Comments (5)
From the traceback it looks like this fails when it tries to read the first element of the data set data = zarr_obj[0]
and it looks like the error occurs in numcodec
rather than Zarr
. What confuses me is the error ValueError: buffer source array is read-only
, which seems to indicate that blosc
wants write access even when reading from file. I'm wondering whether this may be an issue in Zarr
or numcodec
instead of hdmf_zarr
A couple of things to try:
- Change the mode during reading to
a
instead ofr
to see if that fixes the issue, i.e., change this line towith BACKEND_NWB_IO[backend](path=nwbfile_path, mode="a") as io:
. If that works, then I think this may be an issue in Zarr. - Can you also try reading the file with just Zarr, i.e,. open the file and try to read
data = zarr_obj[0]
from the dataset that causes the issue? If that works, another thing to try is to open with consolidated metadata (because hdmf_zarr uses consolidated metadata by default)
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@mavaylon1 can you take this from here.
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@oruebel I can, but I probably won't take a look till earliest end of next week. Does that fit your timeline?
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Possibly related: #195
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This seems to have been resolved by my fix and release in #195
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Related Issues (20)
- [Bug]: Deploy and release workflow fails due to unsupported actions
- [Feature]: support Python 3.12 HOT 4
- [Feature]: Refactor tox.ini to match HDMF
- [Feature]: Write zarr without using pickle HOT 5
- kerchunk considerations HOT 23
- [Feature]: write `xarray`-compatible Zarr files HOT 9
- [Documentation]: `linkable` key has been deprecated HOT 2
- [Bug]: `export` fails to correctly save units after adding columns HOT 7
- [Feature]: Support pathlib.Path in ZarrIO
- [Bug]: NWBZarrIO appending HOT 7
- [Bug]: Remote read with/without consolidated metadata is not being tested
- Zarr datasets info lack compression data HOT 3
- [Feature]: Use `copy_store` for copying existing zarr data HOT 5
- [Feature]: Explore use of Zarrita HOT 2
- [Bug]: Writing NWB with `experimenter` (or any `ArrayLike[str]`) fails HOT 4
- [Feature]: NWBZarrIO should have load_namespaces=True by default HOT 2
- [Bug]: Pre-release daily workflows failing with zarr 3.0.0a0 HOT 2
- [Feature]: Support zarr-python v3
- [Bug]: `[0.7.0, 0.8.0]` Fails to open file with consolidated metadata from S3
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