[MOBY-guts] biomoby commit

[Paul Gordon]

gordonp
Wed Oct 25 20:32:20 EDT 2006
Update of /home/repository/moby/moby-live/Java/src/main/org/biomoby/shared/data
In directory dev.open-bio.org:/tmp/cvs-serv14885/src/main/org/biomoby/shared/data

Modified Files:
	MobyContentInstance.java MobyDataUtils.java 
Log Message:
Became more lenient in namespace resoltion (moby-s allowed, but give warnings)
moby-live/Java/src/main/org/biomoby/shared/data MobyContentInstance.java,1.4,1.5 MobyDataUtils.java,1.3,1.4
===================================================================
RCS file: /home/repository/moby/moby-live/Java/src/main/org/biomoby/shared/data/MobyContentInstance.java,v
retrieving revision 1.4
retrieving revision 1.5
diff -u -r1.4 -r1.5
--- /home/repository/moby/moby-live/Java/src/main/org/biomoby/shared/data/MobyContentInstance.java	2006/09/22 23:01:04	1.4
+++ /home/repository/moby/moby-live/Java/src/main/org/biomoby/shared/data/MobyContentInstance.java	2006/10/26 00:32:20	1.5
@@ -87,10 +87,18 @@
 				    ") was not " + MobyTags.MOBYCONTENT);
 	}
 	if(!MobyPrefixResolver.MOBY_XML_NAMESPACE.equals(objectTag.getNamespaceURI())){
-	    throw new MobyException("The content element's namespace (" + 
-				    objectTag.getNamespaceURI() +
-				    ") did not have the MOBY namespace " + 
-				    MobyPrefixResolver.MOBY_XML_NAMESPACE);
+	    if(!MobyPrefixResolver.MOBY_XML_NAMESPACE_INVALID.equals(objectTag.getNamespaceURI())){
+		throw new MobyException("The content element's namespace (" + 
+					objectTag.getNamespaceURI() +
+					") did not have the MOBY namespace " + 
+					MobyPrefixResolver.MOBY_XML_NAMESPACE);
+	    }
+	    else{
+		System.err.println("Invalid namespace used for content element (was " + 
+				   objectTag.getNamespaceURI() + 
+				   ", but should be " + MobyPrefixResolver.MOBY_XML_NAMESPACE + 
+				   ", proceeding anyway");
+	    }
 	}
 	
 	members = new HashMap();
@@ -100,11 +108,12 @@
 	NodeList mobyData = MobyPrefixResolver.getChildElements(objectTag, 
 								MobyTags.MOBYDATA);
 
-	if(mobyData.getLength() == 0){
-	    throw new MobyException("The document's " + MobyTags.MOBYCONTENT +
-				    " element does not have a " + MobyTags.MOBYDATA + 
-				    " child. It must have one or more according to the MOBY API");
-	}
+	// The case below is no longer true: an empty content block is a "ping" request as per mailing list 2006-08
+// 	if(mobyData.getLength() == 0){
+// 	    throw new MobyException("The document's " + MobyTags.MOBYCONTENT +
+// 				    " element does not have a " + MobyTags.MOBYDATA + 
+// 				    " child. It must have one or more according to the MOBY API");
+// 	}
 
 	// Now back to the main data
 	for(int i = 0; i < mobyData.getLength(); i++){

===================================================================
RCS file: /home/repository/moby/moby-live/Java/src/main/org/biomoby/shared/data/MobyDataUtils.java,v
retrieving revision 1.3
retrieving revision 1.4
diff -u -r1.3 -r1.4
--- /home/repository/moby/moby-live/Java/src/main/org/biomoby/shared/data/MobyDataUtils.java	2006/07/07 04:12:40	1.3
+++ /home/repository/moby/moby-live/Java/src/main/org/biomoby/shared/data/MobyDataUtils.java	2006/10/26 00:32:20	1.4
@@ -57,14 +57,25 @@
 				    doc_root.getLocalName() +
 				    ") was not " + MobyTags.MOBY);
 	}
+	NodeList envelope = null;
 	if(!MobyPrefixResolver.MOBY_XML_NAMESPACE.equals(doc_root.getNamespaceURI())){
-	    throw new MobyException("The XML document's root element namespace (" + 
-				    doc_root.getNamespaceURI() +
-				    ") is not the MOBY namespace " + 
-				    MobyPrefixResolver.MOBY_XML_NAMESPACE);
+	   if(!MobyPrefixResolver.MOBY_XML_NAMESPACE_INVALID.equals(doc_root.getNamespaceURI())){
+	       throw new MobyException("The XML document's root element namespace (" + 
+				       doc_root.getNamespaceURI() +
+				       ") is not the MOBY namespace " + 
+				       MobyPrefixResolver.MOBY_XML_NAMESPACE);
+	   }
+	   System.err.println("Invalid namespace used for root element (was " + doc_root.getNamespaceURI() + 
+			      ", but should be " + MobyPrefixResolver.MOBY_XML_NAMESPACE + 
+			      ", proceeding anyway");
+	   envelope = doc_root.getElementsByTagNameNS(MobyPrefixResolver.MOBY_XML_NAMESPACE_INVALID, 
+						      MobyTags.MOBYCONTENT);
+	}
+	else{
+	    envelope = doc_root.getElementsByTagNameNS(MobyPrefixResolver.MOBY_XML_NAMESPACE, 
+						       MobyTags.MOBYCONTENT);
 	}
-	NodeList envelope = doc_root.getElementsByTagNameNS(MobyPrefixResolver.MOBY_XML_NAMESPACE, 
-							    MobyTags.MOBYCONTENT);
+
 	if(envelope.getLength() == 0){
 	    throw new MobyException("The document's " + MobyTags.MOBY + 
 				    " element does not contain a " +