Merge branch 'main' into feat/sort-by-physical-size

ami/jobs/tests.py

@@ -48,6 +48,7 @@ def setUp(self):
         self.job = Job.objects.create(project=self.project, name="Test job", delay=0)
         self.user = User.objects.create_user(  # type: ignore
             email="[email protected]",
+            is_staff=True,
         )
         self.factory = APIRequestFactory()
 
@@ -99,7 +100,6 @@ def test_run_job(self):
         jobs_run_url = reverse_with_params("api:job-run", args=[self.job.pk], params={"no_async": True})
         self.client.force_authenticate(user=self.user)
         resp = self.client.post(jobs_run_url)
-        self.client.force_authenticate(user=None)
         self.assertEqual(resp.status_code, 200)
         data = resp.json()
         self.assertEqual(data["id"], self.job.pk)

ami/main/api/serializers.py

@@ -552,6 +552,7 @@ class Meta:
             "withdrawn",
             "agreed_with_identification_id",
             "agreed_with_prediction_id",
+            "comment",
             "created_at",
             "updated_at",
         ]
@@ -706,7 +707,7 @@ class Meta:
             "classifications",
         ]
 
-    def get_classifications(self, obj):
+    def get_classifications(self, obj) -> str:
         """
         Return URL to the classifications endpoint filtered by this detection.
         """
@@ -899,10 +900,38 @@ def validate_image(self, value):
         return value
 
 
+class SourceImageCollectionCommonKwargsSerializer(serializers.Serializer):
+    # The most common kwargs for the sampling methods
+    # use for the "common_combined" method
+    minute_interval = serializers.IntegerField(required=False, allow_null=True)
+    max_num = serializers.IntegerField(required=False, allow_null=True)
+    month_start = serializers.IntegerField(required=False, allow_null=True)
+    month_end = serializers.IntegerField(required=False, allow_null=True)
+
+    hour_start = serializers.IntegerField(required=False, allow_null=True)
+    hour_end = serializers.IntegerField(required=False, allow_null=True)
+
+    # Kwargs for other sampling methods, this is not complete
+    # see the SourceImageCollection model for all available kwargs.
+    size = serializers.IntegerField(required=False, allow_null=True)
+    num_each = serializers.IntegerField(required=False, allow_null=True)
+    exclude_events = serializers.CharField(required=False, allow_null=True)
+    deployment_id = serializers.IntegerField(required=False, allow_null=True)
+    position = serializers.IntegerField(required=False, allow_null=True)
+
+    # Don't return the kwargs if they are empty
+    def to_representation(self, instance):
+        data = super().to_representation(instance)
+        return {key: value for key, value in data.items() if value is not None}
+
+
 class SourceImageCollectionSerializer(DefaultSerializer):
+    # @TODO can sampling kwargs be a nested serializer instead??
+
     source_images = serializers.SerializerMethodField()
-    kwargs = serializers.JSONField(initial=dict, required=False)
+    kwargs = SourceImageCollectionCommonKwargsSerializer(required=False, partial=True)
     jobs = JobStatusSerializer(many=True, read_only=True)
+    project = serializers.PrimaryKeyRelatedField(queryset=Project.objects.all())
 
     class Meta:
         model = SourceImageCollection
@@ -920,7 +949,7 @@ class Meta:
             "updated_at",
         ]
 
-    def get_source_images(self, obj):
+    def get_source_images(self, obj) -> str:
         """
         Return URL to the captures endpoint filtered by this collection.
         """
@@ -944,6 +973,7 @@ class Meta:
             "taxon",
             "user",
             "withdrawn",
+            "comment",
             "created_at",
         ]
 

ami/main/api/views.py

@@ -12,11 +12,13 @@
 from rest_framework import viewsets
 from rest_framework.decorators import action
 from rest_framework.filters import SearchFilter
+from rest_framework.generics import GenericAPIView
 from rest_framework.response import Response
 from rest_framework.views import APIView
 
 from ami import tasks
 from ami.base.filters import NullsLastOrderingFilter
+from ami.base.pagination import LimitOffsetPaginationWithPermissions
 from ami.base.permissions import IsActiveStaffOrReadOnly
 from ami.utils.requests import get_active_classification_threshold
 
@@ -98,13 +100,18 @@ class DefaultReadOnlyViewSet(DefaultViewSetMixin, viewsets.ReadOnlyModelViewSet)
     pass
 
 
+class ProjectPagination(LimitOffsetPaginationWithPermissions):
+    default_limit = 20
+
+
 class ProjectViewSet(DefaultViewSet):
     """
     API endpoint that allows projects to be viewed or edited.
     """
 
     queryset = Project.objects.filter(active=True).prefetch_related("deployments").all()
     serializer_class = ProjectSerializer
+    pagination_class = ProjectPagination
 
     def get_serializer_class(self):
         """
@@ -317,6 +324,7 @@ def populate(self, request, pk=None):
         Populate a collection with source images using the configured sampling method and arguments.
         """
         collection = self.get_object()
+        collection.images.clear()
         task = tasks.populate_collection.apply_async([collection.pk])
         return Response({"task": task.id})
 
