Sign upLogin

sanger/sequencescape

View on GitHub
Star

Showing 5,431 of 5,433 total issues

Complex method BatchesController#show (36.0)
Open

  def show # rubocop:todo Metrics/AbcSize
    respond_to do |format|
      format.html do
        @submenu_presenter = Presenters::BatchSubmenuPresenter.new(current_user, @batch)
Severity: Minor
Found in app/controllers/batches_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 Plate::Creator#create_plates_from_tube_racks! (35.8)
Open

  def create_plates_from_tube_racks!(
    tube_racks,
    barcode_printer,
    scanned_user,
    should_create_asset_group,
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 Ability::Manager#grant_privileges (35.5)
Open

  def grant_privileges # rubocop:todo Metrics/AbcSize, Metrics/MethodLength
    Rails.logger.debug { 'Granting Manager privileges' }

    can(:edit, Labware) { |lw| !lw.is_a?(PlateTemplate) }
    cannot :edit, PlateTemplate
Severity: Minor
Found in app/models/ability/manager.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::UsersController#update (35.4)
Open

  def update # rubocop:todo Metrics/AbcSize, Metrics/MethodLength
    @user = User.find(params[:id])
    Role.general_roles.each do |role|
      params[:role] && params[:role][role.name] ? @user.grant_role(role.name) : @user.remove_role(role.name)
    end
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 QcReportsController#index (35.3)
Open

  def index # rubocop:todo Metrics/AbcSize
    # Build a conditions hash of acceptable parameters, ignoring those that are blank

    @qc_reports = QcReport.for_report_page(conditions).page(params[:page]).includes(:study, :product)
    @qc_report = QcReport.new(exclude_existing: true, study_id: params[:study_id])
Severity: Minor
Found in app/controllers/qc_reports_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 ReceptaclesController#update (35.3)
Open

  def update # rubocop:todo Metrics/AbcSize, Metrics/MethodLength
    respond_to do |format|
      if @asset.update(asset_params.merge(params.to_unsafe_h.fetch(:lane, {})))
        flash[:notice] = 'Receptacle was successfully updated.'
        if params[:lab_view]
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

Complex method Batch#generate_target_assets_for_requests (35.1)
Open

  def generate_target_assets_for_requests # rubocop:todo Metrics/AbcSize
    requests_to_update = []

    asset_type = pipeline.asset_type.constantize
    requests.reload.each do |request|
Severity: Minor
Found in app/models/batch.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 serialize has a Cognitive Complexity of 13 (exceeds 5 allowed). Consider refactoring.
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 - About 1 hr 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

Method _check_mandatory_field has a Cognitive Complexity of 13 (exceeds 5 allowed). Consider refactoring.
Open

        def _check_mandatory_field(mandatory_field) # rubocop:todo Metrics/CyclomaticComplexity, Metrics/AbcSize
          return unless upload.respond_to?(:rows)
          upload.rows.each do |row|
            next if row.columns.blank? || row.data.blank?
            col_num = row.columns.find_column_or_null(:name, mandatory_field).number
Severity: Minor
Found in app/sample_manifest_excel/sample_manifest_excel/upload/processor/base.rb - About 1 hr 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

Method duplicate_barcodes has a Cognitive Complexity of 13 (exceeds 5 allowed). Consider refactoring.
Open

        def duplicate_barcodes # rubocop:todo Metrics/CyclomaticComplexity
          return unless upload.respond_to?(:rows)

          unique_bcs = []
          upload.rows.each do |row|
Severity: Minor
Found in app/sample_manifest_excel/sample_manifest_excel/upload/processor/base.rb - About 1 hr 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

Method non_matching_retention_instructions_for_plates has a Cognitive Complexity of 13 (exceeds 5 allowed). Consider refactoring.
Open

        def non_matching_retention_instructions_for_plates
          return nil, nil unless upload.respond_to?(:rows)

          # Initialize empty retention_instructions hash to store retention instructions
          upload
Severity: Minor
Found in app/sample_manifest_excel/sample_manifest_excel/upload/processor/plate.rb - About 1 hr 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

Method non_matching_retention_instructions has a Cognitive Complexity of 13 (exceeds 5 allowed). Consider refactoring.
Open

        def non_matching_retention_instructions
          return nil, nil unless upload.respond_to?(:rows)

          upload
            .rows
Severity: Minor
Found in app/sample_manifest_excel/sample_manifest_excel/upload/processor/one_d_tube.rb - About 1 hr 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 Asset::Finder#find_wells_in_array (35.0)
Open

  def find_wells_in_array(plate, well_array) # rubocop:todo Metrics/CyclomaticComplexity
    return plate.wells.in_column_major_order.with_aliquots.distinct if well_array.empty?

    well_array.flat_map do |map_description|
      case map_description
Severity: Minor
Found in app/models/asset/finder.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 SequencingQcBatch::adjacent_state_helper (34.8)
Open

  def self.adjacent_state_helper(direction, offset, delimiter) # rubocop:todo Metrics/AbcSize
    define_method(:"qc_#{direction}_state") do
      unless qc_states.include?(qc_state.to_s)
        raise StandardError, "Current QC state appears to be invalid: '#{qc_state}'"
      end
Severity: Minor
Found in lib/sequencing_qc_batch.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 swap has 39 lines of code (exceeds 25 allowed). Consider refactoring.
Open

  def swap(current_user, batch_info = {}) # rubocop:todo Metrics/CyclomaticComplexity
    return false if batch_info.empty?

    # Find the two lanes that are to be swapped
    batch_request_left =
Severity: Minor
Found in app/models/batch.rb - About 1 hr to fix

    Complex method SampleManifestExcel::Upload::Processor::Plate#duplicate_barcodes (34.7)
    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 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

          expect(state.plates).toEqual({
        1: {
          id: 1,
          barcode: "DN12345",
          batches: ["1", "2", "3"],
    Severity: Major
    Found in app/frontend/plate-picks/store/mutations.test.js and 1 other location - About 1 hr to fix
    app/frontend/plate-picks/store/mutations.test.js on lines 95..97

    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 66.

    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

          expect(state.plates).toEqual({
        1: { id: 1, barcode: "DN12345", batches: ["1", "2", "3"], picks: { 1: ["Pick"], 2: ["Other", "New"] } },
      });
    Severity: Major
    Found in app/frontend/plate-picks/store/mutations.test.js and 1 other location - About 1 hr to fix
    app/frontend/plate-picks/store/mutations.test.js on lines 104..111

    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 66.

    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

            def non_matching_retention_instructions
          return nil, nil unless upload.respond_to?(:rows)

          upload
            .rows
    Severity: Major
    Found in app/sample_manifest_excel/sample_manifest_excel/upload/processor/one_d_tube.rb and 1 other location - About 1 hr to fix
    app/sample_manifest_excel/sample_manifest_excel/upload/processor/plate.rb on lines 79..100

    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 64.

    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

            def non_matching_retention_instructions_for_plates
          return nil, nil unless upload.respond_to?(:rows)

          # Initialize empty retention_instructions hash to store retention instructions
          upload
    Severity: Major
    Found in app/sample_manifest_excel/sample_manifest_excel/upload/processor/plate.rb and 1 other location - About 1 hr to fix
    app/sample_manifest_excel/sample_manifest_excel/upload/processor/one_d_tube.rb on lines 21..42

    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 64.

    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

    Severity
    Category
    Status
    Source
    Language