wurmlab/sequenceserver

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bin/sequenceserver

Summary

Maintainability
Test Coverage

Method has too many lines. [20/15]
Open

def ask_to_join
  asked_to_join = File.join(SequenceServer::DOTDIR, 'asked_to_join')
  unless File.exist?(asked_to_join)
    puts
    puts <<~MSG
Severity: Minor
Found in bin/sequenceserver 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.

You can set literals you want to fold with CountAsOne. Available are: 'array', 'hash', and 'heredoc'. Each literal will be counted as one line regardless of its actual size.

NOTE: The ExcludedMethods configuration is deprecated and only kept for backwards compatibility. Please use IgnoredMethods instead.

Example: CountAsOne: ['array', 'heredoc']

def m
  array = [       # +1
    1,
    2
  ]

  hash = {        # +3
    key: 'value'
  }

  <<~HEREDOC      # +1
    Heredoc
    content.
  HEREDOC
end               # 5 points

Favor modifier unless usage when having a single-line body. Another good alternative is the usage of control flow &&/||.
Open

          unless File.basename(response) == 'bin'
Severity: Minor
Found in bin/sequenceserver by rubocop

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

Redundant single-element character class, [n] can be replaced with n.
Open

          SequenceServer.makeblastdb.run unless response =~ /^[n]$/i
Severity: Minor
Found in bin/sequenceserver by rubocop

This cop checks for unnecessary single-element Regexp character classes.

Example:

# bad
r = /[x]/

# good
r = /x/

# bad
r = /[\s]/

# good
r = /\s/

# bad
r = %r{/[b]}

# good
r = %r{/b}

# good
r = /[ab]/

Align the elements of an array literal if they span more than one line.
Open

        SequenceServer::BLAST_DATABASE_ERROR,
Severity: Minor
Found in bin/sequenceserver by rubocop

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]

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"

Use $stdin instead of STDIN.
Open

    response = STDIN.gets.to_s.strip
Severity: Minor
Found in bin/sequenceserver 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

Incorrect indentation detected (column 4 instead of 7).
Open

    # on 'doctor',
Severity: Minor
Found in bin/sequenceserver by rubocop

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

Use 2 spaces for indentation in a heredoc.
Open

          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).
Severity: Minor
Found in bin/sequenceserver by rubocop

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

Avoid rescuing without specifying an error class.
Open

      rescue => e
Severity: Minor
Found in bin/sequenceserver 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

      post_email_cmd = "curl -m 5 https://docs.google.com/forms/u/0/d/e/" \
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"

Align the elements of an array literal if they span more than one line.
Open

        SequenceServer::CONFIG_FILE_ERROR,
Severity: Minor
Found in bin/sequenceserver by rubocop

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]

Use the new Ruby 1.9 hash syntax.
Open

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

This cop checks hash literal syntax.

It can enforce either the use of the class hash rocket syntax or the use of the newer Ruby 1.9 syntax (when applicable).

A separate offense is registered for each problematic pair.

The supported styles are:

  • ruby19 - forces use of the 1.9 syntax (e.g. {a: 1}) when hashes have all symbols for keys
  • hash_rockets - forces use of hash rockets for all hashes
  • nomixedkeys - simply checks for hashes with mixed syntaxes
  • ruby19nomixed_keys - forces use of ruby 1.9 syntax and forbids mixed syntax hashes

Example: EnforcedStyle: ruby19 (default)

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

# good
{a: 2, b: 1}
{:c => 2, 'd' => 2} # acceptable since 'd' isn't a symbol
{d: 1, 'e' => 2} # technically not forbidden

Example: EnforcedStyle: hash_rockets

# bad
{a: 1, b: 2}
{c: 1, 'd' => 5}

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

Example: EnforcedStyle: nomixedkeys

# bad
{:a => 1, b: 2}
{c: 1, 'd' => 2}

# good
{:a => 1, :b => 2}
{c: 1, d: 2}

Example: EnforcedStyle: ruby19nomixed_keys

# bad
{:a => 1, :b => 2}
{c: 2, 'd' => 3} # should just use hash rockets

# good
{a: 1, b: 2}
{:c => 3, 'd' => 4}

Use 2 spaces for indentation in a heredoc.
Open

    Do you want to be notified of SequenceServer releases and any
    other important announcements (3-12 messages a year)? If yes,
    please provide your email address below or press enter to
    continue (you won't be prompted again).
    MSG
Severity: Minor
Found in bin/sequenceserver by rubocop

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

Use a guard clause (return if File.exist?(asked_to_join)) instead of wrapping the code inside a conditional expression.
Open

  unless File.exist?(asked_to_join)
Severity: Minor
Found in bin/sequenceserver 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

# bad
if something
  foo || raise('exception')
else
  ok
end

# good
foo || raise('exception') if something
ok

Incorrect indentation detected (column 7 instead of 4).
Open

       # 'Run SequenceServer doctor'
Severity: Minor
Found in bin/sequenceserver by rubocop

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

Final newline missing.
Open

end
Severity: Minor
Found in bin/sequenceserver 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

Use $stdin instead of STDIN.
Open

          response = STDIN.gets.to_s.strip
Severity: Minor
Found in bin/sequenceserver 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

Use $stdin instead of STDIN.
Open

          response = STDIN.gets.to_s.strip
Severity: Minor
Found in bin/sequenceserver 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

Redundant single-element character class, [n] can be replaced with n.
Open

          unless response =~ /^[n]$/i
Severity: Minor
Found in bin/sequenceserver by rubocop

This cop checks for unnecessary single-element Regexp character classes.

Example:

# bad
r = /[x]/

# good
r = /x/

# bad
r = /[\s]/

# good
r = /\s/

# bad
r = %r{/[b]}

# good
r = %r{/b}

# good
r = /[ab]/

Align the elements of an array literal if they span more than one line.
Open

        SequenceServer::NUM_THREADS_INCORRECT => e
Severity: Minor
Found in bin/sequenceserver by rubocop

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]

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 = {     }

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 = {     }

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