Add filter to relationships tab

.env-example

@@ -5,3 +5,5 @@ EBI_SEARCH_ENDPOINT=http://example.com  # if not specified, www will be used
 SECRET_KEY=super_secret_key  # if not specified, it uses get_random_secret_key
 DJANGO_DEBUG=True  # if not specified, it uses DJANGO_DEBUG=False
 LOCAL_DEVELOPMENT=True  # use this variable if you need the django-debug-toolbar, coverage and mock packages
+DOORBELL_API_KEY=your_doorbell_api_key  # Doorbell.io API key for feedback integration
+DOORBELL_API_ID=your_doorbell_app_id  # Doorbell.io application ID

kubernetes/helm/templates/rnacentral.yaml

@@ -62,6 +62,16 @@ spec:
           env:
             - name: RNACENTRAL_ENV
               value: {{ .Values.setEnv }}
+            - name: DOORBELL_API_KEY
+              valueFrom:
+                secretKeyRef:
+                  name: doorbell-credentials
+                  key: DOORBELL_API_KEY
+            - name: DOORBELL_API_ID
+              valueFrom:
+                secretKeyRef:
+                  name: doorbell-credentials
+                  key: DOORBELL_API_ID
           envFrom:
           - secretRef:
               name: {{ .Values.database }}

rnacentral/apiv1/views.py

@@ -1244,42 +1244,72 @@ class RelationshipsView(generics.ListAPIView):
 
