sanger/sequencescape

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app/models/plate/creator.rb

Summary

Maintainability
A
2 hrs
Test Coverage
A
97%

Complex method Plate::Creator#create_child_plates_from (46.6)
Open

  def create_child_plates_from(plate, current_user, creator_parameters) # rubocop:todo Metrics/AbcSize
    stock_well_picker = plate.plate_purpose.stock_plate? ? ->(w) { [w] } : ->(w) { w.stock_wells }
    parent_wells = plate.wells

    parent_barcode = plate.human_barcode
Severity: Minor
Found in app/models/plate/creator.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

Complex method Plate::Creator#create_plates (41.3)
Open

  def create_plates(source_plate_barcodes, current_user, creator_parameters = nil) # rubocop:todo Metrics/AbcSize
    if source_plate_barcodes.blank?
      # No barcodes have been scanned. This results in empty plates. This behaviour
      # is used in a few circumstances. User comment:
      # bs6: we use it to create 'pico standard' barcodes, as well as 'aliquot' barcodes.
Severity: Minor
Found in app/models/plate/creator.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

Complex method Plate::Creator#create_plates_from_tube_racks! (35.8)
Open

  def create_plates_from_tube_racks!(
    tube_racks,
    barcode_printer,
    scanned_user,
    should_create_asset_group,
Severity: Minor
Found in app/models/plate/creator.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

Method create_plates has a Cognitive Complexity of 9 (exceeds 5 allowed). Consider refactoring.
Open

  def create_plates(source_plate_barcodes, current_user, creator_parameters = nil) # rubocop:todo Metrics/AbcSize
    if source_plate_barcodes.blank?
      # No barcodes have been scanned. This results in empty plates. This behaviour
      # is used in a few circumstances. User comment:
      # bs6: we use it to create 'pico standard' barcodes, as well as 'aliquot' barcodes.
Severity: Minor
Found in app/models/plate/creator.rb - About 55 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

Plate::Creator#create_plates_from_tube_racks! is controlled by argument 'should_create_asset_group'
Open

    @created_asset_group = create_asset_group(created_plates) if should_create_asset_group
Severity: Minor
Found in app/models/plate/creator.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".

Plate::Creator#create_child_plates_from contains iterators nested 2 deep
Open

          target_plate_purpose.create!(
            :without_wells,
            sanger_barcode: child_plate_barcode,
            size: plate.size
          ) { |child| child.name = "#{target_plate_purpose.name} #{child.human_barcode}" }
Severity: Minor
Found in app/models/plate/creator.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::Creator#execute has 5 parameters
Open

  def execute(source_plate_barcodes, barcode_printer, scanned_user, should_create_asset_group, creator_parameters = nil)
Severity: Minor
Found in app/models/plate/creator.rb by reek

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.

Plate::Creator#create_asset_group has approx 10 statements
Open

  def create_asset_group(created_plates) # rubocop:todo Metrics/MethodLength
Severity: Minor
Found in app/models/plate/creator.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.)

Plate::Creator#execute is controlled by argument 'should_create_asset_group'
Open

    @created_asset_group = create_asset_group(created_plates) if should_create_asset_group
Severity: Minor
Found in app/models/plate/creator.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".

Plate::Creator#asset_group_name refers to 'now' more than self (maybe move it to another class?)
Open

    time_now_formatted = "#{now.year}-#{now.month}-#{now.day}-#{now.hour}#{now.min}#{now.sec}"
Severity: Minor
Found in app/models/plate/creator.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.

Plate::Creator#execute has approx 9 statements
Open

  def execute(source_plate_barcodes, barcode_printer, scanned_user, should_create_asset_group, creator_parameters = nil)
Severity: Minor
Found in app/models/plate/creator.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.)

Plate::Creator#create_child_plates_from has approx 18 statements
Open

  def create_child_plates_from(plate, current_user, creator_parameters) # rubocop:todo Metrics/AbcSize
Severity: Minor
Found in app/models/plate/creator.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.)

