Adds autcomplete to ontology term lookups. Need to do the same for

taxons, dbxrefs. Use JS in annotation_add.html to see how to use the
autocomplete. Closes #64 and closes #41, partial work for #49

annotations/forms.py

@@ -1,7 +1,7 @@
 from django import forms
 
 # models import
-from .models import Annotation, AnnotationDocument, AnnotationApproval
+from .models import Annotation, AnnotationDocument, AnnotationApproval, AnnotationOntologyTerm
 from taxon.models import Taxon
 
 
@@ -14,6 +14,8 @@ class Meta:
 
 
 class AnnotationAddForm(forms.ModelForm):
+    ontology_term = forms.CharField(widget=forms.TextInput)
+    onto_pk = forms.IntegerField(widget=forms.HiddenInput)
     class Meta:
         model = AnnotationApproval
         exclude = ['datetime', 'action', 'status', 'requestor', 'internal_gene', 'source_annotation', 'assigned_by', 'date']
@@ -22,15 +24,35 @@ class Meta:
     taxon = forms.ModelChoiceField(
         queryset=Taxon.objects.order_by('name').filter(rank__contains='species'))
 
+    def clean(self):
+        cleaned_data = super().clean()
+        # Need to get the ontology term pk from the hidden field in the form filled in by the autocomplete
+        onto_pk = cleaned_data.get('onto_pk')
+        if onto_pk:
+            ontology_term = AnnotationOntologyTerm.objects.get(pk=onto_pk)
+            self.cleaned_data['ontology_term']=ontology_term
+        return  self.cleaned_data
+
 
 class AnnotationAddByGeneForm(forms.ModelForm):
+    ontology_term = forms.CharField(widget=forms.TextInput())
+    onto_pk = forms.IntegerField(widget=forms.HiddenInput)
     class Meta:
         model = AnnotationApproval
         exclude = ['datetime', 'action', 'status', 'requestor', 'internal_gene', 'source_annotation', 'assigned_by', 'date']
 
     taxon = forms.ModelChoiceField(
         queryset=Taxon.objects.order_by('name').filter(rank__contains='species'))
 
+    def clean(self):
+        cleaned_data = super().clean()
+        # Need to get the ontology term pk from the hidden field in the form filled in by the autocomplete
+        onto_pk = cleaned_data.get('onto_pk')
+        if onto_pk:
+            ontology_term = AnnotationOntologyTerm.objects.get(pk=onto_pk)
+            self.cleaned_data['ontology_term']=ontology_term
+        return  self.cleaned_data
+
     def __init__(self, *args, **kwargs):
         db_obj_id = kwargs.pop('db_obj_id', None)
         taxon = kwargs.pop('taxon', None)

annotations/serializers.py

@@ -0,0 +1,18 @@
+from django_elasticsearch_dsl_drf.serializers import DocumentSerializer
+
+from annotations import documents as annotations_documents
+
+
+class OntologyTermDocumentSerializer(DocumentSerializer):
+    class Meta:
+        document = annotations_documents.OntologyTermDocument
+        fields = (
+            'id',
+            'onto_term',
+            'term_name',
+            'term_definition',
+            'term_synonyms',
+            'term_is_obsolete',
+            'aspect',
+        )
+

