def add_document_and_foreign_keys(
database: Database,
) -> Tuple[Document, Patient, Session, SensorInfo]:
session = add_session(database)
patient = add_patient(database)
sensor_info = add_sensor_info(database)
with database.session_scope() as s:
document = Document(
session_id=session.session_id,
patient_id=patient.patient_id,
sensor_serial_number=sensor_info.sensor_serial_number,
distractor_type=Config.DEFAULT_DISTRACTOR,
)
s.add(document)
return document, patient, session, sensor_info
#!/usr/bin/env python
import argparse
import pandas as pd
from pathlib import Path
from cranio.model import Database, session_scope, Base, Measurement
from cranio.utils import logger, configure_logging
parser = argparse.ArgumentParser()
parser.add_argument('path', help='Path to SQLite file (.db)', type=str)
if __name__ == '__main__':
configure_logging()
args = parser.parse_args()
path = Path(args.path)
database = Database(drivername='sqlite', database=str(path))
database.create_engine()
with session_scope(database) as s:
for table_name, table in Base.metadata.tables.items():
path_out = path.parent / (table_name + '.csv')
logger.info(f'Read table {table_name} from {database.url} to {path_out}')
df = pd.read_sql_table(table_name, con=database.engine)
df.to_csv(path_out, sep=';', index=False)
def select_most_recently_used_patient(self, database: Database):
with database.session_scope() as s:
patient = (s.query(Patient).join(Document).join(Session).order_by(
Session.started_at.desc()).first())
if patient is not None:
self.select_patient(patient_id=patient.patient_id)
def enter_info_to_database(cls, database: Database) -> SensorInfo:
""" Enter copy of self.sensor_info to a database. """
logger.debug(f'Enter sensor info: {str(cls.sensor_info)}')
database.insert(cls.sensor_info, insert_if_exists=False)
return cls.sensor_info
def add_sensor_info(database: Database) -> SensorInfo:
with database.session_scope() as s:
sensor_info = SensorInfo(sensor_serial_number='pytest', turns_in_full_turn=3)
s.add(sensor_info)
return sensor_info
def add_patient(database: Database) -> Patient:
with database.session_scope() as s:
patient = Patient(patient_id=generate_unique_id())
s.add(patient)
return patient
def add_session(database: Database) -> Session:
with database.session_scope() as s:
session = Session()
s.add(session)
return session
def database_fixture():
database = Database(drivername='sqlite')
database.create_engine()
database.init()
yield database
database.clear()