Merge branch 'master' into symlinksNutil

Author: tetron

setup.py

@@ -11,7 +11,7 @@
     long_description = readmeFile.read()
 
 setup(name='wes-service',
-      version='2.5',
+      version='2.6',
       description='GA4GH Workflow Execution Service reference implementation',
       long_description=long_description,
       author='GA4GH Containers and Workflows task team',

wes_client/wes_client_main.py

@@ -75,6 +75,10 @@ def main(argv=sys.argv[1:]):
         json.dump(response.result(), sys.stdout, indent=4)
         return 0
 
+    if not args.workflow_url:
+        parser.print_help()
+        return 1
+      
     if not args.job_order:
         logging.error("Missing json/yaml file.")
         return 1

wes_service/arvados_wes.py

@@ -155,8 +155,6 @@ def invoke_cwl_runner(self, cr_uuid, workflow_url, workflow_params,
     def RunWorkflow(self, **args):
         tempdir, body = self.collect_attachments()
 
-        print(body)
-
         if not connexion.request.headers.get('Authorization'):
             raise MissingAuthorization()
 
@@ -214,7 +212,10 @@ def GetRunLog(self, run_id):
         if request["output_uuid"]:
             c = arvados.collection.CollectionReader(request["output_uuid"], api_client=api)
             with c.open("cwl.output.json") as f:
-                outputobj = json.load(f)
+                try:
+                    outputobj = json.load(f)
+                except ValueError:
+                    pass
 
                 def keepref(d):
                     if isinstance(d, dict) and "location" in d: