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Method has too many lines. [26/10]
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 if the length of a method exceeds some maximum value. Comment lines can optionally be ignored. The maximum allowed length is configurable.

Method merge_bidir_tmp has a Cognitive Complexity of 24 (exceeds 5 allowed). Consider refactoring.
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 - 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

Method perform has a Cognitive Complexity of 24 (exceeds 5 allowed). Consider refactoring.
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 - 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

Method perform has a Cognitive Complexity of 24 (exceeds 5 allowed). Consider refactoring.
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 - 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

Assignment Branch Condition size for test_daemon_launch is too high. [30.59/15]
Open

  def test_daemon_launch
    lair = MiGA::Lair.new(tmpfile('sub'), latency: 1)
    p = MiGA::Project.load(File.join(lair.path, 'project3'))
    d = MiGA::Daemon.new(p)
    assert_not_predicate(d, :active?)
Severity: Minor
Found in test/lair_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 save is too high. [30.68/15]
Open

  def save
    return if self[:never_save]
    return if !saved_hash.nil? && saved_hash == data.hash

    MiGA::MiGA.DEBUG "Metadata.save #{path}"
Severity: Minor
Found in lib/miga/metadata.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. [25/10]
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 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 tabulate is too high. [30.1/15]
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 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 is too high. [30.23/15]
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 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. [25/10]
Open

  def parse_cli
    cli.defaults = {
      query: false, unlink: false,
      reference: false, add_version: true, dry: false,
      get_md: false, only_md: false, save_every: 1
Severity: Minor
Found in lib/miga/cli/action/gtdb_get.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. [25/10]
Open

  def configure_daemon
    cli.puts 'Default daemon configuration:'
    daemon_f = File.expand_path('.miga_daemon.json', ENV['MIGA_HOME'])
    unless File.exist?(daemon_f) and cli.ask_user(
      'A template daemon already exists, do you want to preserve it?',
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.

Method has too many lines. [25/10]
Open

  def partial_bidir_tmp(project, ref_ds)
    n = ref_ds.size

    # Read data first (threaded)
    tmp = File.join(project.path, 'doctor-bidirectional.tmp')
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.

Method has too many lines. [25/10]
Open

  def parse_cli
    cli.defaults = {
      query: false, unlink: false, reference: false,
      complete: false, chromosome: false,
      scaffold: false, contig: false, add_version: true, dry: false,
Severity: Minor
Found in lib/miga/cli/action/ncbi_get.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.

Block has too many lines. [62/25]
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/daemon.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. [25/10]
Open

  def parse_cli
    cli.defaults = { try_load: false, thr: 1, env: false, check_first: false }
    cli.parse do |opt|
      cli.opt_object(opt, [:project, :dataset_opt, :result_opt])
      opt.on(
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. [25/10]
Open

  def parse_cli
    cli.opt_common = false
    cli.parse do |opt|
      descriptions = cli.class.TASK_DESC.keep_if { |k, v| k != :generic }
      opt.separator MiGA::MiGA.tabulate(
Severity: Minor
Found in lib/miga/cli/action/generic.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_gtdb_alt_taxonomy is too high. [29.15/15]
Open

  def test_gtdb_alt_taxonomy
    declare_remote_access
    rd = MiGA::RemoteDataset.new('GCA_018200315.1', :assembly, :gtdb)
    rd.metadata[:get_ncbi_taxonomy] = true
    md = rd.get_metadata
Severity: Minor
Found in test/remote_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

Assignment Branch Condition size for test_cds is too high. [29.27/15]
Open

  def test_cds
    # Prepare result
    dir = 'data/06.cds'
    fa = file_path(dir, '.faa')
    File.open(fa, 'w') { |fh| fh.puts '>1', 'M' }
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

Assignment Branch Condition size for test_result_source is too high. [29.07/15]
Open

  def test_result_source
    r = dataset.add_result(:trimmed_reads)
    assert_equal(dataset.name, r.source.name)
    assert_equal(:trimmed_reads, r.key)
    assert_equal('data/02.trimmed_reads', r.relative_dir)
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_generic_transfer is too high. [29.07/15]
Open

  def test_generic_transfer
    hello = File.expand_path('Hello', tmpdir)
    world = File.expand_path('World', tmpdir)
    assert_respond_to(File, :generic_transfer)
    FileUtils.touch(hello)
Severity: Minor
Found in test/common_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

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