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

Open

  def sorted_pre_cap_pool_json(current_plate) # rubocop:todo Metrics/AbcSize
    unsorted =
      current_plate
        .wells_in_columns
        .each_with_object({}) do |well, pool_store|

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

Open

  newElement: function () {
    let scanned = this
    this.listElement = $(document.createElement('li'))
      .attr('id', 'listElement[' + this.tubeBarcode + ']')
      .attr('class', 'wait-tube')

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

Open

function extractParentWellSubmissionDetails(parentPlate) {
  if (!parentPlate) {
    return {}
  }

Function jsonFactory has 26 lines of code (exceeds 25 allowed). Consider refactoring.

Open

const jsonFactory = (factoryName, userAttributes = {}) => {
  const factory = findFactory(factoryName)
  const type = resourceName(factoryName)
  const resource_config = new ResourceConfig(type)

Function plateFactory has 26 lines of code (exceeds 25 allowed). Consider refactoring.

Open

const plateFactory = function (options = {}) {
  const { _filledWells, _wellOptions, ...plateOptions } = options
  let uuid = plateOptions.uuid || 'plate-uuid'
  let id = plateOptions.id || '1'
  // Bit inefficient, in that we generate wells even if we immediately override them

Function extractSubmDetailsFromAliquots has a Cognitive Complexity of 9 (exceeds 5 allowed). Consider refactoring.

Open

function extractSubmDetailsFromAliquots(well) {
  let submDetails = { id: null, usedTags: [] }

  const requestsLen = well.aliquots.length
  for (let i = 0; i < requestsLen; i++) {

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Function checkDuplicates has a Cognitive Complexity of 9 (exceeds 5 allowed). Consider refactoring.

Open

const checkDuplicates = (plateList) => {
  return (plate) => {
    let occurrences = 0
    for (let i = 0; i < plateList.length; i++) {
      if (plateList[i] && plate && plateList[i].uuid === plate.uuid) {

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Function checkDuplicates has a Cognitive Complexity of 9 (exceeds 5 allowed). Consider refactoring.

Open

const checkDuplicates = (tubeList) => {
  return (tube) => {
    let occurrences = 0
    for (let i = 0; i < tubeList.length; i++) {
      if (tubeList[i] && tube && tubeList[i].uuid === tube.uuid) {

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Method validate has a Cognitive Complexity of 9 (exceeds 5 allowed). Consider refactoring.

Open

    def validate(presenter) # rubocop:todo Metrics/AbcSize
      analyzer = Analyzer.new(presenter.labware)
      if analyzer.no_submission?
        presenter.errors.add(:plate, 'has no requests. Please check that your submission built correctly.')
      elsif analyzer.no_samples?

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Method mould_data_for_view has a Cognitive Complexity of 9 (exceeds 5 allowed). Consider refactoring.

Open

  def mould_data_for_view(purposes, labware_records)
    {}.tap do |output|
      # Make sure there's an entry for each of the purposes, even if no records
      purposes.each { |p| output[p] = [] }

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Function extractSubmDetailsFromRequestsAsSource has a Cognitive Complexity of 9 (exceeds 5 allowed). Consider refactoring.

Open

function extractSubmDetailsFromRequestsAsSource(well) {
  let submDetails = { id: null, usedTags: [] }

  const requestsLen = well.requests_as_source.length
  for (let i = 0; i < requestsLen; i++) {

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Method generate_msg_list_for_file_not_matching_submission has a Cognitive Complexity of 9 (exceeds 5 allowed). Consider refactoring.

Open

    def generate_msg_list_for_file_not_matching_submission
      parent_wells = parent.wells.map(&:location)
      parent_wells.filter_map do |well_locn|
        well_in_submission = parent_wells_with_requests.include?(well_locn)
        valid_well_row_in_file = well_locns_from_filtered_well_details.include?(well_locn)

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Function byFixedGroupByPlate has 6 arguments (exceeds 4 allowed). Consider refactoring.

Open

function byFixedGroupByPlate(_well, tags, _relIndex, absIndex, offset, _counters) {

Function byPool has 6 arguments (exceeds 4 allowed). Consider refactoring.

Open

function byPool(well, tags, _relIndex, _absIndex, offset, counters) {

Method check_control_rules_from_config has a Cognitive Complexity of 8 (exceeds 5 allowed). Consider refactoring.

Open

    def check_control_rules_from_config(control_locations)
      list_of_rules.each do |rule|
        case rule.type
        when 'not'
          # locations must not match this combination of wells (order is important)

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Method generate_tag_layout has a Cognitive Complexity of 8 (exceeds 5 allowed). Consider refactoring.

Open

  def generate_tag_layout(plate) # rubocop:todo Metrics/AbcSize
    tags = tag_ids
    groups = group_wells_of_plate(plate)
    pools = groups.filter_map { |w| w.try(:[], 1) }.uniq
    groups.each_with_object({}) do |(well, pool_id, _well_empty), tagged_wells|

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Method build_transfers_hash has a Cognitive Complexity of 8 (exceeds 5 allowed). Consider refactoring.

Open

    def build_transfers_hash(bins, number_of_rows, compression_reqd) # rubocop:todo Metrics/AbcSize
      binner = Binner.new(compression_reqd, number_of_rows)
      bins
        .values
        .each_with_object({})

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Method update_all_labware_metadata has a Cognitive Complexity of 8 (exceeds 5 allowed). Consider refactoring.

Open

  def update_all_labware_metadata(robot_barcode)
    @robot.beds.each_value do |bed|
      next unless bed.transitions? && bed.labware
      update_bed_labware_metadata(bed, robot_barcode)
    rescue Sequencescape::Api::ResourceNotFound

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Function byGroupByPlate has 6 arguments (exceeds 4 allowed). Consider refactoring.

Open

function byGroupByPlate(_well, tags, relIndex, _absIndex, offset, _counters) {

Function processTagsPerWell has 6 arguments (exceeds 4 allowed). Consider refactoring.

Open

function processTagsPerWell(acc, well, relIndex, absIndex, tagsPerWell, walker) {