File sample.rb
has 386 lines of code (exceeds 250 allowed). Consider refactoring. Open
require 'rexml/text'
#
# A {Sample} is an abstract concept, with represents the life of a sample of DNA/RNA
# as it moves through our processes. As a result, a sample may exist in multiple
Sample has 7 constants Open
class Sample < ApplicationRecord # rubocop:todo Metrics/ClassLength
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Too Many Constants
is a special case of LargeClass
.
Example
Given this configuration
TooManyConstants:
max_constants: 3
and this code:
class TooManyConstants
CONST_1 = :dummy
CONST_2 = :dummy
CONST_3 = :dummy
CONST_4 = :dummy
end
Reek would emit the following warning:
test.rb -- 1 warnings:
[1]:TooManyConstants has 4 constants (TooManyConstants)
Sample has at least 20 methods Open
class Sample < ApplicationRecord # rubocop:todo Metrics/ClassLength
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Too Many Methods
is a special case of LargeClass
.
Example
Given this configuration
TooManyMethods:
max_methods: 3
and this code:
class TooManyMethods
def one; end
def two; end
def three; end
def four; end
end
Reek would emit the following warning:
test.rb -- 1 warning:
[1]:TooManyMethods has at least 4 methods (TooManyMethods)
Sample#accession_service has approx 7 statements Open
def accession_service
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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.)
Sample#accession_service refers to 'services' more than self (maybe move it to another class?) Open
return UnsuitableAccessionService.new([]) if services.empty?
highest_priority = services.keys.max
suitable_study = services[highest_priority].detect(&:send_samples_to_service?)
return suitable_study.accession_service if suitable_study
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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.
Sample#accession_service calls 'services[highest_priority]' 2 times Open
suitable_study = services[highest_priority].detect(&:send_samples_to_service?)
return suitable_study.accession_service if suitable_study
UnsuitableAccessionService.new(services[highest_priority])
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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.
Sample#sample_reference_genome calls 'sample_metadata.reference_genome' 2 times Open
return sample_metadata.reference_genome if sample_metadata.reference_genome.try(:name).present?
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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.
Complex method Sample#validate_ena_required_fields! (21.6) Open
def validate_ena_required_fields!
(valid?(:accession) && valid?(accession_service.provider)) || raise(ActiveRecord::RecordInvalid, self)
rescue ActiveRecord::RecordInvalid => e
ena_study.errors.full_messages.each { |message| errors.add(:base, "#{message} on study") } unless ena_study.nil?
raise e
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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 validate_ena_required_fields!
has a Cognitive Complexity of 6 (exceeds 5 allowed). Consider refactoring. Open
def validate_ena_required_fields!
(valid?(:accession) && valid?(accession_service.provider)) || raise(ActiveRecord::RecordInvalid, self)
rescue ActiveRecord::RecordInvalid => e
ena_study.errors.full_messages.each { |message| errors.add(:base, "#{message} on study") } unless ena_study.nil?
raise e
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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
Sample has missing safe method 'rename_to!' Open
def rename_to!(new_name)
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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.
Sample#sample_supplier_name_empty? doesn't depend on instance state (maybe move it to another class?) Open
def sample_supplier_name_empty?(supplier_sample_name)
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A Utility Function is any instance method that has no dependency on the state of the instance.
Sample has missing safe method 'validate_ena_required_fields!' Open
def validate_ena_required_fields!
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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.
Sample#control_formatted performs a nil-check Open
return nil if control.nil?
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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)
Sample#validate_ena_required_fields! performs a nil-check Open
ena_study.errors.full_messages.each { |message| errors.add(:base, "#{message} on study") } unless ena_study.nil?
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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)
Sample#shorten_sanger_sample_id performs a nil-check Open
when nil
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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)
Sample has the variable name 'b' Open
}.transform_values { |v| v.index_by { |b| b.downcase } }
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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.
Sample#validate_ena_required_fields! has the variable name 'e' Open
rescue ActiveRecord::RecordInvalid => e
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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.
Sample#accession_service has the variable name 's' Open
services = studies.group_by { |s| s.accession_service.priority }
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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.
Sample has the variable name 'v' Open
}.transform_values { |v| v.index_by { |b| b.downcase } }
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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.
TODO found Open
custom_attribute(:date_of_sample_extraction) # TODO[xxx]: Date field?
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TODO found Open
custom_attribute(:date_of_sample_collection) # TODO[xxx]: Date field?
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TODO found Open
custom_attribute(:is_resubmitted) # TODO[xxx]: selection of yes/no?
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TODO found Open
custom_attribute(:sample_purified) # TODO[xxx]: selection of yes/no?
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TODO found Open
# TODO: split age in two fields and use a composed_of
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TODO found Open
custom_attribute(:compound) # TODO : yes/no?
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TODO found Open
custom_attribute(:purification_method) # TODO[xxx]: tied to the field above?
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Identical blocks of code found in 2 locations. Consider refactoring. Open
before_validation do |record|
record.reference_genome_id = 1 if record.reference_genome_id.blank?
# Unfortunately it appears that some of the functionality of this implementation relies on non-capitalisation!
# So we remap the lowercased versions to their proper values here
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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 38.
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
- Extract Method
- Extract Class
- Form Template Method
- Introduce Null Object
- Pull Up Method
- Pull Up Field
- Substitute Algorithm
Further Reading
- Don't Repeat Yourself on the C2 Wiki
- Duplicated Code on SourceMaking
- Refactoring: Improving the Design of Existing Code by Martin Fowler. Duplicated Code, p76