Class: TaxonNameRelationship

Inherits:

ApplicationRecord

• Object
• ActiveRecord::Base
• ApplicationRecord
• TaxonNameRelationship

Includes:

Housekeeping, Shared::Citations, Shared::DwcOccurrenceHooks, Shared::IsData, Shared::Notes, SoftValidation

Defined in:

app/models/taxon_name_relationship.rb

Overview

TODO:

SourceClassifiedAs is not really Combination in the other sense

TODO:

validate, that all the relationships in the table could be linked to relationships in classes (if those had changed)

TODO:

Check if more than one species associated with the genus in the original paper

A NOMEN github.com/SpeciesFileGroup/nomen relationship between two Protonyms.

Unless otherwise noted relationships read left to right, and can be interpreted by inserting “of” after the class name.

For example the triple:

Subject: Aus aus - TaxonNameRelationship::Iczn::Invalidating::Synonym - Object: Bus bus

Can be read as:

  aus synonym OF bus

Note that not all relationships are reflective.  We can't say, for the example above we can't say

  bus valid_name OF aus

Note that we can not say that all names that are subjects are valid, this is determined on a case by case basis.

TaxonNameRelationships have a domain (attributes on the subject) and range (attributes on the object). So if you use a relationship you may be asserting a TaxonNameClassification also exists for the subject or object.

Direct Known Subclasses

Combination, CurrentCombination, Hybrid, Icn, Icnp, Icvcn, Iczn, OriginalCombination, SourceClassifiedAs, Typification

Defined Under Namespace

Classes: Combination, CurrentCombination, Hybrid, Icn, Icnp, Icvcn, Iczn, OriginalCombination, SourceClassifiedAs, Typification

Constant Summary

Constants included from SoftValidation

SoftValidation::ANCESTORS_WITH_SOFT_VALIDATIONS

Instance Attribute Summary

• #no_cached ⇒ Boolean^?

  When true, cached values are not built.

• #object_taxon_name_id ⇒ Integer

  The object taxon name.

• #project_id ⇒ Integer

  the project ID.

• #subject_taxon_name_id ⇒ Integer

  The subject taxon name.

• #type ⇒ String

  The relationship/“predicate” between the subject and object taxon names.

Class Method Summary

• .assignable ⇒ Object
• .collect_descendants_and_itself_to_s(*classes) ⇒ Object protected
• .collect_descendants_to_s(*classes) ⇒ Object protected
• .collect_to_s(*args) ⇒ Object protected
• .disjoint_object_classes ⇒ Object
• .disjoint_subject_classes ⇒ Object
• .disjoint_taxon_name_relationships ⇒ Array of TaxonNameRelationships

  If this relationships is set for the subject, then others in this array should not be used for that subject.

• .gbif_status_of_object ⇒ Object
• .gbif_status_of_subject ⇒ Object
• .nomen_uri ⇒ String^?

  The NOMEN uri for this type.

• .nomenclatural_priority ⇒ Symbol

  Determine the relative age of subject and object :direct - subject is younger than object :reverse - object is younger than subject.

• .parent ⇒ Object

  Class this method calls Module#module_parent.

• .required_taxon_name_relationships ⇒ Object

  TODO: why isn’t this disjoint? disjoint relationships for the taxon as a object.

• .valid_object_ranks ⇒ Array of NomenclatureRank

  The valid ranks to which the object name can belong, set in subclasses.

• .valid_subject_ranks ⇒ Array of NomenclatureRank

  The valid ranks to which the subject name can belong, set in subclasses.

Instance Method Summary

• #dwc_occurrences ⇒ Object
• #is_combination? ⇒ Boolean
• #is_invalidating? ⇒ Boolean protected
• #nomenclature_date ⇒ Time

  Effective date of publication, used to determine nomenclatural priorities !! Careful, if no date is present the current year is given, rather than nil, @proceps is this a safe inference?.

• #object_properties ⇒ Array of TaxonNameClassification

  The inferable TaxonNameClassification(s) added to the subject when this relationship is used !! Not implmented.

• #object_status ⇒ String

  The status inferred by the relationship to the object name.

• #object_status_connector_to_subject ⇒ String

  The connecting word in the relationship from the object name to subject name.

• #object_status_tag ⇒ String

  A readable fragement combining status and connector.

• #set_cached_names_for_taxon_names ⇒ Object protected
• #subject_and_object_in_same_project ⇒ Object protected
• #subject_invalid_statuses ⇒ Object protected
• #subject_properties ⇒ Array of TaxonNameClassification

  The inferable TaxonNameClassification(s) added to the subject when this relationship is used !! Not implemented.

• #subject_status ⇒ String

  The status inferred by the relationship to the subject name.

• #subject_status_connector_to_object ⇒ String

  The connecting word in the relationship from the subject name to object name.

• #subject_status_tag ⇒ String

  A readable fragement combining status and connector.

• #sv_coordinated_taxa ⇒ Object protected
• #sv_coordinated_taxa_object ⇒ Object protected
• #sv_fix_combination_relationship ⇒ Object protected
• #sv_fix_coordinated_object_taxa ⇒ Object protected
• #sv_fix_coordinated_subject_taxa ⇒ Object protected
• #sv_fix_not_specific_relationship ⇒ Object protected
• #sv_fix_objective_synonym_relationship ⇒ Object protected
• #sv_fix_subject_parent_update ⇒ Object protected
• #sv_not_specific_relationship ⇒ Object protected
• #sv_objective_synonym_relationship ⇒ Object protected
• #sv_specific_relationship ⇒ Object protected
• #sv_synonym_linked_to_valid_name ⇒ Object protected
• #sv_synonym_relationship ⇒ Object protected
• #sv_validate_disjoint_object ⇒ Object protected
• #sv_validate_disjoint_relationships ⇒ Object protected
• #sv_validate_disjoint_subject ⇒ Object protected
• #sv_validate_priority ⇒ Object protected
• #sv_validate_required_relationships ⇒ Object protected
• #sv_validate_seniority ⇒ Object protected
• #type_class ⇒ Object
• #type_class=(value) ⇒ Object
• #type_name ⇒ String^?

  The type of this relationship, IF the type is a valid name, else nil.

• #validate_object_and_subject_both_protonyms ⇒ Object protected
• #validate_object_must_equal_subject_for_uncertain_placement ⇒ Object protected
• #validate_rank_group ⇒ Object protected
• #validate_subject_and_object_are_not_identical ⇒ Object protected
• #validate_subject_and_object_ranks ⇒ Object protected
• #validate_subject_and_object_share_code ⇒ Object protected
• #validate_type ⇒ Object protected
• #validate_uniqueness_of_typification_object ⇒ Object protected

  Protonym historically could be listed as a synonym to different taxa def validate_uniqueness_of_synonym_subject if !self.type.nil? && /Synonym/.match(self.type_name) && !TaxonNameRelationship.where(subject_taxon_name_id: self.subject_taxon_name_id).with_type_contains(‘Synonym’).not_self(self).empty? errors.add(:subject_taxon_name_id, ‘Only one synonym relationship is allowed’) end end.

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 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::Notes

#concatenated_notes_string, #reject_notes

Methods included from Shared::Citations

#cited?, #mark_citations_for_destruction, #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

#no_cached ⇒ Boolean^?

Returns When true, cached values are not built.

Returns:

• (Boolean, nil) —

  When true, cached values are not built

# File 'app/models/taxon_name_relationship.rb', line 54

def no_cached
  @no_cached
end

#object_taxon_name_id ⇒ Integer

Returns the object taxon name.

Returns:

• (Integer) —

  the object taxon name

# File 'app/models/taxon_name_relationship.rb', line 44

class TaxonNameRelationship < ApplicationRecord
  include Housekeeping
  include Shared::Citations
  include Shared::Notes
  include SoftValidation
  include Shared::DwcOccurrenceHooks
  include Shared::IsData

  # @return [Boolean, nil]
  #   When true, cached values are not built
  attr_accessor :no_cached

  belongs_to :subject_taxon_name, class_name: 'TaxonName', inverse_of: :taxon_name_relationships # left side
  belongs_to :object_taxon_name, class_name: 'TaxonName', inverse_of: :related_taxon_name_relationships # right side

  # !! Keep as after_commit unless you are wanting to spend a lot of time
  # !! refactoring tests
  after_commit :set_cached_names_for_taxon_names, unless: -> {self.no_cached || destroyed?}
  after_destroy :set_cached_names_for_taxon_names, unless: -> {self.no_cached}

  # TODO: remove, it's required by STI
  validates_presence_of :type, message: 'Relationship type should be specified'
  validates_presence_of :subject_taxon_name, message: 'Missing taxon name on the left side'
  validates_presence_of :object_taxon_name, message: 'Missing taxon name on the right side'
  validates_uniqueness_of :object_taxon_name_id, scope: [:type, :project_id], if: :is_combination?
  validates_uniqueness_of :object_taxon_name_id, scope: [:type, :subject_taxon_name_id, :project_id], unless: :is_combination?

  validate :validate_type, :validate_subject_and_object_are_not_identical
  validate :subject_and_object_in_same_project

  with_options unless: -> {!subject_taxon_name || !object_taxon_name} do
    validate :validate_subject_and_object_share_code,
      :validate_uniqueness_of_typification_object,
      #:validate_uniqueness_of_synonym_subject,
      :validate_object_and_subject_both_protonyms,
      :validate_object_must_equal_subject_for_uncertain_placement,
      :validate_subject_and_object_ranks,
      :validate_rank_group
  end

  # TODO: isolate to an include file sensu protonym
  soft_validate(
    :sv_validate_required_relationships,
    set: :validate_required_relationships,
    name: 'Required relationships',
    description: 'Required relationships' )

  soft_validate(
    :sv_validate_disjoint_relationships,
    set: :validate_disjoint_relationships,
    name: 'Conflicting relationships',
    description: 'Detect conflicting relationships' )

  soft_validate(
    :sv_validate_disjoint_object,
    set: :validate_disjoint_object,
    name: 'Conflicting object taxon',
    description: 'Object taxon has a status conflicting with the relationship' )

  soft_validate(
    :sv_validate_disjoint_subject,
    set: :validate_disjoint_subject,
    name: 'Conflicting subject taxon',
    description: 'Subject taxon has a status conflicting with the relationship' )

  soft_validate(
    :sv_specific_relationship,
    set: :specific_relationship,
    name: 'validate relationship',
    description: 'Validate integrity of the relationship, for example, the year applicability range' )

  soft_validate(
    :sv_objective_synonym_relationship,
    set: :objective_synonym_relationship,
    fix: :sv_fix_objective_synonym_relationship,
    name: 'Objective synonym relationship',
    description: 'Objective synonyms should have the same type' )

  soft_validate(
    :sv_synonym_relationship,
    set: :synonym_relationship,
    name: 'Synonym relationship',
    description: 'Validate integrity of synonym relationship' )

  soft_validate(
    :sv_not_specific_relationship,
    set: :not_specific_relationship,
    fix: :sv_fix_not_specific_relationship,
    name: 'Not specific relationship',
    description: 'More specific relationship is preferred, for example "Subjective synonym" instead of "Synonym".' )

  soft_validate(
    :sv_synonym_linked_to_valid_name,
    set: :synonym_linked_to_valid_name,
    fix: :sv_fix_subject_parent_update,
    name: 'Synonym not linked to valid taxon',
    description: 'Synonyms should be linked to valid taxon.' )

  soft_validate(
    :sv_validate_priority,
    set: :validate_priority,
    name: 'Priority validation',
    description: 'Junior synonym should be younger than senior synonym' )

  soft_validate(
    :sv_validate_seniority,
    set: :validate_seniority,
    name: 'Seniority validation',
    description: 'Of two synonyms described in the same paper, one described at a higher rank has a priority' )

  soft_validate(
    :sv_coordinated_taxa,
    set: :coordinated_taxa,
    fix: :sv_fix_coordinated_subject_taxa,
    name: 'Move relationship to coordinate taxon',
    description: 'Relationship should be moved to the lowest rank coordinate taxon (for example from species to nomynotypical subspecies). It could be updated automatically with the Fix.' )

  soft_validate(
    :sv_coordinated_taxa_object,
    set: :coordinated_taxa,
    fix: :sv_fix_coordinated_object_taxa,
    name: 'Move object relationship to coordinate taxon',
    description: 'Relationship should be moved to the lowest rank coordinate object taxon (for example from species to nomynotypical subspecies). It could be updated automatically with the Fix.')

