wurmlab/sequenceserver

      def extract_params
        # Parse/get params from the job first.
        job_params = parse_advanced(job.advanced)
        # Old jobs from beta releases may not have the advanced key but they
        # will have the deprecated advanced_params key.

Close

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 and https://en.wikipedia.org/wiki/ABC_Software_Metric.

Interpreting ABC size:

• <= 17 satisfactory
• 18..30 unsatisfactory
• > 30 dangerous

You can have repeated "attributes" calls count as a single "branch". For this purpose, attributes are any method with no argument; no attempt is meant to distinguish actual attr_reader from other methods.

Example: CountRepeatedAttributes: false (default is true)

# `model` and `current_user`, refenced 3 times each,
 # are each counted as only 1 branch each if
 # `CountRepeatedAttributes` is set to 'false'

 def search
   @posts = model.active.visible_by(current_user)
             .search(params[:q])
   @posts = model.some_process(@posts, current_user)
   @posts = model.another_process(@posts, current_user)

   render 'pages/search/page'
 end

This cop also takes into account IgnoredMethods (defaults to [])

      return nil unless id.match(PFAM_ID_PATTERN) or title.match(PFAM_ID_PATTERN)

Close

This cop enforces empty line after guard clause

Example:

# bad
def foo
  return if need_return?
  bar
end

# good
def foo
  return if need_return?

  bar
end

# good
def foo
  return if something?
  return if something_different?

  bar
end

# also good
def foo
  if something?
    do_something
    return if need_return?
  end
end

        url:   url,

Close

Check that the keys, separators, and values of a multi-line hash literal are aligned according to configuration. The configuration options are:

• key (left align keys, one space before hash rockets and values)
• separator (align hash rockets and colons, right align keys)
• table (left align keys, hash rockets, and values)

The treatment of hashes passed as the last argument to a method call can also be configured. The options are:

• always_inspect
• always_ignore
• ignore_implicit (without curly braces)

Alternatively you can specify multiple allowed styles. That's done by passing a list of styles to EnforcedStyles.

Example: EnforcedHashRocketStyle: key (default)

# bad
{
  :foo => bar,
   :ba => baz
}
{
  :foo => bar,
  :ba  => baz
}

# good
{
  :foo => bar,
  :ba => baz
}

Example: EnforcedHashRocketStyle: separator

# bad
{
  :foo => bar,
  :ba => baz
}
{
  :foo => bar,
  :ba  => baz
}

# good
{
  :foo => bar,
   :ba => baz
}

Example: EnforcedHashRocketStyle: table

# bad
{
  :foo => bar,
   :ba => baz
}

# good
{
  :foo => bar,
  :ba  => baz
}

Example: EnforcedColonStyle: key (default)

# bad
{
  foo: bar,
   ba: baz
}
{
  foo: bar,
  ba:  baz
}

# good
{
  foo: bar,
  ba: baz
}

Example: EnforcedColonStyle: separator

# bad
{
  foo: bar,
  ba: baz
}

# good
{
  foo: bar,
   ba: baz
}

Example: EnforcedColonStyle: table

# bad
{
  foo: bar,
  ba: baz
}

# good
{
  foo: bar,
  ba:  baz
}

Example: EnforcedLastArgumentHashStyle: always_inspect (default)

# Inspect both implicit and explicit hashes.

# bad
do_something(foo: 1,
  bar: 2)

# bad
do_something({foo: 1,
  bar: 2})

# good
do_something(foo: 1,
             bar: 2)

# good
do_something(
  foo: 1,
  bar: 2
)

# good
do_something({foo: 1,
              bar: 2})

# good
do_something({
  foo: 1,
  bar: 2
})

Example: EnforcedLastArgumentHashStyle: always_ignore

# Ignore both implicit and explicit hashes.

# good
do_something(foo: 1,
  bar: 2)

# good
do_something({foo: 1,
  bar: 2})

Example: EnforcedLastArgumentHashStyle: ignore_implicit

# Ignore only implicit hashes.

# bad
do_something({foo: 1,
  bar: 2})

# good
do_something(foo: 1,
  bar: 2)

Example: EnforcedLastArgumentHashStyle: ignore_explicit

# Ignore only explicit hashes.

# bad
do_something(foo: 1,
  bar: 2)

# good
do_something({foo: 1,
  bar: 2})

      response = STDIN.gets.to_s.strip

Close

This cop enforces the use of $stdout/$stderr/$stdin instead of STDOUT/STDERR/STDIN. STDOUT/STDERR/STDIN are constants, and while you can actually reassign (possibly to redirect some stream) constants in Ruby, you'll get an interpreter warning if you do so.

