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Merged
yuanzhou merged 3 commits into from
Apr 21, 2026
Merged

Derek furst/optimize generate doc #1024

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6523e62
added support for field 'donors' for datasets and publications
DerekFurstPitt Apr 21, 2026
8d5ede7
fixed potential logging bug
DerekFurstPitt Apr 21, 2026
c46fc7c
Merge branch 'Derek-Furst/multiple-donors' into Derek-Furst/optimize-…
DerekFurstPitt Apr 21, 2026
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8 changes: 5 additions & 3 deletions src/hubmap_translator.py
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Original file line number Diff line number Diff line change
Expand Up @@ -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)

Expand Down Expand Up @@ -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:
Expand Down Expand Up @@ -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:
Expand Down
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