Merge pull request #5 from Health-RI/main

Add Support for mongo+srv Connection String in MongoDB Configuration

beacon/connections/mongo/__init__.py

@@ -2,14 +2,21 @@
 from beacon.connections.mongo import conf
 import os
 
-uri = "mongodb://{}:{}@{}:{}/{}?authSource={}".format(
-    conf.database_user,
-    conf.database_password,
-    conf.database_host,
-    conf.database_port,
-    conf.database_name,
-    conf.database_auth_source
-)
+if conf.database_cluster:
+    uri = "mongodb+srv://{}:{}@{}/?tls=true&authMechanism=SCRAM-SHA-256&retrywrites=false&maxIdleTimeMS=120000".format(
+        conf.database_user,
+        conf.database_password,
+        conf.database_host
+    )
+else:
+    uri = "mongodb://{}:{}@{}:{}/{}?authSource={}".format(
+        conf.database_user,
+        conf.database_password,
+        conf.database_host,
+        conf.database_port,
+        conf.database_name,
+        conf.database_auth_source
+    )
 
 if os.path.isfile(conf.database_certificate):
     uri += '&tls=true&tlsCertificateKeyFile={}'.format(conf.database_certificate)

beacon/connections/mongo/conf.py

@@ -5,4 +5,5 @@
 database_name = 'beacon'
 database_auth_source = 'admin'
 database_certificate = ''
-database_cafile = ''
+database_cafile = ''
+database_cluster = False

beacon/connections/mongo/extract_filtering_terms.py

@@ -28,14 +28,21 @@
 ICD_REGEX = re.compile(r"(ICD[_A-Za-z0-9]+):([_A-Za-z0-9^\./-]+)")
 
 
-uri = "mongodb://{}:{}@{}:{}/{}?authSource={}".format(
-    conf.database_user,
-    conf.database_password,
-    conf.database_host,
-    conf.database_port,
-    conf.database_name,
-    conf.database_auth_source
-)
+if conf.database_cluster:
+    uri = "mongodb+srv://{}:{}@{}/?tls=true&authMechanism=SCRAM-SHA-256&retrywrites=false&maxIdleTimeMS=120000".format(
+        conf.database_user,
+        conf.database_password,
+        conf.database_host
+    )
+else:
+    uri = "mongodb://{}:{}@{}:{}/{}?authSource={}".format(
+        conf.database_user,
+        conf.database_password,
+        conf.database_host,
+        conf.database_port,
+        conf.database_name,
+        conf.database_auth_source
+    )
 
 if os.path.isfile(conf.database_certificate):
     uri += '&tls=true&tlsCertificateKeyFile={}'.format(conf.database_certificate)

beacon/connections/mongo/get_descendants.py

@@ -13,14 +13,21 @@
 import conf
 
 
-uri = "mongodb://{}:{}@{}:{}/{}?authSource={}".format(
-    conf.database_user,
-    conf.database_password,
-    conf.database_host,
-    conf.database_port,
-    conf.database_name,
-    conf.database_auth_source
-)
+if conf.database_cluster:
+    uri = "mongodb+srv://{}:{}@{}/?tls=true&authMechanism=SCRAM-SHA-256&retrywrites=false&maxIdleTimeMS=120000".format(
+        conf.database_user,
+        conf.database_password,
+        conf.database_host
+    )
+else:
+    uri = "mongodb://{}:{}@{}:{}/{}?authSource={}".format(
+        conf.database_user,
+        conf.database_password,
+        conf.database_host,
+        conf.database_port,
+        conf.database_name,
+        conf.database_auth_source
+    )
 
 if os.path.isfile(conf.database_certificate):
     uri += '&tls=true&tlsCertificateKeyFile={}'.format(conf.database_certificate)

beacon/connections/mongo/ping.py

@@ -5,14 +5,21 @@
 from beacon.logs.logs import LOG
 
 
-uri = "mongodb://{}:{}@{}:{}/{}?authSource={}".format(
-    conf.database_user,
-    conf.database_password,
-    conf.database_host,
-    conf.database_port,
-    conf.database_name,
-    conf.database_auth_source
-)
+if conf.database_cluster:
+    uri = "mongodb+srv://{}:{}@{}/?tls=true&authMechanism=SCRAM-SHA-256&retrywrites=false&maxIdleTimeMS=120000".format(
+        conf.database_user,
+        conf.database_password,
+        conf.database_host
+    )
+else:
+    uri = "mongodb://{}:{}@{}:{}/{}?authSource={}".format(
+        conf.database_user,
+        conf.database_password,
+        conf.database_host,
+        conf.database_port,
+        conf.database_name,
+        conf.database_auth_source
+    )
 
 if os.path.isfile(conf.database_certificate):
     uri += '&tls=true&tlsCertificateKeyFile={}'.format(conf.database_certificate)

beacon/connections/mongo/reindex.py

@@ -3,14 +3,21 @@
 import os
 
 
-uri = "mongodb://{}:{}@{}:{}/{}?authSource={}".format(
-    conf.database_user,
-    conf.database_password,
-    conf.database_host,
-    conf.database_port,
-    conf.database_name,
-    conf.database_auth_source
-)
+if conf.database_cluster:
+    uri = "mongodb+srv://{}:{}@{}/?tls=true&authMechanism=SCRAM-SHA-256&retrywrites=false&maxIdleTimeMS=120000".format(
+        conf.database_user,
+        conf.database_password,
+        conf.database_host
+    )
+else:
+    uri = "mongodb://{}:{}@{}:{}/{}?authSource={}".format(
+        conf.database_user,
+        conf.database_password,
+        conf.database_host,
+        conf.database_port,
+        conf.database_name,
+        conf.database_auth_source
+    )
 
 if os.path.isfile(conf.database_certificate):
     uri += '&tls=true&tlsCertificateKeyFile={}'.format(conf.database_certificate)

requirements.txt

@@ -16,7 +16,7 @@ jsonschema-specifications==2023.12.1
 loguru==0.7.2
 pyyaml==6.0.1
 dataclasses-json==0.5.6
-pymongo==4.0.1
+pymongo[srv]==4.0.1
 coverage==7.6.0
 requests==2.25.1
 pydantic==2.6.2