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Derek furst/bulk ids #983

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1f8d65c
added endpoint /entities/batch-ids/ and its corresponding neo4j query
DerekFurstPitt Feb 4, 2026
2241fb6
added comment block describing get_batch_ids
DerekFurstPitt Feb 4, 2026
546cd3a
uncommented out locked_entity_update_override_key
DerekFurstPitt Feb 4, 2026
8fea7e5
removed trailing slash in endpoint path for batch-ids
DerekFurstPitt Feb 5, 2026
25cdbf7
added entity spec yaml for the new batch ids endpoint. Fixed docstrin…
DerekFurstPitt Feb 6, 2026
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43 changes: 43 additions & 0 deletions entity-api-spec.yaml
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Original file line number Diff line number Diff line change
Expand Up @@ -3140,3 +3140,46 @@ paths:
description: The given dataset is unpublished and the user does not have the authorization to view it.
'500':
description: Internal error
'/entities/batch-ids':
post:
summary: Retrieve the HuBMAP ID and UUID for each entity id provided in a list.
requestBody:
required: true
content:
application/json:
schema:
type: array
description: List of entity identifiers (HuBMAP IDs or UUIDs)
items:
type: string
responses:
'200':
description: Mapping of input entity identifiers to their resolved HuBMAP ID and UUID. If no items are found, will simply return empty.
content:
application/json:
schema:
type: object
additionalProperties:
type: object
properties:
hubmap_id:
type: string
description: Canonical HuBMAP ID for the entity
uuid:
type: string
format: uuid
description: UUID for the entity
required:
- hubmap_id
- uuid
examples:
batchidsexample:
value:
HBM123.ABCD.456:
hubmap_id: "HBM123.ABCD.456"
uuid: "a8098c1a-f86e-11da-bd1a-00112444be1e"
abcd1234-ef56-gh78-ij90-klmnop123456:
hubmap_id: "HBM987.WXYZ.321"
uuid: "abcd1234-ef56-gh78-ij90-klmnop123456"
'500':
description: Internal Error
27 changes: 27 additions & 0 deletions src/app.py
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Expand Up @@ -4319,6 +4319,33 @@ def entity_bulk_update():
return jsonify(list(uuids)), 202


"""
Retrieve ids (uuid, hubmap_id) for a given id

Request Body
------------
JSON array of entity identifiers (either uuids or HuBMAP IDs)

Example:
[
"HBM123.ABCD.456",
"a1234b56-c78d-90de-fg1h-23456789i01j"
]

Returns
-------
json
JSON object keyed by the entity identifier. Each value is a mapping containing the HuBMAP ID and UUID for that entity
"""
@app.route('/entities/batch-ids', methods = ['POST'])
def get_batch_ids():
validate_token_if_auth_header_exists(request)
require_json(request)
json_data_dict = request.get_json()
ids = app_neo4j_queries.get_batch_ids(neo4j_driver_instance, json_data_dict)
return jsonify(ids)


####################################################################################################
## Internal Functions
####################################################################################################
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33 changes: 33 additions & 0 deletions src/app_neo4j_queries.py
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Expand Up @@ -1181,3 +1181,36 @@ def get_entities_by_uuid(neo4j_driver,
return None

return records

"""
Get the uuid and hubmap_id for each entity in a list of ids.

Parameters
----------
neo4j_driver : neo4j.Driver object
The neo4j database connection pool
id_list : list
The list of ids

Returns
-------
Dictionary containing the uuid and hubmap_id of each entity in the list, keyed by that entities original id given
"""
def get_batch_ids(neo4j_driver, id_list):
query = """
MATCH (e)
WHERE e.uuid IN $id_list OR e.hubmap_id IN $id_list
WITH e, [id IN $id_list WHERE id = e.uuid OR id = e.hubmap_id][0] AS original_id
RETURN original_id, e.uuid AS uuid, e.hubmap_id AS hubmap_id
"""

result_map = {}

with neo4j_driver.session() as session:
result = session.run(query, id_list=id_list)
for record in result:
result_map[record['original_id']] = {
"uuid": record['uuid'],
"hubmap_id": record['hubmap_id']
}
return result_map