bio-miga/miga

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Method seqs_length has a Cognitive Complexity of 31 (exceeds 5 allowed). Consider refactoring.
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 - About 4 hrs to fix

Cognitive Complexity

Cognitive Complexity is a measure of how difficult a unit of code is to intuitively understand. Unlike Cyclomatic Complexity, which determines how difficult your code will be to test, Cognitive Complexity tells you how difficult your code will be to read and comprehend.

A method's cognitive complexity is based on a few simple rules:

  • Code is not considered more complex when it uses shorthand that the language provides for collapsing multiple statements into one
  • Code is considered more complex for each "break in the linear flow of the code"
  • Code is considered more complex when "flow breaking structures are nested"

Further reading

File result.rb has 310 lines of code (exceeds 250 allowed). Consider refactoring.
Open

require 'sqlite3'
require 'miga/result'
require 'miga/dataset/base'
require 'miga/common/with_result'

Severity: Minor
Found in lib/miga/dataset/result.rb - About 3 hrs to fix

Method check_mts has a Cognitive Complexity of 24 (exceeds 5 allowed). Consider refactoring.
Open

  def check_mts(cli)
    cli.say 'Looking for unarchived MyTaxa Scan runs'
    cli.load_project.each_dataset do |d|
      res = d.result(:mytaxa_scan)
      next if res.nil?
Severity: Minor
Found in lib/miga/cli/action/doctor.rb - About 3 hrs to fix

Cognitive Complexity

Cognitive Complexity is a measure of how difficult a unit of code is to intuitively understand. Unlike Cyclomatic Complexity, which determines how difficult your code will be to test, Cognitive Complexity tells you how difficult your code will be to read and comprehend.

A method's cognitive complexity is based on a few simple rules:

  • Code is not considered more complex when it uses shorthand that the language provides for collapsing multiple statements into one
  • Code is considered more complex for each "break in the linear flow of the code"
  • Code is considered more complex when "flow breaking structures are nested"

Further reading

Method perform has a Cognitive Complexity of 24 (exceeds 5 allowed). Consider refactoring.
Open

  def perform
    cli.ensure_par(result: '-r')
    ds = cli.load_and_filter_datasets
    cli.say 'Loading results'
    stats = ds.map do |d|
Severity: Minor
Found in lib/miga/cli/action/summary.rb - About 3 hrs to fix

Cognitive Complexity

Cognitive Complexity is a measure of how difficult a unit of code is to intuitively understand. Unlike Cyclomatic Complexity, which determines how difficult your code will be to test, Cognitive Complexity tells you how difficult your code will be to read and comprehend.

A method's cognitive complexity is based on a few simple rules:

  • Code is not considered more complex when it uses shorthand that the language provides for collapsing multiple statements into one
  • Code is considered more complex for each "break in the linear flow of the code"
  • Code is considered more complex when "flow breaking structures are nested"

Further reading

Method traverse_taxonomy has a Cognitive Complexity of 23 (exceeds 5 allowed). Consider refactoring.
Open

  def traverse_taxonomy(tab, dist)
    cli.say 'Traversing taxonomy'
    rank_i = 0
    Taxonomy.KNOWN_RANKS.each do |rank|
      next if rank == :ns
Severity: Minor
Found in lib/miga/cli/action/tax_dist.rb - About 3 hrs to fix

Cognitive Complexity

Cognitive Complexity is a measure of how difficult a unit of code is to intuitively understand. Unlike Cyclomatic Complexity, which determines how difficult your code will be to test, Cognitive Complexity tells you how difficult your code will be to read and comprehend.

A method's cognitive complexity is based on a few simple rules:

  • Code is not considered more complex when it uses shorthand that the language provides for collapsing multiple statements into one
  • Code is considered more complex for each "break in the linear flow of the code"
  • Code is considered more complex when "flow breaking structures are nested"

Further reading

Method load_and_filter_datasets has a Cognitive Complexity of 23 (exceeds 5 allowed). Consider refactoring.
Open

  def load_and_filter_datasets(silent = false)
    return @objects[:filtered_datasets] unless @objects[:filtered_datasets].nil?

    say 'Listing datasets'
    ds =
Severity: Minor
Found in lib/miga/cli/objects_helper.rb - About 3 hrs to fix

Cognitive Complexity

Cognitive Complexity is a measure of how difficult a unit of code is to intuitively understand. Unlike Cyclomatic Complexity, which determines how difficult your code will be to test, Cognitive Complexity tells you how difficult your code will be to read and comprehend.

