Add metadata to dtype when kind is 'O'

In order to get pynwb validation to pass I needed to make the tweak of this PR. It seems that h5py uses a vlen field in metadata for a numpy dtype, and pynwb inspects that. I don't understand exactly what this is about. But when I set it to bytes in this case, the validation passes.

Here's a test validation script where things are passing with this PR


import pynwb
from pynwb import CORE_NAMESPACE
from pynwb.validate import ValidatorMap
import h5py
import remfile
import lindi

def test_validate(io: pynwb.NWBHDF5IO):
    namespace = CORE_NAMESPACE
    validator = ValidatorMap(namespace=io.manager.namespace_catalog.get_namespace(name=namespace))
    builder = io.read_builder()
    validation_errors = validator.validate(builder=builder)
    if len(validation_errors) == 0:
        print('Validation passed!')
    else:
        print('Validation failed!')
        for ve in validation_errors:
            print(ve)

if __name__ == "__main__":
    # https://neurosift.app/?p=/nwb&dandisetId=000409&dandisetVersion=draft&url=https://api.dandiarchive.org/api/assets/c04f6b30-82bf-40e1-9210-34f0bcd8be24/download/

    print('')
    print('Validating with HDF5 URL...')
    h5_url = 'https://api.dandiarchive.org/api/assets/c04f6b30-82bf-40e1-9210-34f0bcd8be24/download/'
    remf = remfile.File(h5_url)
    h5f = h5py.File(remf, mode='r')
    with pynwb.NWBHDF5IO(file=h5f, mode='r', load_namespaces=True) as io:
        test_validate(io)

    print('')
    print('Validating with LINDI URL...')
    lindi_url = 'https://lindi.neurosift.org/dandi/dandisets/000409/assets/c04f6b30-82bf-40e1-9210-34f0bcd8be24/zarr.json'
    ff = lindi.LindiH5pyFile.from_reference_file_system(lindi_url)
    with pynwb.NWBHDF5IO(file=ff, mode='r', load_namespaces=True) as io:
        test_validate(io)

NeurodataWithoutBorders / lindi

Add metadata to dtype when kind is 'O' #47

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