[Bug]: "Nothing found at path ''" once again

[rcpeene]

What happened?

I'm attempting to append coordinate information to my NWB, but getting an error seen before in #205 and #255 .
This NWB I'm using is directly from @alejoe91 's ephys pipeline on Allen Institute's Code Ocean. He may have more relevant details about the packaging.
Since #255 was closed, ensuring hdmf_zarr and hdmf were up-to-date would suffice whenever I had this problem, but now I have ensured my packages are latest and still get this problem.

Steps to Reproduce

with NWBZarrIO(nwb_path, mode="a") as read_io:
        nwb = read_io.read()

Traceback

Traceback (most recent call last):
  File "/root/capsule/code/run_capsule.py", line 256, in <module>
    run()
  File "/root/capsule/code/run_capsule.py", line 231, in run
    with io_class(str(result_nwb_path), mode="a") as read_io:
  File "/opt/conda/lib/python3.9/site-packages/hdmf/utils.py", line 577, in func_call
    return func(args[0], **pargs)
  File "/opt/conda/lib/python3.9/site-packages/hdmf_zarr/nwb.py", line 47, in __init__
    super().load_namespaces(tm, path, storage_options)
  File "/opt/conda/lib/python3.9/site-packages/hdmf/utils.py", line 577, in func_call
    return func(args[0], **pargs)
  File "/opt/conda/lib/python3.9/site-packages/hdmf_zarr/backend.py", line 270, in load_namespaces
    f = zarr.open(path, mode="r", storage_options=storage_options)
  File "/opt/conda/lib/python3.9/site-packages/zarr/convenience.py", line 137, in open
    raise PathNotFoundError(path)
zarr.errors.PathNotFoundError: nothing found at path ''

Operating System

Windows

Python Version

3.13

Package Versions

hdmf==4.0.0
hdmf_zarr==0.11.1

[oruebel]

Thanks for letting us know. @mavaylon1 can you please take a look and respond to this issue.

[rcpeene]

Ah I'll add that there is more to the traceback

Traceback (most recent call last):
  File "/opt/conda/lib/python3.9/site-packages/hdmf_zarr/backend.py", line 566, in __open_file_consolidated
    return zarr.open_consolidated(
  File "/opt/conda/lib/python3.9/site-packages/zarr/convenience.py", line 1360, in open_consolidated
    meta_store = ConsolidatedStoreClass(store, metadata_key=metadata_key)
  File "/opt/conda/lib/python3.9/site-packages/zarr/storage.py", line 3046, in __init__
    meta = json_loads(self.store[metadata_key])
  File "/opt/conda/lib/python3.9/site-packages/zarr/storage.py", line 1120, in __getitem__
    raise KeyError(key)
KeyError: '.zmetadata'

despite .zmetadata being a visible file in the NWB.

[mavaylon1]

Hi @rcpeene thank for reporting this issue. Since this is not a common issue, I am not entirely sure what aspect of your NWBFile to recreate. Are you on our slack channel? We can discuss sharing your NWBFile for me to recreate the issue.

[rcpeene]

I made some changes and haven't reproduced the error since.

I believe when the issue was made, zarr was upgraded after installing hdmf-zarr. After I wrote them into the same environment and installed the latest versions together in pip, the error disappeared. Perhaps some pip chicanery.

Can close for now, will reopen if becomes an issue again.