequest request = new TestHttpServletRequest();
-	    TestHttpServletResponse response = new TestHttpServletResponse();
-	    StringBufferServletOutputStream out = new StringBufferServletOutputStream();
-	    request.setParameter(WSDL_HTTP_PARAM, args[0]);
-	    response.setOutputStream(out);
-	    
-	    try{
-		servlet.doGet(request, response);
-	    } catch(Exception e){
-		e.printStackTrace();
-	    } finally{
-		System.out.print(out.getBuffer().toString());
-	    }
-	}
-	else{
-// 	    TestHttpServletRequest request2 = new TestHttpServletRequest();
-// 	    request2.setParameter("wsdl", "http://soap.genome.jp/KEGG.wsdl");
-// 	    request2.setParameter("service", "SOAP/KEGG KEGG SOAP/KEGG KEGGPort " +
-// 				  "SOAP/KEGG get_compounds_by_enzyme SOAP/KEGG#get_compounds_by_enzyme encoded");
-// 	    request2.setParameter("enzyme_id", "ec:1.1.1.1");
-
-// 	    TestHttpServletRequest request2 = new TestHttpServletRequest();
-// 	    request2.setParameter("wsdl", "http://www.ebi.ac.uk/ontology-lookup/OntologyQuery.wsdl");
-// 	    request2.setParameter("service", "http://www.ebi.ac.uk/ontology-lookup/OntologyQuery QueryService " +
-// 				  "http://www.ebi.ac.uk/ontology-lookup/OntologyQuery OntologyQuery " +
-// 				  "http://www.ebi.ac.uk/ontology-lookup/OntologyQuery getTermsByName " +
-// 				  "getTermsByName literal");
-// 	    request2.setParameter("partialName", "seed");
-// 	    request2.setParameter("ontologyName", "GO");
-//  	    request2.setParameter("reverseKeyOrder", "false");
-
-	    TestHttpServletRequest request2 = new TestHttpServletRequest();
- 	    request2.setParameter(WSDL_HTTP_PARAM, "http://www.ncbi.nlm.nih.gov/entrez/eutils/soap/v2.0/eutils.wsdl");
-	    request2.setParameter(SERVICE_SPEC_PARAM, "http://www.ncbi.nlm.nih.gov/soap/eutils/ eUtilsService " +
-				  "http://www.ncbi.nlm.nih.gov/soap/eutils/ eUtilsServiceSoap " +
-				  "http://www.ncbi.nlm.nih.gov/soap/eutils/espell eSpellRequest " +
-				  "espell literal");
-	    request2.setParameter("db:opt", "");
-	    request2.setParameter("term:opt", "brest");
-	    request2.setParameter("tool:opt", "");
-	    request2.setParameter("email:opt", "");
-
-	    TestHttpServletResponse response2 = new TestHttpServletResponse();
-	    StringBufferServletOutputStream out2 = new StringBufferServletOutputStream();
-	    response2.setOutputStream(out2);
-	    
-	    try{
-		servlet.doPost(request2, response2);
-	    }
-	    catch(Exception e){
-            e.printStackTrace();
-	    }
-	    finally{
-		System.err.println(out2.getBuffer().toString());
-	    }
-	}
-    }
-
     public static class MyNodeList implements NodeList{
         private Vector nodes;
         public MyNodeList(){nodes = new Vector();}


From gordonp at dev.open-bio.org  Thu Aug 20 15:52:09 2009
From: gordonp at dev.open-bio.org (Paul Gordon)
Date: Thu, 20 Aug 2009 15:52:09 -0400
Subject: [MOBY-guts] biomoby commit
Message-ID: <200908201952.n7KJq9oQ010311@dev.open-bio.org>


gordonp
Thu Aug 20 15:52:09 EDT 2009
Update of /home/repository/moby/moby-live/Java/src/main/ca/ucalgary/services/test
In directory dev.open-bio.org:/tmp/cvs-serv10255/src/main/ca/ucalgary/services/test

Modified Files:
	SoapServletTestCase.java 
Log Message:
Moved tests from SoapServlet to Test Case class, updated and expanded tests
moby-live/Java/src/main/ca/ucalgary/services/test SoapServletTestCase.java,1.1,1.2
===================================================================
RCS file: /home/repository/moby/moby-live/Java/src/main/ca/ucalgary/services/test/SoapServletTestCase.java,v
retrieving revision 1.1
retrieving revision 1.2
diff -u -r1.1 -r1.2
--- /home/repository/moby/moby-live/Java/src/main/ca/ucalgary/services/test/SoapServletTestCase.java	2009/06/09 19:39:53	1.1
+++ /home/repository/moby/moby-live/Java/src/main/ca/ucalgary/services/test/SoapServletTestCase.java	2009/08/20 19:52:09	1.2
@@ -4,8 +4,7 @@
 import ca.ucalgary.seahawk.gui.*;
 import ca.ucalgary.seahawk.util.*;
 
-import org.biomoby.shared.MobyDataType;
-import org.biomoby.shared.data.*;
+import org.biomoby.service.test.*;
 
 import junit.framework.*;
 
@@ -17,30 +16,117 @@
  * 
  */
 public class SoapServletTestCase extends TestCase{
-    private final static String TEST_WSDL = "http://www.ncbi.nlm.nih.gov/entrez/eutils/soap/v2.0/eutils.wsdl";
+    // The class below should have a nullary c-tor
+    private final static String TEST_DATARECORDER = "ca.ucalgary.services.util.PBERecorder";
 
     public SoapServletTestCase(String name){
 	super(name);
     }
     
-    public void testWSDLLoad(){
-	URL testWSDL = null;
+    /**
+     * Checks against a KEGG service
+     */
+    public void testWSDLRpcEncExecute(){
+	SoapServlet servlet = new SoapServlet();
+	try{
+	    servlet.init(new TestServletConfig("", new TestServletContext()));
+	}catch(Exception e){
+	    e.printStackTrace();
+	    fail("Could not initialize the SoapServlet");
+	}
+
+	TestHttpServletRequest request = new TestHttpServletRequest();
+	request.setParameter(SoapServlet.WSDL_HTTP_PARAM, "http://soap.genome.jp/KEGG.wsdl");
+	request.setParameter(SoapServlet.SERVICE_SPEC_PARAM, "SOAP/KEGG KEGG SOAP/KEGG KEGGPort " +
+			     "SOAP/KEGG get_compounds_by_enzyme SOAP/KEGG#get_compounds_by_enzyme " +
+			     "get_compounds_by_enzyme rpc encoded");
+	request.setParameter("enzyme_id", "ec:1.1.1.1");
+
+	TestHttpServletResponse response = new TestHttpServletResponse();
+	StringBufferServletOutputStream out = new StringBufferServletOutputStream();
+	response.setOutputStream(out);
+	try{
+	    servlet.doPost(request, response);
+	}
+	catch(Exception e){
+	    e.printStackTrace();
+	    fail("Got exception while posting request for RPC/Encoded KEGG Web Service");
+	}
+	assertTrue("Did not find the expected data in the reponse from KEGG", 
+		   out.getBuffer().indexOf("cpd:C00001") != -1);
+    }
+    
+    /**
+     * Checks against both NCBI and EBI services.
+     */
+    public void testWSDLDocLitExecute(){
+	SoapServlet servlet = new SoapServlet();
 	try{
-	    testWSDL = new URL(TEST_WSDL);
-	} catch(Exception e){
+	    servlet.init(new TestServletConfig("", new TestServletContext()));
+	}catch(Exception e){
 	    e.printStackTrace();
-	    fail("Could not create URL from test document (" + TEST_WSDL + "): " + e);
+	    fail("Could not initialize the SoapServlet");
 	}
+
+	TestHttpServletRequest request = new TestHttpServletRequest();
+	request.setParameter(SoapServlet.WSDL_HTTP_PARAM, "http://www.ebi.ac.uk/ontology-lookup/OntologyQuery.wsdl");
+	request.setParameter(SoapServlet.SERVICE_SPEC_PARAM, "http://www.ebi.ac.uk/ontology-lookup/OntologyQuery QueryService " +
+			     "http://www.ebi.ac.uk/ontology-lookup/OntologyQuery OntologyQuery " +
+			     "http://www.ebi.ac.uk/ontology-lookup/OntologyQuery getTermsByName " +
+			     "getTermsByName getTermsByName document literal");
+	request.setParameter("partialName", "seed");
+	request.setParameter("ontologyName", "GO");
+	request.setParameter("reverseKeyOrder", "false");
+
+	TestHttpServletResponse response = new TestHttpServletResponse();
+	StringBufferServletOutputStream out = new StringBufferServletOutputStream();
+	response.setOutputStream(out);
+	try{
+	    servlet.doPost(request, response);
+	}
+	catch(Exception e){
+	    e.printStackTrace();
+	    fail("Got exception while posting request for Document/Literal EBI Web Service");
+	}
+	if(out.getBuffer().indexOf("coat") == -1){
+	    fail("Did not find the expected data in the reponse from EBI.  Response was:\n" + 
+		 out.getBuffer().toString());
+	}
+	TestHttpServletRequest request2 = new TestHttpServletRequest();
+	request2.setParameter(SoapServlet.WSDL_HTTP_PARAM, "http://www.ncbi.nlm.nih.gov/entrez/eutils/soap/v2.0/eutils.wsdl");
+	request2.setParameter(SoapServlet.SERVICE_SPEC_PARAM, "http://www.ncbi.nlm.nih.gov/soap/eutils/ eUtilsService " +
+			      "http://www.ncbi.nlm.nih.gov/soap/eutils/ eUtilsServiceSoap " +
+			      "http://www.ncbi.nlm.nih.gov/soap/eutils/espell eSpellRequest " +
+			      "espell run_eSpell document literal");
+	request2.setParameter("db:opt", "");
+	request2.setParameter("term:opt", "brest");
+	request2.setParameter("tool:opt", "");
+	request2.setParameter("email:opt", "");
 	
