Y24-375 scRNA - refactored shared constants to move them into a central config file

app/models/validators/required_number_of_cells_validator.rb

@@ -14,7 +14,7 @@ module Validators
   # for the user to configure the option after seeing the warning and download
   # the driver file again to use the correct value.
   class RequiredNumberOfCellsValidator < ActiveModel::Validator
-    STUDIES_WITHOUT_REQUIRED_NUMBER_OF_CELLS =
+    STUDIES_WITHOUT_REQUIRED_NUMBER_OF_CELLS_PER_SAMPLE_PER_POOL =
       'The required number of cells is not configured for all studies ' \
         'going into pooling on this plate. If not provided, the default ' \
         'value %s will be used for the samples of the following studies: ' \
@@ -33,16 +33,16 @@ class RequiredNumberOfCellsValidator < ActiveModel::Validator
     def validate(presenter)
       return unless presenter.labware.state == 'pending'
 
-      studies = source_studies_without_config(presenter, study_required_number_of_cells_key(presenter))
+      study_required_number_of_cells_per_sample_in_pool_key =
+        Rails.application.config.scrna_config[:study_required_number_of_cells_per_sample_in_pool_key]
+      default_value = Rails.application.config.scrna_config[:required_number_of_cells_per_sample_in_pool]
+
+      studies = source_studies_without_config(presenter, study_required_number_of_cells_per_sample_in_pool_key)
       return if studies.empty?
 
       formatted_string =
-        format(
-          STUDIES_WITHOUT_REQUIRED_NUMBER_OF_CELLS,
-          default_required_number_of_cells(presenter),
-          studies.join(', ')
-        )
-      presenter.errors.add(:required_number_of_cells, formatted_string)
+        format(STUDIES_WITHOUT_REQUIRED_NUMBER_OF_CELLS_PER_SAMPLE_PER_POOL, default_value, studies.join(', '))
+      presenter.errors.add(:required_number_of_cells_per_sample_in_pool, formatted_string)
     end
 
     private
@@ -65,21 +65,5 @@ def source_studies_without_config(presenter, key)
         .map(&:name)
         .uniq
     end
-
-    # Retrieves the default required number of cells from the purpose config.
-    #
-    # @return [Integer] the default required number of cells
-    # :reek:UtilityFunction { public_methods_only: true }
-    def default_required_number_of_cells(presenter)
-      Settings.purposes[presenter.labware.purpose.uuid][:presenter_class][:args][:default_required_number_of_cells]
-    end
-
-    # Retrieves the poly_metadatum key for the study-specific required number of cells.
-    #
-    # @return [String] the poly_metadatum key
-    # :reek:UtilityFunction { public_methods_only: true }
-    def study_required_number_of_cells_key(presenter)
-      Settings.purposes[presenter.labware.purpose.uuid][:presenter_class][:args][:study_required_number_of_cells_key]
-    end
   end
 end

app/sequencescape/sequencescape/api/v2/shared/has_poly_metadata.rb

@@ -15,6 +15,9 @@ module HasPolyMetadata
     # @param key [String] the key of the PolyMetadatum to find
     # @return [PolyMetadatum, nil] the found PolyMetadatum object, or nil if no match is found
     def poly_metadatum_by_key(key)
+      # if no poly_metadata exist for this model instance, or no key value is passed, return nil
+      return nil if poly_metadata.blank? || key.blank?
+
       poly_metadata.find { |pm| pm.key == key }
     end
   end

app/sequencescape/sequencescape/api/v2/well.rb

@@ -2,6 +2,7 @@
 
 class Sequencescape::Api::V2::Well < Sequencescape::Api::V2::Base # rubocop:todo Style/Documentation
   include Sequencescape::Api::V2::Shared::HasRequests
+  include Sequencescape::Api::V2::Shared::HasPolyMetadata
   has_many :qc_results
   has_many :requests_as_source, class_name: 'Sequencescape::Api::V2::Request'
   has_many :requests_as_target, class_name: 'Sequencescape::Api::V2::Request'

app/views/exports/hamilton_gem_x_5p_chip_loading.csv.erb

@@ -1,9 +1,9 @@
 <%# Driver file for Hamilton robot to transfer from LRC PBMC Pools (or Input) to LRC GEM x 5P chip %>
 <%= CSV.generate_line [
-    'Workflow', 
+    'Workflow',
     @workflow
-  ], 
-  row_sep: '' 
+  ],
+  row_sep: ''
 %>
 <%= CSV.generate_line [], row_sep: "" %>
 <%= CSV.generate_line [
@@ -19,14 +19,16 @@
                       row_sep: ""
 %>
 <%
-  # Configuration specific to this export
+  # Constants from config/initializers/scrna_config.rb
+  scrna_config = Rails.application.config.scrna_config
 