A method's cognitive complexity is based on a few simple rules:

  • Code is not considered more complex when it uses shorthand that the language provides for collapsing multiple statements into one
  • Code is considered more complex for each "break in the linear flow of the code"
  • Code is considered more complex when "flow breaking structures are nested"

Further reading

Method opts_for_wf has 79 lines of code (exceeds 25 allowed). Consider refactoring.
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: Major
Found in lib/miga/cli/action/wf.rb - About 3 hrs to fix

File daemon_test.rb has 290 lines of code (exceeds 250 allowed). Consider refactoring.
Open

require 'test_helper'
require 'daemon_helper'
require 'miga/daemon'

class DaemonTest < Test::Unit::TestCase
Severity: Minor
Found in test/daemon_test.rb - About 2 hrs to fix

Method parse_cli has 68 lines of code (exceeds 25 allowed). Consider refactoring.
Open

  def parse_cli
    cli.defaults = { daemon_opts: [] }
    cli.expect_operation = true
    cli.parse do |opt|
      opt.separator 'Available operations:'
Severity: Major
Found in lib/miga/cli/action/lair.rb - About 2 hrs to fix

Method download_entries has a Cognitive Complexity of 18 (exceeds 5 allowed). Consider refactoring.
Open

  def download_entries(ds, p)
    cli.say "Downloading #{ds.size} " + (ds.size == 1 ? 'entry' : 'entries')
    p.do_not_save = true if cli[:save_every] != 1
    ignore = !cli[:ignore_until].nil?
    downloaded = 0
Severity: Minor
Found in lib/miga/cli/action/ncbi_get.rb - About 2 hrs to fix

Cognitive Complexity

Cognitive Complexity is a measure of how difficult a unit of code is to intuitively understand. Unlike Cyclomatic Complexity, which determines how difficult your code will be to test, Cognitive Complexity tells you how difficult your code will be to read and comprehend.

A method's cognitive complexity is based on a few simple rules:

  • Code is not considered more complex when it uses shorthand that the language provides for collapsing multiple statements into one
  • Code is considered more complex for each "break in the linear flow of the code"
  • Code is considered more complex when "flow breaking structures are nested"

Further reading

Method tabulate has a Cognitive Complexity of 18 (exceeds 5 allowed). Consider refactoring.
Open

  def tabulate(header, values, tabular = false)
    fields = []
    fields << header.map(&:to_s) unless tabular && header.all?(&:nil?)
    fields << fields.first.map { |h| h.gsub(/\S/, '-') } unless tabular
    fields += values.map { |r| r.map { |cell| cell.nil? ? '?' : cell.to_s } }
Severity: Minor
Found in lib/miga/common/format.rb - About 2 hrs to fix

Cognitive Complexity

Cognitive Complexity is a measure of how difficult a unit of code is to intuitively understand. Unlike Cyclomatic Complexity, which determines how difficult your code will be to test, Cognitive Complexity tells you how difficult your code will be to read and comprehend.

A method's cognitive complexity is based on a few simple rules:

  • Code is not considered more complex when it uses shorthand that the language provides for collapsing multiple statements into one
  • Code is considered more complex for each "break in the linear flow of the code"
  • Code is considered more complex when "flow breaking structures are nested"

Further reading

Method parse_cli has 58 lines of code (exceeds 25 allowed). Consider refactoring.
Open

  def parse_cli
    cli.defaults = { query: false, universe: :ncbi, db: :nuccore,
                     get_md: false, only_md: false }
    cli.parse do |opt|
      cli.opt_object(opt, [:project, :dataset, :dataset_type])
Severity: Major
Found in lib/miga/cli/action/get.rb - About 2 hrs to fix

Method parse_cli has 58 lines of code (exceeds 25 allowed). Consider refactoring.
Open

  def parse_cli
    cli.defaults = { daemon_opts: [] }
    cli.expect_operation = true
    cli.parse do |opt|
      opt.separator 'Available operations:'
Severity: Major
Found in lib/miga/cli/action/daemon.rb - About 2 hrs to fix

Method opts_for_wf has a Cognitive Complexity of 17 (exceeds 5 allowed). Consider refactoring.
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 - About 2 hrs to fix

Cognitive Complexity

Cognitive Complexity is a measure of how difficult a unit of code is to intuitively understand. Unlike Cyclomatic Complexity, which determines how difficult your code will be to test, Cognitive Complexity tells you how difficult your code will be to read and comprehend.

