Anyone have an issue writing file with custom extension due to a datatype error?

[josh-steighner]

Hi all,

I have a custom extension that adds an object for partner data designed to generally mimic the built-in subject object (we work with pair-bonded animals). While my code correctly generates the file in Jupyter Notebook, but for some reason when I try to write the file I get an error due to a data type conflict. Specifically, date-of-birth is required to be datetime to be added to the NWB file, but when I try to write the file I get an error that it was expecting a string.

The extensions.yaml and create_extension_spec.py files all say datetime, so why would the write function expect a different type? Apologies if I'm making some glaring oversight, but would appreciate any suggestions!

[rly]

Hi @josh-steighner , PyNWB (and HDMF) have some issues with datetime dtypes in extensions that we are working to resolve:

• [Bug]: Cannot build data (dataset) with dtype datetime hdmf-dev/hdmf#1311
• get_class to handle datetimes hdmf-dev/hdmf#429

The fix is not quite ready yet. When it's ready, I will ping you to see if it works for you. It's not ideal, but in the meantime, you can use dtype text.

You might also be interested in our (early) proposal for storing data from multiple subjects in a NWB file: https://github.com/nehatk17/ndx-multisubjects

There, we use dtype text instead of datetime while we resolve the issue.

[josh-steighner]

Ah, thanks for the help! Setting it as text and saving in iso format worked great.