Safety:

Autocorrection is unsafe because STDOUT and $stdout may point to different objects, for example.

Example:

# bad
STDOUT.puts('hello')

hash = { out: STDOUT, key: value }

def m(out = STDOUT)
  out.puts('hello')
end

# good
$stdout.puts('hello')

hash = { out: $stdout, key: value }

def m(out = $stdout)
  out.puts('hello')
end

    def is_compatible(given, expected)

Close

This cop makes sure that predicates are named properly.

Example:

# bad
def is_even(value)
end

def is_even?(value)
end

# good
def even?(value)
end

# bad
def has_value
end

def has_value?
end

# good
def value?
end

      return nil unless id.match(PFAM_ID_PATTERN) or title.match(PFAM_ID_PATTERN)

Close

This cop checks for uses of and and or, and suggests using && and || instead. It can be configured to check only in conditions or in all contexts.

Safety:

Auto-correction is unsafe because there is a different operator precedence between logical operators (&& and ||) and semantic operators (and and or), and that might change the behaviour.

Example: EnforcedStyle: always

# bad
foo.save and return

# bad
if foo and bar
end

# good
foo.save && return

# good
if foo && bar
end

Example: EnforcedStyle: conditionals (default)

# bad
if foo and bar
end

# good
foo.save && return

# good
foo.save and return

# good
if foo && bar
end

      rescue => e

Close

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

           gaps length qcovhsp qseq sseq midline].inject({}) { |h, k|

Close

Check for uses of braces or do/end around single line or multi-line blocks.

Methods that can be either procedural or functional and cannot be categorised from their usage alone is ignored. lambda, proc, and it are their defaults. Additional methods can be added to the IgnoredMethods.

Example: EnforcedStyle: linecountbased (default)

# bad - single line block
items.each do |item| item / 5 end

# good - single line block
items.each { |item| item / 5 }

# bad - multi-line block
things.map { |thing|
  something = thing.some_method
  process(something)
}

# good - multi-line block
things.map do |thing|
  something = thing.some_method
  process(something)
end

Example: EnforcedStyle: semantic

# Prefer `do...end` over `{...}` for procedural blocks.

# return value is used/assigned
# bad
foo = map do |x|
  x
end
puts (map do |x|
  x
end)

# return value is not used out of scope
# good
map do |x|
  x
end

# Prefer `{...}` over `do...end` for functional blocks.

# return value is not used out of scope
# bad
each { |x|
  x
}

# return value is used/assigned
# good
foo = map { |x|
  x
}
map { |x|
  x
}.inspect

# The AllowBracesOnProceduralOneLiners option is ignored unless the
# EnforcedStyle is set to `semantic`. If so:

# If the AllowBracesOnProceduralOneLiners option is unspecified, or
# set to `false` or any other falsey value, then semantic purity is
# maintained, so one-line procedural blocks must use do-end, not
# braces.

# bad
collection.each { |element| puts element }

# good
collection.each do |element| puts element end

# If the AllowBracesOnProceduralOneLiners option is set to `true`, or
# any other truthy value, then one-line procedural blocks may use
# either style. (There is no setting for requiring braces on them.)

# good
collection.each { |element| puts element }

# also good
collection.each do |element| puts element end

Example: EnforcedStyle: bracesforchaining

# bad
words.each do |word|
  word.flip.flop
end.join("-")

# good
words.each { |word|
  word.flip.flop
}.join("-")

Example: EnforcedStyle: always_braces

# bad
words.each do |word|
  word.flip.flop
end

# good
words.each { |word|
  word.flip.flop
}

Example: BracesRequiredMethods: ['sig']

# Methods listed in the BracesRequiredMethods list, such as 'sig'
# in this example, will require `{...}` braces. This option takes
# precedence over all other configurations except IgnoredMethods.

