From 86865a741f902ac008e11d1dec90b87b89822025 Mon Sep 17 00:00:00 2001 From: Peter Amstutz Date: Thu, 10 Mar 2016 08:28:58 -0500 Subject: [PATCH] Fixes --- crunch_scripts/cwl-runner | 10 ++++++++-- 1 file changed, 8 insertions(+), 2 deletions(-) diff --git a/crunch_scripts/cwl-runner b/crunch_scripts/cwl-runner index 3142fab593..8cbf4d876e 100755 --- a/crunch_scripts/cwl-runner +++ b/crunch_scripts/cwl-runner @@ -6,15 +6,20 @@ import arvados.collection import arvados.util from cwltool.process import shortname import cwltool.main +import logging +import os +from arvados.api import OrderedJsonModel api = arvados.api("v1") try: job_order_object = arvados.current_job()['script_parameters'] + print job_order_object + for k,v in job_order_object.items(): if arvados.util.keep_locator_pattern.match(v): - job_order_object[k] = "%s/%s" % (os.environ['TASK_KEEPMOUNT'], v) + job_order_object[k] = "file://%s/%s" % (os.environ['TASK_KEEPMOUNT'], v) runner = arvados_cwl.ArvCwlRunner(api_client=arvados.api('v1', model=OrderedJsonModel())) @@ -32,7 +37,8 @@ try: 'success': True, 'progress':1.0 }).execute() -except: +except Exception as e: + logging.exception("Unhandled exception") api.job_tasks().update(uuid=arvados.current_task()['uuid'], body={ 'output': None, -- 2.30.2