Method generate_json_to_object_mapping has 62 lines of code (exceeds 25 allowed). Consider refactoring.

Open

  def generate_json_to_object_mapping(json_to_attribute) # rubocop:todo Metrics/CyclomaticComplexity
    code = []

    # Split the mappings into two to make things easier.  Read only attributes are easily
    # handled right now, provided there is not a read_write one that shares their name.

File well.rb has 269 lines of code (exceeds 250 allowed). Consider refactoring.

Open

class Well < Receptacle # rubocop:todo Metrics/ClassLength
  include Api::WellIO::Extensions
  include ModelExtensions::Well
  include Cherrypick::VolumeByNanoGrams
  include Cherrypick::VolumeByNanoGramsPerMicroLitre

Method stage has a Cognitive Complexity of 18 (exceeds 5 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]

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Class SampleManifest has 22 methods (exceeds 20 allowed). Consider refactoring.

Open

class SampleManifest < ApplicationRecord # rubocop:todo Metrics/ClassLength
  include Uuid::Uuidable
  include ModelExtensions::SampleManifest
  include SampleManifest::BarcodePrinterBehaviour
  include SampleManifest::CoreBehaviour

Class Base has 22 methods (exceeds 20 allowed). Consider refactoring.

Open

      class Base
        MANDATORY_FIELDS = %w[country_of_origin date_of_sample_collection].freeze

        include ActiveModel::Model
        include SequencescapeExcel::SubclassChecker

Method render_cherrypick_task has a Cognitive Complexity of 17 (exceeds 5 allowed). Consider refactoring.

Open

  def render_cherrypick_task(_task, params) # rubocop:todo Metrics/CyclomaticComplexity
    if flash[:error].present?
      redirect_to action: 'stage', batch_id: @batch.id, workflow_id: @workflow.id, id: (@stage - 1).to_s
      return
    end

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File submissions.js has 258 lines of code (exceeds 250 allowed). Consider refactoring.

Open

// Submission workflow jQuery Plugin...
(function (window, $) {
  "use strict";

  var methods = {

Class Aliquot has 21 methods (exceeds 20 allowed). Consider refactoring.

Open

class Aliquot < ApplicationRecord # rubocop:todo Metrics/ClassLength
  include Uuid::Uuidable
  include Api::Messages::FlowcellIO::AliquotExtensions
  include Api::Messages::QcResultIO::AliquotExtensions
  include AliquotIndexer::AliquotScopes

Class Pooling has 21 methods (exceeds 20 allowed). Consider refactoring.

Open

class Pooling # rubocop:todo Metrics/ClassLength
  include ActiveModel::Model

  attr_writer :barcodes, :source_assets
  attr_accessor :stock_mx_tube_required, :stock_mx_tube, :standard_mx_tube, :barcode_printer, :count

Class Pipeline has 21 methods (exceeds 20 allowed). Consider refactoring.

Open

class Pipeline < ApplicationRecord # rubocop:todo Metrics/ClassLength
  include Uuid::Uuidable
  include Pipeline::BatchValidation
  include SharedBehaviour::Named

Method default_permitted_metadata_fields has 54 lines of code (exceeds 25 allowed). Consider refactoring.

Open

  def default_permitted_metadata_fields
    {
      sample_metadata_attributes: %i[
        consent_withdrawn
        organism

Method included has a Cognitive Complexity of 16 (exceeds 5 allowed). Consider refactoring.

Open

  def self.included(base) # rubocop:todo Metrics/AbcSize, Metrics/MethodLength
    base.class_eval do
      # We probably want to move this validation
      validates_each(:project, if: :checking_project?) do |record, _attr, project|
        record.errors.add(:base, "Project #{project.name} is not approved") unless project.approved?

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Method submit has 52 lines of code (exceeds 25 allowed). Consider refactoring.

Open

  def submit(user, *accessionables) # rubocop:todo Metrics/CyclomaticComplexity
    ActiveRecord::Base.transaction do
      submission = Accessionable::Submission.new(self, user, *accessionables)

      errors = submission.all_accessionables.map(&:errors).flatten

File receptacle.rb has 251 lines of code (exceeds 250 allowed). Consider refactoring.

Open

class Receptacle < Asset # rubocop:todo Metrics/ClassLength
  include Uuid::Uuidable
  include Commentable
  include Transfer::State
  include Aliquot::Remover

Method sample_named has 50 lines of code (exceeds 25 allowed). Consider refactoring.

Open

    def sample_named(name, study)
      {
        'sample_tube_attributes' => {
          'two_dimensional_barcode' => ''
        },

Method render_cherrypick_task has 48 lines of code (exceeds 25 allowed). Consider refactoring.

Open

  def render_cherrypick_task(_task, params) # rubocop:todo Metrics/CyclomaticComplexity
    if flash[:error].present?
      redirect_to action: 'stage', batch_id: @batch.id, workflow_id: @workflow.id, id: (@stage - 1).to_s
      return
    end

Function addOrderHandler has 48 lines of code (exceeds 25 allowed). Consider refactoring.

Open

  var addOrderHandler = function (_event) {
    // Loads this order's parameters into thewindow.SCAPE.submission object...
    $("#order-parameters")
      .find("select, input")
      .each(function () {

Method included has 48 lines of code (exceeds 25 allowed). Consider refactoring.

Open

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

Method handle_has_many has a Cognitive Complexity of 15 (exceeds 5 allowed). Consider refactoring.

Open

    def handle_has_many(attributes, attribute, json, object) # rubocop:todo Metrics/CyclomaticComplexity
      if json.first.is_a?(Hash)
        uuids = Uuid.include_resource.lookup_many_uuids(json.filter_map { |j| j['uuid'] })
        uuid_to_resource = uuids.each_with_object({}) { |uuid, hash| hash[uuid.external_id] = uuid.resource }
        mapped_attributes =

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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 ...