Do minor test reorganization and mypy-placation

services/dcs/README.md

@@ -438,7 +438,7 @@ The service requires the following configuration parameters:
   ```
 
 
-- **`api_route`** *(string)*: Default: `"/ga4gh/drs/v1"`.
+- **`api_route`** *(string)*: DRS API route. Default: `"/ga4gh/drs/v1"`.
 
 ## Definitions
 

services/dcs/config_schema.json

@@ -526,6 +526,7 @@
     },
     "api_route": {
       "default": "/ga4gh/drs/v1",
+      "description": "DRS API route",
       "title": "Api Route",
       "type": "string"
     }

services/dcs/src/dcs/adapters/inbound/fastapi_/configure.py

@@ -20,6 +20,7 @@
 from fastapi import FastAPI
 from fastapi.openapi.utils import get_openapi
 from ghga_service_commons.api import ApiConfigBase, configure_app
+from pydantic import Field
 
 from dcs import __version__
 from dcs.adapters.inbound.fastapi_.routes import router
@@ -28,7 +29,7 @@
 class DrsApiConfig(ApiConfigBase):
     """Configuration parameters for the DRS API."""
 
-    api_route: str = "/ga4gh/drs/v1"
+    api_route: str = Field(default="/ga4gh/drs/v1", description="DRS API route")
 
 
 def get_openapi_schema(app: FastAPI, *, config: DrsApiConfig) -> dict[str, Any]:

services/dcs/src/dcs/main.py

@@ -28,7 +28,7 @@
 
 async def run_rest_app():
     """Run the HTTP REST API."""
-    config = Config()  # type: ignore
+    config = Config()
     configure_logging(config=config)
 
     async with prepare_rest_app(config=config) as app:
@@ -37,7 +37,7 @@ async def run_rest_app():
 
 async def consume_events(run_forever: bool = True):
     """Run an event consumer listening to the specified topic."""
-    config = Config()  # type: ignore
+    config = Config()
     configure_logging(config=config)
 
     async with prepare_event_subscriber(config=config) as event_subscriber:
@@ -46,7 +46,7 @@ async def consume_events(run_forever: bool = True):
 
 async def run_outbox_cleanup():
     """Check if outbox buckets contains files that should be cleaned up and perform clean-up."""
-    config = Config()  # type: ignore
+    config = Config()
     configure_logging(config=config)
 
     async with prepare_outbox_cleaner(config=config) as cleanup_outbox:

services/dcs/tests_dcs/conftest.py

@@ -0,0 +1,37 @@
+# Copyright 2021 - 2023 Universität Tübingen, DKFZ, EMBL, and Universität zu Köln
+# for the German Human Genome-Phenome Archive (GHGA)
+#
+# Licensed under the Apache License, Version 2.0 (the "License");
+# you may not use this file except in compliance with the License.
+# You may obtain a copy of the License at
+#
+#     http://www.apache.org/licenses/LICENSE-2.0
+#
+# Unless required by applicable law or agreed to in writing, software
+# distributed under the License is distributed on an "AS IS" BASIS,
+# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+# See the License for the specific language governing permissions and
+# limitations under the License.
+"""Session-scoped fixture setup"""
+
+from hexkit.providers.akafka.testutils import (  # noqa: F401
+    kafka_container_fixture,
+    kafka_fixture,
+)
+from hexkit.providers.mongodb.testutils import (  # noqa: F401
+    mongodb_container_fixture,
+    mongodb_fixture,
+)
+from hexkit.providers.s3.testutils import (  # noqa: F401
+    file_fixture,  # function-scoped
+    s3_container_fixture,
+    s3_fixture,
+)
+
+# These are function-scoped but importing them here saves imports in test
+# modules and makes it so the noqa: F811 is not required
+from tests_dcs.fixtures.joint import (  # noqa: F401
+    cleanup_fixture,
+    joint_fixture,
+    populated_fixture,
+)

services/dcs/tests_dcs/fixtures/config.py

@@ -38,5 +38,4 @@ def get_config(
         for source in sources:
             sources_dict.update(**source.model_dump())
 
-    # type: ignore
     return Config(config_yaml=default_config_yaml, **sources_dict)

services/dcs/tests_dcs/fixtures/joint.py

@@ -17,15 +17,8 @@
 
 __all__ = [
     "cleanup_fixture",
-    "file_fixture",
     "joint_fixture",
     "JointFixture",
-    "mongodb_fixture",
-    "mongodb_container_fixture",
-    "s3_fixture",
-    "s3_container_fixture",
-    "kafka_fixture",
-    "kafka_container_fixture",
     "populated_fixture",
