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Showing 839 of 1,651 total issues

Method has too many lines. [14/10]
Open

  def ask_user(question, default = nil, answers = nil, force = false)
    ans = " (#{answers.join(' / ')})" unless answers.nil?
    dft = " [#{default}]" unless default.nil?
    print "#{question}#{ans}#{dft} > "
    if self[:auto] && !force
Severity: Minor
Found in lib/miga/cli.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 ask_user is too high. [19.21/15]
Open

  def ask_user(question, default = nil, answers = nil, force = false)
    ans = " (#{answers.join(' / ')})" unless answers.nil?
    dft = " [#{default}]" unless default.nil?
    print "#{question}#{ans}#{dft} > "
    if self[:auto] && !force
Severity: Minor
Found in lib/miga/cli.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. [14/10]
Confirmed

  def get_gtdb_taxonomy
    gtdb_genome = metadata[:gtdb_assembly] or return

    doc = MiGA::Json.parse(
      MiGA::RemoteDataset.download(
Severity: Minor
Found in lib/miga/remote_dataset.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 get_metadata is too high. [19.31/15]
Open

  def get_metadata(metadata_def = {})
    metadata_def.each { |k, v| @metadata[k] = v }
    return @metadata if @metadata[:bypass_metadata]

    case universe
Severity: Minor
Found in lib/miga/remote_dataset.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 get_ncbi_taxid_from_ncbi is too high. [19.62/15]
Open

  def get_ncbi_taxid_from_ncbi
    # Try first from Assembly data
    return get_ncbi_taxid_from_web if db == :assembly

    # Try from previously pulled NCBI data
Severity: Minor
Found in lib/miga/remote_dataset.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_type_status_ncbi_asm is too high. [10/6]
Open

  def get_type_status_ncbi_asm(metadata)
    from_type = nil

    # Try first from previously pulled NCBI metadata
    if metadata[:ncbi_dataset]
Severity: Minor
Found in lib/miga/remote_dataset.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.

Method has too many lines. [14/10]
Confirmed

  def save_assembly_to(project, name, udb)
    dir = MiGA::Dataset.RESULT_DIRS[:assembly]
    base = "#{project.path}/data/#{dir}/#{name}"
    l_ctg = "#{base}.LargeContigs.fna"
    a_ctg = "#{base}.AllContigs.fna"
Severity: Minor
Found in lib/miga/remote_dataset.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. [14/10]
Open

  def unregistered_datasets
    datasets = []
    MiGA::Dataset.RESULT_DIRS.values.each do |dir|
      dir_p = "#{path}/data/#{dir}"
      next unless Dir.exist? dir_p
Severity: Minor
Found in lib/miga/project/dataset.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 runopts is too high. [10/6]
Open

  def runopts(k, v = nil, force = false)
    k = k.to_sym
    unless v.nil?
      case k
      when :latency, :maxjobs, :ppn, :ppn_project, :format_version, :verbosity,
Severity: Minor
Found in lib/miga/daemon/base.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.

Method has too many lines. [14/10]
Open

  def each_file(&blk)
    return to_enum(:each_file) unless block_given?

    @data[:files] ||= {}
    self[:files].each do |k, files|
Severity: Minor
Found in lib/miga/result.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. [14/10]
Open

  def create
    unless MiGA::MiGA.initialized?
      warn 'Projects cannot be processed yet, first run: miga init'
    end
Severity: Minor
Found in lib/miga/project.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. [19.92/15]
Open

  def parse_cli
    cli.defaults = { metric: :aai, external: false, how_many: 5 }
    cli.parse do |opt|
      cli.opt_object(opt, [:project, :dataset_opt])
      cli.opt_filter_datasets(opt)
Severity: Minor
Found in lib/miga/cli/action/relatives.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 add_result is too high. [19.82/15]
Open

  def add_result(task, save = true, opts = {})
    task = task.to_sym
    return nil if result_dirs[task].nil?

    base = File.join(project.path, 'data', result_dirs[task], result_base)
Severity: Minor
Found in lib/miga/common/with_result.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. [14/10]
Open

  def pull_hook(event, *event_args)
    event = event.to_sym
    event_queue = (hooks[event] || [])
    event_queue += (metadata[event] || []) if respond_to? :metadata
    event_queue.each do |i|
Severity: Minor
Found in lib/miga/common/hooks.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 remote_connection is too high. [19.87/15]
Open

  def remote_connection(host)
    host = known_hosts(host) if host.is_a?(Symbol)
    uri = host.is_a?(URI) ? host : URI.parse(host)
    @remote_connection_uri = uri
Severity: Minor
Found in lib/miga/common/net.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 assert_valid_option_value is too high. [19.42/15]
Open

  def assert_valid_option_value(key, value, from_string = false)
    opt = assert_has_option(key)
    value = option_from_string(key, value) if from_string

    # nil is always valid, and so are supported tokens
Severity: Minor
Found in lib/miga/common/with_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. [14/10]
Open

  def parse_cli
    cli.parse do |opt|
      cli.opt_object(opt, [:project])
      cli.opt_filter_datasets(opt)
      opt.on(
Severity: Minor
Found in lib/miga/cli/action/tax_dist.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. [14/10]
Open

  def parse_cli
    cli.defaults = { format: :json }
    cli.parse do |opt|
      cli.opt_object(opt, [:project])
      opt.on(
Severity: Minor
Found in lib/miga/cli/action/tax_index.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. [14/10]
Open

  def net_method(method, uri, *opts)
    attempts ||= 0
    uri = URI.parse(uri) if uri.is_a? String
    DEBUG "#{method.to_s.upcase}: #{uri} #{opts}"
    case method.to_sym
Severity: Minor
Found in lib/miga/common/net.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. [19.31/15]
Open

  def parse_cli
    cli.parse do |opt|
      cli.opt_object(opt, [:project, :project_type_req])
      opt.on(
        '-n', '--name STRING',
Severity: Minor
Found in lib/miga/cli/action/new.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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