from cwltool.load_tool import load_tool
from cwltool.errors import WorkflowException
+from .fsaccess import CollectionFetcher
+
logger = logging.getLogger('arvados.cwl-runner')
def run():
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)
+ t = load_tool(toolpath, runner.arv_make_tool,
+ fetcher_constructor=functools.partial(CollectionFetcher,
+ api_client=api,
+ keep_client=arvados.keep.KeepClient(api_client=api, num_retries=4)))
args = argparse.Namespace()
args.project_uuid = arvados.current_job()["owner_uuid"]