Feature/esckan-35 - Composer REST new generic endpoint - public - Kno…

…wledgeStatement (#260)

* #35 renaming of methods and functions

* #35 rename reference uri to population uri

* #35 use model property instead of repeat logic

backend/composer/admin.py

@@ -100,7 +100,7 @@ class SentenceAdmin(
 class AnatomicalEntityAdmin(admin.ModelAdmin):
     search_fields = ('simple_entity__name', 'region_layer__layer__name', 'region_layer__region__name')
     autocomplete_fields = ('simple_entity', 'region_layer')
-    list_display = ('simple_entity', 'region_layer', "synonyms")
+    list_display = ('simple_entity', 'region_layer', "synonyms", "ontology_uri")
     list_display_links = ('simple_entity', 'region_layer')
     inlines = (SynonymInline,)
 
@@ -114,6 +114,11 @@ def get_queryset(self, request: HttpRequest) -> QuerySet[Any]:
     def synonyms(self, obj):
         synonyms = obj.synonyms.all()
         return ', '.join([synonym.name for synonym in synonyms])
+
+    @admin.display(description="Ontology URI")
+    def ontology_uri(self, obj):
+        return obj.ontology_uri
+
 
 
 class AnatomicalEntityMetaAdmin(admin.ModelAdmin):

backend/composer/api/filtersets.py

@@ -13,6 +13,8 @@
     Via,
     Specie, Destination,
 )
+from django_filters import rest_framework
+from django_filters import CharFilter, BaseInFilter
 
 
 def field_has_content(queryset, name, value):
@@ -95,6 +97,66 @@ class Meta:
         fields = []
 
 
+class ListCharFilter(BaseInFilter, CharFilter):
+    pass
+
+
+class KnowledgeStatementFilterSet(rest_framework.FilterSet):
+    via_uris = ListCharFilter(method='filter_via_uris', label='Via URI')
+    destination_uris = ListCharFilter(method='filter_destination_uris', label='Destination URI')
+    origin_uris = ListCharFilter(method='filter_origin_uris', label='Origin URI')
+    population_uris = ListCharFilter(method='filter_population_uris', label='Reference URI')
+
+    class Meta:
+        model = ConnectivityStatement
+        fields = ['via_uris', 'destination_uris', 'origin_uris', 'population_uris']
+        distinct = True
+
+    @property
+    def qs(self):
+        return super().qs.distinct()
+
+    def filter_population_uris(self, queryset, name, value):
+        return queryset.filter(reference_uri__in=value)
+
+    def filter_via_uris(self, queryset, name, value):
+        via_uris = value
+        via_ids = Via.objects.none()
+        for uri in via_uris:
+            via_ids = via_ids.union(
+                Via.objects.filter(anatomical_entities__simple_entity__ontology_uri=uri).prefetch_related('anatomical_entities__simple_entity')
+                .union(Via.objects.filter(anatomical_entities__region_layer__layer__ontology_uri=uri).prefetch_related('anatomical_entities__region_layer__layer'))
+                .union(Via.objects.filter(anatomical_entities__region_layer__region__ontology_uri=uri).prefetch_related('anatomical_entities__region_layer__region'))
+                .values_list("id", flat=True)
+            )
+        return queryset.filter(via__in=via_ids)
+
+    def filter_destination_uris(self, queryset, name, value):
+        destination_uris = value
+        destination_ids = Destination.objects.none()
+        for uri in destination_uris:
+            destination_ids = destination_ids.union(
+                Destination.objects.filter(anatomical_entities__simple_entity__ontology_uri=uri).prefetch_related('anatomical_entities__simple_entity')
+                .union(Destination.objects.filter(anatomical_entities__region_layer__layer__ontology_uri=uri).prefetch_related('anatomical_entities__region_layer__layer'))
+                .union(Destination.objects.filter(anatomical_entities__region_layer__region__ontology_uri=uri).prefetch_related('anatomical_entities__region_layer__region'))
+                .values_list("id", flat=True)
+            )
+        return queryset.filter(destinations__in=destination_ids)
+
+    def filter_origin_uris(self, queryset, name, value):
+        origin_uris = value
+        origin_ids = AnatomicalEntity.objects.none()
+        for uri in origin_uris:
+            origin_ids = origin_ids.union(
+                AnatomicalEntity.objects.filter(simple_entity__ontology_uri=uri).prefetch_related('simple_entity')
+                .union(AnatomicalEntity.objects.filter(region_layer__layer__ontology_uri=uri).prefetch_related('region_layer__layer'))
+                .union(AnatomicalEntity.objects.filter(region_layer__region__ontology_uri=uri).prefetch_related('region_layer__region'))
+                .values_list("id", flat=True)
+            )
+        return queryset.filter(origins__in=origin_ids)
+
+
+
 class AnatomicalEntityFilter(django_filters.FilterSet):
     name = django_filters.CharFilter(method="filter_name")
     exclude_ids = NumberInFilter(field_name='id', exclude=True)

