From kawas at dev.open-bio.org  Wed Jul  2 16:27:01 2008
From: kawas at dev.open-bio.org (Eddie Kawas)
Date: Wed, 2 Jul 2008 16:27:01 -0400
Subject: [MOBY-guts] biomoby commit
Message-ID: <200807022027.m62KR1eD021387@dev.open-bio.org>


kawas
Wed Jul  2 16:27:00 EDT 2008
Update of /home/repository/moby/moby-live/Perl/MOBY-Server/bin/scripts
In directory dev.open-bio.org:/tmp/cvs-serv21356/Perl/MOBY-Server/bin/scripts

Added Files:
	moby-s-caching.pl 
Log Message:
initial commit of a script that helps build the rdf cache for the registry
moby-live/Perl/MOBY-Server/bin/scripts moby-s-caching.pl,NONE,1.1

From kawas at dev.open-bio.org  Wed Jul  2 16:49:24 2008
From: kawas at dev.open-bio.org (Eddie Kawas)
Date: Wed, 2 Jul 2008 16:49:24 -0400
Subject: [MOBY-guts] biomoby commit
Message-ID: <200807022049.m62KnOZ5021488@dev.open-bio.org>


kawas
Wed Jul  2 16:49:23 EDT 2008
Update of /home/repository/moby/moby-live/Perl/MOBY-Server/bin/scripts
In directory dev.open-bio.org:/tmp/cvs-serv21453/Perl/MOBY-Server/bin/scripts

Modified Files:
	moby-s-install.pl 
Log Message:
when checking for root, we ignore windows.
moby-live/Perl/MOBY-Server/bin/scripts moby-s-install.pl,1.11,1.12
===================================================================
RCS file: /home/repository/moby/moby-live/Perl/MOBY-Server/bin/scripts/moby-s-install.pl,v
retrieving revision 1.11
retrieving revision 1.12
diff -u -r1.11 -r1.12
--- /home/repository/moby/moby-live/Perl/MOBY-Server/bin/scripts/moby-s-install.pl	2008/06/20 19:56:37	1.11
+++ /home/repository/moby/moby-live/Perl/MOBY-Server/bin/scripts/moby-s-install.pl	2008/07/02 20:49:23	1.12
@@ -490,6 +490,8 @@
 }
 
 sub check_root {
+	# assume that windows has no security preventing the copying of files
+	return if MSWIN;
     unless (getpwuid($<) eq 'root') { 
 	print STDOUT <<EOT;
 


From kawas at dev.open-bio.org  Wed Jul  2 16:49:44 2008
From: kawas at dev.open-bio.org (Eddie Kawas)
Date: Wed, 2 Jul 2008 16:49:44 -0400
Subject: [MOBY-guts] biomoby commit
Message-ID: <200807022049.m62KniUQ021528@dev.open-bio.org>


kawas
Wed Jul  2 16:49:44 EDT 2008
Update of /home/repository/moby/moby-live/Perl/MOBY-Server
In directory dev.open-bio.org:/tmp/cvs-serv21493/Perl/MOBY-Server

Modified Files:
	Makefile.PL 
Log Message:
added the caching script to the makefile
moby-live/Perl/MOBY-Server Makefile.PL,1.7,1.8
===================================================================
RCS file: /home/repository/moby/moby-live/Perl/MOBY-Server/Makefile.PL,v
retrieving revision 1.7
retrieving revision 1.8
diff -u -r1.7 -r1.8
--- /home/repository/moby/moby-live/Perl/MOBY-Server/Makefile.PL	2008/06/05 14:13:52	1.7
+++ /home/repository/moby/moby-live/Perl/MOBY-Server/Makefile.PL	2008/07/02 20:49:44	1.8
@@ -106,6 +106,7 @@
 	no_index 'directory' => 'bin/scripts';
 
 	install_script 'bin/scripts/moby-s-install.pl';
+	install_script 'bin/scripts/moby-s-caching.pl';
 
 	install_share 'share';
 


From kawas at dev.open-bio.org  Wed Jul  2 16:51:33 2008
From: kawas at dev.open-bio.org (Eddie Kawas)
Date: Wed, 2 Jul 2008 16:51:33 -0400
Subject: [MOBY-guts] biomoby commit
Message-ID: <200807022051.m62KpXZ2021568@dev.open-bio.org>


kawas
Wed Jul  2 16:51:33 EDT 2008
Update of /home/repository/moby/moby-live/Perl/MOBY-Server
In directory dev.open-bio.org:/tmp/cvs-serv21533/Perl/MOBY-Server

Modified Files:
	Changes 
Log Message:

moby-live/Perl/MOBY-Server Changes,1.10,1.11
===================================================================
RCS file: /home/repository/moby/moby-live/Perl/MOBY-Server/Changes,v
retrieving revision 1.10
retrieving revision 1.11
diff -u -r1.10 -r1.11
--- /home/repository/moby/moby-live/Perl/MOBY-Server/Changes	2008/06/20 19:58:22	1.10
+++ /home/repository/moby/moby-live/Perl/MOBY-Server/Changes	2008/07/02 20:51:33	1.11
@@ -47,6 +47,11 @@
 	- fixed the installer script, username/password, root/root was hardcoded
 	- fixed a bug in MOBY::dbConfig that caused certain parameters to be
 	  ignored in the configuration file if a field was empty.
+	- added a caching script to be used by registry providers needing to
+	  update their cache. 
+	  For more information, run: 
+	      moby-s-caching.pl -h
+	  
 
 1.04
 	- fixed bug in MOBY::Client::Central::DUMP that resulted


From gordonp at dev.open-bio.org  Thu Jul  3 12:29:26 2008
From: gordonp at dev.open-bio.org (Paul Gordon)
Date: Thu, 3 Jul 2008 12:29:26 -0400
Subject: [MOBY-guts] biomoby commit
Message-ID: <200807031629.m63GTQdO024979@dev.open-bio.org>


gordonp
Thu Jul  3 12:29:25 EDT 2008
Update of /home/repository/moby/moby-live/Java/src/main/ca/ucalgary/services/util
In directory dev.open-bio.org:/tmp/cvs-serv24943/src/main/ca/ucalgary/services/util

Modified Files:
	WSDLConfig.java 
Log Message:
Refactored and added implicit collection support
moby-live/Java/src/main/ca/ucalgary/services/util WSDLConfig.java,1.3,1.4
===================================================================
RCS file: /home/repository/moby/moby-live/Java/src/main/ca/ucalgary/services/util/WSDLConfig.java,v
retrieving revision 1.3
retrieving revision 1.4
diff -u -r1.3 -r1.4
--- /home/repository/moby/moby-live/Java/src/main/ca/ucalgary/services/util/WSDLConfig.java	2008/06/30 17:42:29	1.3
+++ /home/repository/moby/moby-live/Java/src/main/ca/ucalgary/services/util/WSDLConfig.java	2008/07/03 16:29:25	1.4
@@ -157,6 +157,7 @@
 	    }
 	    String modelReference = partElement.getAttributeNS(MobyPrefixResolver.SAWSDL_NAMESPACE, SAWSDL_MODEL_ATTR);
 	    if(modelReference == null || modelReference.length() == 0){
+		// TODO deal with schema-only level SAWSDL annotation
 		throw new Exception("Part element " + partName + " of WSDL message " + 
 				    messageName + " has no SAWSDL " + SAWSDL_MODEL_ATTR + " attribute defined");
 	    }
@@ -167,10 +168,10 @@
 		    throw new Exception("Part element " + partName + " of WSDL message " + 
 					messageName + " has no SAWSDL " + SAWSDL_INMAP_ATTR + " attribute defined");
 		}
-		String mobyParam = wsdlParam2MobyParam(partName, partType, modelReference);
+		String mobyParam = wsdlParam2MobyParam(partElement, partName, partType, modelReference);
 		if(mobyParam == null){
 		    // Check if it's a secondary
-		    mobyParam = wsdlParam2MobySecondaryParam(partName, partType, modelReference, partElement);
+		    mobyParam = wsdlParam2MobySecondaryParam(partElement, partName, partType, modelReference);
 		    if(mobyParam == null){
 			throw new Exception("The LSID '" + modelReference + 
 					    "' is not a properly formed Moby primary or secondary param LSID as required");
@@ -189,7 +190,7 @@
 		    throw new Exception("Part element " + partName + " of WSDL message " + 
 					messageName + " has no SAWSDL " + SAWSDL_OUTMAP_ATTR + " attribute defined");
 		}
-		outputs.put(partName, wsdlParam2MobyParam(partName, partType, modelReference));
+		outputs.put(partName, wsdlParam2MobyParam(partElement, partName, partType, modelReference));
 		outputTypes.put(partName, partType);
 		outputMappings.put(partName, schemaMapping);	    
 	    }
@@ -207,7 +208,8 @@
 	}
     }
 
-    public String wsdlParam2MobyParam(String paramName, String paramXSDType, String dataTypeLSID){
+    public String wsdlParam2MobyParam(Element element, String paramName, String paramXSDType, String dataTypeLSID) 
+	throws Exception{
 	String[] dataTypeLSIDFields = dataTypeLSID.split(":");
 	if(dataTypeLSIDFields.length != 5 && dataTypeLSIDFields.length != 6 ||
 	   !dataTypeLSIDFields[0].equals("urn") || !dataTypeLSIDFields[1].equals("lsid") ||
@@ -219,11 +221,29 @@
 	    return paramName+":"+MobyTags.MOBYOBJECT+":"+dataTypeLSIDFields[4];
 	}
 	else{
-	    return paramName+":"+dataTypeLSIDFields[4];
+	    // Deal with the case where the output XSD data type is an array: 
+	    // implicitly make the return data type Collection(Thing)
+
+	    // See if the name is namespace qualified, and separate the local part if so
+	    String nsURI = "";
+	    if(paramXSDType.contains(":")){
+		String nsPrefix = paramXSDType.substring(0, paramXSDType.indexOf(":"));  //XML NS prefix
+		paramXSDType = paramXSDType.substring(paramXSDType.indexOf(":")+1); //local part
+		nsURI = element.lookupNamespaceURI(nsPrefix);  //prefix->URI
+	    }
+	    Element schemaDataTypeElement = getSchemaElement(element.getOwnerDocument(), nsURI, paramXSDType);	    
+	    if(getArrayType(schemaDataTypeElement) != null){
+		return paramName+":Collection("+dataTypeLSIDFields[4]+")";
+	    }
+	    else{
+		return paramName+":"+dataTypeLSIDFields[4];
+	    }
 	}
+	
     }
 
-    public String wsdlParam2MobySecondaryParam(String paramName, String paramXSDType, String dataTypeLSID, Element partElement) throws Exception{
+    public String wsdlParam2MobySecondaryParam(Element partElement, String paramName, 
+					       String paramXSDType, String dataTypeLSID) throws Exception{
 	String[] dataTypeLSIDFields = dataTypeLSID.split(":");
 	if(dataTypeLSIDFields.length != 5 && dataTypeLSIDFields.length != 6 ||
 	   !dataTypeLSIDFields[0].equals("urn") || !dataTypeLSIDFields[1].equals("lsid") ||
@@ -381,7 +401,7 @@
 	    throw new Exception("Could not find a message definition (" + targetMessageName + 
 				") for operation "+ opName);
 	}
-	// The lifting may be defijned at the "part" tag level, as it is for services
+	// The lifting may be defined at the "part" tag level, as it is for services
 	String schemaMapping = partElement.getAttributeNS(MobyPrefixResolver.SAWSDL_NAMESPACE, SAWSDL_OUTMAP_ATTR);
 	if(schemaMapping != null && schemaMapping.length() != 0){
 	    return new URL(schemaMapping);
@@ -403,105 +423,119 @@
 
