Extra logging ... probably don't want exactly this.

Author: jmchilton

planemo/galaxy/activity.py

@@ -35,8 +35,16 @@
 def execute(ctx, config, runnable, job_path, **kwds):
     """Execute a Galaxy activity."""
     try:
-        return _execute(ctx, config, runnable, job_path, **kwds)
+        rval = _execute(ctx, config, runnable, job_path, **kwds)
+        ctx.vlog("execute complete...")
+        return rval
     except Exception as e:
+        ctx.vlog("execute failed...")
+        import sys
+        import traceback
+        exc_type, exc_value, exc_traceback = sys.exc_info()
+        traceback.print_tb(exc_traceback, limit=1, file=sys.stdout)
+        traceback.print_exc()
         return ErrorRunResponse(str(e))
 
 
@@ -87,6 +95,8 @@ def _execute(ctx, config, runnable, job_path, **kwds):
     elif runnable.type in [RunnableType.galaxy_workflow, RunnableType.cwl_workflow]:
         response_class = GalaxyWorkflowRunResponse
         workflow_id = config.workflow_id(runnable.path)
+        with open("imported_workflow.json", "w") as f:
+            json.dump(user_gi.workflows.export_workflow_dict(workflow_id), f)
         ctx.vlog("Found Galaxy workflow ID [%s] for path [%s]" % (workflow_id, runnable.path))
         # TODO: update bioblend to allow inputs_by.
         # invocation = user_gi.worklfows.invoke_workflow(
@@ -382,6 +392,7 @@ def outputs_dict(self):
     def download_output_to(self, dataset_details, output_directory):
         file_name = dataset_details.get("cwl_file_name") or dataset_details.get("name")
         destination = os.path.join(output_directory, file_name)
+        self._ctx.vlog("download for [%s]" % dataset_details)
         self._user_gi.histories.download_dataset(
             self._history_id,
             dataset_details["id"],