sanger/sequencescape

View on GitHub
lib/working_setup/standard_seeder.rb

Summary

Maintainability
A
2 hrs
Test Coverage
F
0%

Method sample_named has 50 lines of code (exceeds 25 allowed). Consider refactoring.
Open

    def sample_named(name, study)
      {
        'sample_tube_attributes' => {
          'two_dimensional_barcode' => ''
        },
Severity: Minor
Found in lib/working_setup/standard_seeder.rb - About 2 hrs to fix

    WorkingSetup::StandardSeeder has at least 16 methods
    Open

      class StandardSeeder
    Severity: Minor
    Found in lib/working_setup/standard_seeder.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)

    WorkingSetup::StandardSeeder#plates_of_purpose has approx 6 statements
    Open

        def plates_of_purpose(name, number) # rubocop:todo Metrics/AbcSize
    Severity: Minor
    Found in lib/working_setup/standard_seeder.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.)

    WorkingSetup::StandardSeeder#plates_of_purpose refers to 'plate' more than self (maybe move it to another class?)
    Open

              plate.wells.each do |w|
                w.aliquots.create!(
                  sample:
                    Sample.create!(name: "sample_#{plate.human_barcode}_#{w.map.description}", studies: [study, study_b])
                )
    Severity: Minor
    Found in lib/working_setup/standard_seeder.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.

    WorkingSetup::StandardSeeder#tag_plates has approx 6 statements
    Open

        def tag_plates( # rubocop:todo Metrics/MethodLength
    Severity: Minor
    Found in lib/working_setup/standard_seeder.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.)

    Complex method WorkingSetup::StandardSeeder#plates_of_purpose (25.5)
    Open

        def plates_of_purpose(name, number) # rubocop:todo Metrics/AbcSize
          purpose = Purpose.find_by!(name: name)
          number.times do
            purpose.create!.tap do |plate|
              plate.wells.each do |w|
    Severity: Minor
    Found in lib/working_setup/standard_seeder.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

    WorkingSetup::StandardSeeder tests 'existing' at least 3 times
    Open

          return existing if existing
    
          User
            .create!(login: 'admin', password: 'admin', swipecard_code: 'abcdef', barcode: 'ID99A')
            .tap(&:grant_administrator)
    Severity: Minor
    Found in lib/working_setup/standard_seeder.rb by reek

    Repeated Conditional is a special case of Simulated Polymorphism. Basically it means you are checking the same value throughout a single class and take decisions based on this.

    Example

    Given

    class RepeatedConditionals
      attr_accessor :switch
    
      def repeat_1
        puts "Repeat 1!" if switch
      end
    
      def repeat_2
        puts "Repeat 2!" if switch
      end
    
      def repeat_3
        puts "Repeat 3!" if switch
      end
    end

    Reek would emit the following warning:

    test.rb -- 4 warnings:
      [5, 9, 13]:RepeatedConditionals tests switch at least 3 times (RepeatedConditional)

    If you get this warning then you are probably not using the right abstraction or even more probable, missing an additional abstraction.

    WorkingSetup::StandardSeeder#plates_of_purpose calls 'plate.human_barcode' 2 times
    Open

                    Sample.create!(name: "sample_#{plate.human_barcode}_#{w.map.description}", studies: [study, study_b])
                )
              end
              puts "#{name}: #{plate.ean13_barcode}-#{plate.human_barcode}"
    Severity: Minor
    Found in lib/working_setup/standard_seeder.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.

    WorkingSetup::StandardSeeder#tag_plates calls 'Time.current' 2 times
    Open

                lot_number: Time.current.to_i.to_s,
                template: TagLayoutTemplate.find_by!(name: template),
                user: user,
                received_at: Time.current
    Severity: Minor
    Found in lib/working_setup/standard_seeder.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.

    Complex method WorkingSetup::StandardSeeder#tag_plates (22.6)
    Open

        def tag_plates( # rubocop:todo Metrics/MethodLength
          lot_type: 'IDT Tags',
          template: 'Sanger_168tags - 10 mer tags in columns ignoring pools (first oligo: ATCACGTT)',
          size: 30
        )
    Severity: Minor
    Found in lib/working_setup/standard_seeder.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

    WorkingSetup::StandardSeeder#create_or_find_user doesn't depend on instance state (maybe move it to another class?)
    Open

        def create_or_find_user
    Severity: Minor
    Found in lib/working_setup/standard_seeder.rb by reek

    A Utility Function is any instance method that has no dependency on the state of the instance.

    WorkingSetup::StandardSeeder#supplier doesn't depend on instance state (maybe move it to another class?)
    Open

        def supplier
    Severity: Minor
    Found in lib/working_setup/standard_seeder.rb by reek

    A Utility Function is any instance method that has no dependency on the state of the instance.

    WorkingSetup::StandardSeeder#create_project doesn't depend on instance state (maybe move it to another class?)
    Open

        def create_project(name)
    Severity: Minor
    Found in lib/working_setup/standard_seeder.rb by reek

    A Utility Function is any instance method that has no dependency on the state of the instance.

    WorkingSetup::StandardSeeder#plates_of_purpose has the variable name 'w'
    Open

              plate.wells.each do |w|
    Severity: Minor
    Found in lib/working_setup/standard_seeder.rb by reek

    An Uncommunicative Variable Name is a variable 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.

    WorkingSetup::StandardSeeder#seed has the variable name 's'
    Open

          Sample.find_each { |s| study_b.samples << s }
    Severity: Minor
    Found in lib/working_setup/standard_seeder.rb by reek

    An Uncommunicative Variable Name is a variable 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.

    Category
    Status