     def get_queryset(self):
         """Return relationship data for a given URS and taxid from RNA-KG API"""
-        
+
         node_id = f"{self.kwargs['pk']}_{self.kwargs['taxid']}"
-        
+
         # Get the relationships using the original endpoint
         rna_kg_url = "https://rna-kg.biodata.di.unimi.it/api/v1/incoming/id"
         relationships_params = {
             'node_id': node_id,
             'node_id_scheme': 'RNAcentral',
             'filter_rnacentral_rels': 'false'
         }
-        
+
         try:
             relationships_response = requests.get(rna_kg_url, params=relationships_params, timeout=10)
             relationships_response.raise_for_status()
             relationships_data = relationships_response.json()
             relationships = relationships_data.get('relationships', [])
-
+
+            # Apply filters if provided
+            search_query = self.request.query_params.get('search', '').strip().lower()
+            relationship_type_filter = self.request.query_params.get('relationship_type', '').strip()
+            source_filter = self.request.query_params.get('source', '').strip()
+
+            if search_query or relationship_type_filter or source_filter:
+                filtered_relationships = []
+                for rel in relationships:
+                    # Text search filter
+                    if search_query:
+                        node_props = rel.get('node_properties', {})
+                        label = (node_props.get('Label') or rel.get('node_id') or '').lower()
+                        description = (node_props.get('Description') or '').lower()
+                        if search_query not in label and search_query not in description:
+                            continue
+
+                    # Relationship type filter
+                    if relationship_type_filter:
+                        if rel.get('relationship_type', '') != relationship_type_filter:
+                            continue
+
+                    # Source filter
+                    if source_filter:
+                        sources = rel.get('relationship_properties', {}).get('Source', [])
+                        if source_filter not in sources:
+                            continue
+
+                    filtered_relationships.append(rel)
+                relationships = filtered_relationships
+
             # Create a mock queryset-like object for pagination
             class RelationshipQuerySet:
                 def __init__(self, data):
                     self.data = data
-                
+
                 def __iter__(self):
                     return iter(self.data)
-                
+
                 def __len__(self):
                     return len(self.data)
-                
+
                 def count(self):
                     return len(self.data)
-                
+
                 def __getitem__(self, key):
                     return self.data[key]
-            
+
             return RelationshipQuerySet(relationships)
-            
+
         except Exception as e:
             # Log the error if you have logging set up
             # print(f"Error fetching RNA-KG relationships data: {e}")
@@ -1293,7 +1323,7 @@ def get_rna_sequence_rnakg_id(self):
             'node_id': node_id,
             'node_id_scheme': 'RNAcentral'
         }
-        
+
         try:
             node_response = requests.get(node_id_url, params=node_id_params, timeout=10)
             if node_response.status_code == 200:
@@ -1302,22 +1332,64 @@ def get_rna_sequence_rnakg_id(self):
         except Exception:
             pass
         return None
-
+
+    def get_filter_options(self):
+        """Extract unique relationship types and sources from the full dataset"""
+        node_id = f"{self.kwargs['pk']}_{self.kwargs['taxid']}"
+        rna_kg_url = "https://rna-kg.biodata.di.unimi.it/api/v1/incoming/id"
+        relationships_params = {
+            'node_id': node_id,
+            'node_id_scheme': 'RNAcentral',
+            'filter_rnacentral_rels': 'false'
+        }
+
+        relationship_types = set()
+        sources = set()
+
+        try:
+            response = requests.get(rna_kg_url, params=relationships_params, timeout=10)
+            response.raise_for_status()
+            relationships = response.json().get('relationships', [])
+
+            for rel in relationships:
+                rel_type = rel.get('relationship_type')
+                if rel_type:
+                    relationship_types.add(rel_type)
+
+                rel_sources = rel.get('relationship_properties', {}).get('Source', [])
+                for source in rel_sources:
+                    sources.add(source)
+        except Exception:
+            pass
+
+        return {
+            'relationship_types': sorted(list(relationship_types)),
+            'sources': sorted(list(sources))
+        }
+
     def list(self, request, *args, **kwargs):
-        """Override list method to include RNA sequence rnakg_id in response"""
+        """Override list method to include RNA sequence rnakg_id and filter options in response"""
         queryset = self.filter_queryset(self.get_queryset())
-        
+
         page = self.paginate_queryset(queryset)
         if page is not None:
             serializer = self.get_serializer(page, many=True)
             paginated_response = self.get_paginated_response(serializer.data)
-            
-            # Add the RNA sequence rnakg_id to the response
+
+            # Add the RNA sequence rnakg_id and filter options to the response
             rna_sequence_rnakg_id = self.get_rna_sequence_rnakg_id()
             paginated_response.data['rna_sequence_rnakg_id'] = rna_sequence_rnakg_id
-
+
+            # Only fetch filter options on initial load (no filters applied)
+            if not any([
+                request.query_params.get('search'),
+                request.query_params.get('relationship_type'),
+                request.query_params.get('source')
+            ]):
+                paginated_response.data['filter_options'] = self.get_filter_options()
+
             return paginated_response
-        
+
         serializer = self.get_serializer(queryset, many=True)
         response_data = {
             'results': serializer.data,

