From bacd0f15463b677190166a7dc0377254d51b60c6 Mon Sep 17 00:00:00 2001
From: Mihai Todor <todormihai@gmail.com>
Date: Thu, 19 Dec 2024 17:05:34 +0000
Subject: [PATCH] Use env var to read MongoDB password

Signed-off-by: Mihai Todor <todormihai@gmail.com>
---
 .github/workflows/cicd.yml |  2 ++
 .gitignore                 |  1 +
 app/common.py              | 20 ++++++++++++--------
 run.py                     |  2 ++
 tests/conftest.py          |  5 +++++
 utilities/common.py        |  6 ++++--
 6 files changed, 26 insertions(+), 10 deletions(-)

diff --git a/.github/workflows/cicd.yml b/.github/workflows/cicd.yml
index 1527e6c94..0aa0c8c23 100644
--- a/.github/workflows/cicd.yml
+++ b/.github/workflows/cicd.yml
@@ -29,6 +29,8 @@ jobs:
 
       - name: Run Tests
         run: ./fetch_utilities_data.sh && python -m pytest
+        env:
+          MONGODB_READONLY_PASSWORD: ${{ secrets.MONGODB_READONLY_PASSWORD }}
 
   deploy:
     name: Deploy to dev
diff --git a/.gitignore b/.gitignore
index d54ff8b0a..daba48198 100644
--- a/.gitignore
+++ b/.gitignore
@@ -7,3 +7,4 @@ __pycache__
 utilities/FASTA
 utilities/mongo_utilities.py
 /data
+secrets.env
diff --git a/app/common.py b/app/common.py
index f52c60581..418d56172 100644
--- a/app/common.py
+++ b/app/common.py
@@ -1,17 +1,19 @@
+import os
+import re
 from collections import OrderedDict
+from datetime import datetime
+from itertools import groupby
 from threading import Lock
 from uuid import uuid4
+
 import pyliftover
-import requests
-from datetime import datetime
 import pymongo
+import requests
 from flask import abort
-from itertools import groupby
-import re
 
 # MongoDB Client URIs
-FHIR_genomics_data_client_uri = "mongodb+srv://download:download@cluster0.8ianr.mongodb.net/FHIRGenomicsData"
-utilities_data_client_uri = "mongodb+srv://download:download@cluster0.8ianr.mongodb.net/UtilitiesData"
+FHIR_genomics_data_client_uri = f"mongodb+srv://readonly:{os.getenv('MONGODB_READONLY_PASSWORD')}@cluster0.8ianr.mongodb.net/FHIRGenomicsData"
+utilities_data_client_uri = f"mongodb+srv://readonly:{os.getenv('MONGODB_READONLY_PASSWORD')}@cluster0.8ianr.mongodb.net/UtilitiesData"
 
 # MongoDB Clients
 client = pymongo.MongoClient(FHIR_genomics_data_client_uri)
@@ -620,9 +622,11 @@ def create_fhir_variant_resource(record, ref_seq, subject):
             inner_end = record['END'] - abs(record['CIEND'][0])
             outer_end = record['END'] + abs(record['CIEND'][1])
 
-        resource["component"].append({"code": {"coding": [{"system": "http://loinc.org", "code": "81301-4", "display": "Variant outer start-end"}]}, "valueRange": {"low": {"value": outer_start}, "high": {"value": outer_end}}})
+        resource["component"].append({"code": {"coding": [{"system": "http://loinc.org", "code": "81301-4", "display": "Variant outer start-end"}]},
+                                     "valueRange": {"low": {"value": outer_start}, "high": {"value": outer_end}}})
 
-        resource["component"].append({"code": {"coding": [{"system": "http://loinc.org", "code": "81302-2", "display": "Variant inner start-end"}]}, "valueRange": {"low": {"value": inner_start}, "high": {"value": inner_end}}})
+        resource["component"].append({"code": {"coding": [{"system": "http://loinc.org", "code": "81302-2", "display": "Variant inner start-end"}]},
+                                     "valueRange": {"low": {"value": inner_start}, "high": {"value": inner_end}}})
 
     # Variant population allele frequency
     if 'popAlleleFreq' in record:
diff --git a/run.py b/run.py
index 35d01fb4a..710ba62b8 100644
--- a/run.py
+++ b/run.py
@@ -3,6 +3,8 @@
 from app import create_app
 
 load_dotenv()
+# Load secrets from secrets.env file if available
+load_dotenv("secrets.env")
 
 app = create_app()
 
diff --git a/tests/conftest.py b/tests/conftest.py
index ccfa7e8e9..2eafd8e38 100644
--- a/tests/conftest.py
+++ b/tests/conftest.py
@@ -1,7 +1,12 @@
 import pytest
+from dotenv import load_dotenv
 
 from app import create_app
 
+load_dotenv()
+# Load secrets from secrets.env file if available
+load_dotenv("secrets.env")
+
 
 @pytest.fixture(scope='module')
 def client():
diff --git a/utilities/common.py b/utilities/common.py
index a27b837c6..1e32ad1cb 100644
--- a/utilities/common.py
+++ b/utilities/common.py
@@ -1,9 +1,11 @@
-from enum import Enum
+import os
 import re
+from enum import Enum
+
 import pandas as pd
 import pymongo
 
-utilities_data_client_uri = "mongodb+srv://download:download@cluster0.8ianr.mongodb.net/UtilitiesData"
+utilities_data_client_uri = f"mongodb+srv://readonly:{os.getenv('MONGODB_READONLY_PASSWORD')}@cluster0.8ianr.mongodb.net/UtilitiesData"
 utilities_client = pymongo.MongoClient(utilities_data_client_uri)
 utilities_db = utilities_client.UtilitiesData
 transcript_data = utilities_db.Transcripts