sanger/sequencescape

      def each(&block) # rubocop:todo Metrics/AbcSize
        Rails.logger.info('API[streaming]: starting JSON streaming')
        start = Time.zone.now

        ::Core::Io::Buffer.new(block) do |buffer|

Close

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

      def each(&block) # rubocop:todo Metrics/AbcSize

Close

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.)

          ::Core::Io::Json::Stream

Close

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)

        start = Time.zone.now

        ::Core::Io::Buffer.new(block) do |buffer|
          ::Core::Io::Json::Stream
            .new(buffer)

Close

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.

      Rails.logger.info("API[start]: #{handler}: #{request.fullpath}")
      yield
    ensure
      Rails.logger.info("API[handled]: #{handler}: #{request.fullpath}")

Close

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.

    class Request

Close

Classes should not assume that instance variables are set or present outside of the current class definition.

Good:

class Foo
  def initialize
    @bar = :foo
  end

  def foo?
    @bar == :foo
  end
end

Good as well:

class Foo
  def foo?
    bar == :foo
  end

  def bar
    @bar ||= :foo
  end
end

Bad:

class Foo
  def go_foo!
    @bar = :foo
  end

  def foo?
    @bar == :foo
  end
end

Example

Running Reek on:

class Dummy
  def test
    @ivar
  end
end

would report:

[1]:InstanceVariableAssumption: Dummy assumes too much for instance variable @ivar

Note that this example would trigger this smell warning as well:

class Parent
  def initialize(omg)
    @omg = omg
  end
end

class Child < Parent
  def foo
    @omg
  end
end

The way to address the smell warning is that you should create an attr_reader to use @omg in the subclass and not access @omg directly like this:

class Parent
  attr_reader :omg

  def initialize(omg)
    @omg = omg
  end
end

class Child < Parent
  def foo
    omg
  end
end

Directly accessing instance variables is considered a smell because it breaks encapsulation and makes it harder to reason about code.

If you don't want to expose those methods as public API just make them private like this:

class Parent
  def initialize(omg)
    @omg = omg
  end

  private
  attr_reader :omg
end

class Child < Parent
  def foo
    omg
  end
end

Current Support in Reek

An instance variable must:

• be set in the constructor
• or be accessed through a method with lazy initialization / memoization.

If not, Instance Variable Assumption will be reported.

  class Service < Sinatra::Base

Close

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

    class Request

Close

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

        @service.request.cookies['api_key'] || @service.request.cookies['WTSISignOn']

Close

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.

      module Behaviour

Close

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

      class Initializer

Close

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

      Rails.logger.info("API[start]: #{handler}: #{request.fullpath}")
      yield
    ensure
      Rails.logger.info("API[handled]: #{handler}: #{request.fullpath}")

Close

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.

          response.general_error(self.class.api_error_code, [self.class.api_error_message || api_error_message])

Close

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.

        start = Time.zone.now

        ::Core::Io::Buffer.new(block) do |buffer|
          ::Core::Io::Json::Stream
            .new(buffer)

Close

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.

        @service.request.cookies['api_key'] || @service.request.cookies['WTSISignOn']

Close

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.

    class UnsupportedAction < Error

Close

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

  class Service < Sinatra::Base

Close

Classes should not assume that instance variables are set or present outside of the current class definition.

Good:

class Foo
  def initialize
    @bar = :foo
  end

  def foo?
    @bar == :foo
  end
end

Good as well:

class Foo
  def foo?
    bar == :foo
  end

  def bar
    @bar ||= :foo
  end
end

Bad:

class Foo
  def go_foo!
    @bar = :foo
  end

  def foo?
    @bar == :foo
  end
end

Example

Running Reek on:

class Dummy
  def test
    @ivar
  end
end

would report:

[1]:InstanceVariableAssumption: Dummy assumes too much for instance variable @ivar

Note that this example would trigger this smell warning as well:

class Parent
  def initialize(omg)
    @omg = omg
  end
end

class Child < Parent
  def foo
    @omg
  end
end

The way to address the smell warning is that you should create an attr_reader to use @omg in the subclass and not access @omg directly like this:

class Parent
  attr_reader :omg

  def initialize(omg)
    @omg = omg
  end
end

class Child < Parent
  def foo
    omg
  end
end

Directly accessing instance variables is considered a smell because it breaks encapsulation and makes it harder to reason about code.

If you don't want to expose those methods as public API just make them private like this:

class Parent
  def initialize(omg)
    @omg = omg
  end

  private
  attr_reader :omg
end

class Child < Parent
  def foo
    omg
  end
end

Current Support in Reek

An instance variable must:

• be set in the constructor
• or be accessed through a method with lazy initialization / memoization.

If not, Instance Variable Assumption will be reported.

    class MethodNotAllowed < Error

Close

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

    class Request

Close

Classes should not assume that instance variables are set or present outside of the current class definition.

Good:

class Foo
  def initialize
    @bar = :foo
  end

  def foo?
    @bar == :foo
  end
end

Good as well:

class Foo
  def foo?
    bar == :foo
  end

  def bar
    @bar ||= :foo
  end
end

Bad:

class Foo
  def go_foo!
    @bar = :foo
  end

  def foo?
    @bar == :foo
  end
end

Example

Running Reek on:

class Dummy
  def test
    @ivar
  end
end

would report:

[1]:InstanceVariableAssumption: Dummy assumes too much for instance variable @ivar

Note that this example would trigger this smell warning as well:

class Parent
  def initialize(omg)
    @omg = omg
  end
end

class Child < Parent
  def foo
    @omg
  end
end

The way to address the smell warning is that you should create an attr_reader to use @omg in the subclass and not access @omg directly like this:

class Parent
  attr_reader :omg

  def initialize(omg)
    @omg = omg
  end
end

class Child < Parent
  def foo
    omg
  end
end

Directly accessing instance variables is considered a smell because it breaks encapsulation and makes it harder to reason about code.

If you don't want to expose those methods as public API just make them private like this:

class Parent
  def initialize(omg)
    @omg = omg
  end

  private
  attr_reader :omg
end

class Child < Parent
  def foo
    omg
  end
end

Current Support in Reek

An instance variable must:

• be set in the constructor
• or be accessed through a method with lazy initialization / memoization.

If not, Instance Variable Assumption will be reported.

    class DeprecatedAction < Error

Close

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

    class Error < StandardError

Close

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

        Rails.logger.info('API[streaming]: starting JSON streaming')
        start = Time.zone.now

        ::Core::Io::Buffer.new(block) do |buffer|
          ::Core::Io::Json::Stream

Close

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.

    def handle_not_found!(_boom)

Close

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.

      attr_writer :io, :file, :filename

Close

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)

      def create!(instance_attributes = attributes)

Close

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.

      attr_writer :io, :file, :filename

Close

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)

      def update!(instance_attributes = attributes)

Close

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.

      attr_writer :io, :file, :filename

Close

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)

        ActiveRecord::Base.transaction { target.tap { |o| o.update!(instance_attributes) } }

Close

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.