Merge pull request #1050 from sanger/dpl-745-revio-sample-sheets

DPL-745: Implement 2-plate sample sheets for Revio

.erd.pacbio.erdconfig

@@ -36,7 +36,7 @@ cluster: true
 indirect: false
 
 # Filter to only include listed models in diagram.
-only: ",Pacbio::Run,Pacbio::Well,TagSet"
+only: ",Pacbio::Run,Pacbio::Well,TagSet,Request"
 
 # Recurses into relations specified by --only up to a depth N.
 only_recursion_depth: 3

app/csv_generator/pacbio_sample_sheet.rb

@@ -30,7 +30,7 @@ def generate
   private
 
   def wells
-    run.plates.first.wells
+    run.plates.flat_map(&:wells)
   end
 
   # Returns a list of wells associated with the plate in column order

app/models/pacbio/well.rb

@@ -73,6 +73,18 @@ def summary
       "#{sample_names} #{comment}".strip
     end
 
+    # return the sequencing_kit_box_barcode of this plate if well belongs to plate 1
+    # used for 2-plate sample sheets
+    def sequencing_kit_box_barcode_plate_1
+      plate.plate_number == 1 ? plate.sequencing_kit_box_barcode : nil
+    end
+
+    # return the sequencing_kit_box_barcode of this plate if well belongs to plate 2
+    # used for 2-plate sample sheets
+    def sequencing_kit_box_barcode_plate_2
+      plate.plate_number == 2 ? plate.sequencing_kit_box_barcode : nil
+    end
+
     # collection of all of the requests for a library
     # useful for messaging
     def request_libraries

config/pipelines/pacbio.yml

@@ -73,6 +73,7 @@ default: &default
                   type: :model
                   value: pool.tube.barcode
 
+    # For instructions on structure and syntax, see: 'app/csv_generator/pacbio_sample_sheet.rb'
     sample_sheet:
       v10:
         columns:
@@ -445,14 +446,14 @@ default: &default
               with: :well
           Plate 1:
             type: :model
-            value: plate.sequencing_kit_box_barcode
+            value: sequencing_kit_box_barcode_plate_1
             populate:
               for:
                 - :well
               with: :well
           Plate 2:
-            type: :string
-            value: null
+            type: :model
+            value: sequencing_kit_box_barcode_plate_2
             populate:
               for:
                 - :well

spec/csv_generator/pacbio_sample_sheet_spec.rb

@@ -2,6 +2,8 @@
 
 require 'rails_helper'
 