-	javax.swing.JOptionPane.showMessageDialog(null, "information",
-				      "information", javax.swing.JOptionPane.INFORMATION_MESSAGE);
-	System.err.println("About to load GUI");
-	MobyContentGUI gui = MobyUtils.getMobyContentGUI(null);
-	System.err.println("About to load " + TEST_WSDL);
-	gui.loadPaneFromURL(testWSDL, true);
+	TestHttpServletResponse response2 = new TestHttpServletResponse();
+	StringBufferServletOutputStream out2 = new StringBufferServletOutputStream();
+	response2.setOutputStream(out2);
 	try{
-	    Thread.sleep(100000);
-	} catch(Exception e){System.err.println("Sleep interrupted: " + e);}
+	    servlet.doPost(request2, response2);
+	}
+	catch(Exception e){
+	    e.printStackTrace();
+	    fail("Got exception while posting request for Document/Literal NCBI Web Service");
+	}
+	assertTrue("Did not find the expected data in the reponse from NCBI", 
+		   out2.getBuffer().indexOf("breast") != -1);
+    }
+
+    public void testDataRecorderAutoLoad(){
+	SoapServlet servlet = new SoapServlet();
+	try{
+	    TestServletConfig config = new TestServletConfig("", new TestServletContext());
+	    config.addInitParameter(SoapServlet.DATARECORDER_CONTEXTPARAM, TEST_DATARECORDER);
+	    servlet.init(config);
+	}catch(Exception e){
+	    e.printStackTrace();
+	    fail("Could not initialize the SoapServlet");
+	}	
     }
 
     /**
@@ -52,7 +138,9 @@
     public static Test suite() {
 
 	TestSuite suite = new TestSuite();
- 	suite.addTest(new SoapServletTestCase("testWSDLLoad"));
+	suite.addTest(new SoapServletTestCase("testWSDLRpcEncExecute"));
+	suite.addTest(new SoapServletTestCase("testWSDLDocLitExecute"));
+	suite.addTest(new SoapServletTestCase("testDataRecorderAutoLoad"));
         return suite;
     }
 


From gordonp at dev.open-bio.org  Wed Aug 26 18:02:18 2009
From: gordonp at dev.open-bio.org (Paul Gordon)
Date: Wed, 26 Aug 2009 18:02:18 -0400
Subject: [MOBY-guts] biomoby commit
Message-ID: <200908262202.n7QM2IfR032508@dev.open-bio.org>


gordonp
Wed Aug 26 18:02:18 EDT 2009
Update of /home/repository/moby/moby-live/Java/src/main/ca/ucalgary/services
In directory dev.open-bio.org:/tmp/cvs-serv32472/src/main/ca/ucalgary/services

Modified Files:
	SoapServlet.java 
Log Message:
Fix to avoid namespace collision between XML scehma elements and XML schema types in the WSDL doc
moby-live/Java/src/main/ca/ucalgary/services SoapServlet.java,1.5,1.6
===================================================================
RCS file: /home/repository/moby/moby-live/Java/src/main/ca/ucalgary/services/SoapServlet.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/SoapServlet.java	2009/08/20 19:52:09	1.5
+++ /home/repository/moby/moby-live/Java/src/main/ca/ucalgary/services/SoapServlet.java	2009/08/26 22:02:18	1.6
@@ -20,6 +20,11 @@
 import java.util.*;
 import java.io.*;
 
+/**
+ * Provides an HTML interface for invoking SOAP-based Web Services. The appearance and functionality of the class
+ * can be extended using stylesheets and registering a DataRecorder (e.g. Daggoo registers PBERecorder to get 
+ * its functionality), please see the documentation at http://biomoby.open-bio.org/CVS_CONTENT/moby-live/Java/docs/soapServlet.html
+ */
 public class SoapServlet extends HttpServlet{
 
     public static final String DATARECORDER_CONTEXTPARAM = "dataRecorder"; // how users spec a DataRecorder in the web.xml
@@ -842,6 +847,8 @@
 									    "types");  
 			    Map> element2Members = 
 				new LinkedHashMap>();	   
+			    Map> type2Members = 
+				new LinkedHashMap>();	   
 			    for(int m = 0; m < types.getLength(); m++){
 				Element typeTag = (Element) types.item(m);
 				MyNodeList typeDefs = new MyNodeList();
@@ -870,8 +877,17 @@
 				    // It could either be a basic type (handled right here), or a complex one with subfields
 				    String elementType = element.getAttribute("type");
 				    if(elementType != null && elementType.trim().length() != 0){
-					memberMap.put(BASIC_TYPE_SENTINEL, getQName(elementType, element));
-					memberMap.put(BASIC_NAME_SENTINEL, new QName(null, elementName));
+					QName eT = getQName(elementType, element);
+					if(eT.getNamespaceURI() == null ||
+					   eT.getNamespaceURI().equals("http://www.w3.org/2001/XMLSchema")){
+					    memberMap.put(BASIC_TYPE_SENTINEL, eT);
+					    memberMap.put(BASIC_NAME_SENTINEL, new QName(null, elementName));
+					}
+					else{
+					    // pointer to complex type elsewhere in the schema tag
+					    memberMap.put(BASIC_TYPE_SENTINEL, getQName(getRef(eT), element));
+					    memberMap.put(BASIC_NAME_SENTINEL, new QName(null, elementName));
+					}
 				    }
 
 				    NodeList subelements = element.getElementsByTagNameNS("http://www.w3.org/2001/XMLSchema",
@@ -884,22 +900,20 @@
 					if(restrictions.getLength() == 0){
 					    restrictions = element.getElementsByTagNameNS("http://www.w3.org/2001/XMLSchema",
 											  "extension");
-					    if(restrictions.getLength() == 0){
-						//out.print("Error: Could not find the restriction or extension " +
-						//	  "attribute for a simple type " +
-						//	  " schema element " + elementName);
+					    if(restrictions.getLength() != 0){
+						String baseAttr = restrictions.getLength() == 0 ? "xs:string" : 
+						    ((Element) restrictions.item(0)).getAttribute("base");
+						QName baseType = getQName(baseAttr, element);
+						QName anonQName = getQName(baseAttr+"SubType"+anonCount++, element);
+						memberMap.put(BASIC_TYPE_SENTINEL, anonQName);
+						memberMap.put(BASIC_NAME_SENTINEL, new QName(null, elementName));
 					    }
+					    // else, some time you just get a blank type...
 					}
 					else{
+					    // TODO handle extension properly
 					    
 					}
-					String baseAttr = restrictions.getLength() == 0 ? "xs:string" : 
-					    ((Element) restrictions.item(0)).getAttribute("base");
-					QName baseType = getQName(baseAttr, element);
-					QName anonQName = getQName(baseAttr+"SubType"+anonCount++, element);
-					// TODO handle extension properly
-					memberMap.put(BASIC_TYPE_SENTINEL, anonQName);
-					memberMap.put(BASIC_NAME_SENTINEL, new QName(null, elementName));
 				    }
 				    for(int p = 0; p < subelements.getLength(); p++){
 					Element subelement = (Element) subelements.item(p);
@@ -973,7 +987,12 @@
 					}
 				    }
 
-				    element2Members.put(getQName(elementName, element), memberMap);
+				    if(element.getLocalName().equals("element")){					
+					element2Members.put(getQName(elementName, element), memberMap);
+				    }
+				    else{ //probably complexType def
+					type2Members.put(getQName(elementName, element), memberMap);
+				    }
 				}  //end for ...
 			    }  //for wsdl:types
 			    
@@ -1013,21 +1032,31 @@
 					Map subpartsMap = element2Members.get(dataType);
 					if(subpartsMap == null){
 					    if(dataType.getNamespaceURI().equals("http://schemas.xmlsoap.org/soap/encoding/")){
-						writeDataType(out, part.getKey(), part.getValue(), element2Members, "");
+						writeDataType(out, part.getKey(),
+							      part.getValue(), element2Members, type2Members, "");
+					    }
+					    else{
+						out.print("Error: cannot find definition for data type " + 
+							  dataType + "\nValid types are:");
+						for(QName key: element2Members.keySet()){
+						    out.print(" "+key);
+						}
 					    }
-					    out.print("Error: cannot find definition for data type " + 
-						      dataType + "\nValid types are:");
-					    for(QName key: element2Members.keySet()){
- 						out.print(" "+key);
- 					    }
 					    continue;
 					}
-					for(Map.Entry subpart: subpartsMap.entrySet()){
-					    writeDataType(out, subpart.getKey(), subpart.getValue(), element2Members, "");
+					if(subpartsMap.containsKey(BASIC_TYPE_SENTINEL)){
+					    writeDataType(out, messageQName.getLocalPart(),
+							  subpartsMap.get(BASIC_TYPE_SENTINEL), 
+							  type2Members, type2Members, "");
+					}
+					else{
+					    for(Map.Entry subpart: subpartsMap.entrySet()){
+						writeDataType(out, subpart.getKey(), subpart.getValue(), type2Members, type2Members, "");
+					    }
 					}
 				    }
 				    else{ // rpc style
-					writeDataType(out, part.getKey(), part.getValue(), element2Members, "");
+					writeDataType(out, part.getKey(), part.getValue(), element2Members, type2Members, "");
 				    }
 				}  // for parts
 				// special condition for rpc calls, still need to give the op ns & name
@@ -1154,7 +1183,8 @@
     }
 
     private void writeDataType(java.io.PrintStream out, String memberName, QName dataType, 
-			       Map> msg2Parts, String prefix){
+			       Map> msg2Parts, 
+			       Map> type2Parts, String prefix){
 
