Merge branch '12991-docker-memory-limit'

[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 d426c1ad6f32fef90e0a5b15a3691fe811c78760..f0f9c77f40fed6c5a27d8160abdfc1d710ddb9f1 100644 (file)
--- a/sdk/cwl/arvados_cwl/arvworkflow.py
+++ b/sdk/cwl/arvados_cwl/arvworkflow.py
@@ -27,9 +27,9 @@ logger = logging.getLogger('arvados.cwl-runner')
 metrics = logging.getLogger('arvados.cwl-runner.metrics')
 
 def upload_workflow(arvRunner, tool, job_order, project_uuid, uuid=None,
-                    submit_runner_ram=0, name=None):
+                    submit_runner_ram=0, name=None, merged_map=None):
 
-    packed = packed_workflow(arvRunner, tool)
+    packed = packed_workflow(arvRunner, tool, merged_map)
 
     adjustDirObjs(job_order, trim_listing)
     adjustFileObjs(job_order, trim_anonymous_location)
@@ -158,7 +158,7 @@ class ArvadosWorkflow(Workflow):
                 "inputs": self.tool["inputs"],
                 "outputs": self.tool["outputs"],
                 "stdout": "cwl.output.json",
-                "requirements": workflowobj["requirements"]+[
+                "requirements": self.requirements+[
                     {
                     "class": "InitialWorkDirRequirement",
                     "listing": [{
@@ -172,8 +172,9 @@ class ArvadosWorkflow(Workflow):
                             "entry": json.dumps(joborder_keepmount, indent=2, sort_keys=True, separators=(',',': ')).replace("\\", "\\\\").replace('$(', '\$(').replace('${', '\${')
                         }]
                 }],
-                "hints": workflowobj["hints"],
-                "arguments": ["--no-container", "--move-outputs", "--preserve-entire-environment", "workflow.cwl#main", "cwl.input.yml"]
+                "hints": self.hints,
+                "arguments": ["--no-container", "--move-outputs", "--preserve-entire-environment", "workflow.cwl#main", "cwl.input.yml"],
+                "id": "#"
             })
             kwargs["loader"] = self.doc_loader
             kwargs["avsc_names"] = self.doc_schema