Failed to extract metadata: Indexing elements must be in increasing order

Inizia in dandi/pynwb_utils.py, in _get_session_duration(), in particolare alla riga indicata nel traceback, e riproduci il problema con il file NWB indicato tramite dandi upload. Confronta i suoi dati di temporizzazione della sessione con quelli dei due file che vengono caricati correttamente. Il lavoro è completato quando l’estrazione dei metadati e il caricamento non falliscono più per questo file, con una copertura per il caso segnalato se viene identificata una posizione di test esistente.

Hello,

I've made some nwb files and am trying to upload them to DANDI using dandi upload. I have three of them. Two upload just fine. The other one hits this error trace:

2026-05-28T16:06:11+0100 [WARNING ] dandi 923713:127939540670144 Failed to extract NWB metadata from /home/nolanlab/fromgit/nolanlab_nwb/001854/sub-M22/sub-M22_ses-D34OF2_ecephys+behavior.nwb: TypeError: Indexing elements must be in increasing order
2026-05-28T16:06:11+0100 [ERROR   ] dandi 923713:127939540670144 Error uploading /home/nolanlab/fromgit/nolanlab_nwb/001854/sub-M22/sub-M22_ses-D34OF2_ecephys+behavior.nwb:
Traceback (most recent call last):
  File "/home/nolanlab/fromgit/nolanlab_nwb/.venv/lib/python3.13/site-packages/dandi/upload.py", line 392, in process_path
    metadata = dfile.get_metadata(
               ~~~~~~~~~~~~~~~~~~^
        digest=file_etag, ignore_errors=allow_any_path
        ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
    ).model_dump(mode="json", exclude_none=True)
    ^
  File "/home/nolanlab/fromgit/nolanlab_nwb/.venv/lib/python3.13/site-packages/dandi/files/bases.py", line 494, in get_metadata
    metadata = nwb2asset(self.filepath, digest=digest)
  File "/home/nolanlab/fromgit/nolanlab_nwb/.venv/lib/python3.13/site-packages/dandi/metadata/nwb.py", line 149, in nwb2asset
    metadata = get_metadata(nwb_path)
  File "/home/nolanlab/fromgit/nolanlab_nwb/.venv/lib/python3.13/site-packages/fscacher/cache.py", line 164, in fingerprinter
    ret = fingerprinted(*args, **kwargs_)
  File "/home/nolanlab/fromgit/nolanlab_nwb/.venv/lib/python3.13/site-packages/joblib/memory.py", line 607, in __call__
    return self._cached_call(args, kwargs, shelving=False)[0]
           ~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/home/nolanlab/fromgit/nolanlab_nwb/.venv/lib/python3.13/site-packages/joblib/memory.py", line 562, in _cached_call
    return self._call(call_id, args, kwargs, shelving)
           ~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/home/nolanlab/fromgit/nolanlab_nwb/.venv/lib/python3.13/site-packages/joblib/memory.py", line 832, in _call
    output = self.func(*args, **kwargs)
  File "/home/nolanlab/fromgit/nolanlab_nwb/.venv/lib/python3.13/site-packages/fscacher/cache.py", line 100, in fingerprinted
    return f(path, *args, **kwargs)
  File "/home/nolanlab/fromgit/nolanlab_nwb/.venv/lib/python3.13/site-packages/dandi/metadata/nwb.py", line 106, in get_metadata
    meta.update(_get_pynwb_metadata(r))
                ~~~~~~~~~~~~~~~~~~~^^^
  File "/home/nolanlab/fromgit/nolanlab_nwb/.venv/lib/python3.13/site-packages/dandi/pynwb_utils.py", line 279, in _get_pynwb_metadata
    session_duration = _get_session_duration(nwb)
  File "/home/nolanlab/fromgit/nolanlab_nwb/.venv/lib/python3.13/site-packages/dandi/pynwb_utils.py", line 350, in _get_session_duration
    start = float(np.min(np.r_[st_data[0], st_data[idxs[:-1]]]))
                                           ~~~~~~~^^^^^^^^^^^
  File "/home/nolanlab/fromgit/nolanlab_nwb/.venv/lib/python3.13/site-packages/hdmf/container.py", line 1002, in __getitem__
    return self.get(args)
           ~~~~~~~~^^^^^^
  File "/home/nolanlab/fromgit/nolanlab_nwb/.venv/lib/python3.13/site-packages/hdmf/common/table.py", line 61, in get
    return super().get(key)
           ~~~~~~~~~~~^^^^^
  File "/home/nolanlab/fromgit/nolanlab_nwb/.venv/lib/python3.13/site-packages/hdmf/container.py", line 1010, in get
    return self.data[args]
           ~~~~~~~~~^^^^^^
  File "h5py/_objects.pyx", line 56, in h5py._objects.with_phil.wrapper
  File "h5py/_objects.pyx", line 57, in h5py._objects.with_phil.wrapper
  File "/home/nolanlab/fromgit/nolanlab_nwb/.venv/lib/python3.13/site-packages/h5py/_hl/dataset.py", line 893, in __getitem__
    selection = sel.select(self.shape, args, dataset=self)
  File "/home/nolanlab/fromgit/nolanlab_nwb/.venv/lib/python3.13/site-packages/h5py/_hl/selections.py", line 82, in select
    return selector.make_selection(args)
           ~~~~~~~~~~~~~~~~~~~~~~~^^^^^^
  File "h5py/_selector.pyx", line 282, in h5py._selector.Selector.make_selection
  File "h5py/_selector.pyx", line 215, in h5py._selector.Selector.apply_args
TypeError: Indexing elements must be in increasing order

