Showing 1,637 of 1,651 total issues
Similar blocks of code found in 2 locations. Consider refactoring. Open
@@LONG_RANKS = {
root: 'root', ns: 'namespace', d: 'domain', k: 'kingdom',
p: 'phylum', c: 'class', o: 'order', f: 'family', g: 'genus', s: 'species',
ssp: 'subspecies', str: 'strain', ds: 'dataset'
}
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Duplicated Code
Duplicated code can lead to software that is hard to understand and difficult to change. The Don't Repeat Yourself (DRY) principle states:
Every piece of knowledge must have a single, unambiguous, authoritative representation within a system.
When you violate DRY, bugs and maintenance problems are sure to follow. Duplicated code has a tendency to both continue to replicate and also to diverge (leaving bugs as two similar implementations differ in subtle ways).
Tuning
This issue has a mass of 28.
We set useful threshold defaults for the languages we support but you may want to adjust these settings based on your project guidelines.
The threshold configuration represents the minimum mass a code block must have to be analyzed for duplication. The lower the threshold, the more fine-grained the comparison.
If the engine is too easily reporting duplication, try raising the threshold. If you suspect that the engine isn't catching enough duplication, try lowering the threshold. The best setting tends to differ from language to language.
See codeclimate-duplication
's documentation for more information about tuning the mass threshold in your .codeclimate.yml
.
Refactorings
- Extract Method
- Extract Class
- Form Template Method
- Introduce Null Object
- Pull Up Method
- Pull Up Field
- Substitute Algorithm
Further Reading
- Don't Repeat Yourself on the C2 Wiki
- Duplicated Code on SourceMaking
- Refactoring: Improving the Design of Existing Code by Martin Fowler. Duplicated Code, p76
Similar blocks of code found in 2 locations. Consider refactoring. Open
@@RESULT_DIRS = {
# Preprocessing
raw_reads: '01.raw_reads',
trimmed_reads: '02.trimmed_reads',
read_quality: '03.read_quality',
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Duplicated Code
Duplicated code can lead to software that is hard to understand and difficult to change. The Don't Repeat Yourself (DRY) principle states:
Every piece of knowledge must have a single, unambiguous, authoritative representation within a system.
When you violate DRY, bugs and maintenance problems are sure to follow. Duplicated code has a tendency to both continue to replicate and also to diverge (leaving bugs as two similar implementations differ in subtle ways).
Tuning
This issue has a mass of 28.
We set useful threshold defaults for the languages we support but you may want to adjust these settings based on your project guidelines.
The threshold configuration represents the minimum mass a code block must have to be analyzed for duplication. The lower the threshold, the more fine-grained the comparison.
If the engine is too easily reporting duplication, try raising the threshold. If you suspect that the engine isn't catching enough duplication, try lowering the threshold. The best setting tends to differ from language to language.
See codeclimate-duplication
's documentation for more information about tuning the mass threshold in your .codeclimate.yml
.
Refactorings
- Extract Method
- Extract Class
- Form Template Method
- Introduce Null Object
- Pull Up Method
- Pull Up Field
- Substitute Algorithm
Further Reading
- Don't Repeat Yourself on the C2 Wiki
- Duplicated Code on SourceMaking
- Refactoring: Improving the Design of Existing Code by Martin Fowler. Duplicated Code, p76
Similar blocks of code found in 2 locations. Consider refactoring. Open
when :result_dataset
opt.on(
'-r', '--result STRING',
'(Mandatory) Name of the result, one of:',
*MiGA::Dataset.RESULT_DIRS.keys.map { |n| " ~ #{n}" }
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Duplicated Code
Duplicated code can lead to software that is hard to understand and difficult to change. The Don't Repeat Yourself (DRY) principle states:
Every piece of knowledge must have a single, unambiguous, authoritative representation within a system.
When you violate DRY, bugs and maintenance problems are sure to follow. Duplicated code has a tendency to both continue to replicate and also to diverge (leaving bugs as two similar implementations differ in subtle ways).
Tuning
This issue has a mass of 27.
We set useful threshold defaults for the languages we support but you may want to adjust these settings based on your project guidelines.
The threshold configuration represents the minimum mass a code block must have to be analyzed for duplication. The lower the threshold, the more fine-grained the comparison.
