SpeciesFileGroup/taxonworks

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Specify a :dependent option.
Open

  has_many :gene_attributes, inverse_of: :sequence
Severity: Minor
Found in app/models/sequence.rb by rubocop

This cop looks for has_many or has_one associations that don't specify a :dependent option. It doesn't register an offense if :through option was specified.

Example:

# bad
class User < ActiveRecord::Base
  has_many :comments
  has_one :avatar
end

# good
class User < ActiveRecord::Base
  has_many :comments, dependent: :restrict_with_exception
  has_one :avatar, dependent: :destroy
  has_many :patients, through: :appointments
end

Prefer 1.month.
Open

      .where(t['updated_at'].gt(1.months.ago))
Severity: Minor
Found in app/models/serial.rb by rubocop

This cop checks for correct grammar when using ActiveSupport's core extensions to the numeric classes.

Example:

# bad
3.day.ago
1.months.ago

# good
3.days.ago
1.month.ago

Use depiction_params.present? instead of depiction_params && !depiction_params.empty?.
Open

    if depiction_params && !depiction_params.empty?
Severity: Minor
Found in app/models/sled_image.rb by rubocop

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

    if siblings.where(project_id:).any?
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.

Avoid using update_column because it skips validations.
Open

          r.update_column(:subject_taxon_name_id, o.id)
Severity: Minor
Found in app/models/protonym/becomes.rb by rubocop

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 more than 3 levels of block nesting.
Open

            name2 = self.cached_primary_homonym_alternative_spelling ? self.cached_primary_homonym_alternative_spelling : nil

This cop checks for excessive nesting of conditional and looping constructs.

You can configure if blocks are considered using the CountBlocks option. When set to false (the default) blocks are not counted towards the nesting level. Set to true to count blocks as well.

The maximum level of nesting allowed is configurable.

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

        otus.create(taxon_name_id: id)

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

Avoid using update_column because it skips validations.
Open

          self.update_column(:year_of_publication, t.year_of_publication)

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, presence: value over validates_presence_of.
Open

  validates_presence_of :name, :minimum_value
Severity: Minor
Found in app/models/ranged_lot_category.rb by rubocop

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

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

  validates_uniqueness_of :name, scope: [:project_id]
Severity: Minor
Found in app/models/ranged_lot_category.rb by rubocop

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

Specify an :inverse_of option.
Open

  belongs_to :translated_from_serial, foreign_key: :translated_from_serial_id, class_name: 'Serial'
Severity: Minor
Found in app/models/serial.rb by rubocop

This cop looks for has(one|many) and belongsto associations where Active Record can't automatically determine the inverse association because of a scope or the options used. Using the blog with order scope example below, traversing the a Blog's association in both directions with blog.posts.first.blog would cause the blog to be loaded from the database twice.

:inverse_of must be manually specified for Active Record to use the associated object in memory, or set to false to opt-out. Note that setting nil does not stop Active Record from trying to determine the inverse automatically, and is not considered a valid value for this.

Example:

# good
class Blog < ApplicationRecord
  has_many :posts
end

class Post < ApplicationRecord
  belongs_to :blog
end

Example:

# bad
class Blog < ApplicationRecord
  has_many :posts, -> { order(published_at: :desc) }
end

class Post < ApplicationRecord
  belongs_to :blog
end

# good
class Blog < ApplicationRecord
  has_many(:posts,
           -> { order(published_at: :desc) },
           inverse_of: :blog)
end

class Post < ApplicationRecord
  belongs_to :blog
end

# good
class Blog < ApplicationRecord
  with_options inverse_of: :blog do
    has_many :posts, -> { order(published_at: :desc) }
  end
end

class Post < ApplicationRecord
  belongs_to :blog
end

# good
# When you don't want to use the inverse association.
class Blog < ApplicationRecord
  has_many(:posts,
           -> { order(published_at: :desc) },
           inverse_of: false)
end

Example:

