wurmlab/sequenceserver

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Use $stdin instead of STDIN.
Open

      user_response = STDIN.gets.strip
Severity: Minor
Found in lib/sequenceserver/makeblastdb.rb by rubocop

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

Final newline missing.
Open

end
Severity: Minor
Found in lib/sequenceserver/refinements.rb by rubocop

This cop looks for trailing blank lines and a final newline in the source code.

Example: EnforcedStyle: finalblankline

# `final_blank_line` looks for one blank line followed by a new line
# at the end of files.

# bad
class Foo; end
# EOF

# bad
class Foo; end # EOF

# good
class Foo; end

# EOF

Example: EnforcedStyle: final_newline (default)

# `final_newline` looks for one newline at the end of files.

# bad
class Foo; end

# EOF

# bad
class Foo; end # EOF

# good
class Foo; end
# EOF

Align the keys of a hash literal if they span more than one line.
Open

      'qa_no_identity'  => [2, :txt],

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})

Align the keys of a hash literal if they span more than one line.
Open

      'asn_text'        => [8, :asn],

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})

Do not use semicolons to terminate expressions.
Open

        properties.inject({}) { |h, k| h[k] = send(k); h }.to_json(*args)
Severity: Minor
Found in lib/sequenceserver/blast/hit.rb by rubocop

This cop checks for multiple expressions placed on the same line. It also checks for lines terminated with a semicolon.

This cop has AllowAsExpressionSeparator configuration option. It allows ; to separate several expressions on the same line.

Example:

# bad
foo = 1; bar = 2;
baz = 3;

# good
foo = 1
bar = 2
baz = 3

Example: AllowAsExpressionSeparator: false (default)

# bad
foo = 1; bar = 2

Example: AllowAsExpressionSeparator: true

# good
foo = 1; bar = 2

Convert if-elsif to case-when.
Open

        if algo_config.is_a?(Array)
          # Very old config files may have a single array with CLI args.
          # e.g. { blastn: ['-task blastn', '-evalue 1e-5'] }
          # Convert the array values into a single hash naming it 'default' if
          # the values match SequenceServer defaults.
Severity: Minor
Found in lib/sequenceserver/config.rb by rubocop

This cop identifies places where if-elsif constructions can be replaced with case-when.

Safety:

This cop is unsafe. case statements use === for equality, so if the original conditional used a different equality operator, the behaviour may be different.

Example:

# bad
if status == :active
  perform_action
elsif status == :inactive || status == :hibernating
  check_timeout
else
  final_action
end

# good
case status
when :active
  perform_action
when :inactive, :hibernating
  check_timeout
else
  final_action
end

Favor a normal unless-statement over a modifier clause in a multiline statement.
Open

        fail(
          InvalidParameterError,
          "Invalid range coordinates: #{coords}"
        ) unless coords =~ /[0-9]+-[0-9]*/
Severity: Minor
Found in lib/sequenceserver/database.rb by rubocop

Checks for uses of if/unless modifiers with multiple-lines bodies.

Example:

# bad
{
  result: 'this should not happen'
} unless cond

# good
{ result: 'ok' } if cond

Align the keys of a hash literal if they span more than one line.
Open

      'qa'              => [1, :txt],

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})

Align the keys of a hash literal if they span more than one line.
Open

      'archive'         => [11, :txt]

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})

Use fail instead of raise to signal exceptions.
Open

                raise SequenceServer::XmlImportError
Severity: Minor
Found in lib/sequenceserver/blast/report.rb by rubocop

This cop checks for uses of fail and raise.

Example: EnforcedStyle: only_raise (default)

# The `only_raise` style enforces the sole use of `raise`.
# bad
begin
  fail
rescue Exception
  # handle it
end

def watch_out
  fail
rescue Exception
  # handle it
end

Kernel.fail

# good
begin
  raise
rescue Exception
  # handle it
end

def watch_out
  raise
rescue Exception
  # handle it
end

Kernel.raise

Example: EnforcedStyle: only_fail

# The `only_fail` style enforces the sole use of `fail`.
# bad
begin
  raise
rescue Exception
  # handle it
end

def watch_out
  raise
rescue Exception
  # handle it
end

Kernel.raise

# good
begin
  fail
rescue Exception
  # handle it
end

def watch_out
  fail
rescue Exception
  # handle it
end

Kernel.fail

Example: EnforcedStyle: semantic

# The `semantic` style enforces the use of `fail` to signal an
# exception, then will use `raise` to trigger an offense after
# it has been rescued.
# bad
begin
  raise
rescue Exception
  # handle it
end

def watch_out
  # Error thrown
rescue Exception
  fail
end

Kernel.fail
Kernel.raise

# good
begin
  fail
rescue Exception
  # handle it
end

def watch_out
  fail
rescue Exception
  raise 'Preferably with descriptive message'
end

explicit_receiver.fail
explicit_receiver.raise

Assignment Branch Condition size for tree is too high. [<10, 30, 6> 32.19/17]
Open

      def tree
        all.each_with_object({}) do |db, data|
          data[db.type] ||= []
          use_parent = '#'
          db.categories.each_with_index do |entry, index|
Severity: Minor
Found in lib/sequenceserver/database.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 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 [])

