Merge pull request #530 from sanger/develop

develop to master for Duplex seq

.rubocop.yml

@@ -190,3 +190,12 @@ Performance/StringInclude: # (new in 1.7)
   Enabled: true
 Performance/Sum: # (new in 1.8)
   Enabled: true
+Layout/BeginEndAlignment: # (new in 0.91)
+  Enabled: true
+Lint/ConstantDefinitionInBlock: # (new in 0.91)
+  Enabled: true
+Lint/IdentityComparison: # (new in 0.91)
+  Enabled: true
+Lint/UselessTimes: # (new in 0.91)
+  Enabled: true
+

Gemfile

@@ -70,5 +70,5 @@ group :development do
   gem 'travis'
   # Ruby jard is a ruby debugger, buit on top of pry and byebug. Invoke it
   # with jard
-  gem 'ruby_jard'
+  # gem 'ruby_jard'
 end

app/assets/javascripts/legacy_scripts_a.js

@@ -20,7 +20,7 @@
       }
     }
 
-    this['concentration-binned-view'] = {
+    this['binned-view'] = {
       activate: function(){
         plateElement.addClass('binning-colours')
       },

app/assets/stylesheets/application.scss

@@ -4,6 +4,6 @@
 @import "bootstrap";
 @import "limber/screen";
 @import "limber/plate";
-@import "limber/concentration-binning";
+@import "limber/binning";
 @import "limber/spinner";
 @import "limber/pipeline-graph";

app/assets/stylesheets/limber/concentration-binning.scss → app/assets/stylesheets/limber/binning.scss

@@ -1,12 +1,12 @@
 /*
- * This css is for the concentration binned plate presenter.
- * In /app/views/aliquots/_concentration_binned_aliquot.html.erb we define two aliquot divs, one specific to the binning
+ * This css is for the binned plate presenter.
+ * In /app/views/aliquots/_binned_aliquot.html.erb we define two aliquot divs, one specific to the binning
  * tab, and the default pooling one for other tabs. This css shows and hides the relevant aliquot div.
  */
 .plate-view {
-  .concentration-binning-id { display: none; }
+  .binning-id { display: none; }
    &.binning-colours {
-    .concentration-binning-id { display: inline; }
+    .binning-id { display: inline; }
   }
 
   .aliquot.aliquot-pooled { display: inline-block; }

app/controllers/exports_controller.rb

@@ -12,50 +12,60 @@ class ExportsController < ApplicationController
   WELL_QC_SAMPLE_INCLUDES = 'wells.qc_results,wells.aliquots.sample.sample_metadata'
   WELL_SRC_ASSET_INCLUDES = 'wells.transfer_requests_as_target.source_asset'
 
-  CSVDetail = Struct.new(:csv, :plate_includes, :workflow) do
+  CSVDetail = Struct.new(:csv, :plate_includes, :workflow, :ancestor_purpose) do
   end
 
