Pull in MANE preferred transcript from the allele registry

app/controllers/variants_controller.rb

@@ -2,8 +2,8 @@ class VariantsController < ApplicationController
   include WithComment
   include WithSoftDeletion
 
-  actions_without_auth :index, :show, :typeahead_results, :datatable, :gene_index, :entrez_gene_index, :variant_group_index, :myvariant_info_proxy, :allele_registry_proxy, :variant_navigation
-  skip_analytics :typeahead_results, :myvariant_info_proxy, :allele_registry_proxy
+  actions_without_auth :index, :show, :typeahead_results, :datatable, :gene_index, :entrez_gene_index, :variant_group_index, :myvariant_info_proxy, :allele_registry_proxy, :mane_preferred_transcript, :variant_navigation
+  skip_analytics :typeahead_results, :myvariant_info_proxy, :allele_registry_proxy, :mane_preferred_transcript
 
   def index
     variants = Variant.index_scope
@@ -78,6 +78,10 @@ def allele_registry_proxy
     render json: AlleleRegistry.new(params[:variant_id]).response
   end
 
+  def mane_preferred_transcript
+    render json: ManePreferredTranscript.new(params[:variant_id]).mane_preferred_transcript
+  end
+
   private
   def variant_params
     params.permit(:name, :description, :genome_build, :chromosome, :start, :stop, :reference_bases, :variant_bases, :representative_transcript, :chromosome2, :start2, :stop2, :reference_build, :representative_transcript2, :ensembl_version, variant_types: [])

app/models/mane_preferred_transcript.rb

@@ -0,0 +1,51 @@
+class ManePreferredTranscript
+  attr_reader :variant
+
+  def initialize(variant_id)
+    @variant = Variant.find(variant_id)
+  end
+
+  def mane_preferred_transcript
+    Rails.cache.fetch(cache_key(variant), expires_in: 24.hours) do
+      if mane_preferred_ref_seq = get_mane_preferred_ref_seq(variant)
+        transcripts = get_allele_registry_transcripts(variant)
+        transcripts.find{ |t| t['hgvs'][0].start_with?(mane_preferred_ref_seq) }
+      end
+    end
+  end
+
+  def get_allele_registry_transcripts(variant)
+    allele_response = make_allele_request(variant.allele_registry_id)
+    JSON.parse(allele_response)['transcriptAlleles']
+  end
+
+  def get_mane_preferred_ref_seq(variant)
+    gene_response = make_gene_request(variant.gene.name)
+    JSON.parse(gene_response)[0]['externalRecords']['MANEPrefRefSeq']['id'] rescue nil
+  end
+
+  private
+  def make_gene_request(gene_name)
+    Scrapers::Util.make_get_request(gene_url(gene_name))
+  rescue StandardError
+    {}
+  end
+
+  def make_allele_request(allele_registry_id)
+    Scrapers::Util.make_get_request(allele_url(allele_registry_id))
+  rescue StandardError
+    {}
+  end
+
+  def gene_url(gene_name)
+    URI.encode("http://reg.genome.network/genes?name=#{gene_name}")
+  end
+
+  def allele_url(allele_registry_id)
+    URI.encode("http://reg.genome.network/allele/#{allele_registry_id}")
+  end
+
+  def cache_key(variant)
+    "mane_preferred_transcript_#{variant.id}_#{variant.hash}"
+  end
+end

config/routes.rb

@@ -100,6 +100,7 @@
     resources 'variants', except: [:edit] do
       get 'myvariant_info_proxy' => 'variants#myvariant_info_proxy'
       get 'allele_registry_proxy' => 'variants#allele_registry_proxy'
+      get 'mane_preferred_transcript' => 'variants#mane_preferred_transcript'
       get 'evidence_items' => 'evidence_items#variant_index'
       get 'variant_groups' => 'variant_groups#variant_index'
       get 'assertions' => 'assertions#variant_index'