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

Open

  def self.construct!(hash) # rubocop:todo Metrics/CyclomaticComplexity
    st = {}

    STRAIGHT_CLONE.each { |key| st[key.to_sym] = hash[key.to_sym] }

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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?

        # checking if the plate this well belongs to already has this foreign barcode set in its list of barcodes.
        # or if it contains a foreign barcode with the same format, then update that existing one

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Method apply_fluidigm_data has 34 lines of code (exceeds 25 allowed). Consider refactoring.

Open

  def apply_fluidigm_data(fluidigm_file) # rubocop:todo Metrics/AbcSize
    qc_assay = QcAssay.new
    raise FluidigmError, 'File does not match plate' unless fluidigm_file.for_plate?(fluidigm_barcode)

    wells

Method configure has 33 lines of code (exceeds 25 allowed). Consider refactoring.

Open

    def configure(model) # rubocop:todo Metrics/CyclomaticComplexity
      conditions = @options.slice(:if, :on)
      save_blank_value = @options.delete(:save_blank)
      allow_blank = save_blank_value
      model.with_options(conditions) do |object|

Method show_summary has 33 lines of code (exceeds 25 allowed). Consider refactoring.

Open

  def show_summary # rubocop:todo Metrics/CyclomaticComplexity
    page_params = { page: params[:page] || 1, per_page: params[:per_page] || 50 }

    if request.xhr?
      @summary = params[:summary] || 'assets-progress'

Method submission_structure has 32 lines of code (exceeds 25 allowed). Consider refactoring.

Open

  def submission_structure # rubocop:todo Metrics/CyclomaticComplexity
    Hash
      .new { |h, i| h[i] = Array.new }
      .tap do |submission|
        csv_data_rows.each_with_index do |row, index|

Method stage has 32 lines of code (exceeds 25 allowed). Consider refactoring.

Open

  def stage # rubocop:todo Metrics/CyclomaticComplexity
    @workflow = Workflow.includes(:tasks).find(params[:workflow_id])
    @stage = params[:id].to_i
    @task = @workflow.tasks[@stage]

Method progress_report_header has 32 lines of code (exceeds 25 allowed). Consider refactoring.

Open

  def progress_report_header
    [
      'Status',
      'Study',
      'Supplier',

Method well_to_destination has a Cognitive Complexity of 11 (exceeds 5 allowed). Consider refactoring.

Open

  def well_to_destination # rubocop:todo Metrics/AbcSize
    {}.tap do |sources_to_target|
      # Group the wells based on the submission
      groups = source.wells.in_column_major_order.with_pool_id.group_by(&:pool_id).delete_if { |k, _| k.nil? }.values

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Method swap has a Cognitive Complexity of 11 (exceeds 5 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 =

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Method sorted_requests_for_destination_plate has a Cognitive Complexity of 11 (exceeds 5 allowed). Consider refactoring.

Open

  def sorted_requests_for_destination_plate(requests_to_sort) # rubocop:todo Metrics/CyclomaticComplexity
    requests_to_sort.sort_by do |req|
      if req.target_asset&.map&.column_order
        [req.target_asset.plate.id, req.asset.plate&.pick_as_control? ? 0 : 1, req.target_asset.map.column_order]
      else

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Method output_aliquot has a Cognitive Complexity of 11 (exceeds 5 allowed). Consider refactoring.

Open

  def output_aliquot(xml, aliquot) # rubocop:todo Metrics/AbcSize, Metrics/MethodLength
    xml.sample(
      sample_id: aliquot.sample_id,
      library_id: aliquot.library_id,
      library_name: aliquot.library_name,

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Method perform_pick has a Cognitive Complexity of 11 (exceeds 5 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 = []

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Method file_addition has 30 lines of code (exceeds 25 allowed). Consider refactoring.

Open

      def file_addition(action, http_method) # rubocop:todo Metrics/AbcSize
        send(
          http_method,
          %r{/([\da-f]{8}(?:-[\da-f]{4}){3}-[\da-f]{12})(?:/([^/]+(?:/[^/]+)*))?},
          file_attached: true

Method create_request has 30 lines of code (exceeds 25 allowed). Consider refactoring.

Open

  def create_request # rubocop:todo Metrics/AbcSize
    @request_type = RequestType.find(params[:request_type_id])
    @study = Study.find(params[:study_id]) if params[:cross_study_request].blank?
    @project = Project.find(params[:project_id]) if params[:cross_project_request].blank?

Method studies_from_scope has 30 lines of code (exceeds 25 allowed). Consider refactoring.

Open

  def studies_from_scope(scope) # rubocop:todo Metrics/CyclomaticComplexity
    studies =
      case scope
      when 'interesting'
        Study.of_interest_to(current_user)

Method included has 29 lines of code (exceeds 25 allowed). Consider refactoring.

Open

  def self.included(base) # rubocop:todo Metrics/AbcSize, Metrics/MethodLength
    base.class_eval do
      include AASM
      aasm column: :state, whiny_persistence: true do
        state :pending, initial: true

Method generate_tecan_data has 29 lines of code (exceeds 25 allowed). Consider refactoring.

Open

  def generate_tecan_data # rubocop:todo Metrics/AbcSize
    source_barcode = "#{plate.machine_barcode}_s"
    destination_barcode = "#{plate.machine_barcode}_d"
    data_object = {
      'user' => user.login,

Method grant_privileges has 29 lines of code (exceeds 25 allowed). Consider refactoring.

Open

  def grant_privileges # rubocop:todo Metrics/AbcSize
    Rails.logger.debug { 'Granting Administrator privileges' }

    # Labware
    can %i[edit rename change_purpose edit_retention_instruction], Labware

Method check_inputs_to_volume_to_cherrypick_by_nano_grams! has 29 lines of code (exceeds 25 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,