from arvados.api import OrderedJsonModel
from cwltool.process import shortname, adjustFileObjs, adjustDirObjs, getListing, normalizeFilesDirs
from cwltool.load_tool import load_tool
+from cwltool.errors import WorkflowException
logger = logging.getLogger('arvados.cwl-runner')
arvados_cwl.add_arv_hints()
+ runner = None
try:
job_order_object = arvados.current_job()['script_parameters']
adjustDirObjs(job_order_object, functools.partial(getListing, arvados_cwl.fsaccess.CollectionFsAccess("", api_client=api)))
output_name = None
+ output_tags = None
+ enable_reuse = True
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_tags" in job_order_object:
+ output_tags = job_order_object["arv:output_tags"]
+ del job_order_object["arv:output_tags"]
+
+ if "arv:enable_reuse" in job_order_object:
+ enable_reuse = job_order_object["arv:enable_reuse"]
+ del job_order_object["arv:enable_reuse"]
+
runner = arvados_cwl.ArvCwlRunner(api_client=arvados.api('v1', model=OrderedJsonModel()),
- output_name=output_name)
+ output_name=output_name, output_tags=output_tags)
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.enable_reuse = enable_reuse
args.submit = False
args.debug = True
args.quiet = 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:
+ except Exception as e:
+ if isinstance(e, WorkflowException):
+ logging.info("Workflow error %s", e)
+ else:
+ logging.exception("Unhandled exception")
+ if runner and 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': outputCollection,
- 'success': True,
- 'progress':1.0
- }).execute()
- except Exception as e:
- logging.exception("Unhandled exception")
- api.job_tasks().update(uuid=arvados.current_task()['uuid'],
- body={
- 'output': None,
'success': False,
'progress':1.0
}).execute()