 	// Now find the definition of the part's data type, and see if it has a schema lifting mapping
 	// Usually, <xsd:schema> -> <xsd:complexType name="partType"/>
-	NodeList schemaElements = wsdlRoot.getElementsByTagNameNS(MobyPrefixResolver.XSD_NAMESPACE, 
-								  "schema");
+	Element schemaDefElement = getSchemaElement(opElement.getOwnerDocument(), partTypeNamespaceURI, partType);
+
+	// If it's an XML Schema definition element with the same name as our part type, we're good to go...
+	// See if the SAWSDL lifting schema attribute is defined
+	schemaMapping = schemaDefElement.getAttributeNS(MobyPrefixResolver.SAWSDL_NAMESPACE, SAWSDL_OUTMAP_ATTR);
+	if(schemaMapping == null || schemaMapping.length() == 0){
+	    // As a last-ditch effort, if the data type is just an array of another datatype, 
+	    // look up the other data type to see if it has a lifting schema mapping, and
+	    // we will take care of the array iteration part opf the transformation
+	    String arrayType = getArrayType(schemaDefElement);
+	    if(arrayType == null){
+		throw new Exception("The definition of XML Schema type " + partType + " used as the output of " + 
+				    opName + " has no SAWSDL " + SAWSDL_OUTMAP_ATTR + " attribute defined, nor is" +
+				    "it simply an array of a type with a lifting schema");
+	    }
+
+	    // We're at the array's data type.  This is the last chance to find a schema lifting mapping
+	    Element sde = getSchemaElement(opElement.getOwnerDocument(), partTypeNamespaceURI, arrayType);
+	    schemaMapping = sde.getAttributeNS(MobyPrefixResolver.SAWSDL_NAMESPACE, SAWSDL_OUTMAP_ATTR);
+
+	    if(schemaMapping != null && schemaMapping.length() != 0){
+		// The ARRAY_SENTINEL as a ref part of the URL indicates the rule should be
+		// applied to each members of the incoming array, not the once to the whole array
+		if(lsidResolver.isLSID(schemaMapping)){
+		    return new URL(lsidResolver.resolveDataURL(schemaMapping).toString()+
+				   "#"+ARRAY_SENTINEL);
+		}
+		else{
+		    return new URL(schemaMapping+"#"+ARRAY_SENTINEL);
+		}
+	    }
+	    throw new Exception("Neither the array datatype ("+partType + ") nor the datatype " +
+				"it stores (" + arrayType + ") has a SAWSDL " + SAWSDL_OUTMAP_ATTR +
+				" attribute");
+	}
+	else{
+	    if(lsidResolver.isLSID(schemaMapping)){
+		return lsidResolver.resolveDataURL(schemaMapping);
+	    }
+	    else{
+		return new URL(schemaMapping);
+	    } 
+	}
+    }
+
+    /**
+     * @return the data type of the array, or null if the data type is not an array
+     */
+    protected String getArrayType(Element schemaDefElement){
+	// The XML must look something like:
+	//<xsd:complexType name="ArrayOfThing">
+	// <xsd:complexContent>
+	//  <xsd:restriction base="soapenc:Array">
+	//   <xsd:attribute ref="soapenc:arrayType" wsdl:arrayType="typens:Thing[]"/>
+	// </xsd:restriction></xsd:complexContent></xsd:complexType>
+	NodeList contentElements = schemaDefElement.getElementsByTagNameNS(MobyPrefixResolver.XSD_NAMESPACE, 
+									   "complexContent");
+	if(contentElements.getLength() == 1){
+	    NodeList restrictionElements = 
+		((Element) contentElements.item(0)).getElementsByTagNameNS(MobyPrefixResolver.XSD_NAMESPACE, 
+									   "restriction");
+	    if(restrictionElements.getLength() == 1){
+		NodeList attributeElements = ((Element) restrictionElements.item(0)).getElementsByTagNameNS(MobyPrefixResolver.XSD_NAMESPACE, 
+													    "attribute");
+		if(attributeElements.getLength() == 1){
+		    // NOTE: WSDL 1.1 only for now
+		    String arrayType = ((Element) attributeElements.item(0)).getAttributeNS(MobyPrefixResolver.WSDL_NAMESPACE, 
+											    "arrayType");
+		    if(arrayType.contains(":")){
+			arrayType = arrayType.substring(arrayType.indexOf(":")+1); //local part
+		    }
+		    if(arrayType.endsWith("[]")){
+			return arrayType.substring(0, arrayType.length()-2); // remove the array square brackets
+		    }
+		}
+	    }
+	}
+	return null;
+    }
+
+    /**
+     * Returns the XML DOM element containing the definition of an XML Schema data type, 
+     * unless that datatype or namespace doesn't exist, in which case an exception is thrown.
+     */
+    protected Element getSchemaElement(Document wsdlDoc, String nsUri, String name) throws Exception{
+	NodeList schemaElements = wsdlDoc.getDocumentElement().getElementsByTagNameNS(MobyPrefixResolver.XSD_NAMESPACE, 
+										      "schema");
+	if(schemaElements.getLength() == 0){
+	    throw new Exception("Could not find XML Schema type definition for " + name + 
+				", cannot find the schema section of the WSDL document");
+	}
+
 	for(int i = 0; i < schemaElements.getLength(); i++){
-	    if(!partTypeNamespaceURI.equals(((Element) schemaElements.item(i)).getAttribute("targetNamespace"))){
+	    if(!nsUri.equals(((Element) schemaElements.item(i)).getAttribute("targetNamespace"))){
 		continue; // only look as schema definitions in the correct namespace
 	    }
-
+	    
 	    NodeList schemaDefElements = ((Element) schemaElements.item(i)).getChildNodes();
 	    for(int j = 0; j < schemaDefElements.getLength(); j++){
-
 		if(!(schemaDefElements.item(j) instanceof Element)){
 		    continue;
 		}
-
-		Element schemaDefElement = (Element) schemaDefElements.item(j);
-		// If it's an XML Schema definition element with the same name as our part type, we're good to go...
-		if((MobyPrefixResolver.XSD_NAMESPACE.equals(schemaDefElement.getNamespaceURI())) &&
-		   partType.equals(schemaDefElement.getAttribute("name"))){
-		    // See if the SAWSDL lifting schema attribute is defined
-		    schemaMapping = partElement.getAttributeNS(MobyPrefixResolver.SAWSDL_NAMESPACE, SAWSDL_OUTMAP_ATTR);
-		    if(schemaMapping == null || schemaMapping.length() == 0){
-			// As a last-ditch effort, if the data type is just an array of another datatype, 
-			// look up the other data type to see if it has a lifting schema mapping, and
-			// we will take care of the array iteration part opf the transformation
-			// The XML must look something like:
-			//<xsd:complexType name="ArrayOfThing">
-			// <xsd:complexContent>
-			//  <xsd:restriction base="soapenc:Array">
-			//   <xsd:attribute ref="soapenc:arrayType" wsdl:arrayType="typens:Thing[]"/>
-			// </xsd:restriction></xsd:complexContent></xsd:complexType>
-			NodeList contentElements = schemaDefElement.getElementsByTagNameNS(MobyPrefixResolver.XSD_NAMESPACE, 
-											   "complexContent");
-			if(contentElements.getLength() == 1){
-			    NodeList restrictionElements = 
-				((Element) contentElements.item(0)).getElementsByTagNameNS(MobyPrefixResolver.XSD_NAMESPACE, 
-											   "restriction");
-			    if(restrictionElements.getLength() == 1){
-				NodeList attributeElements = ((Element) restrictionElements.item(0)).getElementsByTagNameNS(MobyPrefixResolver.XSD_NAMESPACE, 
-															    "attribute");
-				if(attributeElements.getLength() == 1){
-				    // NOTE: WSDL 1.1 only for now
-				    String arrayType = ((Element) attributeElements.item(0)).getAttributeNS(MobyPrefixResolver.WSDL_NAMESPACE, 
-													    "arrayType");
-				    if(arrayType.contains(":")){
-					arrayType = arrayType.substring(arrayType.indexOf(":")+1); //local part
-				    }
-				    if(!arrayType.endsWith("[]")){
-					throw new Exception("The definition of XML Schema type " + partType + 
-							    " used as the output of " + 
-							    opName + " has no SAWSDL " + SAWSDL_OUTMAP_ATTR + 
-							    " attribute defined, nor is" +
-							    "it simply an array of a type with a lifting schema");
-				    }
-				    arrayType = arrayType.substring(0, arrayType.length()-2); // remove the array square brackets
-				    for(int k = 0; k < schemaDefElements.getLength(); k++){
-					if(!(schemaDefElements.item(k) instanceof Element)){
-					    continue;
-					}
-					Element sde = (Element) schemaDefElements.item(k);
-					if((MobyPrefixResolver.XSD_NAMESPACE.equals(sde.getNamespaceURI())) &&
-					   arrayType.equals(sde.getAttribute("name"))){
-					    // We're at the array's data type.  This is the last chance to find a schema lifting mapping
-					    schemaMapping = sde.getAttributeNS(MobyPrefixResolver.SAWSDL_NAMESPACE, SAWSDL_OUTMAP_ATTR);
-					    if(schemaMapping != null && schemaMapping.length() != 0){
-						// The ARRAY_SENTINEL as a ref part of the URL indicates the rule should be
-						// applied to each members of the incoming array, not the once to the whole array
-						if(lsidResolver.isLSID(schemaMapping)){
-						    return new URL(lsidResolver.resolveDataURL(schemaMapping).toString()+
-								   "#"+ARRAY_SENTINEL);
-						}
-						else{
-						    return new URL(schemaMapping+"#"+ARRAY_SENTINEL);
-						}
-					    }
-					    throw new Exception("Neither the array datatype ("+partType + ") nor the datatype " +
-								"it stores (" + arrayType + ") has a SAWSDL " + SAWSDL_OUTMAP_ATTR +
-								" attribute");
-					}
-				    }
-				    throw new Exception("Could not find XML Schema type definition for " + arrayType);
-				}
-			    }
-			}
-
-			throw new Exception("The definition of XML Schema type " + partType + " used as the output of " + 
-					    opName + " has no SAWSDL " + SAWSDL_OUTMAP_ATTR + " attribute defined, nor is" +
-					    "it simply an array of a type with a lifting schema");
-		    }
-		    if(lsidResolver.isLSID(schemaMapping)){
-			return lsidResolver.resolveDataURL(schemaMapping);
-		    }
-		    else{
-			return new URL(schemaMapping);
-		    } 
+		Element e = (Element) schemaDefElements.item(j);
+		if((MobyPrefixResolver.XSD_NAMESPACE.equals(e.getNamespaceURI())) &&
+		   name.equals(e.getAttribute("name"))){
+		    return e;
 		}
 	    }
+	    throw new Exception("Could not find XML Schema type definition for " + name + ", namespace " +
+				nsUri + " exists, but schema element " + name + " does not");
 	}
-	throw new Exception("Could not find the data type definition for " + partType + " in the WSDL");
-	    
+	throw new Exception("Could not find XML Schema type definition for " + name + ", namespace " +
+			    nsUri + " does not exist");
     }
 
     protected String convertSourceToMobySecondaryValues(Source source, URL liftingSchema, boolean arrayRule) throws Exception{


From gordonp at dev.open-bio.org  Thu Jul  3 12:29:26 2008
From: gordonp at dev.open-bio.org (Paul Gordon)
Date: Thu, 3 Jul 2008 12:29:26 -0400
Subject: [MOBY-guts] biomoby commit
Message-ID: <200807031629.m63GTQD2024997@dev.open-bio.org>


gordonp
Thu Jul  3 12:29:26 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-serv24943/src/main/ca/ucalgary/services/util/test

Modified Files:
	WSDLConfigTestCase.java 
Log Message:
Refactored and added implicit collection support
moby-live/Java/src/main/ca/ucalgary/services/util/test WSDLConfigTestCase.java,1.2,1.3
===================================================================
RCS file: /home/repository/moby/moby-live/Java/src/main/ca/ucalgary/services/util/test/WSDLConfigTestCase.java,v
retrieving revision 1.2
retrieving revision 1.3
diff -u -r1.2 -r1.3
--- /home/repository/moby/moby-live/Java/src/main/ca/ucalgary/services/util/test/WSDLConfigTestCase.java	2008/06/30 17:42:29	1.2
+++ /home/repository/moby/moby-live/Java/src/main/ca/ucalgary/services/util/test/WSDLConfigTestCase.java	2008/07/03 16:29:26	1.3
@@ -39,7 +39,7 @@
 
     private final static int NUM_OUTPUTS = 1;
     private final static String OUTPUT_NAME1 = "return";
-    private final static String OUTPUT_TYPE1 = "return:GeneId";
+    private final static String OUTPUT_TYPE1 = "return:Collection(GeneId)";  //should be collection due to XSD array type of return
     private final static String OUTPUT_XSDTYPE1 = "typens:ArrayOfstring";
     private final static String OUTPUT_SCHEMA_MAPPING1 = "urn:lsid:bioxml.info:mobyLiftingSchemaMapping:string2GeneId";
 
@@ -247,8 +247,8 @@
     public static Test suite() {
 
 	TestSuite suite = new TestSuite();
- 	//suite.addTest(new WSDLConfigTestCase("testParsingBasic"));
- 	//suite.addTest(new WSDLConfigTestCase("testMetadata"));
+ 	suite.addTest(new WSDLConfigTestCase("testParsingBasic"));
+ 	suite.addTest(new WSDLConfigTestCase("testMetadata"));
  	suite.addTest(new WSDLConfigTestCase("testIOSpecs"));
 	
         return suite;


From kawas at dev.open-bio.org  Mon Jul  7 12:29:20 2008
From: kawas at dev.open-bio.org (Eddie Kawas)
Date: Mon, 7 Jul 2008 12:29:20 -0400
Subject: [MOBY-guts] biomoby commit
Message-ID: <200807071629.m67GTKCJ006453@dev.open-bio.org>


kawas
Mon Jul  7 12:29:19 EDT 2008
Update of /home/repository/moby/moby-live/Perl/MOBY-Server/lib/MOBY
In directory dev.open-bio.org:/tmp/cvs-serv6418/Perl/MOBY-Server/lib/MOBY

Modified Files:
	MOBY.pm 
Log Message:
mention that moby-s-caching.pl can be used to update the registry cache (if need be).
moby-live/Perl/MOBY-Server/lib/MOBY MOBY.pm,1.2,1.3
===================================================================
RCS file: /home/repository/moby/moby-live/Perl/MOBY-Server/lib/MOBY/MOBY.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/MOBY.pm	2008/03/20 17:35:42	1.2
+++ /home/repository/moby/moby-live/Perl/MOBY-Server/lib/MOBY/MOBY.pm	2008/07/07 16:29:19	1.3
@@ -10,7 +10,7 @@
 	$VERSION = '0.85';
 	@ISA       = qw{ Exporter };
 	@EXPORT    = qw{};
-	@EXPORT_OK = qw{};
+	@EXPORT_OK = qw{}; 
 }
 
 
@@ -54,7 +54,7 @@
 
 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!
+B<Important> if you are upgrading to newer versions, please make sure to remove any files that may be cached by this module! To help you do this, run the script B<moby-s-caching.pl>. For information on using B<moby-s-caching.pl>, use the -h option!
 
 =cut
 


From kawas at dev.open-bio.org  Mon Jul  7 12:29:39 2008
From: kawas at dev.open-bio.org (Eddie Kawas)
Date: Mon, 7 Jul 2008 12:29:39 -0400
Subject: [MOBY-guts] biomoby commit
Message-ID: <200807071629.m67GTdIM006493@dev.open-bio.org>


kawas
Mon Jul  7 12:29:39 EDT 2008
Update of /home/repository/moby/moby-live/Perl/MOBY-Server
In directory dev.open-bio.org:/tmp/cvs-serv6458/Perl/MOBY-Server

Modified Files:
	README 
Log Message:

moby-live/Perl/MOBY-Server README,1.1,1.2
===================================================================
RCS file: /home/repository/moby/moby-live/Perl/MOBY-Server/README,v
retrieving revision 1.1
retrieving revision 1.2
diff -u -r1.1 -r1.2
--- /home/repository/moby/moby-live/Perl/MOBY-Server/README	2008/02/21 00:21:28	1.1
+++ /home/repository/moby/moby-live/Perl/MOBY-Server/README	2008/07/07 16:29:39	1.2
@@ -1,4 +1,4 @@
-Perl MOBY version 0.04
+Perl MOBY version 1.05
 ======================
 
 This directory contains the Perl implementation of the MOBY


From kawas at dev.open-bio.org  Mon Jul  7 12:50:25 2008
From: kawas at dev.open-bio.org (Eddie Kawas)
Date: Mon, 7 Jul 2008 12:50:25 -0400
Subject: [MOBY-guts] biomoby commit
Message-ID: <200807071650.m67GoP0n006780@dev.open-bio.org>


kawas
Mon Jul  7 12:50:25 EDT 2008
Update of /home/repository/moby/moby-live/Perl/MOBY-Server/lib/MOBY
In directory dev.open-bio.org:/tmp/cvs-serv6721/Perl/MOBY-Server/lib/MOBY

Modified Files:
	secondary_input.pm collection_input.pm collection_output.pm 
	simple_input.pm service_type.pm simple_output.pm authority.pm 
Log Message:
fixed the perldoc for the synopsis and in some cases formatted the code.
moby-live/Perl/MOBY-Server/lib/MOBY secondary_input.pm,1.1,1.2 collection_input.pm,1.2,1.3 collection_output.pm,1.1,1.2 simple_input.pm,1.1,1.2 service_type.pm,1.1,1.2 simple_output.pm,1.1,1.2 authority.pm,1.1,1.2
===================================================================
RCS file: /home/repository/moby/moby-live/Perl/MOBY-Server/lib/MOBY/secondary_input.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/secondary_input.pm	2008/02/21 00:21:27	1.1
+++ /home/repository/moby/moby-live/Perl/MOBY-Server/lib/MOBY/secondary_input.pm	2008/07/07 16:50:25	1.2
@@ -12,14 +12,15 @@
 
 =head1 SYNOPSIS
 
-NON FUNCTIONAL AT THIS TIME
+ NON FUNCTIONAL AT THIS TIME
+
  use MOBY::secondary_input;
- my $Instance = MOBY::secondary_input->new(
-          object_type => "Sequence",
-          namespaces => ["genbank/gi", "genbank/Acc"],
-          article_name => "InputSequenceThingy",
- )
 
+ my $Instance = MOBY::secondary_input->new(
+ 	 object_type => "Sequence",
+	 namespaces => ["genbank/gi", "genbank/Acc"],
+	 article_name => "InputSequenceThingy",
+ );
 
 =cut
 
@@ -42,17 +43,17 @@
 	#ATTRIBUTES
 	my %_attr_data =    #     				DEFAULT    	ACCESSIBILITY
 	  (
-		secondary_input_id  => [ undef, 'read/write' ],
-		default_value       => [ undef, 'read/write' ],
-		maximum_value       => [ undef, 'read/write' ],
-		minimum_value       => [ undef, 'read/write' ],
-		enum_value          => [ undef, 'read/write' ],
-		datatype            => [ undef, 'read/write' ],
-		article_name        => [ undef, 'read/write' ],
-		service_instance_id => [ undef, 'read/write' ],
-		service_instance_lsid  => [ undef, 'read/write' ],
-		dbh                 => [ undef, 'read/write' ],
-		description		=> [undef, 'read/write'],
+		secondary_input_id    => [ undef, 'read/write' ],
+		default_value         => [ undef, 'read/write' ],
+		maximum_value         => [ undef, 'read/write' ],
+		minimum_value         => [ undef, 'read/write' ],
+		enum_value            => [ undef, 'read/write' ],
+		datatype              => [ undef, 'read/write' ],
+		article_name          => [ undef, 'read/write' ],
+		service_instance_id   => [ undef, 'read/write' ],
+		service_instance_lsid => [ undef, 'read/write' ],
+		dbh                   => [ undef, 'read/write' ],
+		description           => [ undef, 'read/write' ],
 	  );
 
 	#_____________________________________________________________
@@ -118,15 +119,17 @@
 	$CONFIG ||= MOBY::Config->new;    # exported by Config.pm
 	my $adaptor = $CONFIG->getDataAdaptor( datasource => 'mobycentral' );
 	my $dbh = $self->dbh;
-	my $insertid = $adaptor->insert_secondary_input(default_value => $self->default_value,
-							maximum_value => $self->maximum_value,
-							minimum_value => $self->minimum_value,
-							enum_value => $self->enum_value,
-							datatype => $self->datatype,
-							article_name => $self->article_name,
-							service_instance_lsid => $self->service_instance_lsid,
-							description => $self->description);
-	
+	my $insertid = $adaptor->insert_secondary_input(
+						  default_value         => $self->default_value,
+						  maximum_value         => $self->maximum_value,
+						  minimum_value         => $self->minimum_value,
+						  enum_value            => $self->enum_value,
+						  datatype              => $self->datatype,
+						  article_name          => $self->article_name,
+						  service_instance_lsid => $self->service_instance_lsid,
+						  description           => $self->description
+	);
+
 	return $insertid;
 }
 

