Sign upLogin

bio-miga/miga

View on GitHub
Star

Showing 1,586 of 1,600 total issues

Module has too many lines. [134/100]
Open

module MiGA::Cli::Action::Doctor::Operations
  ##
  # Perform refdb operation with MiGA::Cli +cli+
  def check_refdb(cli)
    cli.say 'Checking index format of reference database'
Severity: Minor
Found in lib/miga/cli/action/doctor/operations.rb by rubocop

This cop checks if the length a module exceeds some maximum value. Comment lines can optionally be ignored. The maximum allowed length is configurable.

Module has too many lines. [132/100]
Open

module MiGA::Cli::OptHelper
  ##
  # Send MiGA's banner to OptionParser +opt+
  def banner(opt)
    usage = "Usage: miga #{action.name}"
Severity: Minor
Found in lib/miga/cli/opt_helper.rb by rubocop

This cop checks if the length a module exceeds some maximum value. Comment lines can optionally be ignored. The maximum allowed length is configurable.

Class has too many lines. [129/100]
Open

class MiGA::Result < MiGA::MiGA
  include MiGA::Result::Dates
  include MiGA::Result::Source
  include MiGA::Result::Stats
  include MiGA::Result::Versions
Severity: Minor
Found in lib/miga/result.rb by rubocop

This cop checks if the length a class exceeds some maximum value. Comment lines can optionally be ignored. The maximum allowed length is configurable.

Class has too many lines. [129/100]
Open

class MiGA::RemoteDataset
  include MiGA::RemoteDataset::Base

  # Class-level
  class << self
Severity: Minor
Found in lib/miga/remote_dataset/download.rb by rubocop

This cop checks if the length a class exceeds some maximum value. Comment lines can optionally be ignored. The maximum allowed length is configurable.

Module has too many lines. [127/100]
Open

module MiGA::Cli::Action::Download::Ncbi
  include MiGA::Cli::Action::Download::Base

  def cli_task_flags(opt)
    cli.opt_flag(
Severity: Minor
Found in lib/miga/cli/action/download/ncbi.rb by rubocop

This cop checks if the length a module exceeds some maximum value. Comment lines can optionally be ignored. The maximum allowed length is configurable.

Class has too many lines. [124/100]
Open

class MiGA::Cli < MiGA::MiGA
  require 'miga/cli/base'
  require 'miga/cli/opt_helper'
  require 'miga/cli/objects_helper'
  require 'miga/cli/action'
Severity: Minor
Found in lib/miga/cli.rb by rubocop

This cop checks if the length a class exceeds some maximum value. Comment lines can optionally be ignored. The maximum allowed length is configurable.

Module has too many lines. [124/100]
Open

module MiGA::Project::Base
  ##
  # Top-level folders inside a project
  @@FOLDERS = %w[data metadata daemon]
Severity: Minor
Found in lib/miga/project/base.rb by rubocop

This cop checks if the length a module exceeds some maximum value. Comment lines can optionally be ignored. The maximum allowed length is configurable.

Module has too many lines. [123/100]
Open

module MiGA::Project::Dataset
  ##
  # Returns Array of MiGA::Dataset
  def datasets
    metadata[:datasets].map { |name| dataset(name) }
Severity: Minor
Found in lib/miga/project/dataset.rb by rubocop

This cop checks if the length a module exceeds some maximum value. Comment lines can optionally be ignored. The maximum allowed length is configurable.

Module has too many lines. [122/100]
Open

module MiGA::Common::WithDaemon
  # Process ID of the forked process declaring the daemon alive
  attr :declare_alive_pid

  # Loop counter
Severity: Minor
Found in lib/miga/common/with_daemon.rb by rubocop

This cop checks if the length a module exceeds some maximum value. Comment lines can optionally be ignored. The maximum allowed length is configurable.

Class has too many lines. [117/100]
Open

class ResultTest < Test::Unit::TestCase
  include TestHelper

  def setup
    initialize_miga_home
Severity: Minor
Found in test/result_test.rb by rubocop

This cop checks if the length a class exceeds some maximum value. Comment lines can optionally be ignored. The maximum allowed length is configurable.

Class has too many lines. [116/100]
Open

class ResultStatsTest < Test::Unit::TestCase
  include TestHelper

  def setup
    initialize_miga_home
Severity: Minor
Found in test/result_stats_test.rb by rubocop

This cop checks if the length a class exceeds some maximum value. Comment lines can optionally be ignored. The maximum allowed length is configurable.

Method has too many lines. [74/10]
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 if the length of a method exceeds some maximum value. Comment lines can optionally be ignored. The maximum allowed length is configurable.

Class has too many lines. [111/100]
Open

class MiGA::Taxonomy < MiGA::MiGA
  include MiGA::Taxonomy::Base

  ##
  # Taxonomic hierarchy Hash.
Severity: Minor
Found in lib/miga/taxonomy.rb by rubocop

This cop checks if the length a class exceeds some maximum value. Comment lines can optionally be ignored. The maximum allowed length is configurable.

Module has too many lines. [111/100]
Open

module MiGA::Cli::Action::Doctor::Distances
  ##
  # Perform databases operation with MiGA::Cli +cli+
  def check_db(cli)
    cli.say 'Checking integrity of databases'
Severity: Minor
Found in lib/miga/cli/action/doctor/distances.rb by rubocop

This cop checks if the length a module exceeds some maximum value. Comment lines can optionally be ignored. The maximum allowed length is configurable.

Method has too many lines. [72/10]
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 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. [72/10]
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 if the length of a method exceeds some maximum value. Comment lines can optionally be ignored. The maximum allowed length is configurable.

Module has too many lines. [109/100]
Open

module MiGA::Project::Result
  include MiGA::Project::Base
  include MiGA::Common::WithResult

  ##
Severity: Minor
Found in lib/miga/project/result.rb by rubocop

This cop checks if the length a module exceeds some maximum value. Comment lines can optionally be ignored. The maximum allowed length is configurable.

Assignment Branch Condition size for test_preprocessing is too high. [76.16/15]
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 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

Module has too many lines. [107/100]
Open

module MiGA::Cli::Action::Init::FilesHelper
  def open_rc_file
    rc_path = File.expand_path('.miga_rc', ENV['MIGA_HOME'])
    if File.exist? rc_path
      if cli.ask_user(
Severity: Minor
Found in lib/miga/cli/action/init/files_helper.rb by rubocop

This cop checks if the length a module exceeds some maximum value. Comment lines can optionally be ignored. The maximum allowed length is configurable.

Class has too many lines. [105/100]
Open

class MiGA::Metadata < MiGA::MiGA
  # Class-level

  ##
  # Does the metadata described in +path+ already exist?
Severity: Minor
Found in lib/miga/metadata.rb by rubocop

This cop checks if the length a class exceeds some maximum value. Comment lines can optionally be ignored. The maximum allowed length is configurable.

Severity
Category
Status
Source
Language