Exclude region with status different than "clustered"

rnacentral/apiv1/views.py

@@ -16,6 +16,7 @@ import requests
 import zlib
 from itertools import chain
 
+from django.db import connection
 from django.http import Http404, HttpResponse
 from django.shortcuts import get_object_or_404
 from django_filters import rest_framework as filters
@@ -31,17 +32,17 @@ from rest_framework_jsonp.renderers import JSONPRenderer
 from rest_framework_yaml.renderers import YAMLRenderer
 
 from apiv1.serializers import RnaNestedSerializer, AccessionSerializer, CitationSerializer, XrefSerializer, \
-                              RnaFlatSerializer, RnaFastaSerializer, RnaGffSerializer, RnaGff3Serializer, RnaBedSerializer, \
-                              RnaSpeciesSpecificSerializer, ExpertDatabaseStatsSerializer, \
+                              RnaFlatSerializer, RnaFastaSerializer, RnaGffSerializer, RnaGff3Serializer, \
+                              RnaBedSerializer, RnaSpeciesSpecificSerializer, ExpertDatabaseStatsSerializer, \
                               RawPublicationSerializer, RnaSecondaryStructureSerializer, \
                               RfamHitSerializer, SequenceFeatureSerializer, \
                               EnsemblAssemblySerializer, ProteinTargetsSerializer, \
                               LncrnaTargetsSerializer, EnsemblComparaSerializer, SecondaryStructureSVGImageSerializer
 
 from apiv1.renderers import RnaFastaRenderer
-from portal.models import Rna, RnaPrecomputed, Accession, Xref, Database, DatabaseStats, RfamHit, EnsemblAssembly,\
-    GoAnnotation, RelatedSequence, ProteinInfo, SequenceFeature,\
-    SequenceRegion, EnsemblCompara, SecondaryStructureWithLayout
+from portal.models import Rna, RnaPrecomputed, Accession, Database, DatabaseStats, RfamHit, EnsemblAssembly, \
+    GoAnnotation, RelatedSequence, ProteinInfo, SequenceFeature, SequenceRegion, EnsemblCompara, \
+    SecondaryStructureWithLayout, dictfetchall
 from portal.config.expert_databases import expert_dbs
 from rnacentral.utils.pagination import Pagination, PaginatedRawQuerySet
 
@@ -449,6 +450,18 @@ class RnaGenomeLocations(generics.ListAPIView):
 
         output = []
         for region in regions:
+            # check the gene status for each region
+            query = '''
+                    SELECT status
+                    FROM rnc_gene_status
+                    WHERE region_id = '{region_id}'
+                    '''.format(region_id=region.id)
+            with connection.cursor() as cursor:
+                cursor.execute(query)
+                data = dictfetchall(cursor)
+
+            # show results only from those with "clustered" status
+            if data[0]['status'] == "clustered":
                 output.append({
                     'chromosome': region.chromosome,
                     'strand': region.strand,