sanger/sequencescape

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app/models/asset/finder.rb

Summary

Maintainability
A
1 hr
Test Coverage
A
91%

Complex method Asset::Finder#find_wells_in_array (35.0)
Open

  def find_wells_in_array(plate, well_array) # rubocop:todo Metrics/CyclomaticComplexity
    return plate.wells.in_column_major_order.with_aliquots.distinct if well_array.empty?

    well_array.flat_map do |map_description|
      case map_description
Severity: Minor
Found in app/models/asset/finder.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

Asset::Finder#find_wells_in_array has approx 8 statements
Open

  def find_wells_in_array(plate, well_array) # rubocop:todo Metrics/CyclomaticComplexity
Severity: Minor
Found in app/models/asset/finder.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.)

Asset::Finder#find_wells_in_array refers to 'plate' more than self (maybe move it to another class?)
Open

    return plate.wells.in_column_major_order.with_aliquots.distinct if well_array.empty?

    well_array.flat_map do |map_description|
      case map_description
      when /^[a-z,A-Z][0-9]+$/
Severity: Minor
Found in app/models/asset/finder.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.

Asset::Finder#resolve has approx 6 statements
Open

  def resolve
Severity: Minor
Found in app/models/asset/finder.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 find_wells_in_array has a Cognitive Complexity of 7 (exceeds 5 allowed). Consider refactoring.
Open

  def find_wells_in_array(plate, well_array) # rubocop:todo Metrics/CyclomaticComplexity
    return plate.wells.in_column_major_order.with_aliquots.distinct if well_array.empty?

    well_array.flat_map do |map_description|
      case map_description
Severity: Minor
Found in app/models/asset/finder.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

Asset::Finder#resolve manually dispatches method call
Open

      labware.respond_to?(:wells) ? find_wells_in_array(labware, well_array) : labware
Severity: Minor
Found in app/models/asset/finder.rb by reek

Reek reports a Manual Dispatch smell if it finds source code that manually checks whether an object responds to a method before that method is called. Manual dispatch is a type of Simulated Polymorphism which leads to code that is harder to reason about, debug, and refactor.

Example

class MyManualDispatcher
  attr_reader :foo

  def initialize(foo)
    @foo = foo
  end

  def call
    foo.bar if foo.respond_to?(:bar)
  end
end

Reek would emit the following warning:

test.rb -- 1 warning:
  [9]: MyManualDispatcher manually dispatches method call (ManualDispatch)

Asset::Finder#find_wells_in_array calls 'plate.size' 2 times
Open

        plate.wells.with_aliquots.in_plate_row(map_description, plate.size).distinct
      when /^[0-9]+$/
        # A column
        plate.wells.with_aliquots.in_plate_column(map_description, plate.size).distinct
Severity: Minor
Found in app/models/asset/finder.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.

Asset::Finder::InvalidInputException has no descriptive comment
Open

  InvalidInputException = Class.new(StandardError)
Severity: Minor
Found in app/models/asset/finder.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

Asset::Finder#find_wells_in_array calls 'plate.wells.with_aliquots' 2 times
Open

        plate.wells.with_aliquots.in_plate_row(map_description, plate.size).distinct
      when /^[0-9]+$/
        # A column
        plate.wells.with_aliquots.in_plate_column(map_description, plate.size).distinct
Severity: Minor
Found in app/models/asset/finder.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.

Asset::Finder#find_wells_in_array calls 'plate.wells' 3 times
Open

    return plate.wells.in_column_major_order.with_aliquots.distinct if well_array.empty?

    well_array.flat_map do |map_description|
      case map_description
      when /^[a-z,A-Z][0-9]+$/
Severity: Minor
Found in app/models/asset/finder.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.

Method resolve has a Cognitive Complexity of 6 (exceeds 5 allowed). Consider refactoring.
Open

  def resolve
    barcodes_wells.flat_map do |labware_barcode, well_locations|
      labware = Labware.find_by_barcode(labware_barcode)
      raise InvalidInputException, "No labware found for barcode #{labware_barcode}." if labware.nil?

Severity: Minor
Found in app/models/asset/finder.rb - About 25 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

Asset::Finder#find_wells_in_array performs a nil-check
Open

        if well.nil? || well.aliquots.empty?
Severity: Minor
Found in app/models/asset/finder.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)

Asset::Finder#resolve performs a nil-check
Open

      raise InvalidInputException, "No labware found for barcode #{labware_barcode}." if labware.nil?
Severity: Minor
Found in app/models/asset/finder.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)

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