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Complex method Submission#next_requests_via_submission (58.5)
Open

  def next_requests_via_submission(request) # rubocop:todo Metrics/CyclomaticComplexity
    raise "Request #{request.id} is not part of submission #{id}" unless request.submission_id == id

    # Pick out the siblings of the request, so we can work out where it is in the list, and all of
    # the requests in the subsequent request type, so that we can tie them up.  We order by ID
Severity: Minor
Found in app/models/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 SubmissionSerializer::construct! (57.8)
Open

  def self.construct!(hash) # rubocop:todo Metrics/CyclomaticComplexity
    st = {}

    STRAIGHT_CLONE.each { |key| st[key.to_sym] = hash[key.to_sym] }
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

File studies_controller.rb has 310 lines of code (exceeds 250 allowed). Consider refactoring.
Open

require 'rexml/document'

# rubocop:todo Metrics/ClassLength
class StudiesController < ApplicationController
  # WARNING! This filter bypasses security mechanisms in rails 4 and mimics rails 2 behviour.
Severity: Minor
Found in app/controllers/studies_controller.rb - About 3 hrs to fix

    Method process has a Cognitive Complexity of 24 (exceeds 5 allowed). Consider refactoring.
    Open

      def process # rubocop:todo Metrics/CyclomaticComplexity
    # Store the details of the successful submissions so the user can be presented with a summary
    @submission_ids = []
    @completed_submissions = {}
    Severity: Minor
    Found in app/models/bulk_submission.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

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

      $("#report_fail_user_code").bind("keydown", function (e) {
    /* We don't take tab index into account here */
    var ENTER = 13,
      TAB = 9,
      code;
    Severity: Major
    Found in app/frontend/entrypoints/report_fails.js and 1 other location - About 3 hrs to fix
    app/frontend/entrypoints/labwhere_reception.js on lines 26..37

    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 103.

    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

        $("#labwhere_reception_user_code").bind("keydown", function (e) {
      /* We don't take tab index into account here */
      var ENTER = 13,
        TAB = 9,
        code;
    Severity: Major
    Found in app/frontend/entrypoints/labwhere_reception.js and 1 other location - About 3 hrs to fix
    app/frontend/entrypoints/report_fails.js on lines 9..20

    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 103.

    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

    Complex method StudyReport::StudyDetails#progress_report_on_all_assets (56.7)
    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 ...
    Severity: Minor
    Found in app/models/study_report/study_details.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::instance_action (56.7)
    Open

          def instance_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_attached: false,
    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

    Complex method namespace#record_loader (56.1)
    Open

    namespace :record_loader do
  desc 'Automatically generate TubeRackPurpose through TubeRackPurposeLoader'
  task tube_rack_purpose: :environment do
    RecordLoader::TubeRackPurposeLoader.new.create!
    Severity: Minor
    Found in lib/tasks/record_loader/tube_rack_purpose.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

    Complex method namespace(benchmark)::task#plate_transfer (56.0)
    Open

      task plate_transfer: :environment do
    $stdout.puts 'Preparing'
    stock = Purpose.find_by(name: 'Shear').create!
    sample = Sample.find_or_create_by(name: 'test_sample')
    stock.wells.each do |w|
    Severity: Minor
    Found in lib/tasks/benchmark_plate_transfer.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 SubmissionCreator has 28 methods (exceeds 20 allowed). Consider refactoring.
    Open

    class Submission::SubmissionCreator < Submission::PresenterSkeleton # rubocop:todo Metrics/ClassLength
  SubmissionsCreaterError = Class.new(StandardError)
  IncorrectParamsException = Class.new(SubmissionsCreaterError)
  InvalidInputException = Class.new(SubmissionsCreaterError)
    Severity: Minor
    Found in app/models/submission/submission_creator.rb - About 3 hrs to fix

      Complex method Accession::Sample#to_xml (55.8)
      Open

          def to_xml # rubocop:todo Metrics/AbcSize
      tag_groups = tags.by_group
      xml = Builder::XmlMarkup.new
      xml.instruct!
      xml.SAMPLE_SET(XML_NAMESPACE) do
      Severity: Minor
      Found in lib/accession/accession/sample.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 Tasks::CherrypickHandler#setup_input_params_for_pass_through (55.6)
      Open

        def setup_input_params_for_pass_through # rubocop:todo Metrics/AbcSize
    @robot_id = params[:robot_id]
    @robot = Robot.find(@robot_id)
    @plate_type = params[:plate_type]
    if params[:nano_grams_per_micro_litre]
      Severity: Minor
      Found in app/models/tasks/cherrypick_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

      Complex method Api::Base::render_class_for_model (55.4)
      Open

          def render_class_for_model(model) # rubocop:todo Metrics/CyclomaticComplexity
      render_class = Class.new(self)

      # NOTE: It's quite annoying that you don't have any access to the inheritable class attributes from
      # within the Class.new block above, so we have to do a separate instance_eval to get it to work.
      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 PlatesController#create_sample_tubes (55.2)
      Open

        def create_sample_tubes # rubocop:todo Metrics/AbcSize, Metrics/MethodLength
    barcode_printer = BarcodePrinter.find(params[:plates][:barcode_printer])
    barcode_array = params[:plates][:source_plates].scan(/\w+/)
    plates = Plate.with_barcode(barcode_array)
    study = Study.find(params[:plates][:study])
      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

      Complex method Api::Base::to_hash (55.1)
      Open

          def to_hash(object) # rubocop:todo Metrics/CyclomaticComplexity
      # If the object is nil we get a chance to use the 'default' object that was specified.  By
      # default the "default" object is nil, but you can override it for associations through the
      # with_association(:name, :if_nil_use => :some_method).
      object ||= default_object
      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 Api::SampleIO::with_association#sample_metadata (54.9)
      Open

        with_association(:sample_metadata) do
    map_attribute_to_json_attribute(:organism)
    map_attribute_to_json_attribute(:cohort)
    map_attribute_to_json_attribute(:country_of_origin)
    map_attribute_to_json_attribute(:geographical_region)
      Severity: Minor
      Found in app/models/api/sample_io.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 Well has 27 methods (exceeds 20 allowed). Consider refactoring.
      Open

      class Well < Receptacle # rubocop:todo Metrics/ClassLength
  include Api::WellIO::Extensions
  include ModelExtensions::Well
  include Cherrypick::VolumeByNanoGrams
  include Cherrypick::VolumeByNanoGramsPerMicroLitre
      Severity: Minor
      Found in app/models/well.rb - About 3 hrs to fix

        Complex method Admin::UsersController#grant_user_role (53.7)
        Open

          def grant_user_role # rubocop:todo Metrics/AbcSize, Metrics/MethodLength
    if request.xhr?
      if params[:role]
        authorizable_object =
          if params[:role][:authorizable_type] == 'Project'
        Severity: Minor
        Found in app/controllers/admin/users_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 AssetsController#lookup (53.6)
        Open

          def lookup # rubocop:todo Metrics/AbcSize, Metrics/MethodLength
    if params[:asset] && params[:asset][:barcode]
      @assets = Labware.with_barcode(params[:asset][:barcode]).limit(50).page(params[:page])

      case @assets.size
        Severity: Minor
        Found in app/controllers/assets_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

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