SpeciesFileGroup/taxonworks

View on GitHub

Showing 12,628 of 12,628 total issues

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

    object.nil? ? SqedDepiction.where(project_id:).order(id: :asc).first : object
Severity: Minor
Found in app/models/sqed_depiction.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 tCOLON (Using Ruby 2.4 parser; configure using TargetRubyVersion parameter, under AllCops)
Open

    object.nil? ? SqedDepiction.where(project_id:).order(id: :asc).first : object
Severity: Minor
Found in app/models/sqed_depiction.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

  scope :with_cached_valid_taxon_name_id, -> (cached_valid_taxon_name_id) {where(cached_valid_taxon_name_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 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.

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

      a = klass.is_species_group.touched_by(user_id).where(project_id:).order(updated_at: :desc).limit(6).to_a
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

    mri = ObservationMatrixRowItem::TaxonNameRowItem.where(taxon_name_id: id, project_id:).limit(1)
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

            t1.update_column(:verbatim_name, t1.cached) if t1.verbatim_name.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

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

  validates_uniqueness_of :taxon_name_id, scope: [:type, :project_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

Use 2 (not 4) spaces for indentation.
Open

      soft_validations.add(:type, 'Please specify if the name is Valid or Invalid')

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 :object_taxon_name_id, scope: :type

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

Do not use to_time on Date objects, because they know nothing about the time zone in use.
Open

      date1 = self.source.cached_nomenclature_date.to_time

This cop checks for the correct use of Date methods, such as Date.today, Date.current etc.

Using Date.today is dangerous, because it doesn't know anything about Rails time zone. You must use Time.zone.today instead.

The cop also reports warnings when you are using to_time method, because it doesn't know about Rails time zone either.

Two styles are supported for this cop. When EnforcedStyle is 'strict' then the Date methods today, current, yesterday, and tomorrow are prohibited and the usage of both to_time and 'totimeincurrentzone' are reported as warning.

When EnforcedStyle is 'flexible' then only Date.today is prohibited and only to_time is reported as warning.

Example: EnforcedStyle: strict

# bad
Date.current
Date.yesterday
Date.today
date.to_time

# good
Time.zone.today
Time.zone.today - 1.day

Example: EnforcedStyle: flexible (default)

# bad
Date.today
date.to_time

# good
Time.zone.today
Time.zone.today - 1.day
Date.current
Date.yesterday
date.in_time_zone

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, uniqueness: value over validates_uniqueness_of.
Open

  validates_uniqueness_of :subject_taxon_name_id, scope: [:type, :object_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

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

  validates_uniqueness_of :subject_taxon_name_id, scope: [:type, :object_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

Use find_by instead of where.first.
Open

    tr = TaxonNameRelationship::Iczn::Invalidating::Synonym::Objective::ReplacedHomonym.where(object_taxon_name_id: subject_taxon_name_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 the new style validations validates :column, uniqueness: value over validates_uniqueness_of.
Open

  validates_uniqueness_of :object_taxon_name_id, scope: :type

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

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

      h[:quick] = (Topic.pinned_by(user_id).pinboard_inserted.where(project_id:).to_a +
Severity: Minor
Found in app/models/topic.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

      a = klass.touched_by(user_id).where(project_id:).order(updated_at: :desc).limit(6).to_a
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_columns because it skips validations.
Open

            s.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

Use 2 (not 0) spaces for indentation.
Open

  NOMEN_URI='http://purl.obolibrary.org/obo/NOMEN_0000195'.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
Severity
Category
Status
Source
Language