Y26-680 Automated buffer addition for cherrypicking

app/frontend/entrypoints/cherrypick_strategies.js

@@ -1,3 +1,15 @@
+// Toggle buffer_volume_for_empty_wells input based on automatic_buffer_addition checkbox
+document.addEventListener("DOMContentLoaded", function () {
+  const bufferInput = document.getElementById("buffer_volume_for_empty_wells");
+  const autoBufferCheckbox = document.getElementById("automatic_buffer_addition");
+  if (bufferInput && autoBufferCheckbox) {
+    function toggleBufferInput() {
+      bufferInput.disabled = !autoBufferCheckbox.checked;
+    }
+    autoBufferCheckbox.addEventListener("change", toggleBufferInput);
+    toggleBufferInput(); // Set initial state
+  }
+});
 // apply a border highlight to the card, based on the cherrypick strategy selected
 // this is admittedly a gratuitous addition to the user experience, but it's a nice touch
 

app/frontend/entrypoints/cherrypick_strategies.test.js

@@ -0,0 +1,33 @@
+// cherrypick_strategies.test.js
+// Tests for cherrypick_strategies.js buffer input toggle logic
+
+/* global describe, it, expect, beforeEach, jest */
+/* @jest-environment jsdom */
+
+describe("Buffer input toggle", () => {
+  let bufferInput, autoBufferCheckbox;
+
+  beforeEach(() => {
+    document.body.innerHTML = `
+      <input id="buffer_volume_for_empty_wells" type="number" />
+      <input id="automatic_buffer_addition" type="checkbox" />
+    `;
+    // Re-require the script to attach event listeners
+    jest.resetModules();
+    require("./cherrypick_strategies.js");
+    bufferInput = document.getElementById("buffer_volume_for_empty_wells");
+    autoBufferCheckbox = document.getElementById("automatic_buffer_addition");
+  });
+
+  it("enables and disables buffer input when checkbox is toggled", () => {
+    // register the change event handler
+    // bufferInput is initially disabled because autoBufferCheckbox is unchecked
+    document.dispatchEvent(new Event("DOMContentLoaded"));
+
+    autoBufferCheckbox.click(); // unchecked to checked
+    expect(bufferInput.disabled).toBe(false);
+
+    autoBufferCheckbox.click(); // checked to unchecked
+    expect(bufferInput.disabled).toBe(true);
+  });
+});

app/models/batch.rb

@@ -16,6 +16,9 @@ class Batch < ApplicationRecord # rubocop:todo Metrics/ClassLength
   include ::Batch::PipelineBehaviour
   include ::Batch::StateMachineBehaviour
   include UnderRepWellCommentsToBroadcast
+  # Added for storing buffer_volume_for_empty_wells option on Cherrypick batches.
+  include HasPolyMetadata
+  include ::Batch::PolyMetadataBehaviour
   extend EventfulRecord
 
   # The three states of {Batch} Also @see {SequencingQcBatch}
@@ -481,18 +484,16 @@ def swap(current_user, batch_info = {}) # rubocop:todo Metrics/CyclomaticComplex
       # Finally record the fact that the batch was swapped
       batch_request_left.batch.lab_events.create!(
         description: 'Lane swap',
-        # rubocop:todo Layout/LineLength
         message:
-          "Lane #{batch_request_right.position} moved to #{batch_request_left.batch_id} lane #{batch_request_left.position}",
-        # rubocop:enable Layout/LineLength
+          "Lane #{batch_request_right.position} moved to #{batch_request_left.batch_id} " \
+          "lane #{batch_request_left.position}",
         user_id: current_user.id
       )
       batch_request_right.batch.lab_events.create!(
         description: 'Lane swap',
-        # rubocop:todo Layout/LineLength
         message:
-          "Lane #{batch_request_left.position} moved to #{batch_request_right.batch_id} lane #{batch_request_right.position}",
-        # rubocop:enable Layout/LineLength
+          "Lane #{batch_request_left.position} moved to #{batch_request_right.batch_id} " \
+          "lane #{batch_request_right.position}",
         user_id: current_user.id
       )
     end

app/models/batch/poly_metadata_behaviour.rb

@@ -0,0 +1,16 @@
+# frozen_string_literal: true
+module Batch::PolyMetadataBehaviour
+  # Returns whether the Cherrypick automatic_buffer_addition option is enabled
+  # @return [Boolean] whether the automatic_buffer_addition option is enabled
+  def automatic_buffer_addition?
+    # tests 1 and on to cover both visible and hidden option in the forms of successive pages
+    %w[1 on].include?(get_poly_metadata(:automatic_buffer_addition))
+  end
+
+  # Returns the Cherrypick buffer_volume_for_empty_wells option value if
+  # automatic_buffer_addition is enabled, nil otherwise.
+  # @return [Float, nil] the buffer_volume_for_empty_wells value
+  def buffer_volume_for_empty_wells
+    get_poly_metadata(:buffer_volume_for_empty_wells).to_f if automatic_buffer_addition?
+  end
+end

