def from_db(cls, eartag, experiment_name, testing=False, postgresql=None):
if testing:
with TestingCursor(postgresql) as cursor:
mouse = Mouse.from_db(eartag,
testing=testing,
postgresql=postgresql)
experiment = Experiment.from_db(experiment_name,
testing=testing,
postgresql=postgresql)
return cls.__from_db(cursor, mouse, experiment)
else:
with Cursor() as cursor:
mouse = Mouse.from_db(eartag)
experiment = Experiment.from_db(experiment_name)
return cls.__from_db(cursor, mouse, experiment)
def test_from_db(self):
self.load_mouse = Mouse.from_db(self.seed_tup[0], testing=True, postgresql=self.postgresql)
self.assertEqual(self.seed_tup[0], self.load_mouse.eartag)
self.assertEqual(self.seed_tup[1], self.load_mouse.birthdate)
self.assertEqual(self.seed_tup[2], self.load_mouse.genotype)
self.assertEqual(self.seed_tup[3], self.load_mouse.sex)
self.assertFalse(self.load_mouse.mouse_id is None)
def test_add_new_mouse(self):
test_mouse = Mouse(1111, self.birthdate, 'wild type', 'female').save_to_db(testing=True,
postgresql=self.postgresql)
self.assertEqual(1111, test_mouse.eartag)
self.assertEqual(util.convert_date_int_yyyymmdd(self.birthdate), test_mouse.birthdate)
self.assertEqual('wild type', test_mouse.genotype)
self.assertEqual('female', test_mouse.sex)
self.assertFalse(test_mouse.mouse_id is None)
def setUp(self):
self.postgresql = Postgresql()
database.handlers.handlers.handler_seed_sessions_table(self.postgresql)
[eartag, _, _, _, _, experiment_name, _, _] = test_mouse_table_seed.pop()
self.mouse = Mouse.from_db(eartag, testing=True, postgresql=self.postgresql)
self.experiment = Experiment.from_db(experiment_name, testing=True, postgresql=self.postgresql)
possible_sessions = test_session_table_seed[eartag, utils.prep_string_for_db(experiment_name)]
self.session_date, self.session_dir = possible_sessions.pop()
def setUp(self):
self.postgresql = Postgresql()
database.handlers.handlers.handler_seed_mouse(self.postgresql)
database.handlers.handlers.handler_seed_experiments(self.postgresql)
self.mouse = Mouse.from_db(9990, testing=True, postgresql=self.postgresql)
self.experiment = Experiment.from_db('test-experiment-one', testing=True, postgresql=self.postgresql)
self.session_date = 20200503
self.session_dir = '/exp/one/dir/9990/20200503_S2'
def main():
pc = Pc()
pc.add_element(Motherboard())
pc.add_element(GraphicCard())
pc.add_element(Keyboard())
pc.add_element(Monitor())
pc.add_element(Mouse())
print(pc)
def test_list_participants(self):
all_participants = ParticipantDetails.list_participants(
self.exp_seed[0], testing=True, postgresql=self.postgresql)
self.assertTrue(len(all_participants) == 5)
for mouse_id in all_participants:
eartag = Mouse.from_db_by_id(mouse_id,
testing=True,
postgresql=self.postgresql).eartag
if 'one' in self.exp_seed[0]:
self.assertTrue((eartag % 2) == 0)
else:
self.assertTrue((eartag % 2) != 0)
def test_from_db(self):
test_details = ParticipantDetails.from_db(self.mouse_seed[0],
self.mouse_seed[5],
testing=True,
postgresql=self.postgresql)
self.assertTrue(
Mouse.from_db(self.mouse_seed[0],
testing=True,
postgresql=self.postgresql) == test_details.mouse)
self.assertTrue(
Experiment.from_db(
self.mouse_seed[5], testing=True, postgresql=self.postgresql)
== test_details.experiment)
self.assertFalse(test_details.detail_id is None)
def test_add_new_participant_details(self):
test_mouse = Mouse.from_db(self.mouse_seed[0],
testing=True,
postgresql=self.postgresql)
test_exp = Experiment.from_db(self.mouse_seed[5],
testing=True,
postgresql=self.postgresql)
test_details = ParticipantDetails(
test_mouse, test_exp, self.mouse_seed[6],
self.mouse_seed[7]).save_to_db(testing=True,
postgresql=self.postgresql)
self.assertTrue(test_mouse == test_details.mouse)
self.assertTrue(test_exp == test_details.experiment)
self.assertFalse(test_details.detail_id is None)
def list_participants(experiment_name='all'):
if experiment_name == 'all':
all_participants = dict()
with Cursor() as cursor:
all_experiments = list_all_experiments(cursor)
for experiment_name in all_experiments:
