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Convert images endpoints to django-ninja
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -1,7 +1,5 @@ | ||
| from .image import ImageViewSet | ||
| from .user import user_me | ||
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| __all__ = [ | ||
| "ImageViewSet", | ||
| "user_me", | ||
| ] |
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -1,109 +1,118 @@ | ||
| from django.utils.decorators import method_decorator | ||
| from drf_yasg.utils import swagger_auto_schema | ||
| from rest_framework.decorators import action | ||
| from rest_framework.response import Response | ||
| from rest_framework.viewsets import ReadOnlyModelViewSet | ||
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| from isic.core.models.collection import Collection | ||
| from isic.core.models.image import Image | ||
| from isic.core.permissions import IsicObjectPermissionsFilter, get_visible_objects | ||
| from django.conf import settings | ||
| from django.http.request import HttpRequest | ||
| from django.shortcuts import get_object_or_404 | ||
| from django.template.loader import render_to_string | ||
| from isic_metadata import FIELD_REGISTRY | ||
| from ninja import Field, ModelSchema, Query, Router, Schema | ||
| from ninja.pagination import paginate | ||
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| from isic.core.models import Collection, Image | ||
| from isic.core.pagination import CursorPagination | ||
| from isic.core.permissions import get_visible_objects | ||
| from isic.core.search import build_elasticsearch_query, facets | ||
| from isic.core.serializers import ImageSerializer, SearchQuerySerializer | ||
| from isic.core.serializers import SearchQueryIn | ||
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| router = Router() | ||
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| @method_decorator( | ||
| name="list", decorator=swagger_auto_schema(operation_summary="Return a list of images.") | ||
| # TODO this originally had "distinct()" on it; I don't think that's needed though | ||
| default_qs = Image.objects.select_related("accession__cohort").defer( | ||
| "accession__unstructured_metadata" | ||
| ) | ||
| @method_decorator( | ||
| name="retrieve", | ||
| decorator=swagger_auto_schema(operation_summary="Retrieve a single image by ISIC ID."), | ||
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| class FileOut(Schema): | ||
| url: str | ||
| size: int | ||
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| class ImageFilesOut(Schema): | ||
| full: FileOut | ||
| thumbnail_256: FileOut | ||
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| class ImageOut(ModelSchema): | ||
| class Config: | ||
| model = Image | ||
| model_fields = ["public"] | ||
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| isic_id: str = Field(alias="isic_id") | ||
| copyright_license: str = Field(alias="accession.copyright_license") | ||
| attribution: str = Field(alias="accession.cohort.attribution") | ||
| files: ImageFilesOut | ||
| metadata: dict | ||
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| @staticmethod | ||
| def resolve_files(image: Image) -> dict: | ||
| if settings.ISIC_PLACEHOLDER_IMAGES: | ||
| full_url = f"https://picsum.photos/seed/{image.id}/1000" | ||
| thumbnail_url = f"https://picsum.photos/seed/{image.id}/256" | ||
| else: | ||
| full_url = image.accession.blob.url | ||
| thumbnail_url = image.accession.thumbnail_256.url | ||
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| full_size = image.accession.blob_size | ||
| thumbnail_size = image.accession.thumbnail_256_size | ||
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| return ImageFilesOut( | ||
| full=FileOut(url=full_url, size=full_size), | ||
| thumbnail_256=FileOut(url=thumbnail_url, size=thumbnail_size), | ||
| ) | ||
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| @staticmethod | ||
| def resolve_metadata(image: Image) -> dict: | ||
| metadata = { | ||
| "acquisition": {"pixels_x": image.accession.width, "pixels_y": image.accession.height}, | ||
| "clinical": {}, | ||
| } | ||
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| for key, value in image.accession.redacted_metadata.items(): | ||
| # this is the only field that we expose that isn't in the FIELD_REGISTRY | ||
| # since it's a derived field. | ||
| if key == "age_approx": | ||
| metadata["clinical"][key] = value | ||
| else: | ||
| metadata[FIELD_REGISTRY[key]["type"]][key] = value | ||
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| return metadata | ||
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| @router.get("/", response=list[ImageOut], summary="Return a list of images.") | ||
| @paginate(CursorPagination) | ||
| def list_images(request: HttpRequest): | ||
| return get_visible_objects(request.user, "core.view_image", default_qs) | ||
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| @router.get( | ||
