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Complex method Submission::SubmissionCreator#save (50.3)
Open

  def save # rubocop:todo Metrics/AbcSize
    begin
      ActiveRecord::Base.transaction do
        # Add assets to the order...
        new_order = create_order.tap { |o| o.update!(order_assets) }
Severity: Minor
Found in app/models/submission/submission_creator.rb by flog

Flog calculates the ABC score for methods. The ABC score is based on assignments, branches (method calls), and conditions.

You can read more about ABC metrics or the flog tool

Complex method Batch::StateMachineBehaviour::included (50.3)
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
Severity: Minor
Found in app/models/batch/state_machine_behaviour.rb by flog

Flog calculates the ABC score for methods. The ABC score is based on assignments, branches (method calls), and conditions.

You can read more about ABC metrics or the flog tool

Complex method SampleManifestExcel::Worksheet::TestWorksheet#record_tube_samples (50.0)
Open

      def record_tube_samples # rubocop:todo Metrics/AbcSize
        tube_counter = 0
        first_to_last.each do |sheet_row|
          row = dynamic_attributes[sheet_row]
          build_tube_sample_manifest_asset do |sample_manifest_asset|
Severity: Minor
Found in app/sample_manifest_excel/sample_manifest_excel/worksheet/test_worksheet.rb by flog

Flog calculates the ABC score for methods. The ABC score is based on assignments, branches (method calls), and conditions.

You can read more about ABC metrics or the flog tool

Complex method CherrypickTask#perform_pick (49.8)
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 = []
Severity: Minor
Found in app/models/cherrypick_task.rb by flog

Flog calculates the ABC score for methods. The ABC score is based on assignments, branches (method calls), and conditions.

You can read more about ABC metrics or the flog tool

Complex method PlatePicksController#batches (49.3)
Open

  def batches # rubocop:todo Metrics/AbcSize, Metrics/MethodLength
    batch = Batch.find(params[:id])

    # Either we're not a cherrypick batch, or we haven't been processed
Severity: Minor
Found in app/controllers/plate_picks_controller.rb by flog

Flog calculates the ABC score for methods. The ABC score is based on assignments, branches (method calls), and conditions.

You can read more about ABC metrics or the flog tool

Complex method SamplesController#taxon_lookup (49.2)
Open

  def taxon_lookup # rubocop:todo Metrics/AbcSize
    if params[:term]
      url = configatron.taxon_lookup_url + "/esearch.fcgi?db=taxonomy&term=#{params[:term].gsub(/\s/, '_')}"
    elsif params[:id]
      url = configatron.taxon_lookup_url + "/efetch.fcgi?db=taxonomy&mode=xml&id=#{params[:id]}"
Severity: Minor
Found in app/controllers/samples_controller.rb by flog

Flog calculates the ABC score for methods. The ABC score is based on assignments, branches (method calls), and conditions.

You can read more about ABC metrics or the flog tool

Method submit has a Cognitive Complexity of 20 (exceeds 5 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
Severity: Minor
Found in app/models/accession_service.rb - About 2 hrs 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

Complex method Api::Base::with_nested_has_many_association (48.3)
Open

  def self.with_nested_has_many_association(association, options = {}, &block) # rubocop:todo Metrics/AbcSize
    association_helper = Class.new(Api::Base)
    association_helper.class_eval(&block)
    association_helper.singleton_class.class_eval do
      define_method(:association) { association }
Severity: Minor
Found in app/models/api/base.rb by flog

Flog calculates the ABC score for methods. The ABC score is based on assignments, branches (method calls), and conditions.

You can read more about ABC metrics or the flog tool

Complex method Admin::StudiesController#managed_update (48.2)
Open

  def managed_update # rubocop:todo Metrics/AbcSize, Metrics/MethodLength
    @study = Study.find(params[:id])

    if params[:study][:uploaded_data].present?
      Document.create!(documentable: @study, uploaded_data: params[:study][:uploaded_data])
Severity: Minor
Found in app/controllers/admin/studies_controller.rb by flog

Flog calculates the ABC score for methods. The ABC score is based on assignments, branches (method calls), and conditions.

You can read more about ABC metrics or the flog tool

Complex method SampleManifestExcel::Worksheet::TestWorksheet#add_cell_data (48.1)
Open

      def add_cell_data(column, row_num, partial) # rubocop:todo Metrics/CyclomaticComplexity
        if partial && empty_row?(row_num)
          (data[column.name] || dynamic_attributes[row_num][column.name]) unless empty_columns.include?(column.name)
        elsif validation_errors.include?(:insert_size_from) && column.name == 'insert_size_from' &&
              row_num == computed_first_row
Severity: Minor
Found in app/sample_manifest_excel/sample_manifest_excel/worksheet/test_worksheet.rb by flog

Flog calculates the ABC score for methods. The ABC score is based on assignments, branches (method calls), and conditions.

