sanger/sequencescape

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app/models/aliquot.rb

Summary

Maintainability
A
2 hrs
Test Coverage
A
93%

Class Aliquot has 21 methods (exceeds 20 allowed). Consider refactoring.
Open

class Aliquot < ApplicationRecord # rubocop:todo Metrics/ClassLength
  include Uuid::Uuidable
  include Api::Messages::FlowcellIO::AliquotExtensions
  include Api::Messages::QcResultIO::AliquotExtensions
  include AliquotIndexer::AliquotScopes
Severity: Minor
Found in app/models/aliquot.rb - About 2 hrs to fix

    Complex method Aliquot#matches? (40.8)
    Open

      def matches?(object) # rubocop:todo Metrics/CyclomaticComplexity
        # NOTE: This function is directional, and assumes that the downstream aliquot
        # is checking the upstream aliquot
        case
        when sample_id != object.sample_id
    Severity: Minor
    Found in app/models/aliquot.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

    Aliquot#set_library has boolean parameter 'force'
    Open

      def set_library(force: false)
    Severity: Minor
    Found in app/models/aliquot.rb by reek

    Boolean Parameter is a special case of Control Couple, where a method parameter is defaulted to true or false. A Boolean Parameter effectively permits a method's caller to decide which execution path to take. This is a case of bad cohesion. You're creating a dependency between methods that is not really necessary, thus increasing coupling.

    Example

    Given

    class Dummy
      def hit_the_switch(switch = true)
        if switch
          puts 'Hitting the switch'
          # do other things...
        else
          puts 'Not hitting the switch'
          # do other things...
        end
      end
    end

    Reek would emit the following warning:

    test.rb -- 3 warnings:
      [1]:Dummy#hit_the_switch has boolean parameter 'switch' (BooleanParameter)
      [2]:Dummy#hit_the_switch is controlled by argument switch (ControlParameter)

    Note that both smells are reported, Boolean Parameter and Control Parameter.

    Getting rid of the smell

    This is highly dependent on your exact architecture, but looking at the example above what you could do is:

    • Move everything in the if branch into a separate method
    • Move everything in the else branch into a separate method
    • Get rid of the hit_the_switch method alltogether
    • Make the decision what method to call in the initial caller of hit_the_switch

    Aliquot#matches? refers to 'object' more than self (maybe move it to another class?)
    Open

        when sample_id != object.sample_id
          false # The samples don't match
        when object.library_id.present? && (library_id != object.library_id)
          false # Our libraries don't match.
        when object.bait_library_id.present? && (bait_library_id != object.bait_library_id)
    Severity: Minor
    Found in app/models/aliquot.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.

    Aliquot has at least 19 methods
    Open

    class Aliquot < ApplicationRecord # rubocop:todo Metrics/ClassLength
    Severity: Minor
    Found in app/models/aliquot.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)

    Aliquot#set_library is controlled by argument 'force'
    Open

        self.library = receptacle if library.nil? || force
    Severity: Minor
    Found in app/models/aliquot.rb by reek

    Control Parameter is a special case of Control Couple

    Example

    A simple example would be the "quoted" parameter in the following method:

    def write(quoted)
      if quoted
        write_quoted @value
      else
        write_unquoted @value
      end
    end

    Fixing those problems is out of the scope of this document but an easy solution could be to remove the "write" method alltogether and to move the calls to "writequoted" / "writeunquoted" in the initial caller of "write".

    Aliquot#matches? has approx 6 statements
    Open

      def matches?(object) # rubocop:todo Metrics/CyclomaticComplexity
    Severity: Minor
    Found in app/models/aliquot.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.)

    Method matches? has a Cognitive Complexity of 7 (exceeds 5 allowed). Consider refactoring.
    Open

      def matches?(object) # rubocop:todo Metrics/CyclomaticComplexity
        # NOTE: This function is directional, and assumes that the downstream aliquot
        # is checking the upstream aliquot
        case
        when sample_id != object.sample_id
    Severity: Minor
    Found in app/models/aliquot.rb - About 35 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

    Aliquot#matches? calls 'object.library_id' 2 times
    Open

        when object.library_id.present? && (library_id != object.library_id)
    Severity: Minor
    Found in app/models/aliquot.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.

    Aliquot#matches? calls 'object.bait_library_id' 2 times
    Open

        when object.bait_library_id.present? && (bait_library_id != object.bait_library_id)
    Severity: Minor
    Found in app/models/aliquot.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.

    Aliquot#no_tag1? performs a nil-check
    Open

        tag_id == UNASSIGNED_TAG || (tag_id.nil? && tag.nil?)
    Severity: Minor
    Found in app/models/aliquot.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)

    Aliquot#set_library performs a nil-check
    Open

        self.library = receptacle if library.nil? || force
    Severity: Minor
    Found in app/models/aliquot.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)

    Aliquot#no_tag2? performs a nil-check
    Open

        tag2_id == UNASSIGNED_TAG || (tag2_id.nil? && tag2.nil?)
    Severity: Minor
    Found in app/models/aliquot.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)

    Aliquot#tag2 has the name 'tag2'
    Open

      def tag2
    Severity: Minor
    Found in app/models/aliquot.rb by reek

    An Uncommunicative Method Name is a method name that doesn't communicate its intent well enough.

    Poor names make it hard for the reader to build a mental picture of what's going on in the code. They can also be mis-interpreted; and they hurt the flow of reading, because the reader must slow down to interpret the names.

    There are no issues that match your filters.

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