bio-miga/miga

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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'
  }
Severity: Minor
Found in lib/miga/taxonomy/base.rb and 1 other location - About 20 mins to fix
lib/miga/dataset/base.rb on lines 66..84

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

Further Reading

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',
Severity: Minor
Found in lib/miga/dataset/base.rb and 1 other location - About 20 mins to fix
lib/miga/taxonomy/base.rb on lines 46..50

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

Further Reading

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}" }
Severity: Minor
Found in lib/miga/cli/opt_helper.rb and 1 other location - About 20 mins to fix
lib/miga/cli/opt_helper.rb on lines 106..111

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

Further Reading

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}" }
Severity: Minor
Found in lib/miga/cli/opt_helper.rb and 1 other location - About 20 mins to fix
lib/miga/cli/opt_helper.rb on lines 100..105

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

Further Reading

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)
Severity: Minor
Found in lib/miga/sqlite.rb and 1 other location - About 15 mins to fix
lib/miga/sqlite.rb on lines 58..70

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

Further Reading

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)
Severity: Minor
Found in lib/miga/sqlite.rb and 1 other location - About 15 mins to fix
lib/miga/sqlite.rb on lines 64..70

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

Further Reading

Missing magic comment # frozen_string_literal: true.
Open

#!/usr/bin/env ruby
Severity: Minor
Found in bin/miga by rubocop

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'
Severity: Minor
Found in Rakefile 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}

Missing magic comment # frozen_string_literal: true.
Open

require 'test_helper'
Severity: Minor
Found in test/dataset_test.rb by rubocop

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) }
Severity: Minor
Found in test/dataset_test.rb by rubocop

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)
Severity: Minor
Found in test/system_call_test.rb by rubocop

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)
Severity: Minor
Found in test/remote_dataset_test.rb by rubocop

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)
Severity: Minor
Found in test/remote_dataset_test.rb by rubocop

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

Severity: Minor
Found in bin/miga by rubocop

Missing magic comment # frozen_string_literal: true.
Open

require 'test_helper'
Severity: Minor
Found in test/project_test.rb by rubocop

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}"
Severity: Minor
Found in test/net_test.rb by rubocop

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'
Severity: Minor
Found in Rakefile by rubocop

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'
Severity: Minor
Found in test/format_test.rb by rubocop

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
Severity: Minor
Found in test/with_daemon_test.rb by rubocop

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|
Severity: Minor
Found in test/dataset_test.rb by rubocop

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
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