backend/composer/api/serializers.py

@@ -680,3 +680,18 @@ class Meta:
             "errors"
         )
 
+
+class KnowledgeStatementSerializer(ConnectivityStatementSerializer):
+    """Knowledge Statement"""
+    class Meta(ConnectivityStatementSerializer.Meta):
+        fields = (
+            "id",
+            "sentence_id",
+            "species",
+            "origins",
+            "vias",
+            "destinations",
+            "apinatomy_model",
+            "phenotype_id",
+            "phenotype",
+        )

backend/composer/api/urls.py

@@ -5,6 +5,7 @@
     AnatomicalEntityViewSet,
     PhenotypeViewSet,
     ConnectivityStatementViewSet,
+	KnowledgeStatementViewSet,
     jsonschemas,
     NoteViewSet,
     ProfileViewSet,
@@ -42,4 +43,5 @@
 urlpatterns = [
     path("", include(router.urls)),
     path("jsonschemas/", jsonschemas, name="jsonschemas"),
+	path("knowledge-statement/", KnowledgeStatementViewSet.as_view(), name="knowledge-statement"),
 ]

backend/composer/api/views.py

@@ -9,6 +9,8 @@
 from rest_framework.renderers import INDENT_SEPARATORS
 from rest_framework.response import Response
 from rest_framework.serializers import ValidationError
+from rest_framework import generics
+from django_filters.rest_framework import DjangoFilterBackend
 
 from composer.services.state_services import (
     ConnectivityStatementStateService,
@@ -17,6 +19,7 @@
 from .filtersets import (
     SentenceFilter,
     ConnectivityStatementFilter,
+    KnowledgeStatementFilterSet,
     AnatomicalEntityFilter,
     NoteFilter,
     ViaFilter,
@@ -26,6 +29,7 @@
     AnatomicalEntitySerializer,
     PhenotypeSerializer,
     ConnectivityStatementSerializer,
+    KnowledgeStatementSerializer,
     NoteSerializer,
     ProfileSerializer,
     SentenceSerializer,
@@ -345,6 +349,34 @@ def partial_update(self, request, *args, **kwargs):
         return super().partial_update(request, *args, **kwargs)
 
 
+@extend_schema(tags=["public"])
+class KnowledgeStatementViewSet(
+    generics.ListAPIView,
+):
+    """
+    KnowledgeStatement that only allows GET to get the list of ConnectivityStatements
+    """
+    model = ConnectivityStatement
+    queryset = ConnectivityStatement.objects.exported()
+    serializer_class = KnowledgeStatementSerializer
+    permission_classes = [
+        permissions.AllowAny,
+    ]
+    filter_backends = [DjangoFilterBackend]
+    filterset_class = KnowledgeStatementFilterSet
+
+    @property
+    def allowed_methods(self):
+        return ['GET']
+
+    def get_serializer_class(self):
+        return KnowledgeStatementSerializer
+
+
+    def list(self, request, *args, **kwargs):
+        return super().list(request, *args, **kwargs)
+
+
 class TagViewSet(viewsets.ReadOnlyModelViewSet):
     """
     Tag

backend/composer/models.py

@@ -97,6 +97,9 @@ def get_queryset(self):
 
     def excluding_draft(self):
         return self.get_queryset().exclude(state=CSState.DRAFT)
+
+    def exported(self):
+        return self.get_queryset().filter(state=CSState.EXPORTED)
 
 
 class SentenceStatementManager(models.Manager):