fix equate IL

app/controllers/private_api/proteins_controller.rb

@@ -1,89 +1,87 @@
 class PrivateApi::ProteinsController < PrivateApi::PrivateApiController
+  include SuffixArrayHelper
+
   def proteins
+    peptide = params[:peptide]
+    equate_il = params[:equate_il].nil? ? true : params[:equate_il]
+
     unless params[:peptide]
       @error_name = 'Invalid peptide provided'
       @error_message = 'No peptide sequence was provided. Please provide a valid peptide sequence.'
       render 'private_api/error'
       return
     end
 
-    # process parameters
-    # the sequence or id of the peptide (filter out all characters that are non-ASCII)
-    seq = params[:peptide].upcase.gsub(/\P{ASCII}/, '')
-    # should we equate I and L? (true by default)
-    equate_il = params.key?(:equate_il) ? params[:equate_il] == 'true' : true
-
-    begin
-      # process the input, convert seq to a valid @sequence
-      sequence = Sequence.single_search(seq, equate_il)
-      @original_sequence = seq
-    rescue SequenceTooShortError
+    unless peptide.length >= 5
       @error_name = 'Sequence too short'
       @error_message = 'The peptide sequence you provided is too short. It should contain at least 5 valid amino acids.'
       render 'private_api/error'
       return
     end
 
-    if sequence.present? && sequence.peptides(equate_il).empty?
-      @entries = []
-      return
-    end
+    # Request the suffix array search service
+    @response = search([ peptide ], equate_il)
 
-    @common_lineage = []
+    # if sequence.present? && sequence.peptides(equate_il).empty?
+    #   @entries = []
+    #   return
+    # end
 
-    # get the uniprot entries of every peptide
-    # only used for the open in uniprot links
-    # and calculate the LCA
-    if sequence.nil?
-      begin
-        # we didn't find the sequence in the database, so let's try to split it
-        long_sequences = Sequence.advanced_single_search(seq, equate_il)
-      rescue NoMatchesFoundError
-        return
-      end
-      # calculate possible uniprot entries
-      temp_entries = long_sequences.map { |s| s.peptides(equate_il).map(&:uniprot_entry).to_set }
-      # take the intersection of all sets
-      @entries = temp_entries.reduce(:&)
-      # check if the protein contains the startsequence
-      @entries.select! { |e| e.protein_contains?(seq, equate_il) }
+    # @common_lineage = []
 
-      # Calculate fa summary
-      @fa_summary = UniprotEntry.summarize_fa(@entries)
+    # # get the uniprot entries of every peptide
+    # # only used for the open in uniprot links
+    # # and calculate the LCA
+    # if sequence.nil?
+    #   begin
+    #     # we didn't find the sequence in the database, so let's try to split it
+    #     long_sequences = Sequence.advanced_single_search(seq, equate_il)
+    #   rescue NoMatchesFoundError
+    #     return
+    #   end
+    #   # calculate possible uniprot entries
+    #   temp_entries = long_sequences.map { |s| s.peptides(equate_il).map(&:uniprot_entry).to_set }
+    #   # take the intersection of all sets
+    #   @entries = temp_entries.reduce(:&)
+    #   # check if the protein contains the startsequence
+    #   @entries.select! { |e| e.protein_contains?(seq, equate_il) }
 
-      return if @entries.empty?
+    #   # Calculate fa summary
+    #   @fa_summary = UniprotEntry.summarize_fa(@entries)
 
-      @lineages = @entries.map(&:lineage).compact
-    else
-      @entries = sequence.peptides(equate_il).map(&:uniprot_entry)
-      @lineages = sequence.lineages(equate_il, true).to_a
+    #   return if @entries.empty?
 
-      # Get FA summary from cache
-      @fa_summary = sequence.calculate_fa(equate_il)
-    end
+    #   @lineages = @entries.map(&:lineage).compact
+    # else
+    #   @entries = sequence.peptides(equate_il).map(&:uniprot_entry)
+    #   @lineages = sequence.lineages(equate_il, true).to_a
 
-    # sort entries
-    @entries = @entries.to_a.sort_by { |e| e.taxon.nil? ? '' : e.taxon.name }
+    #   # Get FA summary from cache
+    #   @fa_summary = sequence.calculate_fa(equate_il)
+    # end
 
-    @lca_taxon = Lineage.calculate_lca_taxon(@lineages)
-    @root = Node.new(1, 'Organism', nil, 'root') # start constructing the tree
-    common_hits = @lineages.map(&:hits).reduce(:+)
-    @root.data['count'] = common_hits
-    last_node = @root
+    # # sort entries
+    # @entries = @entries.to_a.sort_by { |e| e.taxon.nil? ? '' : e.taxon.name }
 
-    # common lineage
-    # construct the common lineage in this array
-    l = @lca_taxon.lineage
-    found = (@lca_taxon.name == 'root')
-    while !found && l.has_next?
-      t = l.next_t
-      next if t.nil?
+    # @lca_taxon = Lineage.calculate_lca_taxon(@lineages)
+    # @root = Node.new(1, 'Organism', nil, 'root') # start constructing the tree
+    # common_hits = @lineages.map(&:hits).reduce(:+)
+    # @root.data['count'] = common_hits
+    # last_node = @root
 
-      found = (@lca_taxon.id == t.id)
-      @common_lineage << t
-      node = Node.new(t.id, t.name, @root, t.rank)
-      node.data['count'] = common_hits
-      last_node = last_node.add_child(node)
-    end
+    # # common lineage
+    # # construct the common lineage in this array
+    # l = @lca_taxon.lineage
+    # found = (@lca_taxon.name == 'root')
+    # while !found && l.has_next?
+    #   t = l.next_t
+    #   next if t.nil?
+
+    #   found = (@lca_taxon.id == t.id)
+    #   @common_lineage << t
+    #   node = Node.new(t.id, t.name, @root, t.rank)
+    #   node.data['count'] = common_hits
+    #   last_node = last_node.add_child(node)
+    # end
   end
 end

app/views/private_api/proteins/proteins.json.jbuilder

@@ -1,10 +1,12 @@
-json.lca @lca_taxon ? @lca_taxon.id : -1
-json.common_lineage(@common_lineage.map(&:id))
-json.proteins @entries do |entry|
-  json.uniprotAccessionId entry.uniprot_accession_number
-  json.name entry.name
-  json.organism entry.taxon_id
-  json.ecNumbers(entry.ec_cross_references.map(&:ec_number_code))
-  json.goTerms(entry.go_cross_references.map(&:go_term_code))
-  json.interproEntries(entry.interpro_cross_references.map(&:interpro_entry_code))
-end
+# json.lca @lca_taxon ? @lca_taxon.id : -1
+# json.common_lineage(@common_lineage.map(&:id))
+# json.proteins @entries do |entry|
+#   json.uniprotAccessionId entry.uniprot_accession_number
+#   json.name entry.name
+#   json.organism entry.taxon_id
+#   json.ecNumbers(entry.ec_cross_references.map(&:ec_number_code))
+#   json.goTerms(entry.go_cross_references.map(&:go_term_code))
+#   json.interproEntries(entry.interpro_cross_references.map(&:interpro_entry_code))
+# end
+
+json.proteins(@response)