Merge pull request #629 from RNAcentral/db-changes

Db changes

rnacentral/apiv1/serializers.py

@@ -423,12 +423,6 @@ def get_secondary_structures(self, obj):
         return obj.get_layout_secondary()
 
 
-class SecondaryStructureSVGImageSerializer(serializers.ModelSerializer):
-    class Meta:
-        model = SecondaryStructureWithLayout
-        fields = ("layout",)
-
-
 class RnaSpeciesSpecificSerializer(serializers.Serializer):
     """
     Serializer class for species-specific RNAcentral ids.

rnacentral/apiv1/views.py

@@ -39,7 +39,6 @@
     RnaNestedSerializer,
     RnaSecondaryStructureSerializer,
     RnaSpeciesSpecificSerializer,
-    SecondaryStructureSVGImageSerializer,
     SequenceFeatureSerializer,
     XrefSerializer,
 )
@@ -478,7 +477,6 @@ class SecondaryStructureSVGImage(generics.ListAPIView):
     SVG image for an RNA sequence.
     """
 
-    serializer_class = SecondaryStructureSVGImageSerializer
     permission_classes = (AllowAny,)
 
     def get(self, request, pk=None, format=None):

rnacentral/portal/models/rfam.py

@@ -131,30 +131,6 @@ def rfam_clan_id(self):
         return self.rfam_model.rfam_clan_id
 
 
-class RfamInitialAnnotations(models.Model):
-    """
-    This table represents the given Rfam annotations for a sequence. For
-    example when we take sequences from Rfam we already know what the
-    'correct' family is. In addition, we get sequences from people who have
-    performed their own Rfam scans. We keep track of this to decide if things
-    should be suppressed or handled differently here.
-    """
-
-    rfam_initial_annotation_id = models.AutoField(primary_key=True)
-    upi = models.ForeignKey(
-        "Rna", db_column="upi", to_field="upi", on_delete=models.CASCADE
-    )
-    rfam_model = models.ForeignKey(
-        RfamModel,
-        db_column="rfam_model_id",
-        to_field="rfam_model_id",
-        on_delete=models.CASCADE,
-    )
-
-    class Meta:
-        db_table = "rfam_initial_annotations"
-
-
 class RfamAnalyzedSequences(models.Model):
     """
     This table keeps track of all sequences which have been analyzed for Rfam

rnacentral/portal/models/secondary_structure.py

@@ -49,7 +49,7 @@ class SecondaryStructureWithLayout(models.Model):
     )
 
     class Meta:
-        db_table = "rnc_secondary_structure_layout"
+        db_table = "r2dt_results"
         unique_together = (("urs",),)
 
 
@@ -64,4 +64,4 @@ class SecondaryStructureLayout(models.Model):
     rna_type = models.TextField()
 
     class Meta:
-        db_table = "rnc_secondary_structure_layout_models"
+        db_table = "r2dt_models"