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Method normalisation_details has a Cognitive Complexity of 6 (exceeds 5 allowed). Consider refactoring.
Open

    def normalisation_details(wells) # rubocop:todo Metrics/AbcSize
      # sort on well coordinate to ensure wells are in plate column order
      wells
        .sort_by(&:coordinate)
        .each_with_object({}) do |well, details|
Severity: Minor
Found in app/models/utility/common_dilution_calculations.rb - About 25 mins to fix

Cognitive Complexity

Cognitive Complexity is a measure of how difficult a unit of code is to intuitively understand. Unlike Cyclomatic Complexity, which determines how difficult your code will be to test, Cognitive Complexity tells you how difficult your code will be to read and comprehend.

A method's cognitive complexity is based on a few simple rules:

  • Code is not considered more complex when it uses shorthand that the language provides for collapsing multiple statements into one
  • Code is considered more complex for each "break in the linear flow of the code"
  • Code is considered more complex when "flow breaking structures are nested"

Further reading

Method check_for_unused_parents has a Cognitive Complexity of 6 (exceeds 5 allowed). Consider refactoring.
Open

    def check_for_unused_parents
      parent_beds.each do |parent_bed|
        next if beds[parent_bed].empty?
        next if used_parents.include?(parent_bed)
Severity: Minor
Found in app/models/robots/pooling_and_splitting_robot.rb - About 25 mins to fix

Cognitive Complexity

Cognitive Complexity is a measure of how difficult a unit of code is to intuitively understand. Unlike Cyclomatic Complexity, which determines how difficult your code will be to test, Cognitive Complexity tells you how difficult your code will be to read and comprehend.

A method's cognitive complexity is based on a few simple rules:

  • Code is not considered more complex when it uses shorthand that the language provides for collapsing multiple statements into one
  • Code is considered more complex for each "break in the linear flow of the code"
  • Code is considered more complex when "flow breaking structures are nested"

Further reading

Method concentration_bins has a Cognitive Complexity of 6 (exceeds 5 allowed). Consider refactoring.
Open

    def concentration_bins(norm_details)
      # Returns eg. { 1 => [], 2 => [], 3 => [] }
      conc_bins = (1..number_of_bins).index_with { |_bin_number| [] }
      norm_details.each do |well_locn, details|
        amount = details['amount_in_target']
Severity: Minor
Found in app/models/utility/normalised_binning_calculator.rb - About 25 mins to fix

Cognitive Complexity

Cognitive Complexity is a measure of how difficult a unit of code is to intuitively understand. Unlike Cyclomatic Complexity, which determines how difficult your code will be to test, Cognitive Complexity tells you how difficult your code will be to read and comprehend.

A method's cognitive complexity is based on a few simple rules:

  • Code is not considered more complex when it uses shorthand that the language provides for collapsing multiple statements into one
  • Code is considered more complex for each "break in the linear flow of the code"
  • Code is considered more complex when "flow breaking structures are nested"

Further reading

Method extract_pools_with_extra_details has a Cognitive Complexity of 6 (exceeds 5 allowed). Consider refactoring.
Open

    def extract_pools_with_extra_details
      extra_details = Hash.new { |hash, pool_name| hash[pool_name] = { locations: [] } }

      parent.wells_in_columns.each do |well|
        next if well.empty?
Severity: Minor
Found in app/models/labware_creators/pooled_tubes_by_sample.rb - About 25 mins to fix

Cognitive Complexity

Cognitive Complexity is a measure of how difficult a unit of code is to intuitively understand. Unlike Cyclomatic Complexity, which determines how difficult your code will be to test, Cognitive Complexity tells you how difficult your code will be to read and comprehend.

A method's cognitive complexity is based on a few simple rules:

  • Code is not considered more complex when it uses shorthand that the language provides for collapsing multiple statements into one
  • Code is considered more complex for each "break in the linear flow of the code"
  • Code is considered more complex when "flow breaking structures are nested"

Further reading

Method tubes_must_have_active_requests_of_expected_type has a Cognitive Complexity of 6 (exceeds 5 allowed). Consider refactoring.
Open

    def tubes_must_have_active_requests_of_expected_type
      return unless file_valid?

      parent_tubes.each do |foreign_barcode, tube_in_db|
        # NB. should be catching missing tubes in previous validation
Severity: Minor
Found in app/models/labware_creators/multi_stamp_tubes_using_tube_rack_scan.rb - About 25 mins to fix

Cognitive Complexity

Cognitive Complexity is a measure of how difficult a unit of code is to intuitively understand. Unlike Cyclomatic Complexity, which determines how difficult your code will be to test, Cognitive Complexity tells you how difficult your code will be to read and comprehend.