   CSV_DETAILS = {
     'concentrations_ngul' =>
-      CSVDetail.new('concentrations_ngul', WELL_QC_INCLUDES, nil),
+      CSVDetail.new('concentrations_ngul', WELL_QC_INCLUDES, nil, nil),
     'concentrations_nm' =>
-      CSVDetail.new('concentrations_nm', WELL_QC_INCLUDES, nil),
+      CSVDetail.new('concentrations_nm', WELL_QC_INCLUDES, nil, nil),
     'duplex_seq_al_lib_concentrations_for_customer' =>
-      CSVDetail.new('duplex_seq_al_lib_concentrations_for_customer', WELL_QC_SAMPLE_INCLUDES, nil),
+      CSVDetail.new('duplex_seq_al_lib_concentrations_for_customer', WELL_QC_SAMPLE_INCLUDES, nil, nil),
+    'duplex_seq_pcr_xp_concentrations_for_custom_pooling' =>
+      CSVDetail.new('duplex_seq_pcr_xp_concentrations_for_custom_pooling', WELL_QC_INCLUDES, nil, 'LDS AL Lib Dil'),
     'hamilton_aggregate_cherrypick' =>
-      CSVDetail.new('hamilton_aggregate_cherrypick', WELL_SRC_ASSET_INCLUDES, 'Cherry Pick'),
+      CSVDetail.new('hamilton_aggregate_cherrypick', WELL_SRC_ASSET_INCLUDES, 'Cherry Pick', nil),
     'hamilton_cherrypick_to_sample_dilution' =>
-      CSVDetail.new('hamilton_fixed_volume_dilutions', WELL_SRC_ASSET_INCLUDES, 'Sample Dilution'),
+      CSVDetail.new('hamilton_fixed_volume_dilutions', WELL_SRC_ASSET_INCLUDES, 'Sample Dilution', nil),
     'hamilton_gex_dil_to_gex_frag_2xp' =>
-      CSVDetail.new('hamilton_plate_stamp', WELL_SRC_ASSET_INCLUDES, '10X Post Repair Double SPRI'),
+      CSVDetail.new('hamilton_plate_stamp', WELL_SRC_ASSET_INCLUDES, '10X Post Repair Double SPRI', nil),
     'hamilton_gex_frag_2xp_to_gex_ligxp' =>
-      CSVDetail.new('hamilton_plate_stamp', WELL_SRC_ASSET_INCLUDES, '10X Post Ligation Single SPRI'),
+      CSVDetail.new('hamilton_plate_stamp', WELL_SRC_ASSET_INCLUDES, '10X Post Ligation Single SPRI', nil),
     'hamilton_cherrypick_to_5p_gex_dilution' =>
-      CSVDetail.new('hamilton_variable_volume_dilutions', WELL_SRC_ASSET_INCLUDES, 'Sample Dilution'),
+      CSVDetail.new('hamilton_variable_volume_dilutions', WELL_SRC_ASSET_INCLUDES, 'Sample Dilution', nil),
     'hamilton_cherrypick_to_bcr_dilution1' =>
-      CSVDetail.new('hamilton_fixed_volume_dilutions', WELL_SRC_ASSET_INCLUDES, 'Sample Dilution'),
+      CSVDetail.new('hamilton_fixed_volume_dilutions', WELL_SRC_ASSET_INCLUDES, 'Sample Dilution', nil),
     'hamilton_lbc_bcr_dil_1_to_lbc_bcr_enrich1_1xspri' =>
-      CSVDetail.new('hamilton_plate_stamp', WELL_SRC_ASSET_INCLUDES, '10X VDJ Post Target Enrichment 1 Single SPRI'),
+      CSVDetail.new('hamilton_plate_stamp', WELL_SRC_ASSET_INCLUDES, '10X VDJ Post Target Enrichment 1 Single SPRI', nil),
     'hamilton_lbc_bcr_enrich1_1xspri_to_lbc_bcr_enrich2_2xspri' =>
-      CSVDetail.new('hamilton_plate_stamp', WELL_SRC_ASSET_INCLUDES, '10X VDJ Post Target Enrichment 2 Double SPRI'),
+      CSVDetail.new('hamilton_plate_stamp', WELL_SRC_ASSET_INCLUDES, '10X VDJ Post Target Enrichment 2 Double SPRI', nil),
     'hamilton_lbc_bcr_enrich2_2xspri_to_lbc_bcr_dil_2' =>
-      CSVDetail.new('hamilton_variable_volume_dilutions', WELL_SRC_ASSET_INCLUDES, 'Sample Dilution'),
+      CSVDetail.new('hamilton_variable_volume_dilutions', WELL_SRC_ASSET_INCLUDES, 'Sample Dilution', nil),
     'hamilton_lbc_bcr_dil_2_to_lbc_bcr_post_lig_1xspri' =>
-      CSVDetail.new('hamilton_plate_stamp', WELL_SRC_ASSET_INCLUDES, '10X VDJ Post Ligation SPRI'),
+      CSVDetail.new('hamilton_plate_stamp', WELL_SRC_ASSET_INCLUDES, '10X VDJ Post Ligation SPRI', nil),
     'hamilton_cherrypick_to_tcr_dilution1' =>
-      CSVDetail.new('hamilton_fixed_volume_dilutions', WELL_SRC_ASSET_INCLUDES, 'Sample Dilution'),
+      CSVDetail.new('hamilton_fixed_volume_dilutions', WELL_SRC_ASSET_INCLUDES, 'Sample Dilution', nil),
     'hamilton_lbc_tcr_dil_1_to_lbc_tcr_enrich1_1xspri' =>
-      CSVDetail.new('hamilton_plate_stamp', WELL_SRC_ASSET_INCLUDES, '10X VDJ Post Target Enrichment 1 Single SPRI'),
+      CSVDetail.new('hamilton_plate_stamp', WELL_SRC_ASSET_INCLUDES, '10X VDJ Post Target Enrichment 1 Single SPRI', nil),
     'hamilton_lbc_tcr_enrich1_1xspri_to_lbc_tcr_enrich2_2xspri' =>
-      CSVDetail.new('hamilton_plate_stamp', WELL_SRC_ASSET_INCLUDES, '10X VDJ Post Target Enrichment 2 Double SPRI'),
+      CSVDetail.new('hamilton_plate_stamp', WELL_SRC_ASSET_INCLUDES, '10X VDJ Post Target Enrichment 2 Double SPRI', nil),
     'hamilton_lbc_tcr_enrich2_2xspri_to_lbc_tcr_dil_2' =>
-      CSVDetail.new('hamilton_variable_volume_dilutions', WELL_SRC_ASSET_INCLUDES, 'Sample Dilution'),
+      CSVDetail.new('hamilton_variable_volume_dilutions', WELL_SRC_ASSET_INCLUDES, 'Sample Dilution', nil),
     'hamilton_lbc_tcr_dil_2_to_lbc_tcr_post_lig_1xspri' =>
-      CSVDetail.new('hamilton_plate_stamp', WELL_SRC_ASSET_INCLUDES, '10X VDJ Post Ligation SPRI')
+      CSVDetail.new('hamilton_plate_stamp', WELL_SRC_ASSET_INCLUDES, '10X VDJ Post Ligation SPRI', nil),
+    'hamilton_lds_al_lib_to_qc1' =>
+      CSVDetail.new('hamilton_plate_stamp_to_qc', WELL_SRC_ASSET_INCLUDES, 'Cherry Pick', nil),
+    'hamilton_lds_al_lib_to_lds_al_lib_dil' =>
+      CSVDetail.new('hamilton_variable_volume_dilutions_with_well_diluents', WELL_SRC_ASSET_INCLUDES, 'Sample Dilution', nil)
   }.freeze
 
