Merge pull request #5 from unipept/feature/pept2filtered

Add new "pept2filtered" endpoint to the Unipept API

app/controllers/mpa_controller.rb

@@ -24,6 +24,34 @@ def pept2data
     end
   end
 
+  def pept2filtered
+    peptides = params[:peptides] || []
+    # missed = params[:missed] || false
+    taxa_filter_ids = (params[:taxa] || []).map(&:to_i)
+
+    @equate_il = params[:equate_il].nil? ? true : params[:equate_il]
+
+    @sequences = Sequence
+                 .joins(peptides: [:uniprot_entry])
+                 .includes(peptides: [:uniprot_entry])
+                 .where(sequence: peptides)
+                 .where(uniprot_entry: { taxon_id: taxa_filter_ids })
+                 .uniq
+
+    uniprot_ids = @sequences.map { |s| s.peptides.map(&:uniprot_entry_id) }.flatten.uniq
+
+    @go_terms = GoCrossReference
+                .where(uniprot_entry_id: uniprot_ids)
+
+    @ec_numbers = EcCrossReference
+                  .where(uniprot_entry_id: uniprot_ids)
+
+    @ipr_entries = InterproCrossReference
+                   .where(uniprot_entry_id: uniprot_ids)
+
+    @seq_entries = @sequences.map { |s| [s, s.peptides.map(&:uniprot_entry).select { |e| taxa_filter_ids.include? e.taxon_id }] }
+  end
+
   private
 
   def default_format_json

app/models/lineage.rb

@@ -139,6 +139,11 @@ def to_a
     array.map { |x| x.nil? ? '' : x.name }
   end
 
+  def to_a_idx
+    array = ORDER_T.map { |rank| send(rank) }
+    array.map { |x| x.nil? ? nil : x.id }
+  end
+
   def self.ranks
     ORDER
   end

app/views/mpa/pept2filtered.json.jbuilder

@@ -0,0 +1,9 @@
+json.peptides @seq_entries do |seq_entry|
+  json.sequence seq_entry[0].sequence
+  json.taxa seq_entry[1].map(&:taxon_id).uniq
+  json.fa do
+    json.go_terms @go_terms.map(&:go_term_code).uniq
+    json.ec_numbers(@ec_numbers.map(&:ec_number_code).reject(&:empty?).uniq.map { |ec| "EC:#{ec}" })
+    json.interpro_entries(@ipr_entries.map(&:interpro_entry_code).uniq.map { |ipr| ipr.sub('IPR', 'IPR:') })
+  end
+end

config/routes.rb

@@ -10,6 +10,16 @@
     match "metadata", via: [:get, :post], :to => "private_api#metadata"
   end
 
+  scope :mpa, as: 'mpa' do
+    match '/*path', via: [:options], to: 'handle_options#handle_options_request'
+    match 'pept2data', via: %i[get post], to: 'mpa#pept2data'
+    match 'pept2filtered', via: %i[get post], to: 'mpa#pept2filtered'
+  end
+
+  scope :datasets, as: 'datasets' do
+    match 'sampledata', via: [:post], to: 'datasets#sampledata'
+  end
+
   namespace :api, path: 'api/v1' do
     match 'pept2taxa' => "api#pept2taxa", via: %i[get post]
     match 'pept2lca' => "api#pept2lca", via: %i[get post]
@@ -34,18 +44,10 @@
     match 'pept2ec' => 'api#pept2ec', via: %i[get post]
     match 'pept2go' => 'api#pept2go', via: %i[get post]
     match 'pept2interpro' => 'api#pept2interpro', via: %i[get post]
+    match 'pept2gm' => 'api#pept2gm', via: %i[get post]
     match 'taxa2tree' => 'api#taxa2tree', via: %i[get post]
     match 'peptinfo' => 'api#peptinfo', via: %i[get post]
     match 'taxonomy' => 'api#taxonomy', via: %i[get post]
     match 'messages' => 'api#messages', via: %i[get post]
   end
-
-  scope :mpa, as: 'mpa' do
-    match '/*path', via: [:options], to: 'handle_options#handle_options_request'
-    match 'pept2data', via: %i[get post], to: 'mpa#pept2data'
-  end
-
-  scope :datasets, as: 'datasets' do
-    match 'sampledata', via: [:post], to: 'datasets#sampledata'
-  end
 end