  scope :where_subject_is_taxon_name, -> (taxon_name) {where(subject_taxon_name_id: taxon_name)}
  scope :where_object_is_taxon_name, -> (taxon_name) {where(object_taxon_name_id: taxon_name)}
  scope :where_object_in_taxon_names, -> (taxon_name_array) {where('"taxon_name_relationships"."object_taxon_name_id" IN (?)', taxon_name_array)}

  scope :with_type_string, -> (type_string) { where(sanitize_sql_array(["taxon_name_relationships.type = '%s'", type_string])) }

  scope :with_type_base, -> (base_string) {where('"taxon_name_relationships"."type" LIKE ?', "#{base_string}%")}
  scope :with_type_contains, -> (base_string) {where('"taxon_name_relationships"."type" LIKE ?', "%#{base_string}%")}

  scope :with_two_type_bases, -> (base_string1, base_string2) {
    where('taxon_name_relationships.type LIKE ? OR taxon_name_relationships.type LIKE ?', "#{base_string1}%", "#{base_string2}%") }

  scope :homonym_or_suppressed, -> {where("taxon_name_relationships.type LIKE 'TaxonNameRelationship::Iczn::Invalidating::Homonym%' OR taxon_name_relationships.type LIKE 'TaxonNameRelationship::Iczn::Invalidating::Suppression::Total'") }
  scope :with_type_array, -> (base_array) {where('taxon_name_relationships.type IN (?)', base_array ) }

  def dwc_occurrences
    DwcOccurrence
      .joins("JOIN collection_objects co on dwc_occurrence_object_id = co.id AND dwc_occurrence_object_type = 'CollectionObject'")
      .joins("JOIN taxon_determinations td on co.id = td.taxon_determination_object_id AND td.taxon_determination_object_type = 'CollectionObject'")
      .joins("JOIN otus o on o.id = td.otu_id")
      .where(o: {taxon_name_id: [subject_taxon_name_id, object_taxon_name_id]})
      .distinct
  end

  # @return [Array of TaxonNameClassification]
  #  the inferable TaxonNameClassification(s) added to the subject when this relationship is used
  #  !! Not implemented
  def subject_properties
    []
  end

  # @return [Array of TaxonNameClassification]
  #  the inferable TaxonNameClassification(s) added to the subject when this relationship is used
  #  !! Not implmented
  def object_properties
    []
  end

  # @return class
  #   this method calls Module#module_parent
  def self.parent
    self.module_parent
  end

  # @return [Array of NomenclatureRank]
  #   the valid ranks to which the subject name can belong, set in subclasses. (left side)
  def self.valid_subject_ranks
    []
  end

  # @return [Array of NomenclatureRank]
  #   the valid ranks to which the object name can belong, set in subclasses. (right side)
  def self.valid_object_ranks
    []
  end

  # @return [Array of TaxonNameRelationships]
  #   if this relationships is set for the subject, then others in this array should not be used for that subject
  def self.disjoint_taxon_name_relationships
    []
  end

  # TODO: why isn't this disjoint?
  # disjoint relationships for the taxon as a object
  def self.required_taxon_name_relationships
    []
  end

  def self.disjoint_subject_classes
    []
  end

  def self.disjoint_object_classes
    []
  end

  def self.gbif_status_of_subject
    nil
  end

  def self.gbif_status_of_object
    nil
  end

  def self.assignable
    false
  end

  # @return [Symbol]
  #   determine the relative age of subject and object
  #   :direct - subject is younger than object
  #   :reverse - object is younger than subject
  def self.nomenclatural_priority
    nil
  end

  # @return [String]
  #    the status inferred by the relationship to the object name
  def object_status
    self.type_name.demodulize.underscore.humanize.downcase.gsub(/\d+/, ' \0 ').squish
  end

  # @return [String]
  #    the status inferred by the relationship to the subject name
  def subject_status
    self.type_name.demodulize.underscore.humanize.downcase.gsub(/\d+/, ' \0 ').squish
  end

  # @return [String]
  #    the connecting word in the relationship from the subject name to object name
  def subject_status_connector_to_object
    ' of'
  end

  # @return [String]
  #    the connecting word in the relationship from the object name to subject name
  def object_status_connector_to_subject
    ' of'
  end

  # @return [String]
  #   a readable fragement combining status and connector
  def subject_status_tag
    subject_status + subject_status_connector_to_object
  end

  # @return [String]
  #   a readable fragement combining status and connector
  def object_status_tag
    object_status + object_status_connector_to_subject
  end

  # @return [String, nil]
  #   the type of this relationship, IF the type is a valid name, else nil
  def type_name
    r = self.type
    TAXON_NAME_RELATIONSHIP_NAMES.include?(r) ? r : nil
  end

  def type_class=(value)
    write_attribute(:type, value.to_s)
  end

  def type_class
    r = read_attribute(:type).to_s
    TAXON_NAME_RELATIONSHIP_NAMES.include?(r) ? r.safe_constantize : nil
  end

  # @return [String, nil]
  #   the NOMEN uri for this type
  def self.nomen_uri
    const_defined?(:NOMEN_URI, false) ? self::NOMEN_URI : nil
  end

  # @return [Time]
  #   effective date of publication, used to determine nomenclatural priorities
  #   !! Careful, if no date is present the current year is given, rather than nil, @proceps is this a safe inference?
  def nomenclature_date
    self.source ? (self.source.cached_nomenclature_date ? self.source.cached_nomenclature_date.to_time : Time.current) : Time.current
  end

  def is_combination?
    !!/TaxonNameRelationship::(OriginalCombination|Combination)/.match(self.type.to_s)
  end

  protected

  def subject_and_object_in_same_project
    if subject_taxon_name && object_taxon_name
      if subject_taxon_name.project_id != object_taxon_name.project_id
        errors.add(:base, 'one name is not in the same project as the other')
      end
    end
  end

  def validate_type
    # TODO: Remove, handled by STI
    if type && !TAXON_NAME_RELATIONSHIP_NAMES.include?(type.to_s)
      errors.add(:type, "'#{type}' is not a valid taxon name relationship")
    elsif self.type_class && object_taxon_name.class.to_s == 'Protonym' && !self.type_class.valid_object_ranks.include?(object_taxon_name.rank_string)
      errors.add(:type, "'#{type}' is not a valid taxon name relationship")
    end

    if object_taxon_name.class.to_s == 'Protonym' || object_taxon_name.class.to_s == 'Hybrid'
      errors.add(:type, "'#{type}' is not a valid taxon name relationship") if /TaxonNameRelationship::Combination::/.match(self.type)
    end

    if object_taxon_name.class.to_s == 'Combination'
      errors.add(:type, "'#{type}' is not a valid taxon name relationship") unless /TaxonNameRelationship::Combination::/.match(self.type)
    end
  end

  # @todo validate, that all the relationships in the table could be linked to relationships in classes (if those had changed)

  def validate_subject_and_object_share_code
    if object_taxon_name.type  == 'Protonym' && subject_taxon_name.type == 'Protonym'
      errors.add(:object_taxon_name_id, 'The related taxon is not in the same monenclatural group (ICZN, ICN, ICNP, ICVCN') if subject_taxon_name.rank_class.try(:nomenclatural_code) != object_taxon_name.rank_class.try(:nomenclatural_code)
    end
  end

  def validate_subject_and_object_are_not_identical
    if !self.object_taxon_name_id.nil? && self.object_taxon_name == self.subject_taxon_name
      errors.add(:object_taxon_name_id, "#{self.object_taxon_name.try(:cached_html)} should not refer to itself") unless self.type =~ /OriginalCombination/
    end
  end

  def validate_object_must_equal_subject_for_uncertain_placement
    if self.object_taxon_name_id != self.subject_taxon_name.parent_id && self.type_name == 'TaxonNameRelationship::Iczn::Validating::UncertainPlacement'
      errors.add(:object_taxon_name_id, "The parent #{self.subject_taxon_name.parent.cached_html} and the Incertae Sedis placement (#{self.object_taxon_name.cached_html}) should match")
    end
  end

  def validate_subject_and_object_ranks
    tname = self.type_name

    if tname =~ /TaxonNameRelationship::(Icnp|Icn|Iczn|Icvcn)/ && tname != 'TaxonNameRelationship::Iczn::Validating::UncertainPlacement'
      rank_group = self.subject_taxon_name.rank_class.try(:parent)
      unless rank_group == self.object_taxon_name.rank_class.try(:parent)
        errors.add(:object_taxon_name_id, "Rank of related taxon should be in the #{rank_group.try(:rank_name)} rank group, not #{self.object_taxon_name.rank_class.try(:rank_name)}")
      end
    end

    if self.type_class.present? # only validate if it is set
      if object_taxon_name && object_taxon_name.rank_class
        if object_taxon_name.type == 'Protonym' || object_taxon_name.type == 'Hybrid'
          unless self.type_class.valid_object_ranks.include?(self.object_taxon_name.rank_string)
            errors.add(:object_taxon_name_id, "#{self.object_taxon_name.rank_class.rank_name.capitalize} rank of #{self.object_taxon_name.cached_html} is not compatible with the #{self.subject_status} relationship")
            errors.add(:type, "Relationship #{self.subject_status} is not compatible with the #{self.object_taxon_name.rank_class.rank_name} rank of #{self.object_taxon_name.cached_html}")
          end
        end
      end

      if subject_taxon_name && subject_taxon_name.rank_class
        if subject_taxon_name.type == 'Protonym' || subject_taxon_name.type == 'Hybrid'
          unless self.type_class.valid_subject_ranks.include?(self.subject_taxon_name.rank_string)
            soft_validations.add(:subject_taxon_name_id, "#{self.subject_taxon_name.rank_class.rank_name.capitalize} rank of #{self.subject_taxon_name.cached_html} is not compatible with the #{self.subject_status} relationship")
            soft_validations.add(:type, "Relationship #{self.subject_status} is not compatible with the #{self.subject_taxon_name.rank_class.rank_name} rank of #{self.subject_taxon_name.cached_html}")
          end
        end
      end
    end
  end

  ##### Protonym historically could be listed as a synonym to different taxa
  #def validate_uniqueness_of_synonym_subject
  #  if !self.type.nil? && /Synonym/.match(self.type_name) && !TaxonNameRelationship.where(subject_taxon_name_id: self.subject_taxon_name_id).with_type_contains('Synonym').not_self(self).empty?
  #    errors.add(:subject_taxon_name_id, 'Only one synonym relationship is allowed')
  #  end
  #end

  def validate_uniqueness_of_typification_object
    if /Typification/.match(self.type_name) && !TaxonNameRelationship.where(object_taxon_name_id: self.object_taxon_name_id).with_type_contains('Typification').not_self(self).empty?
      errors.add(:object_taxon_name_id, 'Only one Type designation relationship is allowed')
    end
  end

  def validate_rank_group
    if self.type =~ /Hybrid/ && self.subject_taxon_name && self.object_taxon_name
      if self.subject_taxon_name.rank_class.parent != self.object_taxon_name.rank_class.parent
        errors.add(:subject_taxon_name_id, "#{self.subject_taxon_name.rank_class.rank_name.capitalize} rank of #{self.subject_taxon_name.cached_html} is not compatible with the rank of hybrid (#{self.object_taxon_name.rank_class.rank_name})")
      end
    end
  end

  def validate_object_and_subject_both_protonyms
    if /TaxonNameRelationship::Combination::/.match(self.type)
      errors.add(:object_taxon_name_id, 'Not a Combination') if object_taxon_name.type != 'Combination'
    else
      errors.add(:object_taxon_name_id, 'Not a Protonym') if object_taxon_name.type == 'Combination'
    end
    errors.add(:subject_taxon_name_id, 'Not a Protonym') if subject_taxon_name.type == 'Combination' && self.type != 'TaxonNameRelationship::CurrentCombination'
  end

  def set_cached_names_for_taxon_names
    # !! only fire if subject_taxon_name changed
    return true unless subject_taxon_name_id_previously_changed? || destroyed?

