+# Copyright (C) The Arvados Authors. All rights reserved.
+#
+# SPDX-License-Identifier: Apache-2.0
+
# Crunch script integration for running arvados-cwl-runner (importing
# arvados_cwl module) inside a crunch job.
#
import functools
from arvados.api import OrderedJsonModel
-from cwltool.process import shortname, adjustFileObjs, adjustDirObjs, getListing, normalizeFilesDirs
+from cwltool.process import shortname
+from cwltool.pathmapper import adjustFileObjs, adjustDirObjs, normalizeFilesDirs
from cwltool.load_tool import load_tool
from cwltool.errors import WorkflowException
+from .fsaccess import CollectionFetcher, CollectionFsAccess
+
logger = logging.getLogger('arvados.cwl-runner')
def run():
+ # Timestamps are added by crunch-job, so don't print redundant timestamps.
+ arvados.log_handler.setFormatter(logging.Formatter('%(name)s %(levelname)s: %(message)s'))
+
# Print package versions
logger.info(arvados_cwl.versionstring())
runner = None
try:
job_order_object = arvados.current_job()['script_parameters']
+ toolpath = "file://%s/%s" % (os.environ['TASK_KEEPMOUNT'], job_order_object.pop("cwl:tool"))
pdh_path = re.compile(r'^[0-9a-f]{32}\+\d+(/.+)?$')
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"])
+ if "location" in v:
+ v["location"] = keeppath(v["location"])
for k,v in job_order_object.items():
if isinstance(v, basestring) and arvados.util.keep_locator_pattern.match(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
output_tags = None
enable_reuse = True
+ on_error = "continue"
+ debug = False
+
if "arv:output_name" in job_order_object:
output_name = job_order_object["arv:output_name"]
del job_order_object["arv:output_name"]
enable_reuse = job_order_object["arv:enable_reuse"]
del job_order_object["arv:enable_reuse"]
+ if "arv:on_error" in job_order_object:
+ on_error = job_order_object["arv:on_error"]
+ del job_order_object["arv:on_error"]
+
+ if "arv:debug" in job_order_object:
+ debug = job_order_object["arv:debug"]
+ del job_order_object["arv:debug"]
+
runner = arvados_cwl.ArvCwlRunner(api_client=arvados.api('v1', model=OrderedJsonModel()),
output_name=output_name, output_tags=output_tags)
- t = load_tool(job_order_object, runner.arv_make_tool)
+ make_fs_access = functools.partial(CollectionFsAccess,
+ collection_cache=runner.collection_cache)
+
+ t = load_tool(toolpath, runner.arv_make_tool,
+ fetcher_constructor=functools.partial(CollectionFetcher,
+ api_client=runner.api,
+ fs_access=make_fs_access(""),
+ num_retries=runner.num_retries))
+
+ if debug:
+ logger.setLevel(logging.DEBUG)
+ logging.getLogger('arvados').setLevel(logging.DEBUG)
+ logging.getLogger("cwltool").setLevel(logging.DEBUG)
args = argparse.Namespace()
args.project_uuid = arvados.current_job()["owner_uuid"]
args.enable_reuse = enable_reuse
+ args.on_error = on_error
args.submit = False
- args.debug = True
+ args.debug = debug
args.quiet = False
args.ignore_docker_for_reuse = False
args.basedir = os.getcwd()
+ args.name = None
args.cwl_runner_job={"uuid": arvados.current_job()["uuid"], "state": arvados.current_job()["state"]}
- outputObj = runner.arv_executor(t, job_order_object, **vars(args))
+ args.make_fs_access = make_fs_access
+ args.trash_intermediate = False
+ args.intermediate_output_ttl = 0
+
+ runner.arv_executor(t, job_order_object, **vars(args))
except Exception as e:
if isinstance(e, WorkflowException):
logging.info("Workflow error %s", e)