more updates

server/lib/genome/groupers/base.rb

@@ -60,7 +60,7 @@ def normalize_claim(primary_term, claim_aliases)
             response = retrieve_normalizer_response(claim_alias.alias)
             match_type = response['match_type']
             if !response.nil? && match_type > 0
-              concept_id = response[@descriptor_name]['id'][15..]
+              concept_id = response['normalized_id']
               if !claim_responses.key?(concept_id)
                 claim_responses[concept_id] = response
               end
@@ -93,6 +93,10 @@ def normalize_claim(primary_term, claim_aliases)
         response
       end
 
+      def get_concept_id(response)
+        response['normalized_id'] unless response['match_type'].zero?
+      end
+
       def retrieve_extension(descriptor, type, default = nil)
         unless descriptor.fetch('extensions').blank?
           descriptor['extensions'].each do |extension|

server/lib/genome/groupers/drug_grouper.rb

@@ -8,7 +8,8 @@ def initialize
         if !url_base.ends_with? "/"
           url_base += "/"
         end
-        @normalizer_host = "#{url_base}/therapy/"
+        @normalizer_host = "#{url_base}therapy/"
+        @descriptor_name = 'therapy'
 
         @term_to_match_dict = {}
 
@@ -52,19 +53,6 @@ def run(source_id = nil)
         end
       end
 
-      def set_response_structure
-        url = URI("#{@normalizer_host}search?q=")
-        body = fetch_json_response(url)
-        version = body['service_meta_']['version']
-        if version < '0.4.0'
-          @descriptor_name = 'therapy_descriptor'
-          @id_name = 'therapy_id'
-        else
-          @descriptor_name = 'therapeutic_descriptor'
-          @id_name = 'therapeutic'
-        end
-      end
-
       def create_sources
         drug_source_type = SourceType.find_by(type: 'drug')
 
@@ -168,10 +156,6 @@ def create_sources
         }
       end
 
-      def get_concept_id(response)
-        response[@descriptor_name][@id_name] unless response['match_type'].zero?
-      end
-
       def produce_concept_id_nomenclature(concept_id)
         case concept_id
         when /rxcui:/
@@ -293,7 +277,7 @@ def add_grouper_claim_aliases(claim, record)
       end
 
       def add_grouper_data(drug, descriptor)
-        drug_data = retrieve_normalizer_data(descriptor[@id_name])
+        gene_data = retrieve_normalizer_data(descriptor['id'][15..])
 
         drug_data.each do |source_name, source_data|
           next if %w[DrugBank ChEMBL GuideToPHARMACOLOGY].include?(source_name)

server/lib/genome/groupers/gene_grouper.rb

@@ -48,28 +48,15 @@ def run(source_id = nil)
           if normalized_gene.is_a? String
             normalized_id = normalized_gene
           else
-            normalized_id = normalized_gene['normalize_id']
-            create_new_gene normalized_gene['gene'] if Gene.find_by(concept_id: normalized_id).nil?
+            normalized_id = normalized_gene['normalized_id']
+            create_new_gene(normalized_gene['gene'], normalized_id) if Gene.find_by(concept_id: normalized_id).nil?
           end
           add_claim_to_gene(gene_claim, normalized_id)
 
           pbar.progress += 1
         end
       end
 
-      # def set_response_structure
-      #   @descriptor_name = 'gene_descriptor'
-      #
-      #   url = URI("#{@normalizer_host}search?q=")
-      #   body = fetch_json_response(url)
-      #   version = body['service_meta_']['version']
-      #   if version < '0.2.0'
-      #     @id_name = 'gene_id'
-      #   else
-      #     @id_name = 'gene'
-      #   end
-      # end
-      #
       def create_sources
         gene_source_type = SourceType.find_by(type: 'gene')
 
@@ -134,10 +121,6 @@ def create_sources
         }
       end
 
-      def get_concept_id(response)
-        response['normalized_id'] unless response['match_type'].zero?
-      end
-
       def create_gene_claim(record, source)
         GeneClaim.where(
           name: record['symbol'],
@@ -212,8 +195,8 @@ def add_grouper_claim_attribute(claim, record)
         )
       end
 
-      def add_grouper_data(gene, descriptor)
-        gene_data = retrieve_normalizer_data(descriptor['id'][15..])
+      def add_grouper_data(gene, descriptor, normalized_id)
+        gene_data = retrieve_normalizer_data(normalized_id)
         gene_data.each do |source_name, source_data|
           source = @sources[source_name.to_sym]
 
@@ -227,19 +210,19 @@ def add_grouper_data(gene, descriptor)
         end
       end
 
-      def create_new_gene(gene_response)
+      def create_new_gene(gene_response, normalized_id)
         name = if gene_response.fetch('label').blank?
-                 gene_response['id'][15..]
+                 normalized_id
                else
                  gene_response['label']
                end
         gene = Gene.where(
-          concept_id: gene_response['id'][15..],
+          concept_id: normalized_id,
           name: name,
           long_name: retrieve_extension(gene_response, 'approved_name')
         ).first_or_create
 
-        add_grouper_data(gene, gene_response)
+        add_grouper_data(gene, gene_response, normalized_id)
       end
 
       def add_claim_attributes(claim, gene)