Merge pull request #330 from EBI-G2P/update_draft_check_v14

Validate curation draft before update

Author: dglemos

gene2phenotype_project/gene2phenotype_app/serializers/curation.py

@@ -45,17 +45,16 @@ class CurationDataSerializer(serializers.ModelSerializer):
 
     def validate_to_save(self, data):
         """
-        Validate the input data for curation.
+        Validate the input data to add or save a curation draft.
 
-        Validation extension step:
-            This step is called in AddCurationData of the views.py
-            The steps of the validation for the save is
-                - Locus is the minimum requirement needed to save a draft
-                - Draft does not already exist as a draft
-                - User has permissions to curate on the selected panel
+        Validation steps:
+            - Locus is the minimum requirement needed to save a draft
+            - Draft does not already exist as a draft
+            - User has permissions to curate on the selected panels
 
         Args:
-            data: The data to be validated.
+            data: The data to be validated. Input format:
+                {'json_data': {...}, 'status': 'manual'} OR {'json_data': {...}}
 
         Returns:
             The validated data.
@@ -290,6 +289,7 @@ def compare_curation_data(self, input_json_data, user_obj):
             # remove session_name field from input json and compare input json with existing curation json
             input_json_data["json_data"].pop("session_name", None)
             data_json.pop("session_name", None)
+
             result = DeepDiff(input_json_data["json_data"], data_json)
 
             if not result:

gene2phenotype_project/gene2phenotype_app/tests/curation/test_update_curation.py

@@ -24,7 +24,9 @@ def setUp(self):
         self.url_update_curation = reverse(
             "update_curation", kwargs={"stable_id": "G2P00004"}
         )
-
+        self.url_update_curation_2 = reverse(
+            "update_curation", kwargs={"stable_id": "G2P00010"}
+        )
         self.url_update_invalid_curation = reverse(
             "update_curation", kwargs={"stable_id": "G2P00123"}
         )
@@ -327,7 +329,6 @@ def test_update_curation_empty_locus(self):
         """
         self.login_user()
 
-        # Define the complex data structure
         curation_to_update = {
             "json_data": {
                 "allelic_requirement": "",
@@ -358,7 +359,45 @@ def test_update_curation_empty_locus(self):
         self.assertEqual(response.status_code, 400)
 
         response_data = response.json()
-        self.assertEqual(response_data["error"],"Invalid gene ''")
+        self.assertEqual(response_data["error"], "To save a draft, the minimum requirement is a locus entry. Please save this draft with locus information")
+
+    def test_update_curation_invalid_locus(self):
+        """
+        Test call to update curation endpoint with invalid locus field
+        """
+        self.login_user()
+
+        curation_to_update = {
+            "json_data": {
+                "allelic_requirement": "",
+                "confidence": "",
+                "cross_cutting_modifier": [],
+                "disease": {"cross_references": [], "disease_name": ""},
+                "locus": "BAAT-21",
+                "mechanism_evidence": [],
+                "mechanism_synopsis": [],
+                "molecular_mechanism": {"name": "", "support": ""},
+                "panels": [],
+                "phenotypes": [],
+                "private_comment": "",
+                "public_comment": "",
+                "publications": [],
+                "session_name": "test session",
+                "variant_consequences": [],
+                "variant_descriptions": [],
+                "variant_types": [],
+            }
+        }
+
+        response = self.client.put(
+            self.url_update_curation,
+            curation_to_update,
+            content_type="application/json",
+        )
+        self.assertEqual(response.status_code, 400)
+
+        response_data = response.json()
+        self.assertEqual(response_data["error"], "Invalid gene 'BAAT-21'")
 
     def test_update_invalid_curation(self):
         """
@@ -396,3 +435,49 @@ def test_update_invalid_curation(self):
             content_type="application/json",
         )
         self.assertEqual(response.status_code, 404)
+
+    def test_update_curation_duplicate(self):
+        """
+        Test to update curation that would create a duplicate entry
+        G2P ID G2P00010 has session name 'test session SRY', this test
+        tries to update the json content to be the same as session 'test session' (G2P00004)
+        """
+        self.login_user()
+
+        curation_to_update = {
+            "json_data": {
+                "allelic_requirement": "",
+                "confidence": "",
+                "cross_cutting_modifier": [],
+                "disease": {
+                    "cross_references": [],
+                    "disease_name": ""
+                    },
+                "locus": "CEP290",
+                "mechanism_evidence": [],
+                "mechanism_synopsis": [],
+                "molecular_mechanism": {
+                    "name": "",
+                    "support": ""
+                    },
+                "panels": [],
+                "phenotypes": [],
+                "private_comment": "",
+                "public_comment": "",
+                "publications": [],
+                "session_name": "test session SRY",
+                "variant_consequences": [],
+                "variant_descriptions": [],
+                "variant_types": []
+            }
+        }
+
+        response = self.client.put(
+            self.url_update_curation_2,
+            curation_to_update,
+            content_type="application/json",
+        )
+        self.assertEqual(response.status_code, 400)
+
+        response_data = response.json()
+        self.assertEqual(response_data["error"], "Data already under curation. Please check session 'test session'")

gene2phenotype_project/gene2phenotype_app/views/curation.py

@@ -287,6 +287,10 @@ def update(self, request, *args, **kwargs):
                 status=status.HTTP_400_BAD_REQUEST,
             )
 
+        # Check if input data (json) is already present for this user
+        # Do not use 'input_data' because it is a result of json.dumps()
+        self.serializer_class(context={"user": user}).validate_to_save(request.data)
+
         # Update data - it replaces the data
         serializer = CurationDataSerializer(
             curation_obj,