sanger/sequencescape

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lib/illumina_c/helper.rb

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55 mins
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IlluminaC::Helper::TemplateConstructor#request_type_ids is controlled by argument 'cherrypick'
Open

      ids << [cherrypick_request_type.id] if cherrypick
Severity: Minor
Found in lib/illumina_c/helper.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".

IlluminaC::Helper::TemplateConstructor#update! refers to 'options' more than self (maybe move it to another class?)
Open

        next if options[:submission_parameters][:input_field_infos].nil?

        SubmissionTemplate
          .find_by!(name: options[:name])
          .update!(submission_parameters: options[:submission_parameters])
Severity: Minor
Found in lib/illumina_c/helper.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.

IlluminaC::Helper::TemplateConstructor#each_submission_template contains iterators nested 2 deep
Open

        sequencing.each do |sequencing_request_type|
Severity: Minor
Found in lib/illumina_c/helper.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)

IlluminaC::Helper::TemplateConstructor#skip_cherrypick= is controlled by argument 'skip'
Open

      @cherrypick_options = skip ? [false] : [true, false]
Severity: Minor
Found in lib/illumina_c/helper.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".

IlluminaC::Helper::TemplateConstructor#self.find_for contains iterators nested 2 deep
Open

        tc.sequencing.map do |sequencing_request_type|
Severity: Minor
Found in lib/illumina_c/helper.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)

IlluminaC::Helper::TemplateConstructor#name_for is controlled by argument 'cherrypick'
Open

      "#{PIPELINE} - #{cherrypick ? 'Cherrypicked - ' : ''}#{name} - #{
Severity: Minor
Found in lib/illumina_c/helper.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".

IlluminaC::Helper::TemplateConstructor#update! calls 'options[:submission_parameters]' 2 times
Open

        next if options[:submission_parameters][:input_field_infos].nil?

        SubmissionTemplate
          .find_by!(name: options[:name])
          .update!(submission_parameters: options[:submission_parameters])
Severity: Minor
Found in lib/illumina_c/helper.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.

IlluminaC::Helper::TemplateConstructor has no descriptive comment
Open

  class TemplateConstructor
Severity: Minor
Found in lib/illumina_c/helper.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

IlluminaC::Helper::TemplateConstructor#role is a writable attribute
Open

    attr_accessor :name, :type, :role, :catalogue
Severity: Minor
Found in lib/illumina_c/helper.rb by reek

A class that publishes a setter for an instance variable invites client classes to become too intimate with its inner workings, and in particular with its representation of state.

The same holds to a lesser extent for getters, but Reek doesn't flag those.

Example

Given:

class Klass
  attr_accessor :dummy
end

Reek would emit the following warning:

reek test.rb

test.rb -- 1 warning:
  [2]:Klass declares the writable attribute dummy (Attribute)

IlluminaC::Helper::TemplateConstructor has missing safe method 'update!'
Open

    def update!
Severity: Minor
Found in lib/illumina_c/helper.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.

IlluminaC::Helper::TemplateConstructor#name is a writable attribute
Open

    attr_accessor :name, :type, :role, :catalogue
Severity: Minor
Found in lib/illumina_c/helper.rb by reek

A class that publishes a setter for an instance variable invites client classes to become too intimate with its inner workings, and in particular with its representation of state.

The same holds to a lesser extent for getters, but Reek doesn't flag those.

Example

Given:

class Klass
  attr_accessor :dummy
end

Reek would emit the following warning:

reek test.rb

test.rb -- 1 warning:
  [2]:Klass declares the writable attribute dummy (Attribute)

IlluminaC::Helper::TemplateConstructor#cherrypick_request_type doesn't depend on instance state (maybe move it to another class?)
Open

    def cherrypick_request_type
Severity: Minor
Found in lib/illumina_c/helper.rb by reek

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

IlluminaC::Helper::TemplateConstructor#multiplexing_request_type doesn't depend on instance state (maybe move it to another class?)
Open

    def multiplexing_request_type
Severity: Minor
Found in lib/illumina_c/helper.rb by reek

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

IlluminaC::Helper::TemplateConstructor#type is a writable attribute
Open

    attr_accessor :name, :type, :role, :catalogue
Severity: Minor
Found in lib/illumina_c/helper.rb by reek

A class that publishes a setter for an instance variable invites client classes to become too intimate with its inner workings, and in particular with its representation of state.

The same holds to a lesser extent for getters, but Reek doesn't flag those.

