diff --git a/app/frontend/entrypoints/cherrypick_strategies.js b/app/frontend/entrypoints/cherrypick_strategies.js
index c0b227d38a..45ed8cddcf 100644
--- a/app/frontend/entrypoints/cherrypick_strategies.js
+++ b/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
diff --git a/app/models/batch.rb b/app/models/batch.rb
index d069a56278..aa156c7abd 100644
--- a/app/models/batch.rb
+++ b/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}
diff --git a/app/models/batch/poly_metadata_behaviour.rb b/app/models/batch/poly_metadata_behaviour.rb
new file mode 100644
index 0000000000..b23dfe76ce
--- /dev/null
+++ b/app/models/batch/poly_metadata_behaviour.rb
@@ -0,0 +1,15 @@
+# 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?
+ %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
diff --git a/app/models/cherrypick/task/buffer_volume_for_empty_wells_option.rb b/app/models/cherrypick/task/buffer_volume_for_empty_wells_option.rb
new file mode 100644
index 0000000000..4fdeb4d321
--- /dev/null
+++ b/app/models/cherrypick/task/buffer_volume_for_empty_wells_option.rb
@@ -0,0 +1,23 @@
+# frozen_string_literal: true
+# frozen_sring_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", or nil if not checked.
+ @batch.set_poly_metadata(key, params[key])
+
+ return unless %w[1 on].include?(params[key])
+
+ # If automatic buffer addition for empty wells is required.
+ 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
+end
diff --git a/app/models/cherrypick/task/pick_helpers.rb b/app/models/cherrypick/task/pick_helpers.rb
index a1ff1891f4..45e349ab19 100644
--- a/app/models/cherrypick/task/pick_helpers.rb
+++ b/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
diff --git a/app/models/concerns/has_poly_metadata.rb b/app/models/concerns/has_poly_metadata.rb
new file mode 100644
index 0000000000..df51d6456a
--- /dev/null
+++ b/app/models/concerns/has_poly_metadata.rb
@@ -0,0 +1,36 @@
+# 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.
+ # @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
diff --git a/app/models/robot/generator/behaviours/tecan_default.rb b/app/models/robot/generator/behaviours/tecan_default.rb
index f7c46f64e6..e716b5b00a 100644
--- a/app/models/robot/generator/behaviours/tecan_default.rb
+++ b/app/models/robot/generator/behaviours/tecan_default.rb
@@ -1,7 +1,7 @@
# frozen_string_literal: true
# Module with the file generation functionality for Tecan robots
-module Robot::Generator::Behaviours::TecanDefault
+module Robot::Generator::Behaviours::TecanDefault # rubocop:disable Metrics/ModuleLength
def mapping(data_object: picking_data)
raise ArgumentError, 'Data object not present for Tecan mapping' if data_object.nil?
@@ -70,10 +70,13 @@ def buffer_separator
'C;'
end
- def buffers(data_object)
+ def buffers(data_object) # rubocop:disable Metrics/AbcSize
+ data_object = data_object_for_buffers(data_object)
buffer = []
each_mapping(data_object) do |mapping, dest_plate_barcode, plate_details|
- next unless total_volume > mapping['volume']
+ # src_well is checked to distinguish between buffer for sample wells
+ # and buffer for empty wells.
+ next if mapping.key?('src_well') && total_volume <= mapping['volume']
dest_name = data_object['destination'][dest_plate_barcode]['name']
volume = mapping['buffer_volume']
@@ -113,4 +116,88 @@ def sorted_destination_plates
def description_to_column_index(well_name, plate_size)
Map::Coordinate.description_to_vertical_plate_position(well_name, plate_size)
end
+
+ def column_index_to_description(index, plate_size)
+ Map::Coordinate.vertical_plate_position_to_description(index, plate_size)
+ end
+
+ # Returns a new data object with buffer entries added for empty destination
+ # wells, if the option is enabled; otherwise returns the original data object.
