pept2prot endpoint

app/controllers/api/pept2prot_controller.rb

@@ -1,35 +1,54 @@
 class Api::Pept2protController < Api::ApiController
   before_action :set_cors_headers
   before_action :set_params
-  before_action :set_sequences
+  # before_action :set_sequences
+  before_action :search_input
 
   # Returns a list of Uniprot entries containing a given tryptic peptide
   # params[:input]: Array, required, List of input peptides
   # params[:equate_il]: "true" or "false" (default), optional, Equate I and L?
   # params[:extra]: "true" or "false" (default), optional, Output extra info?
   def pept2prot
-    lookup = Hash.new { |h, k| h[k] = Set.new }
-    if @extra_info
-      @result = {}
-      # Perform joins and load objects (expensive)
-      ids = []
-      @sequences.pluck(:sequence, 'uniprot_entries.id').each do |sequence, uniprot_id|
-        ids.append uniprot_id
-        lookup[uniprot_id] << sequence
-        @result[sequence] = Set.new
-      end
+    uniprot_accession_numbers = @sequences.map do |sequence| 
+      sequence["uniprot_accession_numbers"]
+    end.flatten.uniq
 
-      ids = ids.uniq.compact.sort
-      UniprotEntry.includes(:taxon, :ec_cross_references, :go_cross_references, :interpro_cross_references)
-                  .where(id: ids).find_in_batches do |group|
-        group.each do |uni|
-          lookup[uni.id].each { |s| @result[s] << uni }
+    uniprot_info = {}
+
+    if @extra_info
+      UniprotEntry
+        .includes(:taxon, :ec_cross_references, :go_cross_references, :interpro_cross_references)
+        .where(uniprot_accession_number: uniprot_accession_numbers)
+        .each do |item| 
+          uniprot_info[item.uniprot_accession_number] = {
+            uniprot_id: item.uniprot_accession_number,
+            name: item.name,
+            taxon_id: item.taxon_id,
+            protein: item.protein,
+            taxon: item.taxon,
+            ec_cross_references: item.ec_cross_references.map(&:ec_number_code).join(" "),
+            go_cross_references: item.go_cross_references.map(&:go_term_code).join(" "),
+            interpro_cross_references: item.interpro_cross_references.map(&:interpro_entry_code).join(" ")
+          }
         end
-      end
     else
-      @result = Hash.new { |h, k| h[k] = Set.new }
-      @sequences.pluck(:sequence, 'uniprot_entries.uniprot_accession_number', 'uniprot_entries.name', 'uniprot_entries.taxon_id', 'uniprot_entries.protein').each do |sequence, uniprot_id, protein_name, taxon_id, protein|
-        @result[sequence] << [uniprot_id, protein_name, taxon_id, protein]
+      UniprotEntry
+        .where(uniprot_accession_number: uniprot_accession_numbers)
+        .pluck(:uniprot_accession_number, :name, :taxon_id, :protein)
+        .each do |item|
+          uniprot_info[item[0]] = {
+            uniprot_id: item[0],
+            name: item[1],
+            taxon_id: item[2],
+            protein: item[3]
+          }
+        end
+    end
+
+    @result = {}
+    @sequences.each do |sequence|
+      sequence["uniprot_accession_numbers"].each do |uniprot_id|
+        @result[sequence["sequence"]] = uniprot_info[uniprot_id]
       end
     end
 

app/views/api/pept2prot/pept2prot.json.jbuilder

@@ -0,0 +1,13 @@
+json.array! @input_order do |peptide|
+  json.peptide peptide
+  json.uniprot_id @result[peptide][:uniprot_id]
+  json.protein_name @result[peptide][:name]
+  json.taxon_id @result[peptide][:taxon_id]
+  json.protein @result[peptide][:protein]
+  if @extra_info
+    json.taxon_name @result[peptide][:taxon][:name]
+    json.ec_references @result[peptide][:ec_cross_references]
+    json.go_references @result[peptide][:go_cross_references]
+    json.interpro_references @result[peptide][:interpro_cross_references]
+  end
+end