   def show
     @workflow = csv_details.workflow
+    if csv_details.ancestor_purpose.present?
+      ancestor_result = @plate.ancestors.where(purpose_name: csv_details.ancestor_purpose).first
+      locate_ancestor(ancestor_result.id) if ancestor_result.present?
+    end
     render csv_details.csv
   end
 
@@ -79,6 +89,10 @@ def locate_labware
                                                                           barcode: params[:limber_plate_id])
   end
 
+  def locate_ancestor(plate_id)
+    @ancestor_plate = Sequencescape::Api::V2.plate_with_custom_includes(include_parameters, id: plate_id)
+  end
+
   def include_parameters
     csv_details.plate_includes || 'wells'
   end

app/models/labware_creators/custom_pooled_tubes/csv_file.rb

@@ -21,6 +21,7 @@ class CustomPooledTubes::CsvFile
 
     def initialize(file)
       @data = CSV.parse(file.read)
+      remove_bom
       @parsed = true
     rescue StandardError => e
       @data = []
@@ -53,6 +54,20 @@ def header_row
 
     private
 
+    # remove byte order marker if present
+    def remove_bom
+      return unless @data.present? && @data[0][0].present?
+
+      # byte order marker will appear at beginning of in first string in @data array
+      s = @data[0][0]
+
+      # NB. had to make byte order marker string mutable here otherwise get frozen string error
+      bom = +"\xEF\xBB\xBF"
+      s_mod = s.gsub!(bom.force_encoding(Encoding::BINARY), '')
+
+      @data[0][0] = s_mod unless s_mod.nil?
+    end
+
     def transfers
       @transfers ||= @data[1..].each_with_index.map do |row_data, index|
         Row.new(header_row, index + 2, row_data)

