sanger/sequencescape

View on GitHub
app/models/submission/asset_submission_finder.rb

Summary

Maintainability
A
0 mins
Test Coverage
A
95%

Complex method Submission::AssetSubmissionFinder#find_wells_including_samples_for! (37.3)
Open

  def find_wells_including_samples_for!(details) # rubocop:todo Metrics/AbcSize
    barcodes, well_list = details['barcode'], details['plate well']
    errors.add(:spreadsheet, 'You can only specify one plate per asset group') unless barcodes.uniq.one?
    barcode = barcodes.first
    plate = Plate.find_from_barcode(barcode)

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

Submission::AssetSubmissionFinder#find_wells_including_samples_for! has approx 9 statements
Open

  def find_wells_including_samples_for!(details) # rubocop:todo Metrics/AbcSize

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.)

Submission::AssetSubmissionFinder#find_wells_including_samples_for! refers to 'details' more than self (maybe move it to another class?)
Open

    barcodes, well_list = details['barcode'], details['plate well']
    errors.add(:spreadsheet, 'You can only specify one plate per asset group') unless barcodes.uniq.one?
    barcode = barcodes.first
    plate = Plate.find_from_barcode(barcode)
    raise StandardError, "Cannot find plate with barcode #{barcode} for #{details['rows']}" if plate.nil?

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.

Submission::AssetSubmissionFinder#find_tubes_including_samples_for! refers to 'details' more than self (maybe move it to another class?)
Open

      .with_barcode(details['barcode'])
      .tap do |found|
        missing = details['barcode'].reject { |barcode| found.any? { |tube| tube.any_barcode_matching?(barcode) } }

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.

Submission::AssetSubmissionFinder#find_all_assets_by_name_including_samples! refers to 'missing' more than self (maybe move it to another class?)
Open

        raise ActiveRecord::RecordNotFound, "Could not find Labware with names #{missing.inspect}" if missing.present?

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.

Submission::AssetSubmissionFinder#find_tubes_including_samples_for! contains iterators nested 2 deep
Open

        missing = details['barcode'].reject { |barcode| found.any? { |tube| tube.any_barcode_matching?(barcode) } }

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)

Submission::AssetSubmissionFinder#find_tubes_including_samples_for! refers to 'missing' more than self (maybe move it to another class?)
Open

        raise ActiveRecord::RecordNotFound, "Could not find Tubes with barcodes #{missing.inspect}" if missing.present?

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.

Submission::AssetSubmissionFinder has no descriptive comment
Open

module Submission::AssetSubmissionFinder

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

Submission::AssetSubmissionFinder#find_tubes_including_samples_for! calls 'details['barcode']' 2 times
Open

      .with_barcode(details['barcode'])
      .tap do |found|
        missing = details['barcode'].reject { |barcode| found.any? { |tube| tube.any_barcode_matching?(barcode) } }

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.

Submission::AssetSubmissionFinder#find_wells_including_samples_for! calls 'details['rows']' 2 times
Open

    raise StandardError, "Cannot find plate with barcode #{barcode} for #{details['rows']}" if plate.nil?

    well_locations = well_list.map(&:strip)
    wells = plate.wells.for_bulk_submission.located_at(well_locations)
    if wells.length != well_locations.size

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.

Submission::AssetSubmissionFinder#is_plate? doesn't depend on instance state (maybe move it to another class?)
Open

  def is_plate?(details)

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

Submission::AssetSubmissionFinder#find_wells_including_samples_for! performs a nil-check
Open

    raise StandardError, "Cannot find plate with barcode #{barcode} for #{details['rows']}" if plate.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)

Submission::AssetSubmissionFinder#is_tube? doesn't depend on instance state (maybe move it to another class?)
Open

  def is_tube?(details)

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

There are no issues that match your filters.

Category
Status