def load_config(args):
if args.config_file:
cfg = import_config(fname_config_file=args.config_file)
elif "CT_INGESTER_CONFIG" in os.environ:
fname_config_file = os.environ["CT_INGESTER_CONFIG"]
cfg = import_config(fname_config_file=fname_config_file)
else:
msg_fmt = "Configuration file path not defined."
raise ValueError(msg_fmt)
return cfg
def setUp(self):
"""Instantiates the DAL and creates the schema."""
# Load the configuration.
self.cfg = import_config(
fname_config_file="/etc/ct-ingester/ct-ingester-test.json", )
self.dal = DalClinicalTrials(sql_username=self.cfg.sql_username,
sql_password=self.cfg.sql_password,
sql_host=self.cfg.sql_host,
sql_port=self.cfg.sql_port,
sql_db=self.cfg.sql_db)
self.ingester = IngesterDocumentClinicalTrial(dal=self.dal)
self.parser = ParserXmlClinicaStudy()
# Drop any schema remnants and recreate it.
Base.metadata.drop_all(self.dal.engine)
Base.metadata.create_all(self.dal.engine)
required=False,
default=False,
action="store_true",
)
argument_parser.add_argument(
"--config-file",
dest="config_file",
help="configuration file",
required=True,
)
arguments = argument_parser.parse_args()
if arguments.dry_run:
logger.info("Performing a dry-run.")
cfg = import_config(arguments.config_file)
# Initialize the Sentry agent.
initialize_sentry(cfg=cfg)
# Create a new DAL.
_dal = DalClinicalTrials(
sql_username=cfg.sql_username,
sql_password=cfg.sql_password,
sql_host=cfg.sql_host,
sql_port=cfg.sql_port,
sql_db=cfg.sql_db,
)
populate(
dal=_dal,
google_place_ids = [
facility.google_place_id for facility in facilities
]
responses = pool.map(_get_place_details, google_place_ids)
for facility, response in zip(facilities, responses):
if not response:
continue
iodu_canonical_facility_from_google(
dal=dal,
google_place_id=facility.google_place_id,
google_response=response)
if __name__ == '__main__':
cfg = import_config("/etc/ct-ingester/ct-ingester-dev.json")
dal = DalClinicalTrials(
sql_username=cfg.sql_username,
sql_password=cfg.sql_password,
sql_host="192.168.0.12",
sql_port=cfg.sql_port,
sql_db=cfg.sql_db,
)
retriever = RetrieverGoogleMaps(api_key=api_keys[0])
populate()