Remove retina endpoints (#154)

See DIAGNijmegen/rse-grand-challenge-admin#236 --------- Co-authored-by: Harm van Zeeland <[email protected]>
DIAGNijmegen · Nov 5, 2024 · 828049e · 828049e
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diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml
@@ -8,7 +8,7 @@ on:
       - published
 
 env:
-  MINIMUM_PYTHON_VERSION: '3.8'
+  MINIMUM_PYTHON_VERSION: '3.9'
 
 concurrency:
   group: ${{ github.head_ref || github.run_id }}
@@ -19,10 +19,10 @@ jobs:
     runs-on: ubuntu-latest
     steps:
       - name: Install Python ${{ env.MINIMUM_PYTHON_VERSION }}
-        uses: actions/setup-python@v4
+        uses: actions/setup-python@v5
         with:
           python-version: ${{ env.MINIMUM_PYTHON_VERSION }}
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
       - name: Install pre-commit
         run: |
           python -m pip install --upgrade pip
@@ -40,19 +40,19 @@ jobs:
     strategy:
       fail-fast: false # Try to work around ECS errors
       matrix:
-        python-version: ["3.8", "3.9", "3.10", "3.11"]
+        python-version: ["3.9", "3.10", "3.11", "3.12"]
     steps:
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
       - name: Set up Python ${{ matrix.python-version }}
-        uses: actions/setup-python@v4
+        uses: actions/setup-python@v5
         with:
           python-version: ${{ matrix.python-version }}
       - name: Install dependencies
         run: |
           python -m pip install --upgrade pip
           python -m pip install tox-gh-actions poetry
       - name: Configure AWS credentials
-        uses: aws-actions/configure-aws-credentials@v2
+        uses: aws-actions/configure-aws-credentials@v4
         with:
           role-to-assume: ${{ secrets.AWS_ROLE_ARN }}
           aws-region: us-east-1
@@ -66,8 +66,6 @@ jobs:
           retry -t 5 -- docker pull public.ecr.aws/diag-nijmegen/grand-challenge/http:latest
       - name: Add gc.localhost to /etc/hosts
         run: sudo echo "127.0.0.1 gc.localhost\n127.0.0.1 minio.localhost" | sudo tee -a /etc/hosts
-      - name: Find the docker compose version (should be at least 2.1.1 for --wait, everything works locally with 2.5.1, 2.4.1+azure-1 does not work)
-        run: docker compose version
       - name: Run tox
         run: tox
 
@@ -77,10 +75,10 @@ jobs:
     runs-on: ubuntu-latest
     steps:
       - name: Install Python ${{ env.MINIMUM_PYTHON_VERSION }}
-        uses: actions/setup-python@v4
+        uses: actions/setup-python@v5
         with:
           python-version: ${{ env.MINIMUM_PYTHON_VERSION }}
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
       - name: Install dependencies
         run: |
           python -m pip install --upgrade pip

diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml
@@ -1,24 +1,24 @@
 repos:
   - repo: https://github.com/pre-commit/pre-commit-hooks
-    rev: v4.4.0
+    rev: v4.6.0
     hooks:
       - id: check-docstring-first
       - id: debug-statements
       - id: end-of-file-fixer
       - id: mixed-line-ending
       - id: trailing-whitespace
   - repo: https://github.com/asottile/pyupgrade
-    rev: v3.3.1
+    rev: v3.17.0
     hooks:
       - id: pyupgrade
         language: python
-        args: [--py38-plus, --keep-runtime-typing]
+        args: [--py39-plus, --keep-runtime-typing]
   - repo: https://github.com/pycqa/isort
-    rev: 5.12.0
+    rev: 5.13.2
     hooks:
       - id: isort
   - repo: https://github.com/ambv/black
-    rev: 23.1.0
+    rev: 24.4.2
     hooks:
       - id: black
         language: python
@@ -35,7 +35,7 @@ repos:
           - mccabe
           - yesqa
   - repo: https://github.com/pre-commit/mirrors-mypy
-    rev: 'v1.0.0'
+    rev: 'v1.11.1'
     hooks:
       - id: mypy
         additional_dependencies:

diff --git a/HISTORY.md b/HISTORY.md
@@ -2,8 +2,10 @@
 
 ## 0.12.0 (UNRELEASED)
 
-  - Removed support for Python 3.6 and 3.7
-  - Added support for Python 3.11
+  - Removed support for Python 3.6, 3.7 and 3.8
+  - Added support for Python 3.11 and 3.12
+  - Removed the retina endpoints
+  - Migrated to use Pydantic models for request and response validation
 
 ## 0.11.0 (2022-12-14)
 

diff --git a/README.md b/README.md
@@ -20,8 +20,8 @@ Challenge](https://grand-challenge.org/documentation/grand-challenge-api/).
 This client is tested using the `tox` framework. This enables testing
 the client in various python-version environments.
 
