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Showing 839 of 1,651 total issues

Assignment Branch Condition size for test_activate is too high. [18.03/15]
Open

  def test_activate
    d = dataset
    assert_equal(:incomplete, d.status)
    assert_predicate(d, :active?)
    d.inactivate! 'Too annoying'
Severity: Minor
Found in test/dataset_test.rb by rubocop

This cop checks that the ABC size of methods is not higher than the configured maximum. The ABC size is based on assignments, branches (method calls), and conditions. See http://c2.com/cgi/wiki?AbcMetric

Assignment Branch Condition size for test_bypass_maintenance is too high. [18.11/15]
Open

  def test_bypass_maintenance
    # Default (run maintenance)
    d = daemon(0)
    d.runopts(:latency, 0, true)
    capture_stderr { d.in_loop }
Severity: Minor
Found in test/daemon_test.rb by rubocop

This cop checks that the ABC size of methods is not higher than the configured maximum. The ABC size is based on assignments, branches (method calls), and conditions. See http://c2.com/cgi/wiki?AbcMetric

Method has too many lines. [13/10]
Open

  def test_in_loop
    declare_forks
    lair = MiGA::Lair.new(tmpdir, name: 'Oh')
    child = lair.start(['--shush'])
    assert_not_nil(child)
Severity: Minor
Found in test/lair_test.rb by rubocop

This cop checks if the length of a method exceeds some maximum value. Comment lines can optionally be ignored. The maximum allowed length is configurable.

Method has too many lines. [13/10]
Open

  def test_in_loop
    p = project
    d = daemon
    d.runopts(:latency, 0, true)
    assert_nil(d.loop_i)
Severity: Minor
Found in test/daemon_test.rb by rubocop

This cop checks if the length of a method exceeds some maximum value. Comment lines can optionally be ignored. The maximum allowed length is configurable.

Method has too many lines. [13/10]
Open

  def test_options
    d1 = daemon
    assert_respond_to(d1, :default_options)
    assert_equal(:normal, d1.default_options[:dir_mode])
    assert_equal(2, d1.runopts(:latency))
Severity: Minor
Found in test/daemon_test.rb by rubocop

This cop checks if the length of a method exceeds some maximum value. Comment lines can optionally be ignored. The maximum allowed length is configurable.

Method has too many lines. [13/10]
Open

  def test_launch_job_ssh
    d1 = daemon(1)
    t = tmpfile('launch_job_ssh')
    d1.runopts(:type, 'ssh')
    d1.runopts(:cmd, "echo {{task_name}} > '#{t}'")
Severity: Minor
Found in test/daemon_test.rb by rubocop

This cop checks if the length of a method exceeds some maximum value. Comment lines can optionally be ignored. The maximum allowed length is configurable.

Assignment Branch Condition size for test_show_log is too high. [18.03/15]
Open

  def test_show_log
    d = daemon
    assert(d.show_log?)
    d.runopts(:show_log, false)
    assert(!d.show_log?)
Severity: Minor
Found in test/daemon_test.rb by rubocop

This cop checks that the ABC size of methods is not higher than the configured maximum. The ABC size is based on assignments, branches (method calls), and conditions. See http://c2.com/cgi/wiki?AbcMetric

Method has too many lines. [13/10]
Open

  def helper_datasets_with_results(n = 1, project_i = 0)
    p1 = project(project_i)
    Array.new(n) do |i|
      d = "d#{i}"
      FileUtils.touch(
Severity: Minor
Found in test/daemon_helper.rb by rubocop

This cop checks if the length of a method exceeds some maximum value. Comment lines can optionally be ignored. The maximum allowed length is configurable.

Method has too many lines. [13/10]
Open

  def initialize(argv)
    @data = {}
    @defaults = { verbose: false, tabular: false }
    @opt_common = true
    @original_argv = argv.dup
Severity: Minor
Found in lib/miga/cli.rb by rubocop

This cop checks if the length of a method exceeds some maximum value. Comment lines can optionally be ignored. The maximum allowed length is configurable.

Cyclomatic complexity for ask_user is too high. [9/6]
Open

  def ask_user(question, default = nil, answers = nil, force = false)
    ans = " (#{answers.join(' / ')})" unless answers.nil?
    dft = " [#{default}]" unless default.nil?
    print "#{question}#{ans}#{dft} > "
    if self[:auto] && !force
Severity: Minor
Found in lib/miga/cli.rb by rubocop

This cop checks that the cyclomatic complexity of methods is not higher than the configured maximum. The cyclomatic complexity is the number of linearly independent paths through a method. The algorithm counts decision points and adds one.

An if statement (or unless or ?:) increases the complexity by one. An else branch does not, since it doesn't add a decision point. The && operator (or keyword and) can be converted to a nested if statement, and ||/or is shorthand for a sequence of ifs, so they also add one. Loops can be said to have an exit condition, so they add one.

Method has too many lines. [13/10]
Open

  def test_update_format_0
    f = tmpfile('daemon.json')
    File.open(f, 'w') do |fh|
      fh.puts(
        <<~DAEMON
Severity: Minor
Found in test/daemon_test.rb by rubocop

This cop checks if the length of a method exceeds some maximum value. Comment lines can optionally be ignored. The maximum allowed length is configurable.

Method has too many lines. [13/10]
Open

  def update_format_0
    {
      cmd: %w[script vars cpus log task_name],
      var: %w[key value],
      alive: %w[pid],
Severity: Minor
Found in lib/miga/daemon.rb by rubocop

This cop checks if the length of a method exceeds some maximum value. Comment lines can optionally be ignored. The maximum allowed length is configurable.