A method's cognitive complexity is based on a few simple rules:

  • Code is not considered more complex when it uses shorthand that the language provides for collapsing multiple statements into one
  • Code is considered more complex for each "break in the linear flow of the code"
  • Code is considered more complex when "flow breaking structures are nested"

Further reading

Method compute_bin_details_by_well has a Cognitive Complexity of 6 (exceeds 5 allowed). Consider refactoring.
Open

    def compute_bin_details_by_well(well_amounts)
      well_amounts.each_with_object({}) do |(well_locn, amount), well_colours|
        bins_template.each do |bin_template|
          next unless (bin_template['min']...bin_template['max']).cover?(amount)
Severity: Minor
Found in app/models/utility/common_dilution_calculations.rb - About 25 mins to fix

Cognitive Complexity

Cognitive Complexity is a measure of how difficult a unit of code is to intuitively understand. Unlike Cyclomatic Complexity, which determines how difficult your code will be to test, Cognitive Complexity tells you how difficult your code will be to read and comprehend.

A method's cognitive complexity is based on a few simple rules:

  • Code is not considered more complex when it uses shorthand that the language provides for collapsing multiple statements into one
  • Code is considered more complex for each "break in the linear flow of the code"
  • Code is considered more complex when "flow breaking structures are nested"

Further reading

Function requestsFromPlates has a Cognitive Complexity of 6 (exceeds 5 allowed). Consider refactoring.
Open

const requestsFromPlates = function (plateObjs) {
  const requestsArray = []
  for (let p = 0; p < plateObjs.length; p++) {
    const plateObj = plateObjs[p]
    const wells = plateObj.plate.wells
Severity: Minor
Found in app/frontend/javascript/shared/requestHelpers.js - About 25 mins to fix

Cognitive Complexity

Cognitive Complexity is a measure of how difficult a unit of code is to intuitively understand. Unlike Cyclomatic Complexity, which determines how difficult your code will be to test, Cognitive Complexity tells you how difficult your code will be to read and comprehend.

A method's cognitive complexity is based on a few simple rules:

  • Code is not considered more complex when it uses shorthand that the language provides for collapsing multiple statements into one
  • Code is considered more complex for each "break in the linear flow of the code"
  • Code is considered more complex when "flow breaking structures are nested"

Further reading

Method concentration_bins has a Cognitive Complexity of 6 (exceeds 5 allowed). Consider refactoring.
Open

    def concentration_bins(well_amounts) # rubocop:todo Metrics/AbcSize
      # Returns eg. { 1 => [], 2 => [], 3 => [] }
      conc_bins = (1..number_of_bins).index_with { |_bin_number| [] }
      well_amounts.each do |well_locn, amount|
        bins_template.each_with_index do |bin_template, bin_index|
Severity: Minor
Found in app/models/utility/concentration_binning_calculator.rb - About 25 mins to fix

Cognitive Complexity

Cognitive Complexity is a measure of how difficult a unit of code is to intuitively understand. Unlike Cyclomatic Complexity, which determines how difficult your code will be to test, Cognitive Complexity tells you how difficult your code will be to read and comprehend.

A method's cognitive complexity is based on a few simple rules:

  • Code is not considered more complex when it uses shorthand that the language provides for collapsing multiple statements into one
  • Code is considered more complex for each "break in the linear flow of the code"
  • Code is considered more complex when "flow breaking structures are nested"

Further reading

Method print_to_pmb has a Cognitive Complexity of 6 (exceeds 5 allowed). Consider refactoring.
Open

  def print_to_pmb
    # Ensure the template exists before attempting to print
    label_template_id = pmb_label_template_id
    return false if label_template_id.nil?
Severity: Minor
Found in app/models/print_job.rb - About 25 mins to fix

Cognitive Complexity

Cognitive Complexity is a measure of how difficult a unit of code is to intuitively understand. Unlike Cyclomatic Complexity, which determines how difficult your code will be to test, Cognitive Complexity tells you how difficult your code will be to read and comprehend.