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
  File "/home/nolanlab/fromgit/nolanlab_nwb/.venv/lib/python3.13/site-packages/dandi/upload.py", line 396, in process_path
    raise UploadError("failed to extract metadata: %s" % str(e))
dandi.exceptions.UploadError: failed to extract metadata: Indexing elements must be in increasing order
2026-05-28T16:06:11+0100 [DEBUG   ] urllib3.connectionpool 923713:127941258118976 Starting new HTTPS connection (1): rig.mit.edu:443
2026-05-28T16:06:16+0100 [DEBUG   ] dandi 923713:127941258118976 Caught exception failed to extract metadata: Indexing elements must be in increasing order
Traceback (most recent call last):
  File "/home/nolanlab/fromgit/nolanlab_nwb/.venv/lib/python3.13/site-packages/dandi/upload.py", line 392, in process_path
    metadata = dfile.get_metadata(
               ~~~~~~~~~~~~~~~~~~^
        digest=file_etag, ignore_errors=allow_any_path
        ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
    ).model_dump(mode="json", exclude_none=True)
    ^
  File "/home/nolanlab/fromgit/nolanlab_nwb/.venv/lib/python3.13/site-packages/dandi/files/bases.py", line 494, in get_metadata
    metadata = nwb2asset(self.filepath, digest=digest)
  File "/home/nolanlab/fromgit/nolanlab_nwb/.venv/lib/python3.13/site-packages/dandi/metadata/nwb.py", line 149, in nwb2asset
    metadata = get_metadata(nwb_path)
  File "/home/nolanlab/fromgit/nolanlab_nwb/.venv/lib/python3.13/site-packages/fscacher/cache.py", line 164, in fingerprinter
    ret = fingerprinted(*args, **kwargs_)
  File "/home/nolanlab/fromgit/nolanlab_nwb/.venv/lib/python3.13/site-packages/joblib/memory.py", line 607, in __call__
    return self._cached_call(args, kwargs, shelving=False)[0]
           ~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/home/nolanlab/fromgit/nolanlab_nwb/.venv/lib/python3.13/site-packages/joblib/memory.py", line 562, in _cached_call
    return self._call(call_id, args, kwargs, shelving)
           ~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/home/nolanlab/fromgit/nolanlab_nwb/.venv/lib/python3.13/site-packages/joblib/memory.py", line 832, in _call
    output = self.func(*args, **kwargs)
  File "/home/nolanlab/fromgit/nolanlab_nwb/.venv/lib/python3.13/site-packages/fscacher/cache.py", line 100, in fingerprinted
    return f(path, *args, **kwargs)
  File "/home/nolanlab/fromgit/nolanlab_nwb/.venv/lib/python3.13/site-packages/dandi/metadata/nwb.py", line 106, in get_metadata
    meta.update(_get_pynwb_metadata(r))
                ~~~~~~~~~~~~~~~~~~~^^^
  File "/home/nolanlab/fromgit/nolanlab_nwb/.venv/lib/python3.13/site-packages/dandi/pynwb_utils.py", line 279, in _get_pynwb_metadata
    session_duration = _get_session_duration(nwb)
  File "/home/nolanlab/fromgit/nolanlab_nwb/.venv/lib/python3.13/site-packages/dandi/pynwb_utils.py", line 350, in _get_session_duration
    start = float(np.min(np.r_[st_data[0], st_data[idxs[:-1]]]))
                                           ~~~~~~~^^^^^^^^^^^
  File "/home/nolanlab/fromgit/nolanlab_nwb/.venv/lib/python3.13/site-packages/hdmf/container.py", line 1002, in __getitem__
    return self.get(args)
           ~~~~~~~~^^^^^^
  File "/home/nolanlab/fromgit/nolanlab_nwb/.venv/lib/python3.13/site-packages/hdmf/common/table.py", line 61, in get
    return super().get(key)
           ~~~~~~~~~~~^^^^^
  File "/home/nolanlab/fromgit/nolanlab_nwb/.venv/lib/python3.13/site-packages/hdmf/container.py", line 1010, in get
    return self.data[args]
           ~~~~~~~~~^^^^^^
  File "h5py/_objects.pyx", line 56, in h5py._objects.with_phil.wrapper
  File "h5py/_objects.pyx", line 57, in h5py._objects.with_phil.wrapper
  File "/home/nolanlab/fromgit/nolanlab_nwb/.venv/lib/python3.13/site-packages/h5py/_hl/dataset.py", line 893, in __getitem__
    selection = sel.select(self.shape, args, dataset=self)
  File "/home/nolanlab/fromgit/nolanlab_nwb/.venv/lib/python3.13/site-packages/h5py/_hl/selections.py", line 82, in select
    return selector.make_selection(args)
           ~~~~~~~~~~~~~~~~~~~~~~~^^^^^^
  File "h5py/_selector.pyx", line 282, in h5py._selector.Selector.make_selection
  File "h5py/_selector.pyx", line 215, in h5py._selector.Selector.apply_args
TypeError: Indexing elements must be in increasing order