    TaxonName.transaction do
      if is_invalidating?
        t = subject_taxon_name

        if type_name =~/Misspelling/
          t.update_column(:cached_misspelling, t.get_cached_misspelling)
          t.update_columns(
              cached_author_year: t.get_author_and_year,
              cached_nomenclature_date: t.nomenclature_date,
              cached_original_combination: t.get_original_combination,
              cached_original_combination_html: t.get_original_combination_html)
        end

        if type_name =~/Misapplication/
          t.update_columns(
            cached_author_year: t.get_author_and_year,
            cached_nomenclature_date: t.nomenclature_date)
        end

        vn = t.get_valid_taxon_name

        # !! NO set cached should do this from TN side of things,
        # !! Not here

        n = t.get_full_name

        t.update_columns(
          cached: n,
          cached_html: t.get_full_name_html(n), # OK to force reload here, otherwise we need an exception in #set_cached
          cached_valid_taxon_name_id: vn.id,
          cached_is_valid: !t.unavailable_or_invalid?)

        t.combination_list_self.each do |c|
          c.update_column(:cached_valid_taxon_name_id, vn.id)
        end

        vn.list_of_invalid_taxon_names.each do |s|
          s.update_columns(
            cached_valid_taxon_name_id: vn.id,
            cached_is_valid: !s.unavailable_or_invalid?)

          s.combination_list_self.each do |c|
            c.update_column(:cached_valid_taxon_name_id, vn.id)
          end
        end

      end

    end

    true
  end

  def is_invalidating?
    TAXON_NAME_RELATIONSHIP_NAMES_INVALID.include?(type_name)
  end

  def sv_validate_required_relationships
    return true if self.subject_taxon_name.not_binominal?
    object_relationships = TaxonNameRelationship.where_object_is_taxon_name(self.object_taxon_name).not_self(self).collect{|r| r.type}
    required = self.type_class.required_taxon_name_relationships - object_relationships
    required.each do |r|
      soft_validations.add(:type, " Presence of #{self.subject_status} requires selection of #{r.demodulize.underscore.humanize.downcase}")
    end
  end

  def sv_validate_disjoint_relationships
    tname = self.type_name
    if tname =~ /TaxonNameRelationship::(Icnp|Icn|Iczn|Icvcn)/ && tname != 'TaxonNameRelationship::Iczn::Validating::UncertainPlacement'
      subject_relationships = TaxonNameRelationship.where_subject_is_taxon_name(self.subject_taxon_name).not_self(self)
      subject_relationships.each  do |i|
        if self.type_class.disjoint_taxon_name_relationships.include?(i.type_name)
          soft_validations.add(:type, "#{self.subject_status.capitalize} relationship is conflicting with another relationship: '#{i.subject_status}'")
        end
      end
    end
  end

  def sv_validate_disjoint_object
    classifications = self.object_taxon_name.taxon_name_classifications.reload.map {|i| i.type_name}
    disjoint_object_classes = self.type_class.disjoint_object_classes
    compare = disjoint_object_classes & classifications
    compare.each do |i|
      c = i.demodulize.underscore.humanize.downcase
      soft_validations.add(:type, "#{self.subject_status.capitalize} relationship is conflicting with the taxon status: '#{c}'")
      soft_validations.add(:object_taxon_name_id, "#{self.object_taxon_name.cached_html} has a conflicting status: '#{c}'")
    end
  end

  def sv_validate_disjoint_subject
    classifications = self.subject_taxon_name.taxon_name_classifications.reload.map {|i| i.type_name}
    disjoint_subject_classes = self.type_class.disjoint_subject_classes
    compare = disjoint_subject_classes & classifications
    compare.each do |i|
      c = i.demodulize.underscore.humanize.downcase
      soft_validations.add(:type, "#{self.subject_status.capitalize} conflicting with the status: '#{c}'")
      soft_validations.add(:subject_taxon_name_id, "#{self.subject_taxon_name.cached_html} has a conflicting status: '#{c}'")
    end
  end

  def sv_specific_relationship
    true # all validations moved to subclasses
  end

  def sv_objective_synonym_relationship
    true # all validations moved to subclasses
  end

  def sv_fix_objective_synonym_relationship
    true # all validations moved to subclasses
  end

  def sv_synonym_relationship
    true # all validations moved to subclasses
  end

  def sv_not_specific_relationship
    true # all validations moved to subclasses
  end

  def sv_fix_not_specific_relationship
    true # all validations moved to subclasses
  end

  def sv_synonym_linked_to_valid_name
    #synonyms and misspellings should be linked to valid names
    if ::TAXON_NAME_RELATIONSHIP_NAMES_SYNONYM.include?(self.type_name)
      obj = self.object_taxon_name
      subj = self.subject_taxon_name
      if subj.rank_class.try(:nomenclatural_code) == :iczn && (obj.parent_id != subj.parent_id || obj.rank_class != subj.rank_class) &&  subj.cached_valid_taxon_name_id == obj.cached_valid_taxon_name_id
        soft_validations.add(:subject_taxon_name_id, "#{self.subject_status.capitalize}  #{subj.cached_html_name_and_author_year} should have the same parent and rank with  #{obj.cached_html_name_and_author_year}",
                             success_message: 'The parent was updated', failure_message:  'The parent was not updated')
      end
    end
  end

  def sv_fix_subject_parent_update
    res = false
    if TAXON_NAME_RELATIONSHIP_NAMES_SYNONYM.include?(self.type_name)
      obj = self.object_taxon_name
      subj = self.subject_taxon_name
      unless obj.parent_id == subj.parent_id
        subj.parent_id = obj.parent_id
        subj.rank_class = obj.rank_class
        begin
          TaxonName.transaction do
            subj.save!
            res = true
          end
        rescue
        end
      end
    end
    res
  end

  def subject_invalid_statuses
    TAXON_NAME_CLASS_NAMES_UNAVAILABLE_AND_INVALID & self.subject_taxon_name.taxon_name_classifications.collect{|c| c.type_class.to_s}
  end

  def sv_validate_priority
    true # all validations moved to subclasses
  end

  def sv_validate_seniority
    true # all validations moved to subclasses
  end

  def sv_coordinated_taxa
    s = subject_taxon_name
    o = object_taxon_name
    s_new = s.lowest_rank_coordinated_taxon
    if s != s_new
      soft_validations.add(:subject_taxon_name_id, "Relationship should move from #{s.rank_class.rank_name} #{s.cached_html} to #{s_new.rank_class.rank_name} #{s_new.cached_html}",
                           success_message: "Relationship moved to  #{s_new.rank_class.rank_name}", failure_message:  'Failed to update relationship')
    end
  end

  def sv_coordinated_taxa_object
    s = subject_taxon_name
    o = object_taxon_name
    o_new = o.lowest_rank_coordinated_taxon
    if o != o_new
      soft_validations.add(:object_taxon_name_id, "Relationship should move from #{o.rank_class.rank_name} #{o.cached_html} to #{o_new.rank_class.rank_name} #{o_new.cached_html}",
                           success_message: "Relationship moved to  #{o_new.rank_class.rank_name}", failure_message:  'Failed to update relationship')
    end
  end

  def sv_fix_coordinated_subject_taxa
    s = subject_taxon_name
    s_new = s.lowest_rank_coordinated_taxon
    if s != s_new
      self.subject_taxon_name = s_new
      begin
        TaxonNameRelationship.transaction do
          self.save
          return true
        end
      rescue
      end
    end
    false
  end

  def sv_fix_coordinated_object_taxa
    o = self.object_taxon_name
    o_new = o.lowest_rank_coordinated_taxon
    if o != o_new
      self.object_taxon_name = o_new
      begin
        TaxonNameRelationship.transaction do
          self.save
          return true
        end
      rescue
      end
    end
    false
  end

  def sv_fix_combination_relationship
    s = self.subject_taxon_name
    list = s.list_of_coordinated_names + [s]
    if s.rank_string =~ /Species/
      s_new = list.detect{|t| t.rank_class.rank_name == 'species'}
    elsif s.rank_string =~ /Genus/
      s_new = list.detect{|t| t.rank_class.rank_name == 'genus'}
    else
      s_new = s
    end
    if s != s_new && !s.nil?
      self.subject_taxon_name = s_new
      begin
        TaxonNameRelationship.transaction do
          self.save
          return true
        end
      rescue
      end
    end
    false
  end

  def self.collect_to_s(*args)
    args.collect{|arg| arg.to_s}
  end

  def self.collect_descendants_to_s(*classes)
    ans = []
    classes.each do |klass|
      ans += klass.descendants.collect{|k| k.to_s}
    end
    ans
  end

  def self.collect_descendants_and_itself_to_s(*classes)
    classes.collect{|k| k.to_s} + self.collect_descendants_to_s(*classes)
  end

  # Force loading all descendants as soon as this class is referenced
  Dir.glob("#{Rails.root.join("app/models/taxon_name_relationship/**/*.rb")}")
    .sort { |a, b| a.split('/').count <=> b.split('/').count }
    .map { |p| p.split('/app/models/').last.sub(/\.rb$/, '') }
    .map { |p| p.split('/') }
    .map { |c| c.map { |n| ActiveSupport::Inflector.camelize(n) } }
    .map { |c| c.join('::') }.map(&:constantize)
end

#project_id ⇒ Integer

the project ID

Returns:

• (Integer)

# File 'app/models/taxon_name_relationship.rb', line 44

class TaxonNameRelationship < ApplicationRecord
  include Housekeeping
  include Shared::Citations
  include Shared::Notes
  include SoftValidation
  include Shared::DwcOccurrenceHooks
  include Shared::IsData

  # @return [Boolean, nil]
  #   When true, cached values are not built
  attr_accessor :no_cached

  belongs_to :subject_taxon_name, class_name: 'TaxonName', inverse_of: :taxon_name_relationships # left side
  belongs_to :object_taxon_name, class_name: 'TaxonName', inverse_of: :related_taxon_name_relationships # right side

  # !! Keep as after_commit unless you are wanting to spend a lot of time
  # !! refactoring tests
  after_commit :set_cached_names_for_taxon_names, unless: -> {self.no_cached || destroyed?}
  after_destroy :set_cached_names_for_taxon_names, unless: -> {self.no_cached}

  # TODO: remove, it's required by STI
  validates_presence_of :type, message: 'Relationship type should be specified'
  validates_presence_of :subject_taxon_name, message: 'Missing taxon name on the left side'
  validates_presence_of :object_taxon_name, message: 'Missing taxon name on the right side'
  validates_uniqueness_of :object_taxon_name_id, scope: [:type, :project_id], if: :is_combination?
  validates_uniqueness_of :object_taxon_name_id, scope: [:type, :subject_taxon_name_id, :project_id], unless: :is_combination?

  validate :validate_type, :validate_subject_and_object_are_not_identical
  validate :subject_and_object_in_same_project

  with_options unless: -> {!subject_taxon_name || !object_taxon_name} do
    validate :validate_subject_and_object_share_code,
      :validate_uniqueness_of_typification_object,
      #:validate_uniqueness_of_synonym_subject,
      :validate_object_and_subject_both_protonyms,
      :validate_object_must_equal_subject_for_uncertain_placement,
      :validate_subject_and_object_ranks,
      :validate_rank_group
  end