If the engine is too easily reporting duplication, try raising the threshold. If you suspect that the engine isn't catching enough duplication, try lowering the threshold. The best setting tends to differ from language to language.
See codeclimate-duplication
's documentation for more information about tuning the mass threshold in your .codeclimate.yml
.
Refactorings
- Extract Method
- Extract Class
- Form Template Method
- Introduce Null Object
- Pull Up Method
- Pull Up Field
- Substitute Algorithm
Further Reading
- Don't Repeat Yourself on the C2 Wiki
- Duplicated Code on SourceMaking
- Refactoring: Improving the Design of Existing Code by Martin Fowler. Duplicated Code, p76
Similar blocks of code found in 2 locations. Consider refactoring. Open
when :result_project
opt.on(
'-r', '--result STRING',
'(Mandatory) Name of the result, one of:',
*MiGA::Project.RESULT_DIRS.keys.map { |n| " ~ #{n}" }
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Duplicated Code
Duplicated code can lead to software that is hard to understand and difficult to change. The Don't Repeat Yourself (DRY) principle states:
Every piece of knowledge must have a single, unambiguous, authoritative representation within a system.
When you violate DRY, bugs and maintenance problems are sure to follow. Duplicated code has a tendency to both continue to replicate and also to diverge (leaving bugs as two similar implementations differ in subtle ways).
Tuning
This issue has a mass of 27.
We set useful threshold defaults for the languages we support but you may want to adjust these settings based on your project guidelines.
The threshold configuration represents the minimum mass a code block must have to be analyzed for duplication. The lower the threshold, the more fine-grained the comparison.
If the engine is too easily reporting duplication, try raising the threshold. If you suspect that the engine isn't catching enough duplication, try lowering the threshold. The best setting tends to differ from language to language.
See codeclimate-duplication
's documentation for more information about tuning the mass threshold in your .codeclimate.yml
.
Refactorings
- Extract Method
- Extract Class
- Form Template Method
- Introduce Null Object
- Pull Up Method
- Pull Up Field
- Substitute Algorithm
Further Reading
- Don't Repeat Yourself on the C2 Wiki
- Duplicated Code on SourceMaking
- Refactoring: Improving the Design of Existing Code by Martin Fowler. Duplicated Code, p76
Similar blocks of code found in 2 locations. Consider refactoring. Open
rescue SQLite3::IOException => e
io_attempts += 1
raise "Database I/O error #{path}: #{e.message}" if io_attempts >= 3
sleep(1)
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Duplicated Code
Duplicated code can lead to software that is hard to understand and difficult to change. The Don't Repeat Yourself (DRY) principle states:
Every piece of knowledge must have a single, unambiguous, authoritative representation within a system.
When you violate DRY, bugs and maintenance problems are sure to follow. Duplicated code has a tendency to both continue to replicate and also to diverge (leaving bugs as two similar implementations differ in subtle ways).
Tuning
This issue has a mass of 25.
We set useful threshold defaults for the languages we support but you may want to adjust these settings based on your project guidelines.
The threshold configuration represents the minimum mass a code block must have to be analyzed for duplication. The lower the threshold, the more fine-grained the comparison.
If the engine is too easily reporting duplication, try raising the threshold. If you suspect that the engine isn't catching enough duplication, try lowering the threshold. The best setting tends to differ from language to language.
See codeclimate-duplication
's documentation for more information about tuning the mass threshold in your .codeclimate.yml
.
Refactorings
- Extract Method
- Extract Class
- Form Template Method
- Introduce Null Object
- Pull Up Method
- Pull Up Field
- Substitute Algorithm
Further Reading
- Don't Repeat Yourself on the C2 Wiki
- Duplicated Code on SourceMaking
- Refactoring: Improving the Design of Existing Code by Martin Fowler. Duplicated Code, p76
Similar blocks of code found in 2 locations. Consider refactoring. Open
rescue SQLite3::BusyException => e
busy_attempts += 1
raise "Database busy #{path}: #{e.message}" if busy_attempts >= 3
sleep(1)
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Duplicated Code
Duplicated code can lead to software that is hard to understand and difficult to change. The Don't Repeat Yourself (DRY) principle states:
Every piece of knowledge must have a single, unambiguous, authoritative representation within a system.
When you violate DRY, bugs and maintenance problems are sure to follow. Duplicated code has a tendency to both continue to replicate and also to diverge (leaving bugs as two similar implementations differ in subtle ways).
