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Showing 838 of 1,651 total issues

Assignment Branch Condition size for test_in_loop is too high. [21.21/15]
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 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_project_result_hooks is too high. [21.59/15]
Open

  def test_project_result_hooks
    $res = :test
    $counter = 1
    project.add_hook(
      :on_result_ready,
Severity: Minor
Found in test/hook_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_versions is too high. [21.1/15]
Open

  def test_versions
    r = dataset.add_result(:trimmed_reads)
    assert_respond_to(r, :add_versions)
    assert_respond_to(r, :versions_md)
    assert_equal(MiGA::VERSION.join('.'), r.versions[:MiGA])
Severity: Minor
Found in test/result_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. [16/10]
Open

  def test_debug_trace
    assert_respond_to(MiGA::MiGA, :DEBUG)
    assert_respond_to(MiGA::MiGA, :DEBUG_ON)
    assert_respond_to(MiGA::MiGA, :DEBUG_OFF)
    MiGA::MiGA.DEBUG_TRACE_ON
Severity: Minor
Found in test/common_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_launch_job_failure is too high. [21.1/15]
Open

  def test_launch_job_failure
    d1 = daemon(1)
    d1.runopts(:type, 'qsub')
    d1.runopts(:cmd, 'echo ""')
    helper_datasets_with_results(1, 1).first.inactivate!
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

Perceived complexity for compute_stats_ssu is too high. [13/7]
Open

  def compute_stats_ssu
    stats = {
      ssu: 0, complete_ssu: 0, ssu_fragment: [0.0, '%'],
      lsu: 0, complete_lsu: 0, lsu_fragment: [0.0, '%']
    }
Severity: Minor
Found in lib/miga/result/stats.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

Method has too many lines. [16/10]
Open

  def taxa_by_rank(rank)
    rank = MiGA::Taxonomy.normalize_rank(rank)
    taxa = [@root]
    select = []
    loop do
Severity: Minor
Found in lib/miga/tax_index.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 compute_stats_essential_genes is too high. [13/7]
Open

  def compute_stats_essential_genes
    stats = {}
    if source.multi?
      stats = { median_copies: 0, mean_copies: 0 }
      File.open(file_path(:report), 'r') do |fh|
Severity: Minor
Found in lib/miga/result/stats.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

Method has too many lines. [16/10]
Open

  def check_datasets
    l_say(2, 'Checking datasets')
    o = false
    project.each_dataset do |ds|
      next unless ds.status == :incomplete
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_type_status_ncbi_asm is too high. [21.79/15]
Open

  def get_type_status_ncbi_asm(metadata)
    from_type = nil

    # Try first from previously pulled NCBI metadata
    if metadata[:ncbi_dataset]
Severity: Minor
Found in lib/miga/remote_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

Cyclomatic complexity for compute_stats_ssu is too high. [12/6]
Open

  def compute_stats_ssu
    stats = {
      ssu: 0, complete_ssu: 0, ssu_fragment: [0.0, '%'],
      lsu: 0, complete_lsu: 0, lsu_fragment: [0.0, '%']
    }
Severity: Minor
Found in lib/miga/result/stats.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 runopts is too high. [21.31/15]
Open

  def runopts(k, v = nil, force = false)
    k = k.to_sym
    unless v.nil?
      case k
      when :latency, :maxjobs, :ppn, :ppn_project, :format_version, :verbosity,
Severity: Minor
Found in lib/miga/daemon/base.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 download_file_ftp is too high. [12/6]
Open

  def download_file_ftp(connection, file = nil, target = nil)
    # Open connection unless passed
    close_conn = false
    if connection.is_a?(String) || connection.is_a?(Symbol) ||
          connection.is_a?(URI)
Severity: Minor
Found in lib/miga/common/net.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.

Cyclomatic complexity for download_entries is too high. [12/6]
Open

  def download_entries(ds, p)
    cli.say "Downloading #{ds.size} " + (ds.size == 1 ? 'entry' : 'entries')
    p.do_not_save = true if cli[:save_every] != 1
    ignore = !cli[:ignore_until].nil?
    downloaded = 0
Severity: Minor
Found in lib/miga/cli/action/download/base.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. [16/10]
Open

  def closest_relative_tax(cr)
    cli.puts "Closest relative: #{cr[0]} with AAI: #{cr[1]}."
    p = cli.load_project
    if cli[:ref_project]
      if (ref = p.option(:ref_project)).nil?
Severity: Minor
Found in lib/miga/cli/action/tax_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. [16/10]
Open

  def save_entry(name, body, p)
    cli.say "  Locating remote dataset: #{name}"
    body[:md][:metadata_only] = true if cli[:only_md]
    rd = MiGA::RemoteDataset.new(body[:ids], body[:db], body[:universe])
    if cli[:get_md]
Severity: Minor
Found in lib/miga/cli/action/download/base.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_tab_index is too high. [21.4/15]
Open

  def get_tab_index(dir)
    if cli[:index].nil?
      ds = cli.load_and_filter_datasets
      ds.keep_if { |d| !d.metadata[:tax].nil? }
Severity: Minor
Found in lib/miga/cli/action/tax_dist.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. [16/10]
Open

  def parse_cli
    cli.parse do |opt|
      cli.opt_object(opt, [:project, :dataset_opt])
      opt.on(
        '-s', '--tax-string STRING',
Severity: Minor
Found in lib/miga/cli/action/tax_set.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. [16/10]
Open

  def perform
    cli.ensure_type(MiGA::Project)
    cli.ensure_par(project: '-P')
    if !cli[:ignore_init] && !MiGA::MiGA.initialized?
      raise 'MiGA has not been initialized, please use "miga init" first'
Severity: Minor
Found in lib/miga/cli/action/new.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 perform is too high. [21.47/15]
Open

  def perform
    cli.operation or raise 'Please specify a daemon operation'

    # Cleanup environment
    %w[PROJECT RUNTYPE CORES DATASET].each { |i| ENV[i] = nil }
Severity: Minor
Found in lib/miga/cli/action/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

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