DPL-947 dna control barcode v12 sequel i ie

app/models/concerns/sample_sheet.rb

@@ -6,11 +6,17 @@
 module SampleSheet
   # Provides run helper methods for sample sheet generation
   module Run
-    # Returns a list of wells associated with the plate in column order
-    # Example: [<Well position:'A1'>, <Well position:'A2'>, <Well position:'B1'>]) =>
-    #          [<Well position:'A1'>, <Well position:'B1'>, <Well position:'A2'>]
+    # Returns a list of wells associated with all plates which are sorted by plate first and
+    # then by wells in column order
+    # Example: ([<Plate plate_number:1>
+    #             [<Well position:'A1'>, <Well position:'A2'>,<Well position:'B1'>]<Plate>
+    #           <Plate plate_number:2>
+    #             [<Well position:'A3'>, <Well position:'A4'>,<Well position:'B3'>]<Plate>]) =>
+    #       [<Well position:'A1'>, <Well position:'B1'>, <Well position:'A2'>,<Well position:'A3'>
+    #        <Well position:'A3'>,<Well position:'B3'>,<Well position:'A4'>],
     def sorted_wells
-      wells.sort_by { |well| [well.column.to_i, well.row] }
+      sorted_plates = plates.sort_by(&:plate_number)
+      sorted_plates.flat_map { |plate| plate.wells.sort_by { |well| [well.column.to_i, well.row] } }
     end
   end
 

app/validators/required_attributes_validator.rb

@@ -1,14 +1,16 @@
 # frozen_string_literal: true
 
 # Validator for required attributes
-# Validates the presence of required attributes
+# Validates the presence of required attributes and versions
 class RequiredAttributesValidator < ActiveModel::Validator
-  attr_reader :required_attributes
+  attr_reader :required_attributes, :versions
 
   # @param [Hash] options
   # @option options [Array] :required_attributes
   def initialize(options)
     super
+
+    @versions = options[:versions]
     @required_attributes = options[:required_attributes]
   end
 
@@ -24,8 +26,14 @@ def validate(record)
   # @param [ActiveRecord::Base] record
   # @param [Symbol] required_attribute
   def validate_required_attribute(record, required_attribute)
-    return if record.send(required_attribute).present?
+    # If versions are specified, check that the record's smrt_link_version version
+    # is included in the list
+    if versions.present? && versions.exclude?(record.smrt_link_version.name)
+      nil
+    else
+      return if record.send(required_attribute).present?
 
-    record.errors.add(required_attribute, "can't be blank")
+      record.errors.add(required_attribute, "can't be blank")
+    end
   end
 end

config/application.rb

@@ -58,6 +58,7 @@ class Application < Rails::Application
 
     # RabbitMQ config
     config.bunny = config_for(:bunny)
+
     config.pacbio_instrument_types = config_for(:pacbio_instrument_types)
 
     # Pacbio default request cost code

config/feature_flags.yml

@@ -1,4 +1,5 @@
 # Add feature flags to this file, example:
 # dpl202_enable_angry_cat_feature: When enabled this will add an angry cat to all pages that will try to catch the mouse pointer
 # The key should be lowecase and snake case, and prefixes with the issue number to allow easy identification
+
 {}

config/pacbio_instrument_types.yml

@@ -16,7 +16,12 @@ default: &default
               attribute: :plates
               minimum: 1
               maximum: 1
-          # TODO: fix this to have separate behaviour for v11 and v12 (see commit 05bfe764a8eafe)
+          required_attributes:
+            options:
+              versions:
+                - v12_sequel_iie
+              required_attributes:
+                - :dna_control_complex_box_barcode
       plates:
         children: :wells
         # we want to validate each plate and plate
@@ -73,31 +78,31 @@ default: &default
             options:
               exclude_marked_for_destruction: true
               valid_positions:
-              - A1
-              - B1
-              - C1
-              - D1
+                - A1
+                - B1
+                - C1
+                - D1
           well_combinations:
             invalid_combinations:
-              - [A1,D1]
-              - [A1,C1]
-              - [B1,D1]
-              - [A1,C1,D1]
-              - [A1,B1,D1]
-              - [D1,B1]
+              - [A1, D1]
+              - [A1, C1]
+              - [B1, D1]
+              - [A1, C1, D1]
+              - [A1, B1, D1]
+              - [D1, B1]
             options:
               exclude_marked_for_destruction: true
               valid_combinations:
-              - [A1]
-              - [A1,B1]
-              - [A1,B1,C1]
-              - [A1,B1,C1,D1]
-              - [B1]
-              - [B1,C1]
-              - [B1,C1,D1]
-              - [C1]
-              - [C1,D1]
-              - [D1]
+                - [A1]
+                - [A1, B1]
+                - [A1, B1, C1]
+                - [A1, B1, C1, D1]
+                - [B1]
+                - [B1, C1]
+                - [B1, C1, D1]
+                - [C1]
+                - [C1, D1]
+                - [D1]
           sequencing_kit_box_barcode:
             options:
               exclude_marked_for_destruction: true