rnacentral/portal/static/js/components/sequence/relationships/relationships.js

@@ -29,18 +29,94 @@
             ctrl.pageSize = 20;
             ctrl.showPagination = false;
             ctrl.rnaSequenceRnakgId = null;
+            ctrl.filterText = '';
+            ctrl.serverSearch = '';
+            ctrl.pageSizeOptions = [10, 20, 50, 100];
+
+            // Dropdown filter options (populated from API)
+            ctrl.relationshipTypeFilter = '';
+            ctrl.sourceFilter = '';
+            ctrl.relationshipTypes = [];
+            ctrl.sources = [];
+
+            ctrl.filterByTargetOrDescription = function(rel) {
+                // Text filter (client-side for current page)
+                if (ctrl.filterText) {
+                    var searchText = ctrl.filterText.toLowerCase();
+                    var target = (rel.node_properties.Label || rel.node_id || '').toLowerCase();
+                    var description = (rel.node_properties.Description || '').toLowerCase();
+                    if (target.indexOf(searchText) === -1 && description.indexOf(searchText) === -1) {
+                        return false;
+                    }
+                }
+                return true;
+            };
+
+            ctrl.applyDropdownFilters = function() {
+                ctrl.loadRelationships(1);
+            };
+
+            ctrl.clearAllFilters = function() {
+                ctrl.filterText = '';
+                ctrl.serverSearch = '';
+                ctrl.relationshipTypeFilter = '';
+                ctrl.sourceFilter = '';
+                ctrl.loadRelationships(1);
+            };
+
+            ctrl.hasActiveFilters = function() {
+                return ctrl.filterText || ctrl.serverSearch || ctrl.relationshipTypeFilter || ctrl.sourceFilter;
+            };
+
+            ctrl.onFilterChange = function() {
+                // Clear server search message when filter text is manually cleared
+                if (!ctrl.filterText && ctrl.serverSearch) {
+                    ctrl.serverSearch = '';
+                    ctrl.loadRelationships(1);
+                }
+            };
+
+            ctrl.onSearchKeypress = function(event) {
+                if (event.keyCode === 13) {
+                    ctrl.searchAll();
+                }
+            };
+
+            ctrl.searchAll = function() {
+                ctrl.serverSearch = ctrl.filterText;
+                ctrl.loadRelationships(1);
+            };
+
+            ctrl.clearFilter = function() {
+                ctrl.filterText = '';
+                ctrl.serverSearch = '';
+                ctrl.loadRelationships(1);
+            };
+
+            ctrl.changePageSize = function() {
+                ctrl.loadRelationships(1);
+            };
 
             ctrl.loadRelationships = function(page, append) {
                 if (!ctrl.taxid || !ctrl.upi) {
                     return;
                 }
-                
+
                 page = page || 1;
                 append = append || false;
                 ctrl.loading = true;
                 ctrl.error = false;
-
-                var relationshipsUrl = '/api/v1/rna/' + ctrl.upi + '/relationships/' + ctrl.taxid + '?page=' + page;
+
+                var relationshipsUrl = '/api/v1/rna/' + ctrl.upi + '/relationships/' + ctrl.taxid + '?page=' + page + '&page_size=' + ctrl.pageSize;
+                if (ctrl.serverSearch) {
+                    relationshipsUrl += '&search=' + encodeURIComponent(ctrl.serverSearch);
+                }
+                if (ctrl.relationshipTypeFilter) {
+                    relationshipsUrl += '&relationship_type=' + encodeURIComponent(ctrl.relationshipTypeFilter);
+                }
+                if (ctrl.sourceFilter) {
+                    relationshipsUrl += '&source=' + encodeURIComponent(ctrl.sourceFilter);
+                }
 
                 $http.get(relationshipsUrl)
                     .then(function(response) {
@@ -55,6 +131,13 @@
                         ctrl.currentPage = page;
                         ctrl.showPagination = ctrl.totalCount > ctrl.pageSize;
                         ctrl.rnaSequenceRnakgId = response.data.rna_sequence_rnakg_id;
+
+                        // Populate filter options from API (only on initial load)
+                        if (response.data.filter_options) {
+                            ctrl.relationshipTypes = response.data.filter_options.relationship_types || [];
+                            ctrl.sources = response.data.filter_options.sources || [];
+                        }
+
                         ctrl.loading = false;
                     })
                     .catch(function(error) {
@@ -147,6 +230,53 @@
                         <span ng-if="ctrl.showPagination">Showing {{ctrl.getStartRecord()}} - {{ctrl.getEndRecord()}} of {{ctrl.totalCount}} relationships.</span>
                     </p>
 