Tuning
This issue has a mass of 25.
We set useful threshold defaults for the languages we support but you may want to adjust these settings based on your project guidelines.
The threshold configuration represents the minimum mass a code block must have to be analyzed for duplication. The lower the threshold, the more fine-grained the comparison.
If the engine is too easily reporting duplication, try raising the threshold. If you suspect that the engine isn't catching enough duplication, try lowering the threshold. The best setting tends to differ from language to language.
See codeclimate-duplication
's documentation for more information about tuning the mass threshold in your .codeclimate.yml
.
Refactorings
- Extract Method
- Extract Class
- Form Template Method
- Introduce Null Object
- Pull Up Method
- Pull Up Field
- Substitute Algorithm
Further Reading
- Don't Repeat Yourself on the C2 Wiki
- Duplicated Code on SourceMaking
- Refactoring: Improving the Design of Existing Code by Martin Fowler. Duplicated Code, p76
Missing magic comment # frozen_string_literal: true
. Open
#!/usr/bin/env ruby
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- Exclude checks
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
Use the new Ruby 1.9 hash syntax. Open
task :test => 'test:all'
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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}
Missing magic comment # frozen_string_literal: true
. Open
require 'test_helper'
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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
Use Hash#key?
instead of Hash#has_key?
. Open
assert { MiGA::Dataset.KNOWN_TYPES.has_key?(:genome) }
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This cop (by default) checks for uses of methods Hash#haskey? and
Hash#hasvalue? where it enforces Hash#key? and Hash#value?
It is configurable to enforce the inverse, using verbose
method
names also.
Example: EnforcedStyle: short (default)
# bad Hash#haskey? Hash#hasvalue?
# good Hash#key? Hash#value?
Example: EnforcedStyle: verbose
# bad Hash#key? Hash#value?
# good Hash#haskey? Hash#hasvalue?
Add parentheses to nested method call o.is_a? Integer
. Open
assert(o.is_a? Integer)
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This cop checks for unparenthesized method calls in the argument list of a parenthesized method call.
Example:
# good
method1(method2(arg), method3(arg))
# bad
method1(method2 arg, method3, arg)
Add parentheses to nested method call u.is_a? URI
. Open
assert(u.is_a? URI)
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- Exclude checks
This cop checks for unparenthesized method calls in the argument list of a parenthesized method call.
Example:
# good
method1(method2(arg), method3(arg))
# bad
method1(method2 arg, method3, arg)
Add parentheses to nested method call h.is_a? Hash
. Open
assert(h.is_a? Hash)
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- Exclude checks
This cop checks for unparenthesized method calls in the argument list of a parenthesized method call.
Example:
# good
method1(method2(arg), method3(arg))
# bad
method1(method2 arg, method3, arg)
1 trailing blank lines detected. Open
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Missing magic comment # frozen_string_literal: true
. Open
require 'test_helper'
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- Exclude checks
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
Prefer to_s
over string interpolation. Open
t2 = "#{t1}"
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This cop checks for strings that are just an interpolated expression.
Example:
# bad
"#{@var}"
# good
@var.to_s
# good if @var is already a String
@var
Missing magic comment # frozen_string_literal: true
. Open
require 'bundler/gem_tasks'
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- Exclude checks
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
Missing magic comment # frozen_string_literal: true
. Open
require 'test_helper'
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- Create a ticketCreate a ticket
- Exclude checks
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
Do not use attr
. Use attr_reader
instead. Open
attr :daemon_home
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This cop checks for uses of Module#attr.
Example:
# bad - creates a single attribute accessor (deprecated in Ruby 1.9)
attr :something, true
attr :one, :two, :three # behaves as attr_reader
# good
attr_accessor :something
attr_reader :one, :two, :three
Align .map
with {
on line 154. Open
.map do |x|
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This cop checks the indentation of the method name part in method calls that span more than one line.
Example: EnforcedStyle: aligned
# bad
while myvariable
.b
# do something
end
# good
while myvariable
.b
# do something
end
# good
Thing.a
.b
.c
Example: EnforcedStyle: indented
# good
while myvariable
.b
# do something
end
Example: EnforcedStyle: indentedrelativeto_receiver
# good
while myvariable
.a
.b
# do something
end
# good
myvariable = Thing
.a
.b
.c