-For example, running a specific `your_test` for only the python 3.8
+For example, running a specific `your_test` for only the python 3.9
 environment can be done as follows:
 ```bash
-tox -e py38 -- -k your_test
+tox -e py39 -- -k your_test
 ```
diff --git a/gcapi/apibase.py b/gcapi/apibase.py
@@ -1,16 +1,6 @@
 import collections
-from typing import (
-    Any,
-    Dict,
-    Generator,
-    Generic,
-    Iterator,
-    List,
-    Sequence,
-    Type,
-    TypeVar,
-    overload,
-)
+from collections.abc import Generator, Iterator, Sequence
+from typing import Any, Generic, TypeVar, overload
 from urllib.parse import urljoin
 
 from httpx import URL, HTTPStatusError
@@ -28,15 +18,12 @@
 
 class ClientInterface:
     @property
-    def base_url(self) -> URL:
-        ...
+    def base_url(self) -> URL: ...
 
     @base_url.setter
-    def base_url(self, v: URLTypes):
-        ...
+    def base_url(self, v: URLTypes): ...
 
-    def validate_url(self, url):
-        ...
+    def validate_url(self, url): ...
 
     def __call__(
         self,
@@ -59,7 +46,7 @@ def __init__(
         offset: int,
         limit: int,
         total_count: int,
-        results: List[T],
+        results: list[T],
         **kwargs,
     ) -> None:
         super().__init__(**kwargs)
@@ -69,12 +56,10 @@ def __init__(
         self._results = results
 
     @overload
-    def __getitem__(self, key: int) -> T:
-        ...
+    def __getitem__(self, key: int) -> T: ...
 
     @overload
-    def __getitem__(self, key: slice) -> Sequence[T]:
-        ...
+    def __getitem__(self, key: slice) -> Sequence[T]: ...
 
     def __getitem__(self, key):
         return self._results[key]
@@ -96,15 +81,15 @@ def total_count(self) -> int:
 
 
 class Common(Generic[T]):
-    model: Type[T]
+    model: type[T]
     _client: ClientInterface
     base_path: str
 
     yield_request = CallCapture()
 
 
 class APIBase(Generic[T], Common[T]):
-    sub_apis: Dict[str, Type["APIBase"]] = {}
+    sub_apis: dict[str, type["APIBase"]] = {}
 
     def __init__(self, client) -> None:
         if isinstance(self, ModifiableMixin):
@@ -123,7 +108,7 @@ def list(self, params=None):
 
     def page(
         self, offset=0, limit=100, params=None
-    ) -> Generator[T, Dict[Any, Any], PageResult[T]]:
+    ) -> Generator[T, dict[Any, Any], PageResult[T]]:
         if params is None:
             params = {}
 
@@ -158,7 +143,7 @@ def iterate_all(self, params=None) -> Iterator[T]:
             yield from current_list
             offset += req_count
 
-    def detail(self, pk=None, **params) -> Generator[T, Dict[Any, Any], T]:
+    def detail(self, pk=None, **params) -> Generator[T, dict[Any, Any], T]:
         if all((pk, params)):
             raise ValueError("Only one of pk or params must be specified")
 

diff --git a/gcapi/client.py b/gcapi/client.py
@@ -2,20 +2,12 @@
 import os
 import re
 import uuid
+from collections.abc import Generator
 from io import BytesIO
 from pathlib import Path
 from random import randint
 from time import sleep
-from typing import (
-    TYPE_CHECKING,
-    Any,
-    Callable,
-    Dict,
-    Generator,
-    List,
-    Optional,
-    Union,
-)
+from typing import TYPE_CHECKING, Any, Callable, Optional, Union
 from urllib.parse import urljoin
 
 import httpx
@@ -206,40 +198,6 @@ class ComponentInterfacesAPI(APIBase[gcapi.models.ComponentInterface]):
     model = gcapi.models.ComponentInterface
 