 	String datatype = dataType.getLocalPart();
 
@@ -1268,11 +1298,14 @@
 	else{  // doc/lit or complex rpc type
 	    Map subparts = msg2Parts.get(dataType);
 	    if(subparts == null){
-		out.print("Error: cannot find definition for data type " + dataType); //+"\nValid types are:");
-	// 	for(QName key: msg2Parts.keySet()){
-// 		    out.print(" "+key);
-// 		}
-		return;
+		subparts = type2Parts.get(dataType);
+		if(subparts == null){
+		    out.print("Error: cannot find definition for data type " + dataType); //+"\nValid types are:");
+		    // 	for(QName key: msg2Parts.keySet()){
+		    // 		    out.print(" "+key);
+		    // 		}
+		    return;
+		}
 	    }
 	    else if(subparts.containsKey(BASIC_TYPE_SENTINEL)){
 		QName typeName = subparts.get(BASIC_TYPE_SENTINEL);
@@ -1282,14 +1315,14 @@
 		if(isOptional){
 		    typeName = new QName(typeName.getNamespaceURI(), typeName.getLocalPart()+"~");
 		}
-		writeDataType(out, memberName, typeName, msg2Parts, prefix);
+		writeDataType(out, memberName, typeName, type2Parts, type2Parts, prefix);
 	    }
 	    else{
 		// currently we don't handle arrays of composites in the form...
-		out.print("Composite "+memberName+
+		out.print("Composite "+ memberName +
 			  " ("+(isOptional?"optional, ":"")+ datatype + "):
");
 		for(Map.Entry subpart: subparts.entrySet()){
-		    writeDataType(out, subpart.getKey(), subpart.getValue(), msg2Parts, prefix+memberName+":");
+		    writeDataType(out, subpart.getKey(), subpart.getValue(), type2Parts, type2Parts, prefix+memberName+":");
 		}
 		out.print("\n");
 	    }


From kawas at dev.open-bio.org  Thu Aug 27 15:37:37 2009
From: kawas at dev.open-bio.org (Eddie Kawas)
Date: Thu, 27 Aug 2009 15:37:37 -0400
Subject: [MOBY-guts] biomoby commit
Message-ID: <200908271937.n7RJbbl6005812@dev.open-bio.org>


kawas
Thu Aug 27 15:37:37 EDT 2009
Update of /home/repository/moby/moby-live/Perl/MOSES-MOBY/lib/MOSES/MOBY/Generators/templates
In directory dev.open-bio.org:/tmp/cvs-serv5776/MOSES-MOBY/lib/MOSES/MOBY/Generators/templates

Modified Files:
	service-base.tt 
Log Message:
fix the warning 'unsuccesful stat on file containing newline' when sending raw data
moby-live/Perl/MOSES-MOBY/lib/MOSES/MOBY/Generators/templates service-base.tt,1.3,1.4
===================================================================
RCS file: /home/repository/moby/moby-live/Perl/MOSES-MOBY/lib/MOSES/MOBY/Generators/templates/service-base.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-base.tt	2008/02/21 00:12:55	1.3
+++ /home/repository/moby/moby-live/Perl/MOSES-MOBY/lib/MOSES/MOBY/Generators/templates/service-base.tt	2009/08/27 19:37:37	1.4
@@ -112,7 +112,9 @@
     Log::Log4perl::NDC->push ($$);
     $LOG->info ('*** REQUEST START *** ' . $self->log_request);
 
+    no warnings 'newline';
     my $in_testing_mode = (-f $data);
+    use warnings 'newline';
     if ($LOG->is_debug) {
        if ($in_testing_mode) {
 	   open (RAWXML, "<$data") or $LOG->logdie ("Cannot open $data: $!\n");


From kawas at dev.open-bio.org  Thu Aug 27 15:39:26 2009
From: kawas at dev.open-bio.org (Eddie Kawas)
Date: Thu, 27 Aug 2009 15:39:26 -0400
Subject: [MOBY-guts] biomoby commit
Message-ID: <200908271939.n7RJdQCb005925@dev.open-bio.org>


kawas
Thu Aug 27 15:39:26 EDT 2009
Update of /home/repository/moby/moby-live/Perl/MOSES-MOBY/lib/MOSES/MOBY/Def
In directory dev.open-bio.org:/tmp/cvs-serv5890/MOSES-MOBY/lib/MOSES/MOBY/Def

Modified Files:
	Service.pm 
Log Message:
added missing categories
moby-live/Perl/MOSES-MOBY/lib/MOSES/MOBY/Def Service.pm,1.4,1.5
===================================================================
RCS file: /home/repository/moby/moby-live/Perl/MOSES-MOBY/lib/MOSES/MOBY/Def/Service.pm,v
retrieving revision 1.4
retrieving revision 1.5
diff -u -r1.4 -r1.5
--- /home/repository/moby/moby-live/Perl/MOSES-MOBY/lib/MOSES/MOBY/Def/Service.pm	2008/04/29 19:41:38	1.4
+++ /home/repository/moby/moby-live/Perl/MOSES-MOBY/lib/MOSES/MOBY/Def/Service.pm	2009/08/27 19:39:26	1.5
@@ -260,7 +260,7 @@
 sub _check_category {
     my ($self, $attr) = @_;
     $self->throw ('Invalid service category: ' . $self->category)
-	unless $self->category =~ /^cgi|wsdl|moby|moby\-async|post$/i;
+	unless $self->category =~ /^cgi|wsdl|moby|moby\-async|post|cgi\-async$/i;
 }
 
 1;


From kawas at dev.open-bio.org  Thu Aug 27 15:40:50 2009
From: kawas at dev.open-bio.org (Eddie Kawas)
Date: Thu, 27 Aug 2009 15:40:50 -0400
Subject: [MOBY-guts] biomoby commit
Message-ID: <200908271940.n7RJeoVe006003@dev.open-bio.org>


kawas
Thu Aug 27 15:40:50 EDT 2009
Update of /home/repository/moby/moby-live/Perl/MOSES-MOBY/lib/MOSES/MOBY/Cache
In directory dev.open-bio.org:/tmp/cvs-serv5968/MOSES-MOBY/lib/MOSES/MOBY/Cache

Modified Files:
	Central.pm 
Log Message:
made relationship regex check case insensitive and less stringent.
moby-live/Perl/MOSES-MOBY/lib/MOSES/MOBY/Cache Central.pm,1.7,1.8
===================================================================
RCS file: /home/repository/moby/moby-live/Perl/MOSES-MOBY/lib/MOSES/MOBY/Cache/Central.pm,v
retrieving revision 1.7
retrieving revision 1.8
diff -u -r1.7 -r1.8
--- /home/repository/moby/moby-live/Perl/MOSES-MOBY/lib/MOSES/MOBY/Cache/Central.pm	2008/06/04 16:14:31	1.7
+++ /home/repository/moby/moby-live/Perl/MOSES-MOBY/lib/MOSES/MOBY/Cache/Central.pm	2009/08/27 19:40:50	1.8
@@ -708,13 +708,13 @@
     while ( $count > 0 ) {
 	my $node         = $nodes->get_node( $count-- );
 	my $relationship = $node->getAttribute('relationshipType');
-	if ( $relationship =~ /.*:isa$/ ) {
+	if ( $relationship =~ /^.*isa$/i ) {
 	    my $parent = $node->getChildrenByTagName('objectType');
 	    my $isa    = $parent->get_node(1)->textContent
 		if ( $parent and $parent->get_node(1) and $parent->get_node(1) );
 	    $datatype->parent($isa);
 	}
-	elsif ( $relationship =~ /.*:hasa$/ ) {
+	elsif ( $relationship =~ /^.*hasa$/i ) {
 	    my $pNode = $node->getChildrenByTagName('objectType');
 	    for ( my $i = 1 ; $i <= $pNode->size() ; $i++ ) {
 		my $article = $pNode->get_node($i)->getAttribute('articleName')
@@ -735,7 +735,7 @@
 		     );
 	    }
 	}
-	elsif ( $relationship =~ /.*:has$/ ) {
+	elsif ( $relationship =~ /^.*has$/i ) {
 	    my $pNode = $node->getChildrenByTagName('objectType');
 	    for ( my $i = 1 ; $i <= $pNode->size() ; $i++ ) {
 		my $article = $pNode->get_node($i)->getAttribute('articleName')


