sanger/sequencescape

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app/models/cherrypick/volume_by_nano_grams.rb

Summary

Maintainability
A
2 hrs
Test Coverage
B
82%

Complex method Cherrypick::VolumeByNanoGrams#check_inputs_to_volume_to_cherrypick_by_nano_grams! (42.2)
Open

  def check_inputs_to_volume_to_cherrypick_by_nano_grams!(minimum_volume, maximum_volume, target_ng, source_well)
    raise 'Source well not found' if source_well.nil?

    if minimum_volume.blank? || minimum_volume <= 0.0
      raise Cherrypick::VolumeError,

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 check_inputs_to_volume_to_cherrypick_by_nano_grams! has 29 lines of code (exceeds 25 allowed). Consider refactoring.
Open

  def check_inputs_to_volume_to_cherrypick_by_nano_grams!(minimum_volume, maximum_volume, target_ng, source_well)
    raise 'Source well not found' if source_well.nil?

    if minimum_volume.blank? || minimum_volume <= 0.0
      raise Cherrypick::VolumeError,
Severity: Minor
Found in app/models/cherrypick/volume_by_nano_grams.rb - About 1 hr to fix

    Method check_inputs_to_volume_to_cherrypick_by_nano_grams! has a Cognitive Complexity of 10 (exceeds 5 allowed). Consider refactoring.
    Open

      def check_inputs_to_volume_to_cherrypick_by_nano_grams!(minimum_volume, maximum_volume, target_ng, source_well)
        raise 'Source well not found' if source_well.nil?
    
        if minimum_volume.blank? || minimum_volume <= 0.0
          raise Cherrypick::VolumeError,
    Severity: Minor
    Found in app/models/cherrypick/volume_by_nano_grams.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

    Cherrypick::VolumeByNanoGrams#volume_to_cherrypick_by_nano_grams has 5 parameters
    Open

      def volume_to_cherrypick_by_nano_grams(

    A Long Parameter List occurs when a method has a lot of parameters.

    Example

    Given

    class Dummy
      def long_list(foo,bar,baz,fling,flung)
        puts foo,bar,baz,fling,flung
      end
    end

    Reek would report the following warning:

    test.rb -- 1 warning:
      [2]:Dummy#long_list has 5 parameters (LongParameterList)

    A common solution to this problem would be the introduction of parameter objects.

    Cherrypick::VolumeByNanoGrams#check_inputs_to_volume_to_cherrypick_by_nano_grams! has 4 parameters
    Open

      def check_inputs_to_volume_to_cherrypick_by_nano_grams!(minimum_volume, maximum_volume, target_ng, source_well)

    A Long Parameter List occurs when a method has a lot of parameters.

    Example

    Given

    class Dummy
      def long_list(foo,bar,baz,fling,flung)
        puts foo,bar,baz,fling,flung
      end
    end

    Reek would report the following warning:

    test.rb -- 1 warning:
      [2]:Dummy#long_list has 5 parameters (LongParameterList)

    A common solution to this problem would be the introduction of parameter objects.

    Cherrypick::VolumeByNanoGrams#check_inputs_to_volume_to_cherrypick_by_nano_grams! refers to 'source_well' more than self (maybe move it to another class?)
    Open

        raise 'Source well not found' if source_well.nil?
    
        if minimum_volume.blank? || minimum_volume <= 0.0
          raise Cherrypick::VolumeError,
                "Minimum volume (#{minimum_volume.inspect}) is invalid for cherrypick by nano grams"

    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.

    Cherrypick::VolumeByNanoGrams#check_inputs_to_volume_to_cherrypick_by_nano_grams! has approx 9 statements
    Open

      def check_inputs_to_volume_to_cherrypick_by_nano_grams!(minimum_volume, maximum_volume, target_ng, source_well)

    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.)