-  required_number_of_cells = 30000 
-  wastage_factor = 0.95238 # accounting for wastage of material when transferring between labware
-  chip_loading_concentration = 2400 
-  desired_number_of_cells_per_chip_well = 90000
-  desired_sample_volume = 37.5 # microlitres
-  volume_taken_for_cell_counting = 10.0 # microlitres
+  # fetch constants from scrna_config for use in calculations on source wells below
+  required_number_of_cells_per_sample_in_pool = scrna_config[:required_number_of_cells_per_sample_in_pool]
+  wastage_factor = scrna_config[:wastage_factor]
+  desired_chip_loading_concentration = scrna_config[:desired_chip_loading_concentration]
+  desired_chip_loading_volume = scrna_config[:desired_chip_loading_volume]
+  volume_taken_for_cell_counting = scrna_config[:volume_taken_for_cell_counting]
+  number_of_cells_per_chip_well_key = scrna_config[:number_of_cells_per_chip_well_key]
 
   # Destination wells are mapped to numbers: A1 -> 17, A2 -> 18, ..., A8 -> 24
   mapping = (1..8).each_with_object({}) { |i, hash| hash["A#{i}"] = (16 + i).to_s }
@@ -35,11 +37,33 @@
   ancestral_plate_wells = @ancestor_plate.wells.index_by(&:location)
   rows_array = []
   each_source_metadata_for_plate(@plate) do |src_barcode, src_location, dest_well|
-    number_of_samples =  ancestral_plate_wells[src_location].aliquots.length
-    resuspension_volume = (number_of_samples * required_number_of_cells * wastage_factor).to_f / chip_loading_concentration
+    src_well = ancestral_plate_wells[src_location]
+    number_of_samples =  src_well.aliquots.length
+
+    # Use the source well's number_of_cells_per_chip_well if available, otherwise error.
+    # Value should have been calculated and stored on the pool well polymetadata.
+    well_poly_metadatum = src_well.poly_metadatum_by_key(number_of_cells_per_chip_well_key)
+
+    # raise error if polymetadata is missing
+    raise "Missing poly metadata for number of cells per chip well for #{src_barcode} #{src_location}, " \
+            'cannot generate driver file' unless well_poly_metadatum
+
+    # extract value from the polymetadata
+    number_of_cells_per_chip_well = well_poly_metadatum&.value.to_f.nonzero?
+
+    # calculations
+
+    # calculate volume we believe is remaining in the source well
+    resuspension_volume = (number_of_samples * required_number_of_cells_per_sample_in_pool * wastage_factor).to_f / desired_chip_loading_concentration
     source_well_volume = resuspension_volume - volume_taken_for_cell_counting
-    sample_volume = desired_number_of_cells_per_chip_well.to_f/chip_loading_concentration 
-    pbs_volume = desired_sample_volume - sample_volume
+
+    # calculate volume of the source sample well to take to load onto the chip
+    sample_volume = number_of_cells_per_chip_well/desired_chip_loading_concentration
+
+    # calculate pbs buffer volume with which to top up the chip loading volume
+    pbs_volume = desired_chip_loading_volume - sample_volume
+
+    # add row to driver file output csv
     rows_array << [
       src_barcode,
       src_location,