From kawas at dev.open-bio.org  Thu Aug 27 15:44:40 2009
From: kawas at dev.open-bio.org (Eddie Kawas)
Date: Thu, 27 Aug 2009 15:44:40 -0400
Subject: [MOBY-guts] biomoby commit
Message-ID: <200908271944.n7RJidME006047@dev.open-bio.org>


kawas
Thu Aug 27 15:44:39 EDT 2009
Update of /home/repository/moby/moby-live/Perl/MOSES-MOBY
In directory dev.open-bio.org:/tmp/cvs-serv6008/MOSES-MOBY

Modified Files:
	Makefile.PL Changes 
Log Message:
updated to reflect current status of the module.
moby-live/Perl/MOSES-MOBY Makefile.PL,1.17,1.18 Changes,1.16,1.17
===================================================================
RCS file: /home/repository/moby/moby-live/Perl/MOSES-MOBY/Makefile.PL,v
retrieving revision 1.17
retrieving revision 1.18
diff -u -r1.17 -r1.18
--- /home/repository/moby/moby-live/Perl/MOSES-MOBY/Makefile.PL	2009/05/22 16:38:39	1.17
+++ /home/repository/moby/moby-live/Perl/MOSES-MOBY/Makefile.PL	2009/08/27 19:44:39	1.18
@@ -6,7 +6,7 @@
     
 	# Define metadata
 	name 'MOSES-MOBY';
-	version '0.90';
+	version '0.91';
 	license 'perl';
 	abstract
 'This distribution aids in the creation of BioMOBY perl based web services.';
@@ -17,7 +17,7 @@
 	requires 'CGI'              	=> 0;
 	requires 'File::Spec'       	=> 0.80;    
 	requires 'SOAP::Lite'       	=> 0.69;
-	requires 'XML::LibXML::Common'  => '0.13';
+	requires 'XML::LibXML::Common'  => 0.13;
 	requires 'XML::LibXML'      	=> 1.62;
 	requires 'Log::Log4perl'    	=> 1.12;
 	requires 'Template'         	=> 1.11;
@@ -25,15 +25,15 @@
 	requires 'IO::String'       	=> 1.08;
 	requires 'Unicode::String'  	=> 2.09;
 	requires 'File::HomeDir'    	=> 0.65;
-	requires 'File::ShareDir'   	=> 0.05;
+	requires 'File::ShareDir'   	=> 1.00;
 	requires 'Class::Inspector' 	=> 1.17;
 	requires 'Params::Util'     	=> 0.38;
 	requires 'HTTP::Date'			=> 5.81;
 
     # windows doesn't need this
 	if ( not MSWIN ) {
-	    requires 'Want'       => '0.18';
-	    requires 'IO::Prompt' => '0.99.2';
+	    requires 'Want'       => 0.18;
+	    requires 'IO::Prompt' => 0.99.2;
 	}
 
 	# for async services	

===================================================================
RCS file: /home/repository/moby/moby-live/Perl/MOSES-MOBY/Changes,v
retrieving revision 1.16
retrieving revision 1.17
diff -u -r1.16 -r1.17
--- /home/repository/moby/moby-live/Perl/MOSES-MOBY/Changes	2009/05/22 16:38:39	1.16
+++ /home/repository/moby/moby-live/Perl/MOSES-MOBY/Changes	2009/08/27 19:44:39	1.17
@@ -3,6 +3,11 @@
 0.91
 	- Updated the Makefile.PL to handle some missing 
 	  dependencies.
+	- bug fix: fixed the unsuccessful stat on filename
+	  warning in service-base.tt
+	- updated the categories in Service.pm
+	- updated Makefile.PL to reflect dependency upgrades
+	  and versioning
 .90
 	- bug fix: when sending data with newlines on
 	  a WinOS, \r was causing problems with the


From gordonp at dev.open-bio.org  Thu Aug 27 17:37:33 2009
From: gordonp at dev.open-bio.org (Paul Gordon)
Date: Thu, 27 Aug 2009 17:37:33 -0400
Subject: [MOBY-guts] biomoby commit
Message-ID: <200908272137.n7RLbX32006322@dev.open-bio.org>


gordonp
Thu Aug 27 17:37:32 EDT 2009
Update of /home/repository/moby/moby-live/Java/src/main/ca/ucalgary/services
In directory dev.open-bio.org:/tmp/cvs-serv6286/src/main/ca/ucalgary/services

Modified Files:
	SoapServlet.java 
Log Message:
Further element reference fixes for WSDL XML schema definitions
moby-live/Java/src/main/ca/ucalgary/services SoapServlet.java,1.6,1.7
===================================================================
RCS file: /home/repository/moby/moby-live/Java/src/main/ca/ucalgary/services/SoapServlet.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/SoapServlet.java	2009/08/26 22:02:18	1.6
+++ /home/repository/moby/moby-live/Java/src/main/ca/ucalgary/services/SoapServlet.java	2009/08/27 21:37:32	1.7
@@ -1045,14 +1045,18 @@
 					    continue;
 					}
 					if(subpartsMap.containsKey(BASIC_TYPE_SENTINEL)){
-					    writeDataType(out, messageQName.getLocalPart(),
-							  subpartsMap.get(BASIC_TYPE_SENTINEL), 
-							  type2Members, type2Members, "");
-					}
-					else{
-					    for(Map.Entry subpart: subpartsMap.entrySet()){
-						writeDataType(out, subpart.getKey(), subpart.getValue(), type2Members, type2Members, "");
+					    QName t = subpartsMap.get(BASIC_TYPE_SENTINEL);
+					    while(DEFERRED_NAMESPACE_URI.equals(t.getNamespaceURI())){
+						String[] p = t.getLocalPart().split("_deferred_");
+						t = new QName(decode(p[0]), p[1]);
+					    }
+					    if(t.getNamespaceURI().equals("http://www.w3.org/2001/XMLSchema")){
+						throw new Exception("Got bare XSD type as contents of WSDL message");
 					    }
+					    subpartsMap = type2Members.get(t);
+					}
+					for(Map.Entry subpart: subpartsMap.entrySet()){
+					    writeDataType(out, subpart.getKey(), subpart.getValue(), type2Members, type2Members, "");
 					}
 				    }
 				    else{ // rpc style


From kawas at dev.open-bio.org  Fri Aug 28 10:15:58 2009
From: kawas at dev.open-bio.org (Eddie Kawas)
Date: Fri, 28 Aug 2009 10:15:58 -0400
Subject: [MOBY-guts] biomoby commit
Message-ID: <200908281415.n7SEFv0S017683@dev.open-bio.org>


kawas
Fri Aug 28 10:15:57 EDT 2009
Update of /home/repository/moby/moby-live/Perl/MOBY-Server/share/cgi
In directory dev.open-bio.org:/tmp/cvs-serv17648/MOBY-Server/share/cgi

Modified Files:
	RESOURCES 
Log Message:
bug fix: sometimes users hit the url with Objects/, or Namespaces/, etc and the trailing slash tripped up the script. 
moby-live/Perl/MOBY-Server/share/cgi RESOURCES,1.3,1.4
===================================================================
RCS file: /home/repository/moby/moby-live/Perl/MOBY-Server/share/cgi/RESOURCES,v
retrieving revision 1.3
retrieving revision 1.4
diff -u -r1.3 -r1.4
--- /home/repository/moby/moby-live/Perl/MOBY-Server/share/cgi/RESOURCES	2008/06/19 17:02:25	1.3
+++ /home/repository/moby/moby-live/Perl/MOBY-Server/share/cgi/RESOURCES	2009/08/28 14:15:57	1.4
@@ -47,7 +47,8 @@
 $url =~ s/%([\da-f][\da-f])/chr( hex($1) )/egi;
 my $form = new CGI;
 
-if ( $url =~ m/^RESOURCES\/MOBY\-S\/Objects(\/[A-Za-z0-9_\-]*)?$/ ) {
+if ( $url =~ m/^RESOURCES\/MOBY\-S\/Objects(\/[A-Za-z0-9_\-]+)?$/ ) {
+    my $byName = length( substr $1, 1) > 0 if $1;
 	do {
 		if ($useCache) {
 			my $x =
@@ -60,14 +61,15 @@
 			$x = $x->createAll();
 			print $form->header('text/xml'), $x if $x;
 		}
-	} unless $1;
+	} unless $byName;
 	do {
 		my $x = MOBY::RDF::Ontologies::Objects->new;
 		my $rdf = $x->createByName( { term => substr $1, 1 } );
 		print $form->header('text/xml'), $rdf if $rdf;
-	} if $1;
+	} if $byName;
 
-} elsif ( $url =~ m/^RESOURCES\/MOBY\-S\/Services(\/[A-Za-z0-9_\-]*)?$/ ) {
+} elsif ( $url =~ m/^RESOURCES\/MOBY\-S\/Services(\/[A-Za-z0-9_\-]+)?$/ ) {
+	my $byName = length( substr $1, 1) > 0 if $1;
 	do {
 		if ($useCache) {
 			my $x =
@@ -80,12 +82,12 @@
 			$x = $x->createAll();
 			print $form->header('text/xml'), $x if $x;
 		}
-	} unless $1;
+	} unless $byName;
 	do {
 		my $x = MOBY::RDF::Ontologies::ServiceTypes->new;
 		my $rdf = $x->createByName( { term => substr $1, 1 } );
 		print $form->header('text/xml'), $rdf if $rdf;
-	} if $1;
+	} if $byName;
 } elsif ( $url =~
 m/^RESOURCES\/MOBY\-S\/ServiceInstances(\/[A-Za-z0-9_\-.]*,[A-Za-z0-9_\-]*){1}$/
   )
@@ -117,7 +119,7 @@
 	} unless $string;
 	
