Merge branch '10583-cwl-salad-ver' refs #10583

[arvados.git] / sdk / cwl / arvados_cwl / arvworkflow.py

diff --git a/sdk/cwl/arvados_cwl/arvworkflow.py b/sdk/cwl/arvados_cwl/arvworkflow.py
index 8eb8fe6fee50e0722ee7066171ff7b7bbc4a10c5..f425ae8df9d2478a566c3dc47aea7e7e1c678d45 100644 (file)
--- a/sdk/cwl/arvados_cwl/arvworkflow.py
+++ b/sdk/cwl/arvados_cwl/arvworkflow.py
@@ -18,7 +18,7 @@ from .perf import Perf
 logger = logging.getLogger('arvados.cwl-runner')
 metrics = logging.getLogger('arvados.cwl-runner.metrics')
 
-def upload_workflow(arvRunner, tool, job_order, project_uuid, update_uuid):
+def upload_workflow(arvRunner, tool, job_order, project_uuid, uuid=None):
     upload_docker(arvRunner, tool)
 
     document_loader, workflowobj, uri = (tool.doc_loader, tool.doc_loader.fetch(tool.tool["id"]), tool.tool["id"])
@@ -39,16 +39,18 @@ def upload_workflow(arvRunner, tool, job_order, project_uuid, update_uuid):
 
     body = {
         "workflow": {
-            "owner_uuid": project_uuid,
             "name": tool.tool.get("label", name),
             "description": tool.tool.get("doc", ""),
             "definition":yaml.safe_dump(packed)
         }}
+    if project_uuid:
+        body["workflow"]["owner_uuid"] = project_uuid
 
-    if update_uuid:
-        return arvRunner.api.workflows().update(uuid=update_uuid, body=body).execute(num_retries=arvRunner.num_retries)["uuid"]
+    if uuid:
+        call = arvRunner.api.workflows().update(uuid=uuid, body=body)
     else:
-        return arvRunner.api.workflows().create(body=body).execute(num_retries=arvRunner.num_retries)["uuid"]
+        call = arvRunner.api.workflows().create(body=body)
+    return call.execute(num_retries=arvRunner.num_retries)["uuid"]
 
 class ArvadosWorkflow(Workflow):
     """Wrap cwltool Workflow to override selected methods."""
@@ -87,6 +89,8 @@ class ArvadosWorkflow(Workflow):
                 joborder_keepmount = copy.deepcopy(joborder)
 
                 def keepmount(obj):
+                    if "location" not in obj:
+                        raise WorkflowException("%s object is missing required 'location' field: %s" % (obj["class"], obj))
                     if obj["location"].startswith("keep:"):
                         obj["location"] = "/keep/" + obj["location"][5:]
                         if "listing" in obj: