sanger/sequencescape

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app/models/transfer/between_plates.rb

Summary

Maintainability
A
25 mins
Test Coverage
A
94%

Complex method Transfer::BetweenPlates#calculate_location_submissions (38.0)
Open

  def calculate_location_submissions # rubocop:todo Metrics/AbcSize
    # We're probably just stamping
    return {} if simple_stamp? || pre_cap_groups.empty?

    destination_sources.each_with_object({}) do |dest_source, store|
Severity: Minor
Found in app/models/transfer/between_plates.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 Transfer::BetweenPlates#each_transfer (32.4)
Open

  def each_transfer # rubocop:todo Metrics/AbcSize
    source_wells = valid_source_wells.index_by(&:map_description)
    destination_locations = transfers.values_at(*source_wells.keys).flatten
    destination_wells = destination.wells.located_at_position(destination_locations).index_by(&:map_description)

Severity: Minor
Found in app/models/transfer/between_plates.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

Transfer::BetweenPlates#destination_sources has approx 6 statements
Open

  def destination_sources
Severity: Minor
Found in app/models/transfer/between_plates.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.)

Transfer::BetweenPlates#each_transfer has approx 8 statements
Open

  def each_transfer # rubocop:todo Metrics/AbcSize
Severity: Minor
Found in app/models/transfer/between_plates.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.)

Transfer::BetweenPlates#calculate_location_submissions has approx 13 statements
Open

  def calculate_location_submissions # rubocop:todo Metrics/AbcSize
Severity: Minor
Found in app/models/transfer/between_plates.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.)

Transfer::BetweenPlates#each_transfer contains iterators nested 2 deep
Open

      Array(transfers[location]).each do |target_well_location|
Severity: Minor
Found in app/models/transfer/between_plates.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)

Transfer::BetweenPlates#calculate_location_submissions contains iterators nested 2 deep
Open

      found_pre_cap_groups = pre_cap_groups.select { |_uuid, group_details| group_details[:wells].sort == sources.sort }
Severity: Minor
Found in app/models/transfer/between_plates.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)

Transfer::BetweenPlates#destination_sources contains iterators nested 2 deep
Open

        transfers.each { |source, dests| dests.each { |dest| dest_sources[dest] << source } }
Severity: Minor
Found in app/models/transfer/between_plates.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)

Transfer::BetweenPlates#calculate_location_submissions calls 'found_pre_cap_groups.length' 2 times
Open

      if found_pre_cap_groups.length > 1
        errors.add(
          :base,
          "Found #{found_pre_cap_groups.length} different pools matching the condition for #{sources} to " \
Severity: Minor
Found in app/models/transfer/between_plates.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.

Transfer::BetweenPlates#calculate_location_submissions calls 'raise ActiveRecord::RecordInvalid, self' 2 times
Open

        raise ActiveRecord::RecordInvalid, self
      end

      uuid = found_pre_cap_groups.keys.first
      transfer_details = found_pre_cap_groups[uuid]
Severity: Minor
Found in app/models/transfer/between_plates.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.

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

  def calculate_location_submissions # rubocop:todo Metrics/AbcSize
    # We're probably just stamping
    return {} if simple_stamp? || pre_cap_groups.empty?

    destination_sources.each_with_object({}) do |dest_source, store|
Severity: Minor
Found in app/models/transfer/between_plates.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

Transfer::BetweenPlates#calculate_location_submissions performs a nil-check
Open

      if transfer_details.nil?
Severity: Minor
Found in app/models/transfer/between_plates.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)

Transfer::BetweenPlates#destination_sources has the variable name 'h'
Open

        dest_sources = Hash.new { |h, i| h[i] = [] }
Severity: Minor
Found in app/models/transfer/between_plates.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.

Transfer::BetweenPlates#destination_sources has the variable name 'i'
Open

        dest_sources = Hash.new { |h, i| h[i] = [] }
Severity: Minor
Found in app/models/transfer/between_plates.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.

Transfer::BetweenPlates#each_transfer has the variable name 'k'
Open

    transfers.keep_if { |k, _| source_wells.key?(k) }
Severity: Minor
Found in app/models/transfer/between_plates.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.

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