 } elsif ( $url =~
-m/^RESOURCES\/MOBY\-S\/ServiceInstances(\/[A-Za-z0-9_\-.]*\/[A-Za-z0-9_\-]*)?$/
+m/^RESOURCES\/MOBY\-S\/ServiceInstances(\/[A-Za-z0-9_\-.]+\/[A-Za-z0-9_\-]+)?$/
   )
 {
 	my $string = $1 || "";
@@ -169,25 +171,28 @@
 		print $form->header('text/xml'), $x if $x;
 	} if $string;
 
-} elsif ( $url =~ m/^RESOURCES\/MOBY\-S\/Namespaces(\/[A-Za-z0-9_\-]*)?$/ ) {
-	do {
-		if ($useCache) {
-			my $x =
-			  MOBY::RDF::Ontologies::Cache::NamespaceCache->new(
-															 cache => "$dir", );
-			$x = $x->get_rdf();
-			print $form->header('text/xml'), $x if $x;
-		} else {
-			my $x = MOBY::RDF::Ontologies::Namespaces->new;
-			$x = $x->createAll();
-			print $form->header('text/xml'), $x if $x;
-		}
-	} unless $1;
+} elsif ( $url =~ m/^RESOURCES\/MOBY\-S\/Namespaces(\/[A-Za-z0-9_\-]+)?$/ ) {
+	my $byName = length( substr $1, 1) > 0 if $1;
 	do {
 		my $x = MOBY::RDF::Ontologies::Namespaces->new;
 		my $rdf = $x->createByName( { term => substr $1, 1 } );
 		print $form->header('text/xml'), $rdf if $rdf;
-	} if $1;
+	} if $byName;
+
+	do {
+        if ($useCache) {
+            my $x =
+              MOBY::RDF::Ontologies::Cache::NamespaceCache->new(
+                                                             cache => "$dir", );
+            $x = $x->get_rdf();
+            print $form->header('text/xml'), $x if $x;
+        } else {
+            my $x = MOBY::RDF::Ontologies::Namespaces->new;
+            $x = $x->createAll();
+            print $form->header('text/xml'), $x if $x;
+        }
+    } unless $byName;
+	
 } elsif ( $url =~ m/^RESOURCES\/MOBY\-S\/FULL$/ ) {
 	my $dom    = undef;
 	my $parser = XML::LibXML->new();


From kawas at dev.open-bio.org  Fri Aug 28 10:19:38 2009
From: kawas at dev.open-bio.org (Eddie Kawas)
Date: Fri, 28 Aug 2009 10:19:38 -0400
Subject: [MOBY-guts] biomoby commit
Message-ID: <200908281419.n7SEJcgp017777@dev.open-bio.org>


kawas
Fri Aug 28 10:19:38 EDT 2009
Update of /home/repository/moby/moby-live/Perl/MOBY-Server/lib/MOBY
In directory dev.open-bio.org:/tmp/cvs-serv17742/MOBY-Server/lib/MOBY

Modified Files:
	Central.pm 
Log Message:
updated the regex expressions that checks the term names when registering new nodes in the ontology.
moby-live/Perl/MOBY-Server/lib/MOBY Central.pm,1.10,1.11
===================================================================
RCS file: /home/repository/moby/moby-live/Perl/MOBY-Server/lib/MOBY/Central.pm,v
retrieving revision 1.10
retrieving revision 1.11
diff -u -r1.10 -r1.11
--- /home/repository/moby/moby-live/Perl/MOBY-Server/lib/MOBY/Central.pm	2009/08/19 15:36:19	1.10
+++ /home/repository/moby/moby-live/Perl/MOBY-Server/lib/MOBY/Central.pm	2009/08/28 14:19:38	1.11
@@ -318,7 +318,7 @@
 	return &_error("Object name may not contain spaces or other characters invalid in a URN",
 		""
 	  )
-	  if $term =~ /[\/\'\\\s\"\&\<\>\[\]\^\`\{\|\}\~\%\+]/;
+	  if $term =~ /[\/\'\\\s\"\&\<\>\[\]\^\`\{\|\}\~\%\!\@\#\$\%\*\+\=]/;
 	if ( $term =~ m"^(([^:/?#]+):)?(//([^/?#]*))?([^?#]*)(\?([^#]*))?(#(.*))?" )
 	{    # matches a URI
 		return &_error( "Object name may not be an URN or URI", "" ) if $1;
@@ -739,6 +739,10 @@
 		""
 	  )
 	  unless $email =~ /\S\@\S+\.\S+/;
+	 return &_error("serviceType name may not contain spaces or other characters invalid in a URN",
+		""
+	  )
+	  if $term =~ /[\/\'\\\s\"\&\<\>\[\]\^\`\{\|\}\~\%\!\@\#\$\%\*\+\=]/;
 
 	# validate that the final ontology will be valid
 	my ( $exists, $exists_message, $existingURI ) =
@@ -999,6 +1003,10 @@
 		);
 	}
 
+	return &_error("Namespace name may not contain spaces or other characters invalid in a URN",
+		""
+	)
+	  if $term =~ /[\/\'\\\s\"\&\<\>\[\]\^\`\{\|\}\~\%\!\@\#\$\%\*\+\=]/;
 	return &_error( "Malformed authURI - must not have an http:// prefix", "" )
 	  if $auth =~ '[/:]';
 	return &_error( "Malformed authURI - must take the form NNN.NNN.NNN", "" )
@@ -1396,6 +1404,7 @@
 	$error .= "missing serviceType \n" unless defined $serviceType;
 	$error .= "invalid character string for serviceName.  Must start with a letter followed by [A-Za-z0-9_]\n" if ($serviceName =~ /^[^A-Za-z]/);
 	$error .= "invalid character string for serviceName.  Must start with a letter followed by [A-Za-z0-9_]\n" if ($serviceName =~ /^.+?[^A-Za-z0-9_]/);
+	$error .= "service name may not contain spaces or other characters invalid in a URN" if $serviceName =~ /[\/\'\\\s\"\&\<\>\[\]\^\`\{\|\}\~\%\!\@\#\$\%\*\+\=]/;
 
 	#	$error .="missing signatureURL \n" unless defined $signatureURL;
 	$error .= "missing authURI \n"      unless defined $AuthURI;
@@ -2946,6 +2955,7 @@
 	if ( $def{description} =~ /[^\]]+))\]\]>/ ) {
 		$def{description} = $1;
 	}
+
 	my $response;
 	$response = "
 	$def{objectType}


From kawas at dev.open-bio.org  Fri Aug 28 10:40:45 2009
From: kawas at dev.open-bio.org (Eddie Kawas)
Date: Fri, 28 Aug 2009 10:40:45 -0400
Subject: [MOBY-guts] biomoby commit
Message-ID: <200908281440.n7SEejaD017919@dev.open-bio.org>


kawas
Fri Aug 28 10:40:44 EDT 2009
Update of /home/repository/moby/moby-live/Perl/MOBY-Server/lib/MOBY
In directory dev.open-bio.org:/tmp/cvs-serv17884/MOBY-Server/lib/MOBY

Modified Files:
	Central.pm 
Log Message:
updated the regex expressions that checks the term names when registering new nodes in the ontology.
moby-live/Perl/MOBY-Server/lib/MOBY Central.pm,1.11,1.12
===================================================================
RCS file: /home/repository/moby/moby-live/Perl/MOBY-Server/lib/MOBY/Central.pm,v
retrieving revision 1.11
retrieving revision 1.12
diff -u -r1.11 -r1.12
--- /home/repository/moby/moby-live/Perl/MOBY-Server/lib/MOBY/Central.pm	2009/08/28 14:19:38	1.11
+++ /home/repository/moby/moby-live/Perl/MOBY-Server/lib/MOBY/Central.pm	2009/08/28 14:40:44	1.12
@@ -318,7 +318,7 @@
 	return &_error("Object name may not contain spaces or other characters invalid in a URN",
 		""
 	  )
-	  if $term =~ /[\/\'\\\s\"\&\<\>\[\]\^\`\{\|\}\~\%\!\@\#\$\%\*\+\=]/;
+	  if $term =~ /[\/\'\\\s"\&\<\>\[\]\^\`\{\|\}\~%\!\@#\$\*\+=]/;
 	if ( $term =~ m"^(([^:/?#]+):)?(//([^/?#]*))?([^?#]*)(\?([^#]*))?(#(.*))?" )
 	{    # matches a URI
 		return &_error( "Object name may not be an URN or URI", "" ) if $1;
@@ -742,7 +742,7 @@
 	 return &_error("serviceType name may not contain spaces or other characters invalid in a URN",
 		""
 	  )
-	  if $term =~ /[\/\'\\\s\"\&\<\>\[\]\^\`\{\|\}\~\%\!\@\#\$\%\*\+\=]/;
+	  if $term =~ /[\/\'\\\s"\&\<\>\[\]\^\`\{\|\}\~%\!\@#\$\*\+=]/;
 