| "/search/", | ||
| response=list[ImageOut], | ||
| summary="Search images with a key:value query string.", | ||
| description=render_to_string("core/swagger_image_search_description.html"), | ||
| ) | ||
| class ImageViewSet(ReadOnlyModelViewSet): | ||
| serializer_class = ImageSerializer | ||
| queryset = ( | ||
| Image.objects.select_related("accession__cohort") | ||
| .defer("accession__unstructured_metadata") | ||
| .distinct() | ||
| @paginate(CursorPagination) | ||
| def search_images(request: HttpRequest, search: SearchQueryIn = Query(...)): # noqa: B008 | ||
| return search.to_queryset(user=request.user, qs=default_qs) | ||
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| @router.get("/facets/", response=dict, include_in_schema=False) | ||
| def get_facets(request: HttpRequest, search: SearchQueryIn = Query(...)): # noqa: B008 | ||
| query = build_elasticsearch_query( | ||
| search.query or "", | ||
| request.user, | ||
| search.collections, | ||
| ) | ||
| filter_backends = [IsicObjectPermissionsFilter] | ||
| lookup_field = "isic_id" | ||
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| @swagger_auto_schema(auto_schema=None) | ||
| @action(detail=False, methods=["get"], pagination_class=None) | ||
| def facets(self, request): | ||
| serializer = SearchQuerySerializer(data=request.query_params) | ||
| serializer.is_valid(raise_exception=True) | ||
| query = build_elasticsearch_query( | ||
| serializer.validated_data.get("query", ""), | ||
| # Manually pass the list of visible collection PKs through so buckets with | ||
| # counts of 0 aren't included in the facets output for non-visible collections. | ||
| collection_pks = list( | ||
| get_visible_objects( | ||
| request.user, | ||
| serializer.validated_data.get("collections"), | ||
| "core.view_collection", | ||
| Collection.objects.values_list("pk", flat=True), | ||
| ) | ||
| # Manually pass the list of visible collection PKs through so buckets with | ||
| # counts of 0 aren't included in the facets output for non-visible collections. | ||
| collection_pks = list( | ||
| get_visible_objects( | ||
| request.user, | ||
| "core.view_collection", | ||
| Collection.objects.values_list("pk", flat=True), | ||
| ) | ||
| ) | ||
| response = facets(query, collection_pks) | ||
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| return Response(response) | ||
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| @swagger_auto_schema( | ||
| operation_summary="Search images with a key:value query string.", | ||
| operation_description=""" | ||
| The search query uses a simple DSL syntax. | ||
| Some example queries are: | ||
| <pre> | ||
| # Display images diagnosed as melanoma from patients that are approximately 50 years old. | ||
| age_approx:50 AND diagnosis:melanoma | ||
| </pre> | ||
| <pre> | ||
| # Display images from male patients that are approximately 20 to 40 years old. | ||
| age_approx:[20 TO 40] AND sex:male | ||
| </pre> | ||
| <pre> | ||
| # Display images from the anterior, posterior, or lateral torso anatomical site where the diagnosis was confirmed by single image expert consensus. | ||
| anatom_site_general:*torso AND diagnosis_confirm_type:"single image expert consensus" | ||
| </pre> | ||
| The following fields are exposed to the query parameter: | ||
| <ul> | ||
| <li>diagnosis</li> | ||
| <li>age_approx</li> | ||
| <li>sex</li> | ||
| <li>benign_malignant</li> | ||
| <li>diagnosis_confirm_type</li> | ||
| <li>personal_hx_mm</li> | ||
| <li>family_hx_mm</li> | ||
| <li>clin_size_long_diam_mm</li> | ||
| <li>melanocytic</li> | ||
| <li>acquisition_day</li> | ||
| <li>nevus_type</li> | ||
| <li>image_type</li> | ||
| <li>dermoscopic_type</li> | ||
| <li>anatom_site_general</li> | ||
| <li>mel_class</li> | ||
| <li>mel_mitotic_index</li> | ||
| <li>mel_thick_mm</li> | ||
| <li>mel_type</li> | ||
| <li>mel_ulcer</li> | ||
| </ul> | ||
| """, # noqa: E501 | ||
| query_serializer=SearchQuerySerializer, | ||
| ) | ||
| @action(detail=False, methods=["get"]) | ||
| def search(self, request): | ||
| serializer = SearchQuerySerializer( | ||
| data=request.query_params, context={"user": request.user} | ||
| ) | ||
| serializer.is_valid(raise_exception=True) | ||
| qs = serializer.to_queryset(self.get_queryset()) | ||
| page = self.paginate_queryset(qs) | ||
| serializer = self.get_serializer(page, many=True) | ||
| paginated_response = self.get_paginated_response(serializer.data) | ||
| return facets(query, collection_pks) | ||
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| return paginated_response | ||
| @router.get("/{isic_id}/", response=ImageOut, summary="Retrieve a single image by ISIC ID.") | ||
| def retrieve_image(request: HttpRequest, isic_id: str): | ||
| qs = get_visible_objects(request.user, "core.view_image", default_qs) | ||
| return get_object_or_404(qs, isic_id=isic_id) |
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