bio-miga/miga

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Redundant begin block detected.
Open

    begin
Severity: Minor
Found in lib/miga/cli.rb by rubocop

This cop checks for redundant begin blocks.

Currently it checks for code like this:

Example:

def redundant
  begin
    ala
    bala
  rescue StandardError => e
    something
  end
end

def preferred
  ala
  bala
rescue StandardError => e
  something
end

Missing magic comment # frozen_string_literal: true.
Open

# @package MiGA
Severity: Minor
Found in lib/miga/tax_index.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

Prefer annotated tokens (like %<foo>s</foo>) over unannotated tokens (like %s).
Open

    say 'MiGA:%s launched' % project.name
Severity: Minor
Found in lib/miga/daemon.rb by rubocop

Use a consistent style for named format string tokens.

Note: unannotated style cop only works for strings which are passed as arguments to those methods: sprintf, format, %. The reason is that unannotated format is very similar to encoded URLs or Date/Time formatting strings.

Example: EnforcedStyle: annotated (default)

# bad
format('%{greeting}', greeting: 'Hello')
format('%s', 'Hello')

# good
format('%<greeting>s', greeting: 'Hello')</greeting>

Example: EnforcedStyle: template

# bad
format('%<greeting>s', greeting: 'Hello')
format('%s', 'Hello')

# good
format('%{greeting}', greeting: 'Hello')</greeting>

Example: EnforcedStyle: unannotated

# bad
format('%<greeting>s', greeting: 'Hello')
format('%{greeting}', 'Hello')

# good
format('%s', 'Hello')</greeting>

Use a guard clause instead of wrapping the code inside a conditional expression.
Open

    if klass.KNOWN_TYPES[self[:type]].nil?
Severity: Minor
Found in lib/miga/cli.rb by rubocop

Use a guard clause instead of wrapping the code inside a conditional expression

Example:

# bad
def test
  if something
    work
  end
end

# good
def test
  return unless something
  work
end

# also good
def test
  work if something
end

# bad
if something
  raise 'exception'
else
  ok
end

# good
raise 'exception' if something
ok

Use ! instead of not.
Open

    if unknown or not datasets.empty? or not name.nil?
Severity: Minor
Found in lib/miga/tax_index.rb by rubocop

This cop checks for uses of the keyword not instead of !.

Example:

# bad - parentheses are required because of op precedence
x = (not something)

# good
x = !something

Avoid single-line method definitions.
Open

  def tax_str; "#{rank}:#{name.nil? ? '?' : name}"; end
Severity: Minor
Found in lib/miga/tax_index.rb by rubocop

This cop checks for single-line method definitions that contain a body. It will accept single-line methods with no body.

Example:

# bad
def some_method; body end
def link_to(url); {:name => url}; end
def @table.columns; super; end

# good
def no_op; end
def self.resource_class=(klass); end
def @table.columns; end

Unnecessary spacing detected.
Open

    ln  = doc.grep(%r{^\s+/db_xref="taxon:}).first
Severity: Minor
Found in lib/miga/remote_dataset.rb by rubocop

This cop checks for extra/unnecessary whitespace.

Example:

# good if AllowForAlignment is true
name      = "RuboCop"
# Some comment and an empty line

website  += "/bbatsov/rubocop" unless cond
puts        "rubocop"          if     debug

# bad for any configuration
set_app("RuboCop")
website  = "https://github.com/bbatsov/rubocop"

Prefer annotated tokens (like %<foo>s</foo>) over unannotated tokens (like %s).
Open

        '%s/%s_genomic.fna.gz' % [url_dir, File.basename(url_dir)]
Severity: Minor
Found in lib/miga/remote_dataset.rb by rubocop

Use a consistent style for named format string tokens.

Note: unannotated style cop only works for strings which are passed as arguments to those methods: sprintf, format, %. The reason is that unannotated format is very similar to encoded URLs or Date/Time formatting strings.