    Cherrypick::VolumeByNanoGrams#volume_to_cherrypick_by_nano_grams has approx 15 statements
    Open

      def volume_to_cherrypick_by_nano_grams(

    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 Cherrypick::VolumeByNanoGrams#volume_to_cherrypick_by_nano_grams (24.4)
    Open

      def volume_to_cherrypick_by_nano_grams(
        minimum_volume,
        maximum_volume,
        target_ng,
        source_well,

    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 volume_to_cherrypick_by_nano_grams has 5 arguments (exceeds 4 allowed). Consider refactoring.
    Open

        minimum_volume,
        maximum_volume,
        target_ng,
        source_well,
        robot_minimum_picking_volume = 0.0
    Severity: Minor
    Found in app/models/cherrypick/volume_by_nano_grams.rb - About 35 mins to fix

      Cherrypick::VolumeByNanoGrams#check_inputs_to_volume_to_cherrypick_by_nano_grams! calls 'source_well.id' 3 times
      Open

            raise Cherrypick::VolumeError, "Missing measured volume for well #{source_well.display_name}(#{source_well.id})"
          end
          if source_concentration.blank?
            raise Cherrypick::ConcentrationError,
                  "Missing measured concentration for well #{source_well.display_name}(#{source_well.id})"

      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.

      Cherrypick::VolumeByNanoGrams has no descriptive comment
      Open

      module Cherrypick::VolumeByNanoGrams

      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

      Cherrypick::VolumeByNanoGrams#check_inputs_to_volume_to_cherrypick_by_nano_grams! calls 'source_well.well_attribute' 2 times
      Open

            source_well.well_attribute.concentration, source_well.well_attribute.measured_volume

      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.

      Cherrypick::VolumeByNanoGrams#check_inputs_to_volume_to_cherrypick_by_nano_grams! calls 'source_well.display_name' 3 times
      Open

            raise Cherrypick::VolumeError, "Missing measured volume for well #{source_well.display_name}(#{source_well.id})"
          end
          if source_concentration.blank?
            raise Cherrypick::ConcentrationError,
                  "Missing measured concentration for well #{source_well.display_name}(#{source_well.id})"

      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.

      Cherrypick::VolumeByNanoGrams#check_inputs_to_volume_to_cherrypick_by_nano_grams! calls 'maximum_volume.inspect' 2 times
      Open

                  "Maximum volume (#{maximum_volume.inspect}) is invalid for cherrypick by nano grams"
          end
          if maximum_volume < minimum_volume
            raise Cherrypick::VolumeError,
                  "Maximum volume (#{maximum_volume.inspect}) is less than minimum (#{minimum_volume.inspect})"

      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.

      Cherrypick::VolumeByNanoGrams#check_inputs_to_volume_to_cherrypick_by_nano_grams! calls 'minimum_volume.inspect' 2 times
      Open

                  "Minimum volume (#{minimum_volume.inspect}) is invalid for cherrypick by nano grams"
          end
          if maximum_volume.blank? || maximum_volume <= 0.0
            raise Cherrypick::VolumeError,
                  "Maximum volume (#{maximum_volume.inspect}) is invalid for cherrypick by nano grams"

      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.

      Cherrypick::VolumeByNanoGrams#volume_to_cherrypick_by_nano_grams calls 'source_well.well_attribute' 2 times
      Open

          source_concentration = source_well.well_attribute.concentration.to_f
      
          # Current volume, fall back to measured if current not set
          source_volume = source_well.well_attribute.estimated_volume

      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.

      Cherrypick::VolumeByNanoGrams#check_inputs_to_volume_to_cherrypick_by_nano_grams! performs a nil-check
      Open

          raise 'Source well not found' if source_well.nil?

      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)

      Cherrypick::VolumeByNanoGrams#calculate_buffer_volume doesn't depend on instance state (maybe move it to another class?)
      Open

        def calculate_buffer_volume(final_volume_desired, volume_so_far, robot_minimum_picking_volume)

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

      There are no issues that match your filters.

      Category
      Status