def get_metadata(self) -> BehaviorMetadata:
"""Return metadata about the session.
:rtype: BehaviorMetadata
"""
metadata = BehaviorMetadata(
extractor=self.extractor,
stimulus_timestamps=self.get_stimulus_timestamps(),
behavior_stimulus_file=self._behavior_stimulus_file())
return metadata
def test_get_behavior_session_uuid(MockBehaviorLimsApi, monkeypatch):
with monkeypatch.context() as ctx:
def dummy_init(self, extractor, behavior_stimulus_file):
self._extractor = extractor
self._behavior_stimulus_file = behavior_stimulus_file
ctx.setattr(BehaviorMetadata, '__init__', dummy_init)
stimulus_file = MockBehaviorLimsApi._behavior_stimulus_file()
metadata = BehaviorMetadata(extractor=MockBehaviorLimsApi.extractor,
behavior_stimulus_file=stimulus_file)
expected = UUID('138531ab-fe59-4523-9154-07c8d97bbe03')
assert expected == metadata.behavior_session_uuid
def get_metadata(self) -> dict:
metadata_nwb_obj = self.nwbfile.lab_meta_data['metadata']
data = OphysBehaviorMetadataSchema(
exclude=['date_of_acquisition']).dump(metadata_nwb_obj)
self._behavior_session_id = data["behavior_session_id"]
# Add pyNWB Subject metadata to behavior session metadata
nwb_subject = self.nwbfile.subject
data['mouse_id'] = int(nwb_subject.subject_id)
data['sex'] = nwb_subject.sex
data['age_in_days'] = BehaviorMetadata.parse_age_in_days(
age=nwb_subject.age)
data['full_genotype'] = nwb_subject.genotype
data['reporter_line'] = nwb_subject.reporter_line
data['driver_line'] = sorted(list(nwb_subject.driver_line))
data['cre_line'] = BehaviorMetadata.parse_cre_line(
full_genotype=nwb_subject.genotype)
# Add other metadata stored in nwb file to behavior session meta
data['date_of_acquisition'] = self.nwbfile.session_start_time
data['behavior_session_uuid'] = uuid.UUID(
data['behavior_session_uuid'])
return data
def test_cre_line(monkeypatch):
"""Tests that cre_line properly parsed from driver_line"""
with monkeypatch.context() as ctx:
def dummy_init(self):
pass
def full_genotype(self):
return 'Sst-IRES-Cre/wt;Ai148(TIT2L-GC6f-ICL-tTA2)/wt'
ctx.setattr(BehaviorMetadata, '__init__', dummy_init)
ctx.setattr(BehaviorMetadata, 'full_genotype', property(full_genotype))
metadata = BehaviorMetadata()
assert metadata.cre_line == 'Sst-IRES-Cre'
def test_get_date_of_acquisition(monkeypatch, tmp_path, test_params,
expected_warn_msg):
mock_session_id = test_params["behavior_session_id"]
pkl_save_path = tmp_path / f"mock_pkl_{mock_session_id}.pkl"
with open(pkl_save_path, 'wb') as handle:
pickle.dump({"start_time": test_params['pkl_expt_date']}, handle)
behavior_stimulus_file = pd.read_pickle(pkl_save_path)
tz = pytz.timezone("America/Los_Angeles")
extractor_expt_date = tz.localize(
test_params['extractor_expt_date']).astimezone(pytz.utc)
class MockExtractor():
def get_date_of_acquisition(self):
return extractor_expt_date
def get_behavior_session_id(self):
return test_params['behavior_session_id']
def get_behavior_stimulus_file(self):
return pkl_save_path
extractor = MockExtractor()
with monkeypatch.context() as ctx:
def dummy_init(self, extractor, behavior_stimulus_file):
self._extractor = extractor
self._behavior_stimulus_file = behavior_stimulus_file
ctx.setattr(BehaviorMetadata,
'__init__',
dummy_init)
metadata = BehaviorMetadata(
extractor=extractor,
behavior_stimulus_file=behavior_stimulus_file)
if expected_warn_msg:
with pytest.warns(Warning, match=expected_warn_msg):
obt_date = metadata.date_of_acquisition
else:
obt_date = metadata.date_of_acquisition
assert obt_date == extractor_expt_date
def test_age_in_days_invalid_age(monkeypatch):
"""Test that age_in_days is None if age not prefixed with P"""
class MockExtractor:
def get_age(self):
return 'Q123'
extractor = MockExtractor()
with monkeypatch.context() as ctx:
def dummy_init(self):
self._extractor = extractor
ctx.setattr(BehaviorMetadata,
'__init__',
dummy_init)
metadata = BehaviorMetadata()
assert metadata.age_in_days is None
def test_reporter_line_no_reporter_line(monkeypatch):
"""Test that if no reporter line, returns None"""
class MockExtractor:
def get_reporter_line(self):
return []
extractor = MockExtractor()
with monkeypatch.context() as ctx:
def dummy_init(self):
self._extractor = extractor
ctx.setattr(BehaviorMetadata,
'__init__',
dummy_init)
metadata = BehaviorMetadata()
assert metadata.reporter_line is None
def test_age_in_days(monkeypatch):