app/views/exports/hamilton_lrc_pbmc_defrost_pbs_to_lrc_pbmc_pools.csv.erb

@@ -17,19 +17,15 @@
   row_sep: ''
 %>
 <%
-  # Configuration specific to this export
-
-  args = Settings.purposes[@plate.purpose.uuid][:presenter_class][:args]
-  default_required_number_of_cells = args[:default_required_number_of_cells]
-  study_required_number_of_cells_key = args[:study_required_number_of_cells_key]
-
-  maximum_sample_volume = 60.0  # microlitres
-  minimum_sample_volume = 5.0  # microlitres
-  resuspension_volume_per_sample = 2.2  # microlitres
-  minimum_resuspension_volume = 10.0  # microlitres
-  millilitres_to_microlitres = 1_000.0
-  wastage_accountment = 0.95238 # Accounting for wastage of material during transfer between labware
-  desired_chip_loading_concentration = 2400
+  # Constants from config/initializers/scrna_config.rb
+  scrna_config = Rails.application.config.scrna_config
+  required_number_of_cells_per_sample_in_pool = scrna_config[:required_number_of_cells_per_sample_in_pool]
+  maximum_sample_volume = scrna_config[:maximum_sample_volume]
+  minimum_sample_volume = scrna_config[:minimum_sample_volume]
+  minimum_resuspension_volume = scrna_config[:minimum_resuspension_volume]
+  millilitres_to_microlitres = scrna_config[:millilitres_to_microlitres]
+  wastage_factor = scrna_config[:wastage_factor]
+  desired_chip_loading_concentration = scrna_config[:desired_chip_loading_concentration]
 
   # Make a mapping { src_barcode => { src_location => src_well } }
 
@@ -45,15 +41,8 @@
     cell_count = src_well.latest_total_cell_count  # cells / millilitres
     next if cell_count.nil?
 
-    # Use the study's required number of cells if available, otherwise use the default
-
-    poly_metadatum = src_well.aliquots.first.study.poly_metadatum_by_key(study_required_number_of_cells_key)
-    study_required_number_of_cells = poly_metadatum&.value.to_i.nonzero?
-    required_number_of_cells = study_required_number_of_cells || default_required_number_of_cells
-
     # Calculate the sample volume required for the number of cells
-
-    required_volume = (millilitres_to_microlitres * required_number_of_cells / cell_count.value.to_f).clamp(minimum_sample_volume, maximum_sample_volume)
+    required_volume = (millilitres_to_microlitres * required_number_of_cells_per_sample_in_pool / cell_count.value.to_f).clamp(minimum_sample_volume, maximum_sample_volume)
 
     transfer_request_data << [
       src_barcode,
@@ -62,7 +51,7 @@
       dest_well.location,
       '%0.1f' % required_volume,
       # We pass in the required number of cells so that we can calculate the resuspension volume later
-      required_number_of_cells
+      required_number_of_cells_per_sample_in_pool
     ]
   end
 
@@ -72,8 +61,8 @@
 
   rows_array = transfer_request_data.map do |data|
     samples_in_pool = samples_by_dest_well[data[3]].count
-    required_number_of_cells = data[5]
-    resuspension_volume = [(samples_in_pool * required_number_of_cells * wastage_accountment) / desired_chip_loading_concentration, minimum_resuspension_volume].max
+    required_number_of_cells_per_sample_in_pool = data[5]
+    resuspension_volume = [(samples_in_pool * required_number_of_cells_per_sample_in_pool * wastage_factor) / desired_chip_loading_concentration, minimum_resuspension_volume].max
     # Replace required number of cells with resuspension volume
     data[5] = '%0.1f' % resuspension_volume
     data

app/views/exports/hamilton_lrc_pbmc_pools_to_cellaca_count.csv.erb

@@ -17,20 +17,21 @@
 <%
   rows_array = []
 
-  # Reading constants
-  args = Settings.purposes[@plate.purpose.uuid][:presenter_class][:args]
-  required_number_of_cells = args[:required_number_of_cells]
-  wastage_factor = args[:wastage_factor]
-  desired_chip_loading_concentration = args[:desired_chip_loading_concentration]
+  # Constants from config/initializers/scrna_config.rb
+  scrna_config = Rails.application.config.scrna_config
+  required_number_of_cells_per_sample_in_pool = scrna_config[:required_number_of_cells_per_sample_in_pool]
+  wastage_factor = scrna_config[:wastage_factor]
+  desired_chip_loading_concentration = scrna_config[:desired_chip_loading_concentration]
 
   filtered_wells = @plate.wells_in_columns.reject { |well| well.empty? || well.failed? }
-  filtered_wells.each do | well |
-    samples_in_pool = well.aliquots.size
-    source_well_volume = (samples_in_pool * required_number_of_cells * wastage_factor) / desired_chip_loading_concentration
+  filtered_wells.each do | src_well |
+    samples_in_pool = src_well.aliquots.size
+
+    source_well_volume = (samples_in_pool * required_number_of_cells_per_sample_in_pool * wastage_factor) / desired_chip_loading_concentration
     row = [
       @plate.labware_barcode.human,
-      well.location,
-      well.name,
+      src_well.location,
+      src_well.name,
       '%0.1f' % source_well_volume
     ]
     rows_array << row

