Fix slow annotation value query

docs/CHANGELOG.rst

@@ -10,6 +10,10 @@ This project adheres to `Semantic Versioning <http://semver.org/>`_.
 Unreleased
 ==========
 
+Fixed
+-----
+- Filter out deleted annotation values in viewset
+
 Changed
 -------
 - **BACKWARD INCOMPATIBLE:** Return all version of processess on process

resolwe/flow/models/annotations.py

@@ -454,11 +454,14 @@ class AnnotationValueManager(BaseManager["AnnotationValue", PermissionQuerySet])
     version_field = "created"
     QuerySet = PermissionQuerySet
 
-    def get_queryset(self) -> PermissionQuerySet:
-        """Return the latest version for every value."""
-        queryset = super().get_queryset()
-        # The old value is deleted so make sure it is never returned.
-        return queryset.filter(pk__in=queryset).exclude(_value__isnull=True)
+    def remove_delete_markers(self) -> PermissionQuerySet:
+        """Remote delete markers from the queryset.
+
+        Due to the nature of the queryset use the method only on small querysets.
+        """
+        return self.filter(pk__in=list(self.values_list("pk", flat=True))).exclude(
+            _value__isnull=True
+        )
 
 
 def _slug_for_annotation_value(instance: "AnnotationValue") -> str:

resolwe/flow/tests/test_annotations.py

@@ -692,13 +692,13 @@ def test_update_annotation_value(self):
             entity=created_value.entity, field=created_value.field
         )
         expected = AnnotationValueSerializer([updated_value], many=True).data
-        print("Got response", response.data)
         self.assertEqual(response.status_code, status.HTTP_200_OK)
         self.assertCountEqual(response.data, expected)
         with self.assertRaises(AnnotationValue.DoesNotExist):
-            AnnotationValue.objects.get(
-                entity=self.annotation_value1.entity, field=self.annotation_value1.field
-            )
+            AnnotationValue.objects.filter(
+                entity=self.annotation_value1.entity,
+                field=self.annotation_value1.field,
+            ).remove_delete_markers().get()
         created_value = AnnotationValue.objects.get(
             entity=created_value.entity, field=created_value.field
         )
@@ -1451,7 +1451,7 @@ def has_value(entity, field_id, value):
         force_authenticate(request, self.contributor)
         response = viewset(request, pk=self.entity1.pk)
         self.assertEqual(response.status_code, status.HTTP_200_OK)
-        self.assertEqual(self.entity1.annotations.count(), 1)
+        self.assertEqual(self.entity1.annotations.remove_delete_markers().count(), 1)
         has_value(self.entity1, self.annotation_field2.pk, 2)
 
         # Re-create deleted annotation value.

resolwe/flow/views/annotations.py

@@ -78,6 +78,15 @@ class AnnotationValueViewSet(
     permission_classes = (get_permissions_class(),)
     ordering_fields = ("created", "id")
 
+    def list(self, request, *args, **kwargs):
+        """List objects."""
+        queryset = self.filter_queryset(self.get_queryset())
+        # Remove the delete markers from the result.
+        serializer = self.get_serializer(
+            (entry for entry in queryset if entry.value is not None), many=True
+        )
+        return response.Response(serializer.data)
+
     def get_serializer(self, *args: Any, **kwargs: Any) -> BaseSerializer:
         """Get serializer instance depending on the request type."""
         kwargs_many = kwargs.get("many", False)

resolwe/permissions/models.py

@@ -133,6 +133,15 @@ def _check_permissions(self):
                 f"Permissions are not supported on model `{self.model._meta.label}`."
             )
 
+    def remove_delete_markers(self) -> "PermissionQuerySet":
+        """Remote delete markers from the queryset.
+
+        Due to the nature of the queryset use the method only on small querysets.
+        """
+        return self.filter(pk__in=list(self.values_list("pk", flat=True))).exclude(
+            _value__isnull=True
+        )
+
     def _filter_by_permission(
         self,
         user: Optional[User],

resolwe/process/tests/test_python_process.py

@@ -157,7 +157,7 @@ def test_annotation_v2(self):
         # Try bulk setting.
         data = self.run_process("test-python-process-annotate-entity-v2-bulk-set")
         self.assertIsNotNone(data.entity)
-        self.assertEqual(data.entity.annotations.count(), 1)
+        self.assertEqual(data.entity.annotations.remove_delete_markers().count(), 1)
         self.assertAnnotation(data.entity, "general.species", "Human Bulk Set")
 
         # Now try reading and updating existing annotations.