Example: EnforcedStyle: annotated (default)

# bad
format('%{greeting}', greeting: 'Hello')
format('%s', 'Hello')

# good
format('%<greeting>s', greeting: 'Hello')</greeting>

Example: EnforcedStyle: template

# bad
format('%<greeting>s', greeting: 'Hello')
format('%s', 'Hello')

# good
format('%{greeting}', greeting: 'Hello')</greeting>

Example: EnforcedStyle: unannotated

# bad
format('%<greeting>s', greeting: 'Hello')
format('%{greeting}', 'Hello')

# good
format('%s', 'Hello')</greeting>

Prefer annotated tokens (like %<foo>s</foo>) over unannotated tokens (like %s).
Open

    say 'Queueing %s:%s' % [to_run[:ds_name], to_run[:job]]
Severity: Minor
Found in lib/miga/daemon.rb by rubocop

Use a consistent style for named format string tokens.

Note: unannotated style cop only works for strings which are passed as arguments to those methods: sprintf, format, %. The reason is that unannotated format is very similar to encoded URLs or Date/Time formatting strings.

Example: EnforcedStyle: annotated (default)

# bad
format('%{greeting}', greeting: 'Hello')
format('%s', 'Hello')

# good
format('%<greeting>s', greeting: 'Hello')</greeting>

Example: EnforcedStyle: template

# bad
format('%<greeting>s', greeting: 'Hello')
format('%s', 'Hello')

# good
format('%{greeting}', greeting: 'Hello')</greeting>

Example: EnforcedStyle: unannotated

# bad
format('%<greeting>s', greeting: 'Hello')
format('%{greeting}', 'Hello')

# good
format('%s', 'Hello')</greeting>

Missing magic comment # frozen_string_literal: true.
Open

# @package MiGA
Severity: Minor
Found in lib/miga/daemon.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

Use =~ in places where the MatchData returned by #match will not be used.
Open

          if /^! (Completeness|Contamination): (.*)%/.match(ln)
Severity: Minor
Found in lib/miga/result/stats.rb by rubocop

This cop identifies the use of Regexp#match or String#match, which returns #<MatchData>/nil. The return value of =~ is an integral index/nil and is more performant.

Example:

# bad
do_something if str.match(/regex/)
while regex.match('str')
  do_something
end

# good
method(str =~ /regex/)
return value unless regex =~ 'str'

Prefer annotated tokens (like %<foo>s</foo>) over unannotated tokens (like %s).
Open

    say '%s launched' % daemon_name
Severity: Minor
Found in lib/miga/lair.rb by rubocop

Use a consistent style for named format string tokens.

Note: unannotated style cop only works for strings which are passed as arguments to those methods: sprintf, format, %. The reason is that unannotated format is very similar to encoded URLs or Date/Time formatting strings.

Example: EnforcedStyle: annotated (default)

# bad
format('%{greeting}', greeting: 'Hello')
format('%s', 'Hello')

# good
format('%<greeting>s', greeting: 'Hello')</greeting>

Example: EnforcedStyle: template

# bad
format('%<greeting>s', greeting: 'Hello')
format('%s', 'Hello')

# good
format('%{greeting}', greeting: 'Hello')</greeting>

Example: EnforcedStyle: unannotated

# bad
format('%<greeting>s', greeting: 'Hello')
format('%{greeting}', 'Hello')

# good
format('%s', 'Hello')</greeting>

Do not prefix reader method names with get_.
Open

  def get_ncbi_taxid_from_ncbi
Severity: Minor
Found in lib/miga/remote_dataset.rb by rubocop

This cop makes sure that accessor methods are named properly.

Example:

# bad
def set_attribute(value)
end

# good
def attribute=(value)
end

# bad
def get_attribute
end

# good
def attribute
end

Indent the first parameter one step more than the start of the previous line.
Open

                to_run[:job], miga: vars['MIGA'], project: project
Severity: Minor
Found in lib/miga/daemon.rb by rubocop

This cop checks the indentation of the first parameter in a method call. Parameters after the first one are checked by Style/AlignParameters, not by this cop.

Example:

# bad
some_method(
first_param,
second_param)

# good
some_method(
  first_param,
second_param)

Avoid rescuing without specifying an error class.
Open

    rescue => err
Severity: Minor
Found in lib/miga/cli.rb by rubocop

This cop checks for rescuing StandardError. There are two supported styles implicit and explicit. This cop will not register an offense if any error other than StandardError is specified.

