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Method ncbi_gb_get has a Cognitive Complexity of 8 (exceeds 5 allowed). Consider refactoring.
Open

    def ncbi_gb_get(opts)
      # Simply use defaults, but ensure that the URL can be properly formed
      o = download_rest(opts.merge(universe: :ncbi, db: :nuccore))
      return o unless o.strip.empty?
Severity: Minor
Found in lib/miga/remote_dataset/download.rb - About 45 mins 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 taxa_by_rank has a Cognitive Complexity of 7 (exceeds 5 allowed). Consider refactoring.
Open

  def taxa_by_rank(rank)
    rank = MiGA::Taxonomy.normalize_rank(rank)
    taxa = [@root]
    select = []
    loop do
Severity: Minor
Found in lib/miga/tax_index.rb - About 35 mins 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 create has a Cognitive Complexity of 7 (exceeds 5 allowed). Consider refactoring.
Open

    def create(path, force = false)
      # Deal with old results first
      r_old = load(path)
      return r_old if r_old && !force
Severity: Minor
Found in lib/miga/result.rb - About 35 mins 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 add_file_to_tar has a Cognitive Complexity of 7 (exceeds 5 allowed). Consider refactoring.
Open

  def add_file_to_tar(tar, rel_path, abs_path)
    if File.directory? abs_path
      Dir["#{abs_path}/*"].each do |f|
        add_file_to_tar(tar, File.join(rel_path, File.basename(f)), f)
      end
Severity: Minor
Found in lib/miga/cli/action/archive.rb - About 35 mins 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 7 (exceeds 5 allowed). Consider refactoring.
Open

  def perform
    # Input data
    norun = %w[
      project_stats haai_distances aai_distances ani_distances clade_finding
    ]
Severity: Minor
Found in lib/miga/cli/action/quality_wf.rb - About 35 mins 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 date_at has a Cognitive Complexity of 7 (exceeds 5 allowed). Consider refactoring.
Open

  def date_at(event)
    date = self[event]
    date ||= self[:started] if event == :start
    if date.nil?
      f = path event
Severity: Minor
Found in lib/miga/result/dates.rb - About 35 mins 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 remote_connection has a Cognitive Complexity of 7 (exceeds 5 allowed). Consider refactoring.
Open

  def remote_connection(host)
    host = known_hosts(host) if host.is_a?(Symbol)
    uri = host.is_a?(URI) ? host : URI.parse(host)
    @remote_connection_uri = uri
Severity: Minor
Found in lib/miga/common/net.rb - About 35 mins 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 normalize_encoding has a Cognitive Complexity of 7 (exceeds 5 allowed). Consider refactoring.
Open

  def normalize_encoding(body)
    # Test encodings
    body.force_encoding('utf-8')
    %w[iso8859-1 windows-1252 us-ascii ascii-8bit].each do |enc|
      break if body.valid_encoding?
Severity: Minor
Found in lib/miga/common/net.rb - About 35 mins 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 last_alive has a Cognitive Complexity of 7 (exceeds 5 allowed). Consider refactoring.
Open

  def last_alive(path)
    f = alive_file(path)
    f = terminated_file(path) unless File.exist? f
    c = File.read(f)
    return nil if c.nil? || c.empty?
Severity: Minor
Found in lib/miga/common/with_daemon_class.rb - About 35 mins 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 add_result_ssu has a Cognitive Complexity of 7 (exceeds 5 allowed). Consider refactoring.
Open

  def add_result_ssu(base, opts)
    return MiGA::Result.new("#{base}.json") if result(:assembly).nil?
    return nil unless result_files_exist?(base, '.ssu.fa')

    r = add_files_to_ds_result(
Severity: Minor
Found in lib/miga/dataset/result/add.rb - About 35 mins 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_type has a Cognitive Complexity of 7 (exceeds 5 allowed). Consider refactoring.
Open

  def check_type
    raise MiGA::Error.new('Undefined dataset type') unless type
    return false if type == :empty

    unless self.class.KNOWN_TYPES[type]
Severity: Minor
Found in lib/miga/dataset/type.rb - About 35 mins 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

Avoid too many return statements within this method.
Open

    check_target and return
Severity: Major
Found in lib/miga/cli/action/db.rb - About 30 mins to fix

Method add_result_clade_finding has a Cognitive Complexity of 6 (exceeds 5 allowed). Consider refactoring.
Open

  def add_result_clade_finding(base, _opts)
    if result_files_exist?(base, %w[.empty])
      r = MiGA::Result.new("#{base}.json")
      r.add_file(:empty, 'miga-project.empty')
      return r
Severity: Minor
Found in lib/miga/project/result.rb - About 25 mins 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 save has a Cognitive Complexity of 6 (exceeds 5 allowed). Consider refactoring.
Open

  def save
    return if self[:never_save]
    return if !saved_hash.nil? && saved_hash == data.hash

    MiGA::MiGA.DEBUG "Metadata.save #{path}"
Severity: Minor
Found in lib/miga/metadata.rb - About 25 mins 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 num_suffix has a Cognitive Complexity of 6 (exceeds 5 allowed). Consider refactoring.
Open

  def num_suffix(n, bin = false)
    p = ''
    { T: 4, G: 3, M: 2, K: 1 }.each do |k, x|
      v = (bin ? 1024 : 1e3)**x
      if n > v
Severity: Minor
Found in lib/miga/common.rb - About 25 mins 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 daemon_loop has a Cognitive Complexity of 6 (exceeds 5 allowed). Consider refactoring.
Open

  def daemon_loop
    l_say(3, 'Daemon loop start')
    reload_project
    check_datasets or check_project
    if shutdown_when_done? && (jobs_running.size + jobs_to_run.size).zero?
Severity: Minor
Found in lib/miga/daemon.rb - About 25 mins 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 assert_valid_option_value has a Cognitive Complexity of 6 (exceeds 5 allowed). Consider refactoring.
Open

  def assert_valid_option_value(key, value, from_string = false)
    opt = assert_has_option(key)
    value = option_from_string(key, value) if from_string

    # nil is always valid, and so are supported tokens
Severity: Minor
Found in lib/miga/common/with_option.rb - About 25 mins 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_ncbi_taxid_from_ncbi has a Cognitive Complexity of 6 (exceeds 5 allowed). Consider refactoring.
Open

  def get_ncbi_taxid_from_ncbi
    # Try first from Assembly data
    return get_ncbi_taxid_from_web if db == :assembly

    # Try from previously pulled NCBI data
Severity: Minor
Found in lib/miga/remote_dataset.rb - About 25 mins 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 6 (exceeds 5 allowed). Consider refactoring.
Open

  def perform
    cli.ensure_par(result: '-r')
    obj = cli.load_project_or_dataset
    cli.say "Registering result: #{cli[:result]}"
    r = obj.add_result(cli[:result], true, force: cli[:force])
Severity: Minor
Found in lib/miga/cli/action/add_result.rb - About 25 mins 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 fix_essential_genes_by_domain has a Cognitive Complexity of 6 (exceeds 5 allowed). Consider refactoring.
Open

  def fix_essential_genes_by_domain
    return if file_path(:raw_report)

    tax = source.metadata[:tax]
    return unless tax.nil? || %w[Archaea Bacteria].include?(tax[:d])
Severity: Minor
Found in lib/miga/result/stats.rb - About 25 mins 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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