Use alias_method instead of alias.
Open

    alias path name
Severity: Minor
Found in lib/sequenceserver/database.rb by rubocop

This cop enforces the use of either #alias or #alias_method depending on configuration. It also flags uses of alias :symbol rather than alias bareword.

Example: EnforcedStyle: prefer_alias (default)

# bad
alias_method :bar, :foo
alias :bar :foo

# good
alias bar foo

Example: EnforcedStyle: preferaliasmethod

# bad
alias :bar :foo
alias bar foo

# good
alias_method :bar, :foo

Call super to initialize state of the parent class.
Open

    def initialize(version)
      @version = version
    end
Severity: Minor
Found in lib/sequenceserver/exceptions.rb by rubocop

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

Assignment Branch Condition size for _make_blast_database is too high. [<5, 17, 3> 17.97/17]
Open

    def _make_blast_database(file, type, title, taxonomy)
      cmd = "makeblastdb -parse_seqids -hash_index -in '#{file}'" \
            " -dbtype #{type.to_s.slice(0, 4)} -title '#{title}'" \
            " #{taxonomy}"

Severity: Minor
Found in lib/sequenceserver/makeblastdb.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 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 [])

Space inside { missing.
Open

        params = {:xml => xml_file_path}
Severity: Minor
Found in bin/sequenceserver by rubocop

Checks that braces used for hash literals have or don't have surrounding space depending on configuration.

Example: EnforcedStyle: space (default)

# The `space` style enforces that hash literals have
# surrounding space.

# bad
h = {a: 1, b: 2}

# good
h = { a: 1, b: 2 }

Example: EnforcedStyle: no_space

# The `no_space` style enforces that hash literals have
# no surrounding space.

# bad
h = { a: 1, b: 2 }

# good
h = {a: 1, b: 2}

Example: EnforcedStyle: compact

# The `compact` style normally requires a space inside
# hash braces, with the exception that successive left
# braces or right braces are collapsed together in nested hashes.

# bad
h = { a: { b: 2 } }
foo = { { a: 1 } => { b: { c: 2 } } }

# good
h = { a: { b: 2 }}
foo = {{ a: 1 } => { b: { c: 2 }}}

Example: EnforcedStyleForEmptyBraces: no_space (default)

# The `no_space` EnforcedStyleForEmptyBraces style enforces that
# empty hash braces do not contain spaces.

# bad
foo = { }
bar = {    }

# good
foo = {}
bar = {}

Example: EnforcedStyleForEmptyBraces: space

# The `space` EnforcedStyleForEmptyBraces style enforces that
# empty hash braces contain space.

# bad
foo = {}

# good
foo = { }
foo = {  }
foo = {     }

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

      "1FAIpQLSe7sOCiKzYbI7LwErid-g3wfIU5Zpi6VTm0ILJyR036RqC8zg/formResponse " \
Severity: Minor
Found in bin/sequenceserver 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"

Add empty line after guard clause.
Open

      return if using_ssh? || verbose?
Severity: Minor
Found in lib/sequenceserver.rb by rubocop

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

Use $stderr instead of STDERR.
Open

                    Logger.new(STDERR, Logger::INFO)
Severity: Minor
Found in lib/sequenceserver.rb by rubocop

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

Align the keys of a hash literal if they span more than one line.
Open

      'fqa'             => [3, :txt],

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})

Missing top-level documentation comment for class SequenceServer::BLAST::Error.
Open

    class Error
Severity: Minor
Found in lib/sequenceserver/blast/error.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, constant definitions or constant visibility declarations.

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

module Math
end

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

# allowed
  # Class without body
  class Person
  end

  # Namespace - A namespace can be a class or a module
  # Containing a class
  module Namespace
    # Description/Explanation of Person class
    class Person
      # ...
    end
  end

  # Containing constant visibility declaration
  module Namespace
    class Private
    end

    private_constant :Private
  end

  # Containing constant definition
  module Namespace
    Public = Class.new
  end

  # Macro calls
  module Namespace
    extend Foo
  end

Example: AllowedConstants: ['ClassMethods']

# good
 module A
   module ClassMethods
     # ...
   end
  end
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