[MOBY-guts] biomoby commit

[Paul Gordon]

gordonp
Mon Jan  7 17:04:17 EST 2008
Update of /home/repository/moby/moby-live/Java/src/main/org/biomoby/client
In directory dev.open-bio.org:/tmp/cvs-serv14667/src/main/org/biomoby/client

Modified Files:
	MobyRequest.java 
Log Message:
Now we fill in default secondary (at Andreas' request), and fixed a potential null pointer exception
moby-live/Java/src/main/org/biomoby/client MobyRequest.java,1.31,1.32
===================================================================
RCS file: /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/MobyRequest.java,v
retrieving revision 1.31
retrieving revision 1.32
diff -u -r1.31 -r1.32
--- /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/MobyRequest.java	2007/12/14 23:04:31	1.31
+++ /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/MobyRequest.java	2008/01/07 22:04:17	1.32
@@ -737,11 +737,13 @@
 	    }
 	}
 
-	if(localResponseString != null && localResponseString.length() == 0){
-	    throw new MobyException("The MOBY payload has no text contents at all"); 
-	}
-	if(Character.isWhitespace(localResponseString.charAt(0))){
-	    localResponseString = localResponseString.trim();
+	if(localResponseString != null){
+	    if(localResponseString.length() == 0){
+		throw new MobyException("The MOBY payload has no text contents at all"); 
+	    }
+	    if(Character.isWhitespace(localResponseString.charAt(0))){
+		localResponseString = localResponseString.trim();
+	    }
 	}
 
 	// Check if the payload is an XML document.  If not, try a last ditch effort 
@@ -860,7 +862,8 @@
     }
 
     /**
-     * Creates an XML representation of the data, renamed to fit the needs of the service if necessary.
+     * Creates an XML representation of the data, renamed to fit the needs of the service if necessary,
+     * and adding any secondary parameter default values if not already specified in the incoming data.
      *
      * @param data the array of input parameters to put in a MOBY XML request
      *
@@ -869,7 +872,7 @@
     public String convertMOBYDataToMOBYRequest(MobyContentInstance data) throws MobyException{
 
 	MobyData[] inputs = mobyService.getPrimaryInputs();
-	MobyData[] secondaries = mobyService.getSecondaryInputs();
+	MobySecondaryData[] secondaries = mobyService.getSecondaryInputs();
 	Iterator queries = data.keySet().iterator();
 
 	// Make sure the number of input args is correct for each query being submitted
@@ -918,14 +921,22 @@
 					" primary input parameter(s), but takes " + inputs.length + 
 					" (query " + queryName + ")");
 	    }
-	    if(secondaries != null && secondaries.length != secondaryParams.size()){
-		throw new MobyException("Service " + mobyService.getName() + " was provided " + 
-					secondaryParams.size() + 
-					" secondary input parameter(s), but takes " + secondaries.length +
-					" (query " + queryName + ")");
+	    if(secondaries != null){
+		// If no secondaries provided, fill them in by default
+		if(secondaries.length != 0 && secondaryParams.isEmpty()){
+		    for(MobySecondaryData secondary: secondaries){
+			secondaryParams.put(secondary.getName(), new MobyDataSecondaryInstance(secondary));
+		    }
+		}
+		else if(secondaries.length != secondaryParams.size()){
+		    throw new MobyException("Service " + mobyService.getName() + " was provided " + 
+					    secondaryParams.size() + 
+					    " secondary input parameter(s), but takes " + secondaries.length +
+					    " (query " + queryName + ")");
+		}
 	    }
 	    
-	    // If there was one anonynmous input, assign the name automatically in
+	    // If there was one anonymous input, assign the name automatically in
 	    // the case the service requires it to be named.  This is the only
 	    // unambiguous case in which we can do this.
 	    if(inputs.length == 1){