sanger/sequencescape

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app/models/sample_manifest.rb

Summary

Maintainability
A
2 hrs
Test Coverage
A
90%

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

    SampleManifest has at least 21 methods
    Open

    class SampleManifest < ApplicationRecord # rubocop:todo Metrics/ClassLength
    Severity: Minor
    Found in app/models/sample_manifest.rb by reek

    Too Many Methods is a special case of LargeClass.

    Example

    Given this configuration

    TooManyMethods:
      max_methods: 3

    and this code:

    class TooManyMethods
      def one; end
      def two; end
      def three; end
      def four; end
    end

    Reek would emit the following warning:

    test.rb -- 1 warning:
      [1]:TooManyMethods has at least 4 methods (TooManyMethods)

    SampleManifest#truncate_errors has approx 7 statements
    Open

      def truncate_errors # rubocop:todo Metrics/MethodLength
    Severity: Minor
    Found in app/models/sample_manifest.rb by reek

    A method with Too Many Statements is any method that has a large number of lines.

    Too Many Statements warns about any method that has more than 5 statements. Reek's smell detector for Too Many Statements counts +1 for every simple statement in a method and +1 for every statement within a control structure (if, else, case, when, for, while, until, begin, rescue) but it doesn't count the control structure itself.

    So the following method would score +6 in Reek's statement-counting algorithm:

    def parse(arg, argv, &error)
      if !(val = arg) and (argv.empty? or /\A-/ =~ (val = argv[0]))
        return nil, block, nil                                         # +1
      end
      opt = (val = parse_arg(val, &error))[1]                          # +2
      val = conv_arg(*val)                                             # +3
      if opt and !arg
        argv.shift                                                     # +4
      else
        val[0] = nil                                                   # +5
      end
      val                                                              # +6
    end

    (You might argue that the two assigments within the first @if@ should count as statements, and that perhaps the nested assignment should count as +2.)

    SampleManifest::Associations has no descriptive comment
    Open

      module Associations
    Severity: Minor
    Found in app/models/sample_manifest.rb by reek

    Classes and modules are the units of reuse and release. It is therefore considered good practice to annotate every class and module with a brief comment outlining its responsibilities.

    Example

    Given

    class Dummy
      # Do things...
    end

    Reek would emit the following warning:

    test.rb -- 1 warning:
      [1]:Dummy has no descriptive comment (IrresponsibleModule)

    Fixing this is simple - just an explaining comment:

    # The Dummy class is responsible for ...
    class Dummy
      # Do things...
    end

    Complex method SampleManifest#truncate_errors (22.1)
    Open

      def truncate_errors # rubocop:todo Metrics/MethodLength
        if last_errors && last_errors.join.length > LIMIT_ERROR_LENGTH
          # First we truncate individual error messages. This ensures that it the first message is already
          # longer than out max limit, we still show something.
          full_last_errors = last_errors.map { |error| error.truncate(INDIVIDUAL_ERROR_LIMIT) }
    Severity: Minor
    Found in app/models/sample_manifest.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 truncate_errors has a Cognitive Complexity of 6 (exceeds 5 allowed). Consider refactoring.
    Open

      def truncate_errors # rubocop:todo Metrics/MethodLength
        if last_errors && last_errors.join.length > LIMIT_ERROR_LENGTH
          # First we truncate individual error messages. This ensures that it the first message is already
          # longer than out max limit, we still show something.
          full_last_errors = last_errors.map { |error| error.truncate(INDIVIDUAL_ERROR_LIMIT) }
    Severity: Minor
    Found in app/models/sample_manifest.rb - About 25 mins 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

    SampleManifest has missing safe method 'find_or_create_qc_assay!'
    Open

      def find_or_create_qc_assay!
    Severity: Minor
    Found in app/models/sample_manifest.rb by reek

    A candidate method for the Missing Safe Method smell are methods whose names end with an exclamation mark.

    An exclamation mark in method names means (the explanation below is taken from here ):

    The ! in method names that end with ! means, “This method is dangerous”—or, more precisely, this method is the “dangerous” version of an otherwise equivalent method, with the same name minus the !. “Danger” is relative; the ! doesn’t mean anything at all unless the method name it’s in corresponds to a similar but bang-less method name. So, for example, gsub! is the dangerous version of gsub. exit! is the dangerous version of exit. flatten! is the dangerous version of flatten. And so forth.

    Such a method is called Missing Safe Method if and only if her non-bang version does not exist and this method is reported as a smell.

    Example

    Given

    class C
      def foo; end
      def foo!; end
      def bar!; end
    end

    Reek would report bar! as Missing Safe Method smell but not foo!.

    Reek reports this smell only in a class context, not in a module context in order to allow perfectly legit code like this:

    class Parent
      def foo; end
    end
    
    module Dangerous
      def foo!; end
    end
    
    class Son < Parent
      include Dangerous
    end
    
    class Daughter < Parent
    end

    In this example, Reek would not report the Missing Safe Method smell for the method foo of the Dangerous module.

    SampleManifest#only_first_label is a writable attribute
    Open

      attr_accessor :override, :only_first_label
    Severity: Minor
    Found in app/models/sample_manifest.rb by reek

    A class that publishes a setter for an instance variable invites client classes to become too intimate with its inner workings, and in particular with its representation of state.

    The same holds to a lesser extent for getters, but Reek doesn't flag those.

    Example

    Given:

    class Klass
      attr_accessor :dummy
    end

    Reek would emit the following warning:

    reek test.rb
    
    test.rb -- 1 warning:
      [2]:Klass declares the writable attribute dummy (Attribute)

    SampleManifest#rows_per_well is a writable attribute
    Open

      attr_writer :rows_per_well
    Severity: Minor
    Found in app/models/sample_manifest.rb by reek

    A class that publishes a setter for an instance variable invites client classes to become too intimate with its inner workings, and in particular with its representation of state.

    The same holds to a lesser extent for getters, but Reek doesn't flag those.

    Example

    Given:

    class Klass
      attr_accessor :dummy
    end

    Reek would emit the following warning:

    reek test.rb
    
    test.rb -- 1 warning:
      [2]:Klass declares the writable attribute dummy (Attribute)

    SampleManifest#override is a writable attribute
    Open

      attr_accessor :override, :only_first_label
    Severity: Minor
    Found in app/models/sample_manifest.rb by reek

    A class that publishes a setter for an instance variable invites client classes to become too intimate with its inner workings, and in particular with its representation of state.

    The same holds to a lesser extent for getters, but Reek doesn't flag those.

    Example

    Given:

    class Klass
      attr_accessor :dummy
    end

    Reek would emit the following warning:

    reek test.rb
    
    test.rb -- 1 warning:
      [2]:Klass declares the writable attribute dummy (Attribute)

    There are no issues that match your filters.

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