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Method has too many lines. [17/10]
Open

  def cli_task_flags(opt)
    cli.opt_flag(
      opt, 'reference',
      'Download all reference genomes (ignore any other status)'
    )
Severity: Minor
Found in lib/miga/cli/action/download/ncbi.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. [17/10]
Open

  def parse_reports_as_datasets(reports)
    ds = {}
    reports.each do |r|
      asm = r[:accession]
      next if asm.nil? || asm.empty? || asm == '-'
Severity: Minor
Found in lib/miga/cli/action/download/ncbi.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 closest_relative_tax is too high. [22.83/15]
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 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. [22.56/15]
Open

  def perform
    dist = read_distances
    Dir.mktmpdir do |dir|
      tab = get_tab_index(dir)
      dist = traverse_taxonomy(tab, dist)
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 check_mts is too high. [22.65/15]
Open

  def check_mts(cli)
    cli.say 'Looking for unarchived MyTaxa Scan runs'
    cli.load_project.each_dataset do |d|
      res = d.result(:mytaxa_scan)
      next if res.nil?
Severity: Minor
Found in lib/miga/cli/action/doctor/operations.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 each_file_listed is too high. [22/15]
Open

  def each_file_listed(datasets, &blk)
    datasets.each_with_index do |ds, k|
      cli.advance('Datasets:', k + 1, datasets.size, false)
      # Metadata
      blk.call(
Severity: Minor
Found in lib/miga/cli/action/archive.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 check_dist_eval is too high. [22.05/15]
Open

  def check_dist_eval(cli, p, res)
    y = { notok: Set.new, fix: Set.new }
    Zlib::GzipReader.open(res.file_path(:matrix)) do |fh|
      lineno = 0
      fh.each_line do |ln|
Severity: Minor
Found in lib/miga/cli/action/doctor/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. [17/10]
Open

  def check_ess(cli)
    cli.say 'Looking for outdated essential genes'
    cli.load_project.each_dataset do |d|
      res = d.result(:essential_genes)
      next if res.nil?
Severity: Minor
Found in lib/miga/cli/action/doctor/operations.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. [17/10]
Open

  def perform
    cli.ensure_par(tarball: '-o')
    unless cli[:tarball] =~ /\.tar\.gz$/
      raise 'The tarball path (-o) must have .tar.gz extension'
    end
Severity: Minor
Found in lib/miga/cli/action/archive.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. [17/10]
Open

  def parse_cli
    default_opts_for_wf
    cli.defaults = { mytaxa: false }
    cli.parse do |opt|
      opt.on(
Severity: Minor
Found in lib/miga/cli/action/preproc_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.

Assignment Branch Condition size for parse_cli is too high. [22.47/15]
Open

  def parse_cli
    cli.expect_files = true
    cli.files_label  = 'CMD'
    cli.defaults = {
      raise: false, return: :status, source: :miga_env,
Severity: Minor
Found in lib/miga/cli/action/cmd.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. [17/10]
Open

  def parse_cli
    cli.parse do |opt|
      cli.opt_object(opt, [:project, :dataset_opt])
      opt.on(
        '-m', '--metadata STRING',
Severity: Minor
Found in lib/miga/cli/action/edit.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. [17/10]
Open

  def add_result_cds(base, opts)
    return nil unless result_files_exist?(base, %w[.faa])

    r = add_files_to_ds_result(
      MiGA::Result.new("#{base}.json"), name,
Severity: Minor
Found in lib/miga/dataset/result/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.

Method compute_stats_essential_genes has a Cognitive Complexity of 18 (exceeds 5 allowed). Consider refactoring.
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 - About 2 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

Method tabulate has a Cognitive Complexity of 18 (exceeds 5 allowed). Consider refactoring.
Open

  def tabulate(header, values, tabular = false)
    fields = []
    fields << header.map(&:to_s) unless tabular && header.all?(&:nil?)
    fields << fields.first.map { |h| h.gsub(/\S/, '-') } unless tabular
    fields += values.map { |r| r.map { |cell| cell.nil? ? '?' : cell.to_s } }
Severity: Minor
Found in lib/miga/common/format.rb - About 2 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

Method flush! has a Cognitive Complexity of 18 (exceeds 5 allowed). Consider refactoring.
Open

  def flush!
    # Check for finished jobs
    l_say(2, 'Checking for finished jobs')
    @jobs_running.select! do |job|
      ongoing =
Severity: Minor
Found in lib/miga/daemon.rb - About 2 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 test_add_result is too high. [21.02/15]
Open

  def test_add_result
    d2 = project.add_dataset('ds_add_result')
    assert_nil(d2.add_result(:koop))
    assert_nil(d2.add_result(:raw_reads))
    FileUtils.touch(
Severity: Minor
Found in test/dataset_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_ncbi_datasets_download_request
    # No remote access needed
    rd = MiGA::RemoteDataset.new(
      'GCF_004684205.1', :genome, :ncbi_datasets_download
    )
Severity: Minor
Found in test/remote_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 test_coupled_raw_reads is too high. [21.38/15]
Open

  def test_coupled_raw_reads
    dir = 'data/01.raw_reads'
    fq = file_path(dir, '.1.fastq')
    File.open(fq, 'w') { |fh| fh.puts '@1', 'ACTAC', '+', '####' }
    fq = file_path(dir, '.2.fastq')
Severity: Minor
Found in test/result_stats_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_defaults
    tmp1 = Tempfile.new('test-parse-1.json')
    tmp1.puts '{"a": 123, "k": false, "t": null}'
    tmp1.close
    assert_equal({ a: 123, k: false, t: nil }, MiGA::Json.parse(tmp1.path))
Severity: Minor
Found in test/json_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.

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