Fix validator not validating on spec of builder data type

[rly]

Motivation

Fix #1049

How to test the behavior?

pytest

Checklist

• Did you update CHANGELOG.md with your changes?
• Does the PR clearly describe the problem and the solution?
• Have you reviewed our Contributing Guide?
• Does the PR use "Fix #XXX" notation to tell GitHub to close the relevant issue numbered XXX when the PR is merged?

[codecov]

Codecov Report

All modified and coverable lines are covered by tests ✅

Comparison is base (3fbe27d) 88.53% compared to head (78f51dd) 88.53%.

Additional details and impacted files

@@           Coverage Diff           @@
##              dev    #1050   +/-   ##
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  Coverage   88.53%   88.53%           
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  Files          45       45           
  Lines        9599     9603    +4     
  Branches     2730     2731    +1     
=======================================
+ Hits         8498     8502    +4     
  Misses        778      778           
  Partials      323      323           

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[rly]

Tests in pynwb dev need to be updated before merging.

[rly]

Note that releasing this has a significant potential to cause issues in existing pipelines because validation will raise more errors than it did before (and it should raise those errors because the files are non-compliant). So NWB files and dandisets that previously passed pynwb validation might now fail.

[bendichter]

I can confirm that this works now using this branch from hdmf:

import h5py
from pynwb.testing.mock.ecephys import mock_ElectricalSeries

from pynwb import NWBHDF5IO, NWBFile
from datetime import datetime
from dateutil.tz import tzlocal

nwbfile = NWBFile(
    session_description="my first synthetic recording",
    identifier="EXAMPLE_ID",
    session_start_time=datetime.now(tzlocal()),
    session_id="LONELYMTN",
)

mock_ElectricalSeries(nwbfile=nwbfile)

with NWBHDF5IO("test_electrodes.nwb", "w") as io:
    io.write(nwbfile)

with h5py.File("test_electrodes.nwb", "r+") as f:
    del f["acquisition"]["ElectricalSeries"]["electrodes"]

python -m pynwb.validate test_electrodes.nwb

Validating /test_electrodes.nwb against cached namespace information using namespace 'core'.
 - found the following errors:
ElectricalSeries (acquisition/ElectricalSeries): missing data type DynamicTableRegion (electrodes)