Standardise error messages

gene2phenotype_project/gene2phenotype_app/serializers/locus_genotype_disease.py

@@ -193,28 +193,35 @@ def get_variant_type(self, id):
         )
         data = {}
 
+        list_of_comments = {}
         for lgd_variant in queryset:
+            # Get the variant type term (ex:frameshift_variant)
+            accession = lgd_variant.variant_type_ot.accession
+
             # Prepare the list of comments
-            list_of_comments = []
             comments = lgd_variant.current_comments # Get the prefetched comments
             for comment_obj in comments:
+                comment_text = comment_obj.comment
                 # Format date
                 date = None
                 if comment_obj.date is not None:
                     date = comment_obj.date.strftime("%Y-%m-%d")
-                list_of_comments.append(
-                    {
-                        "text": comment_obj.comment,
-                        "date": date
-                    }
-                )
 
-            accession = lgd_variant.variant_type_ot.accession
+                if accession not in list_of_comments:
+                    list_of_comments[accession] = [{
+                        "text": comment_text,
+                        "date": date
+                    }]
+                elif not any(comment['text'] == comment_text for comment in list_of_comments[accession]):
+                    list_of_comments[accession].append({
+                        "text": comment_text,
+                        "date": date
+                    })
 
             if accession in data and lgd_variant.publication:
                 # Add pmid to list of publications
                 data[accession]["publications"].append(lgd_variant.publication.pmid)
-                data[accession]["comments"] = list_of_comments
+                data[accession]["comments"] = list_of_comments[accession]
                 # Check the variant inheritance - we group this data for each publication
                 if(lgd_variant.inherited is True):
                     data[accession]["inherited"] = lgd_variant.inherited
@@ -234,7 +241,7 @@ def get_variant_type(self, id):
                     "de_novo": lgd_variant.de_novo,
                     "unknown_inheritance": lgd_variant.unknown_inheritance,
                     "publications": publication_list,
-                    "comments": list_of_comments
+                    "comments": list_of_comments[accession]
                 }
 
         return data.values()
@@ -1160,7 +1167,7 @@ def create(self, validated_data):
                 lgd_variant_type_obj.save()
 
             # The LGDPhenotypeSummary is created - next step is to create the LGDVariantTypeComment
-            if(comment != ""):
+            if comment != "":
                 try:
                     lgd_comment_obj = LGDVariantTypeComment.objects.get(
                         comment = comment,
@@ -1251,7 +1258,7 @@ def create(self, validated_data):
                         lgd_variant_type_obj.save()
 
                     # The LGDPhenotypeSummary is created - next step is to create the LGDVariantTypeComment
-                    if(comment != ""):
+                    if comment != "":
                         try:
                             lgd_comment_obj = LGDVariantTypeComment.objects.get(
                                 comment = comment,
@@ -1283,7 +1290,7 @@ class Meta:
 class LGDVariantTypeListSerializer(serializers.Serializer):
     """
         Serializer to accept a list of variant types.
-        Called by: LGDAddVariantTypes()
+        Called by: LGDEditVariantTypes()
     """
     variant_types = LGDVariantTypeSerializer(many=True)
 

gene2phenotype_project/gene2phenotype_app/tests/views/test_disease.py

@@ -43,7 +43,7 @@ def test_not_found(self):
         response = self.client.get(self.url_disease)
 
         self.assertEqual(response.status_code, 404)
-        self.assertEqual(response.data["message"], "No matching Disease found for: CACNA1F-related Aland Island")
+        self.assertEqual(response.data["error"], "No matching Disease found for: CACNA1F-related Aland Island")
 
 class DiseaseSummaryTests(TestCase):
     """
@@ -98,4 +98,4 @@ def test_not_found(self):
         response = self.client.get(self.url_disease)
 
         self.assertEqual(response.status_code, 404)
-        self.assertEqual(response.data["message"], "No matching Disease found for: CACNA1F-related Aland Island")
+        self.assertEqual(response.data["error"], "No matching Disease found for: CACNA1F-related Aland Island")

gene2phenotype_project/gene2phenotype_app/tests/views/test_publication.py

@@ -48,4 +48,4 @@ def test_invalid(self):
         response = self.client.get(self.url_publication)
 
         self.assertEqual(response.status_code, 404)
-        self.assertEqual(response.data["detail"], "Invalid PMID(s): 0")
+        self.assertEqual(response.data["error"], "Invalid PMID(s): 0")

gene2phenotype_project/gene2phenotype_app/tests/views/test_search.py

@@ -134,4 +134,4 @@ def test_search_not_found(self):
         response = self.client.get(url_search_gene)
 
