Add label

Author: mboudet

biotools_cleaner/cleaner_batch.py

@@ -14,8 +14,10 @@
     parser.add_argument('rse_repo', type=str, help="Research-software-ecosystem data folder")
     parser.add_argument('--dry-run', action='store_true', help="Dry run")
     parser.add_argument('--cleanup', action='store_true', help="Remove old layout files from repository")
+    parser.add_argument('--add-label', action='store_true', help="Make sure all tools in a specific file have the same biotool label")
+
     args = parser.parse_args()
 
     for path in pathlib.Path(args.rse_repo).rglob("biocontainers.yaml"):
         tool = Tool(str(path.resolve()))
-        tool.write_yaml(args.rse_repo, dry_run=args.dry_run, remove_input=args.cleanup)
+        tool.write_yaml(args.rse_repo, dry_run=args.dry_run, remove_input=args.cleanup, add_biotool=args.add_label)

biotools_cleaner/tool.py

@@ -16,7 +16,7 @@ def __init__(self, tool_yaml):
 
         logging.info('Processing ' + tool_yaml)
 
-    def write_yaml(self, output_dir, dry_run=False, remove_input=False):
+    def write_yaml(self, output_dir, dry_run=False, remove_input=False, add_biotool=False):
         to_merge = {}
         if not self.yaml_data.get('softwares'):
             logging.error('"softwares" key not found or empty')
@@ -48,6 +48,9 @@ def write_yaml(self, output_dir, dry_run=False, remove_input=False):
             if tool_name in to_merge:
                 biotool_id = to_merge[tool_name]
                 logging.warn("Assuming {} biotool id is {}".format(tool_name, biotool_id))
+                if add_biotool:
+                    logging.warn("Adding biotool label")
+                    values['labels']['extra.identifiers.biotools'] = biotool_id
 
             data[biotool_id].append({"tool": tool_name, "value": values})