wip(smrtlink): adds initial v25_1 revio config

config/pacbio_smrt_link_versions.yml

@@ -44,6 +44,10 @@ default: &default
       name: v13_1_revio
       active: true
       default: false
+    v25_1_revio:
+      name: v25_1_revio
+      active: true
+      default: false
   options:
     ccs_analysis_output:
       key: ccs_analysis_output
@@ -218,6 +222,7 @@ default: &default
         - v12_revio
         - v13_revio
         - v13_1_revio
+        - v25_1_revio
     include_base_kinetics:
       key: include_base_kinetics
       label: "Include Base Kinetics"
@@ -232,6 +237,7 @@ default: &default
         - v12_revio
         - v13_revio
         - v13_1_revio
+        - v25_1_revio
     library_concentration:
       key: library_concentration
       label: "Library Concentration (pM)"
@@ -243,6 +249,7 @@ default: &default
         - v12_revio
         - v13_revio
         - v13_1_revio
+        - v25_1_revio
     polymerase_kit:
       key: polymerase_kit
       label: "Polymerase Kit"
@@ -254,6 +261,7 @@ default: &default
         - v12_revio
         - v13_revio
         - v13_1_revio
+        - v25_1_revio
     library_type:
       key: library_type
       label: "Library Type"
@@ -268,6 +276,7 @@ default: &default
         - v12_revio
         - v13_revio
         - v13_1_revio
+        - v25_1_revio
 
 development: *default
 test: *default

config/pipelines/pacbio.yml

@@ -340,6 +340,8 @@ default: &default
 
       v13_1_revio: *v13_revio
 
+      v25_1_revio: *v13_revio
+
     # For any EMQ message creation, the section and key name must be same as schema subject in bunny.yml
     volume_tracking:
     # The number suffix '1' is used to identify the schema version of message (created by the

spec/exchanges/run_csv/pacbio_sample_sheet_spec.rb

@@ -10,6 +10,7 @@
   before do
     # Create a default smrt link version
     create(:pacbio_smrt_link_version, name: 'v13_revio', default: true)
+    create(:pacbio_smrt_link_version, name: 'v25_1_revio')
   end
 
