Class has too many lines. [158/100] Open
class MiGA::Cli::Action::Get < MiGA::Cli::Action
require 'miga/cli/action/download/base'
include MiGA::Cli::Action::Download::Base
def parse_cli
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Method has too many lines. [72/10] Open
def parse_cli
cli.defaults = {
query: false, universe: :ncbi, db: :nuccore, get_md: false, only_md: false
}
cli.parse do |opt|
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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.
Assignment Branch Condition size for parse_cli is too high. [47.77/15] Open
def parse_cli
cli.defaults = {
query: false, universe: :ncbi, db: :nuccore, get_md: false, only_md: false
}
cli.parse do |opt|
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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
Assignment Branch Condition size for get_sub_cli is too high. [35/15] Open
def get_sub_cli
return [cli] if cli[:file].nil? || cli[:ignore_file]
glob = []
cli_default = cli.original_argv + ['--ignore-file']
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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
Method has too many lines. [29/10] Open
def get_sub_cli
return [cli] if cli[:file].nil? || cli[:ignore_file]
glob = []
cli_default = cli.original_argv + ['--ignore-file']
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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.
Block has too many lines. [67/25] Open
cli.parse do |opt|
cli.opt_object(opt, [:project, :dataset, :dataset_type])
opt.on(
'-I', '--ids ID1,ID2,...', Array,
'(Mandatory unless -F) IDs in the remote database separated by commas'
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This cop checks if the length of a block exceeds some maximum value. Comment lines can optionally be ignored. The maximum allowed length is configurable. The cop can be configured to ignore blocks passed to certain methods.
Method parse_cli
has 72 lines of code (exceeds 25 allowed). Consider refactoring. Open
def parse_cli
cli.defaults = {
query: false, universe: :ncbi, db: :nuccore, get_md: false, only_md: false
}
cli.parse do |opt|
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Assignment Branch Condition size for create_remote_dataset is too high. [24.92/15] Open
def create_remote_dataset(sub_cli, p)
sub_cli.ensure_par(dataset: '-D', ids: '-I')
unless sub_cli[:api_key].nil?
if sub_cli[:universe] == :web && sub_cli[:db] == :assembly_gz
ENV['NCBI_API_KEY'] = sub_cli[:api_key]
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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
Method get_sub_cli
has a Cognitive Complexity of 17 (exceeds 5 allowed). Consider refactoring. Open
def get_sub_cli
return [cli] if cli[:file].nil? || cli[:ignore_file]
glob = []
cli_default = cli.original_argv + ['--ignore-file']
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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 create_dataset is too high. [19.34/15] Open
def create_dataset(sub_cli, p, rd)
sub_cli.say 'Creating dataset'
if Dataset.exist?(p, sub_cli[:dataset])
raise "Dataset already exists: #{sub_cli[:dataset]}"
end
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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
Method has too many lines. [14/10] Open
def create_remote_dataset(sub_cli, p)
sub_cli.ensure_par(dataset: '-D', ids: '-I')
unless sub_cli[:api_key].nil?
if sub_cli[:universe] == :web && sub_cli[:db] == :assembly_gz
ENV['NCBI_API_KEY'] = sub_cli[:api_key]
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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.
Method has too many lines. [13/10] Open
def perform
glob = get_sub_cli
p = cli.load_project
load_ncbi_taxonomy_dump
glob.each do |sub_cli|
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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.
Cyclomatic complexity for create_remote_dataset is too high. [7/6] Open
def create_remote_dataset(sub_cli, p)
sub_cli.ensure_par(dataset: '-D', ids: '-I')
unless sub_cli[:api_key].nil?
if sub_cli[:universe] == :web && sub_cli[:db] == :assembly_gz
ENV['NCBI_API_KEY'] = sub_cli[:api_key]
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This cop checks that the cyclomatic complexity of methods is not higher than the configured maximum. The cyclomatic complexity is the number of linearly independent paths through a method. The algorithm counts decision points and adds one.
An if statement (or unless or ?:) increases the complexity by one. An else branch does not, since it doesn't add a decision point. The && operator (or keyword and) can be converted to a nested if statement, and ||/or is shorthand for a sequence of ifs, so they also add one. Loops can be said to have an exit condition, so they add one.
