From 2cddd92e172cc20d0b7c1c8013b64fb32056f3df Mon Sep 17 00:00:00 2001 From: Peter Amstutz Date: Thu, 12 Jan 2017 11:14:24 -0500 Subject: [PATCH] 10869: Pass CollectionFetcher to load_tool in crunch_script so that it will recognize keep: URIs. --- sdk/cwl/arvados_cwl/crunch_script.py | 7 ++++++- 1 file changed, 6 insertions(+), 1 deletion(-) diff --git a/sdk/cwl/arvados_cwl/crunch_script.py b/sdk/cwl/arvados_cwl/crunch_script.py index 500fbdd0d7..f33619391d 100644 --- a/sdk/cwl/arvados_cwl/crunch_script.py +++ b/sdk/cwl/arvados_cwl/crunch_script.py @@ -23,6 +23,8 @@ from cwltool.process import shortname, adjustFileObjs, adjustDirObjs, getListing from cwltool.load_tool import load_tool from cwltool.errors import WorkflowException +from .fsaccess import CollectionFetcher + logger = logging.getLogger('arvados.cwl-runner') def run(): @@ -87,7 +89,10 @@ 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"] -- 2.30.2