===================================================================
RCS file: /home/repository/moby/moby-live/Perl/MOBY-Server/lib/MOBY/collection_input.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/collection_input.pm	2008/02/21 17:54:56	1.2
+++ /home/repository/moby/moby-live/Perl/MOBY-Server/lib/MOBY/collection_input.pm	2008/07/07 16:50:25	1.3
@@ -11,14 +11,14 @@
 
 =head1 SYNOPSIS
 
-NON FUNCTIONAL AT THIS TIME
+ #NON FUNCTIONAL AT THIS TIME
 
  use MOBY::collection_input;
  my $Instance = MOBY::collection_input->new(
           object_type => "Sequence",
           namespaces => ["genbank/gi", "genbank/Acc"],
           article_name => "InputSequenceThingy",
- )
+ );
 
 
 

===================================================================
RCS file: /home/repository/moby/moby-live/Perl/MOBY-Server/lib/MOBY/collection_output.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/collection_output.pm	2008/02/21 00:21:27	1.1
+++ /home/repository/moby/moby-live/Perl/MOBY-Server/lib/MOBY/collection_output.pm	2008/07/07 16:50:25	1.2
@@ -12,13 +12,14 @@
 
 =head1 SYNOPSIS
 
-NON FUNCTIONAL AT THIS TIME
+ #NON FUNCTIONAL AT THIS TIME
+ 
  use MOBY::collection_output;
  my $Instance = MOBY::collection_output->new(
           object_type => "Sequence",
           namespaces => ["genbank/gi", "genbank/Acc"],
           article_name => "InputSequenceThingy",
- )
+ );
 
 
 =cut

===================================================================
RCS file: /home/repository/moby/moby-live/Perl/MOBY-Server/lib/MOBY/simple_input.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/simple_input.pm	2008/02/21 00:21:27	1.1
+++ /home/repository/moby/moby-live/Perl/MOBY-Server/lib/MOBY/simple_input.pm	2008/07/07 16:50:25	1.2
@@ -12,14 +12,14 @@
 
 =head1 SYNOPSIS
 
-NON FUNCTIONAL AT THIS TIME
+ #NON FUNCTIONAL AT THIS TIME
 
  use MOBY::simple_input;
  my $Instance = MOBY::simple_input->new(
           object_type => "Sequence",
           namespaces => ["genbank/gi", "genbank/Acc"],
           article_name => "InputSequenceThingy",
- )
+ );
  print $Instance->simple_input_id;
  print $Instance->service_instance_id;
 

===================================================================
RCS file: /home/repository/moby/moby-live/Perl/MOBY-Server/lib/MOBY/service_type.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/service_type.pm	2008/02/21 00:21:27	1.1
+++ /home/repository/moby/moby-live/Perl/MOBY-Server/lib/MOBY/service_type.pm	2008/07/07 16:50:25	1.2
@@ -15,7 +15,7 @@
  my $Instance = MOBY::service_type->new(
       rdf_definition => "URI:LSID:www.biomoby.org:services:Blast",
       name "Blast",
- )
+ );
  print $Instance->service_type_id;
 
 

===================================================================
RCS file: /home/repository/moby/moby-live/Perl/MOBY-Server/lib/MOBY/simple_output.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/simple_output.pm	2008/02/21 00:21:27	1.1
+++ /home/repository/moby/moby-live/Perl/MOBY-Server/lib/MOBY/simple_output.pm	2008/07/07 16:50:25	1.2
@@ -12,13 +12,14 @@
 
 =head1 SYNOPSIS
 
-NON FUNCTIONAL AT THIS TIME
+ #NON FUNCTIONAL AT THIS TIME
+ 
  use MOBY::simple_output;
  my $Instance = MOBY::simple_output->new(
           object_type => "Sequence",
           namespaces => ["genbank/gi", "genbank/Acc"],
           article_name => "InputSequenceThingy",
- )
+ );
  print $Instance->simple_output_id;
  print $Instance->service_instance_id;
 

===================================================================
RCS file: /home/repository/moby/moby-live/Perl/MOBY-Server/lib/MOBY/authority.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/authority.pm	2008/02/21 00:21:27	1.1
+++ /home/repository/moby/moby-live/Perl/MOBY-Server/lib/MOBY/authority.pm	2008/07/07 16:50:25	1.2
@@ -18,7 +18,7 @@
        authority_uri => "ncbi.nlm.nih.gov",
        contact_email => "mr.BIG at ncbi.nlm.nih.gov",
 
- )
+ );
  print $Instance->authority_id;
 
 


From kawas at dev.open-bio.org  Mon Jul  7 13:59:42 2008
From: kawas at dev.open-bio.org (Eddie Kawas)
Date: Mon, 7 Jul 2008 13:59:42 -0400
Subject: [MOBY-guts] biomoby commit
Message-ID: <200807071759.m67HxgLJ006969@dev.open-bio.org>


kawas
Mon Jul  7 13:59:41 EDT 2008
Update of /home/repository/moby/moby-live/Perl/MOBY-Server/bin/scripts
In directory dev.open-bio.org:/tmp/cvs-serv6934/Perl/MOBY-Server/bin/scripts

Modified Files:
	moby-s-caching.pl 
Log Message:
added a brief blurb on using -E if there are issues running the script.
moby-live/Perl/MOBY-Server/bin/scripts moby-s-caching.pl,1.1,1.2
===================================================================
RCS file: /home/repository/moby/moby-live/Perl/MOBY-Server/bin/scripts/moby-s-caching.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-caching.pl	2008/07/02 20:27:00	1.1
+++ /home/repository/moby/moby-live/Perl/MOBY-Server/bin/scripts/moby-s-caching.pl	2008/07/07 17:59:41	1.2
@@ -38,6 +38,11 @@
 
 	-h          ..... shows this message
 
+	If you are running this as root and the user environment is not being set
+	appropriately (for one reason or another), try running the script like the
+	following:
+		sudo -E moby-s-caching.pl [rest of arguments]
+
     Good luck!
 
 


From kawas at dev.open-bio.org  Mon Jul  7 14:27:28 2008
From: kawas at dev.open-bio.org (Eddie Kawas)
Date: Mon, 7 Jul 2008 14:27:28 -0400
Subject: [MOBY-guts] biomoby commit
Message-ID: <200807071827.m67IRSiG007082@dev.open-bio.org>


kawas
Mon Jul  7 14:27:27 EDT 2008
Update of /home/repository/moby/moby-live/Perl/MOBY-Server
In directory dev.open-bio.org:/tmp/cvs-serv7047/Perl/MOBY-Server

Modified Files:
	MANIFEST 
Log Message:
removed the t/MOBY reference
moby-live/Perl/MOBY-Server MANIFEST,1.6,1.7
===================================================================
RCS file: /home/repository/moby/moby-live/Perl/MOBY-Server/MANIFEST,v
retrieving revision 1.6
retrieving revision 1.7
diff -u -r1.6 -r1.7
--- /home/repository/moby/moby-live/Perl/MOBY-Server/MANIFEST	2008/05/07 18:20:29	1.6
+++ /home/repository/moby/moby-live/Perl/MOBY-Server/MANIFEST	2008/07/07 18:27:27	1.7
@@ -118,6 +118,5 @@
 t/CommonSubs.t
 t/Config.t
 t/CrossReference.t
-t/MOBY.t
 t/mobycentral.config
 t/Template.t


From kawas at dev.open-bio.org  Mon Jul  7 14:32:25 2008
From: kawas at dev.open-bio.org (Eddie Kawas)
Date: Mon, 7 Jul 2008 14:32:25 -0400
Subject: [MOBY-guts] biomoby commit
Message-ID: <200807071832.m67IWP5Z007143@dev.open-bio.org>


kawas
Mon Jul  7 14:32:25 EDT 2008
Update of /home/repository/moby/moby-live/Perl/MOBY-Server
In directory dev.open-bio.org:/tmp/cvs-serv7108/Perl/MOBY-Server

Modified Files:
	MANIFEST 
Log Message:
added the caching script to the manifest
moby-live/Perl/MOBY-Server MANIFEST,1.7,1.8
===================================================================
RCS file: /home/repository/moby/moby-live/Perl/MOBY-Server/MANIFEST,v
retrieving revision 1.7
retrieving revision 1.8
diff -u -r1.7 -r1.8
--- /home/repository/moby/moby-live/Perl/MOBY-Server/MANIFEST	2008/07/07 18:27:27	1.7
+++ /home/repository/moby/moby-live/Perl/MOBY-Server/MANIFEST	2008/07/07 18:32:25	1.8
@@ -1,4 +1,5 @@
 bin/scripts/moby-s-install.pl
+bin/scripts/moby-s-caching.pl
 Changes
 drop_tables.sql
 inc/Module/AutoInstall.pm


From gordonp at dev.open-bio.org  Wed Jul 16 16:25:24 2008
From: gordonp at dev.open-bio.org (Paul Gordon)
Date: Wed, 16 Jul 2008 16:25:24 -0400
Subject: [MOBY-guts] biomoby commit
Message-ID: <200807162025.m6GKPO2W016146@dev.open-bio.org>


gordonp
Wed Jul 16 16:25:24 EDT 2008
Update of /home/repository/moby/moby-live/Java/src/main/org/biomoby/client
In directory dev.open-bio.org:/tmp/cvs-serv16110/src/main/org/biomoby/client

Modified Files:
	CentralDigestCachedImpl.java 
Log Message:
Added simpler c-tors
moby-live/Java/src/main/org/biomoby/client CentralDigestCachedImpl.java,1.32,1.33
===================================================================
RCS file: /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/CentralDigestCachedImpl.java,v
retrieving revision 1.32
retrieving revision 1.33
diff -u -r1.32 -r1.33
--- /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/CentralDigestCachedImpl.java	2008/02/28 18:47:32	1.32
+++ /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/CentralDigestCachedImpl.java	2008/07/16 20:25:24	1.33
@@ -74,6 +74,13 @@
     private int datatype_threshold ;
     private int service_threshold ;
     private int service_type_threshold ;
+
+    /**
+     * The same as calling CentralDigestCachedImpl(null)
+     */
+    public CentralDigestCachedImpl () throws MobyException{
+	this(null);
+    }
     
     /***************************************************************************
      * Create an instance that will access a default Moby registry and
@@ -85,6 +92,15 @@
     }
 
     /***************************************************************************
+     * Create an instance that will access a specific Moby registry and
+     * will cache results in the default cache directory.  <p>
+     **************************************************************************/
+    public CentralDigestCachedImpl (String endpoint, String namespace)
+	throws MobyException{
+	this (endpoint, namespace, null);
+    }
+
+    /***************************************************************************
      * Create an instance that will access a Moby registry defined by
      * its 'endpoint' and 'namespace', and will cache results in the
      * 'cacheDir' directory. Note that the same 'cacheDir' can be


From gordonp at dev.open-bio.org  Wed Jul 16 16:33:32 2008
From: gordonp at dev.open-bio.org (Paul Gordon)
Date: Wed, 16 Jul 2008 16:33:32 -0400
Subject: [MOBY-guts] biomoby commit
Message-ID: <200807162033.m6GKXWYb016192@dev.open-bio.org>


gordonp
Wed Jul 16 16:33:32 EDT 2008
Update of /home/repository/moby/moby-live/Java/src/main/org/biomoby/client
In directory dev.open-bio.org:/tmp/cvs-serv16156/src/main/org/biomoby/client

Modified Files:
	CentralImpl.java 
Log Message:
Added methods to get a CentralImpl from a Registry
moby-live/Java/src/main/org/biomoby/client CentralImpl.java,1.55,1.56
===================================================================
RCS file: /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/CentralImpl.java,v
retrieving revision 1.55
retrieving revision 1.56
diff -u -r1.55 -r1.56
--- /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/CentralImpl.java	2008/03/03 11:54:28	1.55
+++ /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/CentralImpl.java	2008/07/16 20:33:32	1.56
@@ -7,6 +7,7 @@
 
 package org.biomoby.client;
 
+import org.biomoby.registry.meta.Registry;
 import org.biomoby.shared.Central;
 import org.biomoby.shared.MobyData;
 import org.biomoby.shared.MobyDataType;
@@ -48,8 +49,11 @@
 import java.io.File;
 import java.io.FileOutputStream;
 import java.io.IOException;
+import java.io.InputStreamReader;
+import java.io.LineNumberReader;
 import java.io.PrintStream;
 import java.io.InputStream;
+import java.lang.reflect.Constructor;
 import java.net.HttpURLConnection;
 import java.net.MalformedURLException;
 import java.net.URL;
@@ -62,6 +66,7 @@
 import java.util.TreeMap;
 import java.util.Comparator;
 import java.util.zip.GZIPInputStream;
+import java.util.logging.*;
 
 /**
  * A default implementation of the
@@ -109,12 +114,25 @@
     private String uri;
     protected boolean debug = false;
 
+    /** Common central used to if getDefaultCentral() is called */
+    protected static Map<String,Central> defaultCentrals = new HashMap<String,Central>();
+
     /** Default location (endpoint) of a Moby registry. */
     public static final String DEFAULT_ENDPOINT = "http://moby.ucalgary.ca/moby/MOBY-Central.pl";
 
     /** Default namespace used by the contacted Moby registry. */
     public static final String DEFAULT_NAMESPACE = "http://moby.ucalgary.ca/MOBY/Central";
 
+    /**
+     * The META-INF resource file that will be checked to determine what
+     * default class should be instantiated in order to create a Central Implementation     
+     * when getDefaultCentral() is called.
+     */
+    public static final String CENTRAL_IMPL_RESOURCE_NAME = "org.biomoby.shared.CentralDefaultImpl";
+    /** The class to use for getDefaultCentral if all else fails */
+    public static final String DEFAULT_CENTRAL_IMPL_CLASSNAME = "org.biomoby.client.CentralDigestCachedImpl";
+    private static Logger logger = Logger.getLogger("org.biomoby.client.CentralImpl");
+
    /**
     * Thread local that gives each thread its own
     * DocumentBuilderFactory (since it is not thread-safe). Code taken
@@ -1836,6 +1854,80 @@
     private static String CHECKED_URI = null;
     
     /**
+     * Using this method to get a Central object will ensure that other parts of the org.biomoby.shared 
+     * class hierarchy that implicitly check the registry will use the same cache.  Otherwise, methods
+     * such as MobyNamespace.getNamespace() must be passed a Central object parameter as well.
+     *
+     * @return a CentralImpl using the default Central URI, and currently a class implementing a caching mechanism
+     */
+    public static Central getDefaultCentral() throws MobyException{
+	return getDefaultCentral(null);
+    }
+
+    public static Central getDefaultCentral(Registry reg) throws MobyException{
+	if(reg == null && defaultCentrals.containsKey("")){
+	    return defaultCentrals.get("");
+	}
+	else if(reg != null && defaultCentrals.containsKey(reg.getEndpoint())){
+	    return defaultCentrals.get(reg.getEndpoint());
+	}
+
+	String className = DEFAULT_CENTRAL_IMPL_CLASSNAME;
+	ClassLoader classLoader = Thread.currentThread().getContextClassLoader();
+	URL resURL = classLoader.getResource("META-INF/"+CENTRAL_IMPL_RESOURCE_NAME);
+	if(resURL != null){
+	    try{
+		LineNumberReader reader = new LineNumberReader(new InputStreamReader(resURL.openStream()));
+		for(String line = reader.readLine(); line != null; line = reader.readLine()){
+		    if(!line.trim().startsWith("#")){
+			className = line.trim();
+			break;
+		    }
+		}
+	    } catch(Exception e){
+		logger.log(Level.WARNING,
+			   "Error reading " + resURL,
+			   e);
+	    }
+	}
+	try{
+	    Class clazz = Class.forName(className);
+	    if(reg == null){  // should use default nullary c-tor
+		defaultCentrals.put("", (Central) clazz.newInstance());
+	    }
+	    else{  // should have (String endpoint, String namespace) c-tor
+		for(Constructor ctor: clazz.getDeclaredConstructors()){
+		    Class[] params = ctor.getParameterTypes();
+		    if(params.length == 2 && params[0].getName().equals("java.lang.String") &&
+		       params[1].getName().equals("java.lang.String") ){
+			defaultCentrals.put(reg.getEndpoint(),
+					    (Central) ctor.newInstance(reg.getEndpoint(), reg.getNamespace()));
+			break;
+		    }
+		}
+		if(!defaultCentrals.containsKey(reg.getEndpoint())){
+		    logger.log(Level.WARNING,
+			       "Could not find required (String endpoint, String namespace)" +
+			       "constructor for class " + className);
+		}
+	    }
+	} catch(Exception e){
+	    logger.log(Level.WARNING,
+		       "Could not load class " + className,
+		       e);
+	    if(reg == null){
+		defaultCentrals.put("", new CentralImpl());  //fallback to this class, no caching, etc.
+	    }
+	    else{
+		defaultCentrals.put(reg.getEndpoint(), 
+				    new CentralImpl(reg.getEndpoint(), reg.getNamespace()));
+	    }
+	}
+
+	return defaultCentrals.get(reg == null ? "" : reg.getEndpoint());
+    }
+
+    /**
      * 
      * @return a String representing the Default mobycentral endpoint. If the
      *         system property 'moby.check.default' exists and is set to true,