 	# validate that the final ontology will be valid
 	my ( $exists, $exists_message, $existingURI ) =
@@ -1006,7 +1006,7 @@
 	return &_error("Namespace name may not contain spaces or other characters invalid in a URN",
 		""
 	)
-	  if $term =~ /[\/\'\\\s\"\&\<\>\[\]\^\`\{\|\}\~\%\!\@\#\$\%\*\+\=]/;
+	  if $term =~ /[\/\'\\\s"\&\<\>\[\]\^\`\{\|\}\~%\!\@#\$\*\+=]/;
 	return &_error( "Malformed authURI - must not have an http:// prefix", "" )
 	  if $auth =~ '[/:]';
 	return &_error( "Malformed authURI - must take the form NNN.NNN.NNN", "" )
@@ -1404,7 +1404,7 @@
 	$error .= "missing serviceType \n" unless defined $serviceType;
 	$error .= "invalid character string for serviceName.  Must start with a letter followed by [A-Za-z0-9_]\n" if ($serviceName =~ /^[^A-Za-z]/);
 	$error .= "invalid character string for serviceName.  Must start with a letter followed by [A-Za-z0-9_]\n" if ($serviceName =~ /^.+?[^A-Za-z0-9_]/);
-	$error .= "service name may not contain spaces or other characters invalid in a URN" if $serviceName =~ /[\/\'\\\s\"\&\<\>\[\]\^\`\{\|\}\~\%\!\@\#\$\%\*\+\=]/;
+	$error .= "service name may not contain spaces or other characters invalid in a URN" if $serviceName =~ /[\/\'\\\s"\&\<\>\[\]\^\`\{\|\}\~%\!\@#\$\*\+=]/;
 
 	#	$error .="missing signatureURL \n" unless defined $signatureURL;
 	$error .= "missing authURI \n"      unless defined $AuthURI;
@@ -2963,9 +2963,9 @@
 	$def{authURI}
 	$def{contactEmail}\n";
 	my %relationships = %{ $def{Relationships} };
-
-	while ( my ( $rel, $objdefs ) = each %relationships ) {
-		$response .= "\n";
+	
+    while ( my ( $rel, $objdefs ) = each %relationships ) {
+        $response .= "\n";
 		foreach my $def ( @{$objdefs} ) {
 			my ( $lsid, $articlename,$type, $def, $auth, $contac ) = @{$def};
 			$articlename = "" unless defined $articlename;


From kawas at dev.open-bio.org  Fri Aug 28 11:03:33 2009
From: kawas at dev.open-bio.org (Eddie Kawas)
Date: Fri, 28 Aug 2009 11:03:33 -0400
Subject: [MOBY-guts] biomoby commit
Message-ID: <200908281503.n7SF3Xf6018095@dev.open-bio.org>


kawas
Fri Aug 28 11:03:33 EDT 2009
Update of /home/repository/moby/moby-live/Perl/MOBY-Server
In directory dev.open-bio.org:/tmp/cvs-serv18060/MOBY-Server

Modified Files:
	Changes 
Log Message:

moby-live/Perl/MOBY-Server Changes,1.29,1.30
===================================================================
RCS file: /home/repository/moby/moby-live/Perl/MOBY-Server/Changes,v
retrieving revision 1.29
retrieving revision 1.30
diff -u -r1.29 -r1.30
--- /home/repository/moby/moby-live/Perl/MOBY-Server/Changes	2009/08/19 15:38:39	1.29
+++ /home/repository/moby/moby-live/Perl/MOBY-Server/Changes	2009/08/28 15:03:33	1.30
@@ -3,8 +3,11 @@
 
 1.11
 	-  Updated the Makefile.PL to handle some missing dependencies.
-        -  Added '%' to the list of characters not allowed in the name of
-           a datatype.
+       Changes
+	  *   Updated the RESOURCES script to better handle trailing slashes
+	      on Objects/, Namespaces, Services/
+	  *  Updated the regex expressions that are applied against terms
+	      when registering new nodes in the biomoby ontologies. 
 
 1.10
     - Added a RESTful WSDL page to the installation. Basically, you do


From kawas at dev.open-bio.org  Fri Aug 28 11:07:18 2009
From: kawas at dev.open-bio.org (Eddie Kawas)
Date: Fri, 28 Aug 2009 11:07:18 -0400
Subject: [MOBY-guts] biomoby commit
Message-ID: <200908281507.n7SF7IFN018280@dev.open-bio.org>


kawas
Fri Aug 28 11:07:18 EDT 2009
Update of /home/repository/moby/moby-live/Perl/MOBY-Server
In directory dev.open-bio.org:/tmp/cvs-serv18245/MOBY-Server

Modified Files:
	Makefile.PL 
Log Message:
updated version for new cpan release.
moby-live/Perl/MOBY-Server Makefile.PL,1.19,1.20
===================================================================
RCS file: /home/repository/moby/moby-live/Perl/MOBY-Server/Makefile.PL,v
retrieving revision 1.19
retrieving revision 1.20
diff -u -r1.19 -r1.20
--- /home/repository/moby/moby-live/Perl/MOBY-Server/Makefile.PL	2009/05/22 16:38:39	1.19
+++ /home/repository/moby/moby-live/Perl/MOBY-Server/Makefile.PL	2009/08/28 15:07:18	1.20
@@ -3,7 +3,7 @@
 
 	# Define metadata
 	name 'MOBY';
-	version '1.10';
+	version '1.11';
 	license 'perl';
 	abstract
 'This distribution is for communicating with or creating your own MOBY Central registry';


From kawas at dev.open-bio.org  Fri Aug 28 11:15:16 2009
From: kawas at dev.open-bio.org (Eddie Kawas)
Date: Fri, 28 Aug 2009 11:15:16 -0400
Subject: [MOBY-guts] biomoby commit
Message-ID: <200908281515.n7SFFGJ4018496@dev.open-bio.org>


kawas
Fri Aug 28 11:15:16 EDT 2009
Update of /home/repository/moby/moby-live/Perl/MOBY-Client/inc/Module
In directory dev.open-bio.org:/tmp/cvs-serv18457/MOBY-Client/inc/Module

Modified Files:
	AutoInstall.pm Install.pm 
Log Message:
updated the module::install inc modules.
moby-live/Perl/MOBY-Client/inc/Module AutoInstall.pm,1.1,1.2 Install.pm,1.2,1.3
===================================================================
RCS file: /home/repository/moby/moby-live/Perl/MOBY-Client/inc/Module/AutoInstall.pm,v
retrieving revision 1.1
retrieving revision 1.2
diff -u -r1.1 -r1.2
--- /home/repository/moby/moby-live/Perl/MOBY-Client/inc/Module/AutoInstall.pm	2008/02/21 00:14:33	1.1
+++ /home/repository/moby/moby-live/Perl/MOBY-Client/inc/Module/AutoInstall.pm	2009/08/28 15:15:15	1.2
@@ -18,7 +18,9 @@
 
 # various lexical flags
 my ( @Missing, @Existing,  %DisabledTests, $UnderCPAN,     $HasCPANPLUS );
-my ( $Config,  $CheckOnly, $SkipInstall,   $AcceptDefault, $TestOnly );
+my (
+    $Config, $CheckOnly, $SkipInstall, $AcceptDefault, $TestOnly, $AllDeps
+);
 my ( $PostambleActions, $PostambleUsed );
 
 # See if it's a testing or non-interactive session
@@ -73,6 +75,9 @@
         elsif ( $arg =~ /^--test(?:only)?$/ ) {
             $TestOnly = 1;
         }
+        elsif ( $arg =~ /^--all(?:deps)?$/ ) {
+            $AllDeps = 1;
+        }
     }
 }
 
@@ -115,6 +120,13 @@
         )[0]
     );
 
+    # We want to know if we're under CPAN early to avoid prompting, but
+    # if we aren't going to try and install anything anyway then skip the
+    # check entirely since we don't want to have to load (and configure)
+    # an old CPAN just for a cosmetic message
+
+    $UnderCPAN = _check_lock(1) unless $SkipInstall;
+
     while ( my ( $feature, $modules ) = splice( @args, 0, 2 ) ) {
         my ( @required, @tests, @skiptests );
         my $default  = 1;
@@ -163,15 +175,24 @@
             }
 
             # XXX: check for conflicts and uninstalls(!) them.
-            if (
-                defined( my $cur = _version_check( _load($mod), $arg ||= 0 ) ) )
+            my $cur = _load($mod);
+            if (_version_cmp ($cur, $arg) >= 0)
             {
                 print "loaded. ($cur" . ( $arg ? " >= $arg" : '' ) . ")\n";
                 push @Existing, $mod => $arg;
                 $DisabledTests{$_} = 1 for map { glob($_) } @skiptests;
             }
             else {
-                print "missing." . ( $arg ? " (would need $arg)" : '' ) . "\n";
+                if (not defined $cur)   # indeed missing
+                {
+                    print "missing." . ( $arg ? " (would need $arg)" : '' ) . "\n";
+                }
+                else
+                {
+                    # no need to check $arg as _version_cmp ($cur, undef) would satisfy >= above
+                    print "too old. ($cur < $arg)\n";
+                }
+
                 push @required, $mod => $arg;
             }
         }
@@ -184,6 +205,8 @@
             !$SkipInstall
             and (
                 $CheckOnly
+                or ($mandatory and $UnderCPAN)
+                or $AllDeps
                 or _prompt(
                     qq{==> Auto-install the }
                       . ( @required / 2 )
@@ -214,8 +237,6 @@
         }
     }
 