You can read more about ABC metrics or the flog tool

Class User has 24 methods (exceeds 20 allowed). Consider refactoring.
Open

class User < ApplicationRecord # rubocop:todo Metrics/ClassLength
  include Authentication
  extend EventfulRecord
  include Uuid::Uuidable
  include Swipecardable
Severity: Minor
Found in app/models/user.rb - About 2 hrs to fix

    Complex method RequestsController#index (47.9)
    Open

      def index # rubocop:todo Metrics/CyclomaticComplexity, Metrics/MethodLength
    @study, @item = nil, nil

    # Ok, here we pick the initial source for the Requests.  They either come from Request (as in all Requests), or they
    # are limited by the Asset / Item.
    Severity: Minor
    Found in app/controllers/requests_controller.rb by flog

    Flog calculates the ABC score for methods. The ABC score is based on assignments, branches (method calls), and conditions.

    You can read more about ABC metrics or the flog tool

    Method prepare_order has 65 lines of code (exceeds 25 allowed). Consider refactoring.
    Open

      def prepare_order(details) # rubocop:todo Metrics/CyclomaticComplexity
    # Retrieve common attributes
    study = Study.find_by_id_or_name!(details['study id'], details['study name'])
    project = Project.find_by_id_or_name!(details['project id'], details['project name'])
    user = User.find_by(login: details['user login']) or
    Severity: Major
    Found in app/models/bulk_submission.rb - About 2 hrs to fix

      Method walk_wells has a Cognitive Complexity of 19 (exceeds 5 allowed). Consider refactoring.
      Open

        def walk_wells # rubocop:todo Metrics/CyclomaticComplexity
    # Adjust each of the groups so that any wells that are in the same pool as those at the same position
    # in the group to the left are moved to a non-clashing position.  Effectively this makes the view of the
    # plate slightly jagged.
    group_size =
      Severity: Minor
      Found in app/models/tag_layout/walk_wells_by_pools.rb - About 2 hrs 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

      Complex method Accessionable::Study#xml (46.9)
      Open

          def xml # rubocop:todo Metrics/AbcSize
      xml = Builder::XmlMarkup.new
      xml.instruct!
      xml.STUDY_SET('xmlns:xsi' => 'http://www.w3.org/2001/XMLSchema-instance') do
        xml.STUDY(alias: self.alias, accession: accession_number) do
      Severity: Minor
      Found in app/models/accessionable/study.rb by flog

      Flog calculates the ABC score for methods. The ABC score is based on assignments, branches (method calls), and conditions.

      You can read more about ABC metrics or the flog tool

      Complex method Plate::Creator#create_child_plates_from (46.6)
      Open

        def create_child_plates_from(plate, current_user, creator_parameters) # rubocop:todo Metrics/AbcSize
    stock_well_picker = plate.plate_purpose.stock_plate? ? ->(w) { [w] } : ->(w) { w.stock_wells }
    parent_wells = plate.wells

    parent_barcode = plate.human_barcode
      Severity: Minor
      Found in app/models/plate/creator.rb by flog

      Flog calculates the ABC score for methods. The ABC score is based on assignments, branches (method calls), and conditions.

      You can read more about ABC metrics or the flog tool

      Complex method namespace(report)::task#purposes (46.4)
      Open

        task purposes: :environment do
    Purpose.descendants.each do |klass|
      puts '=' * 80
      puts klass.name
      puts '-' * 80
      Severity: Minor
      Found in lib/tasks/report.rake by flog

      Flog calculates the ABC score for methods. The ABC score is based on assignments, branches (method calls), and conditions.

      You can read more about ABC metrics or the flog tool

      Class BulkSubmission has 23 methods (exceeds 20 allowed). Consider refactoring.
      Open

      class BulkSubmission # rubocop:todo Metrics/ClassLength
  # Activates the ArrayWithFieldList refinements for this class
  using ArrayWithFieldList

  # This is the default output from excel
      Severity: Minor
      Found in app/models/bulk_submission.rb - About 2 hrs to fix

        Class Basic has 23 methods (exceeds 20 allowed). Consider refactoring.
        Open

        class ProductCriteria::Basic
  SUPPORTED_WELL_ATTRIBUTES = %i[
    gel_pass
    concentration
    rin
        Severity: Minor
        Found in app/models/product_criteria/basic.rb - About 2 hrs to fix

          Class Attribute has 23 methods (exceeds 20 allowed). Consider refactoring.
          Open

            class Attribute # rubocop:todo Metrics/ClassLength
    attr_reader :name, :default

    alias assignable_attribute_name name
          Severity: Minor
          Found in app/models/attributable/attribute.rb - About 2 hrs to fix
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