app/models/labware_creators/pcr_cycles_binned_plate.rb

@@ -0,0 +1,149 @@
+# frozen_string_literal: true
+
+module LabwareCreators
+  # Handles the generation of a plate with wells binned according to the number of
+  # PCR cycles that has been determined by the customer.
+  # Uploads a file supplied by the customer that has a row per each well and
+  # includes Sample Volume, Diluent Volume, PCR Cycles, Sub-Pool and Coverage columns.
+  # Uses the PCR Cycles column to determine the binning arrangement of the wells,
+  # and the Sample Volume and Diluent Volume columns in the well transfers.
+  # Sub-Pool and Coverage need to be stored for a later step downstream in the pipeline,
+  # at the point where custom pooling is performed.
+  # Wells in the bins are applied to the destination by column order.
+  # If there is enough space on the destination plate each new bin will start in a new
+  # column. Otherwise bins will run consecutively without gaps.
+  #
+  #
+  # Source Plate                  Dest Plate
+  # +--+--+--~                    +--+--+--~
+  # |A1| pcr_cycles = 12 (bin 2)  |B1|A1|C1|
+  # +--+--+--~                    +--+--+--~
+  # |B1| pcr_cycles = 15 (bin 1)  |D1|E1|  |
+  # +--+--+--~  +                 +--+--+--~
+  # |C1| pcr_cycles = 10 (bin 3)  |  |G1|  |
+  # +--+--+--~                    +--+--+--~
+  # |D1| pcr_cycles = 15 (bin 1)  |  |  |  |
+  # +--+--+--~                    +--+--+--~
+  # |E1| pcr_cycles = 12 (bin 2)  |  |  |  |
+  # +--+--+--~                    +--+--+--~
+  # |G1| pcr_cycles = 12 (bin 2)  |  |  |  |
+  class PcrCyclesBinnedPlate < StampedPlate
+    include LabwareCreators::CustomPage
+
+    MISSING_WELL_DETAIL = 'is missing a row for well %s, all wells with content must have a row in the uploaded file.'
+    PENDING_WELL = 'contains at least one pending well %s, the plate and all wells in it should be passed before creating the child plate.'
+
+    self.page = 'pcr_cycles_binned_plate'
+    self.attributes += [:file]
+
+    attr_accessor :file
+
+    # delegate method to return well values to csv file handler class
+    delegate :well_details, to: :csv_file
+
+    validates :file, presence: true
+    validates_nested :csv_file, if: :file
+    validate :wells_have_required_information?
+
+    PARENT_PLATE_INCLUDES =
+      'wells.aliquots,wells.qc_results,wells.requests_as_source.request_type,wells.aliquots.request.request_type'
+
+    CHILD_PLATE_INCLUDES =
+      'wells.aliquots'
+
+    def parent
+      @parent ||= Sequencescape::Api::V2.plate_with_custom_includes(PARENT_PLATE_INCLUDES, uuid: parent_uuid)
+    end
+
+    def parent_v1
+      @parent_v1 ||= api.plate.find(parent_uuid)
+    end
+
+    # Configurations from the plate purpose.
+    def csv_file_upload_config
+      @csv_file_upload_config ||= purpose_config.fetch(:csv_file_upload)
+    end
+
+    def dilutions_config
+      @dilutions_config ||= purpose_config.fetch(:dilutions)
+    end
+
+    def save
+      # NB. need the && true!!
+      super && upload_file && true
+    end
+
+    def after_transfer!
+      # called as part of the 'super' call in the 'save' method
+      # retrieve child plate through v2 api, using uuid got through v1 api
+      child_v2 = Sequencescape::Api::V2.plate_with_custom_includes(CHILD_PLATE_INCLUDES, uuid: child.uuid)
+
+      # update fields on each well with various metadata
+      fields_to_update = %w[diluent_volume pcr_cycles submit_for_sequencing sub_pool coverage]
+
+      child_wells_by_location = child_v2.wells.index_by(&:location)
+
+      well_details.each do |parent_location, details|
+        child_position = transfer_hash[parent_location]['dest_locn']
+        child_well = child_wells_by_location[child_position]
+
+        update_well_with_metadata(child_well, details, fields_to_update)
+      end
+    end
+
+    def update_well_with_metadata(well, metadata, fields_to_update)
+      options = fields_to_update.each_with_object({}) { |field, obj| obj[field] = metadata[field] }
+      well.update(options)
+    end
+
+    def wells_have_required_information?
+      filtered_wells.each do |well|
+        next if well.aliquots.empty?
+
+        errors.add(:csv_file, format(MISSING_WELL_DETAIL, well.location)) unless well_details.include? well.location
+        errors.add(:csv_file, format(PENDING_WELL, well.location)) if well.pending?
+      end
+    end
+
+    def dilutions_calculator
+      @dilutions_calculator ||= Utility::PcrCyclesBinningCalculator.new(well_details)
+    end
+
+    private
+
+    # Returns the parent wells selected to be taken forward.
+    def filtered_wells
+      well_filter.filtered.each_with_object([]) do |well_filter_details, wells|
+        wells << well_filter_details[0]
+      end
+    end
+
+    #
+    # Upload the csv file onto the plate via api v1
+    #
+    def upload_file
+      parent_v1.qc_files.create_from_file!(file, 'duplex_seq_customer_file.csv')
+    end
+
+    # Create class that will parse and validate the uploaded file
+    def csv_file
+      @csv_file ||= CsvFile.new(file, csv_file_upload_config, parent.human_barcode)
+    end
+
+    # Override this method in sub-class if required.
+    def request_hash(source_well, child_plate, additional_parameters)
+      {
+        'source_asset' => source_well.uuid,
+        'target_asset' => child_plate.wells.detect do |child_well|
+          child_well.location == transfer_hash[source_well.location]['dest_locn']
+        end&.uuid,
+        'volume' => transfer_hash[source_well.location]['volume'].to_s
+      }.merge(additional_parameters)
+    end
+
+    # Uses the calculator to generate the hash of transfers to be performed on the parent plate
+    def transfer_hash
+      @transfer_hash ||= dilutions_calculator.compute_well_transfers(parent)
+    end
+  end
+end