[Fix conflicts now so it's easier when we merge back in]

Enable deferred annotations everywhere and fix annotations and comments (#206)

* Defer annotations in all files and fix some pre-existing comment quirks

* Applied ruff fixes with and without `--unsafe-fixes` flag

* Some manual fixes

cli/src/pixl_cli/__init__.py

@@ -12,6 +12,7 @@
 #  See the License for the specific language governing permissions and
 #  limitations under the License.
 """PIXL command line interface"""
+from __future__ import annotations
 
 from pixl_cli.main import cli
 

cli/src/pixl_cli/_io.py

@@ -11,8 +11,9 @@
 #  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.
-
 """Reading and writing files from PIXL CLI."""
+from __future__ import annotations
+
 import json
 from datetime import datetime
 from pathlib import Path

cli/src/pixl_cli/_logging.py

@@ -11,6 +11,8 @@
 #  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.
+from __future__ import annotations
+
 import logging
 
 import coloredlogs

cli/src/pixl_cli/_utils.py

@@ -11,6 +11,8 @@
 #  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.
+from __future__ import annotations
+
 from pathlib import Path
 
 

cli/src/pixl_cli/main.py

@@ -12,6 +12,7 @@
 #  See the License for the specific language governing permissions and
 #  limitations under the License.
 """PIXL command line interface functionality"""
+from __future__ import annotations
 
 import json
 import os

cli/tests/conftest.py

@@ -11,8 +11,9 @@
 #  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.
-
 """CLI testing fixtures."""
+from __future__ import annotations
+
 import pathlib
 
 import pytest

cli/tests/test_copy_omop.py

@@ -12,6 +12,8 @@
 #  See the License for the specific language governing permissions and
 #  limitations under the License.
 """Test copying of OMOP ES data for later export."""
+from __future__ import annotations
+
 import datetime
 
 import pytest

cli/tests/test_messages_from_parquet.py

@@ -12,13 +12,17 @@
 #  See the License for the specific language governing permissions and
 #  limitations under the License.
 """Unit tests for reading cohorts from parquet files."""
+from __future__ import annotations
 
 import datetime
-from pathlib import Path
+from typing import TYPE_CHECKING
 
 from core.patient_queue.message import Message
 from pixl_cli._io import copy_parquet_return_logfile_fields, messages_from_parquet
 
+if TYPE_CHECKING:
+    from pathlib import Path
+
 
 def test_messages_from_parquet(resources: Path) -> None:
     """

cli/tests/test_queue_start_and_stop_parquet.py

@@ -12,6 +12,7 @@
 #  See the License for the specific language governing permissions and
 #  limitations under the License.
 """Patient queue tests"""
+from __future__ import annotations
 
 from pathlib import Path
 

hasher/src/hasher/__init__.py

@@ -21,6 +21,7 @@
 The Azure infrastructure (Key Vault, ServicePrincipal & permissions) must be persistent
 and instructions are provided for creating these with the az CLI tool.
 """
+from __future__ import annotations
 
 import importlib.metadata
 

hasher/src/hasher/endpoints.py

@@ -12,6 +12,7 @@
 #  See the License for the specific language governing permissions and
 #  limitations under the License.
 """Sets up endpoints for the hasher-api"""
+from __future__ import annotations
 
 from fastapi import APIRouter
 from starlette.responses import Response

hasher/src/hasher/hashing.py

@@ -20,6 +20,7 @@
 - generate_salt: generate a random text string in hexadecimal to be used as a salt
 
 """
+from __future__ import annotations
 
 import logging
 import os

hasher/src/hasher/main.py

@@ -12,6 +12,7 @@
 #  See the License for the specific language governing permissions and
 #  limitations under the License.
 """Defines the FastAPI app for the hasher"""
+from __future__ import annotations
 
 import logging
 

hasher/src/hasher/settings.py

@@ -22,6 +22,7 @@
 - "AZURE_KEY_VAULT_NAME"
 - "AZURE_KEY_VAULT_SECRET_NAME"
 """
+from __future__ import annotations
 
 import pprint
 import tempfile

hasher/tests/conftest.py

@@ -11,6 +11,7 @@
 #  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.
+from __future__ import annotations
 
 import os
 

hasher/tests/test_endpoints.py

@@ -11,6 +11,8 @@
 #  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.
+from __future__ import annotations
+
 import pytest
 from fastapi.testclient import TestClient
 from hasher.main import app

hasher/tests/test_hashing.py

@@ -11,6 +11,8 @@
 #  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.
+from __future__ import annotations
+
 import pytest
 from hasher.hashing import generate_hash, generate_salt
 from hypothesis import HealthCheck, example, given, settings

orthanc/orthanc-anon/plugin/pixl.py

@@ -1,11 +1,3 @@
-"""
-
-Applies anonymisation scheme to datasets
-
-This module:
--Modifies a DICOM instance received by Orthanc and applies anonymisation
--Upload the resource to a dicom-web server
-
 #  Copyright (c) 2022 University College London Hospitals NHS Foundation Trust
 #
 #  Licensed under the Apache License, Version 2.0 (the "License");
@@ -20,6 +12,13 @@
 #  See the License for the specific language governing permissions and
 #  limitations under the License.
 """
+Applies anonymisation scheme to datasets
+
+This module:
+-Modifies a DICOM instance received by Orthanc and applies anonymisation
+-Upload the resource to a dicom-web server
+"""
+from __future__ import annotations
 