config/initializers/scrna_config.rb

@@ -0,0 +1,31 @@
+# frozen_string_literal: true
+
+# Stores constants used in pooling and chip loading calculations for samples in the scRNA Core pipeline.
+Rails.application.config.scrna_config = {
+  # Maximum volume to take into the pools plate for each sample (in microlitres)
+  maximum_sample_volume: 60.0,
+  # Minimum volume to take into the pools plate for each sample (in microlitres)
+  minimum_sample_volume: 5.0,
+  # Minimum volume required for resuspension in microlitres
+  minimum_resuspension_volume: 10.0,
+  # Conversion factor from millilitres to microlitres
+  millilitres_to_microlitres: 1_000.0,
+  # Number of cells required for each sample going into the pool
+  required_number_of_cells_per_sample_in_pool: 30_000,
+  # Factor accounting for wastage of material when transferring between labware
+  wastage_factor: 0.95,
+  # Desired concentration of cells per microlitre for chip loading
+  desired_chip_loading_concentration: 2400,
+  # Desired volume in the chip well (in microlitres)
+  desired_chip_loading_volume: 37.5,
+  # Volume taken for cell counting in microlitres
+  volume_taken_for_cell_counting: 10.0,
+  # Key for the required number of cells metadata stored on Study (in poly_metadata)
+  study_required_number_of_cells_per_sample_in_pool_key: 'scrna_core_pbmc_donor_pooling_required_number_of_cells',
+  # Default viability threshold when passing/failing samples (in percent)
+  viability_default_threshold: 65,
+  # Default total cell count threshold when passing/failing samples
+  total_cell_count_default_threshold: 50_000,
+  # Key for the number of cells per chip well metadata stored on pool wells (in poly_metadata)
+  number_of_cells_per_chip_well_key: 'scrna_core_pbmc_donor_pooling_number_of_cells_per_chip_well'
+}.freeze

config/purposes/scrna_core_cdna_prep.yml

@@ -32,11 +32,11 @@ LRC PBMC Defrost PBS:
   :qc_thresholds:
     viability:
       units: '%'
-      default_threshold: 65
+      default_threshold: <%= Rails.application.config.scrna_config[:viability_default_threshold] %>
     total_cell_count:
       name: Total cell count
       units: 'cells/ml'
-      default_threshold: 500000
+      default_threshold: <%= Rails.application.config.scrna_config[:total_cell_count_default_threshold] %>
       decimal_places: 0
   :stock_plate: false
   :input_plate: false
@@ -48,23 +48,14 @@ LRC PBMC Pools:
   :qc_thresholds:
     viability:
       units: '%'
-      default_threshold: 65
+      default_threshold: <%= Rails.application.config.scrna_config[:viability_default_threshold] %>
     total_cell_count:
       name: Total cell count
       units: 'cells/ml'
-      default_threshold: 500000
+      default_threshold: <%= Rails.application.config.scrna_config[:total_cell_count_default_threshold] %>
       decimal_places: 0
   :presenter_class:
     name: Presenters::DonorPoolingPlatePresenter
-    args:
-      # The default number of cells to calculate the required volumes.
-      default_required_number_of_cells: 30000
-      # poly_metadatum key for study specific required number of cells.
-      study_required_number_of_cells_key: scrna_core_pbmc_donor_pooling_required_number_of_cells
-      # Constants used to calculate source well volume
-      required_number_of_cells: 30_000
-      wastage_factor: 0.95238
-      desired_chip_loading_concentration: 2_400
   :creator_class:
     name: LabwareCreators::DonorPoolingPlate
     args:

spec/factories/well_factories.rb

@@ -164,6 +164,24 @@
         well._cached_relationship(:transfer_requests_as_target) { evaluator.transfer_requests_as_target || [] }
       end
     end
+
+    factory :v2_well_with_polymetadata do
+      transient { poly_metadata { [] } }
+
+      after(:build) do |well, evaluator|
+        # initialise the poly_metadata array
+        well.poly_metadata = []
+
+        # add each polymetadatum to the well
+        evaluator.poly_metadata.each do |pm|
+          # set the relationship between the polymetadatum and the well
+          pm.relationships.metadatable = well
+
+          # link the polymetadatum to the well
+          well.poly_metadata.push(pm)
+        end
+      end
+    end
   end
 
   # API V1 collection of wells, used mainly for setting up the well association on v1 plates