Assignment Branch Condition size for get_job is too high. [18.44/15]
Open

  def get_job(job, ds = nil)
    (jobs_to_run + jobs_running).find do |j|
      if ds.nil?
        j[:ds].nil? && j[:job] == job
      else
Severity: Minor
Found in lib/miga/daemon.rb by rubocop

This cop checks that the ABC size of methods is not higher than the configured maximum. The ABC size is based on assignments, branches (method calls), and conditions. See http://c2.com/cgi/wiki?AbcMetric

Method has too many lines. [13/10]
Open

  def compute_stats_taxonomy
    stats = {}
    return stats unless file_path(:intax_test)

    File.open(file_path(:intax_test), 'r') do |fh|
Severity: Minor
Found in lib/miga/result/stats.rb by rubocop

This cop checks if the length of a method exceeds some maximum value. Comment lines can optionally be ignored. The maximum allowed length is configurable.

Method has too many lines. [13/10]
Open

  def fix_essential_genes_by_domain
    return if file_path(:raw_report)

    tax = source.metadata[:tax]
    return unless tax.nil? || %w[Archaea Bacteria].include?(tax[:d])
Severity: Minor
Found in lib/miga/result/stats.rb by rubocop

This cop checks if the length of a method exceeds some maximum value. Comment lines can optionally be ignored. The maximum allowed length is configurable.

Perceived complexity for get_ncbi_taxonomy is too high. [10/7]
Open

  def get_ncbi_taxonomy
    tax_id = get_ncbi_taxid or return

    if self.class.ncbi_taxonomy_dump?
      return self.class.taxonomy_from_ncbi_dump(tax_id)
Severity: Minor
Found in lib/miga/remote_dataset.rb by rubocop

This cop tries to produce a complexity score that's a measure of the complexity the reader experiences when looking at a method. For that reason it considers when nodes as something that doesn't add as much complexity as an if or a &&. Except if it's one of those special case/when constructs where there's no expression after case. Then the cop treats it as an if/elsif/elsif... and lets all the when nodes count. In contrast to the CyclomaticComplexity cop, this cop considers else nodes as adding complexity.

Example:

def my_method                   # 1
  if cond                       # 1
    case var                    # 2 (0.8 + 4 * 0.2, rounded)
    when 1 then func_one
    when 2 then func_two
    when 3 then func_three
    when 4..10 then func_other
    end
  else                          # 1
    do_something until a && b   # 2
  end                           # ===
end                             # 7 complexity points

Perceived complexity for ask_user is too high. [10/7]
Open

  def ask_user(question, default = nil, answers = nil, force = false)
    ans = " (#{answers.join(' / ')})" unless answers.nil?
    dft = " [#{default}]" unless default.nil?
    print "#{question}#{ans}#{dft} > "
    if self[:auto] && !force
Severity: Minor
Found in lib/miga/cli.rb by rubocop

This cop tries to produce a complexity score that's a measure of the complexity the reader experiences when looking at a method. For that reason it considers when nodes as something that doesn't add as much complexity as an if or a &&. Except if it's one of those special case/when constructs where there's no expression after case. Then the cop treats it as an if/elsif/elsif... and lets all the when nodes count. In contrast to the CyclomaticComplexity cop, this cop considers else nodes as adding complexity.

Example:

def my_method                   # 1
  if cond                       # 1
    case var                    # 2 (0.8 + 4 * 0.2, rounded)
    when 1 then func_one
    when 2 then func_two
    when 3 then func_three
    when 4..10 then func_other
    end
  else                          # 1
    do_something until a && b   # 2
  end                           # ===
end                             # 7 complexity points

Assignment Branch Condition size for to_tab is too high. [18.68/15]
Open

  def to_tab(unknown, indent = 0)
    o = ''
    if unknown or not datasets.empty? or not name.nil?
      o = "#{' ' * indent}#{tax_str}: #{datasets_count}\n"
    end
Severity: Minor
Found in lib/miga/tax_index.rb by rubocop

This cop checks that the ABC size of methods is not higher than the configured maximum. The ABC size is based on assignments, branches (method calls), and conditions. See http://c2.com/cgi/wiki?AbcMetric

Cyclomatic complexity for parse is too high. [9/6]
Open

    def parse(path, opts = {})
      opts = default_opts(opts)

      # Read JSON
      cont = path
Severity: Minor
Found in lib/miga/json.rb by rubocop

This cop checks that the cyclomatic complexity of methods is not higher than the configured maximum. The cyclomatic complexity is the number of linearly independent paths through a method. The algorithm counts decision points and adds one.

An if statement (or unless or ?:) increases the complexity by one. An else branch does not, since it doesn't add a decision point. The && operator (or keyword and) can be converted to a nested if statement, and ||/or is shorthand for a sequence of ifs, so they also add one. Loops can be said to have an exit condition, so they add one.

Assignment Branch Condition size for unregistered_datasets is too high. [18.68/15]
Open

  def unregistered_datasets
    datasets = []
    MiGA::Dataset.RESULT_DIRS.values.each do |dir|
      dir_p = "#{path}/data/#{dir}"
      next unless Dir.exist? dir_p
Severity: Minor
Found in lib/miga/project/dataset.rb by rubocop

This cop checks that the ABC size of methods is not higher than the configured maximum. The ABC size is based on assignments, branches (method calls), and conditions. See http://c2.com/cgi/wiki?AbcMetric

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