Cyclomatic complexity for get_sub_cli is too high. [7/6] Open
def get_sub_cli
return [cli] if cli[:file].nil? || cli[:ignore_file]
glob = []
cli_default = cli.original_argv + ['--ignore-file']
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- Exclude checks
This cop checks that the cyclomatic complexity of methods is not higher than the configured maximum. The cyclomatic complexity is the number of linearly independent paths through a method. The algorithm counts decision points and adds one.
An if statement (or unless or ?:) increases the complexity by one. An else branch does not, since it doesn't add a decision point. The && operator (or keyword and) can be converted to a nested if statement, and ||/or is shorthand for a sequence of ifs, so they also add one. Loops can be said to have an exit condition, so they add one.
Method get_sub_cli
has 29 lines of code (exceeds 25 allowed). Consider refactoring. Open
def get_sub_cli
return [cli] if cli[:file].nil? || cli[:ignore_file]
glob = []
cli_default = cli.original_argv + ['--ignore-file']
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Method perform
has a Cognitive Complexity of 8 (exceeds 5 allowed). Consider refactoring. Open
def perform
glob = get_sub_cli
p = cli.load_project
load_ncbi_taxonomy_dump
glob.each do |sub_cli|
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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 create_remote_dataset
has a Cognitive Complexity of 8 (exceeds 5 allowed). Consider refactoring. Open
def create_remote_dataset(sub_cli, p)
sub_cli.ensure_par(dataset: '-D', ids: '-I')
unless sub_cli[:api_key].nil?
if sub_cli[:universe] == :web && sub_cli[:db] == :assembly_gz
ENV['NCBI_API_KEY'] = sub_cli[:api_key]
- Read upRead up
- Create a ticketCreate a ticket
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
Use casecmp
instead of downcase ==
. Open
argv_i << "--#{field.downcase}" if r[k].downcase == 'true'
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This cop identifies places where a case-insensitive string comparison
can better be implemented using casecmp
.
Example:
# bad
str.downcase == 'abc'
str.upcase.eql? 'ABC'
'abc' == str.downcase
'ABC'.eql? str.upcase
str.downcase == str.downcase
# good
str.casecmp('ABC').zero?
'abc'.casecmp(str).zero?
Do not prefix reader method names with get_
. Open
def get_sub_cli
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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
Missing top-level class documentation comment. Open
class MiGA::Cli::Action::Get < MiGA::Cli::Action
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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, or constant definitions.
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
# good
# Description/Explanation of Person class
class Person
# ...
end
Missing magic comment # frozen_string_literal: true
. Open
# @package MiGA
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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
Unnecessary splat expansion. Open
when *%w[query ignore-dup get-metadata only-metadata]
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This cop checks for unneeded usages of splat expansion
Example:
# bad
a = *[1, 2, 3]
a = *'a'
a = *1
begin
foo
rescue *[StandardError, ApplicationError]
bar
end
case foo
when *[1, 2, 3]
bar
else
baz
end
Example:
# good
c = [1, 2, 3]
a = *c
a, b = *c
a, *b = *c
a = *1..10
a = ['a']
begin
foo
rescue StandardError, ApplicationError
bar
end
case foo
when *[1, 2, 3]
bar
else
baz
end
Unnecessary splat expansion. Open
when *%w[project file verbose help debug]
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This cop checks for unneeded usages of splat expansion
Example:
# bad
a = *[1, 2, 3]
a = *'a'
a = *1
begin
foo
rescue *[StandardError, ApplicationError]
bar
end
case foo
when *[1, 2, 3]
bar
else
baz
end
Example:
# good
c = [1, 2, 3]
a = *c
a, b = *c
a, *b = *c
a = *1..10
a = ['a']
begin
foo
rescue StandardError, ApplicationError
bar
end
case foo
when *[1, 2, 3]
bar
else
baz
end
Use %i
or %I
for an array of symbols. Open
cli.opt_object(opt, [:project, :dataset, :dataset_type])
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This cop can check for array literals made up of symbols that are not using the %i() syntax.
Alternatively, it checks for symbol arrays using the %i() syntax on projects which do not want to use that syntax.
Configuration option: MinSize
If set, arrays with fewer elements than this value will not trigger the
cop. For example, a MinSize of
3` will not enforce a style on an array
of 2 or fewer elements.
Example: EnforcedStyle: percent (default)
# good
%i[foo bar baz]
# bad
[:foo, :bar, :baz]
Example: EnforcedStyle: brackets
# good
[:foo, :bar, :baz]
# bad
%i[foo bar baz]