Class: TaxonDetermination

Inherits:
ApplicationRecord show all
Includes:
Housekeeping, Shared::Citations, Shared::Confidences, Shared::DataAttributes, Shared::HasRoles, Shared::IsData, Shared::Labels, Shared::Notes
Defined in:
app/models/taxon_determination.rb

Overview

A Taxon determination is an assertion that a collection object belongs to a taxonomic concept.

If you wish to capture verbatim determinations then they should be added to CollectionObject#buffered_determinations, i.e. TaxonDeterminations are fully “normalized”.

Instance Attribute Summary collapse

Instance Method Summary collapse

Methods included from Housekeeping

#has_polymorphic_relationship?

Instance Attribute Details

#biological_collection_object_idInteger

BiologicalCollectionObject, the object being determined

Returns:

  • (Integer)


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# File 'app/models/taxon_determination.rb', line 36

class TaxonDetermination < ApplicationRecord
  acts_as_list scope: [:biological_collection_object_id, :project_id], add_new_at: :top

  include Housekeeping
  include Shared::Citations
  include Shared::DataAttributes
  include Shared::Notes
  include Shared::Confidences
  include Shared::Labels
  include Shared::HasRoles
  include Shared::IsData
  ignore_whitespace_on(:print_label)

  belongs_to :otu, inverse_of: :taxon_determinations
  belongs_to :biological_collection_object, class_name: 'CollectionObject', inverse_of: :taxon_determinations, foreign_key: :biological_collection_object_id

  has_many :determiner_roles, class_name: 'Determiner', as: :role_object
  has_many :determiners, through: :determiner_roles, source: :person

  # validates :biological_collection_object, presence: true
  # validates :otu, presence: true
  # # TODO - probably bad, and preventing nested determinations, should just use DB validation

  accepts_nested_attributes_for :determiners
  accepts_nested_attributes_for :determiner_roles, allow_destroy: true

  # accepts_nested_attributes_for :biological_collection_object
  accepts_nested_attributes_for :otu, allow_destroy: false, reject_if: :reject_otu

  validates :year_made, date_year: { min_year: 1757, max_year: Time.now.year }
  validates :month_made, date_month: true
  validates :day_made, date_day: {year_sym: :year_made, month_sym: :month_made}, unless: -> {year_made.nil? || month_made.nil?}

  # Careful, position must be reset with :update_column!
  validates_uniqueness_of :position, scope: [:biological_collection_object_id, :project_id]

  scope :current, -> { where(position: 1)}
  scope :historical, -> { where.not(position: 1)}

  # @return [String]
  def date
    [year_made, month_made, day_made].compact.join('-')
  end

  # @return [Time]
  def sort_date
    Utilities::Dates.nomenclature_date(day_made, month_made, year_made)
  end

  protected

  # @param [Hash] attributed
  # @return [Boolean]
  def reject_otu(attributed)
    attributed['name'].blank? && attributed['taxon_name_id'].blank?
  end

end

#day_madeInteger

the day of the month the determination was made

Returns:

  • (Integer)


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# File 'app/models/taxon_determination.rb', line 36

class TaxonDetermination < ApplicationRecord
  acts_as_list scope: [:biological_collection_object_id, :project_id], add_new_at: :top

  include Housekeeping
  include Shared::Citations
  include Shared::DataAttributes
  include Shared::Notes
  include Shared::Confidences
  include Shared::Labels
  include Shared::HasRoles
  include Shared::IsData
  ignore_whitespace_on(:print_label)

  belongs_to :otu, inverse_of: :taxon_determinations
  belongs_to :biological_collection_object, class_name: 'CollectionObject', inverse_of: :taxon_determinations, foreign_key: :biological_collection_object_id

  has_many :determiner_roles, class_name: 'Determiner', as: :role_object
  has_many :determiners, through: :determiner_roles, source: :person

  # validates :biological_collection_object, presence: true
  # validates :otu, presence: true
  # # TODO - probably bad, and preventing nested determinations, should just use DB validation

  accepts_nested_attributes_for :determiners
  accepts_nested_attributes_for :determiner_roles, allow_destroy: true