+                    <div class="row" style="margin-bottom: 10px;">
+                        <div class="col-sm-5">
+                            <div class="input-group">
+                                <span class="input-group-addon"><i class="fa fa-search"></i></span>
+                                <input type="text" class="form-control" placeholder="Search by target or description..." ng-model="ctrl.filterText" ng-keypress="ctrl.onSearchKeypress($event)" ng-change="ctrl.onFilterChange()">
+                                <span class="input-group-btn">
+                                    <button class="btn btn-primary" type="button" ng-click="ctrl.searchAll()" title="Search all pages">
+                                        Search all
+                                    </button>
+                                </span>
+                            </div>
+                            <small class="text-muted" ng-if="ctrl.filterText && !ctrl.serverSearch">
+                                Filtering current page. Press Enter or click "Search all" to search all pages.
+                            </small>
+                            <small class="text-muted" ng-if="ctrl.serverSearch">
+                                Showing results matching "{{ctrl.serverSearch}}" across all pages.
+                            </small>
+                        </div>
+                        <div class="col-sm-3">
+                            <select class="form-control" ng-model="ctrl.relationshipTypeFilter" ng-change="ctrl.applyDropdownFilters()">
+                                <option value="">All relationship types</option>
+                                <option ng-repeat="type in ctrl.relationshipTypes" ng-value="type">{{type}}</option>
+                            </select>
+                        </div>
+                        <div class="col-sm-2">
+                            <select class="form-control" ng-model="ctrl.sourceFilter" ng-change="ctrl.applyDropdownFilters()">
+                                <option value="">All sources</option>
+                                <option ng-repeat="source in ctrl.sources" ng-value="source">{{source}}</option>
+                            </select>
+                        </div>
+                        <div class="col-sm-2">
+                            <div class="input-group">
+                                <select class="form-control" ng-model="ctrl.pageSize" ng-change="ctrl.changePageSize()">
+                                    <option ng-repeat="size in ctrl.pageSizeOptions" ng-value="size">{{size}}</option>
+                                </select>
+                                <span class="input-group-addon">/ page</span>
+                            </div>
+                        </div>
+                    </div>
+                    <div class="row" style="margin-bottom: 15px;" ng-if="ctrl.hasActiveFilters()">
+                        <div class="col-sm-12">
+                            <button class="btn btn-default btn-sm" type="button" ng-click="ctrl.clearAllFilters()">
+                                <i class="fa fa-times"></i> Clear all filters
+                            </button>
+                        </div>
+                    </div>
+
                     <div class="table-responsive">
                         <table class="table table-striped table-bordered">
                             <thead>
@@ -159,7 +289,7 @@
                                 </tr>
                             </thead>
                             <tbody>
-                                <tr ng-repeat="rel in ctrl.relationships">
+                                <tr ng-repeat="rel in ctrl.relationships | filter:ctrl.filterByTargetOrDescription">
                                     <td>
                                         <a ng-if="rel.rel_rnakg_id" href="https://rna-kg.biodata.di.unimi.it/relationship/{{rel.rel_rnakg_id}}" target="_blank" class="label label-info" style="text-decoration: none;">
                                             {{ rel.relationship_type || "Unknown" }}
@@ -234,9 +364,18 @@
                     </div>
                 </div>
 
-                <div ng-if="!ctrl.loading && !ctrl.error && (!ctrl.relationships || ctrl.relationships.length === 0)" class="alert alert-info">
-                    <i class="fa fa-info-circle"></i>
-                    No relationship data is currently available for this RNA sequence.
+                <div ng-if="!ctrl.loading && !ctrl.error && (!ctrl.relationships || ctrl.relationships.length === 0)">
+                    <div ng-if="ctrl.hasActiveFilters()" class="alert alert-warning">
+                        <i class="fa fa-filter"></i>
+                        No relationships match the current filters.
+                        <button class="btn btn-default btn-sm" style="margin-left: 10px;" type="button" ng-click="ctrl.clearAllFilters()">
+                            <i class="fa fa-times"></i> Clear all filters
+                        </button>
+                    </div>
+                    <div ng-if="!ctrl.hasActiveFilters()" class="alert alert-info">
+                        <i class="fa fa-info-circle"></i>
+                        No relationship data is currently available for this RNA sequence.
+                    </div>
                 </div>
             `
         };

rnacentral/portal/static/r2dt-web/dist/r2dt-web.js.LICENSE.txt

@@ -0,0 +1 @@
+/*! regenerator-runtime -- Copyright (c) 2014-present, Facebook, Inc. -- license (MIT): https://github.com/babel/babel/blob/main/packages/babel-helpers/LICENSE */