# bad
class Picture < ApplicationRecord
  belongs_to :imageable, polymorphic: true
end

class Employee < ApplicationRecord
  has_many :pictures, as: :imageable
end

class Product < ApplicationRecord
  has_many :pictures, as: :imageable
end

# good
class Picture < ApplicationRecord
  belongs_to :imageable, polymorphic: true
end

class Employee < ApplicationRecord
  has_many :pictures, as: :imageable, inverse_of: :imageable
end

class Product < ApplicationRecord
  has_many :pictures, as: :imageable, inverse_of: :imageable
end

Example:

# bad
# However, RuboCop can not detect this pattern...
class Physician < ApplicationRecord
  has_many :appointments
  has_many :patients, through: :appointments
end

class Appointment < ApplicationRecord
  belongs_to :physician
  belongs_to :patient
end

class Patient < ApplicationRecord
  has_many :appointments
  has_many :physicians, through: :appointments
end

# good
class Physician < ApplicationRecord
  has_many :appointments
  has_many :patients, through: :appointments
end

class Appointment < ApplicationRecord
  belongs_to :physician, inverse_of: :appointments
  belongs_to :patient, inverse_of: :appointments
end

class Patient < ApplicationRecord
  has_many :appointments
  has_many :physicians, through: :appointments
end

@see https://guides.rubyonrails.org/association_basics.html#bi-directional-associations @see https://api.rubyonrails.org/classes/ActiveRecord/Associations/ClassMethods.html#module-ActiveRecord::Associations::ClassMethods-label-Setting+Inverses

else without rescue is useless (Using Ruby 2.4 parser; configure using TargetRubyVersion parameter, under AllCops)
Open

    else
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.

Avoid more than 3 levels of block nesting.
Open

            if !list2.empty?
              list2.each do |s|
                soft_validations.add(:base, "Missing relationship: #{self.cached_html_name_and_author_year} should be a homonym or duplicate of #{s.cached_html_name_and_author_year}")
              end
            end

This cop checks for excessive nesting of conditional and looping constructs.

You can configure if blocks are considered using the CountBlocks option. When set to false (the default) blocks are not counted towards the nesting level. Set to true to count blocks as well.

The maximum level of nesting allowed is configurable.

Avoid more than 3 levels of block nesting.
Open

            possible_primary_homonyms = name1 ? Protonym.with_primary_homonym(name1).without_taxon_name_classification_array(TAXON_NAME_CLASS_NAMES_UNAVAILABLE_AND_INVALID).without_homonym_or_suppressed.not_self(self).with_base_of_rank_class('NomenclaturalRank::Iczn::GenusGroup').with_project(self.project_id) : []

This cop checks for excessive nesting of conditional and looping constructs.

You can configure if blocks are considered using the CountBlocks option. When set to false (the default) blocks are not counted towards the nesting level. Set to true to count blocks as well.

The maximum level of nesting allowed is configurable.

Avoid using update_column because it skips validations.
Open

      self.update_column(:year_of_publication, nil)

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 s['metadata'].present? instead of !s['metadata'].blank?.
Open

      next if !s['metadata'].blank? || _first_identifier.nil?
Severity: Minor
Found in app/models/sled_image.rb by rubocop

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?

Use v.present? instead of !v.blank?.
Open

      errors.add(k, 'can not be provided to a verbatim reference') if !v.blank?
Severity: Minor
Found in app/models/source/verbatim.rb by rubocop

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?

Avoid using update_columns because it skips validations.
Open

        update_columns(b)
Severity: Minor
Found in app/models/source/verbatim.rb by rubocop

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

find_or_create_by returns a model which is always truthy.
Open

    !!ProjectSource.find_or_create_by(project: project, source: tag_object)
Severity: Minor
Found in app/models/tag.rb by rubocop

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

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

      .where(td: {id:} )
Severity: Minor
Found in app/models/taxon_determination.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.

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Status
Source
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