  # TODO: isolate to an include file sensu protonym
  soft_validate(
    :sv_validate_required_relationships,
    set: :validate_required_relationships,
    name: 'Required relationships',
    description: 'Required relationships' )

  soft_validate(
    :sv_validate_disjoint_relationships,
    set: :validate_disjoint_relationships,
    name: 'Conflicting relationships',
    description: 'Detect conflicting relationships' )

  soft_validate(
    :sv_validate_disjoint_object,
    set: :validate_disjoint_object,
    name: 'Conflicting object taxon',
    description: 'Object taxon has a status conflicting with the relationship' )

  soft_validate(
    :sv_validate_disjoint_subject,
    set: :validate_disjoint_subject,
    name: 'Conflicting subject taxon',
    description: 'Subject taxon has a status conflicting with the relationship' )

  soft_validate(
    :sv_specific_relationship,
    set: :specific_relationship,
    name: 'validate relationship',
    description: 'Validate integrity of the relationship, for example, the year applicability range' )

  soft_validate(
    :sv_objective_synonym_relationship,
    set: :objective_synonym_relationship,
    fix: :sv_fix_objective_synonym_relationship,
    name: 'Objective synonym relationship',
    description: 'Objective synonyms should have the same type' )

  soft_validate(
    :sv_synonym_relationship,
    set: :synonym_relationship,
    name: 'Synonym relationship',
    description: 'Validate integrity of synonym relationship' )

  soft_validate(
    :sv_not_specific_relationship,
    set: :not_specific_relationship,
    fix: :sv_fix_not_specific_relationship,
    name: 'Not specific relationship',
    description: 'More specific relationship is preferred, for example "Subjective synonym" instead of "Synonym".' )

  soft_validate(
    :sv_synonym_linked_to_valid_name,
    set: :synonym_linked_to_valid_name,
    fix: :sv_fix_subject_parent_update,
    name: 'Synonym not linked to valid taxon',
    description: 'Synonyms should be linked to valid taxon.' )

  soft_validate(
    :sv_validate_priority,
    set: :validate_priority,
    name: 'Priority validation',
    description: 'Junior synonym should be younger than senior synonym' )

  soft_validate(
    :sv_validate_seniority,
    set: :validate_seniority,
    name: 'Seniority validation',
    description: 'Of two synonyms described in the same paper, one described at a higher rank has a priority' )

  soft_validate(
    :sv_coordinated_taxa,
    set: :coordinated_taxa,
    fix: :sv_fix_coordinated_subject_taxa,
    name: 'Move relationship to coordinate taxon',
    description: 'Relationship should be moved to the lowest rank coordinate taxon (for example from species to nomynotypical subspecies). It could be updated automatically with the Fix.' )

  soft_validate(
    :sv_coordinated_taxa_object,
    set: :coordinated_taxa,
    fix: :sv_fix_coordinated_object_taxa,
    name: 'Move object relationship to coordinate taxon',
    description: 'Relationship should be moved to the lowest rank coordinate object taxon (for example from species to nomynotypical subspecies). It could be updated automatically with the Fix.')

  scope :where_subject_is_taxon_name, -> (taxon_name) {where(subject_taxon_name_id: taxon_name)}
  scope :where_object_is_taxon_name, -> (taxon_name) {where(object_taxon_name_id: taxon_name)}
  scope :where_object_in_taxon_names, -> (taxon_name_array) {where('"taxon_name_relationships"."object_taxon_name_id" IN (?)', taxon_name_array)}

  scope :with_type_string, -> (type_string) { where(sanitize_sql_array(["taxon_name_relationships.type = '%s'", type_string])) }

  scope :with_type_base, -> (base_string) {where('"taxon_name_relationships"."type" LIKE ?', "#{base_string}%")}
  scope :with_type_contains, -> (base_string) {where('"taxon_name_relationships"."type" LIKE ?', "%#{base_string}%")}

  scope :with_two_type_bases, -> (base_string1, base_string2) {
    where('taxon_name_relationships.type LIKE ? OR taxon_name_relationships.type LIKE ?', "#{base_string1}%", "#{base_string2}%") }

  scope :homonym_or_suppressed, -> {where("taxon_name_relationships.type LIKE 'TaxonNameRelationship::Iczn::Invalidating::Homonym%' OR taxon_name_relationships.type LIKE 'TaxonNameRelationship::Iczn::Invalidating::Suppression::Total'") }
  scope :with_type_array, -> (base_array) {where('taxon_name_relationships.type IN (?)', base_array ) }

  def dwc_occurrences
    DwcOccurrence
      .joins("JOIN collection_objects co on dwc_occurrence_object_id = co.id AND dwc_occurrence_object_type = 'CollectionObject'")
      .joins("JOIN taxon_determinations td on co.id = td.taxon_determination_object_id AND td.taxon_determination_object_type = 'CollectionObject'")
      .joins("JOIN otus o on o.id = td.otu_id")
      .where(o: {taxon_name_id: [subject_taxon_name_id, object_taxon_name_id]})
      .distinct
  end

  # @return [Array of TaxonNameClassification]
  #  the inferable TaxonNameClassification(s) added to the subject when this relationship is used
  #  !! Not implemented
  def subject_properties
    []
  end

  # @return [Array of TaxonNameClassification]
  #  the inferable TaxonNameClassification(s) added to the subject when this relationship is used
  #  !! Not implmented
  def object_properties
    []
  end

  # @return class
  #   this method calls Module#module_parent
  def self.parent
    self.module_parent
  end

  # @return [Array of NomenclatureRank]
  #   the valid ranks to which the subject name can belong, set in subclasses. (left side)
  def self.valid_subject_ranks
    []
  end

  # @return [Array of NomenclatureRank]
  #   the valid ranks to which the object name can belong, set in subclasses. (right side)
  def self.valid_object_ranks
    []
  end

  # @return [Array of TaxonNameRelationships]
  #   if this relationships is set for the subject, then others in this array should not be used for that subject
  def self.disjoint_taxon_name_relationships
    []
  end

  # TODO: why isn't this disjoint?
  # disjoint relationships for the taxon as a object
  def self.required_taxon_name_relationships
    []
  end

  def self.disjoint_subject_classes
    []
  end

  def self.disjoint_object_classes
    []
  end

  def self.gbif_status_of_subject
    nil
  end

  def self.gbif_status_of_object
    nil
  end

  def self.assignable
    false
  end

  # @return [Symbol]
  #   determine the relative age of subject and object
  #   :direct - subject is younger than object
  #   :reverse - object is younger than subject
  def self.nomenclatural_priority
    nil
  end

  # @return [String]
  #    the status inferred by the relationship to the object name
  def object_status
    self.type_name.demodulize.underscore.humanize.downcase.gsub(/\d+/, ' \0 ').squish
  end

  # @return [String]
  #    the status inferred by the relationship to the subject name
  def subject_status
    self.type_name.demodulize.underscore.humanize.downcase.gsub(/\d+/, ' \0 ').squish
  end

  # @return [String]
  #    the connecting word in the relationship from the subject name to object name
  def subject_status_connector_to_object
    ' of'
  end

  # @return [String]
  #    the connecting word in the relationship from the object name to subject name
  def object_status_connector_to_subject
    ' of'
  end

  # @return [String]
  #   a readable fragement combining status and connector
  def subject_status_tag
    subject_status + subject_status_connector_to_object
  end

  # @return [String]
  #   a readable fragement combining status and connector
  def object_status_tag
    object_status + object_status_connector_to_subject
  end

  # @return [String, nil]
  #   the type of this relationship, IF the type is a valid name, else nil
  def type_name
    r = self.type
    TAXON_NAME_RELATIONSHIP_NAMES.include?(r) ? r : nil
  end

  def type_class=(value)
    write_attribute(:type, value.to_s)
  end

  def type_class
    r = read_attribute(:type).to_s
    TAXON_NAME_RELATIONSHIP_NAMES.include?(r) ? r.safe_constantize : nil
  end

  # @return [String, nil]
  #   the NOMEN uri for this type
  def self.nomen_uri
    const_defined?(:NOMEN_URI, false) ? self::NOMEN_URI : nil
  end

  # @return [Time]
  #   effective date of publication, used to determine nomenclatural priorities
  #   !! Careful, if no date is present the current year is given, rather than nil, @proceps is this a safe inference?
  def nomenclature_date
    self.source ? (self.source.cached_nomenclature_date ? self.source.cached_nomenclature_date.to_time : Time.current) : Time.current
  end

  def is_combination?
    !!/TaxonNameRelationship::(OriginalCombination|Combination)/.match(self.type.to_s)
  end

  protected

  def subject_and_object_in_same_project
    if subject_taxon_name && object_taxon_name
      if subject_taxon_name.project_id != object_taxon_name.project_id
        errors.add(:base, 'one name is not in the same project as the other')
      end
    end
  end

  def validate_type
    # TODO: Remove, handled by STI
    if type && !TAXON_NAME_RELATIONSHIP_NAMES.include?(type.to_s)
      errors.add(:type, "'#{type}' is not a valid taxon name relationship")
    elsif self.type_class && object_taxon_name.class.to_s == 'Protonym' && !self.type_class.valid_object_ranks.include?(object_taxon_name.rank_string)
      errors.add(:type, "'#{type}' is not a valid taxon name relationship")
    end

    if object_taxon_name.class.to_s == 'Protonym' || object_taxon_name.class.to_s == 'Hybrid'
      errors.add(:type, "'#{type}' is not a valid taxon name relationship") if /TaxonNameRelationship::Combination::/.match(self.type)
    end

    if object_taxon_name.class.to_s == 'Combination'
      errors.add(:type, "'#{type}' is not a valid taxon name relationship") unless /TaxonNameRelationship::Combination::/.match(self.type)
    end
  end

  # @todo validate, that all the relationships in the table could be linked to relationships in classes (if those had changed)

  def validate_subject_and_object_share_code
    if object_taxon_name.type  == 'Protonym' && subject_taxon_name.type == 'Protonym'
      errors.add(:object_taxon_name_id, 'The related taxon is not in the same monenclatural group (ICZN, ICN, ICNP, ICVCN') if subject_taxon_name.rank_class.try(:nomenclatural_code) != object_taxon_name.rank_class.try(:nomenclatural_code)
    end
  end

  def validate_subject_and_object_are_not_identical
    if !self.object_taxon_name_id.nil? && self.object_taxon_name == self.subject_taxon_name
      errors.add(:object_taxon_name_id, "#{self.object_taxon_name.try(:cached_html)} should not refer to itself") unless self.type =~ /OriginalCombination/
    end
  end

  def validate_object_must_equal_subject_for_uncertain_placement
    if self.object_taxon_name_id != self.subject_taxon_name.parent_id && self.type_name == 'TaxonNameRelationship::Iczn::Validating::UncertainPlacement'
      errors.add(:object_taxon_name_id, "The parent #{self.subject_taxon_name.parent.cached_html} and the Incertae Sedis placement (#{self.object_taxon_name.cached_html}) should match")
    end
  end

  def validate_subject_and_object_ranks
    tname = self.type_name

    if tname =~ /TaxonNameRelationship::(Icnp|Icn|Iczn|Icvcn)/ && tname != 'TaxonNameRelationship::Iczn::Validating::UncertainPlacement'
      rank_group = self.subject_taxon_name.rank_class.try(:parent)
      unless rank_group == self.object_taxon_name.rank_class.try(:parent)
        errors.add(:object_taxon_name_id, "Rank of related taxon should be in the #{rank_group.try(:rank_name)} rank group, not #{self.object_taxon_name.rank_class.try(:rank_name)}")
      end
    end

    if self.type_class.present? # only validate if it is set
      if object_taxon_name && object_taxon_name.rank_class
        if object_taxon_name.type == 'Protonym' || object_taxon_name.type == 'Hybrid'
          unless self.type_class.valid_object_ranks.include?(self.object_taxon_name.rank_string)
            errors.add(:object_taxon_name_id, "#{self.object_taxon_name.rank_class.rank_name.capitalize} rank of #{self.object_taxon_name.cached_html} is not compatible with the #{self.subject_status} relationship")
            errors.add(:type, "Relationship #{self.subject_status} is not compatible with the #{self.object_taxon_name.rank_class.rank_name} rank of #{self.object_taxon_name.cached_html}")
          end
        end
      end

      if subject_taxon_name && subject_taxon_name.rank_class
        if subject_taxon_name.type == 'Protonym' || subject_taxon_name.type == 'Hybrid'
          unless self.type_class.valid_subject_ranks.include?(self.subject_taxon_name.rank_string)
            soft_validations.add(:subject_taxon_name_id, "#{self.subject_taxon_name.rank_class.rank_name.capitalize} rank of #{self.subject_taxon_name.cached_html} is not compatible with the #{self.subject_status} relationship")
            soft_validations.add(:type, "Relationship #{self.subject_status} is not compatible with the #{self.subject_taxon_name.rank_class.rank_name} rank of #{self.subject_taxon_name.cached_html}")
          end
        end
      end
    end
  end

  ##### Protonym historically could be listed as a synonym to different taxa
  #def validate_uniqueness_of_synonym_subject
  #  if !self.type.nil? && /Synonym/.match(self.type_name) && !TaxonNameRelationship.where(subject_taxon_name_id: self.subject_taxon_name_id).with_type_contains('Synonym').not_self(self).empty?
  #    errors.add(:subject_taxon_name_id, 'Only one synonym relationship is allowed')
  #  end
  #end

  def validate_uniqueness_of_typification_object
    if /Typification/.match(self.type_name) && !TaxonNameRelationship.where(object_taxon_name_id: self.object_taxon_name_id).with_type_contains('Typification').not_self(self).empty?
      errors.add(:object_taxon_name_id, 'Only one Type designation relationship is allowed')
    end
  end

  def validate_rank_group
    if self.type =~ /Hybrid/ && self.subject_taxon_name && self.object_taxon_name
      if self.subject_taxon_name.rank_class.parent != self.object_taxon_name.rank_class.parent
        errors.add(:subject_taxon_name_id, "#{self.subject_taxon_name.rank_class.rank_name.capitalize} rank of #{self.subject_taxon_name.cached_html} is not compatible with the rank of hybrid (#{self.object_taxon_name.rank_class.rank_name})")
      end
    end
  end

  def validate_object_and_subject_both_protonyms
    if /TaxonNameRelationship::Combination::/.match(self.type)
      errors.add(:object_taxon_name_id, 'Not a Combination') if object_taxon_name.type != 'Combination'
    else
      errors.add(:object_taxon_name_id, 'Not a Protonym') if object_taxon_name.type == 'Combination'
    end
    errors.add(:subject_taxon_name_id, 'Not a Protonym') if subject_taxon_name.type == 'Combination' && self.type != 'TaxonNameRelationship::CurrentCombination'
  end

  def set_cached_names_for_taxon_names
    # !! only fire if subject_taxon_name changed
    return true unless subject_taxon_name_id_previously_changed? || destroyed?

