import ruamel.yaml as yaml
-from .runner import upload_docker, upload_dependencies
+from .runner import upload_docker, upload_dependencies, trim_listing
from .arvtool import ArvadosCommandTool
+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"])
packed = pack(document_loader, workflowobj, uri, tool.metadata)
+ adjustDirObjs(job_order, trim_listing)
+
main = [p for p in packed["$graph"] if p["id"] == "#main"][0]
for inp in main["inputs"]:
sn = shortname(inp["id"])
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."""
if req:
document_loader, workflowobj, uri = (self.doc_loader, self.doc_loader.fetch(self.tool["id"]), self.tool["id"])
- workflowobj["requirements"] = self.requirements + workflowobj.get("requirements", [])
- workflowobj["hints"] = self.hints + workflowobj.get("hints", [])
- packed = pack(document_loader, workflowobj, uri, self.metadata)
-
- upload_dependencies(self.arvrunner,
- kwargs.get("name", ""),
- document_loader,
- packed,
- uri,
- False)
-
- upload_dependencies(self.arvrunner,
- os.path.basename(joborder.get("id", "#")),
- document_loader,
- joborder,
- joborder.get("id", "#"),
- False)
-
- joborder_keepmount = copy.deepcopy(joborder)
-
- def keepmount(obj):
- if obj["location"].startswith("keep:"):
- obj["location"] = "/keep/" + obj["location"][5:]
- elif obj["location"].startswith("_:"):
- pass
- else:
- raise WorkflowException("Location is not a keep reference or a literal: '%s'" % obj["location"])
- if "listing" in obj:
- del obj["listing"]
- adjustFileObjs(joborder_keepmount, keepmount)
- adjustDirObjs(joborder_keepmount, keepmount)
- adjustFileObjs(packed, keepmount)
- adjustDirObjs(packed, keepmount)
+ with Perf(metrics, "subworkflow upload_deps"):
+ workflowobj["requirements"] = self.requirements + workflowobj.get("requirements", [])
+ workflowobj["hints"] = self.hints + workflowobj.get("hints", [])
+ packed = pack(document_loader, workflowobj, uri, self.metadata)
+
+ upload_dependencies(self.arvrunner,
+ kwargs.get("name", ""),
+ document_loader,
+ packed,
+ uri,
+ False)
+
+ upload_dependencies(self.arvrunner,
+ os.path.basename(joborder.get("id", "#")),
+ document_loader,
+ joborder,
+ joborder.get("id", "#"),
+ False)
+
+ with Perf(metrics, "subworkflow adjust"):
+ 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:
+ del obj["listing"]
+ elif obj["location"].startswith("_:"):
+ del obj["location"]
+ else:
+ raise WorkflowException("Location is not a keep reference or a literal: '%s'" % obj["location"])
+
+ adjustFileObjs(joborder_keepmount, keepmount)
+ adjustDirObjs(joborder_keepmount, keepmount)
+ adjustFileObjs(packed, keepmount)
+ adjustDirObjs(packed, keepmount)
wf_runner = {
"class": "CommandLineTool",
"outputs": self.tool["outputs"],
"stdout": "cwl.output.json",
"requirements": workflowobj["requirements"]+[
- {"class": "InlineJavascriptRequirement"},
{
"class": "InitialWorkDirRequirement",
"listing": [{
}]
}],
"hints": workflowobj["hints"],
- "arguments": ["--no-container", "--move-outputs", "workflow.cwl#main", "cwl.input.yml"]
+ "arguments": ["--no-container", "--move-outputs", "--preserve-entire-environment", "workflow.cwl#main", "cwl.input.yml"]
}
kwargs["loader"] = self.doc_loader
kwargs["avsc_names"] = self.doc_schema