CVE-2022-1554: Merge branch 'auth_serve_files' of https://github.com/Clinical-Genomi… · Clinical-Genomics/scout@952a2e2

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#!/usr/bin/python

# -*- coding: utf-8 -*-

import click

from pymongo import MongoClient

CASES_WITH_DIA = {

"diagnosis_phenotypes": {"$exists": True, "$ne": []}

} # MongoDB query to locate cases with any diagnosis

SELECT_FIELDS = {

"owner": 1,

"display_name": 1,

"diagnosis_phenotypes": 1,

} # select only a few important fields using the query above

@click.command()

@click.option(“–db-uri", required=True, help="mongodb://user:password@db_url:db_port”)

@click.option(“–db-name", required=True, help="db name”)

@click.option("–fix", help="Use this flag to fix the OMIM format in old cases", is_flag=True)

def omim_case_fix_format(db_uri, db_name, fix):

try:

client = MongoClient(db_uri)

db = client[db_name]

# test connection

click.echo("database connection info:{}".format(db))

cases_with_dia = list(db.case.find(CASES_WITH_DIA, SELECT_FIELDS))

click.echo(f"Total number of cases with diagnosis:{len(cases_with_dia)}")

# Display cases with old format of diagnosis (a list of integers)

cases_with_old_dia = [

case for case in cases_with_dia if isinstance(case[“diagnosis_phenotypes”][0], int)

]

click.echo(f"Total number of cases with old diagnosis format:{len(cases_with_old_dia)}")

for i, case in enumerate(cases_with_old_dia):

click.echo(f"n:{i}\t{case[‘owner’]}\t{case[‘display_name’]}")

old_dia = case[“diagnosis_phenotypes”]

new_dia = []

for dia_nr in old_dia:

disease_term = db.disease_term.find_one({"disease_nr": dia_nr})

if disease_term is None:

click.echo(f"Could not find a disease term with id:{dia_nr}")

continue

new_dia.append(

{

"disease_nr": dia_nr,

"disease_id": disease_term[“disease_id”],

"description": disease_term[“description”],

}

)

if fix is False:

new_dia = old_dia

else:

db.case.find_one_and_update(

{"_id": case[“_id”]}, {"$set": {"diagnosis_phenotypes": new_dia}}

)

click.echo(f"old dia:{old_dia}—>new dia:{new_dia}\n")

except Exception as err:

click.echo("Error {}".format(err))

if __name__ == "__main__":

omim_case_fix_format()