From gordonp at dev.open-bio.org  Wed Jul 16 16:34:07 2008
From: gordonp at dev.open-bio.org (Paul Gordon)
Date: Wed, 16 Jul 2008 16:34:07 -0400
Subject: [MOBY-guts] biomoby commit
Message-ID: <200807162034.m6GKY7Di016236@dev.open-bio.org>


gordonp
Wed Jul 16 16:34:07 EDT 2008
Update of /home/repository/moby/moby-live/Java/src/main/org/biomoby/shared
In directory dev.open-bio.org:/tmp/cvs-serv16200/src/main/org/biomoby/shared

Modified Files:
	MobyNamespace.java 
Log Message:
Updated getNamespace() to use the new caching mechanism
moby-live/Java/src/main/org/biomoby/shared MobyNamespace.java,1.11,1.12
===================================================================
RCS file: /home/repository/moby/moby-live/Java/src/main/org/biomoby/shared/MobyNamespace.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/MobyNamespace.java	2007/08/24 09:35:27	1.11
+++ /home/repository/moby/moby-live/Java/src/main/org/biomoby/shared/MobyNamespace.java	2008/07/16 20:34:07	1.12
@@ -13,6 +13,7 @@
 import org.biomoby.shared.extended.NamespaceParser;
 
 import java.util.*;
+import java.util.logging.*;
 import java.net.URL;
 
 /**
@@ -37,8 +38,8 @@
     protected String id = null;
     protected Registry registry; //provenance of the namspace definition
 
-    private static Map<String,MobyNamespace[]> namespacesMapBySynonym = new HashMap<String,MobyNamespace[]>();
-    private static Map<URL,MobyNamespace[]> namespacesMapByURL = new HashMap<URL,MobyNamespace[]>();
+    private static Logger logger = Logger.getLogger("org.biomoby.shared.MobyNamespace");
+    private static Map<String,MobyNamespace[]> namespacesMapByURL = new HashMap<String,MobyNamespace[]>();
 
     /**************************************************************************
      * Default constructor. Other characteristics are empty - which is usually
@@ -48,18 +49,6 @@
 	this.name = name;
     }
 
-    protected static String convertRegistryToNamespaceResourceURL(Registry reg) throws MobyException{
-	CentralImpl central = new CentralImpl(reg.getEndpoint());
-	MobyResourceRef[] resources = central.getResourceRefs();
-	for(MobyResourceRef resource: resources){
-	    if(Central.NAMESPACES_RESOURCE_NAME.equals(resource.getResourceName())){
-		return resource.getResourceLocation().toString();
-	    }
-	}
-	System.err.println("Error! Could not find the namespace resource from the registry " + reg.getSynonym());
-	return null;
-    }
-
     public Registry getRegistry(){
 	return registry;
     }
@@ -68,29 +57,6 @@
 	reg = registry;
     }
  
-    /**
-     * Particularly useful for loading namespace definitions from cached file, or
-     * refreshing an in-memory cache.
-     */
-    public static void loadNamespaces(URL namespaceDefURL, Registry reg) throws Exception{
-	synchronized(namespacesMapBySynonym){
-	    if(reg == null){
-		reg = RegistryCache.getDefaultRegistry();
-	    }
-	    
-	    MobyNamespace[] namespaces;
-	    NamespaceParser p = new NamespaceParser(namespaceDefURL);	    
-	    namespaces = p.getMobyNamespacesFromRDF();
-	    
-	    for(MobyNamespace namespace: namespaces){
-		namespace.setRegistry(reg);
-	    }
-	    
-	    namespacesMapBySynonym.put(reg.getSynonym(), namespaces);
-	    namespacesMapByURL.put(namespaceDefURL, namespaces);  
-	}
-    }
-
     public static MobyNamespace getNamespace(String ns){
 	return getNamespace(ns, null);
     }
@@ -100,31 +66,24 @@
 	    return null;
 	}
 	
-	if(reg == null){
-	    reg = RegistryCache.getDefaultRegistry();
-	}
-	if(reg == null){
-	    return null;
-	}
-
 	MobyNamespace[] namespaces = null;
-	// sync makes sure we don't fetch it if it's currently being loaded by loadNamespaces
-	synchronized(namespacesMapBySynonym){  
-	    namespaces = namespacesMapBySynonym.get(reg.getSynonym());
-	}
 
-	// This method has not been called yet in the JVM, populate the namespaces 
+	// This method has not been called yet in the JVM, populate the namespaces, 
+	// ensuring concurrent calls don't collide
 	synchronized(namespacesMapByURL){
+	    namespaces = namespacesMapByURL.get(reg == null ? "" : reg.getEndpoint());
 	    if(namespaces == null){
+		Central central = null;
+		try{
+		    central = CentralImpl.getDefaultCentral(reg);
+		} catch(MobyException e){
+		    logger.log(Level.WARNING,
+			       "Cannot find a default Moby Central implementation",
+			       e);
+		    return null;
+		}
 		try{
-		    URL namespaceDefURL = Registry.findResourceURL(reg, Central.NAMESPACES_RESOURCE_NAME);
-		    namespaces = namespacesMapByURL.get(namespaceDefURL);		    
-		    if(namespaces == null){
-			System.err.println("Fetching namespace ontology from "+namespaceDefURL);
-			loadNamespaces(namespaceDefURL, reg);
-			namespaces = namespacesMapByURL.get(namespaceDefURL);
-		    }
-		    
+		    namespaces = central.getFullNamespaces();
 		}
 		catch(Exception e){
 		    System.err.println("Cannot parse MOBY Namespace Ontology: " + e);


From gordonp at dev.open-bio.org  Wed Jul 16 16:34:54 2008
From: gordonp at dev.open-bio.org (Paul Gordon)
Date: Wed, 16 Jul 2008 16:34:54 -0400
Subject: [MOBY-guts] biomoby commit
Message-ID: <200807162034.m6GKYsRw016298@dev.open-bio.org>


gordonp
Wed Jul 16 16:34:54 EDT 2008
Update of /home/repository/moby/moby-live/Java/src/main/org/biomoby/shared/test
In directory dev.open-bio.org:/tmp/cvs-serv16266/src/main/org/biomoby/shared/test

Added Files:
	MobyNamespaceTestCase.java 
Log Message:
Test case for new ontology caching functionality
moby-live/Java/src/main/org/biomoby/shared/test MobyNamespaceTestCase.java,NONE,1.1

From gordonp at dev.open-bio.org  Wed Jul 16 16:37:21 2008
From: gordonp at dev.open-bio.org (Paul Gordon)
Date: Wed, 16 Jul 2008 16:37:21 -0400
Subject: [MOBY-guts] biomoby commit
Message-ID: <200807162037.m6GKbLpZ016408@dev.open-bio.org>


gordonp
Wed Jul 16 16:37:21 EDT 2008
Update of /home/repository/moby/moby-live/Java/src/main/ca/ucalgary/seahawk/gui
In directory dev.open-bio.org:/tmp/cvs-serv16372/src/main/ca/ucalgary/seahawk/gui

Modified Files:
	MobyContentGUI.java 
Log Message:
Got rid of explicit namespace pre-loading, since new caching mechanism is being used
moby-live/Java/src/main/ca/ucalgary/seahawk/gui MobyContentGUI.java,1.16,1.17
===================================================================
RCS file: /home/repository/moby/moby-live/Java/src/main/ca/ucalgary/seahawk/gui/MobyContentGUI.java,v
retrieving revision 1.16
retrieving revision 1.17
diff -u -r1.16 -r1.17
--- /home/repository/moby/moby-live/Java/src/main/ca/ucalgary/seahawk/gui/MobyContentGUI.java	2008/01/30 00:04:56	1.16
+++ /home/repository/moby/moby-live/Java/src/main/ca/ucalgary/seahawk/gui/MobyContentGUI.java	2008/07/16 20:37:21	1.17
@@ -900,20 +900,10 @@
 	final long allowedAgeMillis = (long) SeahawkOptions.getCacheExpiry()*60*60*1000; // hours to milliseconds
 	RegistryCache.deleteExpiredCacheFiles(allowedAgeMillis);
 
+	// TODO: deal with CentralImpl.getDefaultCentral()
+
 	// Redirect the registry endpoints to local cache files if available
 	// preferredRegistry and/or dataDefURL may be null, if not cached, but that's okay to pass around
-	new Thread(){
-	    public void run(){
-		try{
-		    MobyNamespace.loadNamespaces(RegistryCache.cacheRegistryOntology(preferredRegistry, 
-										     Central.NAMESPACES_RESOURCE_NAME,
-										     allowedAgeMillis).toURI().toURL(),
-						 preferredRegistry);
-		}catch(Exception e){
-		    e.printStackTrace();
-		}
-	    }}.start();
-
 	// The following command will cache all data type definitions for this session
 	new Thread(){
 	    public void run(){
@@ -938,10 +928,6 @@
 		    e.printStackTrace();
 		}
 	    }}.start();
-	// And the service definitions
-	//new Thread(){
-	//	public void run(){org.biomoby.shared.MobyService.getService("","");}
-	//    }.start();
     }
 
     /**


From kawas at dev.open-bio.org  Tue Jul 22 11:49:41 2008
From: kawas at dev.open-bio.org (Eddie Kawas)
Date: Tue, 22 Jul 2008 11:49:41 -0400
Subject: [MOBY-guts] biomoby commit
Message-ID: <200807221549.m6MFnfQI007297@dev.open-bio.org>


kawas
Tue Jul 22 11:49:41 EDT 2008
Update of /home/repository/moby/moby-live/Java/src/main/org/biomoby/shared/extended
In directory dev.open-bio.org:/tmp/cvs-serv7261/src/main/org/biomoby/shared/extended

Modified Files:
	NamespaceParser.java 
Log Message:
fixed a spelling error
moby-live/Java/src/main/org/biomoby/shared/extended NamespaceParser.java,1.11,1.12
===================================================================
RCS file: /home/repository/moby/moby-live/Java/src/main/org/biomoby/shared/extended/NamespaceParser.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/extended/NamespaceParser.java	2008/02/28 17:00:12	1.11
+++ /home/repository/moby/moby-live/Java/src/main/org/biomoby/shared/extended/NamespaceParser.java	2008/07/22 15:49:41	1.12
@@ -164,7 +164,7 @@
 			if (uri.indexOf("#") > 0)
 				name = uri.substring(uri.indexOf("#")+1);
 			else if(uri.lastIndexOf("/Namespaces/") > 0) {
-			    name = uri.substring(uri.lastIndexOf("/Namepaces/")+"/Namespaces/".length());
+			    name = uri.substring(uri.lastIndexOf("/Namespaces/")+"/Namespaces/".length());
 			}
 			
 			MobyNamespace namespace = new MobyNamespace(name);


From kawas at dev.open-bio.org  Tue Jul 22 11:54:30 2008
From: kawas at dev.open-bio.org (Eddie Kawas)
Date: Tue, 22 Jul 2008 11:54:30 -0400
Subject: [MOBY-guts] biomoby commit
Message-ID: <200807221554.m6MFsUKb007412@dev.open-bio.org>


kawas
Tue Jul 22 11:54:29 EDT 2008
Update of /home/repository/moby/moby-live/Perl/MOBY-Server/lib/MOBY/RDF/Ontologies
In directory dev.open-bio.org:/tmp/cvs-serv7377/Perl/MOBY-Server/lib/MOBY/RDF/Ontologies

Modified Files:
	Namespaces.pm 
Log Message:
temporary rollback
moby-live/Perl/MOBY-Server/lib/MOBY/RDF/Ontologies Namespaces.pm,1.5,1.6
===================================================================
RCS file: /home/repository/moby/moby-live/Perl/MOBY-Server/lib/MOBY/RDF/Ontologies/Namespaces.pm,v
retrieving revision 1.5
retrieving revision 1.6
diff -u -r1.5 -r1.6
--- /home/repository/moby/moby-live/Perl/MOBY-Server/lib/MOBY/RDF/Ontologies/Namespaces.pm	2008/06/19 21:49:01	1.5
+++ /home/repository/moby/moby-live/Perl/MOBY-Server/lib/MOBY/RDF/Ontologies/Namespaces.pm	2008/07/22 15:54:29	1.6
@@ -76,8 +76,8 @@
 	
 	# save some information retrieved from mobycentral.config
     my $CONF  = MOBY::Config->new;
-	$self->{uri}       = $CONF->{mobynamespace}->{resourceURL} || 'http://biomoby.org/RESOURCES/MOBY-S/Namespaces/';
-	$self->{uri} = $self->{uri} . "/" unless $self->{uri} =~ m/^.*(\/{1})$/;
+	$self->{uri}       = $CONF->{mobynamespace}->{resourceURL} || 'http://biomoby.org/RESOURCES/MOBY-S/Namespaces#';
+	$self->{uri} = $self->{uri} . "#" unless $self->{uri} =~ m/^.*(\#{1})$/;
 
 	$self->{query_all} = <<END;
 SELECT namespace_type, description, namespace_lsid, authority, contact_email FROM namespace ORDER BY namespace_type asc


From senger at dev.open-bio.org  Wed Jul 23 05:32:35 2008
From: senger at dev.open-bio.org (Martin Senger)
Date: Wed, 23 Jul 2008 05:32:35 -0400
Subject: [MOBY-guts] biomoby commit
Message-ID: <200807230932.m6N9WZWr009126@dev.open-bio.org>


senger
Wed Jul 23 05:32:35 EDT 2008
Update of /home/repository/moby/moby-live/Java/docs
In directory dev.open-bio.org:/tmp/cvs-serv9107/docs

Modified Files:
	ChangeLog 
Log Message:
deployed jMoby 1.1.0
moby-live/Java/docs ChangeLog,1.90,1.91
===================================================================
RCS file: /home/repository/moby/moby-live/Java/docs/ChangeLog,v
retrieving revision 1.90
retrieving revision 1.91
diff -u -r1.90 -r1.91
--- /home/repository/moby/moby-live/Java/docs/ChangeLog	2008/05/22 17:09:30	1.90
+++ /home/repository/moby/moby-live/Java/docs/ChangeLog	2008/07/23 09:32:35	1.91
@@ -1,3 +1,7 @@
+2008-07-23  Martin Senger  <martin.senger&#64;gmail.com>
+
+	* Version 1.1.0 released
+
 2008-05-23  Martin Senger  <senger at ebi.ac.uk>
 
 	* Fixed: registering data types from an XML file, in Dashboard


From senger at dev.open-bio.org  Wed Jul 23 05:32:36 2008
From: senger at dev.open-bio.org (Martin Senger)
Date: Wed, 23 Jul 2008 05:32:36 -0400
Subject: [MOBY-guts] biomoby commit
Message-ID: <200807230932.m6N9WaJo009144@dev.open-bio.org>


senger
Wed Jul 23 05:32:35 EDT 2008
Update of /home/repository/moby/moby-live/Java/xmls
In directory dev.open-bio.org:/tmp/cvs-serv9107/xmls

Modified Files:
	project.pom 
Log Message:
deployed jMoby 1.1.0
moby-live/Java/xmls project.pom,1.10,1.11
===================================================================
RCS file: /home/repository/moby/moby-live/Java/xmls/project.pom,v
retrieving revision 1.10
retrieving revision 1.11
diff -u -r1.10 -r1.11
--- /home/repository/moby/moby-live/Java/xmls/project.pom	2008/03/28 11:19:02	1.10
+++ /home/repository/moby/moby-live/Java/xmls/project.pom	2008/07/23 09:32:35	1.11
@@ -2,7 +2,7 @@
   <modelVersion>4.0.0</modelVersion>
   <groupId>org.biomoby</groupId>
   <artifactId>jmoby</artifactId>
-  <version>1.0.0</version>
+  <version>1.1.0</version>
   <name>jMoby</name>
   <description>
 A sub-project of the BioMoby project. It aims to develop tools in Java for BioMoby.