         self.assertEqual(response.status_code, 404)
-        self.assertEqual(response.data["message"], "No matching Gene found for: TUBB4A")
+        self.assertEqual(response.data["error"], "No matching Gene found for: TUBB4A")

gene2phenotype_project/gene2phenotype_app/views/attrib.py

@@ -111,7 +111,7 @@ def get_queryset(self):
             attrib_type_obj = AttribType.objects.get(code=code)
         except AttribType.DoesNotExist:
             return Response(
-                {"message": f"Attrib type {code} not found"},
+                {"error": f"Attrib type {code} not found"},
                 status=status.HTTP_404_NOT_FOUND
             )
 

gene2phenotype_project/gene2phenotype_app/views/base.py

@@ -25,7 +25,7 @@ def handle_no_permission(self, name_type, name):
 
     def handle_exception(self, exc):
         if isinstance(exc, Http404):
-            return Response({"message": str(exc)}, status=status.HTTP_404_NOT_FOUND)
+            return Response({"error": str(exc)}, status=status.HTTP_404_NOT_FOUND)
 
         return super().handle_exception(exc)
 

gene2phenotype_project/gene2phenotype_app/views/curation.py

@@ -40,29 +40,43 @@ def post(self, request):
             with open(json_file_path, 'r') as file:
                 schema = json.load(file)
         except FileNotFoundError:
-            return Response({"message": "Schema file not found"}, status=status.HTTP_404_NOT_FOUND)
+            return Response(
+                {"error": "Schema file not found"}, status=status.HTTP_404_NOT_FOUND
+            )
 
         # json format accepts null values but in python these values are represented as 'None'
         # dumps() converts 'None' to 'null' before json validation
         input_data = json.dumps(request.data)
         input_json_data = json.loads(input_data)
 
         if "json_data" not in input_json_data:
-            return Response({"message": "Invalid data format: 'json_data' is missing"}, status=status.HTTP_400_BAD_REQUEST)
+            return Response(
+                {"error": "Invalid data format: 'json_data' is missing"},
+                status=status.HTTP_400_BAD_REQUEST
+            )
 
         # Validate the JSON data against the schema
         try:
             validate(instance=input_json_data["json_data"], schema=schema)
         except jsonschema.exceptions.ValidationError as e:
-            return Response({"message": "JSON data does not follow the required format. Required format is" + str(e)}, status=status.HTTP_400_BAD_REQUEST)
+            return Response(
+                {"error": "JSON data does not follow the required format. Required format is" + str(e)},
+                status=status.HTTP_400_BAD_REQUEST
+            )
 
         serializer = self.serializer_class(data=request.data, context={'user': user})
 
         if serializer.is_valid():
             instance = serializer.save()
-            return Response({"message": f"Data saved successfully for session name '{instance.session_name}'", "result": f"{instance.stable_id.stable_id}"}, status=status.HTTP_200_OK)
+            return Response(
+                {
+                    "message": f"Data saved successfully for session name '{instance.session_name}'",
+                    "result": f"{instance.stable_id.stable_id}"
+                },
+                status=status.HTTP_200_OK
+            )
         else:
-            return Response({"errors": serializer.errors}, status=status.HTTP_400_BAD_REQUEST)
+            return Response({"error": serializer.errors}, status=status.HTTP_400_BAD_REQUEST)
 
 class ListCurationEntries(BaseView):
     """
@@ -203,7 +217,10 @@ def update(self, request, *args, **kwargs):
             with open(json_file_path, 'r') as file:
                 schema = json.load(file)
         except FileNotFoundError:
-            return Response({"message": "Schema file not found"}, status=status.HTTP_404_NOT_FOUND)
+            return Response(
+                {"error": "Schema file not found"},
+                status=status.HTTP_404_NOT_FOUND
+            )
 
         # json format accepts null values but in python these values are represented as 'None'
         # dumps() converts 'None' to 'null' before json validation
@@ -214,7 +231,10 @@ def update(self, request, *args, **kwargs):
         try:
             validate(instance=input_json_data["json_data"], schema=schema)
         except jsonschema.exceptions.ValidationError as e:
-            return Response({"message": "JSON data does not follow the required format. Required format is" + str(e)}, status=status.HTTP_400_BAD_REQUEST)
+            return Response(
+                {"error": "JSON data does not follow the required format. Required format is" + str(e)},
+                status=status.HTTP_400_BAD_REQUEST
+            )
 
