Merge branch 'release_16.01' into dev

lib/galaxy/managers/workflows.py

@@ -458,10 +458,13 @@ class WorkflowContentsManager(UsesAnnotations):
 
             # workflow outputs
             outputs = []
-            for output in step.workflow_outputs:
-                outputs.append({"output_name": output.output_name,
-                                "uuid": str(output.uuid) if output.uuid else None,
-                                "label": output.label})
+            for output in step.unique_workflow_outputs:
+                output_label = output.label
+                output_name = output.output_name
+                output_uuid = str(output.uuid) if output.uuid else None
+                outputs.append({"output_name": output_name,
+                                "uuid": output_uuid,
+                                "label": output_label})
             step_dict['workflow_outputs'] = outputs
 
             # Encode input connections as dictionary
@@ -571,7 +574,7 @@ class WorkflowContentsManager(UsesAnnotations):
             # User outputs
 
             workflow_outputs_dicts = []
-            for workflow_output in step.workflow_outputs:
+            for workflow_output in step.unique_workflow_outputs:
                 workflow_output_dict = dict(
                     output_name=workflow_output.output_name,
                     label=workflow_output.label,

lib/galaxy/model/__init__.py

@@ -3630,6 +3630,23 @@ class WorkflowStep( object ):
         self.workflow_outputs = []
         self._input_connections_by_name = None
 
+    @property
+    def unique_workflow_outputs(self):
+        # Older Galaxy workflows may have multiple WorkflowOutputs
+        # per "output_name", when serving these back to the editor
+        # feed only a "best" output per "output_name.""
+        outputs = {}
+        for workflow_output in self.workflow_outputs:
+            output_name = workflow_output.output_name
+
+            if output_name in outputs:
+                found_output = outputs[output_name]
+                if found_output.label is None and workflow_output.label is not None:
+                    outputs[output_name] = workflow_output
+            else:
+                outputs[output_name] = workflow_output
+        return outputs.values()
+
     @property
     def content_id( self ):
         content_id = None

lib/galaxy/workflow/run.py

@@ -177,7 +177,7 @@ class WorkflowInvoker( object ):
                 )
                 raise
 
-            log.debug("Workflow step %s invoked %s" % (step.id, step_timer))
+            log.debug("Workflow step %s of invocation %s invoked %s" % (step.id, workflow_invocation.id, step_timer))
 
         if delayed_steps:
             state = model.WorkflowInvocation.states.READY