    TaxonName.transaction do
      if is_invalidating?
        t = subject_taxon_name

        if type_name =~/Misspelling/
          t.update_column(:cached_misspelling, t.get_cached_misspelling)
          t.update_columns(
              cached_author_year: t.get_author_and_year,
              cached_nomenclature_date: t.nomenclature_date,
              cached_original_combination: t.get_original_combination,
              cached_original_combination_html: t.get_original_combination_html)
        end

        if type_name =~/Misapplication/
          t.update_columns(
            cached_author_year: t.get_author_and_year,
            cached_nomenclature_date: t.nomenclature_date)
        end

        vn = t.get_valid_taxon_name

        # !! NO set cached should do this from TN side of things,
        # !! Not here

        n = t.get_full_name

        t.update_columns(
          cached: n,
          cached_html: t.get_full_name_html(n), # OK to force reload here, otherwise we need an exception in #set_cached
          cached_valid_taxon_name_id: vn.id,
          cached_is_valid: !t.unavailable_or_invalid?)

        t.combination_list_self.each do |c|
          c.update_column(:cached_valid_taxon_name_id, vn.id)
        end

        vn.list_of_invalid_taxon_names.each do |s|
          s.update_columns(
            cached_valid_taxon_name_id: vn.id,
            cached_is_valid: !s.unavailable_or_invalid?)

          s.combination_list_self.each do |c|
            c.update_column(:cached_valid_taxon_name_id, vn.id)
          end
        end

      end

    end

    true
  end

  def is_invalidating?
    TAXON_NAME_RELATIONSHIP_NAMES_INVALID.include?(type_name)
  end

  def sv_validate_required_relationships
    return true if self.subject_taxon_name.not_binominal?
    object_relationships = TaxonNameRelationship.where_object_is_taxon_name(self.object_taxon_name).not_self(self).collect{|r| r.type}
    required = self.type_class.required_taxon_name_relationships - object_relationships
    required.each do |r|
      soft_validations.add(:type, " Presence of #{self.subject_status} requires selection of #{r.demodulize.underscore.humanize.downcase}")
    end
  end

  def sv_validate_disjoint_relationships
    tname = self.type_name
    if tname =~ /TaxonNameRelationship::(Icnp|Icn|Iczn|Icvcn)/ && tname != 'TaxonNameRelationship::Iczn::Validating::UncertainPlacement'
      subject_relationships = TaxonNameRelationship.where_subject_is_taxon_name(self.subject_taxon_name).not_self(self)
      subject_relationships.each  do |i|
        if self.type_class.disjoint_taxon_name_relationships.include?(i.type_name)
          soft_validations.add(:type, "#{self.subject_status.capitalize} relationship is conflicting with another relationship: '#{i.subject_status}'")
        end
      end
    end
  end

  def sv_validate_disjoint_object
    classifications = self.object_taxon_name.taxon_name_classifications.reload.map {|i| i.type_name}
    disjoint_object_classes = self.type_class.disjoint_object_classes
    compare = disjoint_object_classes & classifications
    compare.each do |i|
      c = i.demodulize.underscore.humanize.downcase
      soft_validations.add(:type, "#{self.subject_status.capitalize} relationship is conflicting with the taxon status: '#{c}'")
      soft_validations.add(:object_taxon_name_id, "#{self.object_taxon_name.cached_html} has a conflicting status: '#{c}'")
    end
  end

  def sv_validate_disjoint_subject
    classifications = self.subject_taxon_name.taxon_name_classifications.reload.map {|i| i.type_name}
    disjoint_subject_classes = self.type_class.disjoint_subject_classes
    compare = disjoint_subject_classes & classifications
    compare.each do |i|
      c = i.demodulize.underscore.humanize.downcase
      soft_validations.add(:type, "#{self.subject_status.capitalize} conflicting with the status: '#{c}'")
      soft_validations.add(:subject_taxon_name_id, "#{self.subject_taxon_name.cached_html} has a conflicting status: '#{c}'")
    end
  end

  def sv_specific_relationship
    true # all validations moved to subclasses
  end

  def sv_objective_synonym_relationship
    true # all validations moved to subclasses
  end

  def sv_fix_objective_synonym_relationship
    true # all validations moved to subclasses
  end

  def sv_synonym_relationship
    true # all validations moved to subclasses
  end

  def sv_not_specific_relationship
    true # all validations moved to subclasses
  end

  def sv_fix_not_specific_relationship
    true # all validations moved to subclasses
  end

  def sv_synonym_linked_to_valid_name
    #synonyms and misspellings should be linked to valid names
    if ::TAXON_NAME_RELATIONSHIP_NAMES_SYNONYM.include?(self.type_name)
      obj = self.object_taxon_name
      subj = self.subject_taxon_name
      if subj.rank_class.try(:nomenclatural_code) == :iczn && (obj.parent_id != subj.parent_id || obj.rank_class != subj.rank_class) &&  subj.cached_valid_taxon_name_id == obj.cached_valid_taxon_name_id
        soft_validations.add(:subject_taxon_name_id, "#{self.subject_status.capitalize}  #{subj.cached_html_name_and_author_year} should have the same parent and rank with  #{obj.cached_html_name_and_author_year}",
                             success_message: 'The parent was updated', failure_message:  'The parent was not updated')
      end
    end
  end

  def sv_fix_subject_parent_update
    res = false
    if TAXON_NAME_RELATIONSHIP_NAMES_SYNONYM.include?(self.type_name)
      obj = self.object_taxon_name
      subj = self.subject_taxon_name
      unless obj.parent_id == subj.parent_id
        subj.parent_id = obj.parent_id
        subj.rank_class = obj.rank_class
        begin
          TaxonName.transaction do
            subj.save!
            res = true
          end
        rescue
        end
      end
    end
    res
  end

  def subject_invalid_statuses
    TAXON_NAME_CLASS_NAMES_UNAVAILABLE_AND_INVALID & self.subject_taxon_name.taxon_name_classifications.collect{|c| c.type_class.to_s}
  end

  def sv_validate_priority
    true # all validations moved to subclasses
  end

  def sv_validate_seniority
    true # all validations moved to subclasses
  end

  def sv_coordinated_taxa
    s = subject_taxon_name
    o = object_taxon_name
    s_new = s.lowest_rank_coordinated_taxon
    if s != s_new
      soft_validations.add(:subject_taxon_name_id, "Relationship should move from #{s.rank_class.rank_name} #{s.cached_html} to #{s_new.rank_class.rank_name} #{s_new.cached_html}",
                           success_message: "Relationship moved to  #{s_new.rank_class.rank_name}", failure_message:  'Failed to update relationship')
    end
  end

  def sv_coordinated_taxa_object
    s = subject_taxon_name
    o = object_taxon_name
    o_new = o.lowest_rank_coordinated_taxon
    if o != o_new
      soft_validations.add(:object_taxon_name_id, "Relationship should move from #{o.rank_class.rank_name} #{o.cached_html} to #{o_new.rank_class.rank_name} #{o_new.cached_html}",
                           success_message: "Relationship moved to  #{o_new.rank_class.rank_name}", failure_message:  'Failed to update relationship')
    end
  end

  def sv_fix_coordinated_subject_taxa
    s = subject_taxon_name
    s_new = s.lowest_rank_coordinated_taxon
    if s != s_new
      self.subject_taxon_name = s_new
      begin
        TaxonNameRelationship.transaction do
          self.save
          return true
        end
      rescue
      end
    end
    false
  end

  def sv_fix_coordinated_object_taxa
    o = self.object_taxon_name
    o_new = o.lowest_rank_coordinated_taxon
    if o != o_new
      self.object_taxon_name = o_new
      begin
        TaxonNameRelationship.transaction do
          self.save
          return true
        end
      rescue
      end
    end
    false
  end

  def sv_fix_combination_relationship
    s = self.subject_taxon_name
    list = s.list_of_coordinated_names + [s]
    if s.rank_string =~ /Species/
      s_new = list.detect{|t| t.rank_class.rank_name == 'species'}
    elsif s.rank_string =~ /Genus/
      s_new = list.detect{|t| t.rank_class.rank_name == 'genus'}
    else
      s_new = s
    end
    if s != s_new && !s.nil?
      self.subject_taxon_name = s_new
      begin
        TaxonNameRelationship.transaction do
          self.save
          return true
        end
      rescue
      end
    end
    false
  end

  def self.collect_to_s(*args)
    args.collect{|arg| arg.to_s}
  end

  def self.collect_descendants_to_s(*classes)
    ans = []
    classes.each do |klass|
      ans += klass.descendants.collect{|k| k.to_s}
    end
    ans
  end

  def self.collect_descendants_and_itself_to_s(*classes)
    classes.collect{|k| k.to_s} + self.collect_descendants_to_s(*classes)
  end

  # Force loading all descendants as soon as this class is referenced
  Dir.glob("#{Rails.root.join("app/models/taxon_name_relationship/**/*.rb")}")
    .sort { |a, b| a.split('/').count <=> b.split('/').count }
    .map { |p| p.split('/app/models/').last.sub(/\.rb$/, '') }
    .map { |p| p.split('/') }
    .map { |c| c.map { |n| ActiveSupport::Inflector.camelize(n) } }
    .map { |c| c.join('::') }.map(&:constantize)
end

#subject_taxon_name_id ⇒ Integer

Returns the subject taxon name.