         # Update data - it replaces the data
         serializer = CurationDataSerializer(
@@ -225,10 +245,16 @@ def update(self, request, *args, **kwargs):
 
         if serializer.is_valid():
             instance = serializer.save()
-            return Response({"message": f"Data updated successfully for session name '{instance.session_name}'"}, status=status.HTTP_200_OK)
+            return Response(
+                {"message": f"Data updated successfully for session name '{instance.session_name}'"},
+                status=status.HTTP_200_OK
+            )
 
         else:
-            return Response({"errors": serializer.errors}, status=status.HTTP_400_BAD_REQUEST)
+            return Response(
+                {"error": serializer.errors},
+                status=status.HTTP_400_BAD_REQUEST
+            )
 
 class PublishRecord(APIView):
     """
@@ -264,19 +290,22 @@ def post(self, request, stable_id):
                 # Delete entry from 'curation_data'
                 curation_obj.delete()
 
-                return Response({
-                    "message": f"Record '{lgd_obj.stable_id.stable_id}' published successfully"
-                    }, status=status.HTTP_201_CREATED)
+                return Response(
+                    {"message": f"Record '{lgd_obj.stable_id.stable_id}' published successfully"},
+                    status=status.HTTP_201_CREATED
+                )
 
             except LocusGenotypeDisease.DoesNotExist:
-                Response({
-                    "message": f"Failed to publish record ID '{stable_id}'"
-                    }, status=status.HTTP_400_BAD_REQUEST)
+                Response(
+                    {"error": f"Failed to publish record ID '{stable_id}'"},
+                    status=status.HTTP_400_BAD_REQUEST
+                )
 
         except CurationData.DoesNotExist:
-            return Response({
-                "message": f"Curation data not found for ID '{stable_id}'"
-                }, status=status.HTTP_404_NOT_FOUND)
+            return Response(
+                {"error": f"Curation data not found for ID '{stable_id}'"},
+                status=status.HTTP_404_NOT_FOUND
+            )
 
 class DeleteCurationData(generics.DestroyAPIView):
     """
@@ -331,12 +360,21 @@ def destroy(self, request, *args, **kwargs):
         stable_id = self.kwargs['stable_id']
 
         if not curation_obj or len(curation_obj) == 0:
-            return Response({"error": f"Cannot find ID {stable_id}"}, status=status.HTTP_404_NOT_FOUND)
+            return Response(
+                {"error": f"Cannot find ID {stable_id}"},
+                status=status.HTTP_404_NOT_FOUND
+            )
 
         try:
             # delete record + G2P ID
             self.perform_destroy(curation_obj, stable_id)
         except:
-            return Response({"message": f"Cannot delete data for ID {stable_id}"}, status=status.HTTP_404_NOT_FOUND)
-
-        return Response({"message": f"Data deleted successfully for ID {stable_id}"}, status=status.HTTP_204_NO_CONTENT)
+            return Response(
+                {"error": f"Cannot delete data for ID {stable_id}"},
+                status=status.HTTP_404_NOT_FOUND
+            )
+
+        return Response(
+            {"message": f"Data deleted successfully for ID {stable_id}"},
+            status=status.HTTP_204_NO_CONTENT
+        )

gene2phenotype_project/gene2phenotype_app/views/disease.py

@@ -193,7 +193,10 @@ def post(self, request):
         diseases = request.data  # list of diseases {'id': ..., 'name': ...}
 
         if not isinstance(diseases, list):
-            return Response({"error": "Request should be a list"}, status=status.HTTP_400_BAD_REQUEST)
+            return Response(
+                {"error": "Request should be a list"},
+                status=status.HTTP_400_BAD_REQUEST
+            )
 
         updated_diseases = []
         errors = []
@@ -230,7 +233,7 @@ def post(self, request):
             response_data["updated"] = updated_diseases
 
         if errors:
-            response_data["errors"] = errors
+            response_data["error"] = errors
 
         return Response(response_data, status=status.HTTP_200_OK if updated_diseases else status.HTTP_400_BAD_REQUEST)
 
@@ -242,7 +245,10 @@ def post(self, request):
         data_to_update = request.data
 
         if not isinstance(data_to_update, list):
-            return Response({"error": "Request should be a list"}, status=status.HTTP_400_BAD_REQUEST)
+            return Response(
+                {"error": "Request should be a list"},
+                status=status.HTTP_400_BAD_REQUEST
+            )
 
         updated_records = []
         errors = []
@@ -279,6 +285,6 @@ def post(self, request):
             response_data["Updated records"] = updated_records
 
         if errors:
-            response_data["Errors"] = errors
+            response_data["error"] = errors
 
         return Response(response_data, status=status.HTTP_200_OK if updated_records else status.HTTP_400_BAD_REQUEST)