From kawas at dev.open-bio.org  Wed Jul  2 20:27:01 2008
From: kawas at dev.open-bio.org (Eddie Kawas)
Date: Wed, 2 Jul 2008 16:27:01 -0400
Subject: [MOBY-guts] biomoby commit
Message-ID: <200807022027.m62KR1eD021387@dev.open-bio.org>


kawas
Wed Jul  2 16:27:00 EDT 2008
Update of /home/repository/moby/moby-live/Perl/MOBY-Server/bin/scripts
In directory dev.open-bio.org:/tmp/cvs-serv21356/Perl/MOBY-Server/bin/scripts

Added Files:
	moby-s-caching.pl 
Log Message:
initial commit of a script that helps build the rdf cache for the registry
moby-live/Perl/MOBY-Server/bin/scripts moby-s-caching.pl,NONE,1.1


From kawas at dev.open-bio.org  Wed Jul  2 20:49:24 2008
From: kawas at dev.open-bio.org (Eddie Kawas)
Date: Wed, 2 Jul 2008 16:49:24 -0400
Subject: [MOBY-guts] biomoby commit
Message-ID: <200807022049.m62KnOZ5021488@dev.open-bio.org>


kawas
Wed Jul  2 16:49:23 EDT 2008
Update of /home/repository/moby/moby-live/Perl/MOBY-Server/bin/scripts
In directory dev.open-bio.org:/tmp/cvs-serv21453/Perl/MOBY-Server/bin/scripts

Modified Files:
	moby-s-install.pl 
Log Message:
when checking for root, we ignore windows.
moby-live/Perl/MOBY-Server/bin/scripts moby-s-install.pl,1.11,1.12
===================================================================
RCS file: /home/repository/moby/moby-live/Perl/MOBY-Server/bin/scripts/moby-s-install.pl,v
retrieving revision 1.11
retrieving revision 1.12
diff -u -r1.11 -r1.12
--- /home/repository/moby/moby-live/Perl/MOBY-Server/bin/scripts/moby-s-install.pl	2008/06/20 19:56:37	1.11
+++ /home/repository/moby/moby-live/Perl/MOBY-Server/bin/scripts/moby-s-install.pl	2008/07/02 20:49:23	1.12
@@ -490,6 +490,8 @@
 }
 
 sub check_root {
+	# assume that windows has no security preventing the copying of files
+	return if MSWIN;
     unless (getpwuid($<) eq 'root') { 
 	print STDOUT <<EOT;
 



From kawas at dev.open-bio.org  Wed Jul  2 20:49:44 2008
From: kawas at dev.open-bio.org (Eddie Kawas)
Date: Wed, 2 Jul 2008 16:49:44 -0400
Subject: [MOBY-guts] biomoby commit
Message-ID: <200807022049.m62KniUQ021528@dev.open-bio.org>


kawas
Wed Jul  2 16:49:44 EDT 2008
Update of /home/repository/moby/moby-live/Perl/MOBY-Server
In directory dev.open-bio.org:/tmp/cvs-serv21493/Perl/MOBY-Server

Modified Files:
	Makefile.PL 
Log Message:
added the caching script to the makefile
moby-live/Perl/MOBY-Server Makefile.PL,1.7,1.8
===================================================================
RCS file: /home/repository/moby/moby-live/Perl/MOBY-Server/Makefile.PL,v
retrieving revision 1.7
retrieving revision 1.8
diff -u -r1.7 -r1.8
--- /home/repository/moby/moby-live/Perl/MOBY-Server/Makefile.PL	2008/06/05 14:13:52	1.7
+++ /home/repository/moby/moby-live/Perl/MOBY-Server/Makefile.PL	2008/07/02 20:49:44	1.8
@@ -106,6 +106,7 @@
 	no_index 'directory' => 'bin/scripts';
 
 	install_script 'bin/scripts/moby-s-install.pl';
+	install_script 'bin/scripts/moby-s-caching.pl';
 
 	install_share 'share';
 



From kawas at dev.open-bio.org  Wed Jul  2 20:51:33 2008
From: kawas at dev.open-bio.org (Eddie Kawas)
Date: Wed, 2 Jul 2008 16:51:33 -0400
Subject: [MOBY-guts] biomoby commit
Message-ID: <200807022051.m62KpXZ2021568@dev.open-bio.org>


kawas
Wed Jul  2 16:51:33 EDT 2008
Update of /home/repository/moby/moby-live/Perl/MOBY-Server
In directory dev.open-bio.org:/tmp/cvs-serv21533/Perl/MOBY-Server

Modified Files:
	Changes 
Log Message:

moby-live/Perl/MOBY-Server Changes,1.10,1.11
===================================================================
RCS file: /home/repository/moby/moby-live/Perl/MOBY-Server/Changes,v
retrieving revision 1.10
retrieving revision 1.11
diff -u -r1.10 -r1.11
--- /home/repository/moby/moby-live/Perl/MOBY-Server/Changes	2008/06/20 19:58:22	1.10
+++ /home/repository/moby/moby-live/Perl/MOBY-Server/Changes	2008/07/02 20:51:33	1.11
@@ -47,6 +47,11 @@
 	- fixed the installer script, username/password, root/root was hardcoded
 	- fixed a bug in MOBY::dbConfig that caused certain parameters to be
 	  ignored in the configuration file if a field was empty.
+	- added a caching script to be used by registry providers needing to
+	  update their cache. 
+	  For more information, run: 
+	      moby-s-caching.pl -h
+	  
 
 1.04
 	- fixed bug in MOBY::Client::Central::DUMP that resulted



From gordonp at dev.open-bio.org  Thu Jul  3 16:29:26 2008
From: gordonp at dev.open-bio.org (Paul Gordon)
Date: Thu, 3 Jul 2008 12:29:26 -0400
Subject: [MOBY-guts] biomoby commit
Message-ID: <200807031629.m63GTQdO024979@dev.open-bio.org>


gordonp
Thu Jul  3 12:29:25 EDT 2008
Update of /home/repository/moby/moby-live/Java/src/main/ca/ucalgary/services/util
In directory dev.open-bio.org:/tmp/cvs-serv24943/src/main/ca/ucalgary/services/util

Modified Files:
	WSDLConfig.java 
Log Message:
Refactored and added implicit collection support
moby-live/Java/src/main/ca/ucalgary/services/util WSDLConfig.java,1.3,1.4
===================================================================
RCS file: /home/repository/moby/moby-live/Java/src/main/ca/ucalgary/services/util/WSDLConfig.java,v
retrieving revision 1.3
retrieving revision 1.4
diff -u -r1.3 -r1.4
--- /home/repository/moby/moby-live/Java/src/main/ca/ucalgary/services/util/WSDLConfig.java	2008/06/30 17:42:29	1.3
+++ /home/repository/moby/moby-live/Java/src/main/ca/ucalgary/services/util/WSDLConfig.java	2008/07/03 16:29:25	1.4
@@ -157,6 +157,7 @@
 	    }
 	    String modelReference = partElement.getAttributeNS(MobyPrefixResolver.SAWSDL_NAMESPACE, SAWSDL_MODEL_ATTR);
 	    if(modelReference == null || modelReference.length() == 0){
+		// TODO deal with schema-only level SAWSDL annotation
 		throw new Exception("Part element " + partName + " of WSDL message " + 
 				    messageName + " has no SAWSDL " + SAWSDL_MODEL_ATTR + " attribute defined");
 	    }
@@ -167,10 +168,10 @@
 		    throw new Exception("Part element " + partName + " of WSDL message " + 
 					messageName + " has no SAWSDL " + SAWSDL_INMAP_ATTR + " attribute defined");
 		}
-		String mobyParam = wsdlParam2MobyParam(partName, partType, modelReference);
+		String mobyParam = wsdlParam2MobyParam(partElement, partName, partType, modelReference);
 		if(mobyParam == null){
 		    // Check if it's a secondary
-		    mobyParam = wsdlParam2MobySecondaryParam(partName, partType, modelReference, partElement);
+		    mobyParam = wsdlParam2MobySecondaryParam(partElement, partName, partType, modelReference);
 		    if(mobyParam == null){
 			throw new Exception("The LSID '" + modelReference + 
 					    "' is not a properly formed Moby primary or secondary param LSID as required");
@@ -189,7 +190,7 @@
 		    throw new Exception("Part element " + partName + " of WSDL message " + 
 					messageName + " has no SAWSDL " + SAWSDL_OUTMAP_ATTR + " attribute defined");
 		}
-		outputs.put(partName, wsdlParam2MobyParam(partName, partType, modelReference));
+		outputs.put(partName, wsdlParam2MobyParam(partElement, partName, partType, modelReference));
 		outputTypes.put(partName, partType);
 		outputMappings.put(partName, schemaMapping);	    
 	    }
@@ -207,7 +208,8 @@
 	}
     }
 
-    public String wsdlParam2MobyParam(String paramName, String paramXSDType, String dataTypeLSID){
+    public String wsdlParam2MobyParam(Element element, String paramName, String paramXSDType, String dataTypeLSID) 
+	throws Exception{
 	String[] dataTypeLSIDFields = dataTypeLSID.split(":");
 	if(dataTypeLSIDFields.length != 5 && dataTypeLSIDFields.length != 6 ||
 	   !dataTypeLSIDFields[0].equals("urn") || !dataTypeLSIDFields[1].equals("lsid") ||
@@ -219,11 +221,29 @@
 	    return paramName+":"+MobyTags.MOBYOBJECT+":"+dataTypeLSIDFields[4];
 	}
 	else{
-	    return paramName+":"+dataTypeLSIDFields[4];
+	    // Deal with the case where the output XSD data type is an array: 
+	    // implicitly make the return data type Collection(Thing)
+
+	    // See if the name is namespace qualified, and separate the local part if so
+	    String nsURI = "";
+	    if(paramXSDType.contains(":")){
+		String nsPrefix = paramXSDType.substring(0, paramXSDType.indexOf(":"));  //XML NS prefix
+		paramXSDType = paramXSDType.substring(paramXSDType.indexOf(":")+1); //local part
+		nsURI = element.lookupNamespaceURI(nsPrefix);  //prefix->URI
+	    }
+	    Element schemaDataTypeElement = getSchemaElement(element.getOwnerDocument(), nsURI, paramXSDType);	    
+	    if(getArrayType(schemaDataTypeElement) != null){
+		return paramName+":Collection("+dataTypeLSIDFields[4]+")";
+	    }
+	    else{
+		return paramName+":"+dataTypeLSIDFields[4];
+	    }
 	}
+	
     }
 
-    public String wsdlParam2MobySecondaryParam(String paramName, String paramXSDType, String dataTypeLSID, Element partElement) throws Exception{
+    public String wsdlParam2MobySecondaryParam(Element partElement, String paramName, 
+					       String paramXSDType, String dataTypeLSID) throws Exception{
 	String[] dataTypeLSIDFields = dataTypeLSID.split(":");
 	if(dataTypeLSIDFields.length != 5 && dataTypeLSIDFields.length != 6 ||
 	   !dataTypeLSIDFields[0].equals("urn") || !dataTypeLSIDFields[1].equals("lsid") ||
@@ -381,7 +401,7 @@
 	    throw new Exception("Could not find a message definition (" + targetMessageName + 
 				") for operation "+ opName);
 	}
-	// The lifting may be defijned at the "part" tag level, as it is for services
+	// The lifting may be defined at the "part" tag level, as it is for services
 	String schemaMapping = partElement.getAttributeNS(MobyPrefixResolver.SAWSDL_NAMESPACE, SAWSDL_OUTMAP_ATTR);
 	if(schemaMapping != null && schemaMapping.length() != 0){
 	    return new URL(schemaMapping);
@@ -403,105 +423,119 @@
 
