Troubleshoot Object x Analyte Dataset

[yuanzhou]

From Brendan:

Object x Analyte Dataset for CMU: https://ingest.hubmapconsortium.org/dataset/HBM842.TRKL.652/. It's not indexed in the portal just yet, but reorganization from the big (500 GB/300+ parent) upload worked.

From Juan:

reindexing is not immediate anymore - it’s probably going to take a long time since it has so many parent datasets. UUID in question is 728d02be5fada1541decd1091a4b17e3

[yuanzhou]

The response payload of this dataset is quite large 35MB (S3 link returned by entity-api /entities/<id> with 377 parents) and the response used by reindex from /documents/<id> is only 9.6KB. This is not causing the reindex issue though.

After manually triggered the reindex, it became available on data portal https://portal.hubmapconsortium.org/browse/dataset/728d02be5fada1541decd1091a4b17e3. However, the vis errored out and the call to ingest-api's POST /accessible-data-directories also returned 500.

[2026-02-25 17:25:43] ERROR in app: Unable to get data to determine accessibility of '728d02be5fada1541decd1091a4b17e3'
Traceback (most recent call last):
  File "/usr/local/python3.13/lib/python3.13/site-packages/requests/models.py", line 976, in json
    return complexjson.loads(self.text, **kwargs)
           ~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^
  File "/usr/local/python3.13/lib/python3.13/json/__init__.py", line 346, in loads
    return _default_decoder.decode(s)
           ~~~~~~~~~~~~~~~~~~~~~~~^^^
  File "/usr/local/python3.13/lib/python3.13/json/decoder.py", line 345, in decode
    obj, end = self.raw_decode(s, idx=_w(s, 0).end())
               ~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^
  File "/usr/local/python3.13/lib/python3.13/json/decoder.py", line 363, in raw_decode
    raise JSONDecodeError("Expecting value", s, err.value) from None
json.decoder.JSONDecodeError: Expecting value: line 1 column 1 (char 0)

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
  File "/usr/local/python3.13/lib/python3.13/site-packages/hubmap_sdk/sdk_helper.py", line 77, in make_request
    error = r.json()['error']
            ~~~~~~^^
  File "/usr/local/python3.13/lib/python3.13/site-packages/requests/models.py", line 980, in json
    raise RequestsJSONDecodeError(e.msg, e.doc, e.pos)
requests.exceptions.JSONDecodeError: Expecting value: line 1 column 1 (char 0)

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
  File "/usr/src/app/src/dataset_helper_object.py", line 137, in get_entity_accessibility
    sdk_entity = entity_api.get_entity_by_id(entity_id)
  File "/usr/local/python3.13/lib/python3.13/site-packages/hubmap_sdk/entitysdk.py", line 79, in get_entity_by_id
    output = sdk_helper.make_request('get', self, url)
  File "/usr/local/python3.13/lib/python3.13/site-packages/hubmap_sdk/sdk_helper.py", line 86, in make_request
    raise json.decoder.JSONDecodeError
TypeError: JSONDecodeError.__init__() missing 3 required positional arguments: 'msg', 'doc', and 'pos'

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
  File "/usr/src/app/src/app.py", line 619, in get_accessible_data_directories
    identifier_accessibility_dict = dataset_helper.get_entity_accessibility(identifier
                                                                            , user_token
                                                                            , user_data_access_level=user_data_access_level)
  File "/usr/src/app/src/dataset_helper_object.py", line 159, in get_entity_accessibility
    raise Exception(msg)
Exception: Unable to get data to determine accessibility of '728d02be5fada1541decd1091a4b17e3'
[pid: 306|app: 0|req: 63995/285855] 172.18.0.3 () {86 vars in 1391 bytes} [Wed Feb 25 17:25:24 2026] POST /entities/accessible-data-directories => generated 101 bytes in 19805 msecs (HTTP/1.0 500) 2 headers in 99 bytes (1 switches on core 3)