tidy

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():