[Bug]: Extension namespaces not exported from HDF5 NWB #145
Labels
category: bug
errors in the code or code behavior
priority: medium
non-critical problem and/or affecting only a small set of users
Milestone
What happened?
Testing an export of a dataset that has a custom namespace/schema, and found that it isn't exported and so a subsequent read errors.
Taking a look at the
__cache_spec
method, it seems like the writer uses its own manager rather than the source file's manager:hdmf-zarr/src/hdmf_zarr/backend.py
Line 284 in 5e48ab5
which is confirmed in a debugger. Setting a breakpoint at the start of that function:
and then going up to the initial call which has the source IO object:
If I do this just before calling
__cache_spec
:then the namespace is correctly written, but the read still errors. The namespace is listed in
namespaces
here:hdmf-zarr/src/hdmf_zarr/backend.py
Line 207 in 5e48ab5
but when it reaches
BuildManager.load_namespaces
, thedeps
are empty. That's as far as i'm gonna make it tonight.Steps to Reproduce
Traceback
Operating System
macOS
Python Executable
Python
Python Version
3.11
Package Versions
environment_for_issue.txt
Code of Conduct
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