Class: GeneAttribute

Inherits:
ApplicationRecord show all
Includes:
Housekeeping, Shared::Identifiers, Shared::IsData, Shared::Notes, Shared::Tags
Defined in:
app/models/gene_attribute.rb

Overview

A GeneAttribute defines an attribute that must be matched for a Sequence to be classified as a Descriptor::Gene. There are two key attributes, sequence, and sequence relationship. A GeneAttribute will return all sequences who are the object of a taxon name relationship whose subject is Sequence and whose Type is #sequence_relationship_type

! Deprecated?

Instance Attribute Summary collapse

Instance Method Summary collapse

Methods included from Shared::IsData

#errors_excepting, #full_error_messages_excepting, #identical, #is_community?, #is_destroyable?, #is_editable?, #is_in_use?, #is_in_users_projects?, #metamorphosize, #similar

Methods included from Shared::Tags

#reject_tags, #tag_with, #tagged?, #tagged_with?

Methods included from Shared::Notes

#concatenated_notes_string, #reject_notes

Methods included from Shared::Identifiers

#dwc_occurrence_id, #identified?, #next_by_identifier, #previous_by_identifier, #reject_identifiers, #uri, #uuid

Methods included from Housekeeping

#has_polymorphic_relationship?

Methods inherited from ApplicationRecord

transaction_with_retry

Instance Attribute Details

#controlled_vocabulary_term_id ⇒ Integer

Returns not yet implemented, intent/idea is to define a subclass of CVT that represents GO terms.

Returns:

  • (Integer) —

    not yet implemented, intent/idea is to define a subclass of CVT that represents GO terms.



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# File 'app/models/gene_attribute.rb', line 26

class GeneAttribute < ApplicationRecord
  include Housekeeping
  include Shared::Identifiers
  include Shared::Notes
  include Shared::Tags
  include Shared::IsData

  acts_as_list scope: [:descriptor_id, :project_id]

  belongs_to :descriptor, class_name: 'Descriptor::Gene', inverse_of: :gene_attributes
  belongs_to :sequence, inverse_of: :gene_attributes

  # Not yet implemented.
  # Deprecated: Use Tag/Keyword
  # belongs_to :controlled_vocabulary_term

  validates :descriptor, presence: true
  validates :sequence, presence: true

  validates_uniqueness_of :sequence, scope: [:descriptor, :sequence_relationship_type]

  after_save :add_to_descriptor_logic_if_absent

  def to_logic_literal
    "#{sequence_relationship_type}.#{sequence_id}"
  end

  protected

  def add_to_descriptor_logic_if_absent 
    descriptor.extend_gene_attribute_logic(self, :and) unless descriptor.contains_logic_for?(self)
  end

end

#descriptor_id ⇒ Integer

Returns the descriptor id (Gene) that this attribute defines.

Returns:

  • (Integer) —

    the descriptor id (Gene) that this attribute defines



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# File 'app/models/gene_attribute.rb', line 26

class GeneAttribute < ApplicationRecord
  include Housekeeping
  include Shared::Identifiers
  include Shared::Notes
  include Shared::Tags
  include Shared::IsData

  acts_as_list scope: [:descriptor_id, :project_id]

  belongs_to :descriptor, class_name: 'Descriptor::Gene', inverse_of: :gene_attributes
  belongs_to :sequence, inverse_of: :gene_attributes

  # Not yet implemented.
  # Deprecated: Use Tag/Keyword
  # belongs_to :controlled_vocabulary_term

  validates :descriptor, presence: true
  validates :sequence, presence: true

  validates_uniqueness_of :sequence, scope: [:descriptor, :sequence_relationship_type]

  after_save :add_to_descriptor_logic_if_absent

  def to_logic_literal
    "#{sequence_relationship_type}.#{sequence_id}"
  end

  protected

  def add_to_descriptor_logic_if_absent 
    descriptor.extend_gene_attribute_logic(self, :and) unless descriptor.contains_logic_for?(self)
  end

end

#project_id ⇒ Integer

the project ID

Returns:

  • (Integer) 