+ # Only the fields used by the buffer steps are added to the new data object.
+ # @param data_object [Hash] the original data object
+ # @return [Hash] the new data object with buffer entries for empty wells,
+ # or the original data object if the option is not enabled
+ # @example input data_object
+ # {"destination" =>
+ # {"SQPD-9101" =>
+ # {"name" => "ABgene 0765",
+ # "plate_size" => 96,
+ # "control" => false,
+ # "mapping" =>
+ # [{"src_well" => ["SQPD-9089", "A1"], "dst_well" => "A1", "volume" => 100.0, "buffer_volume" => 0.0},
+ # {"src_well" => ["SQPD-9089", "A2"], "dst_well" => "B1", "volume" => 100.0, "buffer_volume" => 0.0}]},
+ # "source" =>
+ # {"SQPD-9089" => {"name" => "ABgene 0800", "plate_size" => 96, "control" => false},
+ # "SQPD-9090" => {"name" => "ABgene 0800", "plate_size" => 96, "control" => false}},
+ # "time" => Thu, 19 Feb 2026 15:20:20.785717000 GMT +00:00,
+ # "user" => "admin"}
+ #
+ # @example output data_object
+ # {"destination" =>
+ # {"SQPD-9101" =>
+ # {"name" => "ABgene 0765",
+ # "plate_size" => 96,
+ # "control" => false,
+ # "mapping" =>
+ # [{"src_well" => ["SQPD-9089", "A1"], "dst_well" => "A1", "volume" => 100.0, "buffer_volume" => 0.0},
+ # {"src_well" => ["SQPD-9089", "A2"], "dst_well" => "B1", "volume" => 100.0, "buffer_volume" => 0.0},
+ # {"dst_well" => "C1", "buffer_volume" => 120.0}]},
+ # {"dst_well" => "D1", "buffer_volume" => 120.0}]},
+ # ...
+ # ]},
+ # }
+ # }
+ def data_object_for_buffers(data_object) # rubocop:disable Metrics/AbcSize,Metrics/MethodLength,Metrics/CyclomaticComplexity
+ buffer_volume_for_empty_wells = @batch&.buffer_volume_for_empty_wells
+ return data_object unless buffer_volume_for_empty_wells
+
+ obj = { 'destination' => {} }
+ data_object['destination'].each do |dest_plate_barcode, plate_details|
+ plate = Plate.find_by_barcode(dest_plate_barcode)
+ plate_size = plate_details['plate_size']
+ # Initialise the destination section
+ obj['destination'][dest_plate_barcode] = {
+ 'name' => plate_details['name'],
+ 'plate_size' => plate_size
+ }
+ # Create a hash of column index to the existing mapping entries
+ index_to_mapping = plate_details['mapping'].index_by do |entry|
+ description_to_column_index(entry['dst_well'], plate_size)
+ end
+
+ # Loop through the column order and generate new mapping entries
+ # Add existing mappings if present and skip non-empty wells in case it is partial plate.
+ mapping = []
+ (1..plate_size).each do |index|
+ # Add existing mapping if present for this column index.
+ if index_to_mapping.key?(index)
+ mapping << index_to_mapping[index]
+ next
+ end
+
+ # Check if the destination well empty, in case of partial plate.
+ dst_well = column_index_to_description(index, plate_size) # A1, B1, etc.
