-from cwltool.process import shortname, adjustFileObjs, adjustDirObjs, getListing, normalizeFilesDirs
+from cwltool.process import shortname, adjustFileObjs, adjustDirObjs, normalizeFilesDirs
for k,v in job_order_object.items():
if isinstance(v, basestring) and arvados.util.keep_locator_pattern.match(v):
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)
adjustFileObjs(job_order_object, keeppathObj)
adjustDirObjs(job_order_object, keeppathObj)
normalizeFilesDirs(job_order_object)
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)
t = load_tool(toolpath, runner.arv_make_tool,
fetcher_constructor=functools.partial(CollectionFetcher,
t = load_tool(toolpath, runner.arv_make_tool,
fetcher_constructor=functools.partial(CollectionFetcher,
args.basedir = os.getcwd()
args.name = None
args.cwl_runner_job={"uuid": arvados.current_job()["uuid"], "state": arvados.current_job()["state"]}
args.basedir = os.getcwd()
args.name = None
args.cwl_runner_job={"uuid": arvados.current_job()["uuid"], "state": arvados.current_job()["state"]}
runner.arv_executor(t, job_order_object, **vars(args))
except Exception as e:
if isinstance(e, WorkflowException):
runner.arv_executor(t, job_order_object, **vars(args))
except Exception as e:
if isinstance(e, WorkflowException):