Returns:

• (Integer) —

  the subject taxon name

# File 'app/models/taxon_name_relationship.rb', line 44

class TaxonNameRelationship < ApplicationRecord
  include Housekeeping
  include Shared::Citations
  include Shared::Notes
  include SoftValidation
  include Shared::DwcOccurrenceHooks
  include Shared::IsData

  # @return [Boolean, nil]
  #   When true, cached values are not built
  attr_accessor :no_cached

  belongs_to :subject_taxon_name, class_name: 'TaxonName', inverse_of: :taxon_name_relationships # left side
  belongs_to :object_taxon_name, class_name: 'TaxonName', inverse_of: :related_taxon_name_relationships # right side

  # !! Keep as after_commit unless you are wanting to spend a lot of time
  # !! refactoring tests
  after_commit :set_cached_names_for_taxon_names, unless: -> {self.no_cached || destroyed?}
  after_destroy :set_cached_names_for_taxon_names, unless: -> {self.no_cached}

  # TODO: remove, it's required by STI
  validates_presence_of :type, message: 'Relationship type should be specified'
  validates_presence_of :subject_taxon_name, message: 'Missing taxon name on the left side'
  validates_presence_of :object_taxon_name, message: 'Missing taxon name on the right side'
  validates_uniqueness_of :object_taxon_name_id, scope: [:type, :project_id], if: :is_combination?
  validates_uniqueness_of :object_taxon_name_id, scope: [:type, :subject_taxon_name_id, :project_id], unless: :is_combination?

  validate :validate_type, :validate_subject_and_object_are_not_identical
  validate :subject_and_object_in_same_project

  with_options unless: -> {!subject_taxon_name || !object_taxon_name} do
    validate :validate_subject_and_object_share_code,
      :validate_uniqueness_of_typification_object,
      #:validate_uniqueness_of_synonym_subject,
      :validate_object_and_subject_both_protonyms,
      :validate_object_must_equal_subject_for_uncertain_placement,
      :validate_subject_and_object_ranks,
      :validate_rank_group
  end

  # TODO: isolate to an include file sensu protonym
  soft_validate(
    :sv_validate_required_relationships,
    set: :validate_required_relationships,
    name: 'Required relationships',
    description: 'Required relationships' )

  soft_validate(
    :sv_validate_disjoint_relationships,
    set: :validate_disjoint_relationships,
    name: 'Conflicting relationships',
    description: 'Detect conflicting relationships' )

  soft_validate(
    :sv_validate_disjoint_object,
    set: :validate_disjoint_object,
    name: 'Conflicting object taxon',
    description: 'Object taxon has a status conflicting with the relationship' )

  soft_validate(
    :sv_validate_disjoint_subject,
    set: :validate_disjoint_subject,
    name: 'Conflicting subject taxon',
    description: 'Subject taxon has a status conflicting with the relationship' )

  soft_validate(
    :sv_specific_relationship,
    set: :specific_relationship,
    name: 'validate relationship',
    description: 'Validate integrity of the relationship, for example, the year applicability range' )

  soft_validate(
    :sv_objective_synonym_relationship,
    set: :objective_synonym_relationship,
    fix: :sv_fix_objective_synonym_relationship,
    name: 'Objective synonym relationship',
    description: 'Objective synonyms should have the same type' )

  soft_validate(
    :sv_synonym_relationship,
    set: :synonym_relationship,
    name: 'Synonym relationship',
    description: 'Validate integrity of synonym relationship' )

  soft_validate(
    :sv_not_specific_relationship,
    set: :not_specific_relationship,
    fix: :sv_fix_not_specific_relationship,
    name: 'Not specific relationship',
    description: 'More specific relationship is preferred, for example "Subjective synonym" instead of "Synonym".' )

  soft_validate(
    :sv_synonym_linked_to_valid_name,
    set: :synonym_linked_to_valid_name,
    fix: :sv_fix_subject_parent_update,
    name: 'Synonym not linked to valid taxon',
    description: 'Synonyms should be linked to valid taxon.' )

  soft_validate(
    :sv_validate_priority,
    set: :validate_priority,
    name: 'Priority validation',
    description: 'Junior synonym should be younger than senior synonym' )

  soft_validate(
    :sv_validate_seniority,
    set: :validate_seniority,
    name: 'Seniority validation',
    description: 'Of two synonyms described in the same paper, one described at a higher rank has a priority' )

  soft_validate(
    :sv_coordinated_taxa,
    set: :coordinated_taxa,
    fix: :sv_fix_coordinated_subject_taxa,
    name: 'Move relationship to coordinate taxon',
    description: 'Relationship should be moved to the lowest rank coordinate taxon (for example from species to nomynotypical subspecies). It could be updated automatically with the Fix.' )

  soft_validate(
    :sv_coordinated_taxa_object,
    set: :coordinated_taxa,
    fix: :sv_fix_coordinated_object_taxa,
    name: 'Move object relationship to coordinate taxon',
    description: 'Relationship should be moved to the lowest rank coordinate object taxon (for example from species to nomynotypical subspecies). It could be updated automatically with the Fix.')

  scope :where_subject_is_taxon_name, -> (taxon_name) {where(subject_taxon_name_id: taxon_name)}
  scope :where_object_is_taxon_name, -> (taxon_name) {where(object_taxon_name_id: taxon_name)}
  scope :where_object_in_taxon_names, -> (taxon_name_array) {where('"taxon_name_relationships"."object_taxon_name_id" IN (?)', taxon_name_array)}

  scope :with_type_string, -> (type_string) { where(sanitize_sql_array(["taxon_name_relationships.type = '%s'", type_string])) }

  scope :with_type_base, -> (base_string) {where('"taxon_name_relationships"."type" LIKE ?', "#{base_string}%")}
  scope :with_type_contains, -> (base_string) {where('"taxon_name_relationships"."type" LIKE ?', "%#{base_string}%")}

  scope :with_two_type_bases, -> (base_string1, base_string2) {
    where('taxon_name_relationships.type LIKE ? OR taxon_name_relationships.type LIKE ?', "#{base_string1}%", "#{base_string2}%") }

  scope :homonym_or_suppressed, -> {where("taxon_name_relationships.type LIKE 'TaxonNameRelationship::Iczn::Invalidating::Homonym%' OR taxon_name_relationships.type LIKE 'TaxonNameRelationship::Iczn::Invalidating::Suppression::Total'") }
  scope :with_type_array, -> (base_array) {where('taxon_name_relationships.type IN (?)', base_array ) }

  def dwc_occurrences
    DwcOccurrence
      .joins("JOIN collection_objects co on dwc_occurrence_object_id = co.id AND dwc_occurrence_object_type = 'CollectionObject'")
      .joins("JOIN taxon_determinations td on co.id = td.taxon_determination_object_id AND td.taxon_determination_object_type = 'CollectionObject'")
      .joins("JOIN otus o on o.id = td.otu_id")
      .where(o: {taxon_name_id: [subject_taxon_name_id, object_taxon_name_id]})
      .distinct
  end

  # @return [Array of TaxonNameClassification]
  #  the inferable TaxonNameClassification(s) added to the subject when this relationship is used
  #  !! Not implemented
  def subject_properties
    []
  end

  # @return [Array of TaxonNameClassification]
  #  the inferable TaxonNameClassification(s) added to the subject when this relationship is used
  #  !! Not implmented
  def object_properties
    []
  end

  # @return class
  #   this method calls Module#module_parent
  def self.parent
    self.module_parent
  end

  # @return [Array of NomenclatureRank]
  #   the valid ranks to which the subject name can belong, set in subclasses. (left side)
  def self.valid_subject_ranks
    []
  end

  # @return [Array of NomenclatureRank]
  #   the valid ranks to which the object name can belong, set in subclasses. (right side)
  def self.valid_object_ranks
    []
  end

  # @return [Array of TaxonNameRelationships]
  #   if this relationships is set for the subject, then others in this array should not be used for that subject
  def self.disjoint_taxon_name_relationships
    []
  end

  # TODO: why isn't this disjoint?
  # disjoint relationships for the taxon as a object
  def self.required_taxon_name_relationships
    []
  end

  def self.disjoint_subject_classes
    []
  end

  def self.disjoint_object_classes
    []
  end

  def self.gbif_status_of_subject
    nil
  end

  def self.gbif_status_of_object
    nil
  end

  def self.assignable
    false
  end

  # @return [Symbol]
  #   determine the relative age of subject and object
  #   :direct - subject is younger than object
  #   :reverse - object is younger than subject
  def self.nomenclatural_priority
    nil
  end

  # @return [String]
  #    the status inferred by the relationship to the object name
  def object_status
    self.type_name.demodulize.underscore.humanize.downcase.gsub(/\d+/, ' \0 ').squish
  end

  # @return [String]
  #    the status inferred by the relationship to the subject name
  def subject_status
    self.type_name.demodulize.underscore.humanize.downcase.gsub(/\d+/, ' \0 ').squish
  end

  # @return [String]
  #    the connecting word in the relationship from the subject name to object name
  def subject_status_connector_to_object
    ' of'
  end

  # @return [String]
  #    the connecting word in the relationship from the object name to subject name
  def object_status_connector_to_subject
    ' of'
  end

  # @return [String]
  #   a readable fragement combining status and connector
  def subject_status_tag
    subject_status + subject_status_connector_to_object
  end

  # @return [String]
  #   a readable fragement combining status and connector
  def object_status_tag
    object_status + object_status_connector_to_subject
  end

  # @return [String, nil]
  #   the type of this relationship, IF the type is a valid name, else nil
  def type_name
    r = self.type
    TAXON_NAME_RELATIONSHIP_NAMES.include?(r) ? r : nil
  end

  def type_class=(value)
    write_attribute(:type, value.to_s)
  end

  def type_class
    r = read_attribute(:type).to_s
    TAXON_NAME_RELATIONSHIP_NAMES.include?(r) ? r.safe_constantize : nil
  end

  # @return [String, nil]
  #   the NOMEN uri for this type
  def self.nomen_uri
    const_defined?(:NOMEN_URI, false) ? self::NOMEN_URI : nil
  end

  # @return [Time]
  #   effective date of publication, used to determine nomenclatural priorities
  #   !! Careful, if no date is present the current year is given, rather than nil, @proceps is this a safe inference?
  def nomenclature_date
    self.source ? (self.source.cached_nomenclature_date ? self.source.cached_nomenclature_date.to_time : Time.current) : Time.current
  end

  def is_combination?
    !!/TaxonNameRelationship::(OriginalCombination|Combination)/.match(self.type.to_s)
  end

  protected

  def subject_and_object_in_same_project
    if subject_taxon_name && object_taxon_name
      if subject_taxon_name.project_id != object_taxon_name.project_id
        errors.add(:base, 'one name is not in the same project as the other')
      end
    end
  end

  def validate_type
    # TODO: Remove, handled by STI
    if type && !TAXON_NAME_RELATIONSHIP_NAMES.include?(type.to_s)
      errors.add(:type, "'#{type}' is not a valid taxon name relationship")
    elsif self.type_class && object_taxon_name.class.to_s == 'Protonym' && !self.type_class.valid_object_ranks.include?(object_taxon_name.rank_string)
      errors.add(:type, "'#{type}' is not a valid taxon name relationship")
    end

    if object_taxon_name.class.to_s == 'Protonym' || object_taxon_name.class.to_s == 'Hybrid'
      errors.add(:type, "'#{type}' is not a valid taxon name relationship") if /TaxonNameRelationship::Combination::/.match(self.type)
    end

    if object_taxon_name.class.to_s == 'Combination'
      errors.add(:type, "'#{type}' is not a valid taxon name relationship") unless /TaxonNameRelationship::Combination::/.match(self.type)
    end
  end

  # @todo validate, that all the relationships in the table could be linked to relationships in classes (if those had changed)

  def validate_subject_and_object_share_code
    if object_taxon_name.type  == 'Protonym' && subject_taxon_name.type == 'Protonym'
      errors.add(:object_taxon_name_id, 'The related taxon is not in the same monenclatural group (ICZN, ICN, ICNP, ICVCN') if subject_taxon_name.rank_class.try(:nomenclatural_code) != object_taxon_name.rank_class.try(:nomenclatural_code)
    end
  end

  def validate_subject_and_object_are_not_identical
    if !self.object_taxon_name_id.nil? && self.object_taxon_name == self.subject_taxon_name
      errors.add(:object_taxon_name_id, "#{self.object_taxon_name.try(:cached_html)} should not refer to itself") unless self.type =~ /OriginalCombination/
    end
  end

  def validate_object_must_equal_subject_for_uncertain_placement
    if self.object_taxon_name_id != self.subject_taxon_name.parent_id && self.type_name == 'TaxonNameRelationship::Iczn::Validating::UncertainPlacement'
      errors.add(:object_taxon_name_id, "The parent #{self.subject_taxon_name.parent.cached_html} and the Incertae Sedis placement (#{self.object_taxon_name.cached_html}) should match")
    end
  end

  def validate_subject_and_object_ranks
    tname = self.type_name

    if tname =~ /TaxonNameRelationship::(Icnp|Icn|Iczn|Icvcn)/ && tname != 'TaxonNameRelationship::Iczn::Validating::UncertainPlacement'
      rank_group = self.subject_taxon_name.rank_class.try(:parent)
      unless rank_group == self.object_taxon_name.rank_class.try(:parent)
        errors.add(:object_taxon_name_id, "Rank of related taxon should be in the #{rank_group.try(:rank_name)} rank group, not #{self.object_taxon_name.rank_class.try(:rank_name)}")
      end
    end

    if self.type_class.present? # only validate if it is set
      if object_taxon_name && object_taxon_name.rank_class
        if object_taxon_name.type == 'Protonym' || object_taxon_name.type == 'Hybrid'
          unless self.type_class.valid_object_ranks.include?(self.object_taxon_name.rank_string)
            errors.add(:object_taxon_name_id, "#{self.object_taxon_name.rank_class.rank_name.capitalize} rank of #{self.object_taxon_name.cached_html} is not compatible with the #{self.subject_status} relationship")
            errors.add(:type, "Relationship #{self.subject_status} is not compatible with the #{self.object_taxon_name.rank_class.rank_name} rank of #{self.object_taxon_name.cached_html}")
          end
        end
      end

      if subject_taxon_name && subject_taxon_name.rank_class
        if subject_taxon_name.type == 'Protonym' || subject_taxon_name.type == 'Hybrid'
          unless self.type_class.valid_subject_ranks.include?(self.subject_taxon_name.rank_string)
            soft_validations.add(:subject_taxon_name_id, "#{self.subject_taxon_name.rank_class.rank_name.capitalize} rank of #{self.subject_taxon_name.cached_html} is not compatible with the #{self.subject_status} relationship")
            soft_validations.add(:type, "Relationship #{self.subject_status} is not compatible with the #{self.subject_taxon_name.rank_class.rank_name} rank of #{self.subject_taxon_name.cached_html}")
          end
        end
      end
    end
  end

