Merge branch 'master' into 13822-nm-delayed-daemon

[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 94b8568db7e94dd22059a4a605b8638d950131b7..ae90625102ff155cd67daa44d4ab4384aa996866 100644 (file)
--- a/sdk/cwl/arvados_cwl/arvworkflow.py
+++ b/sdk/cwl/arvados_cwl/arvworkflow.py
@@ -52,13 +52,24 @@ def upload_workflow(arvRunner, tool, job_order, project_uuid, uuid=None,
     upload_dependencies(arvRunner, name, tool.doc_loader,
                         packed, tool.tool["id"], False)
 
-    # TODO nowhere for submit_runner_ram to go.
+    if submit_runner_ram:
+        hints = main.get("hints", [])
+        found = False
+        for h in hints:
+            if h["class"] == "http://arvados.org/cwl#WorkflowRunnerResources":
+                h["ramMin"] = submit_runner_ram
+                found = True
+                break
+        if not found:
+            hints.append({"class": "http://arvados.org/cwl#WorkflowRunnerResources",
+                          "ramMin": submit_runner_ram})
+        main["hints"] = hints
 
     body = {
         "workflow": {
             "name": name,
             "description": tool.tool.get("doc", ""),
-            "definition":yaml.round_trip_dump(packed)
+            "definition":json.dumps(packed, sort_keys=True, indent=4, separators=(',',': '))
         }}
     if project_uuid:
         body["workflow"]["owner_uuid"] = project_uuid
@@ -143,11 +154,10 @@ class ArvadosWorkflow(Workflow):
 
                     packed = pack(document_loader, workflowobj, uri, self.metadata)
 
-                    builder = Builder()
-                    builder.job = joborder
-                    builder.requirements = workflowobj["requirements"]
-                    builder.hints = workflowobj["hints"]
-                    builder.resources = {}
+                    builder = Builder(joborder,
+                                      requirements=workflowobj["requirements"],
+                                      hints=workflowobj["hints"],
+                                      resources={})
 
                     def visit(item):
                         for t in ("hints", "requirements"):
@@ -188,11 +198,10 @@ class ArvadosWorkflow(Workflow):
 
 
             if self.dynamic_resource_req:
-                builder = Builder()
-                builder.job = joborder
-                builder.requirements = self.requirements
-                builder.hints = self.hints
-                builder.resources = {}
+                builder = Builder(joborder,
+                                  requirements=self.requirements,
+                                  hints=self.hints,
+                                  resources={})
 
                 # Evaluate dynamic resource requirements using current builder
                 rs = copy.copy(self.static_resource_req)
@@ -259,14 +268,12 @@ class ArvadosWorkflow(Workflow):
                 "outputs": self.tool["outputs"],
                 "stdout": "cwl.output.json",
                 "requirements": self.requirements+job_res_reqs+[
+                    {"class": "InlineJavascriptRequirement"},
                     {
                     "class": "InitialWorkDirRequirement",
                     "listing": [{
                             "entryname": "workflow.cwl",
-                            "entry": {
-                                "class": "File",
-                                "location": "keep:%s/workflow.cwl" % self.wf_pdh
-                            }
+                            "entry": '$({"class": "File", "location": "keep:%s/workflow.cwl"})' % self.wf_pdh
                         }, {
                             "entryname": "cwl.input.yml",
                             "entry": json.dumps(joborder_keepmount, indent=2, sort_keys=True, separators=(',',': ')).replace("\\", "\\\\").replace('$(', '\$(').replace('${', '\${')