remaining pept endpoints

app/controllers/api/pept2funct_controller.rb

@@ -18,8 +18,6 @@ def pept2funct
     interpro_result = pept2interpro_helper
 
     @input_order.each do |seq|
-      seq_index = @equate_il ? seq.tr('I', 'L') : seq
-
       next unless go_result.key? seq_index
 
       @result[seq_index] = {

app/controllers/api/pept2lca_controller.rb

@@ -13,5 +13,6 @@ class Api::Pept2lcaController < Api::ApiController
   # param[names]: "true" or "false", Include the lineage names
   def pept2lca
     @result = pept2lca_helper
+    filter_input_order
   end
 end

app/controllers/api/pept2prot_controller.rb

@@ -1,7 +1,6 @@
 class Api::Pept2protController < Api::ApiController
   before_action :set_cors_headers
   before_action :set_params
-  # before_action :set_sequences
   before_action :search_input
 
   # Returns a list of Uniprot entries containing a given tryptic peptide
@@ -45,15 +44,13 @@ def pept2prot
         end
     end
 
-    @result = {}
+    @result = Hash.new { |h, k| h[k] = Set.new }
     @sequences.each do |sequence|
       sequence["uniprot_accession_numbers"].each do |uniprot_id|
-        @result[sequence["sequence"]] = uniprot_info[uniprot_id]
+        @result[sequence["sequence"]] << uniprot_info[uniprot_id]
       end
     end
 
     filter_input_order
-
-    respond_with(@result)
   end
 end

app/controllers/api/pept2taxa_controller.rb

@@ -1,49 +1,18 @@
 class Api::Pept2taxaController < Api::ApiController
+  include TaxonomyHelper
+
   before_action :set_cors_headers
   before_action :set_params
   before_action :set_query
+  before_action :search_input
 
   # Returns a list of taxa retrieved from the Uniprot entries containing a given tryptic peptide
   # param[input]: Array, required, List of input peptides
   # param[equate_il]: "true" or "false", Indicate if you want to equate I and L
   # param[extra]: "true" or "false", Include lineage
   # param[names]: "true" or "false", Include the lineage names
   def pept2taxa
-    @result = {}
-    lookup = Hash.new { |h, k| h[k] = Set.new }
-    ids = Set.new
-
-    seqid2seq = {}
-    Sequence.where(sequence: @input).select(:id, :sequence).each do |seq|
-      seqid2seq[seq[:id]] = seq[:sequence]
-      @result[seq[:sequence]] = Set.new
-    end
-
-    rel_name = @equate_il ? :sequence_id : :original_sequence_id
-    Peptide.where(rel_name => seqid2seq.keys).select(:id, rel_name, :uniprot_entry_id).find_in_batches do |items|
-      uniprot2seqids = Hash.new { |h, k| h[k] = [] }
-      items.each { |i| uniprot2seqids[i[:uniprot_entry_id]] << i[rel_name] }
-
-      UniprotEntry.where(id: uniprot2seqids.keys).select(:id, :taxon_id).each do |entry|
-        uniprot2seqids[entry[:id]].each do |seqid|
-          sequence = seqid2seq[seqid]
-          lookup[entry[:taxon_id]] << sequence
-          ids << entry[:taxon_id]
-        end
-      end
-    end
-
-    ids.delete nil
-    ids = ids.to_a.sort
-
-    @query.where(id: ids).find_in_batches do |group|
-      group.each do |t|
-        lookup[t.id].each { |s| @result[s] << t }
-      end
-    end
-
+    @result = pept2taxa_helper
     filter_input_order
-
-    respond_with(@result)
   end
 end

app/controllers/api/peptinfo_controller.rb

@@ -5,6 +5,7 @@ class Api::PeptinfoController < Api::ApiController
   before_action :set_cors_headers
   before_action :set_params
   before_action :set_query
+  before_action :search_input
 
   # Returns both the lca, ec and go information for a given tryptic peptide
   # param[input]: Array, required, List of input peptides
@@ -20,8 +21,6 @@ def peptinfo
     interpro_result = pept2interpro_helper
 
     @input_order.each do |seq|
-      seq_index = @equate_il ? seq.tr('I', 'L') : seq
-
       next unless go_result.key? seq_index
 
       @result[seq_index] = {
@@ -32,7 +31,5 @@ def peptinfo
         lca: lca_result[seq_index]
       }
     end
-
-    respond_with(@result)
   end
 end

app/controllers/api/protinfo_controller.rb

@@ -20,7 +20,5 @@ def protinfo
           }
         end
       end
-
-    respond_with(@result)
   end
 end

app/helpers/taxonomy_helper.rb

@@ -21,4 +21,27 @@ def pept2lca_helper
 
     output
   end
+
+  def pept2taxa_helper
+    output = Hash.new { |h, k| h[k] = Set.new }
+    lookup = Hash.new { |h, k| h[k] = Set.new }
+    ids = []
+
+    @sequences.each do |seq|
+      seq["taxa"].each do |taxon|
+        ids.append taxon
+        lookup[taxon] << seq["sequence"]
+      end
+    end
+
+    ids = ids.uniq.compact.sort
+
+    @query.where(id: ids).find_in_batches do |group|
+      group.each do |t|
+        lookup[t.id].each { |s| output[s] << t }
+      end
+    end
+
+    output
+  end
 end

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

@@ -1,13 +1,15 @@
-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]
+@input_order.map do |peptide|
+  json.array! @result[peptide].map do |prot|
+    json.peptide peptide
+    json.uniprot_id prot[:uniprot_id]
+    json.protein_name prot[:name]
+    json.taxon_id prot[:taxon_id]
+    json.protein prot[:protein]
+    if @extra_info
+      json.taxon_name prot[:taxon][:name]
+      json.ec_references prot[:ec_cross_references]
+      json.go_references prot[:go_cross_references]
+      json.interpro_references prot[:interpro_cross_references]
+    end
   end
 end