failing validation of matnwb-generated files with cached namespace

[cechava]

matnwb-generated NWB files fail validation due to missing experimental.yaml file. The following replicates the error:

nwb = NwbFile( ...
    'session_description', 'mouse in open exploration',...
    'identifier', 'Mouse5_Day3', ...
    'session_start_time', datetime(2018, 4, 25, 2, 30, 3) ...
);
nwbExport(nwb, 'simple_file_export.nwb')

$  python -m pynwb.validate simple_file_export.nwb

full traceback:

Traceback (most recent call last):
  File "/Users/cesar/anaconda3/envs/pynwb-dev/lib/python3.9/runpy.py", line 197, in _run_module_as_main
    return _run_code(code, main_globals, None,
  File "/Users/cesar/anaconda3/envs/pynwb-dev/lib/python3.9/runpy.py", line 87, in _run_code
    exec(code, run_globals)
  File "/Users/cesar/anaconda3/envs/pynwb-dev/lib/python3.9/site-packages/pynwb/validate.py", line 136, in <module>
    main()
  File "/Users/cesar/anaconda3/envs/pynwb-dev/lib/python3.9/site-packages/pynwb/validate.py", line 72, in main
    ns_deps = NWBHDF5IO.load_namespaces(catalog, path)
  File "/Users/cesar/anaconda3/envs/pynwb-dev/lib/python3.9/site-packages/hdmf/utils.py", line 583, in func_call
    return func(args[0], **pargs)
  File "/Users/cesar/anaconda3/envs/pynwb-dev/lib/python3.9/site-packages/hdmf/backends/hdf5/h5tools.py", line 147, in load_namespaces
    return cls.__load_namespaces(namespace_catalog, namespaces, open_file_obj)
  File "/Users/cesar/anaconda3/envs/pynwb-dev/lib/python3.9/site-packages/hdmf/backends/hdf5/h5tools.py", line 181, in __load_namespaces
    d.update(namespace_catalog.load_namespaces(cls.__ns_spec_path, reader=reader))
  File "/Users/cesar/anaconda3/envs/pynwb-dev/lib/python3.9/site-packages/hdmf/utils.py", line 583, in func_call
    return func(args[0], **pargs)
  File "/Users/cesar/anaconda3/envs/pynwb-dev/lib/python3.9/site-packages/hdmf/spec/namespace.py", line 538, in load_namespaces
    ret[ns['name']] = self.__load_namespace(ns, reader, resolve=resolve)
  File "/Users/cesar/anaconda3/envs/pynwb-dev/lib/python3.9/site-packages/hdmf/spec/namespace.py", line 448, in __load_namespace
    self.__load_spec_file(reader, s['source'], catalog, types_to_load=types_to_load, resolve=resolve)
  File "/Users/cesar/anaconda3/envs/pynwb-dev/lib/python3.9/site-packages/hdmf/spec/namespace.py", line 393, in __load_spec_file
    d = reader.read_spec(spec_source)
  File "/Users/cesar/anaconda3/envs/pynwb-dev/lib/python3.9/site-packages/hdmf/backends/hdf5/h5_utils.py", line 331, in read_spec
    return self.__read(spec_path)
  File "/Users/cesar/anaconda3/envs/pynwb-dev/lib/python3.9/site-packages/hdmf/backends/hdf5/h5_utils.py", line 320, in __read
    s = self.__group[path][()]
  File "h5py/_objects.pyx", line 54, in h5py._objects.with_phil.wrapper
  File "h5py/_objects.pyx", line 55, in h5py._objects.with_phil.wrapper
  File "/Users/cesar/anaconda3/envs/pynwb-dev/lib/python3.9/site-packages/h5py/_hl/group.py", line 305, in __getitem__
    oid = h5o.open(self.id, self._e(name), lapl=self._lapl)
  File "h5py/_objects.pyx", line 54, in h5py._objects.with_phil.wrapper
  File "h5py/_objects.pyx", line 55, in h5py._objects.with_phil.wrapper
  File "h5py/h5o.pyx", line 190, in h5py.h5o.open

No issue when the pynwb validator is is run with the --no-cached-namespace There's also no issue with pynwb-generated files.

[cechava]

@ln-vidrio let me know if you have an idea of how to address this.

[lawrence-mbf]

This is because we're assuming that there is only one namespace per namespace.yaml file. In fact, nothing from that experimental namespace is actually generated as class files anyway.

[oruebel]

@rly this issue may be of interest for you