main_create_metadata.py

import pdb
import argparse
import sys
import os
import utils.create_metadata as comp_pt_nums
import logging

sys.path.append(os.getcwd())
parser = argparse.ArgumentParser()
parser.add_argument("--cohort_name", type=str, default='mci', choices = ['mci','nonmci'])    
parser.add_argument("--followup_window_size", type=int, default=12)    
args = parser.parse_args()

# pdb.set_trace()
if  args.cohort_name == "mci":
	client_name = "mining-clinical-decisions"
	patient_id = 'anon_id'
	time_field_name = 'start_date_utc'
	query_diag = "select * from `mining-clinical-decisions.proj_sage_sf2.mci_cohort_metadata_diagnosis` A"
	query_demog = "select * from `mining-clinical-decisions.proj_sage_sf2.mci_cohort_metadata_demographic`"
	comp_pt_nums.compute_paients_numbers(args.cohort_name, client_name, patient_id, time_field_name, query_diag, query_demog,args.followup_window_size)

elif  args.cohort_name == "nonmci":
	client_name = "mining-clinical-decisions"
	patient_id = 'anon_id'
	time_field_name = 'start_date_utc'
	query_diag = "select * from `mining-clinical-decisions.proj_sage_sf2.nonmci_cohort_metadata_age_matched_diagnosis` A"
	query_demog = "select * from `mining-clinical-decisions.proj_sage_sf2.nonmci_cohort_metadata_age_matched_demographic`"	
	comp_pt_nums.compute_paients_numbers(args.cohort_name, client_name, patient_id, time_field_name, query_diag,query_demog, args.followup_window_size)