+ well = plate.find_well_by_name(dst_well) # Well object or nil
+ next if well.present? && !well.empty? # Skip non-empty wells
+
+ # Add buffer for empty well
+ mapping << {
+ 'dst_well' => dst_well,
+ 'buffer_volume' => buffer_volume_for_empty_wells
+ }
+ end
+ obj['destination'][dest_plate_barcode]['mapping'] = mapping
+ end
+ obj
+ end
end
diff --git a/app/models/robot/generator/tecan_v3.rb b/app/models/robot/generator/tecan_v3.rb
index e6a1bdadde..625ff034b0 100644
--- a/app/models/robot/generator/tecan_v3.rb
+++ b/app/models/robot/generator/tecan_v3.rb
@@ -14,9 +14,12 @@ class Robot::Generator::TecanV3 < Robot::Generator::TecanV2
# @see Robot::Generator::Behaviours::TecanDefault#buffers
# rubocop:disable Metrics/AbcSize,Metrics/MethodLength
def buffers(data_object)
+ data_object = data_object_for_buffers(data_object)
groups = Hash.new { |h, k| h[k] = [] } # channel => [steps]
each_mapping(data_object) do |mapping, dest_plate_barcode, plate_details|
- next unless total_volume > mapping['volume']
+ # src_well is checked to distinguish between buffer for sample wells
+ # and buffer for empty wells.
+ next if mapping.key?('src_well') && total_volume <= mapping['volume']
dest_name = data_object['destination'][dest_plate_barcode]['name']
volume = mapping['buffer_volume']
diff --git a/app/models/tasks/cherrypick_handler.rb b/app/models/tasks/cherrypick_handler.rb
index 9461e8d4b1..926e3952cc 100644
--- a/app/models/tasks/cherrypick_handler.rb
+++ b/app/models/tasks/cherrypick_handler.rb
@@ -92,6 +92,9 @@ def setup_input_params_for_pass_through # rubocop:todo Metrics/AbcSize
else
raise StandardError, "Invalid cherrypicking strategy '#{params[:cherrypick][:strategy]}'"
end
+ # Add buffer volume for empty wells option to params for pass through
+ @automatic_buffer_addition = params[:automatic_buffer_addition]
+ @buffer_volume_for_empty_wells = params[:buffer_volume_for_empty_wells]
@plate_purpose_id = params[:plate_purpose_id]
@fluidigm_barcode = params[:fluidigm_plate]
end
@@ -129,6 +132,9 @@ def do_cherrypick_task(_task, params) # rubocop:todo Metrics/CyclomaticComplexit
raise StandardError, "Invalid cherrypicking type #{params[:cherrypick_strategy]}"
end
+ # Store the buffer volume for empty wells option in the batch's poly_metadata
+ create_buffer_volume_for_empty_wells_option(params)
+
# We can preload the well locations so that we can do efficient lookup later.
well_locations =
Map
diff --git a/app/views/batches/_cherrypick_single_worksheet.html.erb b/app/views/batches/_cherrypick_single_worksheet.html.erb
index 6bb66c2c36..09a5e40a01 100644
--- a/app/views/batches/_cherrypick_single_worksheet.html.erb
+++ b/app/views/batches/_cherrypick_single_worksheet.html.erb
@@ -14,6 +14,8 @@
<%# see Robot::Verification::Base#pick_number_to_expected_layout for structure of robot_plate_layout %>
<% destination_layout, source_layout, control_layout = robot_plate_layout %>
<% source_plate_colour = source_layout.transform_values { |sort_order| "colour#{sort_order%12}" } %>
+<%# Get buffer_volume_for_empty_wells from batch as float or nil -%>
+<% buffer_volume_for_empty_wells = batch.buffer_volume_for_empty_wells %>
<%= render partial: 'cherrypick_worksheet_plate_list', locals: { section_name: 'Source plates', plates: source_layout, bed_prefix: 'SCRC' } %>
@@ -48,6 +50,8 @@
<%= rowchar %> |
<% (num_columns).times do |column| -%>
<% well = plate_wells[row*num_columns+column] -%>
