yannickwurm/sequenceserver

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lib/sequenceserver/database.rb

Summary

Maintainability
A
2 hrs
Test Coverage

Method has too many lines. [19/15]
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 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

Method tree has a Cognitive Complexity of 11 (exceeds 5 allowed). Consider refactoring.
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 - 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 retrieve has a Cognitive Complexity of 9 (exceeds 5 allowed). Consider refactoring.
Open

      def retrieve(loci)
        # Exit early if loci is nil.
        return unless loci

        # String -> Array
Severity: Minor
Found in lib/sequenceserver/database.rb - About 55 mins 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

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

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

      if coords
Severity: Minor
Found in lib/sequenceserver/database.rb 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

Extra empty line detected at block body beginning.
Open


    extend Forwardable
Severity: Minor
Found in lib/sequenceserver/database.rb by rubocop

This cop checks if empty lines around the bodies of blocks match the configuration.

Example: EnforcedStyle: empty_lines

# good

foo do |bar|

  # ...

end

Example: EnforcedStyle: noemptylines (default)

# good

foo do |bar|
  # ...
end

Unnecessary spacing detected.
Open

      args[2].downcase!   # type
Severity: Minor
Found in lib/sequenceserver/database.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  += "/rubocop/rubocop" unless cond
puts        "rubocop"          if     debug

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

# good only if AllowBeforeTrailingComments is true
object.method(arg)  # this is a comment

# good even if AllowBeforeTrailingComments is false or not set
object.method(arg) # this is a comment

# good with either AllowBeforeTrailingComments or AllowForAlignment
object.method(arg)         # this is a comment
another_object.method(arg) # this is another comment
some_object.method(arg)    # this is some comment

Add empty line after guard clause.
Open

      return if alias?
Severity: Minor
Found in lib/sequenceserver/database.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

#to_json requires an optional argument to be parsable via JSON.generate(obj).
Open

      def to_json
        collection.values.to_json
      end
Severity: Minor
Found in lib/sequenceserver/database.rb by rubocop

This cop checks to make sure #to_json includes an optional argument. When overriding #to_json, callers may invoke JSON generation via JSON.generate(your_obj). Since JSON#generate allows for an optional argument, your method should too.

Example:

class Point
  attr_reader :x, :y

  # bad, incorrect arity
  def to_json
    JSON.generate([x, y])
  end

  # good, preserving args
  def to_json(*args)
    JSON.generate([x, y], *args)
  end

  # good, discarding args
  def to_json(*_args)
    JSON.generate([x, y])
  end
end

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

          unless seq
Severity: Minor
Found in lib/sequenceserver/database.rb 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

Use the double pipe equals operator ||= instead.
Open

          unless seq
            seq = "# ERROR: #{locus} not found in any database"
          end
Severity: Minor
Found in lib/sequenceserver/database.rb by rubocop

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'

Avoid using rescue in its modifier form.
Open

      sys(cmd, path: config[:bin]) rescue false
Severity: Minor
Found in lib/sequenceserver/database.rb by rubocop

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

There are no issues that match your filters.

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