Fix file discovery

galaxyproject · Sep 12, 2023 · cddc58b · cddc58b
1 parent 01d4d43
commit cddc58b
Showing 1 changed file with 2 additions and 1 deletion.
diff --git a/lib/galaxy/metadata/set_metadata.py b/lib/galaxy/metadata/set_metadata.py
@@ -435,9 +435,10 @@ def set_meta(new_dataset_instance, file_dict):
                 if not object_store or not export_store:
                     # Can't happen, but type system doesn't know
                     raise Exception("object_store not built")
-                if not is_deferred and not link_data_only:
+                if not is_deferred and not link_data_only and os.path.getsize(external_filename):
                     # Here we might be updating a disk based objectstore when outputs_to_working_directory is used,
                     # or a remote object store from its cache path.
+                    # empty files could happen when outputs are discovered
                     object_store_update_actions.append(
                         partial(
                             object_store.update_from_file, dataset.dataset, file_name=external_filename, create=True