Method accession_submission_xml has 28 lines of code (exceeds 25 allowed). Consider refactoring.

Open

  def accession_submission_xml(submission, accession_number) # rubocop:todo Metrics/AbcSize
    xml = Builder::XmlMarkup.new
    xml.instruct!
    xml.SUBMISSION(
      'xmlns:xsi' => 'http://www.w3.org/2001/XMLSchema-instance',

Method encode has 28 lines of code (exceeds 25 allowed). Consider refactoring.

Open

    def encode(object, options = {}) # rubocop:todo Metrics/CyclomaticComplexity
      case object
      when NilClass
        unencoded('null')
      when Symbol

Method create has 28 lines of code (exceeds 25 allowed). Consider refactoring.

Open

  def create # rubocop:todo Metrics/AbcSize
    @creator = plate_creator = Plate::Creator.find(params[:plates][:creator_id])
    barcode_printer = BarcodePrinter.find(params[:plates][:barcode_printer])
    source_plate_barcodes = params[:plates][:source_plates]
    create_asset_group = params[:plates][:create_asset_group] == 'Yes'

Method check_inputs_to_volume_to_cherrypick_by_nano_grams! has a Cognitive Complexity of 10 (exceeds 5 allowed). Consider refactoring.

Open

  def check_inputs_to_volume_to_cherrypick_by_nano_grams!(minimum_volume, maximum_volume, target_ng, source_well)
    raise 'Source well not found' if source_well.nil?

    if minimum_volume.blank? || minimum_volume <= 0.0
      raise Cherrypick::VolumeError,

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Method accession_submission_xml has a Cognitive Complexity of 10 (exceeds 5 allowed). Consider refactoring.

Open

  def accession_submission_xml(submission, accession_number) # rubocop:todo Metrics/AbcSize
    xml = Builder::XmlMarkup.new
    xml.instruct!
    xml.SUBMISSION(
      'xmlns:xsi' => 'http://www.w3.org/2001/XMLSchema-instance',

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Method convert_json_attributes_to_attributes has a Cognitive Complexity of 10 (exceeds 5 allowed). Consider refactoring.

Open

    def convert_json_attributes_to_attributes(json_attributes) # rubocop:todo Metrics/AbcSize
      return {} if json_attributes.blank?

      attributes = {}
      attribute_to_json_attribute_mappings.each do |attribute, json_attribute|

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Method stock_wells has a Cognitive Complexity of 10 (exceeds 5 allowed). Consider refactoring.

Open

  def stock_wells # rubocop:todo Metrics/AbcSize, Metrics/MethodLength
    # Optimisation: if the plate is a stock plate then it's wells are it's stock wells!]
    if stock_plate?
      wells.with_pool_id.index_with { |w| [w] }
    else

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Method xml has a Cognitive Complexity of 10 (exceeds 5 allowed). Consider refactoring.

Open

    def xml # rubocop:todo Metrics/AbcSize
      xml = Builder::XmlMarkup.new
      xml.instruct!
      xml.SAMPLE_SET('xmlns:xsi' => 'http://www.w3.org/2001/XMLSchema-instance') do
        xml.SAMPLE(sample_element_attributes) do

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Method transfer_requests_io= has a Cognitive Complexity of 10 (exceeds 5 allowed). Consider refactoring.

Open

  def transfer_requests_io=(parameters) # rubocop:todo Metrics/AbcSize
    uuid_cache = UuidCache.new(parameters)

    updated_attributes =
      parameters.map do |parameter|

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Method check_entered_oligos has a Cognitive Complexity of 10 (exceeds 5 allowed). Consider refactoring.

Open

  def check_entered_oligos # rubocop:todo Metrics/AbcSize
    invalid_oligos_list = []
    valid_oligos_hash = {}
    parse_oligos_list.each do |cur_oligo|
      if cur_oligo.match?(/^[ACGTacgt]*$/)

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Method save has a Cognitive Complexity of 10 (exceeds 5 allowed). Consider refactoring.

Open

  def save
    return false unless valid?

    ActiveRecord::Base.transaction do
      fail_requests if requested_fail.present?

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Method record_plate_samples has a Cognitive Complexity of 10 (exceeds 5 allowed). Consider refactoring.

Open

      def record_plate_samples # rubocop:todo Metrics/AbcSize
        sm_sample_assets = sample_manifest.sample_manifest_assets.to_a

        first_to_last.each_with_index do |sheet_row, sample_index|
          cur_sm_sample_asset = sm_sample_assets.fetch(sample_index)

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Method filter_barcode_to_plate_index has a Cognitive Complexity of 10 (exceeds 5 allowed). Consider refactoring.

Open

  def filter_barcode_to_plate_index(destinations)
    destinations.each_with_object({}) do |(destination_barcode, destination_info), all_barcodes|
      mapping_sorted = sort_mapping_by_destination_well(destination_barcode, destination_info['mapping'])
      mapping_sorted.each do |map_well|
        barcode, _well = map_well['src_well']

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Method run has a Cognitive Complexity of 10 (exceeds 5 allowed). Consider refactoring.

Open

        def run(tag_group) # rubocop:todo Metrics/MethodLength
          return unless valid?

          unless @tube_rack_information_previously_processed
            @rack_size = upload.sample_manifest.tube_rack_purpose.size

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Method add_cell_data has a Cognitive Complexity of 10 (exceeds 5 allowed). Consider refactoring.

Open

      def add_cell_data(column, row_num, partial) # rubocop:todo Metrics/CyclomaticComplexity
        if partial && empty_row?(row_num)
          (data[column.name] || dynamic_attributes[row_num][column.name]) unless empty_columns.include?(column.name)
        elsif validation_errors.include?(:insert_size_from) && column.name == 'insert_size_from' &&
              row_num == computed_first_row

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Method page_title has a Cognitive Complexity of 10 (exceeds 5 allowed). Consider refactoring.

Open

  def page_title(title, subtitle = nil, titlecase: true, badges: []) # rubocop:todo Metrics/AbcSize
    tag.div(class: 'page-header') do
      title_class = title.length > 25 ? 'title-long' : 'title-short'
      tag.h1(class: title_class) do
        if titlecase

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Method to_hash has 27 lines of code (exceeds 25 allowed). Consider refactoring.

Open

    def to_hash(object) # rubocop:todo Metrics/CyclomaticComplexity
      # If the object is nil we get a chance to use the 'default' object that was specified.  By
      # default the "default" object is nil, but you can override it for associations through the
      # with_association(:name, :if_nil_use => :some_method).
      object ||= default_object

Method authenticate_with_ldap has 27 lines of code (exceeds 25 allowed). Consider refactoring.

Open

    def authenticate_with_ldap(login, password) # rubocop:todo Metrics/AbcSize, Metrics/MethodLength
      # TODO: - Extract LDAP specifics to configuration
      username = "uid=#{login},ou=people,dc=sanger,dc=ac,dc=uk"
      ldap =
        Net::LDAP.new(

Method post_files has 27 lines of code (exceeds 25 allowed). Consider refactoring.

Open

  def post_files(file_params) # rubocop:todo Metrics/CyclomaticComplexity
    rc = rest_client_resource

    if configatron.disable_web_proxy == true
      RestClient.proxy = nil

Function validateOrganism has 27 lines of code (exceeds 25 allowed). Consider refactoring.

Open

const validateOrganism = function (common_name_field, taxon_id_field) {
  // Empty fields can be ignored
  if (common_name_field.value == "" || common_name_field.value == undefined) {
    return;
  }