Laboratory experiment with samples and reagents

experiment.rb

# The Experiment class represents a laboratory experiment involving samples and reagents.
# It provides methods to assign samples and reagents to wells on a plate.
# Each well can contain one sample-reagent combination.
# Plates come in two sizes: 96 wells or 384 wells, arranged in a rectangular grid.
# Each experiment can have multiple replicates, where each replicate is a set of sample-reagent combinations.
# The class aims to minimize the number of plates used by efficiently arranging the samples and reagents.

# frozen_string_literal: true

require 'matrix'

class Experiment
  attr_reader :plate_size, :samples_names, :reagents_names, :replicates_number

  def initialize(params)
    @plate_size = params[:plate_size]
    @samples_names = params[:samples_names]
    @reagents_names = params[:reagents_names]
    @replicates_number = params[:replicates_number]
  end

  def assign_samples_to_plate_wells
    fill_plate_wells(empty_plate_wells)
  end

  def display_plates
    assign_samples_to_plate_wells.each_with_index do |plate, index|
      puts "Plate #{index + 1}:"
      plate.each do |row|
        puts row.map { |well| well.nil? ? '[   ]' : "[#{well.join(', ')}]" }.join(' ')
      end
      puts "\n"
    end
  end

  private

  def fill_plate_wells(plate_wells)
    pos = { row: 0, col: 0, plate_index: 0 }

    @samples_names.each_with_index do |samples, experiment_index|
      fill_wells_for_experiment(samples, @reagents_names[experiment_index], @replicates_number[experiment_index],
                                plate_wells, pos)
    end

    plate_wells.map(&:to_a)
  end

  def empty_plate_wells
    Array.new(total_plates_needed) { build_empty_plate }
  end

  def total_plates_needed
    @total_plates_needed ||= (total_replicates * total_samples * total_reagents / plate_size.to_f).ceil
  end

  def total_replicates
    @replicates_number.sum
  end

  def total_samples
    @samples_names.flatten.count
  end

  def total_reagents
    @reagents_names.flatten.count
  end

  def build_empty_plate
    Matrix.build(plate_dimensions[:rows], plate_dimensions[:cols]) { nil }
  end

  def plate_dimensions
    if @plate_size == 96
      { rows: 8, cols: 12 }
    elsif @plate_size == 384
      { rows: 16, cols: 24 }
    else
      raise ArgumentError, 'Invalid plate size. Please enter either 96 or 384.'
    end
  end

  def fill_wells_for_experiment(samples, reagents, replicates, plate_wells, pos)
    experiment_combinations = samples.product(reagents).cycle.first(replicates)
    experiment_combinations.each do |sample, reagent|
      fill_well(sample, reagent, plate_wells, pos)
    end
  end

  def fill_well(sample, reagent, plate_wells, pos)
    plate_wells[pos[:plate_index]][pos[:row], pos[:col]] = [sample, reagent]
    increment_position(pos)
  end

  def increment_position(pos)
    pos[:col] += 1
    if pos[:col] >= plate_dimensions[:cols]
      pos[:col] = 0
      pos[:row] += 1
    end

    return unless pos[:row] >= plate_dimensions[:rows]

    pos[:row] = 0
    pos[:plate_index] += 1
  end
end

experiment = Experiment.new(
  plate_size: 384,
  samples_names: [['Sample 1', 'Sam 2', 'Sam 3'], ['Sam 1', 'Sam 3', 'Sam 4']],
  reagents_names: [['Reagent X', 'Reag Y'], ['Reag Y', 'Reag Z']],
  replicates_number: [1, 3]
)
experiment.display_plates