+ <%# Flag to check if well is empty and needs to be represented on the chart with 'e' followed by the buffer volume for empty wells, for example e120.00 -%>
+ <% empty_well = true %>
<% if well.present? -%>
<% request = indexed_requests[well.id] %>
<% source_well = request&.asset %>
@@ -62,6 +66,8 @@
<% else %>
<% end -%>
+ <%# Flag to set if the well is not empty -%>
+ <% empty_well = false %>
<%= source_well.map_description %>
<%= source_well.plate.barcode_number %>
v<%= "%.#{configatron.tecan_precision}f" % well.get_picked_volume %> b<%= "%.#{configatron.tecan_precision}f" % well.get_buffer_volume %>
@@ -74,6 +80,9 @@
<% else %>
|
<% end -%>
+ <% if empty_well && buffer_volume_for_empty_wells.present? -%>
+ e<%= "%.#{configatron.tecan_precision}f" % buffer_volume_for_empty_wells %>
+ <% end %>
|
<% end -%>
<%= rowchar %> |
@@ -92,7 +101,11 @@
diff --git a/app/views/workflows/_cherrypick_batches.html.erb b/app/views/workflows/_cherrypick_batches.html.erb
index 6d378979b9..a20af1374e 100644
--- a/app/views/workflows/_cherrypick_batches.html.erb
+++ b/app/views/workflows/_cherrypick_batches.html.erb
@@ -40,6 +40,9 @@
<%= hidden_field_tag 'robot_id', @robot_id %>
<%= hidden_field_tag 'cherrypick_strategy', @cherrypick_strategy %>
<%= hidden_field_tag 'plate_type', @plate_type %>
+ <%# Add hidden fields for the buffer volume for empty wells option to carry over -%>
+ <%= hidden_field_tag 'automatic_buffer_addition', @automatic_buffer_addition %>
+ <%= hidden_field_tag 'buffer_volume_for_empty_wells', @buffer_volume_for_empty_wells %>
<%= render(partial: 'next_stage_submit', locals: { check_selection: true }) %>
<% end %>
diff --git a/app/views/workflows/_cherrypick_strategies.html.erb b/app/views/workflows/_cherrypick_strategies.html.erb
index c72f3e9d84..07cad95a5c 100644
--- a/app/views/workflows/_cherrypick_strategies.html.erb
+++ b/app/views/workflows/_cherrypick_strategies.html.erb
@@ -1,4 +1,4 @@
-<%# locals: { form: } -%>
+<%# locals: { form: } %>
Choose a strategy below:
@@ -26,5 +26,24 @@
+<%# Add form controls to collect the options for the buffer volume for empty wells -%>
+Additional options:
+
+
<%= vite_javascript_tag 'cherrypick_strategies' %>
diff --git a/spec/models/robot/generator/tecan_spec.rb b/spec/models/robot/generator/tecan_spec.rb
index 3fae3deba7..e94a2702bb 100644
--- a/spec/models/robot/generator/tecan_spec.rb
+++ b/spec/models/robot/generator/tecan_spec.rb
@@ -1,7 +1,10 @@
# frozen_string_literal: true
describe Robot::Generator::Tecan do
- before { create(:full_plate) }
+ before do
+ create(:full_plate)
+ allow(batch).to receive(:buffer_volume_for_empty_wells).and_return(nil)
+ end
shared_examples 'a generator' do
describe '.as_text' do
diff --git a/spec/models/robot/generator/tecan_v3_spec.rb b/spec/models/robot/generator/tecan_v3_spec.rb
index 72b1d5fb18..f505550678 100644
--- a/spec/models/robot/generator/tecan_v3_spec.rb
+++ b/spec/models/robot/generator/tecan_v3_spec.rb
@@ -69,6 +69,11 @@
# Expected output for the test cases.
let(:expected_output) { File.read("spec/data/tecan_v3/case_#{case_num}.gwl") }
+ before do
+ allow(batch).to receive(:get_poly_metadata).with(:buffer_volume_for_empty_wells).and_return(nil)
+ allow(batch).to receive(:buffer_volume_for_empty_wells).and_return(nil)
+ end
+
shared_examples 'a TecanV3 generator' do
it 'generates the expected output' do
expect(generator.as_text).to eq expected_output