Class Batch has 55 methods (exceeds 20 allowed). Consider refactoring.

Open

class Batch < ApplicationRecord # rubocop:todo Metrics/ClassLength
  include Api::BatchIO::Extensions
  include Api::Messages::FlowcellIO::Extensions
  include AASM
  include SequencingQcBatch

Class Plate has 51 methods (exceeds 20 allowed). Consider refactoring.

Open

class Plate < Labware # rubocop:todo Metrics/ClassLength
  include Api::PlateIO::Extensions
  include ModelExtensions::Plate
  include Transfer::Associations
  include Transfer::State::PlateState

File batch.rb has 416 lines of code (exceeds 250 allowed). Consider refactoring.

Open

require 'timeout'
require 'aasm'

# A {Batch} groups 1 or more {Request requests} together to enable processing in a
# {Pipeline}. All requests in a batch get usually processed together, although it is

Class Request has 43 methods (exceeds 20 allowed). Consider refactoring.

Open

class Request < ApplicationRecord # rubocop:todo Metrics/ClassLength
  # Include
  include ModelExtensions::Request
  include Aliquot::DeprecatedBehaviours::Request
  include Api::RequestIO::Extensions

File study.rb has 396 lines of code (exceeds 250 allowed). Consider refactoring.

Open

require 'aasm'

# A Study is a collection of various {Sample samples} and the work done on them.
# They are perhaps slightly overloaded, and provide:
# - A means of grouping together samples for administrative purposes

File request.rb has 392 lines of code (exceeds 250 allowed). Consider refactoring.

Open

require 'aasm'

# A Request represents work which needs to be done, either to fulfil a customers
# needs {CustomerRequest} or for internal reasons {SystemRequest}.
# The progress of a request is tracked through its {Request::Statemachine state machine}.

File sample.rb has 386 lines of code (exceeds 250 allowed). Consider refactoring.

Open

require 'rexml/text'

#
# A {Sample} is an abstract concept, with represents the life of a sample of DNA/RNA
# as it moves through our processes. As a result, a sample may exist in multiple

Class Order has 38 methods (exceeds 20 allowed). Consider refactoring.

Open

class Order < ApplicationRecord # rubocop:todo Metrics/ClassLength
  # Ensure order methods behave correctly
  AssetTypeError = Class.new(StandardError)
  DEFAULT_ASSET_INPUT_METHODS = ['select an asset group'].freeze

Class Map has 38 methods (exceeds 20 allowed). Consider refactoring.

Open

class Map < ApplicationRecord
  validates :description, :asset_size, :location_id, :row_order, :column_order, :asset_shape, presence: true
  validates :asset_size, :row_order, :column_order, numericality: true

  # @!attribute description

Method create_request_chain! has a Cognitive Complexity of 32 (exceeds 5 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

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Class BatchesController has 36 methods (exceeds 20 allowed). Consider refactoring.

Open

class BatchesController < ApplicationController # rubocop:todo Metrics/ClassLength
  # WARNING! This filter bypasses security mechanisms in rails 4 and mimics rails 2 behaviour.
  # It should be removed wherever possible and the correct Strong  Parameter options applied in its place.

  before_action :evil_parameter_hack!

Method login_required has a Cognitive Complexity of 30 (exceeds 5 allowed). Consider refactoring.

Open

  def login_required # rubocop:todo Metrics/CyclomaticComplexity
    username, passwd = get_auth_data

    if username && passwd
      user = User.authenticate(username, passwd)

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Method do_cherrypick_task has a Cognitive Complexity of 29 (exceeds 5 allowed). Consider refactoring.

Open

  def do_cherrypick_task(_task, params) # rubocop:todo Metrics/CyclomaticComplexity
    plates = params[:plate]
    size = params[:plate_size]
    plate_type = params[:plate_type]

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Class Study has 33 methods (exceeds 20 allowed). Consider refactoring.

Open

class Study < ApplicationRecord # rubocop:todo Metrics/ClassLength
  # It has to be here, as there are has_many through: :roles associations in modules
  # Includes / Extendes
  has_many :roles

Method duplicate_barcodes has a Cognitive Complexity of 27 (exceeds 5 allowed). Consider refactoring.

Open

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

          unique_bcs = {}
          unique_plates = {}

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Class StudiesController has 31 methods (exceeds 20 allowed). Consider refactoring.

Open

class StudiesController < ApplicationController
  # WARNING! This filter bypasses security mechanisms in rails 4 and mimics rails 2 behviour.
  # It should be removed wherever possible and the correct Strong  Parameter options applied in its place.
  before_action :evil_parameter_hack!
  include REXML

Class Row has 31 methods (exceeds 20 allowed). Consider refactoring.

Open

    class Row # rubocop:todo Metrics/ClassLength
      include ActiveModel::Model
      include Converters

      attr_accessor :number, :data, :columns, :cache

Class TestWorksheet has 31 methods (exceeds 20 allowed). Consider refactoring.

Open

    class TestWorksheet < SequencescapeExcel::Worksheet::Base # rubocop:todo Metrics/ClassLength
      include SequencescapeExcel::Helpers::Worksheet

      self.worksheet_name = 'DNA Collections Form'

File bulk_submission.rb has 325 lines of code (exceeds 250 allowed). Consider refactoring.

Open

module ArrayWithFieldList
  refine Array do
    def comma_separate_field_list_for_display(*fields)
      field_list(*fields).join(', ')
    end

File batches_controller.rb has 325 lines of code (exceeds 250 allowed). Consider refactoring.

Open

class BatchesController < ApplicationController # rubocop:todo Metrics/ClassLength
  # WARNING! This filter bypasses security mechanisms in rails 4 and mimics rails 2 behaviour.
  # It should be removed wherever possible and the correct Strong  Parameter options applied in its place.

  before_action :evil_parameter_hack!