sanger/sequencescape

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app/models/plate/fluidigm_behaviour.rb

Summary

Maintainability
A
1 hr
Test Coverage
F
31%

Method apply_fluidigm_data has 34 lines of code (exceeds 25 allowed). Consider refactoring.
Open

  def apply_fluidigm_data(fluidigm_file) # rubocop:todo Metrics/AbcSize
    qc_assay = QcAssay.new
    raise FluidigmError, 'File does not match plate' unless fluidigm_file.for_plate?(fluidigm_barcode)

    wells
Severity: Minor
Found in app/models/plate/fluidigm_behaviour.rb - About 1 hr to fix

    Complex method Plate::FluidigmBehaviour#apply_fluidigm_data (28.3)
    Open

      def apply_fluidigm_data(fluidigm_file) # rubocop:todo Metrics/AbcSize
        qc_assay = QcAssay.new
        raise FluidigmError, 'File does not match plate' unless fluidigm_file.for_plate?(fluidigm_barcode)
    
        wells
    Severity: Minor
    Found in app/models/plate/fluidigm_behaviour.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

    Plate::FluidigmBehaviour#apply_fluidigm_data contains iterators nested 2 deep
    Open

            well.stock_wells.each do |sw|
    Severity: Minor
    Found in app/models/plate/fluidigm_behaviour.rb by reek

    A Nested Iterator occurs when a block contains another block.

    Example

    Given

    class Duck
      class << self
        def duck_names
          %i!tick trick track!.each do |surname|
            %i!duck!.each do |last_name|
              puts "full name is #{surname} #{last_name}"
            end
          end
        end
      end
    end

    Reek would report the following warning:

    test.rb -- 1 warning:
      [5]:Duck#duck_names contains iterators nested 2 deep (NestedIterators)

    Plate::FluidigmBehaviour#apply_fluidigm_data has approx 8 statements
    Open

      def apply_fluidigm_data(fluidigm_file) # rubocop:todo Metrics/AbcSize
    Severity: Minor
    Found in app/models/plate/fluidigm_behaviour.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 Plate::FluidigmBehaviour::included (25.1)
    Open

      def self.included(base) # rubocop:todo Metrics/MethodLength
        base.class_eval do
          scope :requiring_fluidigm_data,
                -> {
                  fluidigm_request_ids = RequestType.where(key: 'pick_to_fluidigm').ids
    Severity: Minor
    Found in app/models/plate/fluidigm_behaviour.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

    Plate::FluidigmBehaviour#apply_fluidigm_data calls 'well.map_description' 2 times
    Open

              gender_markers = fluidigm_file.well_at(well.map_description).gender_markers.join('')
              loci_passed = fluidigm_file.well_at(well.map_description).count
    Severity: Minor
    Found in app/models/plate/fluidigm_behaviour.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.

    Plate::FluidigmBehaviour#apply_fluidigm_data calls 'fluidigm_file.well_at(well.map_description)' 2 times
    Open

              gender_markers = fluidigm_file.well_at(well.map_description).gender_markers.join('')
              loci_passed = fluidigm_file.well_at(well.map_description).count
    Severity: Minor
    Found in app/models/plate/fluidigm_behaviour.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.

    Plate::FluidigmBehaviour::FluidigmError has no descriptive comment
    Open

      class FluidigmError < StandardError
    Severity: Minor
    Found in app/models/plate/fluidigm_behaviour.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

    Plate::FluidigmBehaviour has no descriptive comment
    Open

    module Plate::FluidigmBehaviour
    Severity: Minor
    Found in app/models/plate/fluidigm_behaviour.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

    There are no issues that match your filters.

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