Method progress_report_on_all_assets has 45 lines of code (exceeds 25 allowed). Consider refactoring.

Open

  def progress_report_on_all_assets # rubocop:todo Metrics/AbcSize
    yield(progress_report_header)

    each_stock_well_id_in_study_in_batches do |asset_ids|
      # eager loading of well_attribute , can only be done on  wells ...

Method perform_pick has 44 lines of code (exceeds 25 allowed). Consider refactoring.

Open

  def perform_pick(requests, robot, control_source_plate, workflow_controller) # rubocop:todo Metrics/AbcSize
    max_plates = robot.max_beds
    raise StandardError, 'The chosen robot has no beds!' if max_plates.zero?

    destination_plates = []

Method render_class_for_model has a Cognitive Complexity of 14 (exceeds 5 allowed). Consider refactoring.

Open

    def render_class_for_model(model) # rubocop:todo Metrics/CyclomaticComplexity
      render_class = Class.new(self)

      # NOTE: It's quite annoying that you don't have any access to the inheritable class attributes from
      # within the Class.new block above, so we have to do a separate instance_eval to get it to work.

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Method record_tube_samples has a Cognitive Complexity of 14 (exceeds 5 allowed). Consider refactoring.

Open

      def record_tube_samples # rubocop:todo Metrics/AbcSize
        tube_counter = 0
        first_to_last.each do |sheet_row|
          row = dynamic_attributes[sheet_row]
          build_tube_sample_manifest_asset do |sample_manifest_asset|

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Method generate_picking_data_hash has a Cognitive Complexity of 14 (exceeds 5 allowed). Consider refactoring.

Open

  def generate_picking_data_hash(target_barcode, requests: requests_for_destination_plate)
    data_objects = {}
    source_barcode_to_pick_number = {}

    current_pick_size = lambda { data_objects[data_objects.size]['source'].size }

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Method create_request_chain! has 43 lines of code (exceeds 25 allowed). Consider refactoring.

Open

  def create_request_chain!(request_type_and_multiplier_pairs, source_data_set, multiplexing_assets, &block) # rubocop:todo Metrics/CyclomaticComplexity
    raise StandardError, 'No request types specified!' if request_type_and_multiplier_pairs.empty?

    request_type, multiplier = request_type_and_multiplier_pairs.shift

Method process has 43 lines of code (exceeds 25 allowed). Consider refactoring.

Open

  def process # rubocop:todo Metrics/CyclomaticComplexity
    # Store the details of the successful submissions so the user can be presented with a summary
    @submission_ids = []
    @completed_submissions = {}

Method _check_mandatory_field has a Cognitive Complexity of 13 (exceeds 5 allowed). Consider refactoring.

Open

        def _check_mandatory_field(mandatory_field) # rubocop:todo Metrics/CyclomaticComplexity, Metrics/AbcSize
          return unless upload.respond_to?(:rows)
          upload.rows.each do |row|
            next if row.columns.blank? || row.data.blank?
            col_num = row.columns.find_column_or_null(:name, mandatory_field).number

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Method non_matching_retention_instructions_for_plates has a Cognitive Complexity of 13 (exceeds 5 allowed). Consider refactoring.

Open

        def non_matching_retention_instructions_for_plates
          return nil, nil unless upload.respond_to?(:rows)

          # Initialize empty retention_instructions hash to store retention instructions
          upload

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Method serialize has a Cognitive Complexity of 13 (exceeds 5 allowed). Consider refactoring.

Open

  def self.serialize(st) # rubocop:todo Metrics/CyclomaticComplexity
    attributes = st.attributes
    new_attributes = {}

    STRAIGHT_CLONE.each do |key|

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Method duplicate_barcodes has a Cognitive Complexity of 13 (exceeds 5 allowed). Consider refactoring.

Open

        def duplicate_barcodes # rubocop:todo Metrics/CyclomaticComplexity
          return unless upload.respond_to?(:rows)

          unique_bcs = []
          upload.rows.each do |row|

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Method non_matching_retention_instructions has a Cognitive Complexity of 13 (exceeds 5 allowed). Consider refactoring.

Open

        def non_matching_retention_instructions
          return nil, nil unless upload.respond_to?(:rows)

          upload
            .rows

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Method swap has 39 lines of code (exceeds 25 allowed). Consider refactoring.

Open

  def swap(current_user, batch_info = {}) # rubocop:todo Metrics/CyclomaticComplexity
    return false if batch_info.empty?

    # Find the two lanes that are to be swapped
    batch_request_left =

Method included has 38 lines of code (exceeds 25 allowed). Consider refactoring.

Open

    def self.included(base) # rubocop:todo Metrics/MethodLength
      base.class_eval do
        def mx_library
          asset.external_identifier || 'UNKNOWN'
        end

Function exports has 37 lines of code (exceeds 25 allowed). Consider refactoring.

Open

module.exports = function (api) {
  var validEnv = ["development", "test", "production"];
  var currentEnv = api.env();
  var isDevelopmentEnv = api.env("development");
  var isProductionEnv = api.env("production");

Method included has 36 lines of code (exceeds 25 allowed). Consider refactoring.

Open

  def self.included(base) # rubocop:todo Metrics/AbcSize, Metrics/MethodLength
    base.class_eval do
      ## State machine
      ## namespace: true as destroyed clashes with rails, but we can't easily rename the state
      aasm column: :state, whiny_persistence: true, namespace: true, name: 'qc_state' do

Method build_association has 36 lines of code (exceeds 25 allowed). Consider refactoring.

Open

  def build_association(as_class, options) # rubocop:todo Metrics/MethodLength
    # First we build the association into the current ActiveRecord::Base class
    as_name = as_class.name.demodulize.underscore
    association_name = "#{as_name}_metadata".underscore.to_sym
    class_name = "#{name}::Metadata"

Method validate_each has a Cognitive Complexity of 12 (exceeds 5 allowed). Consider refactoring.

Open

  def validate_each(record, attribute, value)
    return unless check_hash(record, attribute, value)

    value.each do |program, params|
      record.errors.add attribute, "invalid label #{program}" unless program.in?(PROGRAMS_LABELS)

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Function plateBarcodeScan has a Cognitive Complexity of 12 (exceeds 5 allowed). Consider refactoring.

Open

  plateBarcodeScan: async ({ commit, dispatch, state }, plate_barcode) => {
    // Firstly we record that the plate has been scanned.
    commit("scanPlate", { barcode: plate_barcode });
    const scanned_plate_id = state.scanStore[`_${plate_barcode}`].id;

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Method update has a Cognitive Complexity of 12 (exceeds 5 allowed). Consider refactoring.

Open

      def update(_attributes = {}) # rubocop:todo Metrics/CyclomaticComplexity, Metrics/MethodLength
        return unless valid? && foreign_barcode_format.present?

        # if this tube's list of barcodes already contains a foreign barcode with the same format then update the
        # existing one

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