A method's cognitive complexity is based on a few simple rules:

  • Code is not considered more complex when it uses shorthand that the language provides for collapsing multiple statements into one
  • Code is considered more complex for each "break in the linear flow of the code"
  • Code is considered more complex when "flow breaking structures are nested"

Further reading

Method active_wells_with_terminated_requests has a Cognitive Complexity of 6 (exceeds 5 allowed). Consider refactoring.
Open

    def active_wells_with_terminated_requests(labware)
      labware.wells.filter_map do |well|
        next if well.inactive? || well.active_requests.empty?

        well.location if well.active_requests.all?(&:failed?)
Severity: Minor
Found in app/models/validators/failed_validator.rb - About 25 mins to fix

Cognitive Complexity

Cognitive Complexity is a measure of how difficult a unit of code is to intuitively understand. Unlike Cyclomatic Complexity, which determines how difficult your code will be to test, Cognitive Complexity tells you how difficult your code will be to read and comprehend.

A method's cognitive complexity is based on a few simple rules:

  • Code is not considered more complex when it uses shorthand that the language provides for collapsing multiple statements into one
  • Code is considered more complex for each "break in the linear flow of the code"
  • Code is considered more complex when "flow breaking structures are nested"

Further reading

Method compute_well_amounts has a Cognitive Complexity of 6 (exceeds 5 allowed). Consider refactoring.
Open

    def compute_well_amounts(wells, multiplication_factor)
      # sort on well coordinate to ensure wells are in plate column order
      wells
        .sort_by(&:coordinate)
        .each_with_object({}) do |well, well_amounts|
Severity: Minor
Found in app/models/utility/concentration_binning_calculator.rb - About 25 mins to fix

Cognitive Complexity

Cognitive Complexity is a measure of how difficult a unit of code is to intuitively understand. Unlike Cyclomatic Complexity, which determines how difficult your code will be to test, Cognitive Complexity tells you how difficult your code will be to read and comprehend.

A method's cognitive complexity is based on a few simple rules:

  • Code is not considered more complex when it uses shorthand that the language provides for collapsing multiple statements into one
  • Code is considered more complex for each "break in the linear flow of the code"
  • Code is considered more complex when "flow breaking structures are nested"

Further reading

Method initialize has a Cognitive Complexity of 6 (exceeds 5 allowed). Consider refactoring.
Open

  def initialize(params = {})
    @user_uuid = params.fetch(:user_uuid, nil)
    @user = Sequencescape::Api::V2::User.find(uuid: @user_uuid).first unless @user_uuid.nil?
    @barcode = params.fetch(:barcode, nil)
    if barcode.present?
Severity: Minor
Found in app/models/labware_metadata.rb - About 25 mins to fix

Cognitive Complexity

Cognitive Complexity is a measure of how difficult a unit of code is to intuitively understand. Unlike Cyclomatic Complexity, which determines how difficult your code will be to test, Cognitive Complexity tells you how difficult your code will be to read and comprehend.

A method's cognitive complexity is based on a few simple rules:

  • Code is not considered more complex when it uses shorthand that the language provides for collapsing multiple statements into one
  • Code is considered more complex for each "break in the linear flow of the code"
  • Code is considered more complex when "flow breaking structures are nested"

Further reading

Method tubes_must_be_of_expected_purpose_type has a Cognitive Complexity of 6 (exceeds 5 allowed). Consider refactoring.
Open

    def tubes_must_be_of_expected_purpose_type
      return unless file_valid?

      parent_tubes.each do |foreign_barcode, tube_in_db|
        # NB. should be catching missing tubes in previous validation
Severity: Minor
Found in app/models/labware_creators/multi_stamp_tubes_using_tube_rack_scan.rb - About 25 mins to fix

Cognitive Complexity

Cognitive Complexity is a measure of how difficult a unit of code is to intuitively understand. Unlike Cyclomatic Complexity, which determines how difficult your code will be to test, Cognitive Complexity tells you how difficult your code will be to read and comprehend.

