[MOBY-guts] biomoby commit

[Paul Gordon]

gordonp
Tue Jan 15 15:56:38 EST 2008
Update of /home/repository/moby/moby-live/Java/src/main/org/biomoby/service
In directory dev.open-bio.org:/tmp/cvs-serv15074/src/main/org/biomoby/service

Modified Files:
	MobyServlet.java 
Log Message:
Removed unncessary properties, blank job on ping, and fixed typos
moby-live/Java/src/main/org/biomoby/service MobyServlet.java,1.11,1.12
===================================================================
RCS file: /home/repository/moby/moby-live/Java/src/main/org/biomoby/service/MobyServlet.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/service/MobyServlet.java	2008/01/07 22:16:35	1.11
+++ /home/repository/moby/moby-live/Java/src/main/org/biomoby/service/MobyServlet.java	2008/01/15 20:56:38	1.12
@@ -555,14 +555,6 @@
 	    return;
 	}
 
-	// It's possible we got here due to an early error, in which
-	// case there will be no MobyData blocks in the response.  Since
-	// this is technically illegal according to MOBY, throw a blank one 
-	// in there are none at all
-	if(mobyResults.isEmpty()){
-	    mobyResults.put(new MobyDataJob());
-	}
-
 	response.setContentType("text/xml");
 
 	try{
@@ -599,7 +591,6 @@
      */
     protected void addException(ServiceException se){
 	MobyContentInstance currentContent = getResponseContentInstance();
-	(new Exception("createing exception " +se)).printStackTrace(); 
 	if(currentContent != null){
 	    currentContent.addException(se);
 	    if(isInitialized){
@@ -612,10 +603,10 @@
 	}
 	else{
 	    if(isInitialized){
-		log("Caught exception, but had no results contents to append it to", se);
+		log("Caught exception, but had no results contents to which it could be appended", se);
 	    }
 	    else{
-		System.err.println("Caught exception, but had no results contents to append it to");
+		System.err.println("Caught exception, but had no results contents to which it could be appended");
 	    }
 	}
     }
@@ -670,10 +661,6 @@
      */
     public void init(){
 	try{
-	    if(System.getProperty("javax.xml.parsers.DocumentBuilderFactory") == null){
-		System.setProperty("javax.xml.parsers.DocumentBuilderFactory", 
-				   "org.apache.xerces.jaxp.DocumentBuilderFactoryImpl");
-	    }
 	    DocumentBuilderFactory dbf = DocumentBuilderFactory.newInstance();
 	    dbf.setNamespaceAware(true);	
 	    docBuilder = dbf.newDocumentBuilder();
@@ -688,12 +675,6 @@
 				   "org.apache.axis.soap.MessageFactoryImpl");
 	    }
 	    soapMessageFactory = MessageFactory.newInstance();  // Should find Axis by default
-	    //log("SOAP Message Factory (when init is called) is " + soapMessageFactory);
-
-	    if(System.getProperty("javax.xml.soap.SOAPFactory") == null){
-		System.setProperty("javax.xml.soap.SOAPFactory", 
-				   "org.apache.axis.soap.SOAPFactoryImpl");
-	    }
 	    SOAPFactory soapFactory = SOAPFactory.newInstance();
 	    bodyContentsName = soapFactory.createName(getServiceName()+"Return",
 						      MobyPrefixResolver.MOBY_TRANSPORT_PREFIX,