sanger/sequencescape

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lib/accession/accession/sample.rb

Summary

Maintainability
A
1 hr
Test Coverage
A
100%

Complex method Accession::Sample#to_xml (55.8)
Open

    def to_xml # rubocop:todo Metrics/AbcSize
      tag_groups = tags.by_group
      xml = Builder::XmlMarkup.new
      xml.instruct!
      xml.SAMPLE_SET(XML_NAMESPACE) do
Severity: Minor
Found in lib/accession/accession/sample.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 to_xml has 26 lines of code (exceeds 25 allowed). Consider refactoring.
Open

    def to_xml # rubocop:todo Metrics/AbcSize
      tag_groups = tags.by_group
      xml = Builder::XmlMarkup.new
      xml.instruct!
      xml.SAMPLE_SET(XML_NAMESPACE) do
Severity: Minor
Found in lib/accession/accession/sample.rb - About 1 hr to fix

    Accession::Sample#to_xml has approx 19 statements
    Open

        def to_xml # rubocop:todo Metrics/AbcSize
    Severity: Minor
    Found in lib/accession/accession/sample.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.)

    Accession::Sample has at least 5 instance variables
    Open

      class Sample
    Severity: Minor
    Found in lib/accession/accession/sample.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)

    Accession::Sample#to_xml refers to 'xml' more than self (maybe move it to another class?)
    Open

          xml.instruct!
          xml.SAMPLE_SET(XML_NAMESPACE) do
            xml.SAMPLE(alias: ebi_alias) do
              xml.TITLE title if title.present?
              xml.SAMPLE_NAME { tag_groups[:sample_name].each { |_k, tag| xml.tag!(tag.label, tag.value) } }
    Severity: Minor
    Found in lib/accession/accession/sample.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.

    Method to_xml has a Cognitive Complexity of 7 (exceeds 5 allowed). Consider refactoring.
    Open

        def to_xml # rubocop:todo Metrics/AbcSize
          tag_groups = tags.by_group
          xml = Builder::XmlMarkup.new
          xml.instruct!
          xml.SAMPLE_SET(XML_NAMESPACE) do
    Severity: Minor
    Found in lib/accession/accession/sample.rb - About 35 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

    Accession::Sample#to_xml calls 'xml.VALUE tag.value' 2 times
    Open

                    xml.VALUE tag.value
                  end
                end
                if service.ena?
                  tag_groups[:array_express].each do |_k, tag|
    Severity: Minor
    Found in lib/accession/accession/sample.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.

    Accession::Sample#to_xml calls 'xml.SAMPLE_ATTRIBUTE' 2 times
    Open

                  xml.SAMPLE_ATTRIBUTE do
                    xml.TAG tag.label
                    xml.VALUE tag.value
                  end
                end
    Severity: Minor
    Found in lib/accession/accession/sample.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.

    Accession::Sample has no descriptive comment
    Open

      class Sample
    Severity: Minor
    Found in lib/accession/accession/sample.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

    Accession::Sample#to_xml calls 'tag.label' 2 times
    Open

              xml.SAMPLE_NAME { tag_groups[:sample_name].each { |_k, tag| xml.tag!(tag.label, tag.value) } }
              xml.SAMPLE_ATTRIBUTES do
                tag_groups[:sample_attributes].each do |_k, tag|
                  xml.SAMPLE_ATTRIBUTE do
                    xml.TAG tag.label
    Severity: Minor
    Found in lib/accession/accession/sample.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.

    Accession::Sample#to_xml calls 'tag.value' 3 times
    Open

              xml.SAMPLE_NAME { tag_groups[:sample_name].each { |_k, tag| xml.tag!(tag.label, tag.value) } }
              xml.SAMPLE_ATTRIBUTES do
                tag_groups[:sample_attributes].each do |_k, tag|
                  xml.SAMPLE_ATTRIBUTE do
                    xml.TAG tag.label
    Severity: Minor
    Found in lib/accession/accession/sample.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.

    Accession::Sample has the variable name 's'
    Open

        validate :check_required_fields, if: proc { |s| s.service.valid? }
    Severity: Minor
    Found in lib/accession/accession/sample.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.

    There are no issues that match your filters.

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