Error in reading nwb files in matnwb

[cmikkelsen]

When we are trying to use nwbRead to open the data from this experiment: https://dandiarchive.org/dandiset/000114?search=oxytocin%20neurons%20social%20transmission&pos=1 we are getting an error using matnwb, " Unable to resolve the name 'types.hdmf_experimental.DynamicTableRegion'. " when trying to load the data . It seems to be occuring for a number of files, but we are able to open data from other dandisets successfully. Thank you for any guidance on how to resolve this issue!

[yarikoptic]

attn @lawrence-mbf @bendichter @rly

[lawrence-mbf]

Without access to a computer, my guess would be that this file is missing a schema. If so (and using the most recent matnwb version), calling

generateCore(util.getSchemaVersion(<filename>))

Should allow you to then read the file. If that throws please let us know.

,Lawrence

Nov 23, 2023 06:57:01 Yaroslav Halchenko @.***>:

attn @lawrence-mbf[https://github.com/lawrence-mbf] @bendichter[https://github.com/bendichter] @rly[https://github.com/rly]

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[rly]

Copying my response from Slack here so that it can be searchable:

Sorry you are having trouble with this dandiset. I see the issue. There are multiple places in the files where the namespace for DynamicTableRegion and VectorData objects is hdmf-experimental instead of hdmf-common.

Do you know how to run a Python script? I wrote a quick Python script to modify the NWB files to fix the above issue here https://gist.github.com/rly/7b3365d157ebb7d0a565bbd48eb12fdd . Download that file and run python fix_dandiset_000114.py [path to directory containing your dandiset NWB files] and let me know if that fixes it.

The python script modifies any NWB files from dandiset 000114 that you have downloaded into a directory. After that, you should be able to open the file in matnwb and continue to use matnwb for your analysis if you wish.

@bendichter added me to the 000114 dandiset so that I can update the NWB files, but my dandihub died (Satra was helping troubleshoot), so that will have to wait.

[lawrence-mbf]

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[rly]

It looks like the issue has been fixed in the latest draft version of the dandiset: https://dandiarchive.org/dandiset/000114/draft so I think this issue can be closed.