+# Copyright (C) The Arvados Authors. All rights reserved.
+#
+# SPDX-License-Identifier: Apache-2.0
+
import os
import json
import copy
import logging
+from schema_salad.sourceline import SourceLine, cmap
+
from cwltool.pack import pack
from cwltool.load_tool import fetch_document
from cwltool.process import shortname
import ruamel.yaml as yaml
-from .runner import upload_docker, upload_dependencies
+from .runner import upload_dependencies, packed_workflow, upload_workflow_collection, trim_anonymous_location
+from .pathmapper import 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):
- upload_docker(arvRunner, tool)
+def upload_workflow(arvRunner, tool, job_order, project_uuid, uuid=None,
+ submit_runner_ram=0, name=None):
- document_loader, workflowobj, uri = (tool.doc_loader, tool.doc_loader.fetch(tool.tool["id"]), tool.tool["id"])
+ packed = packed_workflow(arvRunner, tool)
- packed = pack(document_loader, workflowobj, uri, tool.metadata)
+ adjustDirObjs(job_order, trim_listing)
+ adjustFileObjs(job_order, trim_anonymous_location)
+ adjustDirObjs(job_order, trim_anonymous_location)
main = [p for p in packed["$graph"] if p["id"] == "#main"][0]
for inp in main["inputs"]:
if sn in job_order:
inp["default"] = job_order[sn]
- name = os.path.basename(tool.tool["id"])
- upload_dependencies(arvRunner, name, document_loader,
- packed, uri, False)
+ if not name:
+ name = tool.tool.get("label", os.path.basename(tool.tool["id"]))
+
+ upload_dependencies(arvRunner, name, tool.doc_loader,
+ packed, tool.tool["id"], False)
+
+ # TODO nowhere for submit_runner_ram to go.
body = {
"workflow": {
- "owner_uuid": project_uuid,
- "name": tool.tool.get("label", name),
+ "name": name,
"description": tool.tool.get("doc", ""),
- "definition":yaml.safe_dump(packed)
+ "definition":yaml.round_trip_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"]
+
+def dedup_reqs(reqs):
+ dedup = {}
+ for r in reversed(reqs):
+ if r["class"] not in dedup and not r["class"].startswith("http://arvados.org/cwl#"):
+ dedup[r["class"]] = r
+ return [dedup[r] for r in sorted(dedup.keys())]
class ArvadosWorkflow(Workflow):
"""Wrap cwltool Workflow to override selected methods."""
super(ArvadosWorkflow, self).__init__(toolpath_object, **kwargs)
self.arvrunner = arvrunner
self.work_api = kwargs["work_api"]
+ self.wf_pdh = None
def job(self, joborder, output_callback, **kwargs):
kwargs["work_api"] = self.work_api
req, _ = self.get_requirement("http://arvados.org/cwl#RunInSingleContainer")
if req:
+ with SourceLine(self.tool, None, WorkflowException):
+ if "id" not in self.tool:
+ raise WorkflowException("%s object must have 'id'" % (self.tool["class"]))
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)
-
- wf_runner = {
+ with Perf(metrics, "subworkflow upload_deps"):
+ upload_dependencies(self.arvrunner,
+ os.path.basename(joborder.get("id", "#")),
+ document_loader,
+ joborder,
+ joborder.get("id", "#"),
+ False)
+
+ if self.wf_pdh is None:
+ workflowobj["requirements"] = dedup_reqs(self.requirements)
+ workflowobj["hints"] = dedup_reqs(self.hints)
+
+ packed = pack(document_loader, workflowobj, uri, self.metadata)
+
+ upload_dependencies(self.arvrunner,
+ kwargs.get("name", ""),
+ document_loader,
+ packed,
+ uri,
+ False)
+
+ with Perf(metrics, "subworkflow adjust"):
+ joborder_keepmount = copy.deepcopy(joborder)
+
+ def keepmount(obj):
+ with SourceLine(obj, None, WorkflowException):
+ if "location" not in obj:
+ raise WorkflowException("%s object is missing required 'location' field: %s" % (obj["class"], obj))
+ with SourceLine(obj, "location", WorkflowException):
+ 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)
+
+ if self.wf_pdh is None:
+ adjustFileObjs(packed, keepmount)
+ adjustDirObjs(packed, keepmount)
+ self.wf_pdh = upload_workflow_collection(self.arvrunner, shortname(self.tool["id"]), packed)
+
+ wf_runner = cmap({
"class": "CommandLineTool",
"baseCommand": "cwltool",
"inputs": self.tool["inputs"],
"outputs": self.tool["outputs"],
"stdout": "cwl.output.json",
"requirements": workflowobj["requirements"]+[
- {"class": "InlineJavascriptRequirement"},
{
"class": "InitialWorkDirRequirement",
"listing": [{
"entryname": "workflow.cwl",
- "entry": yaml.safe_dump(packed).replace("\\", "\\\\").replace('$(', '\$(').replace('${', '\${')
+ "entry": {
+ "class": "File",
+ "location": "keep:%s/workflow.cwl" % self.wf_pdh
+ }
}, {
"entryname": "cwl.input.yml",
- "entry": yaml.safe_dump(joborder_keepmount).replace("\\", "\\\\").replace('$(', '\$(').replace('${', '\${')
+ "entry": json.dumps(joborder_keepmount, indent=2, sort_keys=True, separators=(',',': ')).replace("\\", "\\\\").replace('$(', '\$(').replace('${', '\${')
}]
}],
"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
return ArvadosCommandTool(self.arvrunner, wf_runner, **kwargs).job(joborder, output_callback, **kwargs)
projects / arvados.git / blobdiff