[Bug]: get_ancestor checks for neurodata type name not class

[rly]

What happened?

The method AbstractContainer.get_ancestor: https://github.com/hdmf-dev/hdmf/blob/12864bb253908e3bd48e6610ee8bca4816f85be7/src/hdmf/container.py#L369

is called by NWBMixin.get_ancestor: https://github.com/NeurodataWithoutBorders/pynwb/blob/43cfa7b4b31cd2506793faaf8a6297f78bfd47e2/src/pynwb/core.py#L36

which is called by UnitsMap.electrodes_column: https://github.com/NeurodataWithoutBorders/pynwb/blob/43cfa7b4b31cd2506793faaf8a6297f78bfd47e2/src/pynwb/io/misc.py#L46

and Units.addUnit: https://github.com/NeurodataWithoutBorders/pynwb/blob/43cfa7b4b31cd2506793faaf8a6297f78bfd47e2/src/pynwb/misc.py#L222

to find the ancestor container that has neurodata type "NWBFile". This is fine when the root class is NWBFile, but in ndx-events and some extensions, NWBFile is extended, e.g., to NdxEventsNWBFile. Then this method fails to find the root NdxEventsNWBFile object.

In the example below, when nwbfile is an instance of NdxEventsNWBFile, nwbfile.units.get_ancestor(data_type='NWBFile') returns None.

We should add a method like get_ancestor_by_class that accepts a class and finds all instances of that class or subclasses of it.

Source issue: https://github.com/rly/ndx-events/issues/22

Note that Container.get_ancestor: https://github.com/hdmf-dev/hdmf/blob/12864bb253908e3bd48e6610ee8bca4816f85be7/src/hdmf/container.py#L369

is not used by anything else, so we can start deprecating this method and use get_ancestor_by_class instead.

Steps to Reproduce

from datetime import datetime
from pynwb import NWBHDF5IO

from ndx_events import NdxEventsNWBFile

nwbfile = NdxEventsNWBFile(
    session_description="session description",
    identifier="cool_experiment_001",
    session_start_time=datetime.now().astimezone(),
)
electrode_group = nwbfile.create_electrode_group(
                name='test_group',
                description="test",
                location='unknown',
                device=nwbfile.create_device(name='test_device'))


nwbfile.add_electrode(
        id = 0,
        group=electrode_group,
        location="brain area"
    )

nwbfile.add_unit(spike_times=[0,1],electrodes=[0])

Traceback

Traceback (most recent call last):
  File "<python-input-0>", line 24, in <module>
    nwbfile.add_unit(spike_times=[0,1],electrodes=[0])
    ~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/Users/rly/miniconda3/envs/test/lib/python3.13/site-packages/hdmf/utils.py", line 578, in func_call
    return func(args[0], **pargs)
  File "/Users/rly/miniconda3/envs/test/lib/python3.13/site-packages/pynwb/file.py", line 729, in add_unit
    self.units.add_unit(**kwargs)
    ~~~~~~~~~~~~~~~~~~~^^^^^^^^^^
  File "/Users/rly/miniconda3/envs/test/lib/python3.13/site-packages/hdmf/utils.py", line 578, in func_call
    return func(args[0], **pargs)
  File "/Users/rly/miniconda3/envs/test/lib/python3.13/site-packages/pynwb/misc.py", line 223, in add_unit
    elec_col.table = nwbfile.electrodes
                     ^^^^^^^^^^^^^^^^^^
AttributeError: 'NoneType' object has no attribute 'electrodes'

Operating System

macOS

Python Version

3.13

Package Versions

pynwb==3.1.1 hdmf==4.1.0