   describe '#payload' do
@@ -270,5 +271,260 @@
         end
       end
     end
+
+    context 'v25_1_revio' do
+      before do
+        run.smrt_link_version = Pacbio::SmrtLinkVersion.find_by(name: 'v25_1_revio')
+      end
+
+      it 'must return a string' do
+        expect(sample_sheet_string.class).to eq String
+      end
+
+      it 'must have the three required sections' do
+        expect(sample_sheet_string).to include('[Run Settings]')
+        expect(sample_sheet_string).to include('[SMRT Cell Settings]')
+        expect(sample_sheet_string).to include('[Samples]')
+      end
+
+      it 'must have the three required sections in the correct order' do
+        run_settings_index = sample_sheet_string.index('[Run Settings]')
+        cell_settings_index = sample_sheet_string.index('[SMRT Cell Settings]')
+        samples_index = sample_sheet_string.index('[Samples]')
+
+        expect(run_settings_index).to be < cell_settings_index
+        expect(cell_settings_index).to be < samples_index
+      end
+
+      it 'must have the correct run settings' do
+        expect(parsed_sample_sheet['Run Settings']).to eq(
+          {
+            'Instrument Type' => 'Revio',
+            'Run Name' => run.name,
+            'Run Comments' => run.comments,
+            'Plate 1' => run.plates[0].sequencing_kit_box_barcode,
+            'Plate 2' => run.plates[1].sequencing_kit_box_barcode,
+            'CSV Version' => '1'
+          }
+        )
+      end
+
+      it 'must have the cells used listed on the same line as the section header' do
+        # get the line from sample_sheet_string containing [SMRT Cell Settings]
+        smrt_cell_settings_line = sample_sheet_string.lines.find { |line| line.include?('[SMRT Cell Settings]') }.strip
+        expect(smrt_cell_settings_line).to eq('[SMRT Cell Settings],1_A01,1_B01,2_A01')
+      end
+
+      it 'must have the correct SMRT cell settings' do
+        smrt_cell_settings = parsed_sample_sheet['SMRT Cell Settings']
+
+        # create a hash of plate_well_name => well for easy comparison
+        plate_wells = run.plates.flat_map(&:wells).each_with_object({}) do |well, hash|
+          plate_well_name = "#{well.plate.plate_number}_#{well.position_leading_zero}"
+          hash[plate_well_name] = well
+        end
+
+        # confirm that the wells are as expected
+        plate_well_names = plate_wells.keys
+        expect(plate_well_names).to contain_exactly('1_A01', '1_B01', '2_A01')
+        expect(smrt_cell_settings.keys).to match_array(plate_well_names)
+
+        plate_well_names.each do |plate_well_name|
+          well = plate_wells[plate_well_name]
+          expected_settings = {
+            # for all wells
+            'Well Name' => well.used_aliquots.first.source.tube.barcode,
+            'Library Type' => 'Standard',
+            'Movie Acquisition Time (hours)' => well.movie_acquisition_time.to_s,
+            'Insert Size (bp)' => well.insert_size.to_s,
+            'Assign Data To Project' => '1',
+            'Library Concentration (pM)' => well.library_concentration.to_s,
+            'Include Base Kinetics' => well.include_base_kinetics.downcase == 'true', # is a string
+            'Polymerase Kit' => well.polymerase_kit,
+            'Use Adaptive Loading' => false,
+            'Consensus Mode' => 'molecule',
+
+            # specific to tagged wells
+            'Bio Sample Name' => '',
+            'Sample is indexed' => true,
+            'Indexes' => well.barcode_set,
+            'Same Barcodes on Both Ends of Sequence' => true
+          }
+
+          expect(smrt_cell_settings[plate_well_name]).to eq(expected_settings)
+        end
+      end
+
+      context 'when the libraries are tagged' do
+        let(:well1) do
+          create(
+            :pacbio_well,
+            pre_extension_time: 2,
+            generate_hifi: 'In SMRT Link',
+            ccs_analysis_output: 'Yes',
+            row: 'A',
+            column: 1
+          )
+        end
+        let(:well2) do
+          create(
+            :pacbio_well,
+            pre_extension_time: 2,
+            generate_hifi: 'In SMRT Link',
+            ccs_analysis_output: 'No',
+            row: 'A',
+            column: 1
+          )
+        end
+        let(:well3) do
+          create(
+            :pacbio_well,
+            pre_extension_time: 2,
+            generate_hifi: 'In SMRT Link',
+            ccs_analysis_output: 'No',
+            row: 'B',
+            column: 1
+          )
+        end
+        let(:plate1_wells)   { [well1] }
+        let(:plate2_wells)   { [well2, well3] }
+        let(:plate1)  { build(:pacbio_plate, wells: plate1_wells, plate_number: 1) }
+        let(:plate2)  { build(:pacbio_plate, wells: plate2_wells, plate_number: 2) }
+        let(:run)     { create(:pacbio_revio_run, plates: [plate1, plate2]) }
+
+        it 'must have the correct headers' do
+          # get the line from sample_sheet_string after the one containing [Samples]
+          sample_sheet_lines = sample_sheet_string.lines
+          samples_section_index = sample_sheet_lines.find_index { |line| line.include?('[Samples]') }
+          headers_line = sample_sheet_lines[samples_section_index + 1]
+          headers = headers_line.strip.split(',')
