[Bug]: PyNWB validation fails on Zarr data: 'NWBZarrIO' object has no attribute '_file' #293
Description
What happened?
Validating a Zarr NWB file with pynwb fails. Related to NeurodataWithoutBorders/pynwb#2119
As a quick fix, I suggest we add attribute _file while the other changes in hdmf-dev/hdmf#1299 and #292 are gradually merged (the HDMF change is a major breaking change).
Steps to Reproduce
with hdmf_zarr.NWBZarrIO(path=nwbfile_path, mode="r") as io:
invalidations = pynwb.validate(io=io)Traceback
Traceback (most recent call last):
File "<stdin>", line 2, in <module>
File "/Users/rly/Documents/NWB/hdmf/src/hdmf/utils.py", line 582, in func_call
return func(**pargs)
^^^^^^^^^^^^^
File "/Users/rly/Documents/NWB/pynwb/src/pynwb/validation.py", line 165, in validate
validation_errors = _validate_single_file(path=path, **kwargs)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/Users/rly/Documents/NWB/pynwb/src/pynwb/validation.py", line 183, in _validate_single_file
cached_namespaces, manager, namespace_dependencies = get_cached_namespaces_to_validate(path=path,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/Users/rly/Documents/NWB/pynwb/src/pynwb/validation.py", line 66, in get_cached_namespaces_to_validate
file=io._file)
^^^^^^^^
AttributeError: 'NWBZarrIO' object has no attribute '_file'. Did you mean: 'file'?Operating System
macOS
Python Version
3.13
Package Versions
No response