Add endpoint to delete variant type comment

gene2phenotype_project/gene2phenotype_app/tests/delete_data/test_delete_lgd_variant_type_comment.py

@@ -0,0 +1,124 @@
+from django.conf import settings
+from django.test import TestCase
+from django.urls import reverse
+from rest_framework_simplejwt.tokens import RefreshToken
+
+from gene2phenotype_app.models import (
+    LGDVariantTypeComment,
+    LocusGenotypeDisease,
+    User,
+)
+
+
+class LGDEditVariantTypeCommentEndpoint(TestCase):
+    """
+    Test endpoint to delete variant type comments from a record (LGD)
+    """
+
+    fixtures = [
+        "gene2phenotype_app/fixtures/attribs.json",
+        "gene2phenotype_app/fixtures/cv_molecular_mechanism.json",
+        "gene2phenotype_app/fixtures/disease.json",
+        "gene2phenotype_app/fixtures/g2p_stable_id.json",
+        "gene2phenotype_app/fixtures/lgd_panel.json",
+        "gene2phenotype_app/fixtures/locus_genotype_disease.json",
+        "gene2phenotype_app/fixtures/locus.json",
+        "gene2phenotype_app/fixtures/publication.json",
+        "gene2phenotype_app/fixtures/sequence.json",
+        "gene2phenotype_app/fixtures/user_panels.json",
+        "gene2phenotype_app/fixtures/ontology_term.json",
+        "gene2phenotype_app/fixtures/source.json",
+        "gene2phenotype_app/fixtures/lgd_publication.json",
+        "gene2phenotype_app/fixtures/lgd_variant_type.json",
+        "gene2phenotype_app/fixtures/lgd_variant_type_publication.json",
+        "gene2phenotype_app/fixtures/lgd_variant_type_comment.json",
+    ]
+
+    def setUp(self):
+        self.url_delete = reverse(
+            "lgd_variant_type_comment", kwargs={"stable_id": "G2P00002"}
+        )
+        self.comment_to_delete = {"comment_id": 1}
+
+    def _authenticate(self, email):
+        user = User.objects.get(email=email)
+        refresh = RefreshToken.for_user(user)
+        access_token = str(refresh.access_token)
+        self.client.cookies[settings.SIMPLE_JWT["AUTH_COOKIE"]] = access_token
+
+    def test_invalid_delete(self):
+        """
+        Cannot delete a variant type comment that does not exist.
+        """
+        self._authenticate("john@test.ac.uk")
+
+        response = self.client.patch(
+            self.url_delete, {"comment_id": 1000}, content_type="application/json"
+        )
+        self.assertEqual(response.status_code, 404)
+        self.assertEqual(
+            response.json()["error"],
+            "Cannot find variant type comment for record 'G2P00002'",
+        )
+
+        response_2 = self.client.patch(
+            self.url_delete, {}, content_type="application/json"
+        )
+        self.assertEqual(response_2.status_code, 400)
+
+    def test_delete_non_superuser(self):
+        """
+        Only super users can delete variant type comments.
+        """
+        self._authenticate("mary@test.ac.uk")
+
+        response = self.client.patch(
+            self.url_delete, self.comment_to_delete, content_type="application/json"
+        )
+        self.assertEqual(response.status_code, 403)
+        self.assertEqual(
+            response.json()["error"],
+            "You do not have permission to perform this action.",
+        )
+
+    def test_delete_no_permission(self):
+        """
+        Super users still need panel permission to edit the record.
+        """
+        self._authenticate("sofia@test.ac.uk")
+
+        response = self.client.patch(
+            self.url_delete, self.comment_to_delete, content_type="application/json"
+        )
+        self.assertEqual(response.status_code, 403)
+        self.assertEqual(
+            response.json()["error"], "No permission to update record 'G2P00002'"
+        )
+
+    def test_lgd_variant_type_comment_delete(self):
+        """
+        Test successfully deleting the variant type comment from the record (LGD)
+        """
+        self._authenticate("john@test.ac.uk")
+
+        lgd_variant_type_comments = LGDVariantTypeComment.objects.filter(
+            lgd_variant_type__lgd__stable_id__stable_id="G2P00002", is_deleted=0
+        )
+        self.assertEqual(len(lgd_variant_type_comments), 1)
+
+        response = self.client.patch(
+            self.url_delete, self.comment_to_delete, content_type="application/json"
+        )
+        self.assertEqual(response.status_code, 200)
+
+        lgd_deleted_variant_type_comments = LGDVariantTypeComment.objects.filter(
+            lgd_variant_type__lgd__stable_id__stable_id="G2P00002", is_deleted=1
+        )
+        self.assertEqual(len(lgd_deleted_variant_type_comments), 1)
+
+        history_records = LGDVariantTypeComment.history.all()
+        self.assertEqual(len(history_records), 1)
+        self.assertEqual(history_records[0].is_deleted, 1)
+
+        history_records_lgd = LocusGenotypeDisease.history.all()
+        self.assertEqual(len(history_records_lgd), 0)