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
  File "/home/nolanlab/fromgit/nolanlab_nwb/.venv/lib/python3.13/site-packages/dandi/cli/base.py", line 126, in wrapper
    return f(*args, **kwargs)
  File "/home/nolanlab/fromgit/nolanlab_nwb/.venv/lib/python3.13/site-packages/dandi/cli/cmd_upload.py", line 113, in upload
    upload_(
    ~~~~~~~^
        paths,
        ^^^^^^
    ...<9 lines>...
        validation_log_path=companion,
        ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
    )
    ^
  File "/home/nolanlab/fromgit/nolanlab_nwb/.venv/lib/python3.13/site-packages/dandi/upload.py", line 505, in upload
    raise upload_err
  File "/home/nolanlab/fromgit/nolanlab_nwb/.venv/lib/python3.13/site-packages/dandi/upload.py", line 396, in process_path
    raise UploadError("failed to extract metadata: %s" % str(e))
dandi.exceptions.UploadError: failed to extract metadata: Indexing elements must be in increasing order

I don't know what this means, or how to proceed.

Strange things:

• dandi validate runs fine.
• the metadata is generated in the same way for all nwb files, so I don' t understand why only one of them would fail.
• When I open the nwb file using pynwb, it looks fine and all the metadata looks reasonable.

Any advice very welcome!