add pept2filtered without filtering

app/controllers/mpa/pept2filtered_controller.rb

@@ -1,64 +1,19 @@
 class Mpa::Pept2filteredController < Mpa::MpaController
   def pept2filtered
     peptides = params[:peptides] || []
+    missed = params[:missed].nil? ? false : params[:missed]
+    equate_il = params[:equate_il].nil? ? true : params[:equate_il]
     cutoff = params[:cutoff] || 1000
-    # missed = params[:missed] || false
-    taxa_filter_ids = (params[:taxa] || []).map(&:to_i)
-
-    @equate_il = params[:equate_il].nil? ? true : params[:equate_il]
-
-    @seq_entries = {}
-    uniprot_ids = []
-
-    peptides_under_cutoff = Sequence
-                            .joins(:peptides)
-                            .where(sequence: peptides)
-                            .group('sequences.id')
-                            .having('count(peptides.id) < ?', cutoff)
-                            .pluck(:sequence)
-
-    taxa_filter_ids.each_slice(5000) do |taxa_slice|
-      # For all given taxon id's, filter out those that are invalid according to Unipept's filter
-      # i.e. these taxa are typically rubbish (for example those that end in bacterium and are classified at the
-      # species rank).
-      taxa_slice = Taxon
-                   .where(id: taxa_slice)
-                   .where(valid_taxon: 1)
-                   .pluck(:id)
-
-      # If none of the taxa in this slice are valid, skip this iteration of the loop and continue with the next one.
-      next if taxa_slice.empty?
 
-      sequence_subset = Sequence
-                        .joins(peptides: [:uniprot_entry])
-                        .includes(peptides: [:uniprot_entry])
-                        .where(sequence: peptides_under_cutoff)
-                        .where(uniprot_entry: { taxon_id: taxa_slice })
-                        .uniq
+    @response = Hash.new
 
-      sequence_subset.each do |seq_info|
-        @seq_entries[seq_info.sequence] = [] unless @seq_entries.key?(seq_info.sequence)
-
-        @seq_entries[seq_info.sequence] += seq_info
-                                           .peptides
-                                           .map(&:uniprot_entry)
-                                           .select { |e| taxa_filter_ids.include? e.taxon_id }
-
-        @seq_entries[seq_info.sequence].uniq!
-      end
-
-      uniprot_ids += sequence_subset.map { |s| s.peptides.map(&:uniprot_entry_id) }.flatten.uniq
+    if peptides.empty?
+      return
     end
 
-    uniprot_ids = uniprot_ids.uniq
-
-    @go_terms = GoCrossReference
-                .where(uniprot_entry_id: uniprot_ids)
-
-    @ec_numbers = EcCrossReference
-                  .where(uniprot_entry_id: uniprot_ids)
+    taxa_filter_ids = (params[:taxa] || []).map(&:to_i)
 
-    @ipr_entries = InterproCrossReference
-                   .where(uniprot_entry_id: uniprot_ids)
+    # Request the suffix array search service
+    @response = search(peptides, equate_il).uniq
   end
 end

app/views/mpa/pept2filtered/pept2filtered.json.jbuilder

@@ -1,25 +1,8 @@
-json.peptides @seq_entries.each do |sequence, uniprot_entries|
-  json.sequence sequence
-  json.taxa uniprot_entries.map(&:taxon_id).uniq
+json.peptides @response do |peptide|
+  json.sequence peptide["sequence"]
+  json.taxa peptide["taxa"]
   json.fa do
-    json.go_terms(@go_terms
-                  .select { |go| uniprot_entries.map(&:id).include? go.uniprot_entry_id }
-                  .map(&:go_term_code)
-                  .reject(&:empty?)
-                  .uniq)
-
-    json.ec_numbers(@ec_numbers
-                    .select { |ec| uniprot_entries.map(&:id).include? ec.uniprot_entry_id }
-                    .map(&:ec_number_code)
-                    .reject(&:empty?)
-                    .uniq
-                    .map { |ec| "EC:#{ec}" })
-
-    json.interpro_entries(@ipr_entries
-                          .select { |ipr| uniprot_entries.map(&:id).include? ipr.uniprot_entry_id }
-                          .map(&:interpro_entry_code)
-                          .reject(&:empty?)
-                          .uniq
-                          .map { |ipr| ipr.sub('IPR', 'IPR:') })
+    json.counts peptide["fa"]["counts"]
+    json.data peptide["fa"]["data"]
   end
 end