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+(/.+)?$')
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"])
-
for k,v in job_order_object.items():
if isinstance(v, basestring) and arvados.util.keep_locator_pattern.match(v):
job_order_object[k] = {
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"]
+
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)
+ t = load_tool(toolpath, runner.arv_make_tool)
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 = False
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))
except Exception as e: