Regarding reading of NWB files with PyNWB and Python-Neo

[appukuttan-shailesh]

Describe the bug We are trying to read NWB files from the Allen Brain Atlas. E.g.: https://celltypes.brain-map.org/experiment/electrophysiology/643575207 Download URL: https://celltypes.brain-map.org/api/v2/well_known_file_download/742807112

We are having problems reading the file with PyNWB and Python-Neo. A ticket has been opened on this subject, presenting the error obtained. https://github.com/NeuralEnsemble/python-neo/issues/1131

These files are readable with the allendsk package. However, we want to use PyNWB, in order to be able to read it again later with python-Neo. We believe this is because of differences in internal structures of these files, and they probably follow an older NWB specification? Are there already tools for converting these as per current specs, or plans for upgrading these files?

To Reproduce

from neo.io import NWBIO
reader = NWBIO(filename="525011725_ephys.nwb")
reader.read_all_blocks()

Expected behavior For PyNWB, and therefore Python-Neo, to be able to read the files.

Actual Behavior ValueError: 'comments' already exists in Sweep_10.attributes, cannot set in datasets.

Environment (please complete the following information):

• OS & version: Ubuntu 20.04
• Python version: 3.8

Additional context Add any other context about the problem here.

Do you want to work on this issue? I don't have the expertise to handle this. The Python-Neo and/or NWB teams are aware of the issue and might be able to help.

Tagging others following this issue: @apdavison, @legouee