A method's cognitive complexity is based on a few simple rules:

  • Code is not considered more complex when it uses shorthand that the language provides for collapsing multiple statements into one
  • Code is considered more complex for each "break in the linear flow of the code"
  • Code is considered more complex when "flow breaking structures are nested"

Further reading

Method child_labware_of_plate has a Cognitive Complexity of 6 (exceeds 5 allowed). Consider refactoring.
Open

    def child_labware_of_plate
      labware
        .wells
        .sort_by(&well_order)
        .each_with_object([]) do |well, plates|
Severity: Minor
Found in app/models/robots/bed/splitting.rb - About 25 mins to fix

Cognitive Complexity

Cognitive Complexity is a measure of how difficult a unit of code is to intuitively understand. Unlike Cyclomatic Complexity, which determines how difficult your code will be to test, Cognitive Complexity tells you how difficult your code will be to read and comprehend.

A method's cognitive complexity is based on a few simple rules:

  • Code is not considered more complex when it uses shorthand that the language provides for collapsing multiple statements into one
  • Code is considered more complex for each "break in the linear flow of the code"
  • Code is considered more complex when "flow breaking structures are nested"

Further reading

Function checkQCableWalkingBy has a Cognitive Complexity of 6 (exceeds 5 allowed). Consider refactoring.
Open

const checkQCableWalkingBy = (allowedWalkingByList) => {
  return (qcable) => {
    if (!qcable.lot || !qcable.lot.tag_layout_template || !qcable.lot.tag_layout_template.walking_by) {
      return {
        valid: false,
Severity: Minor
Found in app/frontend/javascript/shared/components/plateScanValidators.js - About 25 mins to fix

Cognitive Complexity

Cognitive Complexity is a measure of how difficult a unit of code is to intuitively understand. Unlike Cyclomatic Complexity, which determines how difficult your code will be to test, Cognitive Complexity tells you how difficult your code will be to read and comprehend.

A method's cognitive complexity is based on a few simple rules:

  • Code is not considered more complex when it uses shorthand that the language provides for collapsing multiple statements into one
  • Code is considered more complex for each "break in the linear flow of the code"
  • Code is considered more complex when "flow breaking structures are nested"

Further reading

Function checkForUnacceptablePlatePurpose has a Cognitive Complexity of 6 (exceeds 5 allowed). Consider refactoring.
Open

const checkForUnacceptablePlatePurpose = (acceptable_purposes) => {
  return (plate) => {
    if (!acceptable_purposes || acceptable_purposes.length == 0) {
      // return valid if no acceptable purposes are provided
      return validScanMessage()
Severity: Minor
Found in app/frontend/javascript/shared/components/plateScanValidators.js - About 25 mins to fix

Cognitive Complexity

Cognitive Complexity is a measure of how difficult a unit of code is to intuitively understand. Unlike Cyclomatic Complexity, which determines how difficult your code will be to test, Cognitive Complexity tells you how difficult your code will be to read and comprehend.

A method's cognitive complexity is based on a few simple rules:

  • Code is not considered more complex when it uses shorthand that the language provides for collapsing multiple statements into one
  • Code is considered more complex for each "break in the linear flow of the code"
  • Code is considered more complex when "flow breaking structures are nested"

Further reading

Method stock_barcodes_by_quadrant has a Cognitive Complexity of 6 (exceeds 5 allowed). Consider refactoring.
Open

    def stock_barcodes_by_quadrant
      quadrants = {}
      source_plates_by_quadrant.each_with_index do |uuid, index|
        next if uuid.nil?
Severity: Minor
Found in app/models/labware_creators/quadrant_stamp_base.rb - About 25 mins to fix

Cognitive Complexity

Cognitive Complexity is a measure of how difficult a unit of code is to intuitively understand. Unlike Cyclomatic Complexity, which determines how difficult your code will be to test, Cognitive Complexity tells you how difficult your code will be to read and comprehend.

