sanger/sequencescape

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app/sample_manifest_excel/sample_manifest_excel/upload/processor/plate.rb

Summary

Maintainability
C
7 hrs
Test Coverage
A
100%

Method duplicate_barcodes has a Cognitive Complexity of 27 (exceeds 5 allowed). Consider refactoring.
Open

        def duplicate_barcodes # rubocop:todo Metrics/CyclomaticComplexity
          return nil, nil unless upload.respond_to?(:rows)

          unique_bcs = {}
          unique_plates = {}

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

Method non_matching_retention_instructions_for_plates has a Cognitive Complexity of 13 (exceeds 5 allowed). Consider refactoring.
Open

        def non_matching_retention_instructions_for_plates
          return nil, nil unless upload.respond_to?(:rows)

          # Initialize empty retention_instructions hash to store retention instructions
          upload

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

Complex method SampleManifestExcel::Upload::Processor::Plate#duplicate_barcodes (34.7)
Open

        def duplicate_barcodes # rubocop:todo Metrics/CyclomaticComplexity
          return nil, nil unless upload.respond_to?(:rows)

          unique_bcs = {}
          unique_plates = {}

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 SampleManifestExcel::Upload::Processor::Plate#non_matching_retention_instructions_for_plates (29.7)
Open

        def non_matching_retention_instructions_for_plates
          return nil, nil unless upload.respond_to?(:rows)

          # Initialize empty retention_instructions hash to store retention instructions
          upload

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

SampleManifestExcel::Upload::Processor::Plate#duplicate_barcodes refers to 'row' more than self (maybe move it to another class?)
Open

            next if row.columns.blank? || row.data.blank?

            plate_barcode = row.value('sanger_plate_id')
            sample_id = row.value('sanger_sample_id')

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.

SampleManifestExcel::Upload::Processor::Plate#check_row_retention_value has approx 7 statements
Open

        def check_row_retention_value(row, plate_barcode, retention_instructions)

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.)

SampleManifestExcel::Upload::Processor::Plate#non_matching_retention_instructions_for_plates has approx 9 statements
Open

        def non_matching_retention_instructions_for_plates

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.)

SampleManifestExcel::Upload::Processor::Plate#non_matching_retention_instructions_for_plates refers to 'row' more than self (maybe move it to another class?)
Open

                row.columns.blank? || row.data.blank? || row.columns.extract(['retention_instruction']).count.zero?

              plate_barcode = row.value('sanger_plate_id')
              sample_id = row.value('sanger_sample_id')

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.

SampleManifestExcel::Upload::Processor::Plate#check_row_retention_value refers to 'retention_instructions' more than self (maybe move it to another class?)
Open

          if retention_instructions.key?(plate_barcode)
            if retention_instructions[plate_barcode] != retention_instruction_key
              return "Plate (#{plate_barcode}) cannot have different retention instruction values."
            end
          else

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.

SampleManifestExcel::Upload::Processor::Plate#duplicate_barcodes has approx 17 statements
Open

        def duplicate_barcodes # rubocop:todo Metrics/CyclomaticComplexity

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.)

SampleManifestExcel::Upload::Processor::Plate#duplicate_barcodes manually dispatches method call
Open

          return nil, nil unless upload.respond_to?(:rows)

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)

SampleManifestExcel::Upload::Processor::Plate#non_matching_retention_instructions_for_plates manually dispatches method call
Open

          return nil, nil unless upload.respond_to?(:rows)

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)

SampleManifestExcel::Upload::Processor::Plate#non_matching_retention_instructions_for_plates calls 'row.columns' 2 times
Open

                row.columns.blank? || row.data.blank? || row.columns.extract(['retention_instruction']).count.zero?

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.

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

        def check_row_retention_value(row, plate_barcode, retention_instructions)
          # if present the column is mandatory
          row_retention_value = row.value('retention_instruction')
          return 'Value cannot be blank.' if row_retention_value.nil?

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

SampleManifestExcel::Upload::Processor::Plate#check_for_retention_instruction_by_plate performs a nil-check
Open

          return if retention_error_row.nil?

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)

SampleManifestExcel::Upload::Processor::Plate#duplicate_barcodes performs a nil-check
Open

            next if plate_barcode.nil? || sample_id.nil?

            plate_id_for_sample = find_plate_id_for_sample_id(sample_id)
            next if plate_id_for_sample.nil?

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)

SampleManifestExcel::Upload::Processor::Plate#check_for_barcodes_unique performs a nil-check
Open

          return if duplicated_barcode_row.nil?

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)

SampleManifestExcel::Upload::Processor::Plate#check_row_retention_value performs a nil-check
Open

          return 'Value cannot be blank.' if row_retention_value.nil?

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)

SampleManifestExcel::Upload::Processor::Plate#find_plate_id_for_sample_id doesn't depend on instance state (maybe move it to another class?)
Open

        def find_plate_id_for_sample_id(sample_id)

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

TODO found
Open

      # TODO: had to explicitly specify the namespace for Base here otherwise it picks up Upload::Base

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

        def non_matching_retention_instructions_for_plates
          return nil, nil unless upload.respond_to?(:rows)

          # Initialize empty retention_instructions hash to store retention instructions
          upload
app/sample_manifest_excel/sample_manifest_excel/upload/processor/one_d_tube.rb on lines 21..42

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 64.

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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