diff --git a/src/hubmap_translator.py b/src/hubmap_translator.py index 2710393d..4c91f025 100644 --- a/src/hubmap_translator.py +++ b/src/hubmap_translator.py @@ -1303,11 +1303,11 @@ def translate_collection(self, entity, reindex=False): , es_index=private_index , delete_existing_doc_first=reindex) - logger.info(f"Finished executing translate_collection() for {entity_id}") + logger.info(f"Finished executing translate_collection() for {entity.get('uuid')}") except requests.exceptions.RequestException as e: logger.exception(e) # Log the error and will need fix later and reindex, rather than sys.exit() - logger.error(f"translate_collection() failed to get collection of uuid: {entity_id} via entity-api") + logger.error(f"translate_collection() failed to get collection of uuid: {entity.get('uuid')} via entity-api") except Exception as e: logger.error(e) @@ -1764,6 +1764,7 @@ def filter_fields(entity_list): immediate_ancestor_ids = [e['uuid'] for e in immediate_ancestors_full] immediate_descendant_ids = [e['uuid'] for e in immediate_descendants_full] donor = copy.deepcopy(reindex_info['donor']) if reindex_info.get('donor') else None + donors = copy.deepcopy(reindex_info['donors']) if reindex_info.get('donors') else None origin_samples = reindex_info.get('origin_samples', []) source_samples = reindex_info.get('source_samples', []) else: @@ -1849,12 +1850,13 @@ def filter_fields(entity_list): self.exclude_added_calculated_fields(origin_sample) if entity['entity_type'] in ['Dataset', 'Publication']: entity['source_samples'] = source_samples + entity['donors'] = donors entity['ancestors'] = filter_fields(ancestors) if reindex_info is not None else \ self._relatives_for_index_group(relative_ids=ancestor_ids, index_group=index_group) self._entity_keys_rename(entity) - for field in ['donor', 'origin_samples', 'source_samples', 'ancestors', + for field in ['donor', 'donors', 'origin_samples', 'source_samples', 'ancestors', 'descendants', 'immediate_descendants', 'immediate_ancestors']: items = entity.get(field) if items is None: