def test_registration_session(self):
behavior_path = self.session_path.joinpath('raw_behavior_data')
behavior_path.mkdir()
settings_file = behavior_path.joinpath('_iblrig_taskSettings.raw.json')
with open(settings_file, 'w') as fid:
json.dump(MOCK_SESSION_SETTINGS, fid)
rc = registration.RegistrationClient(one=one)
rc.register_session(self.session_path)
eid = one.search(subjects=SUBJECT, date_range=['2018-04-01', '2018-04-01'])[0]
datasets = one.alyx.rest('datasets', 'list', session=eid)
for ds in datasets:
self.assertTrue(ds['hash'] is not None)
self.assertTrue(ds['file_size'] is not None)
self.assertTrue(ds['version'] == version.ibllib())
# checks the procedure of the session
ses_info = one.alyx.rest('sessions', 'read', id=eid)
self.assertTrue(ses_info['procedures'] == ['Ephys recording with acute probe(s)'])
one.alyx.rest('sessions', 'delete', id=eid)
# re-register the session as behaviour this time
MOCK_SESSION_SETTINGS['PYBPOD_PROTOCOL'] = '_iblrig_tasks_trainingChoiceWorld6.3.1'
with open(settings_file, 'w') as fid:
json.dump(MOCK_SESSION_SETTINGS, fid)
rc.register_session(self.session_path)
eid = one.search(subjects=SUBJECT, date_range=['2018-04-01', '2018-04-01'])[0]
ses_info = one.alyx.rest('sessions', 'read', id=eid)
self.assertTrue(ses_info['procedures'] == ['Behavior training/tasks'])
def job_creator(root_path,
one=None,
dry=False,
rerun=False,
max_md5_size=None):
"""
Server function that will look for creation flags and for each:
1) create the sessions on Alyx
2) register the corresponding raw data files on Alyx
3) create the tasks to be run on Alyx
:param root_path: main path containing sessions or session path
:param one
:param dry
:param rerun
:param max_md5_size
:return:
"""
if not one:
one = ONE()
rc = registration.RegistrationClient(one=one)
flag_files = list(Path(root_path).glob('**/extract_me.flag'))
flag_files += list(Path(root_path).glob('**/raw_session.flag'))
all_datasets = []
for flag_file in flag_files:
session_path = flag_file.parent
_logger.info(f'creating session for {session_path}')
if dry:
continue
flag_file.unlink()
# if the subject doesn't exist in the database, skip
try:
rc.create_session(session_path)
except ibllib.exceptions.AlyxSubjectNotFound:
continue
files, dsets = registration.register_session_raw_data(
session_path, one=one, max_md5_size=max_md5_size)
if dsets is not None:
all_datasets.extend(dsets)
session_type = rawio.get_session_extractor_type(session_path)
if session_type in ['biased', 'habituation', 'training']:
pipe = training_preprocessing.TrainingExtractionPipeline(
session_path, one=one)
# only start extracting ephys on a raw_session.flag
elif session_type in ['ephys'
] and flag_file.name == 'raw_session.flag':
pipe = ephys_preprocessing.EphysExtractionPipeline(session_path,
one=one)
else:
_logger.info(
f"Session type {session_type} as no matching extractor {session_path}"
)
return
if rerun:
rerun__status__in = '__all__'
else:
rerun__status__in = ['Waiting']
pipe.create_alyx_tasks(rerun__status__in=rerun__status__in)
return all_datasets
def test_registration_session(self):
settings = {
'SESSION_DATE':
'2018-04-01',
'SESSION_DATETIME':
'2018-04-01T12:48:26.795526',
'PYBPOD_CREATOR':
['test_user', 'f092c2d5-c98a-45a1-be7c-df05f129a93c', 'local'],
'SESSION_NUMBER':
'002',
'SUBJECT_NAME':
'clns0730',
'PYBPOD_BOARD':
'_iblrig_mainenlab_behavior_1',
'PYBPOD_PROTOCOL':
'_iblrig_tasks_ephysChoiceWorld',
'IBLRIG_VERSION_TAG':
'5.4.1',
'SUBJECT_WEIGHT':
22,
}
with tempfile.TemporaryDirectory() as td:
# creates the local session
session_path = Path(td).joinpath('clns0730', '2018-04-01', '002')
alf_path = session_path.joinpath('alf')
alf_path.mkdir(parents=True)
alf_path.joinpath('spikes.times.npy').touch()
alf_path.joinpath('spikes.amps.npy').touch()
behavior_path = session_path.joinpath('raw_behavior_data')
behavior_path.mkdir()
settings_file = behavior_path.joinpath(
'_iblrig_taskSettings.raw.json')
with open(settings_file, 'w') as fid:
json.dump(settings, fid)
rc = registration.RegistrationClient(one=one)
rc.register_session(session_path)
eid = one.search(subjects='clns0730',
date_range=['2018-04-01', '2018-04-01'])[0]
datasets = one.alyx.get(
'/datasets?subject=clns0730&date=2018-04-01')
for ds in datasets:
self.assertTrue(ds['hash'] is not None)
self.assertTrue(ds['file_size'] is not None)
self.assertTrue(ds['version'] == version.ibllib())
one.alyx.rest('sessions', 'delete', id=eid)