[MOBY-guts] biomoby commit

[Paul Gordon]

gordonp
Tue Nov 21 16:03:48 EST 2006
Update of /home/repository/moby/moby-live/Java/src/main/org/biomoby/client
In directory dev.open-bio.org:/tmp/cvs-serv16310/src/main/org/biomoby/client

Modified Files:
	MobyRequest.java 
Log Message:
Made code more lenient about receiving MOBY payloads without XML declarations (to accomodate Taverna's bug)
moby-live/Java/src/main/org/biomoby/client MobyRequest.java,1.20,1.21
===================================================================
RCS file: /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/MobyRequest.java,v
retrieving revision 1.20
retrieving revision 1.21
diff -u -r1.20 -r1.21
--- /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/MobyRequest.java	2006/10/25 02:33:23	1.20
+++ /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/MobyRequest.java	2006/11/21 21:03:48	1.21
@@ -622,17 +622,28 @@
 	// by base64 decoding the contents.  This is technically not allowable in the 
 	// MOBY spec, but we are being lenient.
 	if(!localResponseString.startsWith("<?xml")){
-	    localResponseString = new String(org.apache.axis.encoding.Base64.decode(localResponseString));
-	    if(!localResponseString.startsWith("<?xml")){
-		throw new MobyException("The SOAP payload defining the MOBY contents " +
-					"does not start with <?xml, and is therefore not " +
-					"an XML document, as specified in the MOBY API. " +
-					"Please contact the service provider.  Contents is: " + localResponseString);
-	    }
-	    debugPS.println("Warning: The MOBY contents was needlessly base64 encoded (the SOAP " +
-			    "envelope does this for you).  It has been decoded, but this is not " +
-			    "part of the MOBY API, and may stop working in the future.  Please " +
-			    "contact the service provider to correct this.");
+	    // Is the XML declaration missing?
+	    if(localResponseString.startsWith("<moby:MOBY") || localResponseString.startsWith("<MOBY")){
+		localResponseString = "<?xml version=\"1.0\"?>\n"+localResponseString;
+		debugPS.println("Warning: The MOBY contents was missing an XML declaration, but it is " +
+				"required by the MOBY API, and may stop working in the future without it.  Please " +
+				"contact the client's provider to correct this.");
+	    }
+	    else{
+		String oldResponse = localResponseString;
+		localResponseString = new String(org.apache.axis.encoding.Base64.decode(localResponseString));
+		if(!localResponseString.startsWith("<?xml")){
+		    throw new MobyException("The SOAP payload defining the MOBY contents " +
+					    "does not start with the xml processing instruction, and is therefore not " +
+					    "an XML document, as specified in the MOBY API. " +
+					    "Please contact the service provider.  Contents was: " + 
+					    oldResponse);
+		}
+		debugPS.println("Warning: The MOBY contents was needlessly base64 encoded (the SOAP " +
+				"envelope does this for you).  It has been decoded, but this is not " +
+				"part of the MOBY API, and may stop working in the future.  Please " +
+				"contact the service provider to correct this.");
+	    }
 	}
 
 	// A bit of a hack: most MOBY data represented in string form