sanger/sequencescape

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app/models/well.rb

Summary

Maintainability
B
6 hrs
Test Coverage
A
95%

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

    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 Well#update_gender_markers! (26.1)
      Open

        def update_gender_markers!(gender_markers, resource) # rubocop:todo Metrics/AbcSize
          if well_attribute.gender_markers == gender_markers
            gender_marker_event = events.where(family: 'update_gender_markers').order('id desc').first
            if gender_marker_event.blank?
              events.update_gender_markers!(resource)
      Severity: Minor
      Found in app/models/well.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

      Well has at least 27 methods
      Open

      class Well < Receptacle # rubocop:todo Metrics/ClassLength
      Severity: Minor
      Found in app/models/well.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)

      Well#display_name has approx 6 statements
      Open

        def display_name
      Severity: Minor
      Found in app/models/well.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.)

      Well#get_sequenom_pass refers to 'markers' more than self (maybe move it to another class?)
      Open

          markers.is_a?(Array) ? markers.join : markers
      Severity: Minor
      Found in app/models/well.rb by reek

      Feature Envy occurs when a code fragment references another object more often than it references itself, or when several clients do the same series of manipulations on a particular type of object.

      Feature Envy reduces the code's ability to communicate intent: code that "belongs" on one class but which is located in another can be hard to find, and may upset the "System of Names" in the host class.

      Feature Envy also affects the design's flexibility: A code fragment that is in the wrong class creates couplings that may not be natural within the application's domain, and creates a loss of cohesion in the unwilling host class.

      Feature Envy often arises because it must manipulate other objects (usually its arguments) to get them into a useful form, and one force preventing them (the arguments) doing this themselves is that the common knowledge lives outside the arguments, or the arguments are of too basic a type to justify extending that type. Therefore there must be something which 'knows' about the contents or purposes of the arguments. That thing would have to be more than just a basic type, because the basic types are either containers which don't know about their contents, or they are single objects which can't capture their relationship with their fellows of the same type. So, this thing with the extra knowledge should be reified into a class, and the utility method will most likely belong there.

      Example

      Running Reek on:

      class Warehouse
        def sale_price(item)
          (item.price - item.rebate) * @vat
        end
      end

      would report:

      Warehouse#total_price refers to item more than self (FeatureEnvy)

      since this:

      (item.price - item.rebate)

      belongs to the Item class, not the Warehouse.

      Well#qc_result_for has approx 6 statements
      Open

        def qc_result_for(key)
      Severity: Minor
      Found in app/models/well.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.)

      Well#qc_result_for refers to 'result' more than self (maybe move it to another class?)
      Open

          return if result.nil?
          return result.to_f.round(3) if result.to_s.include?('.')
      
          result.to_i
      Severity: Minor
      Found in app/models/well.rb by reek

      Feature Envy occurs when a code fragment references another object more often than it references itself, or when several clients do the same series of manipulations on a particular type of object.

      Feature Envy reduces the code's ability to communicate intent: code that "belongs" on one class but which is located in another can be hard to find, and may upset the "System of Names" in the host class.

      Feature Envy also affects the design's flexibility: A code fragment that is in the wrong class creates couplings that may not be natural within the application's domain, and creates a loss of cohesion in the unwilling host class.

      Feature Envy often arises because it must manipulate other objects (usually its arguments) to get them into a useful form, and one force preventing them (the arguments) doing this themselves is that the common knowledge lives outside the arguments, or the arguments are of too basic a type to justify extending that type. Therefore there must be something which 'knows' about the contents or purposes of the arguments. That thing would have to be more than just a basic type, because the basic types are either containers which don't know about their contents, or they are single objects which can't capture their relationship with their fellows of the same type. So, this thing with the extra knowledge should be reified into a class, and the utility method will most likely belong there.

      Example

      Running Reek on:

      class Warehouse
        def sale_price(item)
          (item.price - item.rebate) * @vat
        end
      end

      would report:

      Warehouse#total_price refers to item more than self (FeatureEnvy)

      since this:

      (item.price - item.rebate)

      belongs to the Item class, not the Warehouse.

