sanger/sequencescape

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app/models/accessionable/study.rb

Summary

Maintainability
A
1 hr
Test Coverage
A
100%

Complex method Accessionable::Study#xml (46.9)
Open

    def xml # rubocop:todo Metrics/AbcSize
      xml = Builder::XmlMarkup.new
      xml.instruct!
      xml.STUDY_SET('xmlns:xsi' => 'http://www.w3.org/2001/XMLSchema-instance') do
        xml.STUDY(alias: self.alias, accession: accession_number) do
Severity: Minor
Found in app/models/accessionable/study.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

Complex method Accessionable::Study#initialize (30.3)
Open

    def initialize(study) # rubocop:todo Metrics/AbcSize
      @study = study
      data = {}

      study_title = study.study_metadata.study_study_title
Severity: Minor
Found in app/models/accessionable/study.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

Method xml has a Cognitive Complexity of 9 (exceeds 5 allowed). Consider refactoring.
Open

    def xml # rubocop:todo Metrics/AbcSize
      xml = Builder::XmlMarkup.new
      xml.instruct!
      xml.STUDY_SET('xmlns:xsi' => 'http://www.w3.org/2001/XMLSchema-instance') do
        xml.STUDY(alias: self.alias, accession: accession_number) do
Severity: Minor
Found in app/models/accessionable/study.rb - About 55 mins 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

Accessionable::Study#xml has approx 19 statements
Open

    def xml # rubocop:todo Metrics/AbcSize
Severity: Minor
Found in app/models/accessionable/study.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.)

Accessionable::Study#xml refers to 'xml' more than self (maybe move it to another class?)
Open

      xml.instruct!
      xml.STUDY_SET('xmlns:xsi' => 'http://www.w3.org/2001/XMLSchema-instance') do
        xml.STUDY(alias: self.alias, accession: accession_number) do
          xml.DESCRIPTOR do
            xml.STUDY_TITLE study_title
Severity: Minor
Found in app/models/accessionable/study.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.

Accessionable::Study has at least 10 instance variables
Open

  class Study < Base
Severity: Minor
Found in app/models/accessionable/study.rb by reek

Too Many Instance Variables is a special case of LargeClass.

Example

Given this configuration

TooManyInstanceVariables:
  max_instance_variables: 3

and this code:

class TooManyInstanceVariables
  def initialize
    @arg_1 = :dummy
    @arg_2 = :dummy
    @arg_3 = :dummy
    @arg_4 = :dummy
  end
end

Reek would emit the following warning:

test.rb -- 5 warnings:
  [1]:TooManyInstanceVariables has at least 4 instance variables (TooManyInstanceVariables)

Accessionable::Study#initialize calls 'study.study_metadata' 6 times
Open

      study_title = study.study_metadata.study_study_title
      @name = study_title.blank? ? '' : study_title.gsub(/[^a-z\d]/i, '_')

      study_type = study.study_metadata.study_type.name
      @existing_study_type = study_type # the study type if validated is exactly the one submission need
Severity: Minor
Found in app/models/accessionable/study.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.

Accessionable::Study has no descriptive comment
Open

  class Study < Base
Severity: Minor
Found in app/models/accessionable/study.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

Method initialize has a Cognitive Complexity of 6 (exceeds 5 allowed). Consider refactoring.
Open

    def initialize(study) # rubocop:todo Metrics/AbcSize
      @study = study
      data = {}

      study_title = study.study_metadata.study_study_title
Severity: Minor
Found in app/models/accessionable/study.rb - About 25 mins 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

Accessionable::Study has missing safe method 'update_accession_number!'
Open

    def update_accession_number!(user, accession_number)
Severity: Minor
Found in app/models/accessionable/study.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.

Accessionable::Study has missing safe method 'update_array_express_accession_number!'
Open

    def update_array_express_accession_number!(number)
Severity: Minor
Found in app/models/accessionable/study.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.

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