gene2phenotype_project/gene2phenotype_app/urls.py

@@ -153,6 +153,13 @@ def perform_create(self, serializer):
         views.LGDEditVariantTypes.as_view(),
         name="lgd_variant_type",
     ),
+    # Delete variant type comment from LGD record.
+    # Action: PATCH
+    path(
+        "lgd/<str:stable_id>/variant_type/comment/",
+        views.LGDEditVariantTypeComment.as_view(),
+        name="lgd_variant_type_comment",
+    ),
     # Add or delete variant description(s) from LGD record.
     # Actions: PATCH (to delete one variant description), POST (to add multiple variant descriptions)
     path(

gene2phenotype_project/gene2phenotype_app/views/__init__.py

@@ -67,6 +67,7 @@
     LocusGenotypeDiseaseDetail,
     LGDEditCCM,
     LGDEditComment,
+    LGDEditVariantTypeComment,
     LGDEditVariantConsequences,
     LGDEditVariantTypes,
     LGDEditVariantTypeDescriptions,

gene2phenotype_project/gene2phenotype_app/views/locus_genotype_disease.py

@@ -1678,6 +1678,74 @@ def patch(self, request, stable_id):
             )
 
 
+@extend_schema(exclude=True)
+class LGDEditVariantTypeComment(CustomPermissionAPIView):
+    """
+    Delete a variant type comment from a G2P record (LGD).
+    """
+
+    http_method_names = ["patch", "options"]
+
+    method_permissions = {
+        "patch": [permissions.IsAuthenticated, IsSuperUser],
+    }
+
+    @transaction.atomic
+    def patch(self, request, stable_id):
+        """
+        Soft-delete a variant type comment by comment_id.
+        """
+        comment_id = request.data.get("comment_id", None)
+        user = request.user
+
+        if not comment_id:
+            return Response(
+                {"error": "Missing input key 'comment_id'"},
+                status=status.HTTP_400_BAD_REQUEST,
+            )
+
+        lgd_obj = get_object_or_404(
+            LocusGenotypeDisease, stable_id__stable_id=stable_id, is_deleted=0
+        )
+
+        # Check if user has permission to update panel
+        user_obj = get_object_or_404(User, email=user, is_active=1)
+        serializer_user = UserSerializer(user_obj, context={"user": user})
+        user_panel_list = [panel for panel in serializer_user.panels_names(user_obj)]
+        has_common = LocusGenotypeDiseaseSerializer(
+            lgd_obj, context={"user": user}
+        ).check_user_permission(lgd_obj, user_panel_list)
+        if has_common is False:
+            return Response(
+                {"error": f"No permission to update record '{stable_id}'"},
+                status=status.HTTP_403_FORBIDDEN,
+            )
+
+        try:
+            variant_type_comment = LGDVariantTypeComment.objects.get(
+                lgd_variant_type__lgd=lgd_obj, id=comment_id, is_deleted=0
+            )
+        except LGDVariantTypeComment.DoesNotExist:
+            return Response(
+                {
+                    "error": f"Cannot find variant type comment for record '{stable_id}'"
+                },
+                status=status.HTTP_404_NOT_FOUND,
+            )
+
+        variant_type_comment.is_deleted = 1
+        variant_type_comment.save()
+        lgd_obj.date_review = get_date_now()
+        lgd_obj.save_without_historical_record()
+
+        return Response(
+            {
+                "message": f"Variant type comment successfully deleted for record '{stable_id}'"
+            },
+            status=status.HTTP_200_OK,
+        )
+
+
 @extend_schema(exclude=True)
 class LGDEditReview(APIView):
     http_method_names = ["post", "options"]