def test_get_behavior_stimulus_file(behavior_experiment_id, compare_val):
if compare_val is None:
expected_fail = False
try:
api = BehaviorLimsApi(behavior_experiment_id)
api.extractor.get_behavior_stimulus_file()
except OneResultExpectedError:
expected_fail = True
assert expected_fail is True
else:
api = BehaviorLimsApi(behavior_experiment_id)
assert api.extractor.get_behavior_stimulus_file() == compare_val
def test_get_ori_info_from_trial(
behavior_experiment_id,
ti,
expected,
exception,
):
"""was feeling worried that the values would be wrong,
this helps reaffirm that maybe they are not...
Notes
-----
- i may be rewriting code here but its more a sanity check really...
"""
lims_api = BehaviorLimsApi(behavior_session_id=behavior_experiment_id)
stim_output = pd.read_pickle(
lims_api.extractor.get_behavior_stimulus_file())
trial_log = stim_output['items']['behavior']['trial_log']
if exception:
with pytest.raises(exception):
trials_processing.get_ori_info_from_trial(
trial_log,
ti,
)
else:
assert trials_processing.get_ori_info_from_trial(
trial_log,
ti,
) == expected # noqa: E501
def write_behavior_nwb(session_data, nwb_filepath):
nwb_filepath_inprogress = nwb_filepath+'.inprogress'
nwb_filepath_error = nwb_filepath+'.error'
# Clean out files from previous runs:
for filename in [nwb_filepath_inprogress,
nwb_filepath_error,
nwb_filepath]:
if os.path.exists(filename):
os.remove(filename)
try:
json_session = BehaviorSession(api=BehaviorJsonApi(session_data))
lims_api = BehaviorLimsApi(
behavior_session_id=session_data['behavior_session_id'])
lims_session = BehaviorSession(api=lims_api)
logging.info("Comparing a BehaviorSession created from JSON "
"with a BehaviorSession created from LIMS")
assert sessions_are_equal(json_session, lims_session, reraise=True)
BehaviorNwbApi(nwb_filepath_inprogress).save(json_session)
logging.info("Comparing a BehaviorSession created from JSON "
"with a BehaviorSession created from NWB")
nwb_api = BehaviorNwbApi(nwb_filepath_inprogress)
nwb_session = BehaviorSession(api=nwb_api)
assert sessions_are_equal(json_session, nwb_session, reraise=True)
os.rename(nwb_filepath_inprogress, nwb_filepath)
return {'output_path': nwb_filepath}
except Exception as e:
os.rename(nwb_filepath_inprogress, nwb_filepath_error)
raise e
def get_behavior_session(self,
behavior_session_id: int) -> BehaviorSession:
"""Returns a BehaviorSession object that contains methods to
analyze a single behavior session.
:param behavior_session_id: id that corresponds to a behavior session
:type behavior_session_id: int
:rtype: BehaviorSession
"""
return BehaviorSession(BehaviorLimsApi(behavior_session_id))
def test_get_extended_trials(behavior_experiment_id):
api = BehaviorLimsApi(behavior_experiment_id)
df = api.get_extended_trials()
ets = ExtendedTrialSchema(partial=False, many=True)
data_list_cs = df.to_dict('records')
data_list_cs_sc = ets.dump(data_list_cs)
ets.load(data_list_cs_sc)
df_fail = df.drop(['behavior_session_uuid'], axis=1)
ets = ExtendedTrialSchema(partial=False, many=True)
data_list_cs = df_fail.to_dict('records')
data_list_cs_sc = ets.dump(data_list_cs)
try:
ets.load(data_list_cs_sc)
raise RuntimeError("This should have failed with "
"marshmallow.schema.ValidationError")
except ValidationError:
pass
def get_session(self, behavior_session_uuid=None, behavior_session_id=None):
assert not all(v is None for v in [
behavior_session_uuid, behavior_session_id]), 'must enter either a behavior_session_uuid or a behavior_session_id'
if behavior_session_uuid is not None and behavior_session_id is not None:
# if both a behavior session uuid and a lims id are entered, ensure that they match
behavior_api = BehaviorLimsApi(behavior_session_id)
assert behavior_session_uuid == behavior_api.get_behavior_session_uuid(), 'behavior_session {} does not match behavior_session_id {}'.format(behavior_session_uuid, behavior_session_id)
if behavior_session_uuid is None and behavior_session_id is not None:
# get a behavior session uuid if a lims ID was entered
behavior_api = BehaviorLimsApi(behavior_session_id)
behavior_session_uuid = behavior_api.get_behavior_session_uuid()
filters = [{"name": "id", "op": "eq", "val": behavior_session_uuid}]
behavior_df = self.get_df('behavior_sessions', filters=filters).rename(columns={'id': 'behavior_session_uuid'})
state_df = self.get_df('states').rename(columns={'id': 'state_id'})
regimen_df = self.get_df('regimens').rename(columns={'id': 'regimen_id', 'name': 'regimen_name'}).drop(['states', 'active'], axis=1)
stage_df = self.get_df('stages').rename(columns={'id': 'stage_id'}).drop(['states'], axis=1)
behavior_df = pd.merge(behavior_df, state_df, how='left', on='state_id')
behavior_df = pd.merge(behavior_df, stage_df, how='left', on='stage_id')
behavior_df = pd.merge(behavior_df, regimen_df, how='left', on='regimen_id')
behavior_df.drop(['state_id', 'stage_id', 'regimen_id'], inplace=True, axis=1)
if len(behavior_df) == 0:
raise RuntimeError("Session not found %s:" % behavior_session_uuid)
assert len(behavior_df) == 1
session_dict = behavior_df.iloc[0].to_dict()
filters = [{"name": "behavior_session_uuid", "op": "eq", "val": behavior_session_uuid}]
trials_df = self.get_df('trials', filters=filters).sort_values('index').drop(['id', 'behavior_session'], axis=1).set_index('index', drop=False)
trials_df['behavior_session_uuid'] = trials_df['behavior_session_uuid'].map(uuid.UUID)
del trials_df.index.name
session_dict['trials'] = trials_df[EDF_COLUMNS]
return session_dict
def setup_class(cls):
cls.bd = BehaviorLimsApi(976012750)
cls.od = BehaviorOphysLimsApi(976255949)
def from_lims(cls, behavior_session_id: int) -> "BehaviorSession":
return cls(api=BehaviorLimsApi(behavior_session_id))
def test_behavior_session_id_to_foraging_id(behavior_session_id):
session = BehaviorLimsApi(behavior_session_id=behavior_session_id)
behavior_session_uuid = session.get_metadata().behavior_session_uuid
expected = UUID('394a910e-94c7-4472-9838-5345aff59ed8')
assert behavior_session_uuid == expected
def test_behavior_session_id_to_foraging_id(behavior_session_id):
session = BehaviorLimsApi(behavior_session_id=behavior_session_id)
foraging_id = session.get_behavior_session_uuid()
assert foraging_id == '394a910e-94c7-4472-9838-5345aff59ed8'
def test_foraging_id_to_behavior_session_id(behavior_session_uuid):
session = BehaviorLimsApi.from_foraging_id(behavior_session_uuid)
assert session.behavior_session_id == 823847007