A method's cognitive complexity is based on a few simple rules:

  • Code is not considered more complex when it uses shorthand that the language provides for collapsing multiple statements into one
  • Code is considered more complex for each "break in the linear flow of the code"
  • Code is considered more complex when "flow breaking structures are nested"

Further reading

Method aai_pvalues has a Cognitive Complexity of 17 (exceeds 5 allowed). Consider refactoring.
Open

    def aai_pvalues(aai, test, opts = {})
      y = {}
      Zlib::GzipReader.open(aai_path(test, opts)) do |fh|
        keys = nil
        fh.each_line do |ln|
Severity: Minor
Found in lib/miga/tax_dist.rb - About 2 hrs to fix

Cognitive Complexity

Cognitive Complexity is a measure of how difficult a unit of code is to intuitively understand. Unlike Cyclomatic Complexity, which determines how difficult your code will be to test, Cognitive Complexity tells you how difficult your code will be to read and comprehend.

A method's cognitive complexity is based on a few simple rules:

  • Code is not considered more complex when it uses shorthand that the language provides for collapsing multiple statements into one
  • Code is considered more complex for each "break in the linear flow of the code"
  • Code is considered more complex when "flow breaking structures are nested"

Further reading

Method get_files_and_type has a Cognitive Complexity of 17 (exceeds 5 allowed). Consider refactoring.
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 - About 2 hrs to fix

Cognitive Complexity

Cognitive Complexity is a measure of how difficult a unit of code is to intuitively understand. Unlike Cyclomatic Complexity, which determines how difficult your code will be to test, Cognitive Complexity tells you how difficult your code will be to read and comprehend.

A method's cognitive complexity is based on a few simple rules:

  • Code is not considered more complex when it uses shorthand that the language provides for collapsing multiple statements into one
  • Code is considered more complex for each "break in the linear flow of the code"
  • Code is considered more complex when "flow breaking structures are nested"

Further reading

Class Daemon has 21 methods (exceeds 20 allowed). Consider refactoring.
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 - About 2 hrs to fix

Class DaemonTest has 21 methods (exceeds 20 allowed). Consider refactoring.
Open

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

  def setup
Severity: Minor
Found in test/daemon_test.rb - About 2 hrs to fix

Method compute_stats_essential_genes has a Cognitive Complexity of 16 (exceeds 5 allowed). Consider refactoring.
Open

  def compute_stats_essential_genes
    stats = {}
    if source.is_multi?
      stats = { median_copies: 0, mean_copies: 0 }
      File.open(file_path(:report), 'r') do |fh|
Severity: Minor
Found in lib/miga/result/stats.rb - About 2 hrs to fix

Cognitive Complexity

Cognitive Complexity is a measure of how difficult a unit of code is to intuitively understand. Unlike Cyclomatic Complexity, which determines how difficult your code will be to test, Cognitive Complexity tells you how difficult your code will be to read and comprehend.

A method's cognitive complexity is based on a few simple rules:

  • Code is not considered more complex when it uses shorthand that the language provides for collapsing multiple statements into one
  • Code is considered more complex for each "break in the linear flow of the code"
  • Code is considered more complex when "flow breaking structures are nested"

Further reading

Method get_sub_cli has a Cognitive Complexity of 16 (exceeds 5 allowed). Consider refactoring.
Open

  def get_sub_cli
    return [cli] if cli[:file].nil?

    glob = []
    File.open(cli[:file], 'r') do |fh|
Severity: Minor
Found in lib/miga/cli/action/get.rb - About 2 hrs to fix

Cognitive Complexity

Cognitive Complexity is a measure of how difficult a unit of code is to intuitively understand. Unlike Cyclomatic Complexity, which determines how difficult your code will be to test, Cognitive Complexity tells you how difficult your code will be to read and comprehend.

A method's cognitive complexity is based on a few simple rules:

  • Code is not considered more complex when it uses shorthand that the language provides for collapsing multiple statements into one
  • Code is considered more complex for each "break in the linear flow of the code"
  • Code is considered more complex when "flow breaking structures are nested"

Further reading

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