# bad
sig do
  params(
    foo: string,
  ).void
end
def bar(foo)
  puts foo
end

# good
sig {
  params(
    foo: string,
  ).void
}
def bar(foo)
  puts foo
end

Example: IgnoredMethods: ['lambda', 'proc', 'it' ] (default)

# good
foo = lambda do |x|
  puts "Hello, #{x}"
end

foo = lambda do |x|
  x * 100
end

    def initialize(des, ent)
      @des = des
      @ent = ent
    end

Close

This cop checks for the presence of constructors and lifecycle callbacks without calls to super.

This cop does not consider method_missing (and respond_to_missing?) because in some cases it makes sense to overtake what is considered a missing method. In other cases, the theoretical ideal handling could be challenging or verbose for no actual gain.

Example:

# bad
class Employee < Person
  def initialize(name, salary)
    @salary = salary
  end
end

# good
class Employee < Person
  def initialize(name, salary)
    super(name)
    @salary = salary
  end
end

# bad
class Parent
  def self.inherited(base)
    do_something
  end
end

# good
class Parent
  def self.inherited(base)
    super
    do_something
  end
end

      Find.find(database_dir + '/') do |path|

Close

This cop checks for places where string concatenation can be replaced with string interpolation.

The cop can autocorrect simple cases but will skip autocorrecting more complex cases where the resulting code would be harder to read. In those cases, it might be useful to extract statements to local variables or methods which you can then interpolate in a string.

NOTE: When concatenation between two strings is broken over multiple lines, this cop does not register an offense; instead, Style/LineEndConcatenation will pick up the offense if enabled.

Two modes are supported: 1. aggressive style checks and corrects all occurrences of + where either the left or right side of + is a string literal. 2. conservative style on the other hand, checks and corrects only if left side (receiver of + method call) is a string literal. This is useful when the receiver is some expression that returns string like Pathname instead of a string literal.

Safety:

This cop is unsafe in aggressive mode, as it cannot be guaranteed that the receiver is actually a string, which can result in a false positive.

Example: Mode: aggressive (default)

# bad
email_with_name = user.name + ' <' + user.email + '>'
Pathname.new('/') + 'test'

# good
email_with_name = "#{user.name} <#{user.email}>"
email_with_name = format('%s <%s>', user.name, user.email)
"#{Pathname.new('/')}test"

# accepted, line-end concatenation
name = 'First' +
  'Last'

Example: Mode: conservative

# bad
'Hello' + user.name

# good
"Hello #{user.name}"
user.name + '!!'
Pathname.new('/') + 'test'

    # on 'doctor',

Close

This cop checks the indentation of comments.

Example:

# bad
  # comment here
def method_name
end

  # comment here
a = 'hello'

# yet another comment
  if true
    true
  end

# good
# comment here
def method_name
end

# comment here
a = 'hello'

# yet another comment
if true
  true
end

          SequenceServer has scanned your databases directory and will now offer
          to convert FASTA files into BLAST databases. It will also offer to
          reformat any old-format BLAST databases and those created without
          the -parse_seqids option of makeblastdb (-parse_seqids option is
          required for sequence retrieval to correctly work).

Close

This cop checks the indentation of the here document bodies. The bodies are indented one step.

Note: When Layout/LineLength's AllowHeredoc is false (not default), this cop does not add any offenses for long here documents to avoid Layout/LineLength's offenses.

Example:

# bad
<<-RUBY
something
RUBY

# good
<<~RUBY
  something
RUBY

        unless File.exist?(config[:bin]) && File.directory?(config[:bin])

Close

Checks for if and unless statements that would fit on one line if written as modifier if/unless. The cop also checks for modifier if/unless lines that exceed the maximum line length.

The maximum line length is configured in the Layout/LineLength cop. The tab size is configured in the IndentationWidth of the Layout/IndentationStyle cop.