app/models/cherrypick/task/buffer_volume_for_empty_wells_option.rb

@@ -0,0 +1,39 @@
+# frozen_string_literal: true
+
+module Cherrypick::Task::BufferVolumeForEmptyWellsOption
+  def create_buffer_volume_for_empty_wells_option(params)
+    return unless @batch
+
+    key = :automatic_buffer_addition
+
+    # The checkbox value is either '1', 'on' or nil if not checked.
+    # Store a consistent value
+    value = %w[1 on].include?(params[key]) ? '1' : params[key]
+    @batch.set_poly_metadata(key, value)
+
+    if value == '1'
+      record_buffer_addition_volume(params)
+    else
+      clear_buffer_addition_volume(params)
+    end
+  end
+
+  private
+
+  def record_buffer_addition_volume(params)
+    key = :buffer_volume_for_empty_wells
+
+    unless valid_float_param?(params[key])
+      raise Cherrypick::VolumeError,
+            "Invalid buffer volume for empty wells: #{params[key]}"
+    end
+    @batch.set_poly_metadata(key, params[key])
+  end
+
+  # Most likely it's not set, but if it is, clear it to avoid confusion.
+  def clear_buffer_addition_volume(_params)
+    return if @batch.get_poly_metadata(:buffer_volume_for_empty_wells).blank?
+
+    @batch.set_poly_metadata(:buffer_volume_for_empty_wells, nil)
+  end
+end

app/models/cherrypick/task/pick_helpers.rb

@@ -5,6 +5,7 @@ def self.included(base)
       include Cherrypick::Task::PickByNanoGramsPerMicroLitre
       include Cherrypick::Task::PickByNanoGrams
       include Cherrypick::Task::PickByMicroLitre
+      include Cherrypick::Task::BufferVolumeForEmptyWellsOption
     end
   end
 

app/models/concerns/has_poly_metadata.rb

@@ -0,0 +1,38 @@
+# frozen_string_literal: true
+
+module HasPolyMetadata
+  extend ActiveSupport::Concern
+
+  included do
+    has_many :poly_metadata, as: :metadatable, dependent: :destroy, inverse_of: :metadatable
+  end
+
+  # Sets a PolyMetaDatum for the given key and value.
+  # If value is present, it will create or update the PolyMetaDatum with the
+  # given key and value, otherwise it will destroy the PolyMetaDatum with the
+  # given key if that exists.
+  # NB: this is because PolyMetaDatum validations prevent key duplication and blank values,
+  # although there are no such DB constraints.
+  # @param key [String] The key of the PolyMetaDatum to set.
+  # @param value [String] The value of the PolyMetaDatum to set. If nil or empty, the PolyMetaDatum will be destroyed.
+  # @return [void]
+  def set_poly_metadata(key, value)
+    record = poly_metadata.find_by(key:)
+    if value.present?
+      if record
+        record.update!(value:)
+      else
+        poly_metadata.create!(key:, value:)
+      end
+    else
+      record&.destroy!
+    end
+  end
+
+  # Returns the value of the PolyMetaDatum with the given key.
+  # @param key [String] The key of the PolyMetaDatum to retrieve.
+  # @return [String, nil] The value of the PolyMetaDatum, or nil if it does not exist.
+  def get_poly_metadata(key)
+    poly_metadata.find_by(key:)&.value
+  end
+end

app/models/map.rb

@@ -52,7 +52,9 @@ def self.description_to_horizontal_plate_position(well_description, plate_size)
       (width * split_well[:row]) + split_well[:col]
     end
 
-    def self.description_to_vertical_plate_position(well_description, plate_size)
+    # e.g. B5 returns 34 for a 96 well plate
+    # So 4 columns of 8 rows each, plus 2 for the B row
+    def self.well_description_to_by_column_map_index(well_description, plate_size)
       return nil unless Map.valid_well_description_and_plate_size?(well_description, plate_size)
 
       split_well = Map.split_well_description(well_description)
@@ -62,7 +64,9 @@ def self.description_to_vertical_plate_position(well_description, plate_size)
       (length * (split_well[:col] - 1)) + split_well[:row] + 1
     end
 
-    def self.horizontal_plate_position_to_description(well_position, plate_size)
+    # e.g. 23 returns B11 for a 96 well plate
+    # So 1 full row of 12, plus 11, to give row B, column 11
+    def self.by_row_map_index_to_well_description(well_position, plate_size)
       return nil unless Map.valid_plate_position_and_plate_size?(well_position, plate_size)
 
       width = plate_width(plate_size)
@@ -71,7 +75,9 @@ def self.horizontal_plate_position_to_description(well_position, plate_size)
       horizontal_position_to_description(well_position, width)
     end
 
-    def self.vertical_plate_position_to_description(well_position, plate_size)
+    # e.g. 23 returns G3 for a 96 well plate
+    # So 2 full columns of 8, plus 7, to give row G, column 3
+    def self.by_column_map_index_to_well_description(well_position, plate_size)
       return nil unless Map.valid_plate_position_and_plate_size?(well_position, plate_size)
 
       length = plate_length(plate_size)
@@ -96,6 +102,8 @@ def self.plate_length(plate_size)
       PLATE_DIMENSIONS[plate_size].last
     end
 
+    # well number counting by columns, length is the number of rows in the plate
+    # e.g. B5 sends this 34 and 8
     def self.vertical_position_to_description(well_position, length)
       desc_letter = (((well_position - 1) % length) + 65).chr
       desc_number = ((well_position - 1) / length) + 1
@@ -117,7 +125,7 @@ def self.vertical_to_horizontal(well_position, plate_size)
     end
 
     def self.location_from_index(index, size)
-      horizontal_plate_position_to_description(index + 1, size)
+      by_row_map_index_to_well_description(index + 1, size)
     end
 
     class << self

app/models/robot/generator/behaviours/hamilton_default.rb

@@ -37,7 +37,7 @@ def each_mapping(data_object) # rubocop:todo Metrics/AbcSize
       mapping_by_well = Hash.new { |h, i| h[i] = [] }
       plate_details['mapping'].each do |mapping|
         destination_position =
-          Map::Coordinate.description_to_vertical_plate_position(mapping['dst_well'], plate_details['plate_size'])
+          Map::Coordinate.well_description_to_by_column_map_index(mapping['dst_well'], plate_details['plate_size'])
         mapping_by_well[destination_position] << mapping
       end