      Well::Link has no descriptive comment
      Open

        class Link < ApplicationRecord
      Severity: Minor
      Found in app/models/well.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

      Well#update_gender_markers! calls 'events.update_gender_markers!(resource)' 3 times
      Open

              events.update_gender_markers!(resource)
            elsif resource == 'SNP' && gender_marker_event.content != resource
              events.update_gender_markers!(resource)
            end
          else
      Severity: Minor
      Found in app/models/well.rb by reek

      Duplication occurs when two fragments of code look nearly identical, or when two fragments of code have nearly identical effects at some conceptual level.

      Reek implements a check for Duplicate Method Call.

      Example

      Here's a very much simplified and contrived example. The following method will report a warning:

      def double_thing()
        @other.thing + @other.thing
      end

      One quick approach to silence Reek would be to refactor the code thus:

      def double_thing()
        thing = @other.thing
        thing + thing
      end

      A slightly different approach would be to replace all calls of double_thing by calls to @other.double_thing:

      class Other
        def double_thing()
          thing + thing
        end
      end

      The approach you take will depend on balancing other factors in your code.

      Method update_gender_markers! has a Cognitive Complexity of 6 (exceeds 5 allowed). Consider refactoring.
      Open

        def update_gender_markers!(gender_markers, resource) # rubocop:todo Metrics/AbcSize
          if well_attribute.gender_markers == gender_markers
            gender_marker_event = events.where(family: 'update_gender_markers').order('id desc').first
            if gender_marker_event.blank?
              events.update_gender_markers!(resource)
      Severity: Minor
      Found in app/models/well.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

      Method qc_result_for has a Cognitive Complexity of 6 (exceeds 5 allowed). Consider refactoring.
      Open

        def qc_result_for(key)
          result =
            if key == 'quantity_in_nano_grams'
              well_attribute.quantity_in_nano_grams
            else
      Severity: Minor
      Found in app/models/well.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

      Well has missing safe method 'update_gender_markers!'
      Open

        def update_gender_markers!(gender_markers, resource) # rubocop:todo Metrics/AbcSize
      Severity: Minor
      Found in app/models/well.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.

      Well#qc_result_for performs a nil-check
      Open

          return if result.nil?
      Severity: Minor
      Found in app/models/well.rb by reek

      A NilCheck is a type check. Failures of NilCheck violate the "tell, don't ask" principle.

      Additionally, type checks often mask bigger problems in your source code like not using OOP and / or polymorphism when you should.

      Example

      Given

      class Klass
        def nil_checker(argument)
          if argument.nil?
            puts "argument isn't nil!"
          end
        end
      end

      Reek would emit the following warning:

      test.rb -- 1 warning:
        [3]:Klass#nil_checker performs a nil-check. (NilCheck)

      Well has missing safe method 'update_sequenom_count!'
      Open

        def update_sequenom_count!(sequenom_count, resource)
      Severity: Minor
      Found in app/models/well.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.

      Well#details performs a nil-check
      Open

          return 'Not yet picked' if plate.nil?
      Severity: Minor
      Found in app/models/well.rb by reek

      A NilCheck is a type check. Failures of NilCheck violate the "tell, don't ask" principle.

      Additionally, type checks often mask bigger problems in your source code like not using OOP and / or polymorphism when you should.

      Example

      Given

      class Klass
        def nil_checker(argument)
          if argument.nil?
            puts "argument isn't nil!"
          end
        end
      end

      Reek would emit the following warning:

      test.rb -- 1 warning:
        [3]:Klass#nil_checker performs a nil-check. (NilCheck)

      Well#update_volume performs a nil-check
      Open

          value_current_volume = get_current_volume.nil? ? 0 : get_current_volume
      Severity: Minor
      Found in app/models/well.rb by reek

      A NilCheck is a type check. Failures of NilCheck violate the "tell, don't ask" principle.

      Additionally, type checks often mask bigger problems in your source code like not using OOP and / or polymorphism when you should.

      Example

      Given

      class Klass
        def nil_checker(argument)
          if argument.nil?
            puts "argument isn't nil!"
          end
        end
      end

      Reek would emit the following warning:

      test.rb -- 1 warning:
        [3]:Klass#nil_checker performs a nil-check. (NilCheck)

      There are no issues that match your filters.

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