all_participants[experiment_name] = sorted(set(
(Mouse.from_db_by_id(mouse_id).eartag
for mouse_id in list_participants(experiment_name))),
key=int)
return all_participants
experiment_participant_details = ParticipantDetails.list_participants(
experiment_name)
return sorted(set(experiment_participant_details), key=int)
def handler_seed_sessions_table(postgresql):
handler_seed_mouse(postgresql)
handler_seed_experiments(postgresql)
with TestingCursor(postgresql) as cursor:
for [mouse_eartag, experiment_name] in session_seed.keys():
all_sessions = session_seed[mouse_eartag, experiment_name]
mouse = Mouse.from_db(mouse_eartag,
testing=True,
postgresql=postgresql)
experiment = Experiment.from_db(experiment_name,
testing=True,
postgresql=postgresql)
for [session_date, session_dir] in all_sessions:
database.seed_tables.seed_tables.seed_sessions_table(
cursor, mouse.mouse_id, experiment.experiment_id,
utils.convert_date_int_yyyymmdd(session_date), session_dir)
def handler_seed_participant_details(postgresql):
with TestingCursor(postgresql) as cursor:
seed_id.seed_mouse_table(cursor)
seed_id.seed_experiments_table(cursor)
with TestingCursor(postgresql) as cursor:
all_mice = list_all_mice(cursor)
for eartag in all_mice:
mouse = Mouse.from_db(eartag, testing=True, postgresql=postgresql)
for m in mouse_seed:
if m[0] == mouse.eartag:
experiment = Experiments.from_db(m[5],
testing=True,
postgresql=postgresql)
seed_pd.seed_participant_details(cursor,
mouse.mouse_id,
experiment.experiment_id,
start_date=m[6],
end_date=m[7])
def handler_seed_trials(postgresql):
with TestingCursor(postgresql) as cursor:
seed_id.seed_mouse_table(cursor)
seed_id.seed_experiments_table(cursor)
with TestingCursor(postgresql) as cursor:
all_mice = list_all_mice(cursor)
for eartag in all_mice:
mouse = Mouse.from_db(eartag, testing=True, postgresql=postgresql)
for m in mouse_seed:
if m[0] == mouse.eartag:
experiment = Experiments.from_db(m[5],
testing=True,
postgresql=postgresql)
seed_mouse_all_trials = trial_seed[(
mouse.eartag, experiment.experiment_name)]
for trial in seed_mouse_all_trials:
trial_date, trial_dir = trial
seed_tr.seed_trials(
cursor, mouse.mouse_id, experiment.experiment_id,
utils.convert_date_int_yyyymmdd(trial_date),
trial_dir)
def test_delete_mouse(self):
mouse_to_delete = Mouse.from_db(self.seed_tup[0], testing=True, postgresql=self.postgresql)
mouse_to_delete.delete_from_db(testing=True, postgresql=self.postgresql)
test_reload_mouse = Mouse.from_db(self.seed_tup[0], testing=True, postgresql=self.postgresql)
self.assertIsNone(test_reload_mouse)
def test_duplicate_mouse(self):
test_mouse = Mouse(1111, self.birthdate, 'wild type', 'female').save_to_db(testing=True,
postgresql=self.postgresql)
dup_mouse = test_mouse.save_to_db(testing=True, postgresql=self.postgresql)
self.assertFalse(dup_mouse.mouse_id is None)
from templates.experiment_specific_details import skilled_reaching
from utilities import read_table_csv_to_list
Database.initialize(**dbDetails, **dbUser_Krista)
project_base_dir = Path(__file__).parent.parent.parent
backup_csv_path = os.path.join(project_base_dir, 'data', 'database_backup_csv')
tables_to_populate = ['mouse', 'experiments', 'participant_details']
# MOUSE TABLE
all_mouses = read_table_csv_to_list(backup_csv_path, 'mouse')
for [mouse_id, eartag, birthdate, genotype, sex] in all_mouses:
eartag = int(eartag)
birthdate = ''.join(birthdate.split('-'))
Mouse(eartag, int(birthdate), genotype, sex).save_to_db()
# EXPERIMENTS TABLE
all_experiments = read_table_csv_to_list(backup_csv_path, 'experiments')
for [experiment_id, experiment_dir, experiment_name] in all_experiments:
Experiment(experiment_name, experiment_dir).save_to_db()
# PARTICIPANT DETAILS TABLE
all_participant_details = read_table_csv_to_list(backup_csv_path,
'participant_details')
for participant_detail in all_participant_details:
detail_id = participant_detail[0]
mouse_id = participant_detail[1]
experiment_id = participant_detail[2]
start_date = participant_detail[3]
start_date = int(''.join(start_date.split('-')))