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validating an hdmf file can no longer be done by executing the module #473
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I tagged this as a bug because it sounds like it was intended functionality that no longer works, but I don't know what the bug criteria is for this project, so this could very easily be an enhancement. I'd be happy to submit a PR for this. @rly suggested it could be very similar to this: https://github.com/NeurodataWithoutBorders/pynwb/blob/dev/src/pynwb/validate.py |
Depending on the timeline for the fix, I would suggest to do 1 as a quick "hot fix" (i.e, simply comment this out in the documentation) and then implement 2 (and add back the appropriate documentation) once ready. If the timeline for implementing this is only a few weeks, then simply doing 2 is fine, but if plan to have additional releases in-between, then I would suggest to do 1 first.
That is a reasonable label. In this particular case, it would also be fine to label it as an enhancement since this is functionality that by itself has not existed in HDMF, but I think either option is fine. |
I made a PR to update the documentation in #482. Should we keep this open, or create a new enhancement issue for implementing the documented functionality and close this issue? It seems like implementing this in the code might not be a high priority since the validation functionality is currently available in pynwb, do you guys agree? |
I think its simplest to just keep this issue open for now. I changed the label from bug to enhancement and added a short update to the description of the issue above to clarify what the state of this issue is and what remains to be done. Thanks @dsleiter for identifying this issue and the quick fix!
I don't think there are any pressing use cases that need this functionality in HDMF itself right now, but I'm sure it will become necessary at some point. It is good to at least have an issue that documents that this still needs to be done. |
Description
The HDMF documentation shows the following process for validating a file: https://hdmf.readthedocs.io/en/stable/validation.html
In talking with @rly, this used to work prior to extracting HDFM out of PyNWB, and now only works through the
pynwb.validate
module: https://pynwb.readthedocs.io/en/stable/validation.htmlTwo options for resolving are to:
@rly suggested that we implement the second.
Update
Option 1. has been implemented in #482
This issue has been kept open until option 2 (i.e., adding validation functionality back) has been implemented.
Steps to Reproduce
Attempt to validate a hdmf file using the command provided in the documentation:
Environment
Checklist
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