+# 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, 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
return v
def keeppathObj(v):
- v["location"] = keeppath(v["location"])
+ 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):
args.name = None
args.cwl_runner_job={"uuid": arvados.current_job()["uuid"], "state": arvados.current_job()["state"]}
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: