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figure out what to do about h5py dtype having metadata.vlen in order to get pynwb validator to work with Lindi #53

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magland opened this issue Apr 19, 2024 · 0 comments

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@magland
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magland commented Apr 19, 2024

See #47

and see code comments here

if ret.kind == 'O':
if not ret.metadata:
# The following correction is needed because of
# this code in hdmf/backends/hdf5/h5tools.py:
# def _check_str_dtype(self, h5obj):
# dtype = h5obj.dtype
# if dtype.kind == 'O':
# if dtype.metadata.get('vlen') == str and H5PY_3:
# return StrDataset(h5obj, None)
# return h5obj
# We cannot have a dtype with kind 'O' and no metadata
# There is also this section in pynwb validator.py
# if isinstance(received, np.dtype):
# if received.char == 'O':
# if 'vlen' in received.metadata:
# received = received.metadata['vlen']
# else:
# raise ValueError("Unrecognized type: '%s'" % received)
# received = 'utf' if received is str else 'ascii'
# elif received.char == 'U':
# received = 'utf'
# elif received.char == 'S':
# received = 'ascii'
# else:
# received = received.name
# ------------------------------------------
# I don't know how to figure out when vlen should be str or bytes
# but validate seems to work only when I put in vlen = bytes
#
vlen = bytes
ret = np.dtype(str(ret), metadata={'vlen': vlen})

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