sanger/sequencescape

View on GitHub
app/api/core/io/json/grammar.rb

Summary

Maintainability
A
0 mins
Test Coverage
A
91%

Complex method Core::Io::Json::Grammar::Intermediate#merge_children_with (30.8)
Open

    def merge_children_with(node) # rubocop:todo Metrics/AbcSize
      (node.children.keys + @children.keys)
        .uniq
        .each_with_object({}) do |k, store|
          cloned =
Severity: Minor
Found in app/api/core/io/json/grammar.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

Core::Io::Json::Grammar::Intermediate#initialize is controlled by argument 'children'
Open

      @children = children || {}
Severity: Minor
Found in app/api/core/io/json/grammar.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".

Core::Io::Json::Grammar::Resource#resource_details contains iterators nested 2 deep
Open

        endpoint
Severity: Minor
Found in app/api/core/io/json/grammar.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)

Core::Io::Json::Grammar::Intermediate#merge_children_with has approx 6 statements
Open

    def merge_children_with(node) # rubocop:todo Metrics/AbcSize
Severity: Minor
Found in app/api/core/io/json/grammar.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.)

Core::Io::Json::Grammar::Root#rooted_json is controlled by argument 'nested'
Open

      return yield(stream) if nested
Severity: Minor
Found in app/api/core/io/json/grammar.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".

Core::Io::Json::Grammar::Resource#resource_details has 4 parameters
Open

    def resource_details(endpoint, object, options, stream)
Severity: Minor
Found in app/api/core/io/json/grammar.rb by reek

A Long Parameter List occurs when a method has a lot of parameters.

Example

Given

class Dummy
  def long_list(foo,bar,baz,fling,flung)
    puts foo,bar,baz,fling,flung
  end
end

Reek would report the following warning:

test.rb -- 1 warning:
  [2]:Dummy#long_list has 5 parameters (LongParameterList)

A common solution to this problem would be the introduction of parameter objects.

Core::Io::Json::Grammar::Root#object_encoder has approx 6 statements
Open

    def object_encoder(object, options)
Severity: Minor
Found in app/api/core/io/json/grammar.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.)

Core::Io::Json::Grammar::Resource#resource_details refers to 'stream' more than self (maybe move it to another class?)
Open

      stream.block('actions') do |nested_stream|
        endpoint
          .send(:actions, object, options.merge(target: object))
          .map { |action, url| nested_stream.attribute(action, url) }
        actions(object, options, nested_stream)
Severity: Minor
Found in app/api/core/io/json/grammar.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.

Core::Io::Json::Grammar::Intermediate#merge_children_with calls '@children.key?(k)' 2 times
Open

            when @children.key?(k) && node.children.key?(k)
              node.children[k].merge(@children[k])
            when @children.key?(k)
Severity: Minor
Found in app/api/core/io/json/grammar.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.

Core::Io::Json::Grammar::Actions has no descriptive comment
Open

  class Actions
Severity: Minor
Found in app/api/core/io/json/grammar.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

Core::Io::Json::Grammar::Intermediate#merge_children_with calls 'node.children[k]' 2 times
Open

              node.children[k].merge(@children[k])
            when @children.key?(k)
              @children[k]
            when node.children.key?(k)
              node.children[k]
Severity: Minor
Found in app/api/core/io/json/grammar.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.

Core::Io::Json::Grammar::Leaf has no descriptive comment
Open

  class Leaf
Severity: Minor
Found in app/api/core/io/json/grammar.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

Core::Io::Json::Grammar::Node has no descriptive comment
Open

  class Node
Severity: Minor
Found in app/api/core/io/json/grammar.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

Core::Io::Json::Grammar::Intermediate has initialize method
Open

  module Intermediate
Severity: Minor
Found in app/api/core/io/json/grammar.rb by reek

A module is usually a mixin, so when an #initialize method is present it is hard to tell initialization order and parameters so having #initialize in a module is usually a bad idea.

Example

The Foo module below contains a method initialize. Although class B inherits from A, the inclusion of Foo stops A#initialize from being called.

class A
  def initialize(a)
    @a = a
  end
end

module Foo
  def initialize(foo)
    @foo = foo
  end
end

class B < A
  include Foo

  def initialize(b)
    super('bar')
    @b = b
  end
end

A simple solution is to rename Foo#initialize and call that method by name:

module Foo
  def setup_foo_module(foo)
    @foo = foo
  end
end

class B < A
  include Foo

  def initialize(b)
    super 'bar'
    setup_foo_module('foo')
    @b = b
  end
end

Core::Io::Json::Grammar::Intermediate#merge_children_with calls '@children[k]' 2 times
Open

              node.children[k].merge(@children[k])
            when @children.key?(k)
              @children[k]
Severity: Minor
Found in app/api/core/io/json/grammar.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.

