Class: TaxonDetermination

Inherits:
ApplicationRecord show all
Includes:
Housekeeping, Shared::Citations, Shared::Confidences, Shared::DataAttributes, Shared::Depictions, Shared::IsData, Shared::Labels, Shared::Notes, Shared::ProtocolRelationships, SoftValidation
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”.

Constant Summary

Constants included from SoftValidation

SoftValidation::ANCESTORS_WITH_SOFT_VALIDATIONS

Instance Attribute Summary collapse

Class Method Summary collapse

Instance Method Summary collapse

Methods included from SoftValidation

#clear_soft_validations, #fix_for, #fix_soft_validations, #soft_fixed?, #soft_valid?, #soft_validate, #soft_validated?, #soft_validations, #soft_validators

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::ProtocolRelationships

#protocolled?, #reject_protocols

Methods included from Shared::Depictions

#has_depictions?, #image_array=, #reject_depictions, #reject_images

Methods included from Shared::Labels

#labeled?

Methods included from Shared::Confidences

#reject_confidences

Methods included from Shared::Notes

#concatenated_notes_string, #reject_notes

Methods included from Shared::DataAttributes

#import_attributes, #internal_attributes, #keyword_value_hash, #reject_data_attributes

Methods included from Shared::Citations

#cited?, #mark_citations_for_destruction, #nomenclature_date, #origin_citation_source_id, #reject_citations, #requires_citation?, #sources_by_topic_id

Methods included from Housekeeping

#has_polymorphic_relationship?

Methods inherited from ApplicationRecord

transaction_with_retry

Instance Attribute Details

#biological_collection_object_id ⇒ Integer

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::Depictions
  include Shared::ProtocolRelationships
  include Shared::IsData
  include SoftValidation
  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
  has_many :determiners_organization, through: :determiner_roles, source: :organization

  validates :biological_collection_object, presence: true
  validates :otu, presence: true
  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]

  # TODO: Add uniquiness constraint that also checks roles

  accepts_nested_attributes_for :determiners
  accepts_nested_attributes_for :determiner_roles, allow_destroy: true
  accepts_nested_attributes_for :otu, allow_destroy: false, reject_if: :reject_otu

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

  # @params params [Hash]
  # @params collection_objectt_id [Array, Integer]
  #   an Array or single id 
  # @return Hash
  def self.batch_create(collection_object_id, params)
    collection_object_ids = [collection_object_id].flatten.compact.uniq
    result = {
      failed: [],
      total_created: 0
    }

    collection_object_ids.each do |id|
      begin
        TaxonDetermination.create!(
          params.merge(
            biological_collection_object_id: id
          )
        )

        result[:total_created] += 1

      rescue ActiveRecord::RecordInvalid
        result[:failed].push id
        next
      end
    end
    result
  end

  # @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_made ⇒ Integer

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::Depictions
  include Shared::ProtocolRelationships
  include Shared::IsData
  include SoftValidation
  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
  has_many :determiners_organization, through: :determiner_roles, source: :organization

  validates :biological_collection_object, presence: true
  validates :otu, presence: true
  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]

  # TODO: Add uniquiness constraint that also checks roles

  accepts_nested_attributes_for :determiners
  accepts_nested_attributes_for :determiner_roles, allow_destroy: true
  accepts_nested_attributes_for :otu, allow_destroy: false, reject_if: :reject_otu

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

  # @params params [Hash]
  # @params collection_objectt_id [Array, Integer]
  #   an Array or single id 
  # @return Hash
  def self.batch_create(collection_object_id, params)
    collection_object_ids = [collection_object_id].flatten.compact.uniq
    result = {
      failed: [],
      total_created: 0
    }

    collection_object_ids.each do |id|
      begin
        TaxonDetermination.create!(
          params.merge(
            biological_collection_object_id: id
          )
        )

        result[:total_created] += 1

      rescue ActiveRecord::RecordInvalid
        result[:failed].push id
        next
      end
    end
    result
  end

  # @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_made ⇒ Integer

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::Depictions
  include Shared::ProtocolRelationships
  include Shared::IsData
  include SoftValidation
  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
  has_many :determiners_organization, through: :determiner_roles, source: :organization

  validates :biological_collection_object, presence: true
  validates :otu, presence: true
  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]

  # TODO: Add uniquiness constraint that also checks roles

  accepts_nested_attributes_for :determiners
  accepts_nested_attributes_for :determiner_roles, allow_destroy: true
  accepts_nested_attributes_for :otu, allow_destroy: false, reject_if: :reject_otu

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

  # @params params [Hash]
  # @params collection_objectt_id [Array, Integer]
  #   an Array or single id 
  # @return Hash
  def self.batch_create(collection_object_id, params)
    collection_object_ids = [collection_object_id].flatten.compact.uniq
    result = {
      failed: [],
      total_created: 0
    }

    collection_object_ids.each do |id|
      begin
        TaxonDetermination.create!(
          params.merge(
            biological_collection_object_id: id
          )
        )

        result[:total_created] += 1

      rescue ActiveRecord::RecordInvalid
        result[:failed].push id
        next
      end
    end
    result
  end

  # @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_id ⇒ Integer

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::Depictions
  include Shared::ProtocolRelationships
  include Shared::IsData
  include SoftValidation
  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
  has_many :determiners_organization, through: :determiner_roles, source: :organization

  validates :biological_collection_object, presence: true
  validates :otu, presence: true
  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]

