From 5a6883bdd94893401565a04c74d2817bf763f512 Mon Sep 17 00:00:00 2001
From: Alex Kanitz <alexander.kanitz@alumni.ethz.ch>
Date: Mon, 20 May 2024 02:19:05 +0200
Subject: [PATCH] fix mypy issues

---
 foca/database/register_mongodb.py                   | 13 ++++++++-----
 .../access_control/access_control_server.py         | 11 ++++++-----
 .../access_control/foca_casbin_adapter/adapter.py   |  8 +++++---
 foca/utils/db.py                                    |  2 +-
 requirements.txt                                    |  2 +-
 5 files changed, 21 insertions(+), 15 deletions(-)

diff --git a/foca/database/register_mongodb.py b/foca/database/register_mongodb.py
index ed8285d4..4433515d 100644
--- a/foca/database/register_mongodb.py
+++ b/foca/database/register_mongodb.py
@@ -43,16 +43,19 @@ def register_mongodb(
             db_conf.client = mongo.db
 
             # Add collections
-            if db_conf.collections is not None:
+            if db_conf.collections is not None and db_conf.client is not None:
                 for coll_name, coll_conf in db_conf.collections.items():
 
-                    coll_conf.client = mongo.db[coll_name]
+                    coll_conf.client = db_conf.client[coll_name]
                     logger.info(
                         f"Added database collection '{coll_name}'."
                     )
 
                     # Add indexes
-                    if coll_conf.indexes is not None:
+                    if (
+                        coll_conf.indexes is not None
+                        and coll_conf.client is not None
+                    ):
                         # Remove already created indexes if any
                         coll_conf.client.drop_indexes()
                         for index in coll_conf.indexes:
@@ -94,10 +97,10 @@ def add_new_database(
     db_conf.client = mongo.db
 
     # Add collections
-    if db_conf.collections is not None:
+    if db_conf.collections is not None and db_conf.client is not None:
         for coll_name, coll_conf in db_conf.collections.items():
 
-            coll_conf.client = mongo.db[coll_name]
+            coll_conf.client = db_conf.client[coll_name]
             logger.info(
                 f"Added database collection '{coll_name}'."
             )
diff --git a/foca/security/access_control/access_control_server.py b/foca/security/access_control/access_control_server.py
index 6521c017..e55474a6 100644
--- a/foca/security/access_control/access_control_server.py
+++ b/foca/security/access_control/access_control_server.py
@@ -113,11 +113,12 @@ def getAllPermissions(limit=None) -> List[Dict]:
 
     if not limit:
         limit = 0
-    permissions = db_coll_permission.find(
-        filter={},
-        projection={'_id': False}
-    ).sort([('$natural', -1)]).limit(limit)
-    permissions = list(permissions)
+    permissions = list(
+        db_coll_permission.find(
+            filter={},
+            projection={'_id': False}
+        ).sort([('$natural', -1)]).limit(limit)
+    )
     user_permission_list = []
     for _permission in permissions:
         policy_type = _permission.get("ptype", None)
diff --git a/foca/security/access_control/foca_casbin_adapter/adapter.py b/foca/security/access_control/foca_casbin_adapter/adapter.py
index 76bcf3ca..26f1fe45 100644
--- a/foca/security/access_control/foca_casbin_adapter/adapter.py
+++ b/foca/security/access_control/foca_casbin_adapter/adapter.py
@@ -36,8 +36,9 @@ def __init__(
         self, uri: str, dbname: str, collection: Optional[str] = "casbin_rule"
     ):
         """Create an adapter for Mongodb."""
-        client = MongoClient(uri)
+        client: MongoClient = MongoClient(uri)
         db = client[dbname]
+        assert collection is not None
         self._collection = db[collection]
 
     def load_policy(self, model: CasbinRule):
@@ -100,8 +101,9 @@ def _delete_policy_lines(self, ptype: str, rule: List[str]) -> int:
                 for result in results
                 if line_dict_keys_len == len(result.keys()) - 1
             ]
-            results = self._collection.delete_many({"_id": {"$in": to_delete}})
-            return results.deleted_count
+            return self._collection.delete_many(
+                {"_id": {"$in": to_delete}}
+            ).deleted_count
 
     def save_policy(self, model: Model) -> bool:
         """Method to save a casbin model.
diff --git a/foca/utils/db.py b/foca/utils/db.py
index 2b80d0d5..e44604c5 100644
--- a/foca/utils/db.py
+++ b/foca/utils/db.py
@@ -3,7 +3,7 @@
 from typing import (Any, Mapping, Optional)
 
 from bson.objectid import ObjectId
-from pymongo import collection as Collection
+from pymongo.collection import Collection
 
 
 def find_one_latest(collection: Collection) -> Optional[Mapping[Any, Any]]:
diff --git a/requirements.txt b/requirements.txt
index 5aac9bbb..2a549a25 100644
--- a/requirements.txt
+++ b/requirements.txt
@@ -8,7 +8,7 @@ Flask-Cors==4.0.1
 Flask-PyMongo==2.3.0
 pydantic==1.10.13
 PyJWT==2.4.0
-pymongo==3.12.3
+pymongo==4.7.2
 PyYAML==6.0.1
 requests==2.31.0
 swagger-ui-bundle==0.0.6