     "PopulatedFixture",
     "generate_work_order_token",
@@ -60,19 +53,12 @@
 from hexkit.providers.akafka import KafkaEventSubscriber
 from hexkit.providers.akafka.testutils import (
     KafkaFixture,
-    kafka_container_fixture,
-    kafka_fixture,
 )
 from hexkit.providers.mongodb.testutils import (
     MongoDbFixture,
-    mongodb_container_fixture,
-    mongodb_fixture,
 )
 from hexkit.providers.s3.testutils import (
     S3Fixture,
-    file_fixture,
-    s3_container_fixture,
-    s3_fixture,
     temp_file_object,
 )
 from jwcrypto.jwk import JWK

services/dcs/tests_dcs/test_edge_cases.py

@@ -30,8 +30,11 @@
 from ghga_service_commons.utils.utc_dates import now_as_utc
 from pytest_httpx import HTTPXMock, httpx_mock  # noqa: F401
 
-from tests_dcs.fixtures.joint import *  # noqa: F403
-from tests_dcs.fixtures.joint import EXAMPLE_FILE, JointFixture, PopulatedFixture
+from tests_dcs.fixtures.joint import (
+    EXAMPLE_FILE,
+    JointFixture,
+    PopulatedFixture,
+)
 from tests_dcs.fixtures.mock_api.app import router
 from tests_dcs.fixtures.utils import (
     generate_token_signing_keys,
@@ -40,6 +43,8 @@
 
 unintercepted_hosts: list[str] = ["localhost"]
 
+pytestmark = pytest.mark.asyncio()
+
 
 @dataclass
 class StorageUnavailableFixture:
@@ -85,7 +90,6 @@ def non_mocked_hosts() -> list:
     return unintercepted_hosts
 
 
-@pytest.mark.asyncio
 async def test_get_health(joint_fixture: JointFixture):
     """Test the GET /health endpoint"""
     response = await joint_fixture.rest_client.get("/health")
@@ -94,7 +98,6 @@ async def test_get_health(joint_fixture: JointFixture):
     assert response.json() == {"status": "OK"}
 
 
-@pytest.mark.asyncio
 async def test_access_non_existing(joint_fixture: JointFixture):
     """Checks that requesting access to a non-existing DRS object fails with the
     expected exception.
@@ -136,7 +139,6 @@ async def test_access_non_existing(joint_fixture: JointFixture):
     assert response.status_code == status.HTTP_404_NOT_FOUND
 
 
-@pytest.mark.asyncio
 async def test_deletion_config_error(
     storage_unavailable_fixture: StorageUnavailableFixture,
     httpx_mock: HTTPXMock,  # noqa: F811
@@ -153,7 +155,6 @@ async def test_deletion_config_error(
         await data_repository.delete_file(file_id=storage_unavailable_fixture.file_id)
 
 
-@pytest.mark.asyncio
 async def test_drs_config_error(
     storage_unavailable_fixture: StorageUnavailableFixture,
     httpx_mock: HTTPXMock,  # noqa: F811
@@ -184,7 +185,6 @@ async def test_drs_config_error(
     assert response.status_code == 500
 
 
-@pytest.mark.asyncio
 async def test_register_file_twice(populated_fixture: PopulatedFixture, caplog):
     """Assure that files cannot be registered twice"""
     joint_fixture = populated_fixture.joint_fixture

services/dcs/tests_dcs/test_typical_journey.py

@@ -29,13 +29,17 @@
 from hexkit.providers.s3.testutils import FileObject
 from pytest_httpx import HTTPXMock, httpx_mock  # noqa: F401
 
-from tests_dcs.fixtures.joint import *  # noqa: F403
-from tests_dcs.fixtures.joint import CleanupFixture, PopulatedFixture
+from tests_dcs.fixtures.joint import (
+    CleanupFixture,
+    PopulatedFixture,
+)
 from tests_dcs.fixtures.mock_api.app import router
 from tests_dcs.fixtures.utils import generate_work_order_token
 
 unintercepted_hosts: list[str] = ["localhost"]
 
+pytestmark = pytest.mark.asyncio()
+
 
 @pytest.fixture
 def non_mocked_hosts() -> list:
@@ -47,7 +51,6 @@ def non_mocked_hosts() -> list:
     return unintercepted_hosts
 
 
-@pytest.mark.asyncio
 async def test_happy_journey(
     populated_fixture: PopulatedFixture,
     tmp_file: FileObject,
@@ -165,7 +168,6 @@ async def test_happy_journey(
     assert response.status_code == status.HTTP_401_UNAUTHORIZED
 
 
-@pytest.mark.asyncio
 async def test_happy_deletion(
     populated_fixture: PopulatedFixture,
     tmp_file: FileObject,
@@ -213,7 +215,6 @@ async def test_happy_deletion(
     )
 
 
-@pytest.mark.asyncio
 async def test_bucket_cleanup(cleanup_fixture: CleanupFixture):
     """Test multiple outbox bucket cleanup handling."""
     data_repository = cleanup_fixture.joint.data_repository