 	// Now find the definition of the part's data type, and see if it has a schema lifting mapping
 	// Usually, <xsd:schema> -> <xsd:complexType name="partType"/>
-	NodeList schemaElements = wsdlRoot.getElementsByTagNameNS(MobyPrefixResolver.XSD_NAMESPACE, 
-								  "schema");
+	Element schemaDefElement = getSchemaElement(opElement.getOwnerDocument(), partTypeNamespaceURI, partType);
+
+	// If it's an XML Schema definition element with the same name as our part type, we're good to go...
+	// See if the SAWSDL lifting schema attribute is defined
+	schemaMapping = schemaDefElement.getAttributeNS(MobyPrefixResolver.SAWSDL_NAMESPACE, SAWSDL_OUTMAP_ATTR);
+	if(schemaMapping == null || schemaMapping.length() == 0){
+	    // As a last-ditch effort, if the data type is just an array of another datatype, 
+	    // look up the other data type to see if it has a lifting schema mapping, and
+	    // we will take care of the array iteration part opf the transformation
+	    String arrayType = getArrayType(schemaDefElement);
+	    if(arrayType == null){
+		throw new Exception("The definition of XML Schema type " + partType + " used as the output of " + 
+				    opName + " has no SAWSDL " + SAWSDL_OUTMAP_ATTR + " attribute defined, nor is" +
+				    "it simply an array of a type with a lifting schema");
+	    }
+
+	    // We're at the array's data type.  This is the last chance to find a schema lifting mapping
+	    Element sde = getSchemaElement(opElement.getOwnerDocument(), partTypeNamespaceURI, arrayType);
+	    schemaMapping = sde.getAttributeNS(MobyPrefixResolver.SAWSDL_NAMESPACE, SAWSDL_OUTMAP_ATTR);
+
+	    if(schemaMapping != null && schemaMapping.length() != 0){
+		// The ARRAY_SENTINEL as a ref part of the URL indicates the rule should be
+		// applied to each members of the incoming array, not the once to the whole array
+		if(lsidResolver.isLSID(schemaMapping)){
+		    return new URL(lsidResolver.resolveDataURL(schemaMapping).toString()+
+				   "#"+ARRAY_SENTINEL);
+		}
+		else{
+		    return new URL(schemaMapping+"#"+ARRAY_SENTINEL);
+		}
+	    }
+	    throw new Exception("Neither the array datatype ("+partType + ") nor the datatype " +
+				"it stores (" + arrayType + ") has a SAWSDL " + SAWSDL_OUTMAP_ATTR +
+				" attribute");
+	}
+	else{
+	    if(lsidResolver.isLSID(schemaMapping)){
+		return lsidResolver.resolveDataURL(schemaMapping);
+	    }
+	    else{
+		return new URL(schemaMapping);
+	    } 
+	}
+    }
+
+    /**
+     * @return the data type of the array, or null if the data type is not an array
+     */
+    protected String getArrayType(Element schemaDefElement){
+	// The XML must look something like:
+	//<xsd:complexType name="ArrayOfThing">
+	// <xsd:complexContent>
+	//  <xsd:restriction base="soapenc:Array">
+	//   <xsd:attribute ref="soapenc:arrayType" wsdl:arrayType="typens:Thing[]"/>
+	// </xsd:restriction></xsd:complexContent></xsd:complexType>
+	NodeList contentElements = schemaDefElement.getElementsByTagNameNS(MobyPrefixResolver.XSD_NAMESPACE, 
+									   "complexContent");
+	if(contentElements.getLength() == 1){
+	    NodeList restrictionElements = 
+		((Element) contentElements.item(0)).getElementsByTagNameNS(MobyPrefixResolver.XSD_NAMESPACE, 
+									   "restriction");
+	    if(restrictionElements.getLength() == 1){
+		NodeList attributeElements = ((Element) restrictionElements.item(0)).getElementsByTagNameNS(MobyPrefixResolver.XSD_NAMESPACE, 
+													    "attribute");
+		if(attributeElements.getLength() == 1){
+		    // NOTE: WSDL 1.1 only for now
+		    String arrayType = ((Element) attributeElements.item(0)).getAttributeNS(MobyPrefixResolver.WSDL_NAMESPACE, 
+											    "arrayType");
+		    if(arrayType.contains(":")){
+			arrayType = arrayType.substring(arrayType.indexOf(":")+1); //local part
+		    }
+		    if(arrayType.endsWith("[]")){
+			return arrayType.substring(0, arrayType.length()-2); // remove the array square brackets
+		    }
+		}
+	    }
+	}
+	return null;
+    }
+
+    /**
+     * Returns the XML DOM element containing the definition of an XML Schema data type, 
+     * unless that datatype or namespace doesn't exist, in which case an exception is thrown.
+     */
+    protected Element getSchemaElement(Document wsdlDoc, String nsUri, String name) throws Exception{
+	NodeList schemaElements = wsdlDoc.getDocumentElement().getElementsByTagNameNS(MobyPrefixResolver.XSD_NAMESPACE, 
+										      "schema");
+	if(schemaElements.getLength() == 0){
+	    throw new Exception("Could not find XML Schema type definition for " + name + 
+				", cannot find the schema section of the WSDL document");
+	}
+
 	for(int i = 0; i < schemaElements.getLength(); i++){
-	    if(!partTypeNamespaceURI.equals(((Element) schemaElements.item(i)).getAttribute("targetNamespace"))){
+	    if(!nsUri.equals(((Element) schemaElements.item(i)).getAttribute("targetNamespace"))){
 		continue; // only look as schema definitions in the correct namespace
 	    }
-
+	    
 	    NodeList schemaDefElements = ((Element) schemaElements.item(i)).getChildNodes();
 	    for(int j = 0; j < schemaDefElements.getLength(); j++){
-
 		if(!(schemaDefElements.item(j) instanceof Element)){
 		    continue;
 		}
-
-		Element schemaDefElement = (Element) schemaDefElements.item(j);
-		// If it's an XML Schema definition element with the same name as our part type, we're good to go...
-		if((MobyPrefixResolver.XSD_NAMESPACE.equals(schemaDefElement.getNamespaceURI())) &&
-		   partType.equals(schemaDefElement.getAttribute("name"))){
-		    // See if the SAWSDL lifting schema attribute is defined
-		    schemaMapping = partElement.getAttributeNS(MobyPrefixResolver.SAWSDL_NAMESPACE, SAWSDL_OUTMAP_ATTR);
-		    if(schemaMapping == null || schemaMapping.length() == 0){
-			// As a last-ditch effort, if the data type is just an array of another datatype, 
-			// look up the other data type to see if it has a lifting schema mapping, and
-			// we will take care of the array iteration part opf the transformation
-			// The XML must look something like:
-			//<xsd:complexType name="ArrayOfThing">
-			// <xsd:complexContent>
-			//  <xsd:restriction base="soapenc:Array">
-			//   <xsd:attribute ref="soapenc:arrayType" wsdl:arrayType="typens:Thing[]"/>
-			// </xsd:restriction></xsd:complexContent></xsd:complexType>
-			NodeList contentElements = schemaDefElement.getElementsByTagNameNS(MobyPrefixResolver.XSD_NAMESPACE, 
-											   "complexContent");
-			if(contentElements.getLength() == 1){
-			    NodeList restrictionElements = 
-				((Element) contentElements.item(0)).getElementsByTagNameNS(MobyPrefixResolver.XSD_NAMESPACE, 
-											   "restriction");
-			    if(restrictionElements.getLength() == 1){
-				NodeList attributeElements = ((Element) restrictionElements.item(0)).getElementsByTagNameNS(MobyPrefixResolver.XSD_NAMESPACE, 
-															    "attribute");
-				if(attributeElements.getLength() == 1){
-				    // NOTE: WSDL 1.1 only for now
-				    String arrayType = ((Element) attributeElements.item(0)).getAttributeNS(MobyPrefixResolver.WSDL_NAMESPACE, 
-													    "arrayType");
-				    if(arrayType.contains(":")){
-					arrayType = arrayType.substring(arrayType.indexOf(":")+1); //local part
-				    }
-				    if(!arrayType.endsWith("[]")){
-					throw new Exception("The definition of XML Schema type " + partType + 
-							    " used as the output of " + 
-							    opName + " has no SAWSDL " + SAWSDL_OUTMAP_ATTR + 
-							    " attribute defined, nor is" +
-							    "it simply an array of a type with a lifting schema");
-				    }
-				    arrayType = arrayType.substring(0, arrayType.length()-2); // remove the array square brackets
-				    for(int k = 0; k < schemaDefElements.getLength(); k++){
-					if(!(schemaDefElements.item(k) instanceof Element)){
-					    continue;
-					}
-					Element sde = (Element) schemaDefElements.item(k);
-					if((MobyPrefixResolver.XSD_NAMESPACE.equals(sde.getNamespaceURI())) &&
-					   arrayType.equals(sde.getAttribute("name"))){
-					    // We're at the array's data type.  This is the last chance to find a schema lifting mapping
-					    schemaMapping = sde.getAttributeNS(MobyPrefixResolver.SAWSDL_NAMESPACE, SAWSDL_OUTMAP_ATTR);
-					    if(schemaMapping != null && schemaMapping.length() != 0){
-						// The ARRAY_SENTINEL as a ref part of the URL indicates the rule should be
-						// applied to each members of the incoming array, not the once to the whole array
-						if(lsidResolver.isLSID(schemaMapping)){
-						    return new URL(lsidResolver.resolveDataURL(schemaMapping).toString()+
-								   "#"+ARRAY_SENTINEL);
-						}
-						else{
-						    return new URL(schemaMapping+"#"+ARRAY_SENTINEL);
-						}
-					    }
-					    throw new Exception("Neither the array datatype ("+partType + ") nor the datatype " +
-								"it stores (" + arrayType + ") has a SAWSDL " + SAWSDL_OUTMAP_ATTR +
-								" attribute");
-					}
-				    }
-				    throw new Exception("Could not find XML Schema type definition for " + arrayType);
-				}
-			    }
-			}
-
-			throw new Exception("The definition of XML Schema type " + partType + " used as the output of " + 
-					    opName + " has no SAWSDL " + SAWSDL_OUTMAP_ATTR + " attribute defined, nor is" +
-					    "it simply an array of a type with a lifting schema");
-		    }
-		    if(lsidResolver.isLSID(schemaMapping)){
-			return lsidResolver.resolveDataURL(schemaMapping);
-		    }
-		    else{
-			return new URL(schemaMapping);
-		    } 
+		Element e = (Element) schemaDefElements.item(j);
+		if((MobyPrefixResolver.XSD_NAMESPACE.equals(e.getNamespaceURI())) &&
+		   name.equals(e.getAttribute("name"))){
+		    return e;
 		}
 	    }
+	    throw new Exception("Could not find XML Schema type definition for " + name + ", namespace " +
+				nsUri + " exists, but schema element " + name + " does not");
 	}
-	throw new Exception("Could not find the data type definition for " + partType + " in the WSDL");
-	    
+	throw new Exception("Could not find XML Schema type definition for " + name + ", namespace " +
+			    nsUri + " does not exist");
     }
 
     protected String convertSourceToMobySecondaryValues(Source source, URL liftingSchema, boolean arrayRule) throws Exception{



From gordonp at dev.open-bio.org  Thu Jul  3 16:29:26 2008
From: gordonp at dev.open-bio.org (Paul Gordon)
Date: Thu, 3 Jul 2008 12:29:26 -0400
Subject: [MOBY-guts] biomoby commit
Message-ID: <200807031629.m63GTQD2024997@dev.open-bio.org>


gordonp
Thu Jul  3 12:29:26 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-serv24943/src/main/ca/ucalgary/services/util/test

Modified Files:
	WSDLConfigTestCase.java 
Log Message:
Refactored and added implicit collection support
moby-live/Java/src/main/ca/ucalgary/services/util/test WSDLConfigTestCase.java,1.2,1.3
===================================================================
RCS file: /home/repository/moby/moby-live/Java/src/main/ca/ucalgary/services/util/test/WSDLConfigTestCase.java,v
retrieving revision 1.2
retrieving revision 1.3
diff -u -r1.2 -r1.3
--- /home/repository/moby/moby-live/Java/src/main/ca/ucalgary/services/util/test/WSDLConfigTestCase.java	2008/06/30 17:42:29	1.2
+++ /home/repository/moby/moby-live/Java/src/main/ca/ucalgary/services/util/test/WSDLConfigTestCase.java	2008/07/03 16:29:26	1.3
@@ -39,7 +39,7 @@
 
     private final static int NUM_OUTPUTS = 1;
     private final static String OUTPUT_NAME1 = "return";
-    private final static String OUTPUT_TYPE1 = "return:GeneId";
+    private final static String OUTPUT_TYPE1 = "return:Collection(GeneId)";  //should be collection due to XSD array type of return
     private final static String OUTPUT_XSDTYPE1 = "typens:ArrayOfstring";
     private final static String OUTPUT_SCHEMA_MAPPING1 = "urn:lsid:bioxml.info:mobyLiftingSchemaMapping:string2GeneId";
 
@@ -247,8 +247,8 @@
     public static Test suite() {
 
 	TestSuite suite = new TestSuite();
- 	//suite.addTest(new WSDLConfigTestCase("testParsingBasic"));
- 	//suite.addTest(new WSDLConfigTestCase("testMetadata"));
+ 	suite.addTest(new WSDLConfigTestCase("testParsingBasic"));
+ 	suite.addTest(new WSDLConfigTestCase("testMetadata"));
  	suite.addTest(new WSDLConfigTestCase("testIOSpecs"));
 	
         return suite;



From kawas at dev.open-bio.org  Mon Jul  7 16:29:20 2008
From: kawas at dev.open-bio.org (Eddie Kawas)
Date: Mon, 7 Jul 2008 12:29:20 -0400
Subject: [MOBY-guts] biomoby commit
Message-ID: <200807071629.m67GTKCJ006453@dev.open-bio.org>


kawas
Mon Jul  7 12:29:19 EDT 2008
Update of /home/repository/moby/moby-live/Perl/MOBY-Server/lib/MOBY
In directory dev.open-bio.org:/tmp/cvs-serv6418/Perl/MOBY-Server/lib/MOBY

Modified Files:
	MOBY.pm 
Log Message:
mention that moby-s-caching.pl can be used to update the registry cache (if need be).
moby-live/Perl/MOBY-Server/lib/MOBY MOBY.pm,1.2,1.3
===================================================================
RCS file: /home/repository/moby/moby-live/Perl/MOBY-Server/lib/MOBY/MOBY.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/MOBY.pm	2008/03/20 17:35:42	1.2
+++ /home/repository/moby/moby-live/Perl/MOBY-Server/lib/MOBY/MOBY.pm	2008/07/07 16:29:19	1.3
@@ -10,7 +10,7 @@
 	$VERSION = '0.85';
 	@ISA       = qw{ Exporter };
 	@EXPORT    = qw{};
-	@EXPORT_OK = qw{};
+	@EXPORT_OK = qw{}; 
 }
 
 
@@ -54,7 +54,7 @@
 
 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!
+B<Important> if you are upgrading to newer versions, please make sure to remove any files that may be cached by this module! To help you do this, run the script B<moby-s-caching.pl>. For information on using B<moby-s-caching.pl>, use the -h option!
 
 =cut
 



From kawas at dev.open-bio.org  Mon Jul  7 16:29:39 2008
From: kawas at dev.open-bio.org (Eddie Kawas)
Date: Mon, 7 Jul 2008 12:29:39 -0400
Subject: [MOBY-guts] biomoby commit
Message-ID: <200807071629.m67GTdIM006493@dev.open-bio.org>


kawas
Mon Jul  7 12:29:39 EDT 2008
Update of /home/repository/moby/moby-live/Perl/MOBY-Server
In directory dev.open-bio.org:/tmp/cvs-serv6458/Perl/MOBY-Server

Modified Files:
	README 
Log Message:

moby-live/Perl/MOBY-Server README,1.1,1.2
===================================================================
RCS file: /home/repository/moby/moby-live/Perl/MOBY-Server/README,v
retrieving revision 1.1
retrieving revision 1.2
diff -u -r1.1 -r1.2
--- /home/repository/moby/moby-live/Perl/MOBY-Server/README	2008/02/21 00:21:28	1.1
+++ /home/repository/moby/moby-live/Perl/MOBY-Server/README	2008/07/07 16:29:39	1.2
@@ -1,4 +1,4 @@
-Perl MOBY version 0.04
+Perl MOBY version 1.05
 ======================
 
 This directory contains the Perl implementation of the MOBY



From kawas at dev.open-bio.org  Mon Jul  7 16:50:25 2008
From: kawas at dev.open-bio.org (Eddie Kawas)
Date: Mon, 7 Jul 2008 12:50:25 -0400
Subject: [MOBY-guts] biomoby commit
Message-ID: <200807071650.m67GoP0n006780@dev.open-bio.org>


kawas
Mon Jul  7 12:50:25 EDT 2008
Update of /home/repository/moby/moby-live/Perl/MOBY-Server/lib/MOBY
In directory dev.open-bio.org:/tmp/cvs-serv6721/Perl/MOBY-Server/lib/MOBY

Modified Files:
	secondary_input.pm collection_input.pm collection_output.pm 
	simple_input.pm service_type.pm simple_output.pm authority.pm 
Log Message:
fixed the perldoc for the synopsis and in some cases formatted the code.
moby-live/Perl/MOBY-Server/lib/MOBY secondary_input.pm,1.1,1.2 collection_input.pm,1.2,1.3 collection_output.pm,1.1,1.2 simple_input.pm,1.1,1.2 service_type.pm,1.1,1.2 simple_output.pm,1.1,1.2 authority.pm,1.1,1.2
===================================================================
RCS file: /home/repository/moby/moby-live/Perl/MOBY-Server/lib/MOBY/secondary_input.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/secondary_input.pm	2008/02/21 00:21:27	1.1
+++ /home/repository/moby/moby-live/Perl/MOBY-Server/lib/MOBY/secondary_input.pm	2008/07/07 16:50:25	1.2
@@ -12,14 +12,15 @@
 
 =head1 SYNOPSIS
 
-NON FUNCTIONAL AT THIS TIME
+ NON FUNCTIONAL AT THIS TIME
+
  use MOBY::secondary_input;
- my $Instance = MOBY::secondary_input->new(
-          object_type => "Sequence",
-          namespaces => ["genbank/gi", "genbank/Acc"],
-          article_name => "InputSequenceThingy",
- )
 
+ my $Instance = MOBY::secondary_input->new(
+ 	 object_type => "Sequence",
+	 namespaces => ["genbank/gi", "genbank/Acc"],
+	 article_name => "InputSequenceThingy",
+ );
 
 =cut
 
@@ -42,17 +43,17 @@
 	#ATTRIBUTES
 	my %_attr_data =    #     				DEFAULT    	ACCESSIBILITY
 	  (
-		secondary_input_id  => [ undef, 'read/write' ],
-		default_value       => [ undef, 'read/write' ],
-		maximum_value       => [ undef, 'read/write' ],
-		minimum_value       => [ undef, 'read/write' ],
-		enum_value          => [ undef, 'read/write' ],
-		datatype            => [ undef, 'read/write' ],
-		article_name        => [ undef, 'read/write' ],
-		service_instance_id => [ undef, 'read/write' ],
-		service_instance_lsid  => [ undef, 'read/write' ],
-		dbh                 => [ undef, 'read/write' ],
-		description		=> [undef, 'read/write'],
+		secondary_input_id    => [ undef, 'read/write' ],
+		default_value         => [ undef, 'read/write' ],
+		maximum_value         => [ undef, 'read/write' ],
+		minimum_value         => [ undef, 'read/write' ],
+		enum_value            => [ undef, 'read/write' ],
+		datatype              => [ undef, 'read/write' ],
+		article_name          => [ undef, 'read/write' ],
+		service_instance_id   => [ undef, 'read/write' ],
+		service_instance_lsid => [ undef, 'read/write' ],
+		dbh                   => [ undef, 'read/write' ],
+		description           => [ undef, 'read/write' ],
 	  );
 
 	#_____________________________________________________________
@@ -118,15 +119,17 @@
 	$CONFIG ||= MOBY::Config->new;    # exported by Config.pm
 	my $adaptor = $CONFIG->getDataAdaptor( datasource => 'mobycentral' );
 	my $dbh = $self->dbh;
-	my $insertid = $adaptor->insert_secondary_input(default_value => $self->default_value,
-							maximum_value => $self->maximum_value,
-							minimum_value => $self->minimum_value,
-							enum_value => $self->enum_value,
-							datatype => $self->datatype,
-							article_name => $self->article_name,
-							service_instance_lsid => $self->service_instance_lsid,
-							description => $self->description);
-	
+	my $insertid = $adaptor->insert_secondary_input(
+						  default_value         => $self->default_value,
+						  maximum_value         => $self->maximum_value,
+						  minimum_value         => $self->minimum_value,
+						  enum_value            => $self->enum_value,
+						  datatype              => $self->datatype,
+						  article_name          => $self->article_name,
+						  service_instance_lsid => $self->service_instance_lsid,
+						  description           => $self->description
+	);
+
 	return $insertid;
 }
 