  ##### Protonym historically could be listed as a synonym to different taxa
  #def validate_uniqueness_of_synonym_subject
  #  if !self.type.nil? && /Synonym/.match(self.type_name) && !TaxonNameRelationship.where(subject_taxon_name_id: self.subject_taxon_name_id).with_type_contains('Synonym').not_self(self).empty?
  #    errors.add(:subject_taxon_name_id, 'Only one synonym relationship is allowed')
  #  end
  #end

  def validate_uniqueness_of_typification_object
    if /Typification/.match(self.type_name) && !TaxonNameRelationship.where(object_taxon_name_id: self.object_taxon_name_id).with_type_contains('Typification').not_self(self).empty?
      errors.add(:object_taxon_name_id, 'Only one Type designation relationship is allowed')
    end
  end

  def validate_rank_group
    if self.type =~ /Hybrid/ && self.subject_taxon_name && self.object_taxon_name
      if self.subject_taxon_name.rank_class.parent != self.object_taxon_name.rank_class.parent
        errors.add(:subject_taxon_name_id, "#{self.subject_taxon_name.rank_class.rank_name.capitalize} rank of #{self.subject_taxon_name.cached_html} is not compatible with the rank of hybrid (#{self.object_taxon_name.rank_class.rank_name})")
      end
    end
  end

  def validate_object_and_subject_both_protonyms
    if /TaxonNameRelationship::Combination::/.match(self.type)
      errors.add(:object_taxon_name_id, 'Not a Combination') if object_taxon_name.type != 'Combination'
    else
      errors.add(:object_taxon_name_id, 'Not a Protonym') if object_taxon_name.type == 'Combination'
    end
    errors.add(:subject_taxon_name_id, 'Not a Protonym') if subject_taxon_name.type == 'Combination' && self.type != 'TaxonNameRelationship::CurrentCombination'
  end

  def set_cached_names_for_taxon_names
    # !! only fire if subject_taxon_name changed
    return true unless subject_taxon_name_id_previously_changed? || destroyed?

    TaxonName.transaction do
      if is_invalidating?
        t = subject_taxon_name

        if type_name =~/Misspelling/
          t.update_column(:cached_misspelling, t.get_cached_misspelling)
          t.update_columns(
              cached_author_year: t.get_author_and_year,
              cached_nomenclature_date: t.nomenclature_date,
              cached_original_combination: t.get_original_combination,
              cached_original_combination_html: t.get_original_combination_html)
        end

        if type_name =~/Misapplication/
          t.update_columns(
            cached_author_year: t.get_author_and_year,
            cached_nomenclature_date: t.nomenclature_date)
        end

        vn = t.get_valid_taxon_name

        # !! NO set cached should do this from TN side of things,
        # !! Not here

        n = t.get_full_name

        t.update_columns(
          cached: n,
          cached_html: t.get_full_name_html(n), # OK to force reload here, otherwise we need an exception in #set_cached
          cached_valid_taxon_name_id: vn.id,
          cached_is_valid: !t.unavailable_or_invalid?)

        t.combination_list_self.each do |c|
          c.update_column(:cached_valid_taxon_name_id, vn.id)
        end

        vn.list_of_invalid_taxon_names.each do |s|
          s.update_columns(
            cached_valid_taxon_name_id: vn.id,
            cached_is_valid: !s.unavailable_or_invalid?)

          s.combination_list_self.each do |c|
            c.update_column(:cached_valid_taxon_name_id, vn.id)
          end
        end

      end

    end

    true
  end

  def is_invalidating?
    TAXON_NAME_RELATIONSHIP_NAMES_INVALID.include?(type_name)
  end

  def sv_validate_required_relationships
    return true if self.subject_taxon_name.not_binominal?
    object_relationships = TaxonNameRelationship.where_object_is_taxon_name(self.object_taxon_name).not_self(self).collect{|r| r.type}
    required = self.type_class.required_taxon_name_relationships - object_relationships
    required.each do |r|
      soft_validations.add(:type, " Presence of #{self.subject_status} requires selection of #{r.demodulize.underscore.humanize.downcase}")
    end
  end

  def sv_validate_disjoint_relationships
    tname = self.type_name
    if tname =~ /TaxonNameRelationship::(Icnp|Icn|Iczn|Icvcn)/ && tname != 'TaxonNameRelationship::Iczn::Validating::UncertainPlacement'
      subject_relationships = TaxonNameRelationship.where_subject_is_taxon_name(self.subject_taxon_name).not_self(self)
      subject_relationships.each  do |i|
        if self.type_class.disjoint_taxon_name_relationships.include?(i.type_name)
          soft_validations.add(:type, "#{self.subject_status.capitalize} relationship is conflicting with another relationship: '#{i.subject_status}'")
        end
      end
    end
  end

  def sv_validate_disjoint_object
    classifications = self.object_taxon_name.taxon_name_classifications.reload.map {|i| i.type_name}
    disjoint_object_classes = self.type_class.disjoint_object_classes
    compare = disjoint_object_classes & classifications
    compare.each do |i|
      c = i.demodulize.underscore.humanize.downcase
      soft_validations.add(:type, "#{self.subject_status.capitalize} relationship is conflicting with the taxon status: '#{c}'")
      soft_validations.add(:object_taxon_name_id, "#{self.object_taxon_name.cached_html} has a conflicting status: '#{c}'")
    end
  end

  def sv_validate_disjoint_subject
    classifications = self.subject_taxon_name.taxon_name_classifications.reload.map {|i| i.type_name}
    disjoint_subject_classes = self.type_class.disjoint_subject_classes
    compare = disjoint_subject_classes & classifications
    compare.each do |i|
      c = i.demodulize.underscore.humanize.downcase
      soft_validations.add(:type, "#{self.subject_status.capitalize} conflicting with the status: '#{c}'")
      soft_validations.add(:subject_taxon_name_id, "#{self.subject_taxon_name.cached_html} has a conflicting status: '#{c}'")
    end
  end

  def sv_specific_relationship
    true # all validations moved to subclasses
  end

  def sv_objective_synonym_relationship
    true # all validations moved to subclasses
  end

  def sv_fix_objective_synonym_relationship
    true # all validations moved to subclasses
  end

  def sv_synonym_relationship
    true # all validations moved to subclasses
  end

  def sv_not_specific_relationship
    true # all validations moved to subclasses
  end

  def sv_fix_not_specific_relationship
    true # all validations moved to subclasses
  end

  def sv_synonym_linked_to_valid_name
    #synonyms and misspellings should be linked to valid names
    if ::TAXON_NAME_RELATIONSHIP_NAMES_SYNONYM.include?(self.type_name)
      obj = self.object_taxon_name
      subj = self.subject_taxon_name
      if subj.rank_class.try(:nomenclatural_code) == :iczn && (obj.parent_id != subj.parent_id || obj.rank_class != subj.rank_class) &&  subj.cached_valid_taxon_name_id == obj.cached_valid_taxon_name_id
        soft_validations.add(:subject_taxon_name_id, "#{self.subject_status.capitalize}  #{subj.cached_html_name_and_author_year} should have the same parent and rank with  #{obj.cached_html_name_and_author_year}",
                             success_message: 'The parent was updated', failure_message:  'The parent was not updated')
      end
    end
  end

  def sv_fix_subject_parent_update
    res = false
    if TAXON_NAME_RELATIONSHIP_NAMES_SYNONYM.include?(self.type_name)
      obj = self.object_taxon_name
      subj = self.subject_taxon_name
      unless obj.parent_id == subj.parent_id
        subj.parent_id = obj.parent_id
        subj.rank_class = obj.rank_class
        begin
          TaxonName.transaction do
            subj.save!
            res = true
          end
        rescue
        end
      end
    end
    res
  end

  def subject_invalid_statuses
    TAXON_NAME_CLASS_NAMES_UNAVAILABLE_AND_INVALID & self.subject_taxon_name.taxon_name_classifications.collect{|c| c.type_class.to_s}
  end

  def sv_validate_priority
    true # all validations moved to subclasses
  end

  def sv_validate_seniority
    true # all validations moved to subclasses
  end

  def sv_coordinated_taxa
    s = subject_taxon_name
    o = object_taxon_name
    s_new = s.lowest_rank_coordinated_taxon
    if s != s_new
      soft_validations.add(:subject_taxon_name_id, "Relationship should move from #{s.rank_class.rank_name} #{s.cached_html} to #{s_new.rank_class.rank_name} #{s_new.cached_html}",
                           success_message: "Relationship moved to  #{s_new.rank_class.rank_name}", failure_message:  'Failed to update relationship')
    end
  end

  def sv_coordinated_taxa_object
    s = subject_taxon_name
    o = object_taxon_name
    o_new = o.lowest_rank_coordinated_taxon
    if o != o_new
      soft_validations.add(:object_taxon_name_id, "Relationship should move from #{o.rank_class.rank_name} #{o.cached_html} to #{o_new.rank_class.rank_name} #{o_new.cached_html}",
                           success_message: "Relationship moved to  #{o_new.rank_class.rank_name}", failure_message:  'Failed to update relationship')
    end
  end

  def sv_fix_coordinated_subject_taxa
    s = subject_taxon_name
    s_new = s.lowest_rank_coordinated_taxon
    if s != s_new
      self.subject_taxon_name = s_new
      begin
        TaxonNameRelationship.transaction do
          self.save
          return true
        end
      rescue
      end
    end
    false
  end

  def sv_fix_coordinated_object_taxa
    o = self.object_taxon_name
    o_new = o.lowest_rank_coordinated_taxon
    if o != o_new
      self.object_taxon_name = o_new
      begin
        TaxonNameRelationship.transaction do
          self.save
          return true
        end
      rescue
      end
    end
    false
  end

  def sv_fix_combination_relationship
    s = self.subject_taxon_name
    list = s.list_of_coordinated_names + [s]
    if s.rank_string =~ /Species/
      s_new = list.detect{|t| t.rank_class.rank_name == 'species'}
    elsif s.rank_string =~ /Genus/
      s_new = list.detect{|t| t.rank_class.rank_name == 'genus'}
    else
      s_new = s
    end
    if s != s_new && !s.nil?
      self.subject_taxon_name = s_new
      begin
        TaxonNameRelationship.transaction do
          self.save
          return true
        end
      rescue
      end
    end
    false
  end

  def self.collect_to_s(*args)
    args.collect{|arg| arg.to_s}
  end

  def self.collect_descendants_to_s(*classes)
    ans = []
    classes.each do |klass|
      ans += klass.descendants.collect{|k| k.to_s}
    end
    ans
  end

  def self.collect_descendants_and_itself_to_s(*classes)
    classes.collect{|k| k.to_s} + self.collect_descendants_to_s(*classes)
  end

  # Force loading all descendants as soon as this class is referenced
  Dir.glob("#{Rails.root.join("app/models/taxon_name_relationship/**/*.rb")}")
    .sort { |a, b| a.split('/').count <=> b.split('/').count }
    .map { |p| p.split('/app/models/').last.sub(/\.rb$/, '') }
    .map { |p| p.split('/') }
    .map { |c| c.map { |n| ActiveSupport::Inflector.camelize(n) } }
    .map { |c| c.join('::') }.map(&:constantize)
end

#type ⇒ String

Returns the relationship/“predicate” between the subject and object taxon names.

