Ultima sample sheet Barcode_Plate_Num and Index_Barcode_Num indexing

app/controllers/ultima_sample_sheet/sample_sheet_generator.rb

@@ -34,6 +34,14 @@ class Generator # rubocop:disable Metrics/ClassLength
       study_id
     ].freeze
     NUM_COLUMS = SAMPLES_HEADERS.size
+    # The names of the Ultima tag groups are mapped to the index numbers for
+    # the Barcode_Plate_Num column, i.e. 1 or 2. The number is also used for
+    # determining the consistent starting index number for the
+    # Index_Barcode_Num column, i.e. Z0001 or Z097.
+    ULTIMA_TAG_GROUPS = {
+      'Ultima P1' => 1,
+      'Ultima P2' => 2
+    }.freeze
 
     # Initializes the generator with the given batch.
     # @param batch [UltimaSequencingBatch] the batch to generate sample sheets for
@@ -115,7 +123,7 @@ def add_global_section(csv, _request)
     def add_samples_section(csv, request)
       csv << pad(SAMPLES_TITLE)
       csv << pad(SAMPLES_HEADERS)
-      request.asset.aliquots.each do |aliquot|
+      request.asset.aliquots.sort_by(&:id).each do |aliquot|
         csv << [
           sample_id_for(aliquot),
           library_name_for(aliquot),
@@ -187,28 +195,30 @@ def study_id_for(aliquot)
       aliquot.study_id.to_s
     end
 
-    # Returns a mapping of tags to their respective 1-based index numbers.
-    # This sorts the tags by their tag group ID and map ID to ensure consistent ordering.
+    # Returns a mapping of all Ultima tags to their respective 1-based index
+    # numbers. This sorts the tags by their tag group ID and map ID to ensure
+    # consistent ordering. The index numbers run across all Ultima tag groups,
+    # i.e. the index is 1 for the first tag in the first tag group and 97 for
+    # the first tag in the second tag group.
     # @return [Hash{Tag => Integer}] mapping of tags to index numbers
     def tag_index_map
       @tag_index_map ||= begin
-        tags = batch_tag_groups.flat_map { |tg| tg.tags.sort_by(&:map_id) }
+        tags = ultima_tag_groups.flat_map { |tg| tg.tags.sort_by(&:map_id) }
         tags.each_with_index.to_h { |tag, i| [tag, i + 1] }
       end
     end
 
-    # Returns a mapping of tag groups to 1-based index numbers.
+    # Returns a mapping of all Ultima tag groups to 1-based index numbers.
+    # This indexes the tag groups as given in the ULTIMA_TAG_GROUPS hash.
     # @return [Hash{TagGroup => Integer}] mapping of tag groups to index numbers
     def tag_group_index_map
-      @tag_group_index_map ||= batch_tag_groups.each_with_index.to_h { |tg, i| [tg, i + 1] }
+      @tag_group_index_map ||= ultima_tag_groups.index_with { |tg| ULTIMA_TAG_GROUPS[tg.name] }
     end
 
-    # Returns all unique tag groups used in the batch.
-    # This sorts the tag groups by their ID to ensure consistent ordering.
-    # @return [Array<TagGroup>] the tag groups of the batch's requests
-    def batch_tag_groups
-      @batch_tag_groups ||= batch_requests
-        .flat_map { |request| request.asset.aliquots.map { |aliquot| aliquot.tag.tag_group } }.uniq.sort_by(&:id)
+    # Returns all unique tag groups used for Ultima sequencing from database.
+    # @return [Array<TagGroup>] the tag groups used for Ultima sequencing
+    def ultima_tag_groups
+      @ultima_tag_groups ||= TagGroup.where(name: ULTIMA_TAG_GROUPS.keys)
     end
 
     # Returns the requests associated with the batch.

spec/controllers/ultima_sample_sheet/sample_sheet_generator_spec.rb

@@ -45,13 +45,28 @@
 # 6,Sample6,Z0099,TCAG,2,C1,native,6
 #
 # rubocop:enable Layout/LineLength
+# rubocop:disable RSpec/MultipleExpectations, RSpec/ExampleLength
 RSpec.describe UltimaSampleSheet::SampleSheetGenerator do
   # Eagerly create the global section record.
   before { create(:ultima_global) }
 
+  # First oligo sequences for the two tag groups.
+  let(:plate1_first_oligo) { 'CAGCTCGAATGCGAT' }
+  let(:plate2_first_oligo) { 'CAGTCAGTTGCAGAT' }
+
   # Eagerly create tag groups and tags to get consistent IDs.
-  let!(:tag_group1) { create(:tag_group_with_tags, tag_count: 96) }
-  let!(:tag_group2) { create(:tag_group_with_tags, tag_count: 96) }
+  let!(:tag_group1) do
+    create(:tag_group_with_tags, tag_count: 96, name: 'Ultima P1').tap do |tg|
+      # To test Z0001 matching with the oligo sequence.
+      tg.tags.first.update!(oligo: plate1_first_oligo)
+    end
+  end
+  let!(:tag_group2) do
+    create(:tag_group_with_tags, tag_count: 96, name: 'Ultima P2').tap do |tg|
+      # To test Z0097 matching with the oligo sequence.
+      tg.tags.first.update!(oligo: plate2_first_oligo)
+    end
+  end
   let(:tag_groups) { [tag_group1, tag_group2] }
 
   let(:request_type) { create(:ultima_sequencing) }
@@ -210,7 +225,7 @@ def map_description(map_id)
       expect(csv2[1].compact_blank).to eq(["Batch #{batch.id} #{tube2.human_barcode}"]) # Second CSV
     end
 
-    it 'generates global sections' do # rubocop:disable RSpec/MultipleExpectations
+    it 'generates global sections' do
       # Test: Add the following hardcoded values, Application(WGS native gDNA),
       # sequencing_recipe(UG_116cycles_Baseline_1.8.5.2) and analysis_recipe(wgs1)
       expect(csv1[3].compact_blank).to eq(generator.class::GLOBAL_TITLE)
@@ -219,11 +234,24 @@ def map_description(map_id)
       expect(csv1[6].compact_blank).to eq([])
     end
 
-    it 'generates samples sections' do # rubocop:disable RSpec/MultipleExpectations
+    it 'generates samples sections' do
       expect(csv1[7].compact_blank).to eq(generator.class::SAMPLES_TITLE)
       expect(csv1[8].compact_blank).to eq(generator.class::SAMPLES_HEADERS)
       expect(csv1[9..]).to eq(csv1_samples) # First CSV
       expect(csv2[9..]).to eq(csv2_samples) # Second CSV
     end
+
+    it 'matches the z-indexes, oligo sequences, and plate numbers' do
+      # First CSV
+      expect(csv1[9][2]).to eq('Z0001') # Index_Barcode_Num
+      expect(csv1[9][3]).to eq(plate1_first_oligo) # Index_Barcode_Sequence
+      expect(csv1[9][4]).to eq('1') # Barcode_Plate_Num
+
+      # Second CSV
+      expect(csv2[9][2]).to eq('Z0097') # Index_Barcode_Num
+      expect(csv2[9][3]).to eq(plate2_first_oligo) # Index_Barcode_Sequence
+      expect(csv2[9][4]).to eq('2') # Barcode_Plate_Num
+    end
   end
 end
+# rubocop:enable RSpec/MultipleExpectations, RSpec/ExampleLength