bio-miga/miga

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Module has too many lines. [104/100]
Open

module MiGA::Project::Result
  include MiGA::Project::Base
  include MiGA::Common::WithResult

  ##
Severity: Minor
Found in lib/miga/project/result.rb by rubocop

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

Class has too many lines. [103/100]
Open

class MiGA::Cli::Action::TaxDist < MiGA::Cli::Action
  def parse_cli
    cli.parse do |opt|
      cli.opt_object(opt, [:project])
      cli.opt_filter_datasets(opt)
Severity: Minor
Found in lib/miga/cli/action/tax_dist.rb by rubocop

This cop checks if the length a class 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. [72.7/15]
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 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. [66/10]
Open

  def parse_cli
    cli.defaults = { daemon_opts: [], show_log: false }
    cli.expect_operation = true
    cli.parse do |opt|
      opt.separator 'Available operations:'
Severity: Minor
Found in lib/miga/cli/action/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 perform is too high. [70.8/15]
Open

  def perform
    ds = cli.load_and_filter_datasets(cli[:silent])
    p  = cli.load_project
    exit(ds.empty? ? 1 : 0) if cli[:silent]

Severity: Minor
Found in lib/miga/cli/action/ls.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 load_and_filter_datasets is too high. [63.78/15]
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 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 opts_for_wf is too high. [62.59/15]
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: Minor
Found in lib/miga/cli/action/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 has too many lines. [54/10]
Open

  def parse_cli
    cli.interactive = true
    cli.defaults = {
      mytaxa: nil,
      rdp: nil,
Severity: Minor
Found in lib/miga/cli/action/init.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. [57.87/15]
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 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. [52/10]
Open

  def parse_cli
    cli.defaults = {
      database: :recommended,
      version: :latest,
      local: File.join(ENV['MIGA_HOME'], '.miga_db'),
Severity: Minor
Found in lib/miga/cli/action/db.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. [50/10]
Open

  def test_add_result_other
    d2 = project.add_dataset('ds_add_result_other')
    Dir.mkdir(
      File.join(
        project.path, 'data', '07.annotation', '01.function', '01.essential',
Severity: Minor
Found in test/dataset_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 compute_stats_ssu is too high. [55.34/15]
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 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. [50/10]
Open

  def seqs_length(file, format, opts = {})
    opts[:gc] = true if opts[:skew]
    fh = file =~ /\.gz/ ? Zlib::GzipReader.open(file) : File.open(file, 'r')
    l = []
    gc = 0
Severity: Minor
Found in lib/miga/common/format.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 advance is too high. [54.48/15]
Open

  def advance(step, n = 0, total = nil, bin = true)
    # Initialize advance timing
    @_advance_time ||= { last: nil, n: 0, avg: nil }
    if @_advance_time[:n] > n
      @_advance_time[:last] = nil
Severity: Minor
Found in lib/miga/common.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. [49/10]
Open

  def perform
    # Load environment variables if requested (typically by the daemon)
    if cli[:env]
      cli[:project] ||= ENV['PROJECT']
      cli[:dataset] ||= ENV['DATASET']
Severity: Minor
Found in lib/miga/cli/action/run.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. [48/10]
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 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_alternative is too high. [52.15/15]
Open

  def test_alternative
    tx = MiGA::Taxonomy.new('ns:a s:Arnie', nil,
                            ['ns:b s:Bernie', 'ns:c s:Cornie', 's:Darnie'])
    # Fields
    assert_equal('ns:a s:Arnie', tx.to_s)
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

Method has too many lines. [46/10]
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 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. [46/10]
Open

  def opt_object(opt, what = %i[project dataset])
    what.each do |w|
      case w
      when :project
        opt.on(
Severity: Minor
Found in lib/miga/cli/opt_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 compute_stats_essential_genes is too high. [50.65/15]
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 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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