Extending Subject with a group results in Orphaned Group

[bendichter]

Bug

Steps to Reproduce

from pynwb.spec import NWBNamespaceBuilder, NWBGroupSpec, NWBAttributeSpec


from pynwb import register_class, load_namespaces, get_class
from pynwb.form.utils import docval, get_docval
from pynwb.file import Subject as CoreSubject
from pynwb import NWBFile, NWBHDF5IO

from datetime import datetime

ext_source = "test.extensions.yaml"
ns_path = 'test.namespace.yaml'

extra_subject = NWBGroupSpec(
    neurodata_type_def='ExtraSubject',
    neurodata_type_inc='Subject',
    name='subject',
    doc='subject',
    groups=[NWBGroupSpec(name='extra', doc='extra arg',
                         neurodata_type_inc='NWBDataInterface',
                         neurodata_type_def='MyGroup')]
)

ns_builder = NWBNamespaceBuilder('test extensions', 'test')
ns_builder.add_spec(ext_source, extra_subject)
ns_builder.export(ns_path)

load_namespaces(ns_path)


MyGroup = get_class('MyGroup', 'test')


@register_class('ExtraSubject', 'test')
class ExtraSubject(CoreSubject):
    __nwbfields__ = ('extra',)

    @docval(*get_docval(CoreSubject.__init__) + ({'name': 'extra', 'type': MyGroup,
                                                  'doc': 'extra arg'},))
    def __init__(self, **kwargs):
        extra = kwargs.pop('extra')
        super(ExtraSubject, self).__init__(**kwargs)
        self.extra = extra


subject = ExtraSubject(age='unknown', description='unknown', genotype='NA',
                       sex='unknown', species='Homo sapiens', subject_id='123',
                       weight='unknown', source='source',
                       extra=MyGroup(name='mygroup', source='source'))


nwbfile = NWBFile('a', 'b', 'c', datetime.now())
nwbfile.subject = subject

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

/Users/bendichter/dev/pynwb/src/pynwb/form/build/map.py:759: OrphanContainerWarning: 'mygroup' (MyGroup) for 'subject' (ExtraSubject)
  warnings.warn(msg, OrphanContainerWarning)

Checklist

• Have you ensured the feature or change was not already reported ?
• Have you included a brief and descriptive title?
• Have you included a clear description of the problem you are trying to solve?
• Have you included a minimal code snippet that reproduces the issue you are encountering?

[ajtritt]

Change the following on line 36

    __nwbfields__ = ('extra',)

to

    __nwbfields__ = ({'name': 'extra', 'child': True},)

[bendichter]

@ajtritt thanks for this. I think I'm going to add some documentation about this. So to be clear, is it the case that you need to do this for any NWBGroupSpec that is within another NWBGroupSpec?

[ajtritt]

Almost... any NWBGroupSpec that has a neurodata_type_def or neurodata_type_inc.

The reason for this is to distinguish between subcontainers "owned" by a container and subcontainers linked to by a container. A subgroup that has no neurodata_type is treated as just another field/attribute of the container.

[bendichter]

@ajtritt Can you give me a counterexample?

[ajtritt]

For example, /acquisition is not a child of NWBFile. The TimeSeries defined in /acquisition/timeseries are children of NWBFile.