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app/models/biological_relationship.rb

Summary

Maintainability
A
1 hr
Test Coverage

Specify a :dependent option.
Open

  has_many :biological_associations, inverse_of: :biological_relationship

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

Specify an :inverse_of option.
Open

  has_many :object_biological_relationship_types, -> () {where(type: 'BiologicalRelationshipType::BiologicalRelationshipObjectType')}, class_name: 'BiologicalRelationshipType', dependent: :destroy

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

Specify a :dependent option.
Open

  has_many :biological_relationship_types, inverse_of: :biological_relationship

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

Specify an :inverse_of option.
Open

  has_many :subject_biological_relationship_types, -> () {where(type: 'BiologicalRelationshipType::BiologicalRelationshipSubjectType')}, class_name: 'BiologicalRelationshipType', dependent: :destroy

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

Similar blocks of code found in 2 locations. Consider refactoring.
Open

  def self.used_recently(user_id, project_id)
    t = BiologicalAssociation.arel_table
    k = BiologicalRelationship.arel_table 

    # i is a select manager
Severity: Major
Found in app/models/biological_relationship.rb and 1 other location - About 1 hr to fix
app/models/repository.rb on lines 55..71

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 70.

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

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

  validates_presence_of :name

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

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