Example:

# bad
if condition
  do_stuff(bar)
end

unless qux.empty?
  Foo.do_something
end

do_something_with_a_long_name(arg) if long_condition_that_prevents_code_fit_on_single_line

# good
do_stuff(bar) if condition
Foo.do_something unless qux.empty?

if long_condition_that_prevents_code_fit_on_single_line
  do_something_with_a_long_name(arg)
end

if short_condition # a long comment that makes it too long if it were just a single line
  do_something
end

      return nil unless id.match(UNIPROT_ID_PATTERN) or title.match(UNIPROT_ID_PATTERN)

Close

This cop enforces empty line after guard clause

Example:

# bad
def foo
  return if need_return?
  bar
end

# good
def foo
  return if need_return?

  bar
end

# good
def foo
  return if something?
  return if something_different?

  bar
end

# also good
def foo
  if something?
    do_something
    return if need_return?
  end
end

      return nil unless id.match(NCBI_ID_PATTERN) or title.match(NCBI_ID_PATTERN)

Close

This cop checks for uses of and and or, and suggests using && and || instead. It can be configured to check only in conditions or in all contexts.

Safety:

Auto-correction is unsafe because there is a different operator precedence between logical operators (&& and ||) and semantic operators (and and or), and that might change the behaviour.

Example: EnforcedStyle: always

# bad
foo.save and return

# bad
if foo and bar
end

# good
foo.save && return

# good
if foo && bar
end

Example: EnforcedStyle: conditionals (default)

# bad
if foo and bar
end

# good
foo.save && return

# good
foo.save and return

# good
if foo && bar
end

      def initialize
        self.datetime_format = '%Y-%m-%d %H:%M:%S'
      end

Close

This cop checks for the presence of constructors and lifecycle callbacks without calls to super.

This cop does not consider method_missing (and respond_to_missing?) because in some cases it makes sense to overtake what is considered a missing method. In other cases, the theoretical ideal handling could be challenging or verbose for no actual gain.

Example:

# bad
class Employee < Person
  def initialize(name, salary)
    @salary = salary
  end
end

# good
class Employee < Person
  def initialize(name, salary)
    super(name)
    @salary = salary
  end
end

# bad
class Parent
  def self.inherited(base)
    do_something
  end
end

# good
class Parent
  def self.inherited(base)
    super
    do_something
  end
end

        SequenceServer::CONFIG_FILE_ERROR,

Close

Here we check if the elements of a multi-line array literal are aligned.

Example: EnforcedStyle: withfirstelement (default)

# good

array = [1, 2, 3,
         4, 5, 6]
array = ['run',
         'forrest',
         'run']

# bad

array = [1, 2, 3,
  4, 5, 6]
array = ['run',
     'forrest',
     'run']

Example: EnforcedStyle: withfixedindentation

# good

array = [1, 2, 3,
  4, 5, 6]

# bad

array = [1, 2, 3,
         4, 5, 6]

      Resolv.getname(ip_address) rescue nil

Close

This cop checks for uses of rescue in its modifier form.

The cop to check rescue in its modifier form is added for following reasons:

• The syntax of modifier form rescue can be misleading because it might led us to believe that rescue handles the given exception but it actually rescue all exceptions to return the given rescue block. In this case, value returned by handle_error or SomeException.

• Modifier form rescue would rescue all the exceptions. It would silently skip all exception or errors and handle the error. Example: If NoMethodError is raised, modifier form rescue would handle the exception.

Example:

# bad
some_method rescue handle_error

# bad
some_method rescue SomeException

# good
begin
  some_method
rescue
  handle_error
end

# good
begin
  some_method
rescue SomeException
  handle_error
end

          unless seq
            seq = "# ERROR: #{locus} not found in any database"
          end

Close

This cop checks for potential usage of the ||= operator.

Example:

# bad
name = name ? name : 'Bozhidar'

# bad
name = if name
         name
       else
         'Bozhidar'
       end

# bad
unless name
  name = 'Bozhidar'
end

# bad
name = 'Bozhidar' unless name

# good - set name to 'Bozhidar', only if it's nil or false
name ||= 'Bozhidar'

      return nil unless id.match(NCBI_ID_PATTERN) or title.match(NCBI_ID_PATTERN)

Close

This cop enforces empty line after guard clause

Example:

# bad
def foo
  return if need_return?
  bar
end

# good
def foo
  return if need_return?

  bar
end

# good
def foo
  return if something?
  return if something_different?

  bar
end

# also good
def foo
  if something?
    do_something
    return if need_return?
  end
end