#!/usr/bin/env python
+# Copyright (C) The Arvados Authors. All rights reserved.
+#
+# SPDX-License-Identifier: Apache-2.0
+
+# Crunch script integration for running arvados-cwl-runner inside a crunch job.
-import arvados
import arvados_cwl
+import sys
+
+try:
+ # Use the crunch script defined in the arvados_cwl package. This helps
+ # prevent the crunch script from going out of sync with the rest of the
+ # arvados_cwl package.
+ import arvados_cwl.crunch_script
+ arvados_cwl.crunch_script.run()
+ sys.exit()
+except ImportError:
+ pass
+
+# When running against an older arvados-cwl-runner package without
+# arvados_cwl.crunch_script, fall back to the old code.
+
+
+# This gets the job record, transforms the script parameters into a valid CWL
+# input object, then executes the CWL runner to run the underlying workflow or
+# tool. When the workflow completes, record the output object in an output
+# collection for this runner job.
+
+import arvados
import arvados.collection
import arvados.util
-from cwltool.process import shortname
import cwltool.main
import logging
import os
import json
import argparse
+import re
+import functools
+
from arvados.api import OrderedJsonModel
-from cwltool.process import adjustFiles
+from cwltool.process import shortname, adjustFileObjs, adjustDirObjs, getListing, normalizeFilesDirs
+from cwltool.load_tool import load_tool
+
+# Print package versions
+logging.info(cwltool.main.versionstring())
api = arvados.api("v1")
try:
job_order_object = arvados.current_job()['script_parameters']
- def keeppath(v):
- if arvados.util.keep_locator_pattern.match(v):
- return "file://%s/%s" % (os.environ['TASK_KEEPMOUNT'], v)
-
- job_order_object["cwl:tool"] = keeppath(job_order_object["cwl:tool"])
-
- adjustFiles(job_order_object, keeppath)
-
- runner = arvados_cwl.ArvCwlRunner(api_client=arvados.api('v1', model=OrderedJsonModel()))
-
- t = cwltool.main.load_tool(job_order_object, False, True, runner.arvMakeTool, True)
-
- np = argparse.Namespace()
- np.project_uuid = arvados.current_job()["owner_uuid"]
- np.enable_reuse = True
- np.submit = False
- np.debug = True
- np.quiet = False
- outputObj = runner.arvExecutor(t, job_order_object, "", np, cwl_runner_job={"uuid": arvados.current_job()["uuid"], "state": arvados.current_job()["state"]})
-
- files = {}
- def capture(path):
- sp = path.split("/")
- col = sp[0][5:]
- if col not in files:
- files[col] = set()
- files[col].add("/".join(sp[1:]))
- return path
+ pdh_path = re.compile(r'^[0-9a-f]{32}\+\d+(/.+)?$')
- adjustFiles(outputObj, capture)
-
- final = arvados.collection.Collection()
-
- for k,v in files.iteritems():
- with arvados.collection.Collection(k) as c:
- for f in c:
- final.copy(f, f, c, True)
-
- def makeRelative(path):
- return "/".join(path.split("/")[1:])
-
- adjustFiles(outputObj, makeRelative)
-
- with final.open("cwl.output.json", "w") as f:
- json.dump(outputObj, f, indent=4)
+ def keeppath(v):
+ if pdh_path.match(v):
+ return "keep:%s" % v
+ else:
+ return v
+
+ def keeppathObj(v):
+ v["location"] = keeppath(v["location"])
+
+ job_order_object["cwl:tool"] = "file://%s/%s" % (os.environ['TASK_KEEPMOUNT'], job_order_object["cwl:tool"])
+
+ for k,v in job_order_object.items():
+ if isinstance(v, basestring) and arvados.util.keep_locator_pattern.match(v):
+ job_order_object[k] = {
+ "class": "File",
+ "location": "keep:%s" % v
+ }
+
+ adjustFileObjs(job_order_object, keeppathObj)
+ adjustDirObjs(job_order_object, keeppathObj)
+ normalizeFilesDirs(job_order_object)
+ adjustDirObjs(job_order_object, functools.partial(getListing, arvados_cwl.fsaccess.CollectionFsAccess("", api_client=api)))
+
+ output_name = None
+ if "arv:output_name" in job_order_object:
+ output_name = job_order_object["arv:output_name"]
+ del job_order_object["arv:output_name"]
+
+ runner = arvados_cwl.ArvCwlRunner(api_client=arvados.api('v1', model=OrderedJsonModel()),
+ output_name=output_name)
+
+ t = load_tool(job_order_object, runner.arv_make_tool)
+
+ args = argparse.Namespace()
+ args.project_uuid = arvados.current_job()["owner_uuid"]
+ args.enable_reuse = True
+ args.submit = False
+ args.debug = True
+ args.quiet = False
+ args.ignore_docker_for_reuse = False
+ args.basedir = os.getcwd()
+ args.cwl_runner_job={"uuid": arvados.current_job()["uuid"], "state": arvados.current_job()["state"]}
+ outputObj = runner.arv_executor(t, job_order_object, **vars(args))
+
+ if runner.final_output_collection:
+ outputCollection = runner.final_output_collection.portable_data_hash()
+ else:
+ outputCollection = None
api.job_tasks().update(uuid=arvados.current_task()['uuid'],
body={
- 'output': final.save_new(create_collection_record=False),
+ 'output': outputCollection,
'success': True,
'progress':1.0
}).execute()
projects / arvados.git / blobdiff