Example: EnforcedStyle: implicit

# `implicit` will enforce using `rescue` instead of
# `rescue StandardError`.

# bad
begin
  foo
rescue StandardError
  bar
end

# good
begin
  foo
rescue
  bar
end

# good
begin
  foo
rescue OtherError
  bar
end

# good
begin
  foo
rescue StandardError, SecurityError
  bar
end

Example: EnforcedStyle: explicit (default)

# `explicit` will enforce using `rescue StandardError`
# instead of `rescue`.

# bad
begin
  foo
rescue
  bar
end

# good
begin
  foo
rescue StandardError
  bar
end

# good
begin
  foo
rescue OtherError
  bar
end

# good
begin
  foo
rescue StandardError, SecurityError
  bar
end

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

      raise "See `miga -h`" if action.nil?
Severity: Minor
Found in lib/miga/cli.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"

Do not prefix reader method names with get_.
Open

  def get_ncbi_taxonomy
Severity: Minor
Found in lib/miga/remote_dataset.rb by rubocop

This cop makes sure that accessor methods are named properly.

Example:

# bad
def set_attribute(value)
end

# good
def attribute=(value)
end

# bad
def get_attribute
end

# good
def attribute
end

Provide an exception class and message as arguments to raise.
Open

        raise MiGA::RemoteDataMissingError.new(
          "NCBI Assembly Accession not found: #{acc}"
        )
Severity: Minor
Found in lib/miga/remote_dataset.rb by rubocop

This cop checks the args passed to fail and raise. For exploded style (default), it recommends passing the exception class and message to raise, rather than construct an instance of the error. It will still allow passing just a message, or the construction of an error with more than one argument.

The exploded style works identically, but with the addition that it will also suggest constructing error objects when the exception is passed multiple arguments.

Example: EnforcedStyle: exploded (default)

# bad
raise StandardError.new("message")

# good
raise StandardError, "message"
fail "message"
raise MyCustomError.new(arg1, arg2, arg3)
raise MyKwArgError.new(key1: val1, key2: val2)

Example: EnforcedStyle: compact

# bad
raise StandardError, "message"
raise RuntimeError, arg1, arg2, arg3

# good
raise StandardError.new("message")
raise MyCustomError.new(arg1, arg2, arg3)
fail "message"

Prefer annotated tokens (like %<foo>s</foo>) over unannotated tokens (like %s).
Open

    say 'Queueing %s:%s' % [to_run[:ds_name], to_run[:job]]
Severity: Minor
Found in lib/miga/daemon.rb by rubocop

Use a consistent style for named format string tokens.

Note: unannotated style cop only works for strings which are passed as arguments to those methods: sprintf, format, %. The reason is that unannotated format is very similar to encoded URLs or Date/Time formatting strings.

Example: EnforcedStyle: annotated (default)

# bad
format('%{greeting}', greeting: 'Hello')
format('%s', 'Hello')

# good
format('%<greeting>s', greeting: 'Hello')</greeting>

Example: EnforcedStyle: template

# bad
format('%<greeting>s', greeting: 'Hello')
format('%s', 'Hello')

# good
format('%{greeting}', greeting: 'Hello')</greeting>

Example: EnforcedStyle: unannotated

# bad
format('%<greeting>s', greeting: 'Hello')
format('%{greeting}', 'Hello')

# good
format('%s', 'Hello')</greeting>

Use next to skip iteration.
Open

      if !runopts(k).nil? && runopts(k) =~ /%(\d+\$)?[ds]/
Severity: Minor
Found in lib/miga/daemon.rb by rubocop

Use next to skip iteration instead of a condition at the end.

Example: EnforcedStyle: skipmodifierifs (default)

# bad
[1, 2].each do |a|
  if a == 1
    puts a
  end
end

# good
[1, 2].each do |a|
  next unless a == 1
  puts a
end

# good
[1, 2].each do |o|
  puts o unless o == 1
end

Example: EnforcedStyle: always

# With `always` all conditions at the end of an iteration needs to be
# replaced by next - with `skip_modifier_ifs` the modifier if like
# this one are ignored: `[1, 2].each { |a| return 'yes' if a == 1 }`

# bad
[1, 2].each do |o|
  puts o unless o == 1
end

# bad
[1, 2].each do |a|
  if a == 1
    puts a
  end
end

# good
[1, 2].each do |a|
  next unless a == 1
  puts a
end
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