bio-miga/miga

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Module has too many lines. [241/100]
Open

module MiGA::Dataset::Result
  
  include MiGA::Dataset::Base
  
  ##
Severity: Minor
Found in lib/miga/dataset/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.

Class has too many lines. [240/100]
Open

class MiGA::Cli::Action::NcbiGet < MiGA::Cli::Action
  def parse_cli
    cli.defaults = {
      query: false, unlink: false,
      reference: false, legacy_name: false,
Severity: Minor
Found in lib/miga/cli/action/ncbi_get.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. [230/100]
Open

class MiGA::Cli::Action::Init < MiGA::Cli::Action
  require 'miga/cli/action/init/daemon_helper'
  include MiGA::Cli::Action::Init::DaemonHelper
  
  def parse_cli
Severity: Minor
Found in lib/miga/cli/action/init.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. [218/100]
Open

class MiGA::Cli::Action::Doctor < MiGA::Cli::Action

  def parse_cli
    @@OPERATIONS.keys.each { |i| cli.defaults = { i => true } }
    cli.parse do |opt|
Severity: Minor
Found in lib/miga/cli/action/doctor.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. [198/100]
Open

class MiGA::Daemon < MiGA::MiGA

  include MiGA::Daemon::Base

  ##
Severity: Minor
Found in lib/miga/daemon.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. [181/100]
Open

class MiGA::Cli::Action::GetDb < MiGA::Cli::Action

  def parse_cli
    cli.defaults = {
      database: :recommended,
Severity: Minor
Found in lib/miga/cli/action/get_db.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. [171/100]
Open

class MiGA::Cli::Action::Stats < MiGA::Cli::Action

  def parse_cli
    cli.defaults = { try_load: false }
    cli.parse do |opt|
Severity: Minor
Found in lib/miga/cli/action/stats.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. [168/100]
Open

class MiGA::RemoteDataset < MiGA::MiGA
  include MiGA::RemoteDataset::Download

  # Class-level

Severity: Minor
Found in lib/miga/remote_dataset.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. [168/100]
Open

module MiGA::Cli::Action::Wf
  def default_opts_for_wf
    cli.expect_files = true
    cli.defaults = {
      clean: false, regexp: MiGA::Cli.FILE_REGEXP,
Severity: Minor
Found in lib/miga/cli/action/wf.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. [153/100]
Open

class MiGA::Cli::Action::Add < MiGA::Cli::Action

  def parse_cli
    cli.expect_files = true
    cli.defaults = {
Severity: Minor
Found in lib/miga/cli/action/add.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. [145/100]
Open

class DatasetTest < Test::Unit::TestCase
  
  def setup
    $tmp = Dir.mktmpdir
    ENV["MIGA_HOME"] = $tmp
Severity: Minor
Found in test/dataset_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. [140/100]
Open

class MiGA::Cli < MiGA::MiGA

  require 'miga/cli/base'
  require 'miga/cli/opt_helper'
  require 'miga/cli/objects_helper'
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.

Class has too many lines. [136/100]
Open

class ProjectTest < Test::Unit::TestCase
  
  def setup
    $tmp = Dir.mktmpdir
    ENV["MIGA_HOME"] = $tmp
Severity: Minor
Found in test/project_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. [132/100]
Open

class MiGA::Cli::Action::Get < MiGA::Cli::Action

  def parse_cli
    cli.defaults = {query: false, universe: :ncbi, db: :nuccore,
      get_md: false, only_md: false}
Severity: Minor
Found in lib/miga/cli/action/get.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. [122/100]
Open

class DaemonTest < Test::Unit::TestCase
  
  def setup
    $jruby_tests = !ENV["JRUBY_TESTS"].nil?
    $tmp = Dir.mktmpdir
Severity: Minor
Found in test/daemon_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.

Module has too many lines. [119/100]
Open

module MiGA::Project::Result

  include MiGA::Project::Base

  ##
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.

Module has too many lines. [119/100]
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.

Module has too many lines. [113/100]
Open

module MiGA::Cli::Action::Init::DaemonHelper
  def configure_daemon
    cli.puts 'Default daemon configuration:'
    daemon_f = File.expand_path('.miga_daemon.json', ENV['HOME'])
    unless File.exist?(daemon_f) and cli.ask_user(

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 opts_for_wf(opt, files_desc, params = {})
    {
      multi: false, cleanup: true, project_type: false, ncbi: true
    }.each { |k, v| params[k] = v if params[k].nil? }
    opt.on(
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.

Class has too many lines. [104/100]
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.

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