Merge pull request #20 from unipept/feature/protinfo-endpoint

Fetch taxonomic and functional information for UniProt id's

app/controllers/api/api_controller.rb

@@ -3,8 +3,8 @@
 class Api::ApiController < ApplicationController
   respond_to :json
 
-  before_action :set_headers, only: %i[pept2taxa pept2lca pept2prot pept2funct pept2ec pept2go pept2interpro peptinfo taxa2lca taxonomy taxa2tree]
-  before_action :set_params, only: %i[pept2taxa pept2lca pept2prot pept2funct pept2ec pept2go pept2interpro peptinfo taxa2lca taxonomy taxa2tree]
+  before_action :set_headers, only: %i[pept2taxa pept2lca pept2prot pept2funct pept2ec pept2go pept2interpro peptinfo taxa2lca taxonomy taxa2tree protinfo]
+  before_action :set_params, only: %i[pept2taxa pept2lca pept2prot pept2funct pept2ec pept2go pept2interpro peptinfo taxa2lca taxonomy taxa2tree protinfo]
   before_action :set_query, only: %i[pept2taxa pept2lca peptinfo taxonomy]
   before_action :set_sequences, only: %i[pept2prot]
 
@@ -270,6 +270,28 @@ def taxonomy
     respond_with(@result)
   end
 
+  # Returns the taxonomic and functional information for given uniprot id's
+  # param[input]: Array, required, List of input uniprot id's
+  def protinfo
+    @result = {}
+
+    UniprotEntry
+      .includes(:taxon, :ec_numbers, :go_terms, :interpro_entries)
+      .where(uniprot_accession_number: @input_order)
+      .find_in_batches do |batch|
+        batch.each do |uniprot_id|
+          @result[uniprot_id.uniprot_accession_number] = {
+            taxon: uniprot_id.taxon,
+            ec: uniprot_id.ec_numbers.map { |ec| { ec_number: ec.code } },
+            go: uniprot_id.go_terms.map { |go| { go_term: go.code } },
+            ipr: uniprot_id.interpro_entries.map { |interpro| { code: interpro.code } }
+          }
+        end
+      end
+
+    respond_with(@result)
+  end
+
   private
 
   # log all api calls to stathat

app/views/api/api/protinfo.json.jbuilder

@@ -0,0 +1,13 @@
+json.array! @input_order do |uniprot_id|
+  if @result.key? uniprot_id
+    json.protein uniprot_id
+
+    json.ec @result[uniprot_id][:ec]
+    json.go @result[uniprot_id][:go]
+    json.ipr @result[uniprot_id][:ipr]
+
+    json.taxon_id @result[uniprot_id][:taxon][:id]
+    json.taxon_name @result[uniprot_id][:taxon][:name]
+    json.taxon_rank @result[uniprot_id][:taxon][:rank]
+  end
+end

config/routes.rb

@@ -33,6 +33,7 @@
     match 'peptinfo' => 'api#peptinfo', via: %i[get post]
     match 'taxonomy' => 'api#taxonomy', via: %i[get post]
     match 'messages' => 'api#messages', via: %i[get post]
+    match 'protinfo' => 'api#protinfo', via: %i[get post]
   end
 
   namespace :api, path: 'api/v2' do
@@ -49,5 +50,6 @@
     match 'peptinfo' => 'api#peptinfo', via: %i[get post]
     match 'taxonomy' => 'api#taxonomy', via: %i[get post]
     match 'messages' => 'api#messages', via: %i[get post]
+    match 'protinfo' => 'api#protinfo', via: %i[get post]
   end
 end