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Method has too many lines. [12/10]
Open

  def parse_cli
    cli.parse do |opt|
      opt.on(
        '-o', '--tarball PATH',
        '(Mandatory) Path to the archive to be created ending in .tar.gz'
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. [12/10]
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 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 check_files is too high. [17.58/15]
Open

  def check_files(cli)
    cli.say 'Looking for outdated files in results'
    n, k = cli.load_project.dataset_names.size, 0
    cli.load_project.each_dataset do |d|
      cli.advance('Datasets:', k += 1, n, false)
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

Method has too many lines. [12/10]
Open

  def add_file_to_tar(tar, rel_path, abs_path)
    if File.directory? abs_path
      Dir["#{abs_path}/*"].each do |f|
        add_file_to_tar(tar, File.join(rel_path, File.basename(f)), f)
      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.

Assignment Branch Condition size for initialize_empty_project is too high. [17.15/15]
Open

  def initialize_empty_project(metadata)
    call_cli(
      ['new', '-P', cli[:outdir], '-t', cli[:project_type]]
    ) unless MiGA::Project.exist? cli[:outdir]
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

Assignment Branch Condition size for create_project is too high. [17.46/15]
Open

  def create_project(stage, p_metadata = {}, d_metadata = {})
    cli.ensure_par(
      outdir: '-o',
      project_type: '--project-type',
      dataset_type: '--dataset-type'
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

Cyclomatic complexity for get_files_and_type is too high. [8/6]
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 that the cyclomatic complexity of methods is not higher than the configured maximum. The cyclomatic complexity is the number of linearly independent paths through a method. The algorithm counts decision points and adds one.

An if statement (or unless or ?:) increases the complexity by one. An else branch does not, since it doesn't add a decision point. The && operator (or keyword and) can be converted to a nested if statement, and ||/or is shorthand for a sequence of ifs, so they also add one. Loops can be said to have an exit condition, so they add one.

Cyclomatic complexity for perform is too high. [8/6]
Open

  def perform
    r = cli.load_result or return

    cli[:compute] = false if cli[:try_load] && !r[:stats]&.empty?
Severity: Minor
Found in lib/miga/cli/action/stats.rb by rubocop

This cop checks that the cyclomatic complexity of methods is not higher than the configured maximum. The cyclomatic complexity is the number of linearly independent paths through a method. The algorithm counts decision points and adds one.

An if statement (or unless or ?:) increases the complexity by one. An else branch does not, since it doesn't add a decision point. The && operator (or keyword and) can be converted to a nested if statement, and ||/or is shorthand for a sequence of ifs, so they also add one. Loops can be said to have an exit condition, so they add one.

Perceived complexity for create_dataset is too high. [9/7]
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 tries to produce a complexity score that's a measure of the complexity the reader experiences when looking at a method. For that reason it considers when nodes as something that doesn't add as much complexity as an if or a &&. Except if it's one of those special case/when constructs where there's no expression after case. Then the cop treats it as an if/elsif/elsif... and lets all the when nodes count. In contrast to the CyclomaticComplexity cop, this cop considers else nodes as adding complexity.

Example:

def my_method                   # 1
  if cond                       # 1
    case var                    # 2 (0.8 + 4 * 0.2, rounded)
    when 1 then func_one
    when 2 then func_two
    when 3 then func_three
    when 4..10 then func_other
    end
  else                          # 1
    do_something until a && b   # 2
  end                           # ===
end                             # 7 complexity points

Method has too many lines. [12/10]
Open

  def summarize(which = %w[cds assembly essential_genes ssu])
    return if cli[:prepare_and_exit]

    which.each do |r|
      cli.say "Summary: #{r}"
Severity: Minor
Found in lib/miga/cli/action/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.

Cyclomatic complexity for create_dataset is too high. [8/6]
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 cyclomatic complexity of methods is not higher than the configured maximum. The cyclomatic complexity is the number of linearly independent paths through a method. The algorithm counts decision points and adds one.

An if statement (or unless or ?:) increases the complexity by one. An else branch does not, since it doesn't add a decision point. The && operator (or keyword and) can be converted to a nested if statement, and ||/or is shorthand for a sequence of ifs, so they also add one. Loops can be said to have an exit condition, so they add one.

