Include taxa view updates from OOD branch

ami/base/filters.py

@@ -1,5 +1,6 @@
 from django.db.models import F, OrderBy
-from rest_framework.filters import OrderingFilter
+from django.forms import FloatField
+from rest_framework.filters import BaseFilterBackend, OrderingFilter
 
 
 class NullsLastOrderingFilter(OrderingFilter):
@@ -8,3 +9,56 @@ def get_ordering(self, request, queryset, view):
         if not values:
             return values
         return [OrderBy(F(value.lstrip("-")), descending=value.startswith("-"), nulls_last=True) for value in values]
+
+
+class ThresholdFilter(BaseFilterBackend):
+    """
+    Filter a numeric field by a minimum value.
+
+    Usage:
+
+    Filter occurrences by their determination score:
+    GET /occurrences/?score=0.5
+    This will return all occurrences with a determination score greater than or equal to 0.5.
+
+    Customize the query_param and filter_param to match your API and model fields using
+    the create method.
+
+    Example:
+
+    DeterminationScoreFilter = ThresholdFilter.create(
+        query_param="classification_threshold",
+        filter_param="determination_score",
+    )
+    OODScoreFilter = ThresholdFilter.create("determination_ood_score")
+
+    class OccurrenceViewSet(DefaultViewSet):
+        filter_backends = DefaultViewSetMixin.filter_backends + [
+            DeterminationScoreFilter,
+            OODScoreFilter,
+        ]
+    """
+
+    query_param = "score"
+    filter_param = "score"
+
+    def filter_queryset(self, request, queryset, view):
+        value = FloatField(required=False).clean(request.query_params.get(self.query_param))
+        if value:
+            filters = {f"{self.filter_param}__gte": value}
+            queryset = queryset.filter(**filters)
+        return queryset
+
+    @classmethod
+    def create(cls, query_param: str, filter_param: str | None = None) -> type["ThresholdFilter"]:
+        class_name = f"{cls.__name__}_{query_param}"
+        if filter_param is None:
+            filter_param = query_param
+        return type(
+            class_name,
+            (cls,),
+            {
+                "query_param": query_param,
+                "filter_param": filter_param,
+            },
+        )

ami/main/api/serializers.py

@@ -731,6 +731,8 @@ class Meta:
             "events_count",
             "occurrences",
             "gbif_taxon_key",
+            "last_detected",
+            "best_determination_score",
         ]
 
 

ami/main/api/views.py

@@ -23,7 +23,7 @@
 from rest_framework.response import Response
 from rest_framework.views import APIView
 
-from ami.base.filters import NullsLastOrderingFilter
+from ami.base.filters import NullsLastOrderingFilter, ThresholdFilter
 from ami.base.pagination import LimitOffsetPaginationWithPermissions
 from ami.base.permissions import (
     CanDeleteIdentification,
@@ -1024,6 +1024,11 @@ def filter_queryset(self, request, queryset, view):
             return queryset
 
 
+OccurrenceDeterminationScoreFilter = ThresholdFilter.create(
+    query_param="classification_threshold", filter_param="determination_score"
+)
+
+
 class OccurrenceViewSet(DefaultViewSet, ProjectMixin):
     """
     API endpoint that allows occurrences to be viewed or edited.
@@ -1041,6 +1046,7 @@ class OccurrenceViewSet(DefaultViewSet, ProjectMixin):
         OccurrenceVerified,
         OccurrenceVerifiedByMeFilter,
         OccurrenceTaxaListFilter,
+        OccurrenceDeterminationScoreFilter,
     ]
     filterset_fields = [
         "event",
@@ -1060,7 +1066,6 @@ class OccurrenceViewSet(DefaultViewSet, ProjectMixin):
         "determination_score",
         "event",
         "detections_count",
-        "created_at",
     ]
 
     def get_serializer_class(self):
@@ -1085,14 +1090,7 @@ def get_queryset(self) -> QuerySet["Occurrence"]:
         qs = qs.with_detections_count().with_timestamps()  # type: ignore
         qs = qs.with_identifications()  # type: ignore
 