annotations/templates/annotations/annotation_add.html

@@ -3,13 +3,63 @@
 
 {% block title %}Add individual Annotation{% endblock title %}
 
+{% block extra_js %}
+    <script>
+        $(function() {
+            $("#id_ontology_term").autocomplete({
+                source: function (request, response) {
+                    $.ajax({
+                        url: "{% url 'annotations:autocomplete' %}",
+                        dataType: "json",
+                        data: {
+                            q: request.term
+                        },
+                        success: function(data) {
+                            response($.map(data, function (item) {
+                              return {
+                                  label: item.term_name + " - " + item.onto_term,
+                                  value: item.id,
+                                  aspect: item.aspect,
+                              };
+                            }));
+                        }
+                    })
+                },
+                minLength: 3,
+                open: function() {
+                    $(this).removeClass("ui-corner-all").addClass("ui-corner-top");
+                },
+                close: function() {
+                    $(this).removeClass("ui-corner-top").addClass("ui-corner-all");
+                },
+                select: function(event, ui) {
+                    event.preventDefault();
+                    $(this).val(ui.item.label);
+                    $("#hidden-auto").val(ui.item.value);
+                    $("#id_aspect").val(ui.item.aspect);
+                    //document.querySelector("label[for='id_aspect']").textContent = "Aspect (already selected by ontology term)";
+                },
+                focus: function(event, ui) {
+                    event.preventDefault();
+                    $(this).val(ui.item.label);
+                    $("#hidden-auto").val(ui.item.value);
+                    $("#id_aspect").val(ui.item.aspect);
+                    //document.querySelector("label[for='id_aspect']").textContent = "Aspect (already selected by ontology term)";
+                }
+            })
+        });
+    </script>
+
+{% endblock %}
+
 {% block main %}
     {% if logged_in and superuser %}
         Use this page to add a single annotation
         <form method="post" enctype="multipart/form-data">
             {% csrf_token %}
             {{ form|crispy }}
             <input type="submit" value="Submit" class="btn btn-primary">
+            <input id="hidden-auto" name="onto_pk" type="hidden">
         </form>
     {% else %}
         <h2>You must be a logged in superuser to use this import page</h2>

annotations/urls.py

@@ -20,6 +20,7 @@
     path('by-reference/<slug:id>', views.SearchByReferenceView.as_view(), name='by-reference'),
     path('by-taxon/<int:id>', views.SearchByTaxonView.as_view(), name='by-taxon'),
     path('ontology_update/', views.OntologyUpdateView.as_view(), name='ontology-update'),
+    path('autocomplete/', views.OntologyTermAPIView.as_view(), name='autocomplete'),
     path('', views.BaseAnnotationView.as_view(), name='base_annotation')
 
 ] + static(settings.STATIC_URL, document_root=settings.STATIC_ROOT)

annotations/views.py

@@ -2,7 +2,7 @@
 from django.utils import timezone
 
 from django.db.models import Q
-from django.http import HttpResponseRedirect, HttpResponse
+from django.http import HttpResponseRedirect, HttpResponse, JsonResponse
 from django.shortcuts import render, get_object_or_404
 from django.urls import reverse_lazy
 from django.views.generic import TemplateView, FormView, ListView
@@ -24,8 +24,14 @@
 
 # ElasticSearch import
 from .documents import AnnotationDocument as ESAnnotationDocument
+from .documents import OntologyTermDocument as ESOntologyTermDocument
 from genes.documents import GeneDocument as ESGeneDocument
-from django_elasticsearch_dsl.search import Search
+
+from .serializers import OntologyTermDocumentSerializer
+
+from rest_framework.views import APIView
+from rest_framework.response import Response
+from rest_framework.renderers import JSONRenderer
 
 # choices import
 import curate.choices as choices
@@ -766,6 +772,28 @@ def get_queryset(self):
         return result
 
 
+class OntologyTermAPIView(APIView):
+    document_class = ESOntologyTermDocument
+    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 + "*"
+            # Use the boosts (^10) to order the results
+            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"])
+            #Convert to JSON
+            serializers = OntologyTermDocumentSerializer(terms, many=True)
+            return Response(serializers.data)
+        else:
+            return Response(None)
+
+
 def adjust_pagination(context):
     adjacent_pages = 2
     page_number = context['page_obj'].number

curate/settings.py

@@ -46,6 +46,7 @@
     'django.contrib.humanize',
 
     'django_elasticsearch_dsl',
+    'django_elasticsearch_dsl_drf',
 
     'mozilla_django_oidc',
 

docker-compose.yml

@@ -33,6 +33,9 @@ services:
       - "3307:3306"
     env_file:
       - .env
+    command: [
+      '--wait_timeout=28800',
+    ]
     volumes:
       - /docker/curate/mysqldata:/var/lib/mysql
       - /docker/curate/mysqld:/var/run/mysql

requirements.txt

@@ -23,6 +23,7 @@ django-timezone-field==4.2.1
 djangorestframework==3.12.4
 elasticsearch-dsl>=7.0.0,<8.0.0
 django-elasticsearch-dsl
+django-elasticsearch-dsl-drf
 idna==3.2
 importlib-metadata==4.8.1
 kombu==5.1.0