def load_config(args):
if args.config_file:
cfg = import_config(fname_config_file=args.config_file)
elif "PUBMED_INGESTER_CONFIG" in os.environ:
fname_config_file = os.environ["PUBMED_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/pubmed-ingester/pubmed-ingester-test.json",
)
self.dal = DalPubmed(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 = IngesterDocumentPubmedArticle(dal=self.dal)
self.parser = ParserXmlPubmedArticle()
# Drop any schema remnants and recreate it.
Base.metadata.drop_all(self.dal.engine)
Base.metadata.create_all(self.dal.engine)
postal_code_suffix=_get_address_component_name(
components, ("postal_code_suffix", )),
postal_town=_get_address_component_name(
components, ("postal_town", )),
premise=_get_address_component_name(
components, ("premise", )),
subpremise=_get_address_component_name(
components, ("subpremise", )),
route=_get_address_component_name(components, ("route", )),
street_address=_get_address_component_name(
components, ("street_address", )),
street_number=_get_address_component_name(
components, ("street_number", )),
)
if __name__ == '__main__':
cfg = import_config("/etc/pubmed-ingester/pubmed-ingester-dev.json")
dal = DalPubmed(
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[1])
populate()