File Validation Error

[MarikeReimer]

Description

When I try to validate my NWB files, I get a value error for the namespace.

Steps to Reproduce

1. Create NWB file in this tutorial:
   https://pynwb.readthedocs.io/en/stable/tutorials/domain/ecephys.html#sphx-glr-tutorials-domain-ecephys-py

2. Attempt validation in Jupyter/command prompt.

3. Observe error:
   ValueError: data type 'NWBFile' not found in namespace hdmf-common

Jupyter:
! python -m pynwb.validate ecephys_example.nwb

Command prompt:
python -m pynwb.validate ecephys_example.nwb

Environment

Python Executable: Python
Python Version: Python 3.7.5
Operating System: Windows
HDMF Version: Version of PyNWB used: 1.1.2

Checklist

• [ X] Have you ensured the feature or change was not already reported?
• [X ] Have you included a brief and descriptive title?
• [ X] Have you included a clear description of the problem you are trying to solve?
• [ X] Have you included a minimal code snippet that reproduces the issue you are encountering?
• [X ] Have you checked our Contributing document?

[t-b]

Is that the same as #1157?

[MarikeReimer]

They are both validation problems, however the error messages are different: 1166: ValueError: builder for container 'root' must have data type defined with attribute 'data_type' 1166: ValueError: data type 'NWBFile' not found in namespace hdmf-common

On 2020/01/30 09:53, Thomas Braun wrote: Is that the same as #1157 [1]? -- You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub [2], or unsubscribe [3].

Links: ------ [1] https://urldefense.com/v3/__https://github.com/NeurodataWithoutBorders/pynwb/issues/1157__;!!C5qS4YX3!VUc8KJr41rt1zyX8u2hlmh-WRM0db3vxuL_QxhmFUYc8zPj9IKXukkYNqtq97uw-Dg$ [2] https://urldefense.com/v3/__https://github.com/NeurodataWithoutBorders/pynwb/issues/1166?email_source=notifications&email_token=AIPFK7HPYL6IHX7IC7MABRTRAMH2JA5CNFSM4KN2H7NKYY3PNVWWK3TUL52HS4DFVREXG43VMVBW63LNMVXHJKTDN5WW2ZLOORPWSZGOEKL5I4A*issuecomment-580375664__;Iw!!C5qS4YX3!VUc8KJr41rt1zyX8u2hlmh-WRM0db3vxuL_QxhmFUYc8zPj9IKXukkYNqtruOcaK8w$ [3] https://urldefense.com/v3/__https://github.com/notifications/unsubscribe-auth/AIPFK7DDBEFN6XLXUX5YRNDRAMH2JANCNFSM4KN2H7NA__;!!C5qS4YX3!VUc8KJr41rt1zyX8u2hlmh-WRM0db3vxuL_QxhmFUYc8zPj9IKXukkYNqtpUCBYS7Q$

[oruebel]

From the errors it sounds like this may have to do with move of things from PyNWB to HDMF.

CC @rly @ajtritt f

[t-b]

I'm happy to (help) tackling that if I can get some pointers.

[oruebel]

Thanks @t-b Luckily the hackathon is coming up next week, so if we can't get to it now, then just ping Andrew or Ryan there ;-)

[rly]

I believe this specific error will be fixed by this commit in #1167: 1e6a513

I believe the errors are different between this and #1157 because PyNWB 1.1.2 does not yet incorporate the recently merged PR #1094