  # accepts_nested_attributes_for :biological_collection_object
  accepts_nested_attributes_for :otu, allow_destroy: false, reject_if: :reject_otu

  validates :year_made, date_year: { min_year: 1757, max_year: Time.now.year }
  validates :month_made, date_month: true
  validates :day_made, date_day: {year_sym: :year_made, month_sym: :month_made}, unless: -> {year_made.nil? || month_made.nil?}

  # Careful, position must be reset with :update_column!
  validates_uniqueness_of :position, scope: [:biological_collection_object_id, :project_id]

  scope :current, -> { where(position: 1)}
  scope :historical, -> { where.not(position: 1)}

  # @return [String]
  def date
    [year_made, month_made, day_made].compact.join('-')
  end

  # @return [Time]
  def sort_date
    Utilities::Dates.nomenclature_date(day_made, month_made, year_made)
  end

  protected

  # @param [Hash] attributed
  # @return [Boolean]
  def reject_otu(attributed)
    attributed['name'].blank? && attributed['taxon_name_id'].blank?
  end

end

#month_madeInteger

Returns the month the determination was made

Returns:

  • (Integer)

    the month the determination was made



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# File 'app/models/taxon_determination.rb', line 36

class TaxonDetermination < ApplicationRecord
  acts_as_list scope: [:biological_collection_object_id, :project_id], add_new_at: :top

  include Housekeeping
  include Shared::Citations
  include Shared::DataAttributes
  include Shared::Notes
  include Shared::Confidences
  include Shared::Labels
  include Shared::HasRoles
  include Shared::IsData
  ignore_whitespace_on(:print_label)

  belongs_to :otu, inverse_of: :taxon_determinations
  belongs_to :biological_collection_object, class_name: 'CollectionObject', inverse_of: :taxon_determinations, foreign_key: :biological_collection_object_id

  has_many :determiner_roles, class_name: 'Determiner', as: :role_object
  has_many :determiners, through: :determiner_roles, source: :person

  # validates :biological_collection_object, presence: true
  # validates :otu, presence: true
  # # TODO - probably bad, and preventing nested determinations, should just use DB validation

  accepts_nested_attributes_for :determiners
  accepts_nested_attributes_for :determiner_roles, allow_destroy: true

  # accepts_nested_attributes_for :biological_collection_object
  accepts_nested_attributes_for :otu, allow_destroy: false, reject_if: :reject_otu

  validates :year_made, date_year: { min_year: 1757, max_year: Time.now.year }
  validates :month_made, date_month: true
  validates :day_made, date_day: {year_sym: :year_made, month_sym: :month_made}, unless: -> {year_made.nil? || month_made.nil?}

  # Careful, position must be reset with :update_column!
  validates_uniqueness_of :position, scope: [:biological_collection_object_id, :project_id]

  scope :current, -> { where(position: 1)}
  scope :historical, -> { where.not(position: 1)}

  # @return [String]
  def date
    [year_made, month_made, day_made].compact.join('-')
  end

  # @return [Time]
  def sort_date
    Utilities::Dates.nomenclature_date(day_made, month_made, year_made)
  end

  protected

  # @param [Hash] attributed
  # @return [Boolean]
  def reject_otu(attributed)
    attributed['name'].blank? && attributed['taxon_name_id'].blank?
  end

end

#otu_idInteger

the OTU (concept) of the determination

Returns:

  • (Integer)


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# File 'app/models/taxon_determination.rb', line 36

class TaxonDetermination < ApplicationRecord
  acts_as_list scope: [:biological_collection_object_id, :project_id], add_new_at: :top

  include Housekeeping
  include Shared::Citations
  include Shared::DataAttributes
  include Shared::Notes
  include Shared::Confidences
  include Shared::Labels
  include Shared::HasRoles
  include Shared::IsData
  ignore_whitespace_on(:print_label)

  belongs_to :otu, inverse_of: :taxon_determinations
  belongs_to :biological_collection_object, class_name: 'CollectionObject', inverse_of: :taxon_determinations, foreign_key: :biological_collection_object_id

  has_many :determiner_roles, class_name: 'Determiner', as: :role_object
  has_many :determiners, through: :determiner_roles, source: :person

  # validates :biological_collection_object, presence: true
  # validates :otu, presence: true
  # # TODO - probably bad, and preventing nested determinations, should just use DB validation

  accepts_nested_attributes_for :determiners
  accepts_nested_attributes_for :determiner_roles, allow_destroy: true