config/pacbio_smrt_link_versions.yml

@@ -16,22 +16,22 @@ default: &default
       default: false
     v11:
       name: v11
-      active: true
-      default: true
+      active: false
+      default: false
     v12_revio:
       name: v12_revio
       active: true
       default: false
     v12_sequel_iie:
       name: v12_sequel_iie
       active: true
-      default: false
+      default: true
 
   options:
     ccs_analysis_output:
       key: ccs_analysis_output
-      label: 'CCS Analysis Output'
-      default_value: 'Yes'
+      label: "CCS Analysis Output"
+      default_value: "Yes"
       validations:
         presence: {}
         inclusion:
@@ -42,20 +42,20 @@ default: &default
         - v10
     generate_hifi:
       key: generate_hifi
-      label: 'Generate HiFi'
-      default_value: On Instrument      
+      label: "Generate HiFi"
+      default_value: On Instrument
       validations:
         presence: {}
         inclusion:
           in: *generate
       data_type: list
       select_options: *select_generate
-      versions: 
+      versions:
         - v10
     ccs_analysis_output_include_kinetics_information:
       key: ccs_analysis_output_include_kinetics_information
-      label: 'Include Kinetics Information'
-      default_value: 'Yes'
+      label: "Include Kinetics Information"
+      default_value: "Yes"
       validations:
         presence: {}
         inclusion:
@@ -67,8 +67,8 @@ default: &default
         - v12_sequel_iie
     ccs_analysis_output_include_low_quality_reads:
       key: ccs_analysis_output_include_low_quality_reads
-      label: 'Include Low Quality Reads'
-      default_value: 'Yes'
+      label: "Include Low Quality Reads"
+      default_value: "Yes"
       validations:
         presence: {}
         inclusion:
@@ -80,8 +80,8 @@ default: &default
         - v12_sequel_iie
     include_fivemc_calls_in_cpg_motifs:
       key: include_fivemc_calls_in_cpg_motifs
-      label: 'Include 5mC Calls In CpG Motifs'
-      default_value: 'Yes'
+      label: "Include 5mC Calls In CpG Motifs"
+      default_value: "Yes"
       validations:
         presence: {}
         inclusion:
@@ -93,8 +93,8 @@ default: &default
         - v12_sequel_iie
     demultiplex_barcodes:
       key: demultiplex_barcodes
-      label: 'Demultiplex Barcodes'
-      default_value: 'In SMRT Link'
+      label: "Demultiplex Barcodes"
+      default_value: "In SMRT Link"
       validations:
         presence: {}
         inclusion:
@@ -106,7 +106,7 @@ default: &default
         - v12_sequel_iie
     on_plate_loading_concentration:
       key: on_plate_loading_concentration
-      label: 'On Plate Loading Concentration (mP)'
+      label: "On Plate Loading Concentration (mP)"
       default_value:
       validations:
         presence: {}
@@ -117,7 +117,7 @@ default: &default
         - v12_sequel_iie
     binding_kit_box_barcode:
       key: binding_kit_box_barcode
-      label: 'Binding Kit Box Barcode'
+      label: "Binding Kit Box Barcode"
       default_value:
       validations:
         presence: {}
@@ -128,8 +128,8 @@ default: &default
         - v12_sequel_iie
     pre_extension_time:
       key: pre_extension_time
-      label: 'Pre-extension time'
-      default_value: '2'
+      label: "Pre-extension time"
+      default_value: "2"
       validations:
         numericality:
           allow_blank: true
@@ -141,8 +141,8 @@ default: &default
         - v12_sequel_iie
     loading_target_p1_plus_p2:
       key: loading_target_p1_plus_p2
-      label: 'Loading Target (P1 + P2)'
-      default_value: '0.85'
+      label: "Loading Target (P1 + P2)"
+      default_value: "0.85"
       validations:
         numericality:
           allow_blank: true
@@ -155,7 +155,7 @@ default: &default
         - v12_sequel_iie
     movie_time:
       key: movie_time
-      label: 'Movie Time (hrs)'
+      label: "Movie Time (hrs)"
       default_value:
       validations:
         presence: {}
@@ -170,7 +170,7 @@ default: &default
         - v12_sequel_iie
     movie_acquisition_time:
       key: movie_acquisition_time
-      label: 'Movie Acquisition Time (hrs)'
+      label: "Movie Acquisition Time (hrs)"
       default_value:
       validations:
         presence: {}
@@ -183,8 +183,8 @@ default: &default
         - v12_revio
     include_base_kinetics:
       key: include_base_kinetics
-      label: 'Include Base Kinetics'
-      default_value: 'True'
+      label: "Include Base Kinetics"
+      default_value: "True"
       validations:
         presence: {}
         inclusion:
@@ -195,7 +195,7 @@ default: &default
         - v12_revio
     library_concentration:
       key: library_concentration
-      label: 'Library Concentration (pM)'
+      label: "Library Concentration (pM)"
       default_value:
       validations:
         presence: {}
@@ -204,16 +204,14 @@ default: &default
         - v12_revio
     polymerase_kit:
       key: polymerase_kit
-      label: 'Polymerase Kit'
+      label: "Polymerase Kit"
       default_value:
       validations:
         presence: {}
       data_type: string
       versions:
         - v12_revio
 
