test

app/controllers/mpa/pept2data_controller.rb

@@ -4,23 +4,26 @@ class Mpa::Pept2dataController < Mpa::MpaController
   def pept2data
     peptides = params[:peptides] || []
     missed = params[:missed] || false
-    @equate_il = params[:equate_il].nil? ? true : params[:equate_il] == 'true'
+    equate_il = params[:equate_il].nil? ? true : params[:equate_il] == 'true'
 
     @response = Hash.new
 
     # Request the suffix array search service
-    search_results = search(peptides, @equate_il)
+    search_results = search(peptides, equate_il)
 
+    # Collect all lca's to look up the lineages
     taxa = []
     search_results["result"].each do |result|
       taxa.append(result["lca"])
     end
 
+    # Retrieve all lineages at once
     @lineages = Hash.new
     Lineage.find(taxa).each do |lineage|
       @lineages[lineage.taxon_id] = lineage.to_a_idx
     end
 
+    # Fill the response hash with the search results
     search_results["result"].each do |result|
       @response[result["sequence"]] = {
         sequence: result["sequence"],
@@ -32,36 +35,5 @@ def pept2data
         }
       }
     end
-
-    # proteins = Set.new
-    # search_results["result"].each do |result|
-    #   proteins.merge(result['uniprot_accessions'])
-    # end
-
-    # entries = UniprotEntry.where(uniprot_accession_number: proteins.to_a.uniq)
-
-    # # Convert the retrieved entries to a hash (for easy retrieval)
-    # accession_to_protein = Hash.new
-    # entries.each do |entry|
-    #   accession_to_protein[entry.uniprot_accession_number] = entry
-    # end
-
-    # taxa = []
-    # search_results["result"].each do |result|
-    #   uniprot_entries = result["uniprot_accessions"].map { |acc| accession_to_protein[acc] }
-    #   result["fa"] = UniprotEntry.summarize_fa(uniprot_entries)
-    #   @response[result["sequence"]] = result
-    #   taxa.append(result["lca"])
-    # end
-
-    # looked_up_lineages = Lineage.find(taxa)
-    # looked_up_lineages.each do |lineage|
-    #   @lineages[lineage.taxon_id] = lineage.to_a_idx
-    # end
-
-    # @response.each do |_, entry|
-
-    #   entry["lineage"] = @lineages[entry["lca"].to_i]
-    # end
   end
 end

app/views/mpa/pept2data/pept2data.json.jbuilder

@@ -1 +1 @@
-json.peptides(@response)
+json.peptides(@response.values)