SpeciesFileGroup/taxonworks

View on GitHub

Showing 12,628 of 12,628 total issues

Prefer symbols instead of strings as hash keys.
Open

      'isosyntypes' => Lot
Severity: Minor
Found in app/models/type_material.rb by rubocop

This cop checks for the use of strings as keys in hashes. The use of symbols is preferred instead.

Example:

# bad
{ 'one' => 1, 'two' => 2, 'three' => 3 }

# good
{ one: 1, two: 2, three: 3 }

Use 2 (not 0) spaces for indentation.
Open

  NOMEN_URI='http://purl.obolibrary.org/obo/NOMEN_0000198'.freeze

This cop checks for indentation that doesn't use the specified number of spaces.

See also the IndentationConsistency cop which is the companion to this one.

Example:

# bad
class A
 def test
  puts 'hello'
 end
end

# good
class A
  def test
    puts 'hello'
  end
end

Example: IgnoredPatterns: ['^\s*module']

# bad
module A
class B
  def test
  puts 'hello'
  end
end
end

# good
module A
class B
  def test
    puts 'hello'
  end
end
end

Prefer the new style validations validates :column, uniqueness: value over validates_uniqueness_of.
Open

  validates_uniqueness_of :taxon_name_id

This cop checks for the use of old-style attribute validation macros.

Example:

# bad
validates_acceptance_of :foo
validates_confirmation_of :foo
validates_exclusion_of :foo
validates_format_of :foo
validates_inclusion_of :foo
validates_length_of :foo
validates_numericality_of :foo
validates_presence_of :foo
validates_absence_of :foo
validates_size_of :foo
validates_uniqueness_of :foo

# good
validates :foo, acceptance: true
validates :foo, confirmation: true
validates :foo, exclusion: true
validates :foo, format: true
validates :foo, inclusion: true
validates :foo, length: true
validates :foo, numericality: true
validates :foo, presence: true
validates :foo, absence: true
validates :foo, size: true
validates :foo, uniqueness: true

Please use Rails.root.join('path', 'to') instead.
Open

  Dir.glob("#{Rails.root.join("app/models/taxon_name_relationship/**/*.rb")}")

This cop is used to identify usages of file path joining process to use Rails.root.join clause. It is used to add uniformity when joining paths.

Example: EnforcedStyle: arguments (default)

# bad
Rails.root.join('app/models/goober')
File.join(Rails.root, 'app/models/goober')
"#{Rails.root}/app/models/goober"

# good
Rails.root.join('app', 'models', 'goober')

Example: EnforcedStyle: slashes

# bad
Rails.root.join('app', 'models', 'goober')
File.join(Rails.root, 'app/models/goober')
"#{Rails.root}/app/models/goober"

# good
Rails.root.join('app/models/goober')

Please use Rails.root.join('path', 'to') instead.
Open

  Dir.glob("#{Rails.root.join("app/models/taxon_name_relationship/**/*.rb")}")

This cop is used to identify usages of file path joining process to use Rails.root.join clause. It is used to add uniformity when joining paths.

Example: EnforcedStyle: arguments (default)

# bad
Rails.root.join('app/models/goober')
File.join(Rails.root, 'app/models/goober')
"#{Rails.root}/app/models/goober"

# good
Rails.root.join('app', 'models', 'goober')

Example: EnforcedStyle: slashes

# bad
Rails.root.join('app', 'models', 'goober')
File.join(Rails.root, 'app/models/goober')
"#{Rails.root}/app/models/goober"

# good
Rails.root.join('app/models/goober')

Avoid using update_column because it skips validations.
Open

          t.update_column(:cached_misspelling, t.get_cached_misspelling)

This cop checks for the use of methods which skip validations which are listed in https://guides.rubyonrails.org/active_record_validations.html#skipping-validations

Methods may be ignored from this rule by configuring a Whitelist.

Example:

# bad
Article.first.decrement!(:view_count)
DiscussionBoard.decrement_counter(:post_count, 5)
Article.first.increment!(:view_count)
DiscussionBoard.increment_counter(:post_count, 5)
person.toggle :active
product.touch
Billing.update_all("category = 'authorized', author = 'David'")
user.update_attribute(:website, 'example.com')
user.update_columns(last_request_at: Time.current)
Post.update_counters 5, comment_count: -1, action_count: 1

# good
user.update(website: 'example.com')
FileUtils.touch('file')

Example: Whitelist: ["touch"]

# bad
DiscussionBoard.decrement_counter(:post_count, 5)
DiscussionBoard.increment_counter(:post_count, 5)
person.toggle :active

# good
user.touch

Prefer the new style validations validates :column, uniqueness: value over validates_uniqueness_of.
Open

  validates_uniqueness_of :object_taxon_name_id, scope: [:type, :project_id], if: :is_combination?

This cop checks for the use of old-style attribute validation macros.

