def run_cwl_workflow_engine_adapter(
publisher,
rjc_api_client,
workflow_uuid=None,
workflow_workspace=None,
workflow_json=None,
workflow_parameters=None,
operational_options={},
**kwargs,
):
"""Run cwl workflow."""
workflow_parameters = parse_str_to_int(workflow_parameters)
log.info(f"running workflow on context: {locals()}")
rcode = main.main(
publisher,
rjc_api_client,
workflow_uuid,
workflow_json,
workflow_parameters,
operational_options,
workflow_workspace,
)
log.info("workflow done")
publisher.publish_workflow_status(workflow_uuid, rcode_to_workflow_status(rcode))
def run_cwl_workflow(workflow_uuid,
workflow_workspace,
workflow_json=None,
workflow_parameters=None,
operational_options={}):
"""Run cwl workflow."""
workflow_parameters = parse_str_to_int(workflow_parameters)
log.info(f'running workflow on context: {locals()}')
try:
check_connection_to_job_controller()
publisher = WorkflowStatusPublisher()
rcode = main.main(workflow_uuid, workflow_json, workflow_parameters,
operational_options, workflow_workspace, publisher)
log.info('workflow done')
publisher.publish_workflow_status(workflow_uuid,
rcode_to_workflow_status(rcode))
except Exception as e:
log.error(f'workflow failed: {e}')
publisher.publish_workflow_status(workflow_uuid, 3, message=str(e))
finally:
if publisher:
publisher.close()
else:
log.error(f'Workflow {workflow_uuid} failed but status '
'could not be published.')
def run_cwl_workflow(workflow_uuid,
workflow_workspace,
workflow_json=None,
workflow_parameters=None,
operational_options={}):
"""Run cwl workflow."""
log.info('running workflow on context: {0}'.format(locals()))
try:
publisher = WorkflowStatusPublisher()
main.main(workflow_uuid, workflow_json, workflow_parameters,
operational_options, workflow_workspace, publisher)
log.info('workflow done')
publisher.publish_workflow_status(workflow_uuid, 2)
except Exception as e:
log.error('workflow failed: {0}'.format(e))
publisher.publish_workflow_status(workflow_uuid, 3, message=str(e))
finally:
if publisher:
publisher.close()
else:
log.error(
'Workflow {workflow_uuid} failed but status '
'could not be published.'.format(workflow_uuid=workflow_uuid))