def main(config):
setup_logging()
logger.info('ETL version {}'.format(__version__))
config = MainConfig(**read_yaml_file(Path(config)))
# Initialize ETL with configuration parameters
etl = Wrapper(config)
etl.run()
def main(database, username, password, hostname, port, source, debug,
skipvocab):
setup_logging(debug)
# Test database connection
uri = f'postgresql://{username}:{password}@{hostname}:{port}/{database}'
if not Database.can_connect(uri):
return
db = Database(uri)
etl = Wrapper(db, source, './resources/mapping_tables', skipvocab)
logger.info('ETL version {}'.format(__version__))
# if etl.is_git_repo():
# logger.info('Git HEAD at ' + etl.get_git_tag_or_branch())
# Run ETL
try:
etl.run()
except Exception as err:
logger.error('##### FATAL ERROR. TRACEBACK: #####')
logger.error(traceback.format_exc())
raise err
else:
death_datetime = None
record = Person(
person_id=int(row['p_id']),
person_source_value=row['p_id'],
year_of_birth=int(row['year_birth']),
death_datetime=death_datetime,
gender_concept_id=8507, # Always male
race_concept_id=0,
ethnicity_concept_id=0,
gender_source_concept_id=0,
race_source_concept_id=0,
ethnicity_source_concept_id=0)
records_to_insert.append(record)
return records_to_insert
if __name__ == '__main__':
from src.main.python.database.database import Database
from src.main.python.wrapper import Wrapper
db = Database(f'postgresql://postgres@localhost:5432/postgres'
) # A mock database object
w = Wrapper(db, '../../../../resources/source_data',
'../../../../resources/mapping_tables')
for x in basedata_to_person(w):
print(x.__dict__)
def cdm_source(wrapper) -> list:
with wrapper.db.session_scope() as session:
records_to_insert = []
# Get vocabulary info
vocab_info = session.query(Vocabulary).filter_by(
vocabulary_id='None').one()
record = CdmSource(
cdm_source_name='PRIAS',
cdm_etl_reference='https://github.com/thehyve/ohdsi-etl-prias',
cdm_release_date=date.today(),
cdm_version='v6.x',
vocabulary_version=vocab_info.vocabulary_version)
records_to_insert.append(record)
return records_to_insert
if __name__ == '__main__':
from src.main.python.database.database import Database
from src.main.python.wrapper import Wrapper
db = Database(f'postgresql://postgres@localhost:5432/postgres'
) # A mock database object
w = Wrapper(db, '../../../../resources/source_data')
for x in cdm_source(w):
print(x.__dict__)