Example:

# bad
validates_acceptance_of :foo
validates_confirmation_of :foo
validates_exclusion_of :foo
validates_format_of :foo
validates_inclusion_of :foo
validates_length_of :foo
validates_numericality_of :foo
validates_presence_of :foo
validates_absence_of :foo
validates_size_of :foo
validates_uniqueness_of :foo

# good
validates :foo, acceptance: true
validates :foo, confirmation: true
validates :foo, exclusion: true
validates :foo, format: true
validates :foo, inclusion: true
validates :foo, length: true
validates :foo, numericality: true
validates :foo, presence: true
validates :foo, absence: true
validates :foo, size: true
validates :foo, uniqueness: true

Use s.cached_original_combination.present? instead of !s.cached_original_combination.blank?.
Open

    if !s.cached_original_combination.blank? && s.cached_original_combination == o.cached_original_combination

This cop checks for code that can be written with simpler conditionals using Object#present? defined by Active Support.

Interaction with Style/UnlessElse: The configuration of NotBlank will not produce an offense in the context of unless else if Style/UnlessElse is inabled. This is to prevent interference between the auto-correction of the two cops.

Example: NotNilAndNotEmpty: true (default)

# Converts usages of `!nil? && !empty?` to `present?`

# bad
!foo.nil? && !foo.empty?

# bad
foo != nil && !foo.empty?

# good
foo.present?

Example: NotBlank: true (default)

# Converts usages of `!blank?` to `present?`

# bad
!foo.blank?

# bad
not foo.blank?

# good
foo.present?

Example: UnlessBlank: true (default)

# Converts usages of `unless blank?` to `if present?`

# bad
something unless foo.blank?

# good
something if foo.present?

unexpected token tCOMMA (Using Ruby 2.4 parser; configure using TargetRubyVersion parameter, under AllCops)
Open

    TaxonName.where(project_id:, updated_by_id: user_id)
Severity: Minor
Found in app/models/taxon_name.rb by rubocop

This is not actually a cop. It does not inspect anything. It just provides methods to repack Parser's diagnostics/errors into RuboCop's offenses.

unexpected token tRPAREN (Using Ruby 2.4 parser; configure using TargetRubyVersion parameter, under AllCops)
Open

      if !parent_is_set? && TaxonName.where(parent_id: nil, project_id:).count > 0
Severity: Minor
Found in app/models/taxon_name.rb by rubocop

This is not actually a cop. It does not inspect anything. It just provides methods to repack Parser's diagnostics/errors into RuboCop's offenses.

unexpected token tRPAREN (Using Ruby 2.4 parser; configure using TargetRubyVersion parameter, under AllCops)
Open

      s = 'WITH tn_anc AS (' + taxon_name_ancestors_sql(taxon_name_scope: tns.all, ranks: ) + '), otu_limit AS (' + otu_scope.select(:id).to_sql + ')' +
Severity: Minor
Found in app/models/taxon_name/hierarchy.rb by rubocop

This is not actually a cop. It does not inspect anything. It just provides methods to repack Parser's diagnostics/errors into RuboCop's offenses.

Avoid using update_columns because it skips validations.
Open

          vn.update_columns(

This cop checks for the use of methods which skip validations which are listed in https://guides.rubyonrails.org/active_record_validations.html#skipping-validations

Methods may be ignored from this rule by configuring a Whitelist.

Example:

# bad
Article.first.decrement!(:view_count)
DiscussionBoard.decrement_counter(:post_count, 5)
Article.first.increment!(:view_count)
DiscussionBoard.increment_counter(:post_count, 5)
person.toggle :active
product.touch
Billing.update_all("category = 'authorized', author = 'David'")
user.update_attribute(:website, 'example.com')
user.update_columns(last_request_at: Time.current)
Post.update_counters 5, comment_count: -1, action_count: 1

# good
user.update(website: 'example.com')
FileUtils.touch('file')

Example: Whitelist: ["touch"]

# bad
DiscussionBoard.decrement_counter(:post_count, 5)
DiscussionBoard.increment_counter(:post_count, 5)
person.toggle :active

# good
user.touch

Avoid using update_columns because it skips validations.
Open

            c.update_columns(cached_valid_taxon_name_id: vn.id)

This cop checks for the use of methods which skip validations which are listed in https://guides.rubyonrails.org/active_record_validations.html#skipping-validations

Methods may be ignored from this rule by configuring a Whitelist.

Example:

# bad
Article.first.decrement!(:view_count)
DiscussionBoard.decrement_counter(:post_count, 5)
Article.first.increment!(:view_count)
DiscussionBoard.increment_counter(:post_count, 5)
person.toggle :active
product.touch
Billing.update_all("category = 'authorized', author = 'David'")
user.update_attribute(:website, 'example.com')
user.update_columns(last_request_at: Time.current)
Post.update_counters 5, comment_count: -1, action_count: 1

# good
user.update(website: 'example.com')
FileUtils.touch('file')

Example: Whitelist: ["touch"]

# bad
DiscussionBoard.decrement_counter(:post_count, 5)
DiscussionBoard.increment_counter(:post_count, 5)
person.toggle :active

# good
user.touch

Use 2 (not 0) spaces for indentation.
Open

  NOMEN_URI='http://purl.obolibrary.org/obo/NOMEN_0000211'.freeze

This cop checks for indentation that doesn't use the specified number of spaces.

