diff --git a/lib/galaxy/tool_util/cwl/util.py b/lib/galaxy/tool_util/cwl/util.py index 427deb0f074..a4605653f18 100644 --- a/lib/galaxy/tool_util/cwl/util.py +++ b/lib/galaxy/tool_util/cwl/util.py @@ -145,7 +145,6 @@ def galactic_job_json( is_file = item_class == "File" is_directory = item_class == "Directory" is_collection = item_class == "Collection" # Galaxy extension. - # is_galaxy_id = item_class == "GalaxyID" # Galaxy dataset/collection ID. if force_to_file: if is_file: @@ -168,14 +167,12 @@ def galactic_job_json( return replacement_directory(value) elif is_collection: return replacement_collection(value) - # elif is_galaxy_id: - # return replacement_galaxy_id(value) else: return replacement_record(value) def replacement_file(value): if value.get('galaxy_id'): - return replacement_galaxy_id(value) + return {"src": "hda", "id": value['galaxy_id']} file_path = value.get("location", None) or value.get("path", None) # format to match output definitions in tool, where did filetype come from? filetype = value.get("filetype", None) or value.get("format", None) @@ -284,7 +281,7 @@ def galactic_job_json( def replacement_collection(value): if value.get('galaxy_id'): - return replacement_galaxy_id(value) + return {"src": "hdca", "id": value['galaxy_id']} assert "collection_type" in value collection_type = value["collection_type"] elements = to_elements(value, collection_type) @@ -294,9 +291,6 @@ def galactic_job_json( hdca_id = collection["id"] return {"src": "hdca", "id": hdca_id} - def replacement_galaxy_id(value): - return {"src": "hda", "id": value['galaxy_id']} - def replacement_record(value): collection_element_identifiers = [] for record_key, record_value in value.items():