@@ -702,7 +710,7 @@ class ClassificationViewSet(DefaultViewSet):
     ]
 
 
-class SummaryView(APIView):
+class SummaryView(GenericAPIView):
     permission_classes = [IsActiveStaffOrReadOnly]
     filterset_fields = ["project"]
 

ami/main/migrations/0030_identification_comment.py

@@ -0,0 +1,17 @@
+# Generated by Django 4.2.2 on 2024-04-16 18:56
+
+from django.db import migrations, models
+
+
+class Migration(migrations.Migration):
+    dependencies = [
+        ("main", "0029_alter_deployment_device_and_more"),
+    ]
+
+    operations = [
+        migrations.AddField(
+            model_name="identification",
+            name="comment",
+            field=models.TextField(blank=True),
+        ),
+    ]

ami/main/models.py

@@ -1133,26 +1133,31 @@ def set_dimensions_for_collection(
 
 
 def sample_captures_by_interval(
-    minute_interval: int = 10, qs: models.QuerySet[SourceImage] | None = None
+    minute_interval: int = 10, qs: models.QuerySet[SourceImage] | None = None, max_num: int | None = None
 ) -> typing.Generator[SourceImage, None, None]:
     """
     Return a sample of captures from the deployment, evenly spaced apart by minute_interval.
     """
 
     last_capture = None
+    total = 0
 
     if not qs:
         qs = SourceImage.objects.all()
     qs = qs.exclude(timestamp=None).order_by("timestamp")
 
     for capture in qs.all():
+        if max_num and total >= max_num:
+            break
         if not last_capture:
+            total += 1
             yield capture
             last_capture = capture
         else:
             assert capture.timestamp and last_capture.timestamp
             delta: datetime.timedelta = capture.timestamp - last_capture.timestamp
             if delta.total_seconds() >= minute_interval * 60:
+                total += 1
                 yield capture
                 last_capture = capture
 
@@ -1285,6 +1290,7 @@ class Identification(BaseModel):
         related_name="agreed_identifications",
     )
     score = 1.0  # Always 1 for humans, at this time
+    comment = models.TextField(blank=True)
 
     class Meta:
         ordering = [
@@ -1390,6 +1396,10 @@ class Classification(BaseModel):
     )
     # job = models.CharField(max_length=255, null=True)
 
+    # Type hints for auto-generated fields
+    taxon_id: int
+    algorithm_id: int
+
     class Meta:
         ordering = ["-created_at", "-score"]
 
@@ -2132,6 +2142,7 @@ def html(self) -> str:
 
 
 _SOURCE_IMAGE_SAMPLING_METHODS = [
+    "common_combined",
     "random",
     "stratified_random",
     "interval",
@@ -2162,7 +2173,12 @@ class SourceImageCollection(BaseModel):
     description = models.TextField(blank=True)
     images = models.ManyToManyField("SourceImage", related_name="collections", blank=True)
     project = models.ForeignKey(Project, on_delete=models.CASCADE, related_name="sourceimage_collections")
-    method = models.CharField(max_length=255, choices=as_choices(_SOURCE_IMAGE_SAMPLING_METHODS))
+    method = models.CharField(
+        max_length=255,
+        choices=as_choices(_SOURCE_IMAGE_SAMPLING_METHODS),
+        default="common_combined",
+    )
+    # @TODO this should be a JSON field with a schema, use a pydantic model
     kwargs = models.JSONField(
         "Arguments",
         null=True,
@@ -2171,7 +2187,7 @@ class SourceImageCollection(BaseModel):
         default=dict,
     )
 
-    def source_image_count(self):
+    def source_image_count(self) -> int:
         # This should always be pre-populated using queryset annotations
         return self.images.count()
 
@@ -2206,6 +2222,33 @@ def sample_manual(self, image_ids: list[int]):
         qs = self.get_queryset()
         return qs.filter(id__in=image_ids)
 
+    def sample_common_combined(
+        self,
+        minute_interval: int | None = None,
+        max_num: int | None = 100,
+        hour_start: int | None = None,
+        hour_end: int | None = None,
+        month_start: datetime.date | None = None,
+        month_end: datetime.date | None = None,
+    ) -> list[SourceImage]:
+        qs = self.get_queryset()
+        if month_start:
+            qs = qs.filter(timestamp__month__gte=month_start)
+        if month_end:
+            qs = qs.filter(timestamp__month__lte=month_end)
+        if hour_start:
+            qs = qs.filter(timestamp__hour__gte=hour_start)
+        if hour_end:
+            qs = qs.filter(timestamp__hour__lte=hour_end)
+        if minute_interval:
+            # @TODO can this be done in the database and return a queryset?
+            # this currently returns a list of source images
+            qs = list(sample_captures_by_interval(minute_interval, qs, max_num=max_num))
+        if max_num:
+            qs = qs[:max_num]
+        captures = list(qs)
+        return captures
+
     def sample_interval(
         self, minute_interval: int = 10, exclude_events: list[int] = [], deployment_id: int | None = None
     ):