Cyclomatic complexity for run_daemon is too high. [8/6]
Open

  def run_daemon
    return if cli[:prepare_and_exit]

    cmd  = ['daemon', 'run', '-P', cli[:outdir], '--shutdown-when-done']
    cmd += ['--json', cli[:daemon_json]] if cli[:daemon_json]
Severity: Minor
Found in lib/miga/cli/action/wf.rb by rubocop

This cop checks that the cyclomatic complexity of methods is not higher than the configured maximum. The cyclomatic complexity is the number of linearly independent paths through a method. The algorithm counts decision points and adds one.

An if statement (or unless or ?:) increases the complexity by one. An else branch does not, since it doesn't add a decision point. The && operator (or keyword and) can be converted to a nested if statement, and ||/or is shorthand for a sequence of ifs, so they also add one. Loops can be said to have an exit condition, so they add one.

Perceived complexity for perform is too high. [9/7]
Open

  def perform
    r = cli.load_result or return

    cli[:compute] = false if cli[:try_load] && !r[:stats]&.empty?
Severity: Minor
Found in lib/miga/cli/action/stats.rb by rubocop

This cop tries to produce a complexity score that's a measure of the complexity the reader experiences when looking at a method. For that reason it considers when nodes as something that doesn't add as much complexity as an if or a &&. Except if it's one of those special case/when constructs where there's no expression after case. Then the cop treats it as an if/elsif/elsif... and lets all the when nodes count. In contrast to the CyclomaticComplexity cop, this cop considers else nodes as adding complexity.

Example:

def my_method                   # 1
  if cond                       # 1
    case var                    # 2 (0.8 + 4 * 0.2, rounded)
    when 1 then func_one
    when 2 then func_two
    when 3 then func_three
    when 4..10 then func_other
    end
  else                          # 1
    do_something until a && b   # 2
  end                           # ===
end                             # 7 complexity points

Assignment Branch Condition size for representatives is too high. [17.15/15]
Open

  def representatives(p)
    cli.say 'Identifying representatives'
    f = File.join(cli[:outdir], 'representatives.txt')
    if cli[:criterion] == :medoids
      FileUtils.cp(p.result(:clade_finding).file_path(:medoids_gsp), f)
Severity: Minor
Found in lib/miga/cli/action/derep_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. [12/10]
Open

  def check_libraries(paths)
    req_libraries = {
      r: %w[ape cluster vegan],
      ruby: %w[sqlite3 daemons json],
      python: %w[numpy sqlite3 pyhmmer pyrodigal]
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 version_requested is too high. [17.38/15]
Open

  def version_requested(db)
    cli[:version] = db[:latest].to_sym if cli[:version] == :latest
    ver = db[:versions][cli[:version]]
    raise 'Cannot find database version' if ver.nil?
    ver[:version] = cli[:version]
Severity: Minor
Found in lib/miga/cli/action/db.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_and_install_library is too high. [17.15/15]
Open

  def check_and_install_library(paths, language, library)
    cli.print "Testing #{library}... "
    if test_library(cli, paths, language, library)
      cli.puts 'yes'
    else
Severity: Minor
Found in lib/miga/cli/action/init.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_file is too high. [17.49/15]
Open

  def download_file(ftp, path, reuse = false)
    cli.say "Downloading '#{path}'"
    file = File.expand_path(path, cli[:local])
    if reuse && File.exist?(file)
      cli.say "Reusing #{file}"
Severity: Minor
Found in lib/miga/cli/action/db.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. [12/10]
Open

    def ncbi_map(id, dbfrom, db)
      doc = download(:ncbi_map, dbfrom, id, :json, nil, db: db)
      return if doc.empty?

      begin
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.

Assignment Branch Condition size for recalculate_status is too high. [17.83/15]
Open

  def recalculate_status(save = true)
    old_status = metadata[:status]
    metadata[:status] =
      !active? ? 'inactive' : done_preprocessing? ? 'complete' : 'incomplete'
    if save && (old_status.nil? || old_status != metadata[:status])
Severity: Minor
Found in lib/miga/dataset/status.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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