===================================================================
RCS file: /home/repository/moby/moby-live/Perl/MOBY-Server/lib/MOBY/collection_input.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/collection_input.pm	2008/02/21 17:54:56	1.2
+++ /home/repository/moby/moby-live/Perl/MOBY-Server/lib/MOBY/collection_input.pm	2008/07/07 16:50:25	1.3
@@ -11,14 +11,14 @@
 
 =head1 SYNOPSIS
 
-NON FUNCTIONAL AT THIS TIME
+ #NON FUNCTIONAL AT THIS TIME
 
  use MOBY::collection_input;
  my $Instance = MOBY::collection_input->new(
           object_type => "Sequence",
           namespaces => ["genbank/gi", "genbank/Acc"],
           article_name => "InputSequenceThingy",
- )
+ );
 
 
 

===================================================================
RCS file: /home/repository/moby/moby-live/Perl/MOBY-Server/lib/MOBY/collection_output.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/collection_output.pm	2008/02/21 00:21:27	1.1
+++ /home/repository/moby/moby-live/Perl/MOBY-Server/lib/MOBY/collection_output.pm	2008/07/07 16:50:25	1.2
@@ -12,13 +12,14 @@
 
 =head1 SYNOPSIS
 
-NON FUNCTIONAL AT THIS TIME
+ #NON FUNCTIONAL AT THIS TIME
+ 
  use MOBY::collection_output;
  my $Instance = MOBY::collection_output->new(
           object_type => "Sequence",
           namespaces => ["genbank/gi", "genbank/Acc"],
           article_name => "InputSequenceThingy",
- )
+ );
 
 
 =cut

===================================================================
RCS file: /home/repository/moby/moby-live/Perl/MOBY-Server/lib/MOBY/simple_input.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/simple_input.pm	2008/02/21 00:21:27	1.1
+++ /home/repository/moby/moby-live/Perl/MOBY-Server/lib/MOBY/simple_input.pm	2008/07/07 16:50:25	1.2
@@ -12,14 +12,14 @@
 
 =head1 SYNOPSIS
 
-NON FUNCTIONAL AT THIS TIME
+ #NON FUNCTIONAL AT THIS TIME
 
  use MOBY::simple_input;
  my $Instance = MOBY::simple_input->new(
           object_type => "Sequence",
           namespaces => ["genbank/gi", "genbank/Acc"],
           article_name => "InputSequenceThingy",
- )
+ );
  print $Instance->simple_input_id;
  print $Instance->service_instance_id;
 

===================================================================
RCS file: /home/repository/moby/moby-live/Perl/MOBY-Server/lib/MOBY/service_type.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/service_type.pm	2008/02/21 00:21:27	1.1
+++ /home/repository/moby/moby-live/Perl/MOBY-Server/lib/MOBY/service_type.pm	2008/07/07 16:50:25	1.2
@@ -15,7 +15,7 @@
  my $Instance = MOBY::service_type->new(
       rdf_definition => "URI:LSID:www.biomoby.org:services:Blast",
       name "Blast",
- )
+ );
  print $Instance->service_type_id;
 
 

===================================================================
RCS file: /home/repository/moby/moby-live/Perl/MOBY-Server/lib/MOBY/simple_output.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/simple_output.pm	2008/02/21 00:21:27	1.1
+++ /home/repository/moby/moby-live/Perl/MOBY-Server/lib/MOBY/simple_output.pm	2008/07/07 16:50:25	1.2
@@ -12,13 +12,14 @@
 
 =head1 SYNOPSIS
 
-NON FUNCTIONAL AT THIS TIME
+ #NON FUNCTIONAL AT THIS TIME
+ 
  use MOBY::simple_output;
  my $Instance = MOBY::simple_output->new(
           object_type => "Sequence",
           namespaces => ["genbank/gi", "genbank/Acc"],
           article_name => "InputSequenceThingy",
- )
+ );
  print $Instance->simple_output_id;
  print $Instance->service_instance_id;
 

===================================================================
RCS file: /home/repository/moby/moby-live/Perl/MOBY-Server/lib/MOBY/authority.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/authority.pm	2008/02/21 00:21:27	1.1
+++ /home/repository/moby/moby-live/Perl/MOBY-Server/lib/MOBY/authority.pm	2008/07/07 16:50:25	1.2
@@ -18,7 +18,7 @@
        authority_uri => "ncbi.nlm.nih.gov",
        contact_email => "mr.BIG at ncbi.nlm.nih.gov",
 
- )
+ );
  print $Instance->authority_id;
 
 



From kawas at dev.open-bio.org  Mon Jul  7 17:59:42 2008
From: kawas at dev.open-bio.org (Eddie Kawas)
Date: Mon, 7 Jul 2008 13:59:42 -0400
Subject: [MOBY-guts] biomoby commit
Message-ID: <200807071759.m67HxgLJ006969@dev.open-bio.org>


kawas
Mon Jul  7 13:59:41 EDT 2008
Update of /home/repository/moby/moby-live/Perl/MOBY-Server/bin/scripts
In directory dev.open-bio.org:/tmp/cvs-serv6934/Perl/MOBY-Server/bin/scripts

Modified Files:
	moby-s-caching.pl 
Log Message:
added a brief blurb on using -E if there are issues running the script.
moby-live/Perl/MOBY-Server/bin/scripts moby-s-caching.pl,1.1,1.2
===================================================================
RCS file: /home/repository/moby/moby-live/Perl/MOBY-Server/bin/scripts/moby-s-caching.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-caching.pl	2008/07/02 20:27:00	1.1
+++ /home/repository/moby/moby-live/Perl/MOBY-Server/bin/scripts/moby-s-caching.pl	2008/07/07 17:59:41	1.2
@@ -38,6 +38,11 @@
 
 	-h          ..... shows this message
 
+	If you are running this as root and the user environment is not being set
+	appropriately (for one reason or another), try running the script like the
+	following:
+		sudo -E moby-s-caching.pl [rest of arguments]
+
     Good luck!
 
 



From kawas at dev.open-bio.org  Mon Jul  7 18:27:28 2008
From: kawas at dev.open-bio.org (Eddie Kawas)
Date: Mon, 7 Jul 2008 14:27:28 -0400
Subject: [MOBY-guts] biomoby commit
Message-ID: <200807071827.m67IRSiG007082@dev.open-bio.org>


kawas
Mon Jul  7 14:27:27 EDT 2008
Update of /home/repository/moby/moby-live/Perl/MOBY-Server
In directory dev.open-bio.org:/tmp/cvs-serv7047/Perl/MOBY-Server

Modified Files:
	MANIFEST 
Log Message:
removed the t/MOBY reference
moby-live/Perl/MOBY-Server MANIFEST,1.6,1.7
===================================================================
RCS file: /home/repository/moby/moby-live/Perl/MOBY-Server/MANIFEST,v
retrieving revision 1.6
retrieving revision 1.7
diff -u -r1.6 -r1.7
--- /home/repository/moby/moby-live/Perl/MOBY-Server/MANIFEST	2008/05/07 18:20:29	1.6
+++ /home/repository/moby/moby-live/Perl/MOBY-Server/MANIFEST	2008/07/07 18:27:27	1.7
@@ -118,6 +118,5 @@
 t/CommonSubs.t
 t/Config.t
 t/CrossReference.t
-t/MOBY.t
 t/mobycentral.config
 t/Template.t



From kawas at dev.open-bio.org  Mon Jul  7 18:32:25 2008
From: kawas at dev.open-bio.org (Eddie Kawas)
Date: Mon, 7 Jul 2008 14:32:25 -0400
Subject: [MOBY-guts] biomoby commit
Message-ID: <200807071832.m67IWP5Z007143@dev.open-bio.org>


kawas
Mon Jul  7 14:32:25 EDT 2008
Update of /home/repository/moby/moby-live/Perl/MOBY-Server
In directory dev.open-bio.org:/tmp/cvs-serv7108/Perl/MOBY-Server

Modified Files:
	MANIFEST 
Log Message:
added the caching script to the manifest
moby-live/Perl/MOBY-Server MANIFEST,1.7,1.8
===================================================================
RCS file: /home/repository/moby/moby-live/Perl/MOBY-Server/MANIFEST,v
retrieving revision 1.7
retrieving revision 1.8
diff -u -r1.7 -r1.8
--- /home/repository/moby/moby-live/Perl/MOBY-Server/MANIFEST	2008/07/07 18:27:27	1.7
+++ /home/repository/moby/moby-live/Perl/MOBY-Server/MANIFEST	2008/07/07 18:32:25	1.8
@@ -1,4 +1,5 @@
 bin/scripts/moby-s-install.pl
+bin/scripts/moby-s-caching.pl
 Changes
 drop_tables.sql
 inc/Module/AutoInstall.pm



From gordonp at dev.open-bio.org  Wed Jul 16 20:25:24 2008
From: gordonp at dev.open-bio.org (Paul Gordon)
Date: Wed, 16 Jul 2008 16:25:24 -0400
Subject: [MOBY-guts] biomoby commit
Message-ID: <200807162025.m6GKPO2W016146@dev.open-bio.org>


gordonp
Wed Jul 16 16:25:24 EDT 2008
Update of /home/repository/moby/moby-live/Java/src/main/org/biomoby/client
In directory dev.open-bio.org:/tmp/cvs-serv16110/src/main/org/biomoby/client

Modified Files:
	CentralDigestCachedImpl.java 
Log Message:
Added simpler c-tors
moby-live/Java/src/main/org/biomoby/client CentralDigestCachedImpl.java,1.32,1.33
===================================================================
RCS file: /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/CentralDigestCachedImpl.java,v
retrieving revision 1.32
retrieving revision 1.33
diff -u -r1.32 -r1.33
--- /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/CentralDigestCachedImpl.java	2008/02/28 18:47:32	1.32
+++ /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/CentralDigestCachedImpl.java	2008/07/16 20:25:24	1.33
@@ -74,6 +74,13 @@
     private int datatype_threshold ;
     private int service_threshold ;
     private int service_type_threshold ;
+
+    /**
+     * The same as calling CentralDigestCachedImpl(null)
+     */
+    public CentralDigestCachedImpl () throws MobyException{
+	this(null);
+    }
     
     /***************************************************************************
      * Create an instance that will access a default Moby registry and
@@ -85,6 +92,15 @@
     }
 
     /***************************************************************************
+     * Create an instance that will access a specific Moby registry and
+     * will cache results in the default cache directory.  <p>
+     **************************************************************************/
+    public CentralDigestCachedImpl (String endpoint, String namespace)
+	throws MobyException{
+	this (endpoint, namespace, null);
+    }
+
+    /***************************************************************************
      * Create an instance that will access a Moby registry defined by
      * its 'endpoint' and 'namespace', and will cache results in the
      * 'cacheDir' directory. Note that the same 'cacheDir' can be



From gordonp at dev.open-bio.org  Wed Jul 16 20:33:32 2008
From: gordonp at dev.open-bio.org (Paul Gordon)
Date: Wed, 16 Jul 2008 16:33:32 -0400
Subject: [MOBY-guts] biomoby commit
Message-ID: <200807162033.m6GKXWYb016192@dev.open-bio.org>


gordonp
Wed Jul 16 16:33:32 EDT 2008
Update of /home/repository/moby/moby-live/Java/src/main/org/biomoby/client
In directory dev.open-bio.org:/tmp/cvs-serv16156/src/main/org/biomoby/client

Modified Files:
	CentralImpl.java 
Log Message:
Added methods to get a CentralImpl from a Registry
moby-live/Java/src/main/org/biomoby/client CentralImpl.java,1.55,1.56
===================================================================
RCS file: /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/CentralImpl.java,v
retrieving revision 1.55
retrieving revision 1.56
diff -u -r1.55 -r1.56
--- /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/CentralImpl.java	2008/03/03 11:54:28	1.55
+++ /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/CentralImpl.java	2008/07/16 20:33:32	1.56
@@ -7,6 +7,7 @@
 
 package org.biomoby.client;
 
+import org.biomoby.registry.meta.Registry;
 import org.biomoby.shared.Central;
 import org.biomoby.shared.MobyData;
 import org.biomoby.shared.MobyDataType;
@@ -48,8 +49,11 @@
 import java.io.File;
 import java.io.FileOutputStream;
 import java.io.IOException;
+import java.io.InputStreamReader;
+import java.io.LineNumberReader;
 import java.io.PrintStream;
 import java.io.InputStream;
+import java.lang.reflect.Constructor;
 import java.net.HttpURLConnection;
 import java.net.MalformedURLException;
 import java.net.URL;
@@ -62,6 +66,7 @@
 import java.util.TreeMap;
 import java.util.Comparator;
 import java.util.zip.GZIPInputStream;
+import java.util.logging.*;
 
 /**
  * A default implementation of the
@@ -109,12 +114,25 @@
     private String uri;
     protected boolean debug = false;
 
+    /** Common central used to if getDefaultCentral() is called */
+    protected static Map<String,Central> defaultCentrals = new HashMap<String,Central>();
+
     /** Default location (endpoint) of a Moby registry. */
     public static final String DEFAULT_ENDPOINT = "http://moby.ucalgary.ca/moby/MOBY-Central.pl";
 
     /** Default namespace used by the contacted Moby registry. */
     public static final String DEFAULT_NAMESPACE = "http://moby.ucalgary.ca/MOBY/Central";
 
+    /**
+     * The META-INF resource file that will be checked to determine what
+     * default class should be instantiated in order to create a Central Implementation     
+     * when getDefaultCentral() is called.
+     */
+    public static final String CENTRAL_IMPL_RESOURCE_NAME = "org.biomoby.shared.CentralDefaultImpl";
+    /** The class to use for getDefaultCentral if all else fails */
+    public static final String DEFAULT_CENTRAL_IMPL_CLASSNAME = "org.biomoby.client.CentralDigestCachedImpl";
+    private static Logger logger = Logger.getLogger("org.biomoby.client.CentralImpl");
+
    /**
     * Thread local that gives each thread its own
     * DocumentBuilderFactory (since it is not thread-safe). Code taken
@@ -1836,6 +1854,80 @@
     private static String CHECKED_URI = null;
     
     /**
+     * Using this method to get a Central object will ensure that other parts of the org.biomoby.shared 
+     * class hierarchy that implicitly check the registry will use the same cache.  Otherwise, methods
+     * such as MobyNamespace.getNamespace() must be passed a Central object parameter as well.
+     *
+     * @return a CentralImpl using the default Central URI, and currently a class implementing a caching mechanism
+     */
+    public static Central getDefaultCentral() throws MobyException{
+	return getDefaultCentral(null);
+    }
+
+    public static Central getDefaultCentral(Registry reg) throws MobyException{
+	if(reg == null && defaultCentrals.containsKey("")){
+	    return defaultCentrals.get("");
+	}
+	else if(reg != null && defaultCentrals.containsKey(reg.getEndpoint())){
+	    return defaultCentrals.get(reg.getEndpoint());
+	}
+
+	String className = DEFAULT_CENTRAL_IMPL_CLASSNAME;
+	ClassLoader classLoader = Thread.currentThread().getContextClassLoader();
+	URL resURL = classLoader.getResource("META-INF/"+CENTRAL_IMPL_RESOURCE_NAME);
+	if(resURL != null){
+	    try{
+		LineNumberReader reader = new LineNumberReader(new InputStreamReader(resURL.openStream()));
+		for(String line = reader.readLine(); line != null; line = reader.readLine()){
+		    if(!line.trim().startsWith("#")){
+			className = line.trim();
+			break;
+		    }
+		}
+	    } catch(Exception e){
+		logger.log(Level.WARNING,
+			   "Error reading " + resURL,
+			   e);
+	    }
+	}
+	try{
+	    Class clazz = Class.forName(className);
+	    if(reg == null){  // should use default nullary c-tor
+		defaultCentrals.put("", (Central) clazz.newInstance());
+	    }
+	    else{  // should have (String endpoint, String namespace) c-tor
+		for(Constructor ctor: clazz.getDeclaredConstructors()){
+		    Class[] params = ctor.getParameterTypes();
+		    if(params.length == 2 && params[0].getName().equals("java.lang.String") &&
+		       params[1].getName().equals("java.lang.String") ){
+			defaultCentrals.put(reg.getEndpoint(),
+					    (Central) ctor.newInstance(reg.getEndpoint(), reg.getNamespace()));
+			break;
+		    }
+		}
+		if(!defaultCentrals.containsKey(reg.getEndpoint())){
+		    logger.log(Level.WARNING,
+			       "Could not find required (String endpoint, String namespace)" +
+			       "constructor for class " + className);
+		}
+	    }
+	} catch(Exception e){
+	    logger.log(Level.WARNING,
+		       "Could not load class " + className,
+		       e);
+	    if(reg == null){
+		defaultCentrals.put("", new CentralImpl());  //fallback to this class, no caching, etc.
+	    }
+	    else{
+		defaultCentrals.put(reg.getEndpoint(), 
+				    new CentralImpl(reg.getEndpoint(), reg.getNamespace()));
+	    }
+	}
+
+	return defaultCentrals.get(reg == null ? "" : reg.getEndpoint());
+    }
+
+    /**
      * 
      * @return a String representing the Default mobycentral endpoint. If the
      *         system property 'moby.check.default' exists and is set to true,