 
-class RetinaLandmarkAnnotationSetsAPI(
-    ModifiableMixin, APIBase[gcapi.models.LandmarkAnnotationSet]
-):
-    base_path = "retina/landmark-annotation/"
-    model = gcapi.models.LandmarkAnnotationSet
-
-    def for_image(self, pk):
-        result = yield self.yield_request(
-            method="GET", path=self.base_path, params={"image_id": pk}
-        )
-        return result
-
-
-class RetinaPolygonAnnotationSetsAPI(
-    ModifiableMixin, APIBase[gcapi.models.NestedPolygonAnnotationSet]
-):
-    base_path = "retina/polygon-annotation-set/"
-    model = gcapi.models.NestedPolygonAnnotationSet
-
-
-class RetinaSinglePolygonAnnotationsAPI(
-    ModifiableMixin, APIBase[gcapi.models.SinglePolygonAnnotation]
-):
-    base_path = "retina/single-polygon-annotation/"
-    model = gcapi.models.SinglePolygonAnnotation
-
-
-class RetinaETDRSGridAnnotationsAPI(
-    ModifiableMixin, APIBase[gcapi.models.ETDRSGridAnnotation]
-):
-    base_path = "retina/etdrs-grid-annotation/"
-    model = gcapi.models.ETDRSGridAnnotation
-
-
 class UploadsAPI(APIBase[gcapi.models.UserUpload]):
     base_path = "uploads/"
     model = gcapi.models.UserUpload
@@ -385,7 +343,7 @@ class WorkstationConfigsAPI(APIBase[gcapi.models.WorkstationConfig]):
     model = gcapi.models.WorkstationConfig
 
 
-def _generate_auth_header(token: str = "") -> Dict:
+def _generate_auth_header(token: str = "") -> dict:
     if not token:
         try:
             token = str(os.environ["GRAND_CHALLENGE_AUTHORIZATION"])
@@ -410,10 +368,6 @@ class ApiDefinitions:
     algorithm_jobs: AlgorithmJobsAPI
     archives: ArchivesAPI
     workstation_configs: WorkstationConfigsAPI
-    retina_landmark_annotations: RetinaLandmarkAnnotationSetsAPI
-    retina_polygon_annotation_sets: RetinaPolygonAnnotationSetsAPI
-    retina_single_polygon_annotations: RetinaSinglePolygonAnnotationsAPI
-    retina_etdrs_grid_annotations: RetinaETDRSGridAnnotationsAPI
     raw_image_upload_sessions: UploadSessionsAPI
     archive_items: ArchiveItemsAPI
     interfaces: ComponentInterfacesAPI
@@ -562,7 +516,7 @@ def _upload_file(self, value):
     def upload_cases(  # noqa: C901
         self,
         *,
-        files: List[str],
+        files: list[str],
         archive: Optional[str] = None,
         answer: Optional[str] = None,
         archive_item: Optional[str] = None,
@@ -660,7 +614,7 @@ def upload_cases(  # noqa: C901
 
         return raw_image_upload_session
 
-    def run_external_job(self, *, algorithm: str, inputs: Dict[str, Any]):
+    def run_external_job(self, *, algorithm: str, inputs: dict[str, Any]):
         """
         Starts an algorithm job with the provided inputs.
         You will need to provide the slug of the algorithm. You can find this in the
@@ -740,7 +694,7 @@ def run_external_job(self, *, algorithm: str, inputs: Dict[str, Any]):
         return (yield from self.__org_api_meta.algorithm_jobs.create(**job))
 
     def update_archive_item(
-        self, *, archive_item_pk: str, values: Dict[str, Any]
+        self, *, archive_item_pk: str, values: dict[str, Any]
     ):
         """
         This function updates an existing archive item with the provided values
@@ -764,17 +718,6 @@ def update_archive_item(
         If you provide a value or file for an existing interface of the archive
         item, the old value will be overwritten by the new one, hence allowing you
         to update existing archive item values.
-        For images that are already associated with an archive item, you can
-        also change the interface type (e.g. from generic medical image to
-        generic overlay) by providing the link to the existing image together
-        with the new interface slug you would like to use:
-        client.update_archive_item(
-            archive_item_pk=items[0]['id'],
-            values={
-                "generic-overlay":
-                "https://grand-challenge.org/api/v1/cases/images/.../",
-            }
-        )
 
         Parameters
         ----------
@@ -788,7 +731,7 @@ def update_archive_item(
         item = yield from self.__org_api_meta.archive_items.detail(
             pk=archive_item_pk
         )
-        civs: Dict[str, list] = {"values": []}
+        civs: dict[str, list] = {"values": []}
 
         for civ_slug, value in values.items():
             try:
@@ -880,7 +823,7 @@ def _validate_display_set_values(self, values, interfaces):
         return interfaces
 
     def add_cases_to_reader_study(
-        self, *, reader_study: str, display_sets: List[Dict[str, Any]]
+        self, *, reader_study: str, display_sets: list[dict[str, Any]]
     ):
         """
         This function takes a reader study slug and a list of diplay sets
@@ -911,7 +854,7 @@ def add_cases_to_reader_study(
         The pks of the newly created display sets.
         """
         res = []
-        interfaces: Dict[str, Dict] = {}
+        interfaces: dict[str, dict] = {}
         for display_set in display_sets:
             new_interfaces = yield from self._validate_display_set_values(
                 display_set.items(), interfaces