From: Peter Amstutz Date: Thu, 26 Jan 2023 16:06:23 +0000 (-0500) Subject: 19385: fast-parser fixups X-Git-Tag: 2.6.0~48^2~9 X-Git-Url: https://git.arvados.org/arvados.git/commitdiff_plain/a5bb9338a46680c3976544618d0a3fd5f0b65a96 19385: fast-parser fixups Arvados-DCO-1.1-Signed-off-by: Peter Amstutz --- diff --git a/sdk/cwl/arvados_cwl/arvworkflow.py b/sdk/cwl/arvados_cwl/arvworkflow.py index e850ebcb29..c38458833a 100644 --- a/sdk/cwl/arvados_cwl/arvworkflow.py +++ b/sdk/cwl/arvados_cwl/arvworkflow.py @@ -188,7 +188,12 @@ def update_refs(d, baseuri, urlexpander, merged_map, jobmapper, set_block_style, else: update_refs(s, baseuri, urlexpander, merged_map, jobmapper, set_block_style, runtimeContext, prefix, replacePrefix) elif isinstance(d, MutableMapping): - if "id" in d: + for field in ("id", "name"): + if isinstance(d.get(field), str) and d[field].startswith("_:"): + # blank node reference, was added in automatically, can get rid of it. + del d[field] + + if "id" in d and not d: baseuri = urlexpander(d["id"], baseuri, scoped_id=True) elif "name" in d and isinstance(d["name"], str): baseuri = urlexpander(d["name"], baseuri, scoped_id=True) @@ -353,6 +358,8 @@ def new_upload_workflow(arvRunner, tool, job_order, project_uuid, col.save_new(name=toolname, owner_uuid=arvRunner.project_uuid, ensure_unique_name=True, properties=properties) + logger.info("Workflow uploaded to %s", col.manifest_locator()) + adjustDirObjs(job_order, trim_listing) adjustFileObjs(job_order, trim_anonymous_location) adjustDirObjs(job_order, trim_anonymous_location)