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13111: Merge branch 'master' into 13111-webdav-projects
[arvados.git]
/
sdk
/
cwl
/
arvados_cwl
/
crunch_script.py
diff --git
a/sdk/cwl/arvados_cwl/crunch_script.py
b/sdk/cwl/arvados_cwl/crunch_script.py
index 821abf9266861b8049116bfd3952e2dd789ac27f..aaeffea24b22ef0a3dc4a2de3b35e78f4d5d8e46 100644
(file)
--- a/
sdk/cwl/arvados_cwl/crunch_script.py
+++ b/
sdk/cwl/arvados_cwl/crunch_script.py
@@
-1,3
+1,7
@@
+# 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.
#
# Crunch script integration for running arvados-cwl-runner (importing
# arvados_cwl module) inside a crunch job.
#
@@
-71,6
+75,8
@@
def run():
output_tags = None
enable_reuse = True
on_error = "continue"
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"]
if "arv:output_name" in job_order_object:
output_name = job_order_object["arv:output_name"]
del job_order_object["arv:output_name"]
@@
-87,6
+93,10
@@
def run():
on_error = job_order_object["arv:on_error"]
del job_order_object["arv:on_error"]
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)
runner = arvados_cwl.ArvCwlRunner(api_client=arvados.api('v1', model=OrderedJsonModel()),
output_name=output_name, output_tags=output_tags)
@@
-99,18
+109,28
@@
def run():
fs_access=make_fs_access(""),
num_retries=runner.num_retries))
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 = 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 =
False
+ 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"]}
args.make_fs_access = make_fs_access
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"]}
args.make_fs_access = make_fs_access
+ args.trash_intermediate = False
+ args.intermediate_output_ttl = 0
+ args.priority = arvados_cwl.DEFAULT_PRIORITY
+ args.do_validate = True
+ args.disable_js_validation = False
runner.arv_executor(t, job_order_object, **vars(args))
except Exception as e:
runner.arv_executor(t, job_order_object, **vars(args))
except Exception as e: