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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

Assignment Branch Condition size for parse_cli is too high. [50.99/15]
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 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 parse_cli is too high. [49.24/15]
Open

  def parse_cli
    cli.defaults = { daemon_opts: [] }
    cli.expect_operation = true
    cli.parse do |opt|
      opt.separator 'Available operations:'
Severity: Minor
Found in lib/miga/cli/action/lair.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. [44/10]
Open

  def parse_cli
    cli.defaults = { info: false, processing: false, silent: 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/ls.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 run_cmd is too high. [48.64/15]
Open

  def run_cmd(cmd, opts = {})
    opts = run_cmd_opts(opts)
    cmd = cmd.shelljoin if cmd.is_a?(Array)
    spawn_opts = {}
    spawn_opts[:out] = opts[:stdout] if opts[:stdout]
Severity: Minor
Found in lib/miga/common/system_call.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. [42/10]
Open

  def run_cmd(cmd, opts = {})
    opts = run_cmd_opts(opts)
    cmd = cmd.shelljoin if cmd.is_a?(Array)
    spawn_opts = {}
    spawn_opts[:out] = opts[:stdout] if opts[:stdout]
Severity: Minor
Found in lib/miga/common/system_call.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. [47.77/15]
Open

  def parse_cli
    cli.defaults = {
      query: false, universe: :ncbi, db: :nuccore, get_md: false, only_md: false
    }
    cli.parse do |opt|
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 configure_qsub_msub_daemon is too high. [45.72/15]
Open

  def configure_qsub_msub_daemon(v)
    flavor      = v[:type] == 'msub' ? 'msub' :
                  cli.ask_user('Select qsub flavor', 'torque', %w[torque sge])
    queue       = cli.ask_user('What queue should I use?', nil, nil, true)
    v[:latency] = cli.ask_user('How long should I sleep? (in secs)', '150').to_i
Severity: Minor
Found in lib/miga/cli/action/init/daemon_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

Method has too many lines. [39/10]
Open

  def test_preprocessing
    d2 = project.add_dataset('ds_preprocessing')
    assert_nil(d2.first_preprocessing)
    assert_nil(d2.next_preprocessing)
    assert_not_predicate(d2, :done_preprocessing?)
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.

Method has too many lines. [39/10]
Open

  def opt_filter_datasets(opt, what = %i[ref multi markers active taxonomy])
    what.each do |w|
      case w
      when :ref
        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.

Method has too many lines. [38/10]
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 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 download_entries is too high. [43.61/15]
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 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. [38/10]
Open

  def parse_cli
    default_opts_for_wf
    cli.defaults = {
      metric: :ani, threshold: 95.0, criterion: :quality,
      summaries: true, collection: true
Severity: Minor
Found in lib/miga/cli/action/derep_wf.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 compute_stats_ssu has a Cognitive Complexity of 33 (exceeds 5 allowed). Consider refactoring.
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 - About 4 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

Assignment Branch Condition size for launch_job is too high. [42.2/15]
Open

  def launch_job(job, hostk = nil)
    # Execute job
    job[:cmd] = job_cmd(job)
    MiGA::MiGA.DEBUG "CMD: #{job[:cmd]}"
    case runopts(:type)
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. [37/10]
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 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. [37/10]
Open

  def clean_fasta_file(file)
    tmp_fh = nil
    tmp_path = nil
    begin
      if file =~ /\.gz/
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 read_distances is too high. [42.4/15]
Open

  def read_distances
    p = cli.load_project
    cli[:metric] ||= p.clade? ? 'ani' : 'aai'
    res_n = "#{cli[:metric]}_distances"
    cli.say "Reading distances: 1-#{cli[:metric].upcase}"
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 download_datasets is too high. [42.2/15]
Open

  def download_datasets
    # Download datasets from NCBI
    unless cli[:ncbi_taxon].nil?
      what = cli[:ncbi_ref] ? '--reference' :
             cli[:ncbi_draft] ? '--all' : '--complete'
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. [36/10]
Open

  def configure_slurm_daemon(v)
    queue       = cli.ask_user('What queue should I use?', nil, nil, true)
    v[:latency] = cli.ask_user('How long should I sleep? (in secs)', '150').to_i
    v[:maxjobs] = cli.ask_user('How many jobs can I launch at once?', '300').to_i
    v[:ppn]     = cli.ask_user('How many CPUs can I use per job?', '2').to_i
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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