+# Copyright (C) The Arvados Authors. All rights reserved.
+#
+# SPDX-License-Identifier: Apache-2.0
+
import os
import json
import copy
from cwltool.load_tool import fetch_document
from cwltool.process import shortname
from cwltool.workflow import Workflow, WorkflowException
-from cwltool.pathmapper import adjustFileObjs, adjustDirObjs
+from cwltool.pathmapper import adjustFileObjs, adjustDirObjs, visit_class
import ruamel.yaml as yaml
-from .runner import upload_docker, upload_dependencies, trim_listing
+from .runner import (upload_dependencies, packed_workflow, upload_workflow_collection,
+ trim_anonymous_location, remove_redundant_fields, discover_secondary_files)
+from .pathmapper import ArvPathMapper, trim_listing
from .arvtool import ArvadosCommandTool
from .perf import Perf
def upload_workflow(arvRunner, tool, job_order, project_uuid, uuid=None,
submit_runner_ram=0, name=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)
+ packed = packed_workflow(arvRunner, tool)
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 not name:
name = tool.tool.get("label", os.path.basename(tool.tool["id"]))
- upload_dependencies(arvRunner, name, document_loader,
- packed, uri, False)
+ upload_dependencies(arvRunner, name, tool.doc_loader,
+ packed, tool.tool["id"], False)
# TODO nowhere for submit_runner_ram to go.
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):
+ with SourceLine(self.tool, None, WorkflowException, logger.isEnabledFor(logging.DEBUG)):
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"])
- 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)
+ discover_secondary_files(self.tool["inputs"], joborder)
+ with Perf(metrics, "subworkflow upload_deps"):
upload_dependencies(self.arvrunner,
os.path.basename(joborder.get("id", "#")),
document_loader,
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_resolved = copy.deepcopy(joborder)
joborder_keepmount = copy.deepcopy(joborder)
+ reffiles = []
+ visit_class(joborder_keepmount, ("File", "Directory"), lambda x: reffiles.append(x))
+
+ mapper = ArvPathMapper(self.arvrunner, reffiles, kwargs["basedir"],
+ "/keep/%s",
+ "/keep/%s/%s",
+ **kwargs)
+
def keepmount(obj):
- with SourceLine(obj, None, WorkflowException):
+ remove_redundant_fields(obj)
+ with SourceLine(obj, None, WorkflowException, logger.isEnabledFor(logging.DEBUG)):
if "location" not in obj:
raise WorkflowException("%s object is missing required 'location' field: %s" % (obj["class"], obj))
- with SourceLine(obj, "location", WorkflowException):
+ with SourceLine(obj, "location", WorkflowException, logger.isEnabledFor(logging.DEBUG)):
if obj["location"].startswith("keep:"):
- obj["location"] = "/keep/" + obj["location"][5:]
+ obj["location"] = mapper.mapper(obj["location"]).target
if "listing" in obj:
del obj["listing"]
elif obj["location"].startswith("_:"):
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)
+ visit_class(joborder_keepmount, ("File", "Directory"), keepmount)
+
+ def resolved(obj):
+ if obj["location"].startswith("keep:"):
+ obj["location"] = mapper.mapper(obj["location"]).resolved
+
+ visit_class(joborder_resolved, ("File", "Directory"), resolved)
+
+ 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",
"inputs": self.tool["inputs"],
"outputs": self.tool["outputs"],
"stdout": "cwl.output.json",
- "requirements": workflowobj["requirements"]+[
+ "requirements": self.requirements+[
{
"class": "InitialWorkDirRequirement",
"listing": [{
"entryname": "workflow.cwl",
- "entry": yaml.round_trip_dump(packed).replace("\\", "\\\\").replace('$(', '\$(').replace('${', '\${')
+ "entry": {
+ "class": "File",
+ "location": "keep:%s/workflow.cwl" % self.wf_pdh
+ }
}, {
"entryname": "cwl.input.yml",
- "entry": yaml.round_trip_dump(joborder_keepmount).replace("\\", "\\\\").replace('$(', '\$(').replace('${', '\${')
+ "entry": json.dumps(joborder_keepmount, indent=2, sort_keys=True, separators=(',',': ')).replace("\\", "\\\\").replace('$(', '\$(').replace('${', '\${')
}]
}],
- "hints": workflowobj["hints"],
+ "hints": self.hints,
"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)
+ return ArvadosCommandTool(self.arvrunner, wf_runner, **kwargs).job(joborder_resolved, output_callback, **kwargs)
else:
return super(ArvadosWorkflow, self).job(joborder, output_callback, **kwargs)
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