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Method parse has a Cognitive Complexity of 19 (exceeds 5 allowed). Consider refactoring.
Open

    def parse(path, opts = {})
      opts = default_opts(opts)

      # Read JSON
      cont = path
Severity: Minor
Found in lib/miga/json.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 ncbi_asm_json_doc has a Cognitive Complexity of 19 (exceeds 5 allowed). Consider refactoring.
Open

  def ncbi_asm_json_doc
    return @_ncbi_asm_json_doc unless @_ncbi_asm_json_doc.nil?

    if db == :assembly && %i[ncbi gtdb seqcode].include?(universe)
      metadata[:ncbi_asm] ||= ids.first
Severity: Minor
Found in lib/miga/remote_dataset.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 advance has a Cognitive Complexity of 19 (exceeds 5 allowed). Consider refactoring.
Open

  def advance(step, n = 0, total = nil, bin = true)
    # Initialize advance timing
    @_advance_time ||= { last: nil, n: 0, avg: nil }
    if @_advance_time[:n] > n
      @_advance_time[:last] = nil
Severity: Minor
Found in lib/miga/common.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 DaemonTest has 23 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 18 (exceeds 5 allowed). Consider refactoring.
Open

  def compute_stats_essential_genes
    stats = {}
    if source.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 flush! has a Cognitive Complexity of 18 (exceeds 5 allowed). Consider refactoring.
Open

  def flush!
    # Check for finished jobs
    l_say(2, 'Checking for finished jobs')
    @jobs_running.select! do |job|
      ongoing =
Severity: Minor
Found in lib/miga/daemon.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

File daemon.rb has 264 lines of code (exceeds 250 allowed). Consider refactoring.
Open

require 'miga/project'
require 'miga/common/with_daemon'
require 'miga/daemon/base'

##
Severity: Minor
Found in lib/miga/daemon.rb - About 2 hrs to fix

File wf.rb has 262 lines of code (exceeds 250 allowed). Consider refactoring.
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 - About 2 hrs to fix

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

  def download_datasets
    # Download datasets from NCBI
    unless cli[:ncbi_taxon].nil?
      what = cli[:ncbi_ref] ? '--reference' :
             cli[:ncbi_draft] ? '--all' : '--complete'
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 get_sub_cli has a Cognitive Complexity of 17 (exceeds 5 allowed). Consider refactoring.
Open

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

    glob = []
    cli_default = cli.original_argv + ['--ignore-file']
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

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

  def partial_bidir_tmp(project, ref_ds)
    n = ref_ds.size

    # Read data first (threaded)
    tmp = File.join(project.path, 'doctor-bidirectional.tmp')
Severity: Minor
Found in lib/miga/cli/action/doctor/distances.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 Result has 21 methods (exceeds 20 allowed). Consider refactoring.
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 - About 2 hrs to fix

Method parse_cli has 54 lines of code (exceeds 25 allowed). Consider refactoring.
Open

  def parse_cli
    cli.interactive = true
    cli.defaults = {
      mytaxa: nil,
      rdp: nil,
Severity: Major
Found in lib/miga/cli/action/init.rb - About 2 hrs to fix

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

  def run_cmd(cmd, opts = {})
    opts = run_cmd_opts(opts)
    cmd = cmd.shelljoin if cmd.is_a?(Array)
    spawn_opts = {}
    spawn_opts[:out] = opts[:stdout] if opts[:stdout]
Severity: Minor
Found in lib/miga/common/system_call.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 check_datasets has a Cognitive Complexity of 16 (exceeds 5 allowed). Consider refactoring.
Open

  def check_datasets
    l_say(2, 'Checking datasets')
    o = false
    project.each_dataset do |ds|
      next unless ds.status == :incomplete
Severity: Minor
Found in lib/miga/daemon.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 52 lines of code (exceeds 25 allowed). Consider refactoring.
Open

  def parse_cli
    cli.defaults = {
      database: :recommended,
      version: :latest,
      local: File.join(ENV['MIGA_HOME'], '.miga_db'),
Severity: Major
Found in lib/miga/cli/action/db.rb - About 2 hrs to fix

Method test_add_result_other has 50 lines of code (exceeds 25 allowed). Consider refactoring.
Open

  def test_add_result_other
    d2 = project.add_dataset('ds_add_result_other')
    Dir.mkdir(
      File.join(
        project.path, 'data', '07.annotation', '01.function', '01.essential',
Severity: Minor
Found in test/dataset_test.rb - About 2 hrs to fix

Method seqs_length has 50 lines of code (exceeds 25 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 2 hrs to fix
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