  # TODO: Add uniquiness constraint that also checks roles

  accepts_nested_attributes_for :determiners
  accepts_nested_attributes_for :determiner_roles, allow_destroy: true
  accepts_nested_attributes_for :otu, allow_destroy: false, reject_if: :reject_otu

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

  # @params params [Hash]
  # @params collection_objectt_id [Array, Integer]
  #   an Array or single id 
  # @return Hash
  def self.batch_create(collection_object_id, params)
    collection_object_ids = [collection_object_id].flatten.compact.uniq
    result = {
      failed: [],
      total_created: 0
    }

    collection_object_ids.each do |id|
      begin
        TaxonDetermination.create!(
          params.merge(
            biological_collection_object_id: id
          )
        )

        result[:total_created] += 1

      rescue ActiveRecord::RecordInvalid
        result[:failed].push id
        next
      end
    end
    result
  end

  # @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

#position ⇒ Integer

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::Depictions
  include Shared::ProtocolRelationships
  include Shared::IsData
  include SoftValidation
  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
  has_many :determiners_organization, through: :determiner_roles, source: :organization

  validates :biological_collection_object, presence: true
  validates :otu, presence: true
  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]

  # TODO: Add uniquiness constraint that also checks roles

  accepts_nested_attributes_for :determiners
  accepts_nested_attributes_for :determiner_roles, allow_destroy: true
  accepts_nested_attributes_for :otu, allow_destroy: false, reject_if: :reject_otu

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

  # @params params [Hash]
  # @params collection_objectt_id [Array, Integer]
  #   an Array or single id 
  # @return Hash
  def self.batch_create(collection_object_id, params)
    collection_object_ids = [collection_object_id].flatten.compact.uniq
    result = {
      failed: [],
      total_created: 0
    }

    collection_object_ids.each do |id|
      begin
        TaxonDetermination.create!(
          params.merge(
            biological_collection_object_id: id
          )
        )

        result[:total_created] += 1

      rescue ActiveRecord::RecordInvalid
        result[:failed].push id
        next
      end
    end
    result
  end

  # @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_id ⇒ Integer

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::Depictions
  include Shared::ProtocolRelationships
  include Shared::IsData
  include SoftValidation
  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
  has_many :determiners_organization, through: :determiner_roles, source: :organization

  validates :biological_collection_object, presence: true
  validates :otu, presence: true
  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]

  # TODO: Add uniquiness constraint that also checks roles

  accepts_nested_attributes_for :determiners
  accepts_nested_attributes_for :determiner_roles, allow_destroy: true
  accepts_nested_attributes_for :otu, allow_destroy: false, reject_if: :reject_otu

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

  # @params params [Hash]
  # @params collection_objectt_id [Array, Integer]
  #   an Array or single id 
  # @return Hash
  def self.batch_create(collection_object_id, params)
    collection_object_ids = [collection_object_id].flatten.compact.uniq
    result = {
      failed: [],
      total_created: 0
    }

    collection_object_ids.each do |id|
      begin
        TaxonDetermination.create!(
          params.merge(
            biological_collection_object_id: id
          )
        )

        result[:total_created] += 1

      rescue ActiveRecord::RecordInvalid
        result[:failed].push id
        next
      end
    end
    result
  end

  # @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_made ⇒ Integer

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::Depictions
  include Shared::ProtocolRelationships
  include Shared::IsData
  include SoftValidation
  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
  has_many :determiners_organization, through: :determiner_roles, source: :organization

  validates :biological_collection_object, presence: true
  validates :otu, presence: true
  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]

  # TODO: Add uniquiness constraint that also checks roles

  accepts_nested_attributes_for :determiners
  accepts_nested_attributes_for :determiner_roles, allow_destroy: true
  accepts_nested_attributes_for :otu, allow_destroy: false, reject_if: :reject_otu

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

  # @params params [Hash]
  # @params collection_objectt_id [Array, Integer]
  #   an Array or single id 
  # @return Hash
  def self.batch_create(collection_object_id, params)
    collection_object_ids = [collection_object_id].flatten.compact.uniq
    result = {
      failed: [],
      total_created: 0
    }

    collection_object_ids.each do |id|
      begin
        TaxonDetermination.create!(
          params.merge(
            biological_collection_object_id: id
          )
        )

        result[:total_created] += 1

      rescue ActiveRecord::RecordInvalid
        result[:failed].push id
        next
      end
    end
    result
  end

  # @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

Class Method Details

.batch_create(collection_object_id, params) ⇒ Object

Returns Hash.

Returns:

  • Hash



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# File 'app/models/taxon_determination.rb', line 80

def self.batch_create(collection_object_id, params)
  collection_object_ids = [collection_object_id].flatten.compact.uniq
  result = {
    failed: [],
    total_created: 0
  }

  collection_object_ids.each do |id|
    begin
      TaxonDetermination.create!(
        params.merge(
          biological_collection_object_id: id
        )
      )

      result[:total_created] += 1

    rescue ActiveRecord::RecordInvalid
      result[:failed].push id
      next
    end
  end
  result
end

Instance Method Details

#date ⇒ String

Returns:

  • (String) 


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# File 'app/models/taxon_determination.rb', line 106

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 119

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

#sort_date ⇒ Time

Returns:

  • (Time) 


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# File 'app/models/taxon_determination.rb', line 111

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