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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
Severity: Minor
Found in app/models/order.rb - About 5 hrs to fix

    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
    Severity: Minor
    Found in app/models/map.rb - About 5 hrs to fix

      Complex method BatchesHelper#output_aliquot (75.6)
      Open

        def output_aliquot(xml, aliquot) # rubocop:todo Metrics/AbcSize, Metrics/MethodLength
    xml.sample(
      sample_id: aliquot.sample_id,
      library_id: aliquot.library_id,
      library_name: aliquot.library_name,
      Severity: Minor
      Found in app/helpers/batches_helper.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 WorkflowsController#stage (74.2)
      Open

        def stage # rubocop:todo Metrics/CyclomaticComplexity
    @workflow = Workflow.includes(:tasks).find(params[:workflow_id])
    @stage = params[:id].to_i
    @task = @workflow.tasks[@stage]
      Severity: Minor
      Found in app/controllers/workflows_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 Api::EndpointHandler::file_model_addition (73.4)
      Open

            def file_model_addition(action, http_method) # rubocop:todo Metrics/AbcSize
        send(http_method, %r{/([^\d/][^/]+(?:/[^/]+){0,2})}, file_attached: true) do
          if request.acceptable_media_types.prioritize(registered_mimetypes).present?
            raise Core::Service::ContentFiltering::InvalidRequestedContentType
          end
      Severity: Minor
      Found in app/middleware/api/endpoint_handler.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 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
      Severity: Minor
      Found in app/models/submission/linear_request_graph.rb - About 4 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 Admin::StudiesController#filter (72.6)
      Open

        def filter # rubocop:todo Metrics/CyclomaticComplexity
    filter_conditions = { approved: false } if params[:filter][:by] == 'not approved' unless params[:filter].nil?

    if params[:filter][:by] == 'not approved' || params[:filter][:by] == 'all'
      @studies = Study.where(filter_conditions).alphabetical.select { |p| p.name.include? params[:q] }
      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 main#perform (72.6)
      Open

          def perform
      Submission.find(submission_id).build_batch
      Severity: Minor
      Found in app/jobs/submission_builder_job.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 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!
      Severity: Minor
      Found in app/controllers/batches_controller.rb - About 4 hrs to fix

        Complex method LabwareController#index (69.9)
        Open

          def index # rubocop:todo Metrics/AbcSize, Metrics/MethodLength
    if params[:study_id]
      @study = Study.find(params[:study_id])
      @assets = @study.assets_through_aliquots.order(:name).page(params[:page])
    else
        Severity: Minor
        Found in app/controllers/labware_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 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)
        Severity: Minor
        Found in lib/authenticated_system.rb - About 4 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 PlatesController#create (67.1)
        Open

          def create # rubocop:todo Metrics/AbcSize
    @creator = plate_creator = Plate::Creator.find(params[:plates][:creator_id])
    barcode_printer = BarcodePrinter.find(params[:plates][:barcode_printer])
    source_plate_barcodes = params[:plates][:source_plates]
    create_asset_group = params[:plates][:create_asset_group] == 'Yes'
        Severity: Minor
        Found in app/controllers/plates_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 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]
        Severity: Minor
        Found in app/models/tasks/cherrypick_handler.rb - About 4 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::EndpointHandler::file_action (66.9)
        Open

              def file_action(action, http_method) # rubocop:todo Metrics/AbcSize, Metrics/MethodLength
        send(
          http_method,
          %r{/([\da-f]{8}(?:-[\da-f]{4}){3}-[\da-f]{12})(?:/([^/]+(?:/[^/]+)*))?},
          file_requested: true
        Severity: Minor
        Found in app/middleware/api/endpoint_handler.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 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
        Severity: Minor
        Found in app/models/study.rb - About 4 hrs to fix

          Complex method Endpoints::Uuids::bind_action#create (64.8)
          Open

              bind_action(:create, to: 'bulk', as: :bulk) do |_, request, response|
      lookup = request.json.respond_to?(:keys) ? request.json['lookup'] : nil
      uuids = Search.create_bulk!(lookup).map(&:find)

      # Hack time ...
          Severity: Minor
          Found in app/api/endpoints/uuids.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 BulkSubmission#submission_structure (64.7)
          Open

            def submission_structure # rubocop:todo Metrics/CyclomaticComplexity
    Hash
      .new { |h, i| h[i] = Array.new }
      .tap do |submission|
        csv_data_rows.each_with_index do |row, index|
          Severity: Minor
          Found in app/models/bulk_submission.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 Attributable::Attribute#configure (63.5)
          Open

              def configure(model) # rubocop:todo Metrics/CyclomaticComplexity
      conditions = @options.slice(:if, :on)
      save_blank_value = @options.delete(:save_blank)
      allow_blank = save_blank_value
      model.with_options(conditions) do |object|
          Severity: Minor
          Found in app/models/attributable/attribute.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 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 = {}
          Severity: Minor
          Found in app/sample_manifest_excel/sample_manifest_excel/upload/processor/plate.rb - About 3 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 SubmissionSerializer::serialize (62.1)
          Open

            def self.serialize(st) # rubocop:todo Metrics/CyclomaticComplexity
    attributes = st.attributes
    new_attributes = {}

    STRAIGHT_CLONE.each do |key|
          Severity: Minor
          Found in lib/submission_serializer.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

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