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Assignment Branch Condition size for test_seqs_length_fasta is too high. [36.67/15]
Open

  def test_seqs_length_fasta
    c = ">a\nACA\n>b\nACG\n>c\nACTGA\n>d\nGTGAG\n"
    f = helper_write_file(c)
    o = MiGA::MiGA.seqs_length(f, :fasta)
    assert_equal(4.0, o[:avg])
Severity: Minor
Found in test/format_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_check_datasets is too high. [36.22/15]
Open

  def test_check_datasets
    p = project
    d = daemon
    d.runopts(:maxjobs, 0, true)
    assert_empty(d.jobs_to_run)
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. [31/10]
Open

  def test_start
    p = project
    d = daemon
    d.runopts(:latency, 0, true)
    assert_equal(0, d.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.

Assignment Branch Condition size for job_cmd is too high. [36.4/15]
Open

  def job_cmd(to_run)
    what = to_run[:ds].nil? ? :project : :dataset
    vars = {
      'PROJECT' => project.path,
      'RUNTYPE' => runopts_for(:type, what),
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. [31/10]
Open

  def load_and_filter_datasets(silent = false)
    return @objects[:filtered_datasets] unless @objects[:filtered_datasets].nil?

    say 'Listing datasets'
    ds =
Severity: Minor
Found in lib/miga/cli/objects_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. [31/10]
Open

  def perform
    p = cli.load_project
    if !cli[:taxfile].nil?
      cli.say 'Reading tax-file and registering taxonomy'
      tfh = File.open(cli[:taxfile], 'r')
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.

Assignment Branch Condition size for perform is too high. [36.01/15]
Open

  def perform
    # Quick check when the database is not an alias
    dir = File.join(cli[:local], cli[:database].to_s)
    if !cli[:overwrite] && Dir.exist?(dir)
      cli.puts "Database exists: #{dir}"
Severity: Minor
Found in lib/miga/cli/action/db.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_start is too high. [35.41/15]
Open

  def test_start
    p = project
    d = daemon
    d.runopts(:latency, 0, true)
    assert_equal(0, d.latency)
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

Assignment Branch Condition size for remote_list is too high. [35.28/15]
Open

  def remote_list
    cli.say 'Downloading genome list'
    current_page = 1
    total_pages  = 1
    ds = {}
Severity: Minor
Found in lib/miga/cli/action/download/seqcode.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 merge_bidir_tmp is too high. [35.52/15]
Open

  def merge_bidir_tmp(tmp)
    dist = { aai: {}, ani: {} }
    cli[:threads].times do |i|
      cli.advance('Merging:', i + 1, cli[:threads], false)
      file = File.join(tmp, "#{i}.json")
Severity: Minor
Found in lib/miga/cli/action/doctor/distances.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. [30/10]
Open

  def configure_ssh_daemon(v)
    v[:latency] = cli.ask_user('How long should I sleep? (in secs)', '3').to_i
    v[:nodelist] = cli.ask_user(
      'What environmental variable points to node list?', '$MIGA_NODELIST'
    )
Severity: Minor
Found in lib/miga/cli/action/init/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.

Assignment Branch Condition size for parse_cli is too high. [35.44/15]
Open

  def parse_cli
    cli.expect_files = true
    cli.defaults = { ref: true, ignore_dups: false }
    cli.parse do |opt|
      opt.separator 'You can create multiple datasets with a single command; ' \
Severity: Minor
Found in lib/miga/cli/action/add.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 get_sub_cli is too high. [35/15]
Open

  def get_sub_cli
    return [cli] if cli[:file].nil? || cli[:ignore_file]

    glob = []
    cli_default = cli.original_argv + ['--ignore-file']
Severity: Minor
Found in lib/miga/cli/action/get.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 perform is too high. [35.92/15]
Open

  def perform
    r = cli.load_result or return

    cli[:compute] = false if cli[:try_load] && !r[:stats]&.empty?
Severity: Minor
Found in lib/miga/cli/action/stats.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 dereplicate is too high. [35.74/15]
Open

  def dereplicate(p)
    return if cli[:prepare_and_exit]

    cli.say 'Extracting genomospecies clades'
    r = p.result(:clade_finding) or raise 'Result unavailable: run failed'
Severity: Minor
Found in lib/miga/cli/action/derep_wf.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 opts_for_wf has 98 lines of code (exceeds 25 allowed). Consider refactoring.
Open

  def opts_for_wf(opt, files_desc, params = {})
    {
      multi: false, cleanup: true, project_type: false, ncbi: true, qual: true
    }.each { |k, v| params[k] = v if params[k].nil? }
    opt.on(
Severity: Major
Found in lib/miga/cli/action/wf.rb - About 3 hrs to fix

Method load_and_filter_datasets has a Cognitive Complexity of 27 (exceeds 5 allowed). Consider refactoring.
Open

  def load_and_filter_datasets(silent = false)
    return @objects[:filtered_datasets] unless @objects[:filtered_datasets].nil?

    say 'Listing datasets'
    ds =
Severity: Minor
Found in lib/miga/cli/objects_helper.rb - About 3 hrs 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

Block has too many lines. [68/25]
Open

    cli.parse do |opt|
      opt.separator 'Available operations:'
      {
        start: 'Start an instance of the application',
        stop: 'Start an instance of the application',
Severity: Minor
Found in lib/miga/cli/action/lair.rb by rubocop

This cop checks if the length of a block exceeds some maximum value. Comment lines can optionally be ignored. The maximum allowed length is configurable. The cop can be configured to ignore blocks passed to certain methods.

Method has too many lines. [29/10]
Open

  def import_dataset(ds, method = :hardlink)
    raise "Impossible to import dataset, it already exists: #{ds.name}." if
      MiGA::Dataset.exist?(self, ds.name)

    # Import dataset results
Severity: Minor
Found in lib/miga/project/dataset.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. [29/10]
Open

  def configure_bash_daemon(v)
    v[:latency] = cli.ask_user('How long should I sleep? (in secs)', '2').to_i
    v[:maxjobs] = cli.ask_user('How many jobs can I launch at once?', '6').to_i
    v[:ppn]     = cli.ask_user('How many CPUs can I use per job?', '2').to_i
    v[:nodelist] = nil # <- To enable non-default with default SSH
Severity: Minor
Found in lib/miga/cli/action/init/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.

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