[MOBY-guts] biomoby commit

[Paul Gordon]

gordonp
Sat Apr 17 20:23:42 EDT 2010
Update of /home/repository/moby/moby-live/Java/src/main/ca/ucalgary/seahawk/util
In directory dev.open-bio.org:/tmp/cvs-serv27510/src/main/ca/ucalgary/seahawk/util

Modified Files:
	DataFlowRecorder.java 
Log Message:
Fixed so no problem when original data comes from the clipboard, or a saved moby xml file
moby-live/Java/src/main/ca/ucalgary/seahawk/util DataFlowRecorder.java,1.5,1.6
===================================================================
RCS file: /home/repository/moby/moby-live/Java/src/main/ca/ucalgary/seahawk/util/DataFlowRecorder.java,v
retrieving revision 1.5
retrieving revision 1.6
diff -u -r1.5 -r1.6
--- /home/repository/moby/moby-live/Java/src/main/ca/ucalgary/seahawk/util/DataFlowRecorder.java	2010/04/16 17:33:26	1.5
+++ /home/repository/moby/moby-live/Java/src/main/ca/ucalgary/seahawk/util/DataFlowRecorder.java	2010/04/18 00:23:42	1.6
@@ -342,6 +342,7 @@
 
 	    // true means treat as a collection if that's what the sample data is
 	    String sinkPortName = getPortName(sampleData, true);
+	    // No user data means non-moby origin...backtracking stops.
 	    if(data != null && data.length != 0){
 		URL dataSrcURL = null;
 		try{
@@ -351,6 +352,16 @@
 			       "a provenance URL as expected URL (" + sampleData.getUserData().toString() + ")");
 		    continue;
 		}
+
+		// If srcService == null, the input source for this param was a Moby doc that wasn't a 
+		// service output, e.g. the clipboard or an old doc loaded from file.
+		MobyService srcService = DataUtils.getService(dataSrcURL);
+		if(srcService == null){
+		    addWorkflowInput(processorName, condPassProcessorAndPorts, sinkPortName, sampleData, 
+				     datalinks, processors, inputPorts, doc);
+		    continue;
+		}
+
 		// recursion for workflow creation by backtracking service input provenance
 		String feedingProcessorName = null;
 		String feedingProcessorPort = null;
@@ -429,52 +440,57 @@
 	    }
 	    // Otherwise it's a workflow input the user will need to specify
 	    else{
-		// pName is editable name for input processor target...
-		// allows injection of condition without affecting method's return value
-		String pName = processorName; 
-		if(condPassProcessorAndPorts != null){
-		    // inject condition filter between data creator and current service 
-		    datalinks.appendChild(createDataLinkElement(condPassProcessorAndPorts[0],
-								condPassProcessorAndPorts[2],
-								pName,
-								sinkPortName,
-								doc));
-		    pName = condPassProcessorAndPorts[0];
-		    sinkPortName = condPassProcessorAndPorts[1];
-		}
-		// The sample data may be used in more than one branch of the flow...avoid duplication
-		// Get the real data XML, to see if we've encountered it before as input (it'd be in the hash)
-		// Remember that sd is the loop's original MobyDataInstance before it's been coerced into a MobyPrimaryData, 
-		// which doesn't have XML modes, etc.
-		String inputKey = getInputKey(sd);
-		//		System.err.println("Input key for " + processorName + " is " + inputKey);
-
-		String[] mobifyingProcessorNameAndPorts = null;
-		if(input2Processor.containsKey(inputKey)){
-		    mobifyingProcessorNameAndPorts = input2Processor.get(inputKey);		    
-		}
-		else{
-		    if(sampleData.getDataType().getName().equals(MobyTags.MOBYOBJECT)){
-			mobifyingProcessorNameAndPorts = addIdMobifyingProcessor(processors, datalinks, inputPorts,
-										 sampleData, doc);
-			input2Processor.put(inputKey, mobifyingProcessorNameAndPorts);
-		    }
-		    else{
-			// TODO: Need to build complex input from MOB rule or spreadsheet fields?
-		    }
-		}
-		// link the created data to the workflow service
-		datalinks.appendChild(createDataLinkElement(mobifyingProcessorNameAndPorts[0], 
-							    mobifyingProcessorNameAndPorts[1], 
-							    pName, sinkPortName, 
-							    doc));
+		addWorkflowInput(processorName, condPassProcessorAndPorts, sinkPortName, sampleData, 
+				 datalinks, processors, inputPorts, doc);
 	    }
-
 	}
 
 	return processorName;
     }
 
+    private void addWorkflowInput(String pName, String[] condPassProcessorAndPorts, String sinkPortName, 
+				  MobyPrimaryData sampleData, Element datalinks, Element processors, 
+				  Element inputPorts, Document doc) throws Exception{
+	// pName is editable name for input processor target...
+	// allows injection of condition without affecting method's return value
+	if(condPassProcessorAndPorts != null){
+	    // inject condition filter between data creator and current service 
+	    datalinks.appendChild(createDataLinkElement(condPassProcessorAndPorts[0],
+							condPassProcessorAndPorts[2],
+							pName,
+							sinkPortName,
+							doc));
+	    pName = condPassProcessorAndPorts[0];
+	    sinkPortName = condPassProcessorAndPorts[1];
+	}
+	// The sample data may be used in more than one branch of the flow...avoid duplication
+	// Get the real data XML, to see if we've encountered it before as input (it'd be in the hash)
+	// Remember that sd is the loop's original MobyDataInstance before it's been coerced into a MobyPrimaryData, 
+	// which doesn't have XML modes, etc.
+	String inputKey = getInputKey((MobyDataInstance) sampleData);
+	//		System.err.println("Input key for " + processorName + " is " + inputKey);
+	
+	String[] mobifyingProcessorNameAndPorts = null;
+	if(input2Processor.containsKey(inputKey)){
+	    mobifyingProcessorNameAndPorts = input2Processor.get(inputKey);		    
+	}
+	else{
+	    if(sampleData.getDataType().getName().equals(MobyTags.MOBYOBJECT)){
+		mobifyingProcessorNameAndPorts = addIdMobifyingProcessor(processors, datalinks, inputPorts,
+									 sampleData, doc);
+		input2Processor.put(inputKey, mobifyingProcessorNameAndPorts);
+	    }
+	    else{
+		// TODO: Need to build complex input from MOB rule or spreadsheet fields?
+	    }
+	}
+	// link the created data to the workflow service
+	datalinks.appendChild(createDataLinkElement(mobifyingProcessorNameAndPorts[0], 
+						    mobifyingProcessorNameAndPorts[1], 
+						    pName, sinkPortName, 
+						    doc));	
+    }
+
     // returns the same value for moby sample data instances containing the same data in XML form
     private String getInputKey(MobyDataInstance sd){
 	int oldXmlMode = sd.getXmlMode();