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Complex method Core::Io::Base::JsonFormattingBehaviour::Input::AssociationHandling#handle_has_many (45.8)
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 =
Severity: Minor
Found in app/api/core/io/base/json_formatting_behaviour/input.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 test_worksheet.rb has 270 lines of code (exceeds 250 allowed). Consider refactoring.
Open

require_dependency 'sample_manifest_excel/tags'

module SampleManifestExcel
  module Worksheet
    ##
Severity: Minor
Found in app/sample_manifest_excel/sample_manifest_excel/worksheet/test_worksheet.rb - About 2 hrs to fix

    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.
    Severity: Major
    Found in app/api/core/io/base/json_formatting_behaviour/input.rb - About 2 hrs to fix

      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
      Severity: Minor
      Found in app/models/well.rb - About 2 hrs to fix

        Complex method ReceptaclesController#index (45.3)
        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(created_at: :desc).page(params[:page])
    else
        Severity: Minor
        Found in app/controllers/receptacles_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 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]
        Severity: Minor
        Found in app/controllers/workflows_controller.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

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

            it("registers a pick if none exists", () => {
      // mock state
      const state = defaultState();
      const new_pick = pick1({ id: 1 });
      // apply mutation
        Severity: Major
        Found in app/frontend/plate-picks/store/mutations.test.js and 1 other location - About 2 hrs to fix
        app/frontend/plate-picks/store/mutations.test.js on lines 28..36

        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 83.

        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

            it("registers a plate if none exists", () => {
      // mock state
      const state = defaultState();
      const new_plate = pendingScannedPlate({ id: 1 });
      // apply mutation
        Severity: Major
        Found in app/frontend/plate-picks/store/mutations.test.js and 1 other location - About 2 hrs to fix
        app/frontend/plate-picks/store/mutations.test.js on lines 54..62

        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 83.

        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 CherrypickTask#build_plate_wells_from_requests (44.8)
        Open

          def build_plate_wells_from_requests(requests, workflow_controller = nil) # rubocop:todo Metrics/AbcSize
    loaded_requests = Request.where(requests: { id: requests }).includes(asset: [{ plate: :barcodes }, :map])

    source_plate_barcodes = loaded_requests.map { |request| request.asset.plate.human_barcode }.uniq
        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 StudiesController::role_helper (44.5)
        Open

          def self.role_helper(name, success_action, error_action) # rubocop:todo Metrics/AbcSize
    define_method(:"#{name}_role") do
      ActiveRecord::Base.transaction do
        @study = Study.find(params[:id])
        @user = User.find(params.require(:role).fetch(:user))
        Severity: Minor
        Found in app/controllers/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 Accessionable::Sample#initialize (44.3)
        Open

            def initialize(sample) # rubocop:todo Metrics/CyclomaticComplexity
      @sample = sample
      super(sample.ebi_accession_number)

      sampname = sample.sample_metadata.sample_public_name
        Severity: Minor
        Found in app/models/accessionable/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

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

          def lookup # rubocop:todo Metrics/AbcSize, Metrics/MethodLength
    return unless params[:asset] && params[:asset][:barcode]

    @assets = Labware.with_barcode(params[:asset][:barcode]).limit(50).page(params[:page])
        Severity: Major
        Found in app/controllers/labware_controller.rb and 1 other location - About 2 hrs to fix
        app/controllers/receptacles_controller.rb on lines 181..199

        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 88.

        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

            const wrapper = shallowMount(PicksSectionBatchPick, {
      propsData: {
        name,
        short,
        id: "1",
        Severity: Major
        Found in app/frontend/plate-picks/components/PicksSectionBatchPick.test.js and 1 other location - About 2 hrs to fix
        app/frontend/plate-picks/components/PicksSectionBatchPick.test.js on lines 48..61

        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 82.

        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

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

          def lookup # rubocop:todo Metrics/AbcSize, Metrics/MethodLength
    return unless params[:asset] && params[:asset][:barcode]

    @assets = Labware.with_barcode(params[:asset][:barcode]).limit(50).page(params[:page])
        Severity: Major
        Found in app/controllers/receptacles_controller.rb and 1 other location - About 2 hrs to fix
        app/controllers/labware_controller.rb on lines 125..143

        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 88.

        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

            const wrapper = shallowMount(PicksSectionBatchPick, {
      propsData: {
        name,
        short,
        id: "1",
        Severity: Major
        Found in app/frontend/plate-picks/components/PicksSectionBatchPick.test.js and 1 other location - About 2 hrs to fix
        app/frontend/plate-picks/components/PicksSectionBatchPick.test.js on lines 66..79

        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 82.

        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 ProjectsController#remove_role (44.2)
        Open

          def remove_role # rubocop:todo Metrics/AbcSize
    @user = User.find(params[:role][:user])
    @project = Project.find(params[:id])
    @role = Role.find_by(name: params[:role][:authorizable_type])
        Severity: Minor
        Found in app/controllers/projects_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 ProjectsController#grant_role (44.2)
        Open

          def grant_role # rubocop:todo Metrics/AbcSize
    @user = User.find(params[:role][:user])
    @project = Project.find(params[:id])
    @role = Role.find_by(name: params[:role][:authorizable_type])
        Severity: Minor
        Found in app/controllers/projects_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 namespace(devour)::task#create_config (44.1)
        Open

          task create_config: :environment do
    # We prettify are json to make it both easier to read and diff
    json_formatting = { indent: '  ', object_nl: "\n", space: ' ', array_nl: "\n" }

    config =
        Severity: Minor
        Found in lib/tasks/devour.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 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
        Severity: Minor
        Found in app/models/sample_manifest.rb - About 2 hrs to fix

          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
          Severity: Minor
          Found in app/sample_manifest_excel/sample_manifest_excel/upload/processor/base.rb - About 2 hrs to fix
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