  # accepts_nested_attributes_for :biological_collection_object
  accepts_nested_attributes_for :otu, allow_destroy: false, reject_if: :reject_otu

  validates :year_made, date_year: { min_year: 1757, max_year: Time.now.year }
  validates :month_made, date_month: true
  validates :day_made, date_day: {year_sym: :year_made, month_sym: :month_made}, unless: -> {year_made.nil? || month_made.nil?}

  # Careful, position must be reset with :update_column!
  validates_uniqueness_of :position, scope: [:biological_collection_object_id, :project_id]

  scope :current, -> { where(position: 1)}
  scope :historical, -> { where.not(position: 1)}

  # @return [String]
  def date
    [year_made, month_made, day_made].compact.join('-')
  end

  # @return [Time]
  def sort_date
    Utilities::Dates.nomenclature_date(day_made, month_made, year_made)
  end

  protected

  # @param [Hash] attributed
  # @return [Boolean]
  def reject_otu(attributed)
    attributed['name'].blank? && attributed['taxon_name_id'].blank?
  end

end

#positionInteger

Returns a cached, field managed by acts_as_list the deterimination of a specimen with position '1' is the accepted determination, it NOT necessarily the most recent determination made

Returns:

  • (Integer)

    a cached, field managed by acts_as_list the deterimination of a specimen with position '1' is the accepted determination, it NOT necessarily the most recent determination made



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# File 'app/models/taxon_determination.rb', line 36

class TaxonDetermination < ApplicationRecord
  acts_as_list scope: [:biological_collection_object_id, :project_id], add_new_at: :top

  include Housekeeping
  include Shared::Citations
  include Shared::DataAttributes
  include Shared::Notes
  include Shared::Confidences
  include Shared::Labels
  include Shared::HasRoles
  include Shared::IsData
  ignore_whitespace_on(:print_label)

  belongs_to :otu, inverse_of: :taxon_determinations
  belongs_to :biological_collection_object, class_name: 'CollectionObject', inverse_of: :taxon_determinations, foreign_key: :biological_collection_object_id

  has_many :determiner_roles, class_name: 'Determiner', as: :role_object
  has_many :determiners, through: :determiner_roles, source: :person

  # validates :biological_collection_object, presence: true
  # validates :otu, presence: true
  # # TODO - probably bad, and preventing nested determinations, should just use DB validation

  accepts_nested_attributes_for :determiners
  accepts_nested_attributes_for :determiner_roles, allow_destroy: true

  # accepts_nested_attributes_for :biological_collection_object
  accepts_nested_attributes_for :otu, allow_destroy: false, reject_if: :reject_otu

  validates :year_made, date_year: { min_year: 1757, max_year: Time.now.year }
  validates :month_made, date_month: true
  validates :day_made, date_day: {year_sym: :year_made, month_sym: :month_made}, unless: -> {year_made.nil? || month_made.nil?}

  # Careful, position must be reset with :update_column!
  validates_uniqueness_of :position, scope: [:biological_collection_object_id, :project_id]

  scope :current, -> { where(position: 1)}
  scope :historical, -> { where.not(position: 1)}

  # @return [String]
  def date
    [year_made, month_made, day_made].compact.join('-')
  end

  # @return [Time]
  def sort_date
    Utilities::Dates.nomenclature_date(day_made, month_made, year_made)
  end

  protected

  # @param [Hash] attributed
  # @return [Boolean]
  def reject_otu(attributed)
    attributed['name'].blank? && attributed['taxon_name_id'].blank?
  end

end

#project_idInteger

the project ID

Returns:

  • (Integer)


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# File 'app/models/taxon_determination.rb', line 36

class TaxonDetermination < ApplicationRecord
  acts_as_list scope: [:biological_collection_object_id, :project_id], add_new_at: :top

  include Housekeeping
  include Shared::Citations
  include Shared::DataAttributes
  include Shared::Notes
  include Shared::Confidences
  include Shared::Labels
  include Shared::HasRoles
  include Shared::IsData
  ignore_whitespace_on(:print_label)

  belongs_to :otu, inverse_of: :taxon_determinations
  belongs_to :biological_collection_object, class_name: 'CollectionObject', inverse_of: :taxon_determinations, foreign_key: :biological_collection_object_id

  has_many :determiner_roles, class_name: 'Determiner', as: :role_object
  has_many :determiners, through: :determiner_roles, source: :person