-        if self.action == "list":
-            qs = (
-                qs.all()
-                .filter(determination_score__gte=get_active_classification_threshold(self.request))
-                .order_by("-determination_score")
-            )
-
-        else:
+        if self.action != "list":
             qs = qs.prefetch_related(
                 Prefetch(
                     "detections", queryset=Detection.objects.order_by("-timestamp").select_related("source_image")
@@ -1101,7 +1099,30 @@ def get_queryset(self) -> QuerySet["Occurrence"]:
 
         return qs
 
-    @extend_schema(parameters=[project_id_doc_param])
+    @extend_schema(
+        parameters=[
+            project_id_doc_param,
+            OpenApiParameter(
+                name="classification_threshold",
+                description="Filter occurrences by minimum determination score.",
+                required=False,
+                type=OpenApiTypes.FLOAT,
+            ),
+            OpenApiParameter(
+                name="taxon",
+                description="Filter occurrences by determination taxon ID. Shows occurrences determined as this taxon "
+                "or any of its child taxa.",
+                required=False,
+                type=OpenApiTypes.INT,
+            ),
+            OpenApiParameter(
+                name="collection_id",
+                description="Filter occurrences by the collection their detections' source images belong to.",
+                required=False,
+                type=OpenApiTypes.INT,
+            ),
+        ]
+    )
     def list(self, request, *args, **kwargs):
         return super().list(request, *args, **kwargs)
 
@@ -1133,6 +1154,9 @@ def filter_queryset(self, request, queryset, view):
         return queryset
 
 
+TaxonBestScoreFilter = ThresholdFilter.create("best_determination_score")
+
+
 class TaxonViewSet(DefaultViewSet, ProjectMixin):
     """
     API endpoint that allows taxa to be viewed or edited.
@@ -1144,6 +1168,7 @@ class TaxonViewSet(DefaultViewSet, ProjectMixin):
         CustomTaxonFilter,
         TaxonCollectionFilter,
         TaxonTaxaListFilter,
+        TaxonBestScoreFilter,
     ]
     filterset_fields = [
         "name",

ui/package.json

@@ -29,7 +29,7 @@
     "leaflet": "^1.9.3",
     "lodash": "^4.17.21",
     "lucide-react": "^0.454.0",
-    "nova-ui-kit": "^1.1.30",
+    "nova-ui-kit": "^1.1.31",
     "plotly.js": "^2.25.2",
     "react": "^18.2.0",
     "react-dom": "^18.2.0",

ui/src/app.module.scss

@@ -28,14 +28,20 @@
   position: relative;
 }
 
-@media only screen and (max-width: $medium-screen-breakpoint) {
+@media (max-width: $medium-screen-breakpoint) {
   .main {
     padding: 24px 24px 96px;
   }
 }
 
-@media only screen and (max-width: $small-screen-breakpoint) {
+@media (max-width: $small-screen-breakpoint) {
   .main {
     padding: 16px 16px 80px;
   }
 }
+
+@media print {
+  .wrapper {
+    height: auto;
+  }
+}

ui/src/app.tsx

@@ -74,7 +74,7 @@ export const App = () => (
       />
     </Helmet>
     <div id={APP_CONTAINER_ID} className={styles.wrapper}>
-      <div id={INTRO_CONTAINER_ID}>
+      <div id={INTRO_CONTAINER_ID} className="no-print">
         <Header />
       </div>
       <Routes>

ui/src/components/blueprint-collection/blueprint-collection.module.scss

@@ -82,16 +82,23 @@
   }
 }
 
-@media only screen and (max-width: $small-screen-breakpoint) {
+@media (max-width: $small-screen-breakpoint) {
   .licenseInfoContent {
     text-align: left;
   }
 
   .blueprintContent {
-    flex-direction: row;
-
     &.empty {
       display: none;
     }
   }
 }
+
+@media print {
+  .blueprintContent {
+    display: grid;
+    align-items: start;
+    grid-template-columns: 1fr 1fr;
+    gap: 24px;
+  }
+}

ui/src/components/blueprint-collection/blueprint-collection.tsx

@@ -3,7 +3,7 @@ import { LicenseInfo } from 'components/license-info/license-info'
 import { Icon, IconType } from 'design-system/components/icon/icon'
 import { EyeIcon } from 'lucide-react'
 import { buttonVariants, Tooltip } from 'nova-ui-kit'
-import { useState } from 'react'
+import { ReactNode, useState } from 'react'
 import { Link } from 'react-router-dom'
 import styles from './blueprint-collection.module.scss'
 
