Merge branch 'ensembl-splice' of https://github.com/RNAcentral/rnacen…

…tral-webcode into export-app
RNAcentral · Sep 6, 2024 · ad2d47e · ad2d47e
2 parents c2a8c95 + 73944c3
commit ad2d47e
Show file tree

Hide file tree

Showing 4 changed files with 42 additions and 8 deletions.
diff --git a/rnacentral/apiv1/serializers.py b/rnacentral/apiv1/serializers.py
@@ -198,7 +198,7 @@ class XrefSerializer(serializers.HyperlinkedModelSerializer):
     refseq_mirna_mature_products = serializers.SerializerMethodField()
     refseq_mirna_precursor = serializers.SerializerMethodField()
     refseq_splice_variants = serializers.SerializerMethodField()
-    ensembl_splice_variants = serializers.SerializerMethodField()
+    # ensembl_splice_variants = serializers.SerializerMethodField()
     # tmrna_mate_upi = serializers.SerializerMethodField('get_tmrna_mate_upi')
     # tmrna_type = serializers.ReadOnlyField(source='get_tmrna_type')
     gencode_transcript_id = serializers.CharField(
@@ -229,7 +229,7 @@ class Meta:
             "refseq_mirna_mature_products",
             "refseq_mirna_precursor",
             "refseq_splice_variants",
-            "ensembl_splice_variants",
+            # "ensembl_splice_variants",
             # 'tmrna_mate_upi',
             # 'tmrna_type',
             "gencode_transcript_id",
@@ -958,3 +958,11 @@ def get_ensembl_assembly(self, obj):
             "example_start": obj.example_start,
             "example_end": obj.example_end,
         }
+
+
+class Md5Serializer(serializers.Serializer):
+    """Serializer class to fetch sequence using md5"""
+
+    rnacentral_id = serializers.CharField(source="id")
+    description = serializers.CharField()
+    sequence = serializers.CharField(source="get_sequence")
diff --git a/rnacentral/apiv1/urls.py b/rnacentral/apiv1/urls.py
@@ -196,6 +196,12 @@
         {},
         name="litsumm-specific-id",
     ),
+    # fetch sequence using md5
+    url(
+        r"md5/(?P<md5>.*?)/?$",
+        cache_page(CACHE_TIMEOUT)(views.Md5SequenceView.as_view()),
+        name="md5-sequence",
+    ),
 ]
 
 urlpatterns = format_suffix_patterns(

diff --git a/rnacentral/apiv1/views.py b/rnacentral/apiv1/views.py
@@ -29,6 +29,7 @@
     InteractionsSerializer,
     LitSummSerializer,
     LncrnaTargetsSerializer,
+    Md5Serializer,
     ProteinTargetsSerializer,
     QcStatusSerializer,
     RawPublicationSerializer,
@@ -1102,3 +1103,22 @@ def get_queryset(self):
         if primary_id is not None:
             queryset = queryset.filter(primary_id=primary_id)
         return queryset
+
+
+class Md5SequenceView(APIView):
+    """API endpoint to fetch sequence using md5 field"""
+
+    permission_classes = (AllowAny,)
+
+    def get(self, request, md5):
+        try:
+            rna = Rna.objects.get(md5=md5)
+        except Rna.DoesNotExist:
+            raise Http404
+
+        precomputed = RnaPrecomputed.objects.filter(upi=rna, taxid__isnull=True).first()
+        if not precomputed:
+            raise Http404
+
+        serializer = Md5Serializer(precomputed)
+        return Response(serializer.data)
diff --git a/rnacentral/portal/models/xref.py b/rnacentral/portal/models/xref.py
@@ -86,7 +86,7 @@ def _fetch_all(self):
                 )
                 refseq_mirna_precursors = self.get_refseq_mirna_precursor(taxid)
                 refseq_splice_variants = self.get_refseq_splice_variants(taxid)
-                ensembl_splice_variants = self.get_ensembl_splice_variants(taxid)
+                # ensembl_splice_variants = self.get_ensembl_splice_variants(taxid)
                 # tmrna_mates = self.get_tmrna_mate(taxid)
 
                 # "annotate" xrefs queryset with additional attributes, retrieved by raw SQL queries
@@ -114,11 +114,11 @@ def _fetch_all(self):
                             splice_variant.upi.upi
                             for splice_variant in refseq_splice_variants[xref.id]
                         ]
-                    if xref.id in ensembl_splice_variants:
-                        xref.ensembl_splice_variants = [
-                            splice_variant.upi.upi
-                            for splice_variant in ensembl_splice_variants[xref.id]
-                        ]
+                    # if xref.id in ensembl_splice_variants:
+                    #     xref.ensembl_splice_variants = [
+                    #         splice_variant.upi.upi
+                    #         for splice_variant in ensembl_splice_variants[xref.id]
+                    #     ]
                     # if xref.id in tmrna_mates:
                     #     xref.tmrna_mates = [
                     #         tmrna_mate.upi.upi for tmrna_mate in tmrna_mates[xref.id]