A method's cognitive complexity is based on a few simple rules:

  • Code is not considered more complex when it uses shorthand that the language provides for collapsing multiple statements into one
  • Code is considered more complex for each "break in the linear flow of the code"
  • Code is considered more complex when "flow breaking structures are nested"

Further reading

Similar blocks of code found in 2 locations. Consider refactoring.
Open

  class MinimalPcrPlatePresenter < MinimalPlatePresenter # rubocop:todo Style/Documentation
    include HasPrimerPanel
    self.summary_partial = 'labware/plates/pcr_summary'
    self.state_transition_name_scope = :pcr
Severity: Minor
Found in app/models/presenters/minimal_pcr_plate_presenter.rb and 1 other location - About 25 mins to fix
app/models/presenters/pcr_with_primer_panel_plate_presenter.rb on lines 11..26

Duplicated Code

Duplicated code can lead to software that is hard to understand and difficult to change. The Don't Repeat Yourself (DRY) principle states:

Every piece of knowledge must have a single, unambiguous, authoritative representation within a system.

When you violate DRY, bugs and maintenance problems are sure to follow. Duplicated code has a tendency to both continue to replicate and also to diverge (leaving bugs as two similar implementations differ in subtle ways).

Tuning

This issue has a mass of 29.

We set useful threshold defaults for the languages we support but you may want to adjust these settings based on your project guidelines.

The threshold configuration represents the minimum mass a code block must have to be analyzed for duplication. The lower the threshold, the more fine-grained the comparison.

If the engine is too easily reporting duplication, try raising the threshold. If you suspect that the engine isn't catching enough duplication, try lowering the threshold. The best setting tends to differ from language to language.

See codeclimate-duplication's documentation for more information about tuning the mass threshold in your .codeclimate.yml.

Refactorings

Further Reading

Similar blocks of code found in 2 locations. Consider refactoring.
Open

  class PcrWithPrimerPanelPlatePresenter < StandardPresenter
    include HasPrimerPanel
    self.summary_partial = 'labware/plates/pcr_with_primer_panel_summary'
    self.state_transition_name_scope = :pcr
Severity: Minor
Found in app/models/presenters/pcr_with_primer_panel_plate_presenter.rb and 1 other location - About 25 mins to fix
app/models/presenters/minimal_pcr_plate_presenter.rb on lines 4..19

Duplicated Code

Duplicated code can lead to software that is hard to understand and difficult to change. The Don't Repeat Yourself (DRY) principle states:

Every piece of knowledge must have a single, unambiguous, authoritative representation within a system.

When you violate DRY, bugs and maintenance problems are sure to follow. Duplicated code has a tendency to both continue to replicate and also to diverge (leaving bugs as two similar implementations differ in subtle ways).

Tuning

This issue has a mass of 29.

We set useful threshold defaults for the languages we support but you may want to adjust these settings based on your project guidelines.

The threshold configuration represents the minimum mass a code block must have to be analyzed for duplication. The lower the threshold, the more fine-grained the comparison.

If the engine is too easily reporting duplication, try raising the threshold. If you suspect that the engine isn't catching enough duplication, try lowering the threshold. The best setting tends to differ from language to language.

See codeclimate-duplication's documentation for more information about tuning the mass threshold in your .codeclimate.yml.

Refactorings

Further Reading

Similar blocks of code found in 2 locations. Consider refactoring.
Open

  def primary_index(row, column, scale, height, width)
    tag_col = (column / scale)
    tag_row = (row / scale)
    ((height / scale) * (width / scale)) - (tag_row + (height / scale * tag_col)) - 1
Severity: Minor
Found in app/models/limber/tag_layout_template/in_inverse_columns.rb and 1 other location - About 20 mins to fix
app/models/limber/tag_layout_template/in_inverse_rows.rb on lines 22..25

Duplicated Code

Duplicated code can lead to software that is hard to understand and difficult to change. The Don't Repeat Yourself (DRY) principle states:

Every piece of knowledge must have a single, unambiguous, authoritative representation within a system.

When you violate DRY, bugs and maintenance problems are sure to follow. Duplicated code has a tendency to both continue to replicate and also to diverge (leaving bugs as two similar implementations differ in subtle ways).

Tuning

This issue has a mass of 27.

We set useful threshold defaults for the languages we support but you may want to adjust these settings based on your project guidelines.

The threshold configuration represents the minimum mass a code block must have to be analyzed for duplication. The lower the threshold, the more fine-grained the comparison.

If the engine is too easily reporting duplication, try raising the threshold. If you suspect that the engine isn't catching enough duplication, try lowering the threshold. The best setting tends to differ from language to language.

See codeclimate-duplication's documentation for more information about tuning the mass threshold in your .codeclimate.yml.

Refactorings

Further Reading

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