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Showing 815 of 1,600 total issues

Class has too many lines. [313/100]
Open

class DaemonTest < Test::Unit::TestCase
  include TestHelper
  include DaemonHelper

  def setup
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.

Class has too many lines. [293/100]
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. [260/100]
Open

module MiGA::Cli::Action::Wf
  def default_opts_for_wf
    cli.expect_files = true
    cli.defaults = {
      clean: false, project_type: :genomes, dataset_type: :popgenome,
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. [259/100]
Open

class MiGA::Daemon < MiGA::MiGA
  include MiGA::Daemon::Base
  include MiGA::Common::WithDaemon
  extend MiGA::Common::WithDaemonClass
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. [232/100]
Open

class MiGA::Cli::Action::Init < MiGA::Cli::Action
  require 'miga/cli/action/init/daemon_helper'
  require 'miga/cli/action/init/files_helper'
  include MiGA::Cli::Action::Init::DaemonHelper
  include MiGA::Cli::Action::Init::FilesHelper
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. [224/100]
Open

class MiGA::Cli::Action::Db < MiGA::Cli::Action
  def parse_cli
    cli.defaults = {
      database: :recommended,
      version: :latest,
Severity: Minor
Found in lib/miga/cli/action/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.

Module has too many lines. [217/100]
Open

module MiGA::Dataset::Result::Add
  ##
  # Add result type +:raw_reads+ at +base+ (no +_opts+ supported)
  def add_result_raw_reads(base, _opts)
    return nil unless result_files_exist?(base, '.1.fastq')
Severity: Minor
Found in lib/miga/dataset/result/add.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. [206/100]
Open

module MiGA::Result::Stats
  ##
  # (Re-)calculate and save the statistics for the result
  def compute_stats
    method = :"compute_stats_#{key}"
Severity: Minor
Found in lib/miga/result/stats.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. [204/100]
Open

module MiGA::Cli::Action::Init::DaemonHelper
  def configure_daemon
    cli.puts 'Default daemon configuration:'
    daemon_f = File.expand_path('.miga_daemon.json', ENV['MIGA_HOME'])
    unless File.exist?(daemon_f) and cli.ask_user(
Severity: Minor
Found in lib/miga/cli/action/init/daemon_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. [188/100]
Open

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

  def setup
    initialize_miga_home
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. [185/100]
Open

class MiGA::Cli::Action::Browse < MiGA::Cli::Action
  def parse_cli
    cli.parse do |opt|
      cli.defaults = { open: true }
      cli.opt_object(opt, [:project])
Severity: Minor
Found in lib/miga/cli/action/browse.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. [182/100]
Open

module MiGA::Cli::Action::Download::Base
  def cli_base_flags(opt)
    opt.on(
      '--max-download INT', Integer,
      'Maximum number of datasets to download (by default: unlimited)'
Severity: Minor
Found in lib/miga/cli/action/download/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.

Class has too many lines. [177/100]
Open

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

  def setup
    initialize_miga_home
Severity: Minor
Found in test/remote_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.

Module has too many lines. [166/100]
Open

module MiGA::RemoteDataset::Base
  @@_NCBI_DATASETS = 'https://api.ncbi.nlm.nih.gov/datasets/v2alpha/'
  @@_EUTILS        = 'https://eutils.ncbi.nlm.nih.gov/entrez/eutils/'
  @@_EBI_API       = 'https://www.ebi.ac.uk/Tools/'
  @@_GTDB_API      = 'https://gtdb-api.ecogenomic.org/'
Severity: Minor
Found in lib/miga/remote_dataset/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.

Method has too many lines. [98/10]
Open

  def opts_for_wf(opt, files_desc, params = {})
    {
      multi: false, cleanup: true, project_type: false, ncbi: true, qual: 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.

Assignment Branch Condition size for perform is too high. [102.7/15]
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 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

Class has too many lines. [158/100]
Open

class MiGA::Cli::Action::Get < MiGA::Cli::Action
  require 'miga/cli/action/download/base'
  include MiGA::Cli::Action::Download::Base

  def parse_cli
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. [154/100]
Open

class MiGA::Cli::Action::Add < MiGA::Cli::Action
  def parse_cli
    cli.expect_files = true
    cli.defaults = { ref: true, ignore_dups: false }
    cli.parse do |opt|
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. [150/100]
Open

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

  def setup
    initialize_miga_home
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.

Assignment Branch Condition size for seqs_length is too high. [96.04/15]
Open

  def seqs_length(file, format, opts = {})
    opts[:gc] = true if opts[:skew]
    fh = file =~ /\.gz/ ? Zlib::GzipReader.open(file) : File.open(file, 'r')
    l = []
    gc = 0
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

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