sanger/sequencescape

# frozen_string_literal: true
class FluidigmFile
  module Finder
    class Directory
      def initialize(barcode)
        @barcode = barcode
      end

      def empty?
        !File.exist?("#{configatron.fluidigm_data.directory}/#{@barcode}/#{@barcode}.csv")
      end

      def content
        file_content = nil
        File.open("#{configatron.fluidigm_data.directory}/#{@barcode}/#{@barcode}.csv") do |file|
          file_content = file.read
        end
        file_content
      end
    end

    def self.default
      { 'directory' => Directory }.fetch(configatron.fluidigm_data.source)
    end

    def self.find(barcode)
      default.new(barcode)
    end
  end

  class InvalidFile < StandardError
  end

  class Assay
    attr_reader :name, :result

    @@valid_markers = %w[XX XY YY]
    @@gender_map = { 'XX' => 'F', 'YY' => 'F', 'XY' => 'M' }

    def initialize(name, result)
      @name = name
      @result = result
    end

    def gender_marker?
      /^GS/.match?(name)
    end

    def gender
      @@gender_map[result] || 'U'
    end

    def pass?
      @@valid_markers.include?(result)
    end
  end

  class FluidigmWell
    attr_reader :description

    def initialize(description)
      @description = description
    end

    def gender_markers
      marker_array.select(&:gender_marker?).map(&:gender)
    end

    def add_assay(assay, marker)
      marker_array << Assay.new(assay, marker)
    end

    def count
      marker_array.count(&:pass?)
    end

    private

    def marker_array
      @gender_markers ||= []
    end
  end

  def initialize(file_contents)
    @csv = CSV.parse(file_contents)
    build_wells
  end

  def each_well
    @wells.each { |_, w| yield(w) }
  end

  def for_plate?(test_plate)
    plate_barcode == test_plate
  end

  def plate_barcode
    @csv[0][2]
  end

  def well_at(description)
    @wells ||= Hash.new { |hash, desc| hash[desc] = FluidigmWell.new(desc) }
    @wells[description]
  end

  def well_locations
    @wells.keys
  end

  private

  def header_start_index
    @header_start_index ||=
      (0..@csv.size).detect { |i| @csv[i][0] == 'Experiment Information' } ||
        raise(InvalidFile, 'Could not find header')
  end

  def data_start_index
    header_start_index + 3
  end

  def headers
    @headers ||=
      @csv[header_start_index]
        .zip(@csv[header_start_index + 1])
        .zip(@csv[header_start_index + 2])
        .map { |h| h.join(' ') }
  end

  def column(head)
    headers.index(head)
  end

  def build_wells
    (data_start_index...@csv.size).each do |row_index|
      row = @csv[row_index]
      next if row[column('Experiment Information Sample Name')] == 'Water'

      well = well_at(row[column('Experiment Information Chamber ID')].split('-').first)
      well.add_assay(
        row[column('Experiment Information SNP Assay and Allele Names Assay')],
        row[column('Results Call Information Final')]
      )
    end
  end
end