  # validates :biological_collection_object, presence: true
  # validates :otu, presence: true
  # # TODO - probably bad, and preventing nested determinations, should just use DB validation

  accepts_nested_attributes_for :determiners
  accepts_nested_attributes_for :determiner_roles, allow_destroy: true

  # accepts_nested_attributes_for :biological_collection_object
  accepts_nested_attributes_for :otu, allow_destroy: false, reject_if: :reject_otu

  validates :year_made, date_year: { min_year: 1757, max_year: Time.now.year }
  validates :month_made, date_month: true
  validates :day_made, date_day: {year_sym: :year_made, month_sym: :month_made}, unless: -> {year_made.nil? || month_made.nil?}

  # Careful, position must be reset with :update_column!
  validates_uniqueness_of :position, scope: [:biological_collection_object_id, :project_id]

  scope :current, -> { where(position: 1)}
  scope :historical, -> { where.not(position: 1)}

  # @return [String]
  def date
    [year_made, month_made, day_made].compact.join('-')
  end

  # @return [Time]
  def sort_date
    Utilities::Dates.nomenclature_date(day_made, month_made, year_made)
  end

  protected

  # @param [Hash] attributed
  # @return [Boolean]
  def reject_otu(attributed)
    attributed['name'].blank? && attributed['taxon_name_id'].blank?
  end

end

#year_madeInteger

Returns the 4 digit year the determination was made

Returns:

  • (Integer)

    the 4 digit year the determination was made



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# File 'app/models/taxon_determination.rb', line 36

class TaxonDetermination < ApplicationRecord
  acts_as_list scope: [:biological_collection_object_id, :project_id], add_new_at: :top

  include Housekeeping
  include Shared::Citations
  include Shared::DataAttributes
  include Shared::Notes
  include Shared::Confidences
  include Shared::Labels
  include Shared::HasRoles
  include Shared::IsData
  ignore_whitespace_on(:print_label)

  belongs_to :otu, inverse_of: :taxon_determinations
  belongs_to :biological_collection_object, class_name: 'CollectionObject', inverse_of: :taxon_determinations, foreign_key: :biological_collection_object_id

  has_many :determiner_roles, class_name: 'Determiner', as: :role_object
  has_many :determiners, through: :determiner_roles, source: :person

  # validates :biological_collection_object, presence: true
  # validates :otu, presence: true
  # # TODO - probably bad, and preventing nested determinations, should just use DB validation

  accepts_nested_attributes_for :determiners
  accepts_nested_attributes_for :determiner_roles, allow_destroy: true

  # accepts_nested_attributes_for :biological_collection_object
  accepts_nested_attributes_for :otu, allow_destroy: false, reject_if: :reject_otu

  validates :year_made, date_year: { min_year: 1757, max_year: Time.now.year }
  validates :month_made, date_month: true
  validates :day_made, date_day: {year_sym: :year_made, month_sym: :month_made}, unless: -> {year_made.nil? || month_made.nil?}

  # Careful, position must be reset with :update_column!
  validates_uniqueness_of :position, scope: [:biological_collection_object_id, :project_id]

  scope :current, -> { where(position: 1)}
  scope :historical, -> { where.not(position: 1)}

  # @return [String]
  def date
    [year_made, month_made, day_made].compact.join('-')
  end

  # @return [Time]
  def sort_date
    Utilities::Dates.nomenclature_date(day_made, month_made, year_made)
  end

  protected

  # @param [Hash] attributed
  # @return [Boolean]
  def reject_otu(attributed)
    attributed['name'].blank? && attributed['taxon_name_id'].blank?
  end

end

Instance Method Details

#dateString

Returns:

  • (String)


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# File 'app/models/taxon_determination.rb', line 76

def date
  [year_made, month_made, day_made].compact.join('-')
end

#reject_otu(attributed) ⇒ Boolean (protected)

Parameters:

  • attributed (Hash)

Returns:

  • (Boolean)


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# File 'app/models/taxon_determination.rb', line 89

def reject_otu(attributed)
  attributed['name'].blank? && attributed['taxon_name_id'].blank?
end

#sort_dateTime

Returns:

  • (Time)


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# File 'app/models/taxon_determination.rb', line 81

def sort_date
  Utilities::Dates.nomenclature_date(day_made, month_made, year_made)
end