Fix typing issues

scripts/script_utils/fastapi_app_location.py

@@ -16,9 +16,7 @@
 
 """Used to define the location of the main FastAPI app object."""
 
-# flake8: noqa
-
-from typing import Any, Dict
+from typing import Any
 
 from fastapi import FastAPI
 
@@ -29,12 +27,13 @@
 app.include_router(router)
 
 
-def custom_openapi() -> Dict[str, Any]:
+def custom_openapi() -> dict[str, Any]:
+    """Get custom OpenAPI schema."""
     if app.openapi_schema:
         return app.openapi_schema
     openapi_schema = get_openapi_schema(app)
     app.openapi_schema = openapi_schema
     return app.openapi_schema
 
 
-app.openapi = custom_openapi  # type: ignore [assignment]
+app.openapi = custom_openapi  # type: ignore[method-assign]

src/wps/adapters/inbound/fastapi_/openapi.py

@@ -28,7 +28,7 @@
 
 def get_openapi_schema(api) -> dict[str, Any]:
     """Generate a custom OpenAPI schema for the service."""
-    config = Config()  # pyright: ignore
+    config = Config()  # type: ignore
 
     return get_openapi(
         title="Work Package Service",

src/wps/main.py

@@ -55,14 +55,14 @@ def custom_openapi():
         api.openapi_schema = openapi_schema
         return api.openapi_schema
 
-    api.openapi = custom_openapi  # type: ignore [assignment]
+    api.openapi = custom_openapi  # type: ignore[method-assign]
 
     return api
 
 
 async def run_rest():
     """Run the HTTP REST API."""
-    config = Config()  # pyright: ignore
+    config = Config()  # type: ignore
 
     async with get_container(config=config):
         api = get_rest_api(config=config)
@@ -71,7 +71,7 @@ async def run_rest():
 
 async def consume_events(run_forever: bool = True):
     """Run an event consumer listening to the configured topic."""
-    config = Config()  # pyright: ignore
+    config = Config()  # type: ignore
 
     async with get_container(config=config) as container:
         event_subscriber = await container.event_subscriber()

tests/fixtures/__init__.py

@@ -99,7 +99,7 @@ def fixture_auth_context() -> AuthContext:
 async def fixture_repository(mongodb_fixture: MongoDbFixture) -> WorkPackageRepository:
     """Fixture for creating a configured repository"""
     work_package_config = WorkPackageConfig(
-        work_package_signing_key=SIGNING_KEY_PAIR.export_private()  # pyright: ignore
+        work_package_signing_key=SIGNING_KEY_PAIR.export_private()  # type: ignore
     )
     dataset_dao = await DatasetDaoConstructor.construct(
         config=work_package_config,

tests/test_models.py

@@ -39,7 +39,7 @@ def test_work_order_token():
         user_id="some-user-id",
         user_public_crypt4gh_key="some-public-key",
         full_user_name="Dr. John Doe",
-        email="john@home.org",  # pyright: ignore
+        email="john@home.org",  # type: ignore
     )
     assert token.full_user_name == "Dr. John Doe"
 
@@ -78,23 +78,23 @@ def test_bad_creation_data():
     """Test instantiating invalid work package creation DTO."""
     with raises(ValidationError, match="dataset_id"):
         WorkPackageCreationData(
-            dataset_id=["foo", "bar"],  # pyright: ignore
+            dataset_id=["foo", "bar"],  # type: ignore
             type=WorkType.DOWNLOAD,
             file_ids=["some-file-id", "another-file-id"],
             user_public_crypt4gh_key=user_public_crypt4gh_key,
         )
     with raises(ValidationError, match="type"):
         WorkPackageCreationData(
             dataset_id="some-dataset-id",
-            type="UNKNOWN_TYPE",  # pyright: ignore
+            type="UNKNOWN_TYPE",  # type: ignore
             file_ids=["some-file-id", "another-file-id"],
             user_public_crypt4gh_key=user_public_crypt4gh_key,
         )
     with raises(ValidationError, match="file_ids"):
         WorkPackageCreationData(
             dataset_id="some-dataset-id",
             type=WorkType.DOWNLOAD,
-            file_ids="some-file-id",  # pyright: ignore
+            file_ids="some-file-id",  # type: ignore
             user_public_crypt4gh_key=user_public_crypt4gh_key,
         )
     with raises(ValidationError, match="user_public_crypt4gh_key"):
@@ -116,7 +116,7 @@ def test_work_package():
         files={"some-file-id": ".sam", "another-file-id": ".bam"},
         user_public_crypt4gh_key=user_public_crypt4gh_key,
         full_user_name="Dr. John Doe",
-        email="john@home.org",  # pyright: ignore
+        email="john@home.org",  # type: ignore
         token_hash="308eda9daf26b7446b284449a5895ab9a04ff30c129d4454e471cfb81bf5557d",
         created=datetime(2022, 2, 2, 2, tzinfo=timezone.utc),  # pyright: ignore
         expires=datetime(2022, 2, 2, 3, tzinfo=timezone.utc),  # pyright: ignore

tests/test_tokens.py

@@ -64,7 +64,7 @@ def test_sign_work_order_token():
         user_id="some-user-id",
         user_public_crypt4gh_key="some-public-key",
         full_user_name="Dr. John Doe",
-        email="john@home.org",  # pyright: ignore
+        email="john@home.org",  # type: ignore
     )
     token_str = sign_work_order_token(work_order_token=work_order_token, key=key)
     assert isinstance(token_str, str)