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Update Healthcode to MD5 hash table for JourneyPro, Presence, ElevateMS
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 = metadat_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)
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