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Assignment Branch Condition size for query_probability_distributions is too high. [32.2/15]
Open

  def query_probability_distributions(d, cr)
    cli.say 'Querying probability distributions'
    tax = closest_relative_tax(cr)
    if %w[intax both].include? cli[:test]
      r = test_closest_relative(cr, tax, :intax)
Severity: Minor
Found in lib/miga/cli/action/tax_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. [27/10]
Open

  def check_db(cli)
    cli.say 'Checking integrity of databases'
    p = cli.load_project
    n = p.dataset_names.size
    (0 .. cli[:threads] - 1).map do |i|
Severity: Minor
Found in lib/miga/cli/action/doctor/distances.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.

File daemon_test.rb has 318 lines of code (exceeds 250 allowed). Consider refactoring.
Open

require 'test_helper'
require 'daemon_helper'
require 'miga/daemon'

class DaemonTest < Test::Unit::TestCase
Severity: Minor
Found in test/daemon_test.rb - About 3 hrs to fix

Assignment Branch Condition size for test_reset is too high. [31.02/15]
Open

  def test_reset
    tx = MiGA::Taxonomy.new(
      'ns:Letters d:Latin s:A', nil,
      ['ns:Words d:English s:A', 'ns:Music d:Tone s:A']
    )
Severity: Minor
Found in test/taxonomy_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_overwrite_result is too high. [31.4/15]
Open

  def test_overwrite_result
    r = dataset.add_result(:trimmed_reads)
    r[:ephemeral] = '@'
    r[:versions] = { you: 'best' }
    r.save
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

Assignment Branch Condition size for test_aai_pvalues is too high. [31.4/15]
Open

  def test_aai_pvalues
    distant_intax = MiGA::TaxDist.aai_pvalues(35.0, :intax)
    assert_lt(distant_intax[:root], 0.05)
    assert_gt(distant_intax[:g], 0.05)
    assert_nil(distant_intax[:ns])
Severity: Minor
Found in test/tax_dist_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_dates is too high. [31.26/15]
Open

  def test_dates
    r = dataset.add_result(:trimmed_reads)
    assert_nil(r.done_at)
    assert_nil(r.started_at)
    tf = File.join(
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. [26/10]
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 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. [26/10]
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 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. [26/10]
Open

  def add_metadata(obj, cli = self)
    raise "Unsupported object: #{obj.class}" unless obj.respond_to? :metadata

    (cli[:metadata] || '').split(',').each do |pair|
      (k, v) = pair.split('=')
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.

Assignment Branch Condition size for perform is too high. [31.21/15]
Open

  def perform
    cli.ensure_par(index: '-i')
    ds = cli.load_and_filter_datasets

    cli.say 'Indexing taxonomy'
Severity: Minor
Found in lib/miga/cli/action/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

Assignment Branch Condition size for traverse_taxonomy is too high. [31.67/15]
Open

  def traverse_taxonomy(tab, dist)
    cli.say 'Traversing taxonomy'
    rank_i = 0
    Taxonomy.KNOWN_RANKS.each do |rank|
      next if rank == :ns
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

Assignment Branch Condition size for save_entry is too high. [31.4/15]
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 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. [26/10]
Open

  def perform
    unless cli[:value].nil?
      cli.ensure_par(
        { key: '-k' },
        '%<name>s is mandatory when --value is set: provide %<flag>s'
Severity: Minor
Found in lib/miga/cli/action/option.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 create_dataset is too high. [31.38/15]
Open

  def create_dataset(file, p)
    name = cli[:dataset]
    if name.nil?
      ref_file = file.is_a?(Array) ? file.first : file
      m = cli[:regexp].match(ref_file)
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

Method has too many lines. [26/10]
Open

  def get_files_and_type
    files = cli.files
    file_type = nil
    if files.empty?
      cli.ensure_par({ dataset: '-D' },
Severity: Minor
Found in lib/miga/cli/action/add.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. [31.46/15]
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 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. [26/10]
Open

  def parse_cli
    cli.defaults = { units: false, tabular: false }
    cli.parse do |opt|
      cli.opt_object(opt, [:project, :dataset_opt])
      cli.opt_filter_datasets(opt)
Severity: Minor
Found in lib/miga/cli/action/summary.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. [26/10]
Open

  def perform
    cli.ensure_par(result: '-r')
    ds = cli.load_and_filter_datasets
    cli.say 'Loading results'
    k = 0
Severity: Minor
Found in lib/miga/cli/action/summary.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 ncbi_asm_get is too high. [31.92/15]
Open

    def ncbi_asm_get(opts)
      require 'tempfile'
      require 'zip'

      zipped = download(
Severity: Minor
Found in lib/miga/remote_dataset/download.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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