From gordonp at dev.open-bio.org  Wed Jul 16 20:34:07 2008
From: gordonp at dev.open-bio.org (Paul Gordon)
Date: Wed, 16 Jul 2008 16:34:07 -0400
Subject: [MOBY-guts] biomoby commit
Message-ID: <200807162034.m6GKY7Di016236@dev.open-bio.org>


gordonp
Wed Jul 16 16:34:07 EDT 2008
Update of /home/repository/moby/moby-live/Java/src/main/org/biomoby/shared
In directory dev.open-bio.org:/tmp/cvs-serv16200/src/main/org/biomoby/shared

Modified Files:
	MobyNamespace.java 
Log Message:
Updated getNamespace() to use the new caching mechanism
moby-live/Java/src/main/org/biomoby/shared MobyNamespace.java,1.11,1.12
===================================================================
RCS file: /home/repository/moby/moby-live/Java/src/main/org/biomoby/shared/MobyNamespace.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/MobyNamespace.java	2007/08/24 09:35:27	1.11
+++ /home/repository/moby/moby-live/Java/src/main/org/biomoby/shared/MobyNamespace.java	2008/07/16 20:34:07	1.12
@@ -13,6 +13,7 @@
 import org.biomoby.shared.extended.NamespaceParser;
 
 import java.util.*;
+import java.util.logging.*;
 import java.net.URL;
 
 /**
@@ -37,8 +38,8 @@
     protected String id = null;
     protected Registry registry; //provenance of the namspace definition
 
-    private static Map<String,MobyNamespace[]> namespacesMapBySynonym = new HashMap<String,MobyNamespace[]>();
-    private static Map<URL,MobyNamespace[]> namespacesMapByURL = new HashMap<URL,MobyNamespace[]>();
+    private static Logger logger = Logger.getLogger("org.biomoby.shared.MobyNamespace");
+    private static Map<String,MobyNamespace[]> namespacesMapByURL = new HashMap<String,MobyNamespace[]>();
 
     /**************************************************************************
      * Default constructor. Other characteristics are empty - which is usually
@@ -48,18 +49,6 @@
 	this.name = name;
     }
 
-    protected static String convertRegistryToNamespaceResourceURL(Registry reg) throws MobyException{
-	CentralImpl central = new CentralImpl(reg.getEndpoint());
-	MobyResourceRef[] resources = central.getResourceRefs();
-	for(MobyResourceRef resource: resources){
-	    if(Central.NAMESPACES_RESOURCE_NAME.equals(resource.getResourceName())){
-		return resource.getResourceLocation().toString();
-	    }
-	}
-	System.err.println("Error! Could not find the namespace resource from the registry " + reg.getSynonym());
-	return null;
-    }
-
     public Registry getRegistry(){
 	return registry;
     }
@@ -68,29 +57,6 @@
 	reg = registry;
     }
  
-    /**
-     * Particularly useful for loading namespace definitions from cached file, or
-     * refreshing an in-memory cache.
-     */
-    public static void loadNamespaces(URL namespaceDefURL, Registry reg) throws Exception{
-	synchronized(namespacesMapBySynonym){
-	    if(reg == null){
-		reg = RegistryCache.getDefaultRegistry();
-	    }
-	    
-	    MobyNamespace[] namespaces;
-	    NamespaceParser p = new NamespaceParser(namespaceDefURL);	    
-	    namespaces = p.getMobyNamespacesFromRDF();
-	    
-	    for(MobyNamespace namespace: namespaces){
-		namespace.setRegistry(reg);
-	    }
-	    
-	    namespacesMapBySynonym.put(reg.getSynonym(), namespaces);
-	    namespacesMapByURL.put(namespaceDefURL, namespaces);  
-	}
-    }
-
     public static MobyNamespace getNamespace(String ns){
 	return getNamespace(ns, null);
     }
@@ -100,31 +66,24 @@
 	    return null;
 	}
 	
-	if(reg == null){
-	    reg = RegistryCache.getDefaultRegistry();
-	}
-	if(reg == null){
-	    return null;
-	}
-
 	MobyNamespace[] namespaces = null;
-	// sync makes sure we don't fetch it if it's currently being loaded by loadNamespaces
-	synchronized(namespacesMapBySynonym){  
-	    namespaces = namespacesMapBySynonym.get(reg.getSynonym());
-	}
 
-	// This method has not been called yet in the JVM, populate the namespaces 
+	// This method has not been called yet in the JVM, populate the namespaces, 
+	// ensuring concurrent calls don't collide
 	synchronized(namespacesMapByURL){
+	    namespaces = namespacesMapByURL.get(reg == null ? "" : reg.getEndpoint());
 	    if(namespaces == null){
+		Central central = null;
+		try{
+		    central = CentralImpl.getDefaultCentral(reg);
+		} catch(MobyException e){
+		    logger.log(Level.WARNING,
+			       "Cannot find a default Moby Central implementation",
+			       e);
+		    return null;
+		}
 		try{
-		    URL namespaceDefURL = Registry.findResourceURL(reg, Central.NAMESPACES_RESOURCE_NAME);
-		    namespaces = namespacesMapByURL.get(namespaceDefURL);		    
-		    if(namespaces == null){
-			System.err.println("Fetching namespace ontology from "+namespaceDefURL);
-			loadNamespaces(namespaceDefURL, reg);
-			namespaces = namespacesMapByURL.get(namespaceDefURL);
-		    }
-		    
+		    namespaces = central.getFullNamespaces();
 		}
 		catch(Exception e){
 		    System.err.println("Cannot parse MOBY Namespace Ontology: " + e);



From gordonp at dev.open-bio.org  Wed Jul 16 20:34:54 2008
From: gordonp at dev.open-bio.org (Paul Gordon)
Date: Wed, 16 Jul 2008 16:34:54 -0400
Subject: [MOBY-guts] biomoby commit
Message-ID: <200807162034.m6GKYsRw016298@dev.open-bio.org>


gordonp
Wed Jul 16 16:34:54 EDT 2008
Update of /home/repository/moby/moby-live/Java/src/main/org/biomoby/shared/test
In directory dev.open-bio.org:/tmp/cvs-serv16266/src/main/org/biomoby/shared/test

Added Files:
	MobyNamespaceTestCase.java 
Log Message:
Test case for new ontology caching functionality
moby-live/Java/src/main/org/biomoby/shared/test MobyNamespaceTestCase.java,NONE,1.1


From gordonp at dev.open-bio.org  Wed Jul 16 20:37:21 2008
From: gordonp at dev.open-bio.org (Paul Gordon)
Date: Wed, 16 Jul 2008 16:37:21 -0400
Subject: [MOBY-guts] biomoby commit
Message-ID: <200807162037.m6GKbLpZ016408@dev.open-bio.org>


gordonp
Wed Jul 16 16:37:21 EDT 2008
Update of /home/repository/moby/moby-live/Java/src/main/ca/ucalgary/seahawk/gui
In directory dev.open-bio.org:/tmp/cvs-serv16372/src/main/ca/ucalgary/seahawk/gui

Modified Files:
	MobyContentGUI.java 
Log Message:
Got rid of explicit namespace pre-loading, since new caching mechanism is being used
moby-live/Java/src/main/ca/ucalgary/seahawk/gui MobyContentGUI.java,1.16,1.17
===================================================================
RCS file: /home/repository/moby/moby-live/Java/src/main/ca/ucalgary/seahawk/gui/MobyContentGUI.java,v
retrieving revision 1.16
retrieving revision 1.17
diff -u -r1.16 -r1.17
--- /home/repository/moby/moby-live/Java/src/main/ca/ucalgary/seahawk/gui/MobyContentGUI.java	2008/01/30 00:04:56	1.16
+++ /home/repository/moby/moby-live/Java/src/main/ca/ucalgary/seahawk/gui/MobyContentGUI.java	2008/07/16 20:37:21	1.17
@@ -900,20 +900,10 @@
 	final long allowedAgeMillis = (long) SeahawkOptions.getCacheExpiry()*60*60*1000; // hours to milliseconds
 	RegistryCache.deleteExpiredCacheFiles(allowedAgeMillis);
 
+	// TODO: deal with CentralImpl.getDefaultCentral()
+
 	// Redirect the registry endpoints to local cache files if available
 	// preferredRegistry and/or dataDefURL may be null, if not cached, but that's okay to pass around
-	new Thread(){
-	    public void run(){
-		try{
-		    MobyNamespace.loadNamespaces(RegistryCache.cacheRegistryOntology(preferredRegistry, 
-										     Central.NAMESPACES_RESOURCE_NAME,
-										     allowedAgeMillis).toURI().toURL(),
-						 preferredRegistry);
-		}catch(Exception e){
-		    e.printStackTrace();
-		}
-	    }}.start();
-
 	// The following command will cache all data type definitions for this session
 	new Thread(){
 	    public void run(){
@@ -938,10 +928,6 @@
 		    e.printStackTrace();
 		}
 	    }}.start();
-	// And the service definitions
-	//new Thread(){
-	//	public void run(){org.biomoby.shared.MobyService.getService("","");}
-	//    }.start();
     }
 
     /**



From kawas at dev.open-bio.org  Tue Jul 22 15:49:41 2008
From: kawas at dev.open-bio.org (Eddie Kawas)
Date: Tue, 22 Jul 2008 11:49:41 -0400
Subject: [MOBY-guts] biomoby commit
Message-ID: <200807221549.m6MFnfQI007297@dev.open-bio.org>


kawas
Tue Jul 22 11:49:41 EDT 2008
Update of /home/repository/moby/moby-live/Java/src/main/org/biomoby/shared/extended
In directory dev.open-bio.org:/tmp/cvs-serv7261/src/main/org/biomoby/shared/extended

Modified Files:
	NamespaceParser.java 
Log Message:
fixed a spelling error
moby-live/Java/src/main/org/biomoby/shared/extended NamespaceParser.java,1.11,1.12
===================================================================
RCS file: /home/repository/moby/moby-live/Java/src/main/org/biomoby/shared/extended/NamespaceParser.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/extended/NamespaceParser.java	2008/02/28 17:00:12	1.11
+++ /home/repository/moby/moby-live/Java/src/main/org/biomoby/shared/extended/NamespaceParser.java	2008/07/22 15:49:41	1.12
@@ -164,7 +164,7 @@
 			if (uri.indexOf("#") > 0)
 				name = uri.substring(uri.indexOf("#")+1);
 			else if(uri.lastIndexOf("/Namespaces/") > 0) {
-			    name = uri.substring(uri.lastIndexOf("/Namepaces/")+"/Namespaces/".length());
+			    name = uri.substring(uri.lastIndexOf("/Namespaces/")+"/Namespaces/".length());
 			}
 			
 			MobyNamespace namespace = new MobyNamespace(name);



From kawas at dev.open-bio.org  Tue Jul 22 15:54:30 2008
From: kawas at dev.open-bio.org (Eddie Kawas)
Date: Tue, 22 Jul 2008 11:54:30 -0400
Subject: [MOBY-guts] biomoby commit
Message-ID: <200807221554.m6MFsUKb007412@dev.open-bio.org>


kawas
Tue Jul 22 11:54:29 EDT 2008
Update of /home/repository/moby/moby-live/Perl/MOBY-Server/lib/MOBY/RDF/Ontologies
In directory dev.open-bio.org:/tmp/cvs-serv7377/Perl/MOBY-Server/lib/MOBY/RDF/Ontologies

Modified Files:
	Namespaces.pm 
Log Message:
temporary rollback
moby-live/Perl/MOBY-Server/lib/MOBY/RDF/Ontologies Namespaces.pm,1.5,1.6
===================================================================
RCS file: /home/repository/moby/moby-live/Perl/MOBY-Server/lib/MOBY/RDF/Ontologies/Namespaces.pm,v
retrieving revision 1.5
retrieving revision 1.6
diff -u -r1.5 -r1.6
--- /home/repository/moby/moby-live/Perl/MOBY-Server/lib/MOBY/RDF/Ontologies/Namespaces.pm	2008/06/19 21:49:01	1.5
+++ /home/repository/moby/moby-live/Perl/MOBY-Server/lib/MOBY/RDF/Ontologies/Namespaces.pm	2008/07/22 15:54:29	1.6
@@ -76,8 +76,8 @@
 	
 	# save some information retrieved from mobycentral.config
     my $CONF  = MOBY::Config->new;
-	$self->{uri}       = $CONF->{mobynamespace}->{resourceURL} || 'http://biomoby.org/RESOURCES/MOBY-S/Namespaces/';
-	$self->{uri} = $self->{uri} . "/" unless $self->{uri} =~ m/^.*(\/{1})$/;
+	$self->{uri}       = $CONF->{mobynamespace}->{resourceURL} || 'http://biomoby.org/RESOURCES/MOBY-S/Namespaces#';
+	$self->{uri} = $self->{uri} . "#" unless $self->{uri} =~ m/^.*(\#{1})$/;
 
 	$self->{query_all} = <<END;
 SELECT namespace_type, description, namespace_lsid, authority, contact_email FROM namespace ORDER BY namespace_type asc



From senger at dev.open-bio.org  Wed Jul 23 09:32:35 2008
From: senger at dev.open-bio.org (Martin Senger)
Date: Wed, 23 Jul 2008 05:32:35 -0400
Subject: [MOBY-guts] biomoby commit
Message-ID: <200807230932.m6N9WZWr009126@dev.open-bio.org>


senger
Wed Jul 23 05:32:35 EDT 2008
Update of /home/repository/moby/moby-live/Java/docs
In directory dev.open-bio.org:/tmp/cvs-serv9107/docs

Modified Files:
	ChangeLog 
Log Message:
deployed jMoby 1.1.0
moby-live/Java/docs ChangeLog,1.90,1.91
===================================================================
RCS file: /home/repository/moby/moby-live/Java/docs/ChangeLog,v
retrieving revision 1.90
retrieving revision 1.91
diff -u -r1.90 -r1.91
--- /home/repository/moby/moby-live/Java/docs/ChangeLog	2008/05/22 17:09:30	1.90
+++ /home/repository/moby/moby-live/Java/docs/ChangeLog	2008/07/23 09:32:35	1.91
@@ -1,3 +1,7 @@
+2008-07-23  Martin Senger  <martin.senger&#64;gmail.com>
+
+	* Version 1.1.0 released
+
 2008-05-23  Martin Senger  <senger at ebi.ac.uk>
 
 	* Fixed: registering data types from an XML file, in Dashboard



From senger at dev.open-bio.org  Wed Jul 23 09:32:36 2008
From: senger at dev.open-bio.org (Martin Senger)
Date: Wed, 23 Jul 2008 05:32:36 -0400
Subject: [MOBY-guts] biomoby commit
Message-ID: <200807230932.m6N9WaJo009144@dev.open-bio.org>


senger
Wed Jul 23 05:32:35 EDT 2008
Update of /home/repository/moby/moby-live/Java/xmls
In directory dev.open-bio.org:/tmp/cvs-serv9107/xmls

Modified Files:
	project.pom 
Log Message:
deployed jMoby 1.1.0
moby-live/Java/xmls project.pom,1.10,1.11
===================================================================
RCS file: /home/repository/moby/moby-live/Java/xmls/project.pom,v
retrieving revision 1.10
retrieving revision 1.11
diff -u -r1.10 -r1.11
--- /home/repository/moby/moby-live/Java/xmls/project.pom	2008/03/28 11:19:02	1.10
+++ /home/repository/moby/moby-live/Java/xmls/project.pom	2008/07/23 09:32:35	1.11
@@ -2,7 +2,7 @@
   <modelVersion>4.0.0</modelVersion>
   <groupId>org.biomoby</groupId>
   <artifactId>jmoby</artifactId>
-  <version>1.0.0</version>
+  <version>1.1.0</version>
   <name>jMoby</name>
   <description>
 A sub-project of the BioMoby project. It aims to develop tools in Java for BioMoby.