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lib/miga/cli/action/classify_wf.rb

Summary

Maintainability
A
3 hrs
Test Coverage

Assignment Branch Condition size for reference_db is too high. [41.23/15]
Open

  def reference_db
    cli.say "Locating reference database"
    ref_db_path = cli[:db_path]
    if ref_db_path.nil?
      if cli[:download]
Severity: Minor
Found in lib/miga/cli/action/classify_wf.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

Method has too many lines. [36/10]
Open

  def parse_cli
    default_opts_for_wf
    cli.defaults = {
      download: false, summaries: true, pvalue: 0.1,
      local: File.expand_path('.miga_db', ENV['MIGA_HOME'])
Severity: Minor
Found in lib/miga/cli/action/classify_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.

Method has too many lines. [21/10]
Open

  def reference_db
    cli.say "Locating reference database"
    ref_db_path = cli[:db_path]
    if ref_db_path.nil?
      if cli[:download]
Severity: Minor
Found in lib/miga/cli/action/classify_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.

Method has too many lines. [21/10]
Open

  def perform
    # Input data
    ref_db = reference_db
    norun = %w[
      haai_distances aai_distances ani_distances clade_finding
Severity: Minor
Found in lib/miga/cli/action/classify_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 parse_cli is too high. [25/15]
Open

  def parse_cli
    default_opts_for_wf
    cli.defaults = {
      download: false, summaries: true, pvalue: 0.1,
      local: File.expand_path('.miga_db', ENV['MIGA_HOME'])
Severity: Minor
Found in lib/miga/cli/action/classify_wf.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

Assignment Branch Condition size for perform is too high. [25.57/15]
Open

  def perform
    # Input data
    ref_db = reference_db
    norun = %w[
      haai_distances aai_distances ani_distances clade_finding
Severity: Minor
Found in lib/miga/cli/action/classify_wf.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

Cyclomatic complexity for reference_db is too high. [7/6]
Open

  def reference_db
    cli.say "Locating reference database"
    ref_db_path = cli[:db_path]
    if ref_db_path.nil?
      if cli[:download]
Severity: Minor
Found in lib/miga/cli/action/classify_wf.rb by rubocop

This cop checks that the cyclomatic complexity of methods is not higher than the configured maximum. The cyclomatic complexity is the number of linearly independent paths through a method. The algorithm counts decision points and adds one.

An if statement (or unless or ?:) increases the complexity by one. An else branch does not, since it doesn't add a decision point. The && operator (or keyword and) can be converted to a nested if statement, and ||/or is shorthand for a sequence of ifs, so they also add one. Loops can be said to have an exit condition, so they add one.

Method reference_db has a Cognitive Complexity of 14 (exceeds 5 allowed). Consider refactoring.
Open

  def reference_db
    cli.say "Locating reference database"
    ref_db_path = cli[:db_path]
    if ref_db_path.nil?
      if cli[:download]
Severity: Minor
Found in lib/miga/cli/action/classify_wf.rb - About 1 hr 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 36 lines of code (exceeds 25 allowed). Consider refactoring.
Open

  def parse_cli
    default_opts_for_wf
    cli.defaults = {
      download: false, summaries: true, pvalue: 0.1,
      local: File.expand_path('.miga_db', ENV['MIGA_HOME'])
Severity: Minor
Found in lib/miga/cli/action/classify_wf.rb - About 1 hr to fix

Block has too many lines. [29/25]
Open

    cli.parse do |opt|
      opt.on(
        '--download-db',
        'Attempt to download the reference database (all default options)',
        'It is recommended to use "miga get_db" separately instead'
Severity: Minor
Found in lib/miga/cli/action/classify_wf.rb by rubocop

This cop checks if the length of a block exceeds some maximum value. Comment lines can optionally be ignored. The maximum allowed length is configurable. The cop can be configured to ignore blocks passed to certain methods.

Prefer single-quoted strings when you don't need string interpolation or special symbols.
Open

      cli.say "Summary: classification"
Severity: Minor
Found in lib/miga/cli/action/classify_wf.rb by rubocop

Checks if uses of quotes match the configured preference.

Example: EnforcedStyle: single_quotes (default)

# bad
"No special symbols"
"No string interpolation"
"Just text"

# good
'No special symbols'
'No string interpolation'
'Just text'
"Wait! What's #{this}!"

Example: EnforcedStyle: double_quotes

# bad
'Just some text'
'No special chars or interpolation'

# good
"Just some text"
"No special chars or interpolation"
"Every string in #{project} uses double_quotes"

Missing top-level class documentation comment.
Open

class MiGA::Cli::Action::ClassifyWf < MiGA::Cli::Action
Severity: Minor
Found in lib/miga/cli/action/classify_wf.rb by rubocop

This cop checks for missing top-level documentation of classes and modules. Classes with no body are exempt from the check and so are namespace modules - modules that have nothing in their bodies except classes, other modules, or constant definitions.

The documentation requirement is annulled if the class or module has a "#:nodoc:" comment next to it. Likewise, "#:nodoc: all" does the same for all its children.

Example:

# bad
class Person
  # ...
end

# good
# Description/Explanation of Person class
class Person
  # ...
end

Prefer single-quoted strings when you don't need string interpolation or special symbols.
Open

    cli.say "Locating reference database"
Severity: Minor
Found in lib/miga/cli/action/classify_wf.rb by rubocop

Checks if uses of quotes match the configured preference.

Example: EnforcedStyle: single_quotes (default)

# bad
"No special symbols"
"No string interpolation"
"Just text"

# good
'No special symbols'
'No string interpolation'
'Just text'
"Wait! What's #{this}!"

Example: EnforcedStyle: double_quotes

# bad
'Just some text'
'No special chars or interpolation'

# good
"Just some text"
"No special chars or interpolation"
"Every string in #{project} uses double_quotes"

Missing magic comment # frozen_string_literal: true.
Open

# @package MiGA
Severity: Minor
Found in lib/miga/cli/action/classify_wf.rb by rubocop

This cop is designed to help upgrade to Ruby 3.0. It will add the comment # frozen_string_literal: true to the top of files to enable frozen string literals. Frozen string literals may be default in Ruby 3.0. The comment will be added below a shebang and encoding comment. The frozen string literal comment is only valid in Ruby 2.3+.

Example: EnforcedStyle: when_needed (default)

# The `when_needed` style will add the frozen string literal comment
# to files only when the `TargetRubyVersion` is set to 2.3+.
# bad
module Foo
  # ...
end

# good
# frozen_string_literal: true

module Foo
  # ...
end

Example: EnforcedStyle: always

# The `always` style will always add the frozen string literal comment
# to a file, regardless of the Ruby version or if `freeze` or `<<` are
# called on a string literal.
# bad
module Bar
  # ...
end

# good
# frozen_string_literal: true

module Bar
  # ...
end

Example: EnforcedStyle: never

# The `never` will enforce that the frozen string literal comment does
# not exist in a file.
# bad
# frozen_string_literal: true

module Baz
  # ...
end

# good
module Baz
  # ...
end

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