to_set

app/controllers/mpa/pept2filtered_controller.rb

@@ -2,7 +2,7 @@ class Mpa::Pept2filteredController < Mpa::MpaController
   include SuffixArrayHelper
 
   def pept2filtered
-    peptides = params[:peptides] || []
+    peptides = (params[:peptides] || []).uniq
     missed = params[:missed].nil? ? false : params[:missed]
     equate_il = params[:equate_il].nil? ? true : params[:equate_il]
     cutoff = params[:cutoff] || 1000
@@ -16,11 +16,18 @@ def pept2filtered
     taxa_filter_ids = (params[:taxa] || []).map(&:to_i)
 
     # Request the suffix array search service
-    @response = search(peptides, equate_il, cutoff).select { |result| !result["cutoff_used"] }.uniq
+    @response = search(peptides, equate_il, cutoff)
+      .select { |result| !result["cutoff_used"] }
+      .each { |result| result["taxa"] = result["taxa"].to_set }
 
-    # TODO: we should remove this or use a different approach
-    @response.each do |result|
-      result["taxa"] = result["taxa"].select { |taxon_id| taxa_filter_ids.include?(taxon_id) }.uniq
+    taxa_filter_ids.each_slice(5000) do |taxa_slice|
+      taxa_slice = Taxon.where(id: taxa_slice).where(valid_taxon: 1).pluck(:id).to_set
+
+      next if taxa_slice.empty?
+
+      @response.each do |result|
+        result["taxa"] = result["taxa"].select { |taxon_id| taxa_slice.include?(taxon_id) }.uniq
+      end
     end
   end
 end