Plate::Creator#find_relevant_study contains iterators nested 2 deep
Open

      plate.contained_samples.each { |sample| return sample.studies.first if sample.studies.first }
Severity: Minor
Found in app/models/plate/creator.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::Creator#create_plates has approx 10 statements
Open

  def create_plates(source_plate_barcodes, current_user, creator_parameters = nil) # rubocop:todo Metrics/AbcSize
Severity: Minor
Found in app/models/plate/creator.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.)

Plate::Creator#find_relevant_study has approx 7 statements
Open

  def find_relevant_study(created_plates)
Severity: Minor
Found in app/models/plate/creator.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.)

Plate::Creator#create_plates_from_tube_racks! has 5 parameters
Open

  def create_plates_from_tube_racks!(
Severity: Minor
Found in app/models/plate/creator.rb by reek

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.

Plate::Creator#create_child_plates_from refers to 'plate' more than self (maybe move it to another class?)
Open

    stock_well_picker = plate.plate_purpose.stock_plate? ? ->(w) { [w] } : ->(w) { w.stock_wells }
    parent_wells = plate.wells

    parent_barcode = plate.human_barcode

Severity: Minor
Found in app/models/plate/creator.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.

Plate::Creator#create_plates_from_tube_racks! has approx 13 statements
Open

  def create_plates_from_tube_racks!(
Severity: Minor
Found in app/models/plate/creator.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 create_plates_from_tube_racks! has 5 arguments (exceeds 4 allowed). Consider refactoring.
Open

    tube_racks,
    barcode_printer,
    scanned_user,
    should_create_asset_group,
    _creator_parameters = nil
Severity: Minor
Found in app/models/plate/creator.rb - About 35 mins to fix

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

      def execute(source_plate_barcodes, barcode_printer, scanned_user, should_create_asset_group, creator_parameters = nil)
    Severity: Minor
    Found in app/models/plate/creator.rb - About 35 mins to fix

      Plate::Creator#find_relevant_study calls 'sample.studies' 2 times
      Open

            plate.contained_samples.each { |sample| return sample.studies.first if sample.studies.first }
      Severity: Minor
      Found in app/models/plate/creator.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::Creator::PlateCreationError has no descriptive comment
      Open

        PlateCreationError = Class.new(StandardError)
      Severity: Minor
      Found in app/models/plate/creator.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::Creator#find_relevant_study calls 'sample.studies.first' 2 times
      Open

            plate.contained_samples.each { |sample| return sample.studies.first if sample.studies.first }
      Severity: Minor
      Found in app/models/plate/creator.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 Plate::Creator#execute (22.4)
      Open

        def execute(source_plate_barcodes, barcode_printer, scanned_user, should_create_asset_group, creator_parameters = nil)
          @created_plates = []
      
          new_plates = transaction { create_plates(source_plate_barcodes, scanned_user, creator_parameters) }
          fail_with_error('Plate creation failed') if new_plates.empty?
      Severity: Minor
      Found in app/models/plate/creator.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::Creator#tube_rack_to_plate_factories doesn't depend on instance state (maybe move it to another class?)
      Open

        def tube_rack_to_plate_factories(tube_racks, plate_purpose)
      Severity: Minor
      Found in app/models/plate/creator.rb by reek

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

      Plate::Creator has missing safe method 'create_plates_from_tube_racks!'
      Open

        def create_plates_from_tube_racks!(
      Severity: Minor
      Found in app/models/plate/creator.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.

      Plate::Creator#find_relevant_study doesn't depend on instance state (maybe move it to another class?)
      Open

        def find_relevant_study(created_plates)
      Severity: Minor
      Found in app/models/plate/creator.rb by reek

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

      Plate::Creator#create_child_plates_from has the variable name 'w'
      Open

          stock_well_picker = plate.plate_purpose.stock_plate? ? ->(w) { [w] } : ->(w) { w.stock_wells }
      Severity: Minor
      Found in app/models/plate/creator.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.

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