@@ -16,26 +16,35 @@ export interface BlueprintItem {
   to?: string
 }
 
-export const BlueprintCollection = ({ items }: { items: BlueprintItem[] }) => (
-  <div
-    className={classNames(styles.blueprint, {
-      [styles.empty]: items.length === 0,
-    })}
-  >
-    {items.length > 0 && (
+export const BlueprintCollection = ({
+  children,
+  showLicenseInfo,
+}: {
+  children: ReactNode
+  showLicenseInfo?: boolean
+}) => (
+  <div className={classNames(styles.blueprint)}>
+    {showLicenseInfo ? (
       <div className={styles.licenseInfoContent}>
         <LicenseInfo />
       </div>
-    )}
-    <div className={styles.blueprintContent}>
-      {items.map((item) => (
-        <BlueprintItem key={item.id} item={item} />
-      ))}
-    </div>
+    ) : null}
+    <div className={styles.blueprintContent}>{children}</div>
   </div>
 )
 
-const BlueprintItem = ({ item }: { item: BlueprintItem }) => {
+export const BlueprintItem = ({
+  item,
+}: {
+  item: {
+    id: string
+    image: { src: string; width: number; height: number }
+    label: string
+    timeLabel: string
+    countLabel: string
+    to?: string
+  }
+}) => {
   const [size, setSize] = useState({
     width: item.image.width,
     height: item.image.height,

ui/src/components/determination-score.tsx

@@ -0,0 +1,28 @@
+import { BasicTooltip } from 'design-system/components/tooltip/basic-tooltip'
+import { IdentificationScore } from 'nova-ui-kit'
+import { STRING, translate } from 'utils/language'
+
+export const DeterminationScore = ({
+  confirmed,
+  score,
+  scoreLabel,
+  tooltip,
+}: {
+  confirmed?: boolean
+  score?: number
+  scoreLabel?: string
+  tooltip?: string
+}) => {
+  if (score === undefined || scoreLabel === undefined) {
+    return <span>{translate(STRING.VALUE_NOT_AVAILABLE)}</span>
+  }
+
+  return (
+    <BasicTooltip content={tooltip}>
+      <div className="flex items-center gap-3">
+        <IdentificationScore confirmed={confirmed} confidenceScore={score} />
+        <span>{scoreLabel}</span>
+      </div>
+    </BasicTooltip>
+  )
+}

ui/src/components/filtering/filter-control.tsx

@@ -2,6 +2,7 @@ import { X } from 'lucide-react'
 import { Button } from 'nova-ui-kit'
 import { useFilters } from 'utils/useFilters'
 import { AlgorithmFilter, NotAlgorithmFilter } from './filters/algorithm-filter'
+import { BooleanFilter } from './filters/boolean-filter'
 import { CollectionFilter } from './filters/collection-filter'
 import { DateFilter } from './filters/date-filter'
 import { ImageFilter } from './filters/image-filter'
@@ -21,21 +22,23 @@ const ComponentMap: {
   [key: string]: (props: FilterProps) => JSX.Element
 } = {
   algorithm: AlgorithmFilter,
+  best_determination_score: ScoreFilter,
   classification_threshold: ScoreFilter,
   collection: CollectionFilter,
   date_end: DateFilter,
   date_start: DateFilter,
   deployment: StationFilter,
   detections__source_image: ImageFilter,
   event: SessionFilter,
+  include_unobserved: BooleanFilter,
   job_type_key: TypeFilter,
   not_algorithm: NotAlgorithmFilter,
   pipeline: PipelineFilter,
   source_image_collection: CollectionFilter,
   source_image_single: ImageFilter,
   status: StatusFilter,
-  taxon: TaxonFilter,
   taxa_list_id: TaxaListFilter,
+  taxon: TaxonFilter,
   verified_by_me: VerifiedByFilter,
   verified: VerificationStatusFilter,
 }

ui/src/components/filtering/filter-section.tsx

@@ -14,7 +14,7 @@ export const FilterSection = ({
   defaultOpen,
   title = 'Filters',
 }: FilterSectionProps) => (
-  <Box className="w-full h-min shrink-0 p-2 rounded-lg md:w-72 md:p-4 md:rounded-xl">
+  <Box className="w-full h-min shrink-0 p-2 rounded-lg md:w-72 md:p-4 md:rounded-xl no-print">
     <Collapsible.Root
       className="space-y-4"
       defaultOpen={window.innerWidth >= BREAKPOINTS.MD ? defaultOpen : false}