Update Healthcode to MD5 hash table for JourneyPro, Presence, ElevateMS

exportMD5.py

import bridgeclient
import hashlib
import pandas as pd
import synapseclient as sc
import argparse

SYNAPSE_TABLES = {
        'journey-pro': 'syn11439373',
        'elevate-ms': 'syn11439398',
        'lilly-presence': 'syn11445782'}

def read_args():
    parser = argparse.ArgumentParser(
            description="Export MD5 hashes of participant's email addresses "
                        "coupled with their healthcode identifier.")
    parser.add_argument("study")
    parser.add_argument("email")
    parser.add_argument("password")
    args = parser.parse_args()
    return args

def getmd5(s):
    m = hashlib.md5()
    m.update(s.encode('utf-8'))
    return m.hexdigest().upper()

def main(study, email, password):
    syn = sc.login()
    bc = bridgeclient.bridgeConnector(
            email=email,
            password=password,
            study=study)
    bridge_data = bc.getParticipants()
    synapse_data = syn.tableQuery(
            "select healthCode from {}".format(SYNAPSE_TABLES[study])).asDataFrame()
    print("Downloading participant metadata...")
    bridge_metadata = map(lambda i: bc.getParticipantMetaData(i),
                          bridge_data.id.values)
    bridge_metadata = pd.DataFrame(list(bridge_metadata))
    metadata_rel = bridge_metadata[['id', 'healthCode']]
    new_health_codes = [hc not in synapse_data.healthCode.values for hc in metadata_rel.healthCode.values]
    if any(new_health_codes):
        metadata_rel = metadata_rel.loc[new_health_codes,:]
        bridge_merged = bridge_data.merge(metadata_rel, on='id', how="inner")
        hashes = list(map(getmd5, bridge_merged.email.values))
        bridge_merged['externalId'] = hashes
        table = sc.Table(SYNAPSE_TABLES[study],
                         bridge_merged.loc[:, ['externalId', 'healthCode']])
        syn.store(table,
                  executed=["https://gist.github.com/philerooski/56c193d63129c83775124ad95bb448eb"])

if __name__ == "__main__":
    args = read_args()
    main(args.study, args.email, args.password)