-
-
 development: *default
 test: *default
 production: *default

config/pipelines/pacbio.yml

@@ -535,6 +535,7 @@ default: &default
           - Binding Kit Box Barcode
           - Sequencing Kit Box Barcode
           - On-Plate Loading Concentration (pM)
+          - DNA Control Complex Box Barcode
           - Run Comments
           - Sample is Barcoded
           - Barcode Name
@@ -586,6 +587,9 @@ default: &default
             On-Plate Loading Concentration (pM):
               type: :model
               value: on_plate_loading_concentration
+            DNA Control Complex Box Barcode:
+              type: :model
+              value: plate.run.dna_control_complex_box_barcode
             Run Comments:
               type: :model
               value: plate.run.comments

lib/tasks/pacbio_data.rake

@@ -61,8 +61,10 @@ namespace :pacbio_data do
 
     print '-> Finding Pacbio SMRT Link versions...'
     v11 = Pacbio::SmrtLinkVersion.find_by!(name: 'v11')
+    v11.update(default: false, active: false)
     v12_revio = Pacbio::SmrtLinkVersion.find_by!(name: 'v12_revio')
     v12_sequel_iie = Pacbio::SmrtLinkVersion.find_by!(name: 'v12_sequel_iie')
+    v12_sequel_iie.update(default: true, active: true)
     print COMPLETED
 
     puts '-> Creating pacbio runs:'
@@ -166,6 +168,7 @@ namespace :pacbio_data do
         name: "RUN-#{v12_sequel_iie.name}-#{pool_name}-#{total_plate}_plate",
         system_name: Pacbio::Run.system_names['Sequel IIe'],
         smrt_link_version: v12_sequel_iie,
+        dna_control_complex_box_barcode: "DCCB_#{barcode}",
         plates: (1..total_plate).map do |plate_number|
           Pacbio::Plate.new(
             sequencing_kit_box_barcode: '130429101826100021624',

spec/exchanges/run_csv/pacbio_sample_sheet_spec.rb

@@ -245,6 +245,7 @@
               well.binding_kit_box_barcode,
               well.plate.sequencing_kit_box_barcode,
               well.on_plate_loading_concentration.to_s,
+              well.plate.run.dna_control_complex_box_barcode,
               well.plate.run.comments,
               well.show_row_per_sample?.to_s,
               nil, # barcode name - does not apply
@@ -287,6 +288,7 @@
               nil,
               nil,
               nil,
+              nil,
               well.libraries.first.barcode_name,
               nil,
               nil,
@@ -348,6 +350,7 @@
               well.binding_kit_box_barcode,
               well.plate.sequencing_kit_box_barcode,
               well.on_plate_loading_concentration.to_s,
+              well.plate.run.dna_control_complex_box_barcode,
               well.plate.run.comments,
               well.sample_is_barcoded.to_s,
               nil, # barcode name - does not apply

spec/lib/tasks/pacbio_data.rake_spec.rb

@@ -9,9 +9,9 @@
 RSpec.describe 'RakeTasks' do
   before do
     Pacbio::SmrtLinkVersion.find_by(name: 'v10') || create(:pacbio_smrt_link_version, name: 'v10')
-    Pacbio::SmrtLinkVersion.find_by(name: 'v11') || create(:pacbio_smrt_link_version, name: 'v11', default: true)
+    Pacbio::SmrtLinkVersion.find_by(name: 'v11') || create(:pacbio_smrt_link_version, name: 'v11')
     Pacbio::SmrtLinkVersion.find_by(name: 'v12_revio') || create(:pacbio_smrt_link_version, name: 'v12_revio')
-    Pacbio::SmrtLinkVersion.find_by(name: 'v12_sequel_iie') || create(:pacbio_smrt_link_version, name: 'v12_sequel_iie')
+    Pacbio::SmrtLinkVersion.find_by(name: 'v12_sequel_iie') || create(:pacbio_smrt_link_version, name: 'v12_sequel_iie', default: true)
   end
 
   describe 'create pacbio runs' do