Finish link annotation to internal gene stub. Closes #81. May still want

to work on changes made by a superuser for that not showing up on the
changes page. Did add a note explaining it though.

annotations/templates/annotations/annotation_link_internal.html

@@ -5,7 +5,37 @@
 
 {% block main %}
     {% if logged_in %}
-        <h2>HI!</h2>
+        <h2>Use this page to link to a known gene in Planteome</h2>
+        <br>
+        <div style="text-align: center">
+            <form class="form-inline my-2 my-lg-0" style="display: inline-block" method="GET" action="{% url 'annotations:link_internal' pk=annotation.pk %}">
+                <div id="search_box">
+                    <input class="form-control mr-sm-2" placeholder="Search for genes: CONSTANS, AT5G15850" type="search" name="search" size="40">
+                    <button class="btn btn-primary" type="submit"><i class="fa fa-search"></i> </button>
+                </div>
+            </form>
+        </div>
+        {%  if search_genes %}
+            <br>
+            Please pick one of these genes to link:
+            <br>
+            <table class="table table-striped table-bordered table-hover">
+                <thead>
+                    <th>Gene Symbol</th>
+                    <th>Gene Name</th>
+                    <th>Gene ID</th>
+                    <th>Species</th>
+                </thead>
+            {% for gene in search_genes %}
+                <tr>
+                <td><a href="{% url 'annotations:link_with_gene' annot_pk=annotation.pk gene_pk=gene.meta.id %}">{{ gene.symbol }}</a></td>
+                <td>{{ gene.name }}</td>
+                <td>{{ gene.gene_id }}</td>
+                <td>{{ gene.species.name }}</td>
+                </tr>
+            {% endfor %}
+            </table>
+        {% endif %}
     {% else %}
         <h2>You must be a logged in user to use this page.</h2>
     {% endif %}

annotations/templates/annotations/changes.html

@@ -27,6 +27,8 @@ <h3>Summary of approved changes to source annotation <a href=" {% url 'annotatio
                 <td><a href="{% url 'accounts:info' delta.changed_by %}">{{ delta.changed_by }}</a></td>
                 <td>{{ delta.datetime }}</td>
             </tr>
+        {% empty %}
+            The changes may have been entered by a superuser internally and will not show up here
         {% endfor %}
         </tbody>
     {% endfor %}

annotations/urls.py

@@ -23,6 +23,7 @@
     path('add_ontology_term/', views.OntologyTermAddView.as_view(), name='add_onto_term'),
     path('onto_term/<int:pk>', views.OntologyTermView.as_view(), name='onto_term'),
     path('link_internal/<int:pk>', views.LinkInternalView.as_view(), name='link_internal'),
+    path('link_with_gene/<int:annot_pk>/<int:gene_pk>', views.LinkInternalGeneView.as_view(), name='link_with_gene'),
     path('', views.BaseAnnotationView.as_view(), name='base_annotation')
 
 ] + static(settings.STATIC_URL, document_root=settings.STATIC_ROOT)

annotations/views.py

@@ -1,5 +1,6 @@
 import json
 
+from django.contrib.auth.mixins import LoginRequiredMixin
 from django.forms import model_to_dict
 from django.utils import timezone
 
@@ -282,8 +283,69 @@ def get_context_data(self, **kwargs):
         annotation = Annotation.objects.get(pk=annotation_id)
         context['annotation'] = annotation
 
+        if self.request.GET.get('search'):
+            s = self.get_queryset()
+            hit_list = []
+            for hit in s:
+                hit_list.append(hit)
+            context['search_genes'] = hit_list
         return context
 
+    def get_queryset(self, **kwargs):
+        search_term = self.request.GET.get('search')
+        if search_term:
+            search_term = "*" + search_term + "*"
+            postresult = ESGeneDocument.search().query("query_string", query=search_term,
+                                                             fields=["symbol", "name", "gene_id"])
+            result = postresult
+        else:
+            result = None
+        return result
+
+
+class LinkInternalGeneView(LoginRequiredMixin, TemplateView):
+    model = Annotation
+    template_name = 'annotations/annotation_request.html'
+
+    def get(self, request, *args, **kwargs):
+        context = super(LinkInternalGeneView, self)
+        user = self.request.user
+
+        existing_annotation = get_object_or_404(Annotation, pk=self.kwargs['annot_pk'])
+        existing_gene = get_object_or_404(Gene, pk=self.kwargs['gene_pk'])
+
+        # initialize the changed annotation to the same as the existing
+        changed_annotation = AnnotationApproval()
+        for field in existing_annotation._meta.fields:
+            setattr(changed_annotation, field.name, getattr(existing_annotation, field.name))
+        # Change the value
+        changed_annotation.internal_gene = existing_gene
+
+        # update status and requestor fields
+        status = choices.ApprovalStates.PENDING
+        requestor = self.request.user
+        curr_time = timezone.now()
+
+        # add new values
+        changed_annotation.status = status
+        changed_annotation.action = choices.ApprovalActions.INITIAL
+        changed_annotation.requestor = requestor
+        changed_annotation.datetime = curr_time
+        changed_annotation.date = curr_time
+        changed_annotation.source_annotation = existing_annotation
+
+        # Set it to approved already if the user was a superuser
+        if requestor.is_superuser:
+            changed_annotation.status = choices.ApprovalStates.APPROVED
+            changed_annotation.action = choices.ApprovalActions.APPROVE
+            existing_annotation.internal_gene = existing_gene
+            existing_annotation.save()
+
+        # save it to the db as a AnnotationApproval model
+        changed_annotation.save()
+
+        return render(self.request, 'annotations/annotation_request.html')
+
 
 class AnnotationSearchGeneView(TemplateView):
     template_name = 'annotations/annotation_search_gene.html'