-    $UnderCPAN = _check_lock();    # check for $UnderCPAN
-
     if ( @Missing and not( $CheckOnly or $UnderCPAN ) ) {
         require Config;
         print
@@ -234,21 +255,38 @@
     *{'main::WriteMakefile'} = \&Write if caller(0) eq 'main';
 }
 
+sub _running_under {
+    my $thing = shift;
+    print <<"END_MESSAGE";
+*** Since we're running under ${thing}, I'll just let it take care
+    of the dependency's installation later.
+END_MESSAGE
+    return 1;
+}
+
 # Check to see if we are currently running under CPAN.pm and/or CPANPLUS;
 # if we are, then we simply let it taking care of our dependencies
 sub _check_lock {
-    return unless @Missing;
+    return unless @Missing or @_;
+
+    my $cpan_env = $ENV{PERL5_CPAN_IS_RUNNING};
 
     if ($ENV{PERL5_CPANPLUS_IS_RUNNING}) {
-        print <<'END_MESSAGE';
+        return _running_under($cpan_env ? 'CPAN' : 'CPANPLUS');
+    }
 
-*** Since we're running under CPANPLUS, I'll just let it take care
-    of the dependency's installation later.
-END_MESSAGE
-        return 1;
+    require CPAN;
+
+    if ($CPAN::VERSION > '1.89') {
+        if ($cpan_env) {
+            return _running_under('CPAN');
+        }
+        return; # CPAN.pm new enough, don't need to check further
     }
 
-    _load_cpan();
+    # last ditch attempt, this -will- configure CPAN, very sorry
+
+    _load_cpan(1); # force initialize even though it's already loaded
 
     # Find the CPAN lock-file
     my $lock = MM->catfile( $CPAN::Config->{cpan_home}, ".lock" );
@@ -284,7 +322,7 @@
     while ( my ( $pkg, $ver ) = splice( @_, 0, 2 ) ) {
 
         # grep out those already installed
-        if ( defined( _version_check( _load($pkg), $ver ) ) ) {
+        if ( _version_cmp( _load($pkg), $ver ) >= 0 ) {
             push @installed, $pkg;
         }
         else {
@@ -313,7 +351,7 @@
         @modules = @newmod;
     }
 
-    if ( _has_cpanplus() ) {
+    if ( _has_cpanplus() and not $ENV{PERL_AUTOINSTALL_PREFER_CPAN} ) {
         _install_cpanplus( \@modules, \@config );
     } else {
         _install_cpan( \@modules, \@config );
@@ -323,7 +361,7 @@
 
     # see if we have successfully installed them
     while ( my ( $pkg, $ver ) = splice( @modules, 0, 2 ) ) {
-        if ( defined( _version_check( _load($pkg), $ver ) ) ) {
+        if ( _version_cmp( _load($pkg), $ver ) >= 0 ) {
             push @installed, $pkg;
         }
         elsif ( $args{do_once} and open( FAILED, '>> .#autoinstall.failed' ) ) {
@@ -378,7 +416,7 @@
         my $success;
         my $obj = $modtree->{$pkg};
 
-        if ( $obj and defined( _version_check( $obj->{version}, $ver ) ) ) {
+        if ( $obj and _version_cmp( $obj->{version}, $ver ) >= 0 ) {
             my $pathname = $pkg;
             $pathname =~ s/::/\\W/;
 
@@ -471,7 +509,7 @@
         my $obj     = CPAN::Shell->expand( Module => $pkg );
         my $success = 0;
 
-        if ( $obj and defined( _version_check( $obj->cpan_version, $ver ) ) ) {
+        if ( $obj and _version_cmp( $obj->cpan_version, $ver ) >= 0 ) {
             my $pathname = $pkg;
             $pathname =~ s/::/\\W/;
 
@@ -535,7 +573,7 @@
     my $ver   = shift;
 
     return
-      if defined( _version_check( _load($class), $ver ) );  # no need to upgrade
+      if _version_cmp( _load($class), $ver ) >= 0;  # no need to upgrade
 
     if (
         _prompt( "==> A newer version of $class ($ver) is required. Install?",
@@ -632,7 +670,7 @@
 
 # Load CPAN.pm and it's configuration
 sub _load_cpan {
-    return if $CPAN::VERSION;
+    return if $CPAN::VERSION and $CPAN::Config and not @_;
     require CPAN;
     if ( $CPAN::HandleConfig::VERSION ) {
         # Newer versions of CPAN have a HandleConfig module
@@ -644,9 +682,11 @@
 }
 
 # compare two versions, either use Sort::Versions or plain comparison
-sub _version_check {
+# return values same as <=>
+sub _version_cmp {
     my ( $cur, $min ) = @_;
-    return unless defined $cur;
+    return -1 unless defined $cur;  # if 0 keep comparing
+    return 1 unless $min;
 
     $cur =~ s/\s+$//;
 
@@ -657,16 +697,13 @@
             ) {
 
             # use version.pm if it is installed.
-            return (
-                ( version->new($cur) >= version->new($min) ) ? $cur : undef );
+            return version->new($cur) <=> version->new($min);
         }
         elsif ( $Sort::Versions::VERSION or defined( _load('Sort::Versions') ) )
         {
 
             # use Sort::Versions as the sorting algorithm for a.b.c versions
-            return ( ( Sort::Versions::versioncmp( $cur, $min ) != -1 )
-                ? $cur
-                : undef );
+            return Sort::Versions::versioncmp( $cur, $min );
         }
 
         warn "Cannot reliably compare non-decimal formatted versions.\n"
@@ -675,7 +712,7 @@
 
     # plain comparison
     local $^W = 0;    # shuts off 'not numeric' bugs
-    return ( $cur >= $min ? $cur : undef );
+    return $cur <=> $min;
 }
 
 # nothing; this usage is deprecated.
@@ -706,7 +743,7 @@
       if $Config;
 
     $PostambleActions = (
-        $missing
+        ($missing and not $UnderCPAN)
         ? "\$(PERL) $0 --config=$config --installdeps=$missing"
         : "\$(NOECHO) \$(NOOP)"
     );
@@ -746,7 +783,7 @@
 sub postamble {
     $PostambleUsed = 1;
 
-    return << ".";
+    return <<"END_MAKE";
 
 config :: installdeps
 \t\$(NOECHO) \$(NOOP)
@@ -757,7 +794,7 @@
 installdeps ::
 \t$PostambleActions
 
-.
+END_MAKE
 
 }
 
@@ -765,4 +802,4 @@
 
 __END__
 
-#line 1003
+#line 1056

===================================================================
RCS file: /home/repository/moby/moby-live/Perl/MOBY-Client/inc/Module/Install.pm,v
retrieving revision 1.2
retrieving revision 1.3
diff -u -r1.2 -r1.3
--- /home/repository/moby/moby-live/Perl/MOBY-Client/inc/Module/Install.pm	2008/05/07 18:15:19	1.2
+++ /home/repository/moby/moby-live/Perl/MOBY-Client/inc/Module/Install.pm	2009/08/28 15:15:16	1.3
@@ -17,12 +17,10 @@
 #     3. The ./inc/ version of Module::Install loads
 # }
 
-BEGIN {
-	require 5.004;
-}
+use 5.005;
 use strict 'vars';
 
-use vars qw{$VERSION};
+use vars qw{$VERSION $MAIN};
 BEGIN {
 	# All Module::Install core packages now require synchronised versions.
 	# This will be used to ensure we don't accidentally load old or
@@ -30,7 +28,10 @@
 	# This is not enforced yet, but will be some time in the next few
 	# releases once we can make sure it won't clash with custom
 	# Module::Install extensions.
-	$VERSION = '0.72';
+	$VERSION = '0.91';
+
+	# Storage for the pseudo-singleton
+	$MAIN    = undef;
 
 	*inc::Module::Install::VERSION = *VERSION;
 	@inc::Module::Install::ISA     = __PACKAGE__;
@@ -69,15 +70,26 @@
 # again. This is bad. Rather than taking action to touch it (which
 # is unreliable on some platforms and requires write permissions)
 # for now we should catch this and refuse to run.
-if ( -f $0 and (stat($0))[9] > time ) { die <<"END_DIE" }
+if ( -f $0 ) {
+	my $s = (stat($0))[9];
 
-Your installer $0 has a modification time in the future.
+	# If the modification time is only slightly in the future,
+	# sleep briefly to remove the problem.
+	my $a = $s - time;
+	if ( $a > 0 and $a < 5 ) { sleep 5 }
+
+	# Too far in the future, throw an error.
+	my $t = time;
+	if ( $s > $t ) { die <<"END_DIE" }
+
+Your installer $0 has a modification time in the future ($s > $t).
 
 This is known to create infinite loops in make.
 
 Please correct this, then run $0 again.
 
 END_DIE
+}
 
 
 
@@ -85,7 +97,7 @@
 
 # Build.PL was formerly supported, but no longer is due to excessive
 # difficulty in implementing every single feature twice.
-if ( $0 =~ /Build.PL$/i or -f 'Build.PL' ) { die <<"END_DIE" }
+if ( $0 =~ /Build.PL$/i ) { die <<"END_DIE" }
 
 Module::Install no longer supports Build.PL.
 