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# File 'app/models/gene_attribute.rb', line 26

class GeneAttribute < ApplicationRecord
  include Housekeeping
  include Shared::Identifiers
  include Shared::Notes
  include Shared::Tags
  include Shared::IsData

  acts_as_list scope: [:descriptor_id, :project_id]

  belongs_to :descriptor, class_name: 'Descriptor::Gene', inverse_of: :gene_attributes
  belongs_to :sequence, inverse_of: :gene_attributes

  # Not yet implemented.
  # Deprecated: Use Tag/Keyword
  # belongs_to :controlled_vocabulary_term

  validates :descriptor, presence: true
  validates :sequence, presence: true

  validates_uniqueness_of :sequence, scope: [:descriptor, :sequence_relationship_type]

  after_save :add_to_descriptor_logic_if_absent

  def to_logic_literal
    "#{sequence_relationship_type}.#{sequence_id}"
  end

  protected

  def add_to_descriptor_logic_if_absent 
    descriptor.extend_gene_attribute_logic(self, :and) unless descriptor.contains_logic_for?(self)
  end

end

#sequence_id ⇒ Integer

Returns the sequence id (Gene), defines the nucleotides in the attribute.

Returns:

  • (Integer) —

    the sequence id (Gene), defines the nucleotides in the attribute



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# File 'app/models/gene_attribute.rb', line 26

class GeneAttribute < ApplicationRecord
  include Housekeeping
  include Shared::Identifiers
  include Shared::Notes
  include Shared::Tags
  include Shared::IsData

  acts_as_list scope: [:descriptor_id, :project_id]

  belongs_to :descriptor, class_name: 'Descriptor::Gene', inverse_of: :gene_attributes
  belongs_to :sequence, inverse_of: :gene_attributes

  # Not yet implemented.
  # Deprecated: Use Tag/Keyword
  # belongs_to :controlled_vocabulary_term

  validates :descriptor, presence: true
  validates :sequence, presence: true

  validates_uniqueness_of :sequence, scope: [:descriptor, :sequence_relationship_type]

  after_save :add_to_descriptor_logic_if_absent

  def to_logic_literal
    "#{sequence_relationship_type}.#{sequence_id}"
  end

  protected

  def add_to_descriptor_logic_if_absent 
    descriptor.extend_gene_attribute_logic(self, :and) unless descriptor.contains_logic_for?(self)
  end

end

#sequence_relationship_type ⇒ String

Returns a SequenceRelationship#type, defines how the sequence was used in this attribute.

Returns:

  • (String) —

    a SequenceRelationship#type, defines how the sequence was used in this attribute



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# File 'app/models/gene_attribute.rb', line 26

class GeneAttribute < ApplicationRecord
  include Housekeeping
  include Shared::Identifiers
  include Shared::Notes
  include Shared::Tags
  include Shared::IsData

  acts_as_list scope: [:descriptor_id, :project_id]

  belongs_to :descriptor, class_name: 'Descriptor::Gene', inverse_of: :gene_attributes
  belongs_to :sequence, inverse_of: :gene_attributes

  # Not yet implemented.
  # Deprecated: Use Tag/Keyword
  # belongs_to :controlled_vocabulary_term

  validates :descriptor, presence: true
  validates :sequence, presence: true

  validates_uniqueness_of :sequence, scope: [:descriptor, :sequence_relationship_type]

  after_save :add_to_descriptor_logic_if_absent

  def to_logic_literal
    "#{sequence_relationship_type}.#{sequence_id}"
  end

  protected

  def add_to_descriptor_logic_if_absent 
    descriptor.extend_gene_attribute_logic(self, :and) unless descriptor.contains_logic_for?(self)
  end

end

Instance Method Details

#add_to_descriptor_logic_if_absent ⇒ Object (protected) 



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# File 'app/models/gene_attribute.rb', line 55

def add_to_descriptor_logic_if_absent 
  descriptor.extend_gene_attribute_logic(self, :and) unless descriptor.contains_logic_for?(self)
end

#to_logic_literal ⇒ Object 



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# File 'app/models/gene_attribute.rb', line 49

def to_logic_literal
  "#{sequence_relationship_type}.#{sequence_id}"
end