Merge pull request #54 from dglemos/update/search_output

Update search to return the confidence

.github/workflows/test.yml

@@ -48,12 +48,12 @@ jobs:
           echo "host=127.0.0.1" >> /home/runner/work/config.ini
           echo "port=3306" >> /home/runner/work/config.ini
         
-      - name: Run tests
+      - name: Run Tests
         run: |
+          export SECRET_KEY=$(openssl rand -base64 12)
           python manage.py makemigrations
           python manage.py migrate
           python manage.py test gene2phenotype_app.tests
         env:
-          SECRET_KEY: ${{ secrets.SECRET_KEY }}
           PROJECT_CONFIG_PATH: /home/runner/work/config.ini
         working-directory: gene2phenotype_project

gene2phenotype_project/gene2phenotype_app/serializers/curation.py

@@ -237,12 +237,13 @@ def check_entry(self, input_json_data):
 
     def get_entry_info_from_json_data(self, json_data):
         """
-            Extracts specific information from a given JSON data structure related to genotype, disease, and panel.
+            Extracts specific information from a given JSON data structure.
 
             This method parses the provided `json_data` dictionary to extract the following fields:
             - "genotype": Retrieved from the "allelic_requirement" key.
             - "disease": Retrieved from the nested "disease_name" key inside the "disease" dictionary.
             - "panel": Retrieved from the "panels" key.
+            - "confidence": Retrieved from the key "level" inside the "confidence" dictionary.
 
             If any of the keys are missing, the method returns `None` for the corresponding fields.
 
@@ -251,13 +252,16 @@ def get_entry_info_from_json_data(self, json_data):
 
             Returns:
                 dict: A dictionary containing the extracted fields with the following keys:
-                    - "genotype" (str or None): The value of the "allelic_requirement" field, or `None` if not present.
-                    - "disease" (str or None): The value of the "disease_name" field inside the "disease" dictionary, or `None` if not present.       
+                    - "genotype" (str): The allelic requirement (genotype) value, or empty string if not present.
+                    - "disease" (str): The disease name, or empty string if not present.
+                    - "panel" (list): The list of panels, or empty list if not present.
+                    - "confidence" (str): The confidence level, or empty string if not present.
         """
         return {
             "genotype": json_data.get("allelic_requirement"),
             "disease": json_data.get("disease", {}).get("disease_name"),
-            "panel": json_data.get("panels")
+            "panel": json_data.get("panels"),
+            "confidence": json_data.get("confidence", {}).get("level")
         }
 
     @transaction.atomic

gene2phenotype_project/gene2phenotype_app/views/search.py

@@ -39,7 +39,7 @@ def get_queryset(self):
             return LocusGenotypeDisease.objects.none()
 
         base_locus = Q(locus__name=search_query, is_deleted=0)
-        base_locus_2 = Q(locus__locusidentifier__isnull=False, locus__locusidentifier__identifier=search_query)
+        base_locus_2 = Q(locus__locusidentifier__isnull=False, locus__locusidentifier__identifier=search_query, is_deleted=0)
         base_locus_3 = Q(locus__locusattrib__isnull=False, locus__locusattrib__value=search_query, locus__locusattrib__is_deleted=0)
         base_disease = Q(disease__name__regex=fr"(?i)(?<![\w]){search_query}(?![\w])", is_deleted=0)
         base_disease_2 = Q(disease__diseasesynonym__synonym__regex=fr"(?i)(?<![\w]){search_query}(?![\w])", is_deleted=0)
@@ -141,26 +141,26 @@ def get_queryset(self):
 
             if not queryset.exists():
                 self.handle_no_permission('g2p_id', search_query)
-        
+
         elif search_type == 'draft' and user.is_authenticated:
             queryset = CurationData.objects.filter(
                 gene_symbol=search_query
                 ).order_by('stable_id__stable_id').distinct()
-            
+
             # to extend the queryset being annotated when it is draft,
             # want to return username so curator can see who is curating
             # adding the curator email, incase of the notification.
             queryset = queryset.annotate(first_name=F('user_id__first_name'), last_name=F('user_id__last_name'), user_email=F('user__email'))
 
             for obj in queryset:
                 obj.json_data_info = CurationDataSerializer.get_entry_info_from_json_data(self, obj.json_data)
-            
+
             if not queryset.exists():
                 self.handle_no_permission("draft", search_query)
-    
+
         else:
             self.handle_no_permission('Search type is not valid', None)
-        
+
         new_queryset = []
         if queryset.exists():
             if search_type != 'draft':
@@ -197,7 +197,8 @@ def list(self, request, *args, **kwargs):
                         'genotype':lgd.genotype.value,
                         'disease':lgd.disease.name,
                         'mechanism':lgd.molecular_mechanism.mechanism.value,
-                        'panel':lgd.panels
+                        'panel':lgd.panels,
+                        'confidence': lgd.confidence.value
                     }
                 list_output.append(data)
         else:
@@ -212,6 +213,7 @@ def list(self, request, *args, **kwargs):
                     "genotype": c_data.json_data_info["genotype"],
                     "disease_name" : c_data.json_data_info["disease"],
                     "panels" : c_data.json_data_info["panel"],
+                    "confidence" : c_data.json_data_info["confidence"],
                     "curator_email": c_data.user_email
                 }
                 list_output.append(data)