 import json
 import logging

orthanc/orthanc-raw/plugin/pixl.py

@@ -1,12 +1,3 @@
-"""
-
-Facilitates routing of stable studies from orthanc-raw to orthanc-anon
-
-This module provides:
--OnChange: route stable studies and if auto-routing enabled
--ShouldAutoRoute: checks whether auto-routing is enabled
--OnHeartBeat: extends the REST API
-
 #  Copyright (c) 2022 University College London Hospitals NHS Foundation Trust
 #
 #  Licensed under the Apache License, Version 2.0 (the "License");
@@ -21,6 +12,15 @@
 #  See the License for the specific language governing permissions and
 #  limitations under the License.
 """
+Facilitates routing of stable studies from orthanc-raw to orthanc-anon
+
+This module provides:
+-OnChange: route stable studies and if auto-routing enabled
+-ShouldAutoRoute: checks whether auto-routing is enabled
+-OnHeartBeat: extends the REST API
+"""
+from __future__ import annotations
+
 import os
 
 import orthanc

pixl_core/src/core/__init__.py

@@ -17,3 +17,4 @@
 to interact with RabbitMQ and ensure suitable rate limiting of requests to the upstream
 services.
 """
+from __future__ import annotations

pixl_core/src/core/models.py

@@ -15,6 +15,8 @@
 PIXL core models
 This module defines the data models used by the PIXL core service
 """
+from __future__ import annotations
+
 from dataclasses import dataclass
 
 from pydantic import BaseModel

pixl_core/src/core/omop.py

@@ -11,7 +11,6 @@
 #  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.
-
 """Processing of OMOP parquet files."""
 from __future__ import annotations
 
@@ -27,6 +26,7 @@
 
     from pixl_ehr._processing import PatientEHRData
 
+
 root_from_install = pathlib.Path(__file__).parents[3]
 
 logger = logging.getLogger(__file__)

pixl_core/src/core/patient_queue/__init__.py

@@ -12,6 +12,7 @@
 #  See the License for the specific language governing permissions and
 #  limitations under the License.
 """RabbitMQ consumer for Pixl"""
+from __future__ import annotations
 
 from .subscriber import PixlConsumer
 

pixl_core/src/core/patient_queue/_base.py

@@ -11,6 +11,8 @@
 #  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.
+from __future__ import annotations
+
 import logging
 import os
 from typing import Any

pixl_core/src/core/patient_queue/message.py

@@ -11,16 +11,18 @@
 #  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.
-
 """Classes to represent messages in the patient queue."""
+from __future__ import annotations
 
 import logging
 from dataclasses import dataclass
-from datetime import date, datetime
-from typing import Any
+from typing import TYPE_CHECKING, Any
 
 from jsonpickle import decode, encode
 
+if TYPE_CHECKING:
+    from datetime import date, datetime
+
 logger = logging.getLogger(__name__)
 
 

pixl_core/src/core/patient_queue/producer.py

@@ -12,14 +12,17 @@
 #  See the License for the specific language governing permissions and
 #  limitations under the License.
 """Producer for RabbitMQ"""
+from __future__ import annotations
 
 import logging
 from time import sleep
-
-from core.patient_queue.message import Message
+from typing import TYPE_CHECKING
 
 from ._base import PixlBlockingInterface
 
+if TYPE_CHECKING:
+    from core.patient_queue.message import Message
+
 LOGGER = logging.getLogger(__name__)
 
 

pixl_core/src/core/patient_queue/subscriber.py

@@ -12,20 +12,26 @@
 #  See the License for the specific language governing permissions and
 #  limitations under the License.
 """Subscriber for RabbitMQ"""
+from __future__ import annotations
 
 import asyncio
 import logging
-from collections.abc import Awaitable, Callable
 from pathlib import Path
-from typing import Any
+from typing import TYPE_CHECKING, Any
 
 import aio_pika
 
 from core.patient_queue.message import Message, deserialise
-from core.token_buffer.tokens import TokenBucket
 
 from ._base import PixlBlockingInterface, PixlQueueInterface
 
+if TYPE_CHECKING:
+    from collections.abc import Awaitable, Callable
+
+    from typing_extensions import Self
+
+    from core.token_buffer.tokens import TokenBucket
+
 logger = logging.getLogger(__name__)
 
 
@@ -44,7 +50,7 @@ def __init__(self, queue_name: str, token_bucket: TokenBucket) -> None:
     def _url(self) -> str:
         return f"amqp://{self._username}:{self._password}@{self._host}:{self._port}/"
 
-    async def __aenter__(self) -> "PixlConsumer":
+    async def __aenter__(self) -> Self:
         """Establishes connection to queue."""
         self._connection = await aio_pika.connect_robust(self._url)
         self._channel = await self._connection.channel()

pixl_core/src/core/router.py

@@ -12,6 +12,7 @@
 #  See the License for the specific language governing permissions and
 #  limitations under the License.
 """Router for the API endpoints"""
+from __future__ import annotations
 
 from fastapi import APIRouter, HTTPException, status
 

pixl_core/src/core/token_buffer/__init__.py

@@ -11,8 +11,8 @@
 #  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.
-
 """Implements the TokenBucket class"""
+from __future__ import annotations
 
 from .tokens import TokenBucket
 

pixl_core/src/core/token_buffer/tokens.py

@@ -1,5 +1,4 @@
 # noqa: D100
-
 #  Copyright (c) 2022 University College London Hospitals NHS Foundation Trust
 #
 #  Licensed under the Apache License, Version 2.0 (the "License");
@@ -13,6 +12,8 @@
 #  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.
+from __future__ import annotations
+
 import token_bucket as tb
 
 

pixl_core/tests/conftest.py

@@ -11,6 +11,8 @@
 #  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.
+from __future__ import annotations
+
 import os
 
 os.environ["ENV"] = "test"

pixl_core/tests/patient_queue/test_message.py

@@ -11,6 +11,8 @@
 #  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.
+from __future__ import annotations
+
 import datetime
 
 from core.patient_queue.message import Message, deserialise