+# See additional sample sheet specs at 'spec/pipelines/pacbio/sample_sheet_spec.rb'
+
 RSpec.describe PacbioSampleSheet, type: :model do
   describe '#generate' do
     subject(:csv_string) { csv.generate }
@@ -288,7 +290,6 @@
           ]
           sample_expectations.each do |sample_data, well|
             expect(sample_data).to eq([
-
               '',
               '',
               'false', # well.collection?
@@ -402,5 +403,181 @@
         end
       end
     end
+
+    context 'v12_revio' do
+      let(:smrt_link_version) { create(:pacbio_smrt_link_version, name: 'v12_revio', default: true) }
+
+      context 'when the libraries are tagged' do
+        let(:well1) do
+          create(
+            :pacbio_well_with_pools,
+            pre_extension_time: 2,
+            generate_hifi: 'In SMRT Link',
+            ccs_analysis_output: 'Yes'
+          )
+        end
+        let(:well2) do
+          create(
+            :pacbio_well_with_pools,
+            pre_extension_time: 2,
+            generate_hifi: 'In SMRT Link',
+            ccs_analysis_output: 'No'
+          )
+        end
+
+        it 'must return a csv string' do
+          expect(csv_string.class).to eq String
+        end
+
+        it 'must have the correct headers' do
+          headers = parsed_csv[0]
+
+          expected_headers = Pipelines.pacbio.sample_sheet.columns.map(&:first)
+          expect(headers).to eq(expected_headers)
+        end
+
+        it 'must have the correct well header rows' do
+          well_data_1 = parsed_csv[1]
+          well_data_2 = parsed_csv[7]
+          #  iterate through the wells under test
+          well_expectations = [
+            [well_data_1, well1],
+            [well_data_2, well2]
+          ]
+          well_expectations.each do |well_data, well|
+            expect(well_data).to eq([
+              'Standard', # library type
+              '1', # reagent plate
+              well.plate.run.sequencing_kit_box_barcode,
+              nil, # plate 2: sequencing_kit_box_barcode
+              well.plate.run.name,
+              well.plate.run.system_name,
+              well.plate.run.comments,
+              'true', # well.collection?
+              well.position_leading_zero,
+              well.pool_barcode,
+              well.movie_acquisition_time.to_s,
+              well.include_base_kinetics.to_s,
+              well.library_concentration.to_s,
+              well.polymerase_kit,
+              well.automation_parameters,
+              well.barcode_set,
+              '', # barcode name - does not apply
+              '' # sample name - does not apply
+            ])
+          end
+        end
+
+        it 'must have the correct sample rows' do
+          # Note the increment in the parsed_csv index
+          sample_data_1 = parsed_csv[2]
+          sample_data_2 = parsed_csv[8]
+
+          #  iterate through the samples under test
+          sample_expectations = [
+            [sample_data_1, well1],
+            [sample_data_2, well2]
+          ]
+          sample_expectations.each do |sample_data, well|
+            expect(sample_data).to eq([
+              '',
+              '1', # reagent plate
+              '',
+              '',
+              '',
+              '',
+              '',
+              'false', # well.collection?
+              well.position,
+              '',
+              '',
+              '',
+              '',
+              '',
+              '',
+              '',
+              well.libraries.first.barcode_name,
+              well.libraries.first.request.sample_name
+            ])
+          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(:well1)   do
+          create(:pacbio_well, pre_extension_time: 2, generate_hifi: 'Do Not Generate',
+                               ccs_analysis_output: 'Yes', pools: pool1)
+        end
+        let(:well2) do
+          create(:pacbio_well, generate_hifi: 'On Instrument', ccs_analysis_output: 'No',
+                               pools: pool2)
+        end
+        let(:plate) { create(:pacbio_plate, wells: [well1, well2]) }
+
+        it 'must return a csv string' do
+          expect(csv_string).to be_a String
+        end
+
+        it 'must have the correct headers' do
+          headers = parsed_csv[0]
+
+          expected_headers = Pipelines.pacbio.sample_sheet.columns.map(&:first)
+          expect(headers).to eq(expected_headers)
+        end
+
+        it 'must have the correct well header rows' do
+          well_data_1 = parsed_csv[1]
+          well_data_2 = parsed_csv[2]
+          #  iterate through the wells under test
+          well_expectations = [
+            [well_data_1, well1],
+            [well_data_2, well2]
+          ]
+          well_expectations.each do |well_data, well|
+            expect(well_data).to eq([
+              'Standard', # library type
+              '1', # reagent plate
+              well.plate.run.sequencing_kit_box_barcode,
+              nil, # plate 2: sequencing_kit_box_barcode
+              well.plate.run.name,
+              well.plate.run.system_name,
+              well.plate.run.comments,
+              'true', # well.collection?
+              well.position_leading_zero,
+              well.pool_barcode,
+              well.movie_acquisition_time.to_s,
+              well.include_base_kinetics.to_s,
+              well.library_concentration.to_s,
+              well.polymerase_kit,
+              well.automation_parameters,
+              well.barcode_set,
+              '', # barcode name - does not apply
+              well.find_sample_name
+            ])
+          end
+        end
+
+        it 'must not have sample rows' do
+          expect(parsed_csv.size).to eq 3
+        end
+      end
+
+      context 'with lots of wells in unpredictable orders' 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)   { create(:pacbio_well, pools: pool1, row: 'A', column: 10) }
+        let(:well2)   { create(:pacbio_well, pools: pool2, row: 'A', column: 5) }
+        let(:well3)   { create(:pacbio_well, pools: pool3, row: 'B', column: 1) }
+        let(:plate)   { create(:pacbio_plate, wells: [well1, well2, well3]) }
+
+        it 'sorts the wells by column' do
+          sorted_well_positions = parsed_csv[1..].pluck(8)
+          expect(sorted_well_positions).to eq(%w[B01 A05 A10])
+        end
+      end
+    end
   end
 end

spec/factories/pacbio/runs.rb

@@ -24,12 +24,17 @@ def build_wells_by_position(positions)
       end
 
       system_name { 'Revio' }
-      plates { [build(:pacbio_plate, wells: build_wells_by_position(well_positions_plate_1)), build(:pacbio_plate, wells: build_wells_by_position(well_positions_plate_2))] }
+      plates do
+        [
+          build(:pacbio_plate, plate_number: 1, wells: build_wells_by_position(well_positions_plate_1)),
+          build(:pacbio_plate, plate_number: 2, wells: build_wells_by_position(well_positions_plate_2))
+        ]
+      end
     end
 
     factory :pacbio_sequel_run do
       system_name { 'Sequel IIe' }
-      plates { build_list(:pacbio_plate, 1, wells: [build(:pacbio_well)]) }
+      plates { build_list(:pacbio_plate, 1, plate_number: 1, wells: [build(:pacbio_well)]) }
     end
   end
 end