Container source not set for some references

[rly]

On write, Container.container_source is set for all built objects not read from a file. This field tracks where a Container object is located on disk (e.g., file path) so that links can be made across files. This also prevents a Container object from being written to multiple files.

Oddly, in some cases, Container.container_source is not set at all. Specifically, when Container A makes a reference to Container B, and Container A gets built first, then Container B does not get a container_source. However, if no container makes a reference to Container B before Container B is built, then Container B does get a container_source.

This occurs in PyNWB when writing an NWBFile with a Device, an ElectrodeGroup, and an ElectricalSeries that references those. The ElectricalSeries gets built first, which results in the Device and ElectrodeGroup being built without a container_source set.

If users are not careful, this can lead to unexpected/inconsistent behavior when interacting with a Container that is missing its container_source. For example, a Container without a container_source can be added to multiple files under different build managers. This creates a broken link in all files after the first. Admittedly, this is a bit of an edge case and is minor.

MWE:

from pynwb import NWBFile, NWBHDF5IO
from pynwb.ecephys import ElectricalSeries
from datetime import datetime
import numpy as np


nwbfile = NWBFile(session_description='ADDME',
                  identifier='ADDME',
                  session_start_time=datetime.now().astimezone())

dev1 = nwbfile.create_device('dev1')
group = nwbfile.create_electrode_group('tetrode1', 'tetrode description', 'tetrode location', dev1)

nwbfile.add_electrode(id=1, x=1.0, y=2.0, z=3.0, imp=-1.0, location='CA1', filtering='none', group=group,
                      group_name='tetrode1')

region = nwbfile.create_electrode_table_region(
    region=(0, ),
    name='electrodes',
    description='desc'
)
ts = ElectricalSeries(
    name='test_data',
    data=np.arange(10),
    timestamps=np.arange(10),
    electrodes=region
)
nwbfile.add_acquisition(ts)

with NWBHDF5IO('nwbfile.nwb', 'w') as io:
    io.write(nwbfile)

# dev1 and group do not have container_source set. all other Containers do.
print(dev1.container_source)
print(group.container_source)

# add dev1 and group to a new file
nwbfile2 = NWBFile(session_description='ADDME',
                   identifier='ADDME',
                   session_start_time=datetime.now().astimezone())
nwbfile2.add_device(dev1)
nwbfile2.add_electrode_group(group)

# using a new build manager, a new file can be written with dev1 and group,
# but the file has broken links for them
with NWBHDF5IO('nwbfile2.nwb', 'w') as io:
    io.write(nwbfile2)