"""Test that age_in_days properly parsed from age"""
class MockExtractor:
def get_age(self):
return 'P123'
extractor = MockExtractor()
with monkeypatch.context() as ctx:
def dummy_init(self):
self._extractor = extractor
ctx.setattr(BehaviorMetadata,
'__init__',
dummy_init)
metadata = BehaviorMetadata()
assert metadata.age_in_days == 123
def test_age_in_days_unkown_age(monkeypatch):
"""Test age in days is None if age is unknown"""
class MockExtractor:
def get_age(self):
return 'unkown'
extractor = MockExtractor()
with monkeypatch.context() as ctx:
def dummy_init(self):
self._extractor = extractor
ctx.setattr(BehaviorMetadata,
'__init__',
dummy_init)
metadata = BehaviorMetadata()
assert metadata.age_in_days is None
def test_reporter_line_str(monkeypatch):
"""Test that reporter line returns itself if str"""
class MockExtractor:
def get_reporter_line(self):
return 'foo'
extractor = MockExtractor()
with monkeypatch.context() as ctx:
def dummy_init(self):
self._extractor = extractor
ctx.setattr(BehaviorMetadata,
'__init__',
dummy_init)
metadata = BehaviorMetadata()
assert metadata.reporter_line == 'foo'
def test_reporter_line_multiple(monkeypatch):
"""Test that if multiple reporter lines, the first is returned"""
class MockExtractor:
def get_reporter_line(self):
return ['foo', 'bar']
extractor = MockExtractor()
with monkeypatch.context() as ctx:
def dummy_init(self):
self._extractor = extractor
ctx.setattr(BehaviorMetadata,
'__init__',
dummy_init)
metadata = BehaviorMetadata()
assert metadata.reporter_line == 'foo'
def test_reporter_line(monkeypatch):
"""Test that reporter line properly parsed from list"""
class MockExtractor:
def get_reporter_line(self):
return ['foo']
extractor = MockExtractor()
with monkeypatch.context() as ctx:
def dummy_init(self):
self._extractor = extractor
ctx.setattr(BehaviorMetadata,
'__init__',
dummy_init)
metadata = BehaviorMetadata()
assert metadata.reporter_line == 'foo'
def test_indicator(monkeypatch):
"""Test that indicator is parsed from full_genotype"""
class MockExtractor:
def get_reporter_line(self):
return 'Ai148(TIT2L-GC6f-ICL-tTA2)'
extractor = MockExtractor()
with monkeypatch.context() as ctx:
def dummy_init(self):
self._extractor = extractor
ctx.setattr(BehaviorMetadata, '__init__', dummy_init)
metadata = BehaviorMetadata()
assert metadata.indicator == 'GCaMP6f'
def test_cre_line_bad_full_genotype(monkeypatch):
"""Test that cre_line is None and no error raised"""
with monkeypatch.context() as ctx:
def dummy_init(self):
pass
def full_genotype(self):
return 'foo'
ctx.setattr(BehaviorMetadata,
'__init__',
dummy_init)
ctx.setattr(BehaviorMetadata,
'full_genotype',
property(full_genotype))
metadata = BehaviorMetadata()
assert metadata.cre_line is None
def test_cre_line_bad_full_genotype(monkeypatch):
"""Test that cre_line is None and no error raised"""
with monkeypatch.context() as ctx:
def dummy_init(self):
pass
def full_genotype(self):
return 'foo'
ctx.setattr(BehaviorMetadata, '__init__', dummy_init)
ctx.setattr(BehaviorMetadata, 'full_genotype', property(full_genotype))
metadata = BehaviorMetadata()
with pytest.warns(UserWarning) as record:
cre_line = metadata.cre_line
assert cre_line is None
assert str(record[0].message) == 'Unable to parse cre_line from ' \
'full_genotype'
def test_age_in_days_edge_cases(monkeypatch, input_age, warning_msg, expected):
"""Test age in days edge cases"""
class MockExtractor:
def get_age(self):
return input_age
extractor = MockExtractor()
with monkeypatch.context() as ctx:
def dummy_init(self):
self._extractor = extractor
ctx.setattr(BehaviorMetadata, '__init__', dummy_init)
metadata = BehaviorMetadata()
with pytest.warns(UserWarning) as record:
age_in_days = metadata.age_in_days
assert age_in_days is None
assert str(record[0].message) == warning_msg
def test_indicator_edge_cases(monkeypatch, input_reporter_line, warning_msg,
expected):
"""Test indicator parsing edge cases"""
class MockExtractor:
def get_reporter_line(self):
return input_reporter_line
extractor = MockExtractor()
with monkeypatch.context() as ctx:
def dummy_init(self):
self._extractor = extractor
ctx.setattr(BehaviorMetadata, '__init__', dummy_init)
metadata = BehaviorMetadata()
with pytest.warns(UserWarning) as record:
indicator = metadata.indicator
assert indicator is expected
assert str(record[0].message) == warning_msg