See also the IndentationConsistency cop which is the companion to this one.

Example:

# bad
class A
 def test
  puts 'hello'
 end
end

# good
class A
  def test
    puts 'hello'
  end
end

Example: IgnoredPatterns: ['^\s*module']

# bad
module A
class B
  def test
  puts 'hello'
  end
end
end

# good
module A
class B
  def test
    puts 'hello'
  end
end
end

Use 2 (not 0) spaces for indentation.
Open

  NOMEN_URI='http://purl.obolibrary.org/obo/NOMEN_0000172'.freeze

This cop checks for indentation that doesn't use the specified number of spaces.

See also the IndentationConsistency cop which is the companion to this one.

Example:

# bad
class A
 def test
  puts 'hello'
 end
end

# good
class A
  def test
    puts 'hello'
  end
end

Example: IgnoredPatterns: ['^\s*module']

# bad
module A
class B
  def test
  puts 'hello'
  end
end
end

# good
module A
class B
  def test
    puts 'hello'
  end
end
end

Use save! instead of save if the return value is not checked.
Open

          self.save

This cop identifies possible cases where Active Record save! or related should be used instead of save because the model might have failed to save and an exception is better than unhandled failure.

This will allow: - update or save calls, assigned to a variable, or used as a condition in an if/unless/case statement. - create calls, assigned to a variable that then has a call to persisted?. - calls if the result is explicitly returned from methods and blocks, or provided as arguments. - calls whose signature doesn't look like an ActiveRecord persistence method.

By default it will also allow implicit returns from methods and blocks. that behavior can be turned off with AllowImplicitReturn: false.

You can permit receivers that are giving false positives with AllowedReceivers: []

Example:

# bad
user.save
user.update(name: 'Joe')
user.find_or_create_by(name: 'Joe')
user.destroy

# good
unless user.save
  # ...
end
user.save!
user.update!(name: 'Joe')
user.find_or_create_by!(name: 'Joe')
user.destroy!

user = User.find_or_create_by(name: 'Joe')
unless user.persisted?
  # ...
end

def save_user
  return user.save
end

Example: AllowImplicitReturn: true (default)

# good
users.each { |u| u.save }

def save_user
  user.save
end

Example: AllowImplicitReturn: false

# bad
users.each { |u| u.save }
def save_user
  user.save
end

# good
users.each { |u| u.save! }

def save_user
  user.save!
end

def save_user
  return user.save
end

Example: AllowedReceivers: ['merchant.customers', 'Service::Mailer']

# bad
merchant.create
customers.builder.save
Mailer.create

module Service::Mailer
  self.create
end

# good
merchant.customers.create
MerchantService.merchant.customers.destroy
Service::Mailer.update(message: 'Message')
::Service::Mailer.update
Services::Service::Mailer.update(message: 'Message')
Service::Mailer::update

Prefer the new style validations validates :column, presence: value over validates_presence_of.
Open

  validates_presence_of :object_taxon_name, message: 'Missing taxon name on the right side'

This cop checks for the use of old-style attribute validation macros.

Example:

# bad
validates_acceptance_of :foo
validates_confirmation_of :foo
validates_exclusion_of :foo
validates_format_of :foo
validates_inclusion_of :foo
validates_length_of :foo
validates_numericality_of :foo
validates_presence_of :foo
validates_absence_of :foo
validates_size_of :foo
validates_uniqueness_of :foo

# good
validates :foo, acceptance: true
validates :foo, confirmation: true
validates :foo, exclusion: true
validates :foo, format: true
validates :foo, inclusion: true
validates :foo, length: true
validates :foo, numericality: true
validates :foo, presence: true
validates :foo, absence: true
validates :foo, size: true
validates :foo, uniqueness: true

Use find_by instead of where.first.
Open

    r2 = TaxonNameRelationship.where(type: 'TaxonNameRelationship::Iczn::Invalidating::Synonym::Objective::UnnecessaryReplacementName', subject_taxon_name_id: s.id, object_taxon_name_id: o.id).first

This cop is used to identify usages of where.first and change them to use find_by instead.

Example:

# bad
User.where(name: 'Bruce').first
User.where(name: 'Bruce').take

# good
User.find_by(name: 'Bruce')

Prefer symbols instead of strings as hash keys.
Open

    'paralectotype' => Specimen,
Severity: Minor
Found in app/models/type_material.rb by rubocop

This cop checks for the use of strings as keys in hashes. The use of symbols is preferred instead.

Example:

# bad
{ 'one' => 1, 'two' => 2, 'three' => 3 }

# good
{ one: 1, two: 2, three: 3 }

Prefer symbols instead of strings as hash keys.
Open

    'neotype' => Specimen,
Severity: Minor
Found in app/models/type_material.rb by rubocop

This cop checks for the use of strings as keys in hashes. The use of symbols is preferred instead.

Example:

# bad
{ 'one' => 1, 'two' => 2, 'three' => 3 }

# good
{ one: 1, two: 2, three: 3 }
Severity
Category
Status
Source
Language