Change navbar search to search both genes and ontology terms. Will

redirect results to page depending on choice. Closes #49
Planteome · Nov 10, 2023 · ae4f9e3 · ae4f9e3
1 parent 54de9d0
commit ae4f9e3
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Showing 4 changed files with 83 additions and 16 deletions.
diff --git a/api/serializers.py b/api/serializers.py
@@ -8,6 +8,10 @@
 
 
 class OntologyTermDocumentSerializer(DocumentSerializer):
+    ESscore = serializers.SerializerMethodField()
+
+    def get_ESscore(self, obj):
+        return obj.meta.score
     class Meta:
         document = annotations_documents.OntologyTermDocument
         fields = (
@@ -22,6 +26,10 @@ class Meta:
 
 
 class GeneDocumentSerializer(DocumentSerializer):
+    ESscore = serializers.SerializerMethodField()
+
+    def get_ESscore(self, obj):
+        return obj.meta.score
     class Meta:
         document = genes_documents.GeneDocument
         fields = (
@@ -42,8 +50,8 @@ class Meta:
             'dbname',
             'fullname',
         )
-        
-    
+
+
 class TaxonSerializer(serializers.ModelSerializer):
     class Meta:
         model = Taxon

diff --git a/api/urls.py b/api/urls.py
@@ -10,5 +10,6 @@
     path('autocomplete_genes/', views.GeneAPIView.as_view(), name='autocomplete_genes'),
     path('autocomplete_dbxrefs/', views.DBXrefAPIView.as_view(), name='autocomplete_dbxrefs'),
     path('autocomplete_taxon/', views.TaxonAPIView.as_view(), name='autcomplete_taxon'),
+    path('autocomplete_genes_and_onto_terms/', views.GenesAndTermsAPIView.as_view(), name='autocomplete_combined'),
 
 ] + static(settings.STATIC_URL, document_root=settings.STATIC_ROOT)
diff --git a/api/views.py b/api/views.py
@@ -32,6 +32,8 @@ def get(self, request, *args, **kwargs):
                                                           fields=["onto_term^10", "term_name^5", "term_definition^3", "term_synonyms"])
             #Convert to JSON
             serializers = OntologyTermDocumentSerializer(terms, many=True)
+            for element in serializers.data:
+                del element['ESscore']
             return Response(serializers.data)
         else:
             return Response(None)
@@ -55,11 +57,48 @@ def get(self, request, *args, **kwargs):
                                                                   "summary", "description", "synonyms"])
             #Convert to JSON
             serializers = GeneDocumentSerializer(terms, many=True)
+            for element in serializers.data:
+                del element['ESscore']
+
             return Response(serializers.data)
         else:
             return Response(None)
 
 
+class GenesAndTermsAPIView(APIView):
+    renderer_classes = [JSONRenderer]
+
+    def get(self, request, *args, **kwargs):
+        max_items = 5
+        q = request.GET.get('q')
+
+        if q:
+            if ':' in q:
+                q = q.replace(':', '\":\"')
+            search_term = "*" + q + "*"
+            gene_terms = ESGeneDocument.search().extra(size=max_items).query("multi_match", query=search_term,
+                                                          fields=["gene_id^10", "name^5", "symbol^3",
+                                                                  "summary", "description", "synonyms"])
+            onto_terms = ESOntologyTermDocument.search().extra(size=max_items).query("multi_match", query=search_term,
+                                                          fields=["onto_term^10", "term_name^5", "term_definition^3", "term_synonyms"])
+            genes_serializer = GeneDocumentSerializer(gene_terms, many=True)
+            onto_serializer = OntologyTermDocumentSerializer(onto_terms, many=True)
+
+            combined_data = genes_serializer.data + onto_serializer.data
+            def ESscore(e):
+                return e['ESscore']
+            combined_data.sort(reverse=True, key=ESscore)
+
+            # Now that they are sorted, remove the ESscore fields
+            for element in combined_data:
+                del element['ESscore']
+
+            return Response(combined_data)
+        else:
+            return Response(None)
+
+
+
 #DBXrefs are few enough in number no need to index in elasticsearch, but an autocomplete endpoint might still be nice
 class DBXrefAPIView(APIView):
     renderer_classes = [JSONRenderer]
@@ -77,8 +116,8 @@ def get(self, request, *args, **kwargs):
             return Response(serializers.data)
         else:
             return Response(None)
-        
-        
+
+
 class TaxonAPIView(APIView):
     renderer_classes = [JSONRenderer]
 

diff --git a/templates/navbar.html b/templates/navbar.html
@@ -5,24 +5,39 @@
         $("#id_genes_search").autocomplete({
             source: function (request, response) {
                 $.ajax({
-                    url: "{% url 'api:autocomplete_genes' %}",
+                    url: "{% url 'api:autocomplete_combined' %}",
                     dataType: "json",
                     data: {
                         q: request.term
                     },
                     success: function(data) {
                         response($.map(data, function (item) {
-                            var label_text = item.gene_id;
-                            if (item.symbol){
-                                label_text = item.symbol + " - " + label_text;
-                            }
-                            if (item.synonyms){
-                                label_text = label_text + " - " + item.synonyms;
+                            if (item.gene_id) {
+                                var label_text = item.gene_id;
+                                if (item.symbol) {
+                                    label_text = item.symbol + " - " + label_text;
+                                }
+                                if (item.synonyms) {
+                                    label_text = label_text + " - " + item.synonyms;
+                                }
+                                return {
+                                    label: label_text,
+                                    value: item.gene_id,
+                                    type: 'gene'
+                                };
+                            }else{
+                                var label_text = item.onto_term;
+                                if (item.term_name) {
+                                    label_text = label_text + " - " + item.term_name;
+                                }
+                                return {
+                                    label: label_text,
+                                    value: item.onto_term,
+                                    type: 'onto_term',
+                                    id: item.id
+
+                                }
                             }
-                            return {
-                                label: label_text,
-                                value: item.gene_id,
-                            };
                         }));
                     }
                 })
@@ -37,6 +52,10 @@
             select: function(event, ui) {
                 event.preventDefault();
                 $(this).val(ui.item.value);
+                if (ui.item.type == 'onto_term') {
+                    // Change the form action in this case
+                    $('form').attr('action', "/annotations/onto_term/" + ui.item.id);
+                }
                 $(this).closest('form').submit();
             },
             focus: function (event, ui) {
@@ -68,7 +87,7 @@
             </ul>
             <form class="form-inline my-2 my-lg-0" method="GET" action="{% url 'genes:search' %}">
                 <div>
-                    <input class="form-control mr-sm-2" placeholder="Search for genes: CONSTANS, AT5G15850" type="search" name="search" size="40" id="id_genes_search">
+                    <input class="form-control mr-sm-2" placeholder="Search: CONSTANS, AT5G15850, PO:0009032 (petal)" type="search" name="search" size="40" id="id_genes_search">
                     <button class="btn btn-primary" type="submit"><i class="fa fa-search"></i> </button>
                 </div>
             </form>