@@ -121,12 +133,22 @@
 	$sym->{$cwd} = sub {
 		my $pwd = Cwd::cwd();
 		if ( my $code = $sym->{$pwd} ) {
-			# delegate back to parent dirs
+			# Delegate back to parent dirs
 			goto &$code unless $cwd eq $pwd;
 		}
 		$$sym =~ /([^:]+)$/ or die "Cannot autoload $who - $sym";
+		my $method = $1;
+		if ( uc($method) eq $method ) {
+			# Do nothing
+			return;
+		} elsif ( $method =~ /^_/ and $self->can($method) ) {
+			# Dispatch to the root M:I class
+			return $self->$method(@_);
+		}
+
+		# Dispatch to the appropriate plugin
 		unshift @_, ( $self, $1 );
-		goto &{$self->can('call')} unless uc($1) eq $1;
+		goto &{$self->can('call')};
 	};
 }
 
@@ -151,6 +173,9 @@
 	delete $INC{"$self->{file}"};
 	delete $INC{"$self->{path}.pm"};
 
+	# Save to the singleton
+	$MAIN = $self;
+
 	return 1;
 }
 
@@ -164,8 +189,7 @@
 
 	my @exts = @{$self->{extensions}};
 	unless ( @exts ) {
-		my $admin = $self->{admin};
-		@exts = $admin->load_all_extensions;
+		@exts = $self->{admin}->load_all_extensions;
 	}
 
 	my %seen;
@@ -248,7 +272,7 @@
 sub load_extensions {
 	my ($self, $path, $top) = @_;
 
-	unless ( grep { lc $_ eq lc $self->{prefix} } @INC ) {
+	unless ( grep { ! ref $_ and lc $_ eq lc $self->{prefix} } @INC ) {
 		unshift @INC, $self->{prefix};
 	}
 
@@ -312,7 +336,7 @@
 
 
 #####################################################################
-# Utility Functions
+# Common Utility Functions
 
 sub _caller {
 	my $depth = 0;
@@ -326,28 +350,81 @@
 
 sub _read {
 	local *FH;
-	open FH, "< $_[0]" or die "open($_[0]): $!";
-	my $str = do { local $/;  };
+	if ( $] >= 5.006 ) {
+		open( FH, '<', $_[0] ) or die "open($_[0]): $!";
+	} else {
+		open( FH, "< $_[0]"  ) or die "open($_[0]): $!";
+	}
+	my $string = do { local $/;  };
 	close FH or die "close($_[0]): $!";
-	return $str;
+	return $string;
+}
+
+sub _readperl {
+	my $string = Module::Install::_read($_[0]);
+	$string =~ s/(?:\015{1,2}\012|\015|\012)/\n/sg;
+	$string =~ s/(\n)\n*__(?:DATA|END)__\b.*\z/$1/s;
+	$string =~ s/\n\n=\w+.+?\n\n=cut\b.+?\n+/\n\n/sg;
+	return $string;
+}
+
+sub _readpod {
+	my $string = Module::Install::_read($_[0]);
+	$string =~ s/(?:\015{1,2}\012|\015|\012)/\n/sg;
+	return $string if $_[0] =~ /\.pod\z/;
+	$string =~ s/(^|\n=cut\b.+?\n+)[^=\s].+?\n(\n=\w+|\z)/$1$2/sg;
+	$string =~ s/\n*=pod\b[^\n]*\n+/\n\n/sg;
+	$string =~ s/\n*=cut\b[^\n]*\n+/\n\n/sg;
+	$string =~ s/^\n+//s;
+	return $string;
 }
 
 sub _write {
 	local *FH;
-	open FH, "> $_[0]" or die "open($_[0]): $!";
-	foreach ( 1 .. $#_ ) { print FH $_[$_] or die "print($_[0]): $!" }
+	if ( $] >= 5.006 ) {
+		open( FH, '>', $_[0] ) or die "open($_[0]): $!";
+	} else {
+		open( FH, "> $_[0]"  ) or die "open($_[0]): $!";
+	}
+	foreach ( 1 .. $#_ ) {
+		print FH $_[$_] or die "print($_[0]): $!";
+	}
 	close FH or die "close($_[0]): $!";
 }
 
-sub _version {
+# _version is for processing module versions (eg, 1.03_05) not
+# Perl versions (eg, 5.8.1).
+sub _version ($) {
 	my $s = shift || 0;
-	   $s =~ s/^(\d+)\.?//;
+	my $d =()= $s =~ /(\.)/g;
+	if ( $d >= 2 ) {
+		# Normalise multipart versions
+		$s =~ s/(\.)(\d{1,3})/sprintf("$1%03d",$2)/eg;
+	}
+	$s =~ s/^(\d+)\.?//;
 	my $l = $1 || 0;
-	my @v = map { $_ . '0' x (3 - length $_) } $s =~ /(\d{1,3})\D?/g;
-	   $l = $l . '.' . join '', @v if @v;
+	my @v = map {
+		$_ . '0' x (3 - length $_)
+	} $s =~ /(\d{1,3})\D?/g;
+	$l = $l . '.' . join '', @v if @v;
 	return $l + 0;
 }
 
+sub _cmp ($$) {
+	_version($_[0]) <=> _version($_[1]);
+}
+
+# Cloned from Params::Util::_CLASS
+sub _CLASS ($) {
+	(
+		defined $_[0]
+		and
+		! ref $_[0]
+		and
+		$_[0] =~ m/^[^\W\d]\w*(?:::\w+)*\z/s
+	) ? $_[0] : undef;
+}
+
 1;
 
-# Copyright 2008 Adam Kennedy.
+# Copyright 2008 - 2009 Adam Kennedy.


From kawas at dev.open-bio.org  Fri Aug 28 11:15:16 2009
From: kawas at dev.open-bio.org (Eddie Kawas)
Date: Fri, 28 Aug 2009 11:15:16 -0400
Subject: [MOBY-guts] biomoby commit
Message-ID: <200908281515.n7SFFGeG018558@dev.open-bio.org>


kawas
Fri Aug 28 11:15:16 EDT 2009
Update of /home/repository/moby/moby-live/Perl/MOBY-Client/inc/Module/Install
In directory dev.open-bio.org:/tmp/cvs-serv18457/MOBY-Client/inc/Module/Install

Modified Files:
	AutoInstall.pm Share.pm Include.pm Makefile.pm WriteAll.pm 
	Base.pm Win32.pm Metadata.pm Fetch.pm Can.pm 
Added Files:
	Scripts.pm 
Log Message:
updated the module::install inc modules.
moby-live/Perl/MOBY-Client/inc/Module/Install Scripts.pm,1.2,1.3 AutoInstall.pm,1.2,1.3 Share.pm,1.2,1.3 Include.pm,1.2,1.3 Makefile.pm,1.2,1.3 WriteAll.pm,1.2,1.3 Base.pm,1.2,1.3 Win32.pm,1.2,1.3 Metadata.pm,1.2,1.3 Fetch.pm,1.2,1.3 Can.pm,1.2,1.3
===================================================================
RCS file: /home/repository/moby/moby-live/Perl/MOBY-Client/inc/Module/Install/Scripts.pm,v
retrieving revision 1.2
retrieving revision 1.3
diff -u -r1.2 -r1.3
--- /home/repository/moby/moby-live/Perl/MOBY-Client/inc/Module/Install/Scripts.pm	2008/05/07 18:15:19	1.2
+++ /home/repository/moby/moby-live/Perl/MOBY-Client/inc/Module/Install/Scripts.pm	2009/08/28 15:15:16	1.3
@@ -1,50 +1,29 @@
 #line 1
 package Module::Install::Scripts;
 
-use strict;
-use Module::Install::Base;
-use File::Basename ();
+use strict 'vars';
+use Module::Install::Base ();
 
-use vars qw{$VERSION $ISCORE @ISA};
+use vars qw{$VERSION @ISA $ISCORE};
 BEGIN {
-	$VERSION = '0.67';
+	$VERSION = '0.91';
+	@ISA     = 'Module::Install::Base';
 	$ISCORE  = 1;
-	@ISA     = qw{Module::Install::Base};
-}
-
-sub prompt_script {
-    my ($self, $script_file) = @_;
-
-    my ($prompt, $abstract, $default);
-    foreach my $line ( $self->_read_script($script_file) ) {
-        last unless $line =~ /^#/;
-        $prompt = $1   if $line =~ /^#\s*prompt:\s+(.*)/;
-        $default = $1  if $line =~ /^#\s*default:\s+(.*)/;
-        $abstract = $1 if $line =~ /^#\s*abstract:\s+(.*)/;
-    }
-    unless (defined $prompt) {
-        my $script_name = File::Basename::basename($script_file);
-        $prompt = "Do you want to install '$script_name'";
-        $prompt .= " ($abstract)" if defined $abstract;
-        $prompt .= '?';
-    }
-    return unless $self->prompt($prompt, ($default || 'n')) =~ /^[Yy]/;
-    $self->install_script($script_file);
 }
 
 sub install_script {
-    my $self = shift;
-    my $args = $self->makemaker_args;
-    my $exe_files = $args->{EXE_FILES} ||= [];
-    push @$exe_files, @_;
-}
-
-sub _read_script {
-    my ($self, $script_file) = @_;
-    local *SCRIPT;
-    open SCRIPT, $script_file
-      or die "Can't open '$script_file' for input: $!\n";
-    return 

The URL specified (" + + out.print("Error\n"+ + "\n"+ + "

The URL specified (" + wsdlLoc + ") could not be parsed

The URL specified (" + endpoint + ") could not be parsed

The URL specified (" + endpoint + ") could not be parsed