Example

Given:

class Klass
  attr_accessor :dummy
end

Reek would emit the following warning:

reek test.rb

test.rb -- 1 warning:
  [2]:Klass declares the writable attribute dummy (Attribute)

IlluminaC::Helper::TemplateConstructor has missing safe method 'build!'
Open

    def build!
Severity: Minor
Found in lib/illumina_c/helper.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.

IlluminaC::Helper::TemplateConstructor has missing safe method 'validate!'
Open

    def validate!
Severity: Minor
Found in lib/illumina_c/helper.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.

IlluminaC::Helper::TemplateConstructor#update! performs a nil-check
Open

        next if options[:submission_parameters][:input_field_infos].nil?
Severity: Minor
Found in lib/illumina_c/helper.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)

IlluminaC::Helper::TemplateConstructor#validate! performs a nil-check
Open

      %i[name type role catalogue].each { |value| raise "Must provide a #{value}" if send(value).nil? }
Severity: Minor
Found in lib/illumina_c/helper.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)

IlluminaC::Helper::TemplateConstructor#catalogue is a writable attribute
Open

    attr_accessor :name, :type, :role, :catalogue
Severity: Minor
Found in lib/illumina_c/helper.rb by reek

A class that publishes a setter for an instance variable invites client classes to become too intimate with its inner workings, and in particular with its representation of state.

The same holds to a lesser extent for getters, but Reek doesn't flag those.

Example

Given:

class Klass
  attr_accessor :dummy
end

Reek would emit the following warning:

reek test.rb

test.rb -- 1 warning:
  [2]:Klass declares the writable attribute dummy (Attribute)

Identical blocks of code found in 2 locations. Consider refactoring.
Open

    def self.find_for(name, sequencing = nil)
      tc = TemplateConstructor.new(name: name, sequencing: sequencing)
      [true, false].map do |cherrypick|
        tc.sequencing.map do |sequencing_request_type|
          SubmissionTemplate.find_by!(name: tc.name_for(cherrypick, sequencing_request_type))
Severity: Minor
Found in lib/illumina_c/helper.rb and 1 other location - About 30 mins to fix
lib/limber/helper.rb on lines 41..45

Duplicated Code

Duplicated code can lead to software that is hard to understand and difficult to change. The Don't Repeat Yourself (DRY) principle states:

Every piece of knowledge must have a single, unambiguous, authoritative representation within a system.

When you violate DRY, bugs and maintenance problems are sure to follow. Duplicated code has a tendency to both continue to replicate and also to diverge (leaving bugs as two similar implementations differ in subtle ways).

Tuning

This issue has a mass of 33.

We set useful threshold defaults for the languages we support but you may want to adjust these settings based on your project guidelines.

The threshold configuration represents the minimum mass a code block must have to be analyzed for duplication. The lower the threshold, the more fine-grained the comparison.

If the engine is too easily reporting duplication, try raising the threshold. If you suspect that the engine isn't catching enough duplication, try lowering the threshold. The best setting tends to differ from language to language.

See codeclimate-duplication's documentation for more information about tuning the mass threshold in your .codeclimate.yml.

Refactorings

Further Reading

Identical blocks of code found in 2 locations. Consider refactoring.
Open

    def request_type_ids(cherrypick, sequencing)
      ids = []
      ids << [cherrypick_request_type.id] if cherrypick
      ids << [library_request_type.id]
      ids << [multiplexing_request_type.id] unless library_request_type.for_multiplexing?
Severity: Minor
Found in lib/illumina_c/helper.rb and 1 other location - About 25 mins to fix
lib/limber/helper.rb on lines 151..156

Duplicated Code

Duplicated code can lead to software that is hard to understand and difficult to change. The Don't Repeat Yourself (DRY) principle states:

Every piece of knowledge must have a single, unambiguous, authoritative representation within a system.

When you violate DRY, bugs and maintenance problems are sure to follow. Duplicated code has a tendency to both continue to replicate and also to diverge (leaving bugs as two similar implementations differ in subtle ways).

Tuning

This issue has a mass of 29.

We set useful threshold defaults for the languages we support but you may want to adjust these settings based on your project guidelines.

The threshold configuration represents the minimum mass a code block must have to be analyzed for duplication. The lower the threshold, the more fine-grained the comparison.

If the engine is too easily reporting duplication, try raising the threshold. If you suspect that the engine isn't catching enough duplication, try lowering the threshold. The best setting tends to differ from language to language.

See codeclimate-duplication's documentation for more information about tuning the mass threshold in your .codeclimate.yml.

Refactorings

Further Reading

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