Core::Io::Json::Grammar::Leaf#merge_children_with calls 'node.children' 2 times
Open

      raise "Cannot merge as existing leaf node '#{key}'" if node.children.key?(key)

      node.children.merge(key => self)
Severity: Minor
Found in app/api/core/io/json/grammar.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.

Core::Io::Json::Grammar::Intermediate#merge_children_with calls 'node.children' 5 times
Open

      (node.children.keys + @children.keys)
        .uniq
        .each_with_object({}) do |k, store|
          cloned =
            case
Severity: Minor
Found in app/api/core/io/json/grammar.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.

Core::Io::Json::Grammar::Resource has no descriptive comment
Open

  module Resource
Severity: Minor
Found in app/api/core/io/json/grammar.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

Core::Io::Json::Grammar::Root has no descriptive comment
Open

  class Root
Severity: Minor
Found in app/api/core/io/json/grammar.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

Core::Io::Json::Grammar::Intermediate#merge_children_with calls 'node.children.key?(k)' 2 times
Open

            when @children.key?(k) && node.children.key?(k)
              node.children[k].merge(@children[k])
            when @children.key?(k)
              @children[k]
            when node.children.key?(k)
Severity: Minor
Found in app/api/core/io/json/grammar.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.

Core::Io::Json::Grammar::Intermediate has no descriptive comment
Open

  module Intermediate
Severity: Minor
Found in app/api/core/io/json/grammar.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

Core::Io::Json::Grammar::Root#object_encoder manually dispatches method call
Open

      return self unless object.respond_to?(:uuid)
Severity: Minor
Found in app/api/core/io/json/grammar.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)

Core::Io::Json::Grammar::Leaf#call performs a nil-check
Open

          return if o.nil?
Severity: Minor
Found in app/api/core/io/json/grammar.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)

Core::Io::Json::Grammar::Root takes parameters ['object', 'options'] to 3 methods
Open

    def encode(object, options)
      object_encoder(object, options).call(object, options, options[:stream])
    end

    # To encode an individual object we use our JSON serialization tree, merged with the actions
Severity: Minor
Found in app/api/core/io/json/grammar.rb by reek

In general, a Data Clump occurs when the same two or three items frequently appear together in classes and parameter lists, or when a group of instance variable names start or end with similar substrings.

The recurrence of the items often means there is duplicate code spread around to handle them. There may be an abstraction missing from the code, making the system harder to understand.

Example

Given

class Dummy
  def x(y1,y2); end
  def y(y1,y2); end
  def z(y1,y2); end
end

Reek would emit the following warning:

test.rb -- 1 warning:
  [2, 3, 4]:Dummy takes parameters [y1, y2] to 3 methods (DataClump)

A possible way to fix this problem (quoting from Martin Fowler):

The first step is to replace data clumps with objects and use the objects whenever you see them. An immediate benefit is that you'll shrink some parameter lists. The interesting stuff happens as you begin to look for behavior to move into the new objects.

Core::Io::Json::Grammar::Leaf#call has the variable name 'k'
Open

        @attribute_path.inject(object) do |o, k|
Severity: Minor
Found in app/api/core/io/json/grammar.rb by reek

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.

Core::Io::Json::Grammar::Leaf#call has the variable name 'o'
Open

        @attribute_path.inject(object) do |o, k|
Severity: Minor
Found in app/api/core/io/json/grammar.rb by reek

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.

Core::Io::Json::Grammar::Leaf#dup has the variable name 'p'
Open

      attribute = @attribute_path.dup.tap { |p| p << @attribute }
Severity: Minor
Found in app/api/core/io/json/grammar.rb by reek

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.

Core::Io::Json::Grammar::Intermediate#merge_children_with has the variable name 'k'
Open

        .each_with_object({}) do |k, store|
Severity: Minor
Found in app/api/core/io/json/grammar.rb by reek

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.

Core::Io::Json::Grammar::Root#object_encoder has the variable name 'e'
Open

    rescue Core::Endpoint::BasicHandler::EndpointLookup::MissingEndpoint => e
Severity: Minor
Found in app/api/core/io/json/grammar.rb by reek

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.

Category
Status