def test_roundtrip(self):
"""Test writing and reading the ontology_terms and ontology_objects tables."""
container = TimeSeries(
name='test_ts',
data=[1, 2, 3],
unit='si_unit',
timestamps=[0.1, 0.2, 0.3],
)
self.nwbfile.add_acquisition(container)
table = DynamicTable(name='test_table',
description='test table description')
table.add_column(name='test_col',
description='test column description')
table.add_row(test_col='Mouse')
self.nwbfile.add_acquisition(table)
self.nwbfile.ontology_terms.add_row(
id=np.uint64(1),
key='meter',
ontology='si_ontology',
uri='si_ontology:m',
)
self.nwbfile.ontology_objects.add_row(
id=np.uint64(5),
object_id=container.object_id,
field='unit',
item=np.uint64(1),
)
self.nwbfile.ontology_terms.add_row(
id=np.uint64(2),
key='Mouse',
ontology='species_ontology',
uri='species_ontology:Mus musculus',
)
self.nwbfile.ontology_objects.add_row(
id=np.uint64(6),
object_id=table.object_id,
field='test_col',
item=np.uint64(2),
)
with NWBHDF5IO(self.path, mode='w') as io:
io.write(self.nwbfile)
with NWBHDF5IO(self.path, mode='r', load_namespaces=True) as io:
read_nwbfile = io.read()
self.assertContainerEqual(self.nwbfile.ontology_objects,
read_nwbfile.ontology_objects)
self.assertContainerEqual(self.nwbfile.ontology_terms,
read_nwbfile.ontology_terms)
def test_basic(self):
"""Test adding rows to the ontology_terms and ontology_objects tables."""
nwbfile = GenotypeNWBFile(session_description='session_description',
identifier='identifier',
session_start_time=datetime.datetime.now(
datetime.timezone.utc))
container = TimeSeries(
name='test_ts',
data=[1, 2, 3],
unit='si_unit',
timestamps=[0.1, 0.2, 0.3],
)
nwbfile.add_acquisition(container)
table = DynamicTable(name='test_table',
description='test table description')
table.add_column(name='test_col',
description='test column description')
table.add_row(test_col='Mouse')
nwbfile.add_acquisition(table)
nwbfile.ontology_terms.add_row(
id=np.uint64(1),
key='meter',
ontology='si_ontology',
uri='si_ontology:m',
)
nwbfile.ontology_objects.add_row(
id=np.uint64(5),
object_id=container.object_id,
field='unit',
item=np.uint64(1),
)
nwbfile.ontology_terms.add_row(
id=np.uint64(2),
key='Mouse',
ontology='species_ontology',
uri='species_ontology:Mus musculus',
)
nwbfile.ontology_objects.add_row(
id=np.uint64(6),
object_id=table.object_id,
field='test_col',
item=np.uint64(2),
)
self.assertEqual(len(nwbfile.ontology_objects), 2)
self.assertEqual(len(nwbfile.ontology_terms), 2)
self.assertTupleEqual(
nwbfile.ontology_objects[0],
(np.uint64(5), container.object_id, 'unit', np.uint64(1)))
self.assertTupleEqual(
nwbfile.ontology_objects[1],
(np.uint64(6), table.object_id, 'test_col', np.uint64(2)))
self.assertTupleEqual(
nwbfile.ontology_terms[0],
(np.uint64(1), 'meter', 'si_ontology', 'si_ontology:m'))
self.assertTupleEqual(nwbfile.ontology_terms[1],
(np.uint64(2), 'Mouse', 'species_ontology',
'species_ontology:Mus musculus'))