ami/main/tests.py

@@ -3,6 +3,7 @@
 
 from django.db import connection
 from django.test import TestCase
+from rest_framework.test import APIRequestFactory, APITestCase
 from rich import print
 
 from ami.main.models import (
@@ -17,6 +18,7 @@
     TaxonRank,
     group_images_into_events,
 )
+from ami.users.models import User
 
 
 def setup_test_project(reuse=True) -> tuple[Project, Deployment]:
@@ -547,3 +549,51 @@ def test_taxon_detail(self):
         response = self.client.get(f"/api/v2/taxa/{taxon.pk}/")
         self.assertEqual(response.status_code, 200)
         self.assertEqual(response.json()["name"], taxon.name)
+
+
+class TestIdentification(APITestCase):
+    def setUp(self) -> None:
+        project, deployment = setup_test_project()
+        create_taxa(project=project)
+        create_captures(deployment=deployment)
+        group_images_into_events(deployment=deployment)
+        create_occurrences(deployment=deployment, num=5)
+        self.project = project
+        self.user = User.objects.create_user(  # type: ignore
+            email="[email protected]",
+            is_staff=True,
+        )
+        self.factory = APIRequestFactory()
+        self.client.force_authenticate(user=self.user)
+        return super().setUp()
+
+    def test_identification(self):
+        from ami.main.models import Identification, Taxon
+
+        """
+        Post a new identification suggestion and check that it changed the occurrence's determination.
+        """
+
+        suggest_id_endpoint = "/api/v2/identifications/"
+        taxa = Taxon.objects.filter(projects=self.project)
+        assert taxa.count() > 1
+
+        occurrence = Occurrence.objects.filter(project=self.project).exclude(determination=None)[0]
+        original_taxon = occurrence.determination
+        assert original_taxon is not None
+        new_taxon = Taxon.objects.exclude(pk=original_taxon.pk)[0]
+        comment = "Test identification comment"
+
+        response = self.client.post(
+            suggest_id_endpoint,
+            {
+                "occurrence_id": occurrence.pk,
+                "taxon_id": new_taxon.pk,
+                "comment": comment,
+            },
+        )
+        self.assertEqual(response.status_code, 201)
+        occurrence.refresh_from_db()
+        self.assertEqual(occurrence.determination, new_taxon)
+        identification = Identification.objects.get(pk=response.json()["id"])
+        self.assertEqual(identification.comment, comment)

config/settings/base.py

@@ -355,8 +355,8 @@
     "TITLE": "Automated Monitoring of Insects ML Platform API",
     "DESCRIPTION": "Documentation of API endpoints of Automated Monitoring of Insects ML Platform",
     "VERSION": "1.0.0",
-    "SERVE_PERMISSIONS": ["rest_framework.permissions.IsAdminUser"],
-    # "SERVE_PERMISSIONS": ["rest_framework.permissions.AllowAny"],
+    # "SERVE_PERMISSIONS": ["rest_framework.permissions.IsAdminUser"],
+    "SERVE_PERMISSIONS": ["rest_framework.permissions.AllowAny"],
 }
 # Your stuff...
 # ------------------------------------------------------------------------------

config/urls.py

@@ -23,7 +23,7 @@
     # API base url
     path("api/v2/", include("config.api_router", namespace="api")),
     # OpenAPI Docs
-    path("api/v2/schema/", SpectacularAPIView.as_view(), name="api-schema"),
+    path("api/v2/schema/", SpectacularAPIView.as_view(api_version="api"), name="api-schema"),
     path(
         "api/v2/docs/",
         SpectacularSwaggerView.as_view(url_name="api-schema"),

ui/src/components/header/user-info-dialog/user-info-form/user-info-form.tsx

@@ -28,7 +28,7 @@ const config: FormConfig = {
     label: translate(STRING.FIELD_LABEL_NAME),
   },
   image: {
-    label: translate(STRING.FIELD_LABEL_IMAGE),
+    label: translate(STRING.FIELD_LABEL_ICON),
     description: [
       translate(STRING.MESSAGE_IMAGE_SIZE, {
         value: bytesToMB(API_MAX_UPLOAD_SIZE),

ui/src/data-services/hooks/collections/usePopulateCollection.ts

@@ -0,0 +1,22 @@
+import { useMutation, useQueryClient } from '@tanstack/react-query'
+import axios from 'axios'
+import { API_ROUTES, API_URL } from 'data-services/constants'
+import { getAuthHeader } from 'data-services/utils'
+import { useUser } from 'utils/user/userContext'
+
+export const usePopulateCollection = () => {
+    const { user } = useUser()
+    const queryClient = useQueryClient()
+
+    const { mutateAsync, isLoading, isSuccess, error } = useMutation({
+        mutationFn: (id: string) =>
+            axios.post<{ id: number }>(`${API_URL}/${API_ROUTES.COLLECTIONS}/${id}/populate/`, undefined, {
+                headers: getAuthHeader(user),
+            }),
+        onSuccess: () => {
+            queryClient.invalidateQueries([API_ROUTES.COLLECTIONS])
+        },
+    })
+
+    return { populateCollection: mutateAsync, isLoading, isSuccess, error }
+}