sanger/sequencescape

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app/models/transfer/between_plates_by_submission.rb

Summary

Maintainability
A
1 hr
Test Coverage
A
100%

Complex method Transfer::BetweenPlatesBySubmission#well_to_destination (43.9)
Open

  def well_to_destination # rubocop:todo Metrics/AbcSize
    {}.tap do |sources_to_target|
      # Group the wells based on the submission
      groups = source.wells.in_column_major_order.with_pool_id.group_by(&:pool_id).delete_if { |k, _| k.nil? }.values

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 well_to_destination has a Cognitive Complexity of 11 (exceeds 5 allowed). Consider refactoring.
Open

  def well_to_destination # rubocop:todo Metrics/AbcSize
    {}.tap do |sources_to_target|
      # Group the wells based on the submission
      groups = source.wells.in_column_major_order.with_pool_id.group_by(&:pool_id).delete_if { |k, _| k.nil? }.values

Severity: Minor
Found in app/models/transfer/between_plates_by_submission.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

Transfer::BetweenPlatesBySubmission#well_to_destination contains iterators nested 2 deep
Open

        groups[index].each do |source|

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)

Transfer::BetweenPlatesBySubmission#well_to_destination has approx 8 statements
Open

  def well_to_destination # rubocop:todo Metrics/AbcSize

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.)

Transfer::BetweenPlatesBySubmission#record_transfer calls 'self.transfers' 2 times
Open

    self.transfers ||= {}
    self.transfers[source.map.description] = destination.map.description

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.

Transfer::BetweenPlatesBySubmission#well_to_destination calls 'position.description' 2 times
Open

        destination_well = destination.wells.located_at(position.description).first or
          raise StandardError, "The destination does not have a well at #{position.description}"

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.

Transfer::BetweenPlatesBySubmission#well_to_destination performs a nil-check
Open

      groups = source.wells.in_column_major_order.with_pool_id.group_by(&:pool_id).delete_if { |k, _| k.nil? }.values

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)

Transfer::BetweenPlatesBySubmission#well_to_destination has the variable name 'k'
Open

      groups = source.wells.in_column_major_order.with_pool_id.group_by(&:pool_id).delete_if { |k, _| k.nil? }.values

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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