+          expected_headers = ['Bio Sample Name', 'Plate Well', 'Adapter', 'Adapter2']
+          expect(headers).to eq(expected_headers)
+        end
+
+        it 'must have the correct sample rows' do
+          # 5 pools per well
+          sample_data_1 = parsed_sample_sheet['Samples'][0]
+          sample_data_2 = parsed_sample_sheet['Samples'][1 * 5]
+          sample_data_3 = parsed_sample_sheet['Samples'][2 * 5]
+
+          #  iterate through the samples under test
+          sample_expectations = [
+            [sample_data_1, well1],
+            [sample_data_2, well2],
+            [sample_data_3, well3]
+          ]
+          sample_expectations.each do |sample_data, well|
+            expect(sample_data).to eq(
+              {
+                'Bio Sample Name' => well.base_used_aliquots.first.bio_sample_name,
+                'Plate Well' => well.plate_well_position,
+                'Adapter' => well.base_used_aliquots.first.tag.group_id,
+                'Adapter2' => well.base_used_aliquots.first.tag.group_id
+              }
+            )
+          end
+        end
+      end
+
+      context 'when the libraries are untagged' do
+        let(:pool1)   { create_list(:pacbio_pool, 1, :untagged) }
+        let(:pool2)   { create_list(:pacbio_pool, 1, :untagged) }
+        let(:pool3)   { create_list(:pacbio_pool, 1, :untagged) }
+        let(:well1) do
+          create(
+            :pacbio_well,
+            pre_extension_time: 2,
+            generate_hifi: 'In SMRT Link',
+            ccs_analysis_output: 'Yes',
+            pools: pool1, # untagged pool
+            row: 'A',
+            column: 1
+          )
+        end
+        let(:well2) do
+          create(
+            :pacbio_well,
+            pre_extension_time: 2,
+            generate_hifi: 'In SMRT Link',
+            ccs_analysis_output: 'No',
+            pools: pool2, # untagged pool
+            row: 'A',
+            column: 1
+          )
+        end
+        let(:well3) do
+          create(
+            :pacbio_well,
+            pre_extension_time: 2,
+            generate_hifi: 'In SMRT Link',
+            ccs_analysis_output: 'No',
+            pools: pool3, # untagged pool
+            row: 'B',
+            column: 1
+          )
+        end
+        let(:plate1_wells)   { [well1] }
+        let(:plate2_wells)   { [well2, well3] }
+        let(:plate1)  { build(:pacbio_plate, wells: plate1_wells, plate_number: 1) }
+        let(:plate2)  { build(:pacbio_plate, wells: plate2_wells, plate_number: 2) }
+        let(:run)     { create(:pacbio_revio_run, plates: [plate1, plate2]) }
+
+        it 'must have the correct headers' do
+          # get the line from sample_sheet_string after the one containing [Samples]
+          sample_sheet_lines = sample_sheet_string.lines
+          samples_section_index = sample_sheet_lines.find_index { |line| line.include?('[Samples]') }
+          headers_line = sample_sheet_lines[samples_section_index + 1]
+          headers = headers_line.strip.split(',')
+          expected_headers = ['Bio Sample Name', 'Plate Well', 'Adapter', 'Adapter2']
+          expect(headers).to eq(expected_headers)
+        end
+
+        it 'must have the wells added to the SMRT Cell Settings section' do
+          smrt_cell_settings = parsed_sample_sheet['SMRT Cell Settings']
+
+          # create a hash of plate_well_name => well for easy comparison
+          plate_wells = run.plates.flat_map(&:wells).each_with_object({}) do |well, hash|
+            plate_well_name = "#{well.plate.plate_number}_#{well.position_leading_zero}"
+            hash[plate_well_name] = well
+          end
+
+          # confirm that the wells are as expected
+          plate_well_names = plate_wells.keys
+          expect(plate_well_names).to contain_exactly('1_A01', '2_A01', '2_B01')
+          expect(smrt_cell_settings.keys).to match_array(plate_well_names)
+
+          #  iterate through the wells under test
+          plate_well_names.each do |plate_well_name|
+            well_data = smrt_cell_settings[plate_well_name]
+            well = plate_wells[plate_well_name]
+
+            expect(well_data).to eq(
+              # for all wells
+              'Well Name' => well.used_aliquots.first.source.tube.barcode,
+              'Library Type' => 'Standard',
+              'Movie Acquisition Time (hours)' => well.movie_acquisition_time.to_s,
+              'Insert Size (bp)' => well.insert_size.to_s,
+              'Assign Data To Project' => '1',
+              'Library Concentration (pM)' => well.library_concentration.to_s,
+              'Include Base Kinetics' => well.include_base_kinetics.downcase == 'true', # is a string
+              'Polymerase Kit' => well.polymerase_kit,
+              'Use Adaptive Loading' => false,
+              'Consensus Mode' => 'molecule',
+
+              # specific to untagged wells
+              'Bio Sample Name' => well.bio_sample_name,
+              'Sample is indexed' => false,
+              'Indexes' => '', # well.barcode_set
+              'Same Barcodes on Both Ends of Sequence' => '' # well.same_barcodes_on_both_ends_of_sequence.to_s
+            )
+          end
+        end
+
+        it 'must not have sample rows' do
+          expect(parsed_sample_sheet['Samples']).to be_empty
+        end
+      end
+    end
   end
 end