agilent_to_analyzerdg.rb

require_relative 'agilentfe'
require 'rest_client'

agilent_coordinates_to_array_number = {
  1 => { nil => 1 },
  2 => { [1,1] => 2, [1,2] => 1 },
  4 => { [1,1] => 4, [1,2] => 3, [1,3] => 2, [1,4] => 1 },
  8 => { [1,1] => 8, [1,2] => 6, [1,3] => 4, [1,4] => 2,
         [2,1] => 7, [2,2] => 5, [2,3] => 3, [2,4] => 1 }
}

agilent_feature_extraction_output.check_every 5.minutes do
  age :greater_than => 2.minutes

  # handle QC PDFs
  files_matching(/(US\d{8}_(\d{12})|(\d{12})_\d{12})_.*?(_(\d)_(\d))?\.pdf/) do |file|
    barcode = match_data[2] || match_data[3]
    design_id = barcode.match(/\d{2}(\d{5})\d{5}/)[1]
    destination_folder = [agilent_quantitation_folder, design_id].join("/")

    copy file, :to => destination_folder
  end

  # handle QC XML files
  files_matching(/(US\d{8}_(\d{12})|(\d{12})_\d{12})_.*\.xml/) do |file|
    barcode = match_data[2] || match_data[3]
    design_id = barcode.match(/\d{2}(\d{5})\d{5}/)[1]

    destination_folder = [agilent_quantitation_folder, design_id].join("/")

    # determine array number
    arrays_per_slide = YAML.load_file("agilent_designs.yml")[design_id.to_i]

    if arrays_per_slide
      coordinate_map = agilent_coordinates_to_array_number[arrays_per_slide]

      copy file, :to => destination_folder do |source_path, destination_path|
        coordinate_map.keys.each do |agilent_coordinates|
          begin
            stats = AgilentQC.parse( file.path, agilent_coordinates.join("_") )
          rescue StandardError => e
            Boatman.logger.error "Could not parse Agilent QC file #{source_path}: #{e.message}"
          end

          begin
            array_number = coordinate_map[agilent_coordinates]

            slimarray_resource = RestClient::Resource.new slimarray_qc_sets_uri, :user => slimarray_user,
              :password => slimarray_password, :timeout => 20

            new_file_path = [destination_folder, File.basename(file.path)].join("/")
            slimarray_resource.post :chip_name => barcode, :array_number => array_number, :file => new_file_path,
              :statistics => stats
          rescue RestClient::RequestFailed => e
            Boatman.logger.error "Could not submit Agilent QC to SLIMarray #{source_path}, HTTP Status = #{e.http_code}, HTTP Body = #{e.http_body} new_file_path #{new_file_path} barcode/chip_name #{barcode} array_number #{array_number} statistics #{stats}"
          rescue StandardError => e
            Boatman.logger.error "Could not submit Agilent QC to SLIMarray #{source_path}: #{e.message}"
          end
        end

        FTPUtils.cp source_path, destination_path
        verify_checksum_matches(source_path, destination_path)
      end
    else
      Boatman.logger.error "Missing coordinate information in agilent_designs.yml for design #{design_id}"
    end
  end

  # handle actual data TXT files
  files_matching(/(US\d{8}_(\d{12})|(\d{12})_\d{12})_.*?(_(\d)_(\d))?\.txt/) do |file|
    match_data = file.match_data

    barcode = match_data[2] || match_data[3]
    agilent_coordinates = [match_data[5].to_i, match_data[6].to_i] if match_data[5] && match_data[6]

    design_id = barcode.match(/\d{2}(\d{5})\d{5}/)[1]
    destination_folder = [agilent_quantitation_folder, design_id].join("/")

    # determine array number
    arrays_per_slide = YAML.load_file("agilent_designs.yml")[design_id.to_i]

    if arrays_per_slide
      array_number = agilent_coordinates_to_array_number[arrays_per_slide][agilent_coordinates]

      # copy the raw Agilent FE text
      copy file, :to => destination_folder do |source_path, destination_path|
        FTPUtils.cp source_path, destination_path
        verify_checksum_matches(source_path, destination_path)

        # let SLIMarray know about this new data file
        begin
          slimarray_resource = RestClient::Resource.new slimarray_raw_data_uri, :user => slimarray_user,
            :password => slimarray_password, :timeout => 20
          new_file_path = [destination_folder, File.basename(file.path)].join("/")

          # hack to get POSIX path
          new_file_path.gsub!(/\//, '/').gsub!(/\/isb\-2\/Arrays/, 'net/arrays')        
          new_file_path.gsub!(/\//, '/').gsub!(/Volumes\/arrays/, 'net/arrays')        
          
          slimarray_resource.post :chip_name => barcode, :array_number => array_number, :path => new_file_path
        rescue RestClient::ResourceNotFound => e
          Boatman.logger.debug "No match found in SLIMarray for barcode = #{barcode}, " + 
            "array number = #{array_number}"
        rescue StandardError => e
          Boatman.logger.error "Could not connect to SLIMarray web service: #{e.message}"
        end
      end

      # convert the Agilent FE format file to an AnalyzerDG format CSV file
      analyzerdg_file_name = "#{barcode}#{array_number}.csv"
      copy file, :to => destination_folder, :rename => analyzerdg_file_name do |old_file_name, new_file_name|
        convert_agilentfe_to_analyzerdg(old_file_name, new_file_name)
      end
    else
      Boatman.logger.error "Missing coordinate information in agilent_designs.yml for design #{design_id}"
    end
  end
end