def update_metadata_option(args):
client = get_google_session(args.gcredentials)
new_dict, errors = get_bio_metadata(client)
update_our_meta(new_dict, client, force_update=False)
# Create Patients field
update_patient_id(client)
def update_civet_option(args):
client = get_google_session(args.gcredentials)
new_dict = get_civet_metadata(args.rundir)
if new_dict:
update_civet_meta(new_dict, client, sheet_name=args.maindata)
def update_ct_option(args):
client = get_google_session(args.gcredentials)
new_dict, errors = get_ct_metadata(client, sheet_name=args.ctdata)
update_ct_meta(new_dict, client, sheet_name=args.maindata)
def update_lineage_option(args):
client = get_google_session(args.gcredentials)
new_dict = get_lineage_metadata(client, sheet_name=args.lineagedata)
update_lineage_meta(new_dict, client)
def export_phe_option(args):
client = get_google_session(args.gcredentials)
config = json.load(open(args.config))
export_phe(client, config['temp_dir'], config['sheet_name'],
config['export_server'], config['export_username'],
config['key_location'])
def export_lineage_option(args):
# Build def info:
client = get_google_session(args.gcredentials)
update_pub_info(client)
def update_surv_option(args):
# TODO: Add to options
# Update surveliannce
client = get_google_session(args.gcredentials)
new_dict, surv_counts = get_surv_metadata(client)
update_surv_meta(new_dict, surv_counts, client)
def main(args):
client = get_google_session(args.gcredentials)
new_dict = get_new_metadata(client, sheet_name=args.newdata)
clean_lab_ids(client, new_dict, sheet_name=args.maindata)
update_new_meta(new_dict, client, sheet_name=args.maindata)