sanger/sequencescape

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app/models/tag_layout/walk_wells_by_pools.rb

Summary

Maintainability
A
2 hrs
Test Coverage
A
100%

Complex method TagLayout::WalkWellsByPools#walk_wells (53.5)
Open

  def walk_wells # rubocop:todo Metrics/CyclomaticComplexity
    # Adjust each of the groups so that any wells that are in the same pool as those at the same position
    # in the group to the left are moved to a non-clashing position.  Effectively this makes the view of the
    # plate slightly jagged.
    group_size =

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 walk_wells has a Cognitive Complexity of 19 (exceeds 5 allowed). Consider refactoring.
Open

  def walk_wells # rubocop:todo Metrics/CyclomaticComplexity
    # Adjust each of the groups so that any wells that are in the same pool as those at the same position
    # in the group to the left are moved to a non-clashing position.  Effectively this makes the view of the
    # plate slightly jagged.
    group_size =
Severity: Minor
Found in app/models/tag_layout/walk_wells_by_pools.rb - About 2 hrs 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

TagLayout::WalkWellsByPools#walk_wells contains iterators nested 2 deep
Open

        .map { |wells| wells.map { |well| [well, well.pool_id] } }
    wells_in_groups.each_with_index do |current_group, group|
      next if group == 0

      prior_group = wells_in_groups[group - 1]

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)

TagLayout::WalkWellsByPools#walk_wells has approx 18 statements
Open

  def walk_wells # rubocop:todo Metrics/CyclomaticComplexity

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.)

TagLayout::WalkWellsByPools#walk_wells calls 'plate.size' 2 times
Open

      direction.to_sym == :column ? Map::Coordinate.plate_length(plate.size) : Map::Coordinate.plate_width(plate.size)

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.

TagLayout::WalkWellsByPools#walk_wells calls 'well_and_pool.last' 2 times
Open

        next unless prior_group[index].last == well_and_pool.last

        current_group.push(well_and_pool) # Move the well to the end of the group

        # rubocop:todo Layout/LineLength

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.

TagLayout::WalkWellsByPools has no descriptive comment
Open

class TagLayout::WalkWellsByPools < TagLayout::Walker

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

TagLayout::WalkWellsByPools#walk_wells performs a nil-check
Open

    wells_in_groups.each { |group| group.each_with_index { |(well, _), index| yield(well, index) unless 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)

There are no issues that match your filters.

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