Returns:

• (String) —

  the relationship/“predicate” between the subject and object taxon names

# File 'app/models/taxon_name_relationship.rb', line 44

class TaxonNameRelationship < ApplicationRecord
  include Housekeeping
  include Shared::Citations
  include Shared::Notes
  include SoftValidation
  include Shared::DwcOccurrenceHooks
  include Shared::IsData

  # @return [Boolean, nil]
  #   When true, cached values are not built
  attr_accessor :no_cached

  belongs_to :subject_taxon_name, class_name: 'TaxonName', inverse_of: :taxon_name_relationships # left side
  belongs_to :object_taxon_name, class_name: 'TaxonName', inverse_of: :related_taxon_name_relationships # right side

  # !! Keep as after_commit unless you are wanting to spend a lot of time
  # !! refactoring tests
  after_commit :set_cached_names_for_taxon_names, unless: -> {self.no_cached || destroyed?}
  after_destroy :set_cached_names_for_taxon_names, unless: -> {self.no_cached}

  # TODO: remove, it's required by STI
  validates_presence_of :type, message: 'Relationship type should be specified'
  validates_presence_of :subject_taxon_name, message: 'Missing taxon name on the left side'
  validates_presence_of :object_taxon_name, message: 'Missing taxon name on the right side'
  validates_uniqueness_of :object_taxon_name_id, scope: [:type, :project_id], if: :is_combination?
  validates_uniqueness_of :object_taxon_name_id, scope: [:type, :subject_taxon_name_id, :project_id], unless: :is_combination?

  validate :validate_type, :validate_subject_and_object_are_not_identical
  validate :subject_and_object_in_same_project

  with_options unless: -> {!subject_taxon_name || !object_taxon_name} do
    validate :validate_subject_and_object_share_code,
      :validate_uniqueness_of_typification_object,
      #:validate_uniqueness_of_synonym_subject,
      :validate_object_and_subject_both_protonyms,
      :validate_object_must_equal_subject_for_uncertain_placement,
      :validate_subject_and_object_ranks,
      :validate_rank_group
  end

  # TODO: isolate to an include file sensu protonym
  soft_validate(
    :sv_validate_required_relationships,
    set: :validate_required_relationships,
    name: 'Required relationships',
    description: 'Required relationships' )

  soft_validate(
    :sv_validate_disjoint_relationships,
    set: :validate_disjoint_relationships,
    name: 'Conflicting relationships',
    description: 'Detect conflicting relationships' )

  soft_validate(
    :sv_validate_disjoint_object,
    set: :validate_disjoint_object,
    name: 'Conflicting object taxon',
    description: 'Object taxon has a status conflicting with the relationship' )

  soft_validate(
    :sv_validate_disjoint_subject,
    set: :validate_disjoint_subject,
    name: 'Conflicting subject taxon',
    description: 'Subject taxon has a status conflicting with the relationship' )

  soft_validate(
    :sv_specific_relationship,
    set: :specific_relationship,
    name: 'validate relationship',
    description: 'Validate integrity of the relationship, for example, the year applicability range' )

  soft_validate(
    :sv_objective_synonym_relationship,
    set: :objective_synonym_relationship,
    fix: :sv_fix_objective_synonym_relationship,
    name: 'Objective synonym relationship',
    description: 'Objective synonyms should have the same type' )

  soft_validate(
    :sv_synonym_relationship,
    set: :synonym_relationship,
    name: 'Synonym relationship',
    description: 'Validate integrity of synonym relationship' )

  soft_validate(
    :sv_not_specific_relationship,
    set: :not_specific_relationship,
    fix: :sv_fix_not_specific_relationship,
    name: 'Not specific relationship',
    description: 'More specific relationship is preferred, for example "Subjective synonym" instead of "Synonym".' )

  soft_validate(
    :sv_synonym_linked_to_valid_name,
    set: :synonym_linked_to_valid_name,
    fix: :sv_fix_subject_parent_update,
    name: 'Synonym not linked to valid taxon',
    description: 'Synonyms should be linked to valid taxon.' )

  soft_validate(
    :sv_validate_priority,
    set: :validate_priority,
    name: 'Priority validation',
    description: 'Junior synonym should be younger than senior synonym' )

  soft_validate(
    :sv_validate_seniority,
    set: :validate_seniority,
    name: 'Seniority validation',
    description: 'Of two synonyms described in the same paper, one described at a higher rank has a priority' )

  soft_validate(
    :sv_coordinated_taxa,
    set: :coordinated_taxa,
    fix: :sv_fix_coordinated_subject_taxa,
    name: 'Move relationship to coordinate taxon',
    description: 'Relationship should be moved to the lowest rank coordinate taxon (for example from species to nomynotypical subspecies). It could be updated automatically with the Fix.' )

  soft_validate(
    :sv_coordinated_taxa_object,
    set: :coordinated_taxa,
    fix: :sv_fix_coordinated_object_taxa,
    name: 'Move object relationship to coordinate taxon',
    description: 'Relationship should be moved to the lowest rank coordinate object taxon (for example from species to nomynotypical subspecies). It could be updated automatically with the Fix.')

  scope :where_subject_is_taxon_name, -> (taxon_name) {where(subject_taxon_name_id: taxon_name)}
  scope :where_object_is_taxon_name, -> (taxon_name) {where(object_taxon_name_id: taxon_name)}
  scope :where_object_in_taxon_names, -> (taxon_name_array) {where('"taxon_name_relationships"."object_taxon_name_id" IN (?)', taxon_name_array)}

  scope :with_type_string, -> (type_string) { where(sanitize_sql_array(["taxon_name_relationships.type = '%s'", type_string])) }

  scope :with_type_base, -> (base_string) {where('"taxon_name_relationships"."type" LIKE ?', "#{base_string}%")}
  scope :with_type_contains, -> (base_string) {where('"taxon_name_relationships"."type" LIKE ?', "%#{base_string}%")}

  scope :with_two_type_bases, -> (base_string1, base_string2) {
    where('taxon_name_relationships.type LIKE ? OR taxon_name_relationships.type LIKE ?', "#{base_string1}%", "#{base_string2}%") }

  scope :homonym_or_suppressed, -> {where("taxon_name_relationships.type LIKE 'TaxonNameRelationship::Iczn::Invalidating::Homonym%' OR taxon_name_relationships.type LIKE 'TaxonNameRelationship::Iczn::Invalidating::Suppression::Total'") }
  scope :with_type_array, -> (base_array) {where('taxon_name_relationships.type IN (?)', base_array ) }

  def dwc_occurrences
    DwcOccurrence
      .joins("JOIN collection_objects co on dwc_occurrence_object_id = co.id AND dwc_occurrence_object_type = 'CollectionObject'")
      .joins("JOIN taxon_determinations td on co.id = td.taxon_determination_object_id AND td.taxon_determination_object_type = 'CollectionObject'")
      .joins("JOIN otus o on o.id = td.otu_id")
      .where(o: {taxon_name_id: [subject_taxon_name_id, object_taxon_name_id]})
      .distinct
  end

  # @return [Array of TaxonNameClassification]
  #  the inferable TaxonNameClassification(s) added to the subject when this relationship is used
  #  !! Not implemented
  def subject_properties
    []
  end

  # @return [Array of TaxonNameClassification]
  #  the inferable TaxonNameClassification(s) added to the subject when this relationship is used
  #  !! Not implmented
  def object_properties
    []
  end

  # @return class
  #   this method calls Module#module_parent
  def self.parent
    self.module_parent
  end

  # @return [Array of NomenclatureRank]
  #   the valid ranks to which the subject name can belong, set in subclasses. (left side)
  def self.valid_subject_ranks
    []
  end

  # @return [Array of NomenclatureRank]
  #   the valid ranks to which the object name can belong, set in subclasses. (right side)
  def self.valid_object_ranks
    []
  end

  # @return [Array of TaxonNameRelationships]
  #   if this relationships is set for the subject, then others in this array should not be used for that subject
  def self.disjoint_taxon_name_relationships
    []
  end

  # TODO: why isn't this disjoint?
  # disjoint relationships for the taxon as a object
  def self.required_taxon_name_relationships
    []
  end

  def self.disjoint_subject_classes
    []
  end

  def self.disjoint_object_classes
    []
  end

  def self.gbif_status_of_subject
    nil
  end

  def self.gbif_status_of_object
    nil
  end

  def self.assignable
    false
  end

  # @return [Symbol]
  #   determine the relative age of subject and object
  #   :direct - subject is younger than object
  #   :reverse - object is younger than subject
  def self.nomenclatural_priority
    nil
  end

  # @return [String]
  #    the status inferred by the relationship to the object name
  def object_status
    self.type_name.demodulize.underscore.humanize.downcase.gsub(/\d+/, ' \0 ').squish
  end

  # @return [String]
  #    the status inferred by the relationship to the subject name
  def subject_status
    self.type_name.demodulize.underscore.humanize.downcase.gsub(/\d+/, ' \0 ').squish
  end

  # @return [String]
  #    the connecting word in the relationship from the subject name to object name
  def subject_status_connector_to_object
    ' of'
  end

  # @return [String]
  #    the connecting word in the relationship from the object name to subject name
  def object_status_connector_to_subject
    ' of'
  end

  # @return [String]
  #   a readable fragement combining status and connector
  def subject_status_tag
    subject_status + subject_status_connector_to_object
  end

  # @return [String]
  #   a readable fragement combining status and connector
  def object_status_tag
    object_status + object_status_connector_to_subject
  end

  # @return [String, nil]
  #   the type of this relationship, IF the type is a valid name, else nil
  def type_name
    r = self.type
    TAXON_NAME_RELATIONSHIP_NAMES.include?(r) ? r : nil
  end

  def type_class=(value)
    write_attribute(:type, value.to_s)
  end

  def type_class
    r = read_attribute(:type).to_s
    TAXON_NAME_RELATIONSHIP_NAMES.include?(r) ? r.safe_constantize : nil
  end

  # @return [String, nil]
  #   the NOMEN uri for this type
  def self.nomen_uri
    const_defined?(:NOMEN_URI, false) ? self::NOMEN_URI : nil
  end

  # @return [Time]
  #   effective date of publication, used to determine nomenclatural priorities
  #   !! Careful, if no date is present the current year is given, rather than nil, @proceps is this a safe inference?
  def nomenclature_date
    self.source ? (self.source.cached_nomenclature_date ? self.source.cached_nomenclature_date.to_time : Time.current) : Time.current
  end

  def is_combination?
    !!/TaxonNameRelationship::(OriginalCombination|Combination)/.match(self.type.to_s)
  end

  protected

  def subject_and_object_in_same_project
    if subject_taxon_name && object_taxon_name
      if subject_taxon_name.project_id != object_taxon_name.project_id
        errors.add(:base, 'one name is not in the same project as the other')
      end
    end
  end

  def validate_type
    # TODO: Remove, handled by STI
    if type && !TAXON_NAME_RELATIONSHIP_NAMES.include?(type.to_s)
      errors.add(:type, "'#{type}' is not a valid taxon name relationship")
    elsif self.type_class && object_taxon_name.class.to_s == 'Protonym' && !self.type_class.valid_object_ranks.include?(object_taxon_name.rank_string)
      errors.add(:type, "'#{type}' is not a valid taxon name relationship")
    end

    if object_taxon_name.class.to_s == 'Protonym' || object_taxon_name.class.to_s == 'Hybrid'
      errors.add(:type, "'#{type}' is not a valid taxon name relationship") if /TaxonNameRelationship::Combination::/.match(self.type)
    end

    if object_taxon_name.class.to_s == 'Combination'
      errors.add(:type, "'#{type}' is not a valid taxon name relationship") unless /TaxonNameRelationship::Combination::/.match(self.type)
    end
  end

  # @todo validate, that all the relationships in the table could be linked to relationships in classes (if those had changed)

  def validate_subject_and_object_share_code
    if object_taxon_name.type  == 'Protonym' && subject_taxon_name.type == 'Protonym'
      errors.add(:object_taxon_name_id, 'The related taxon is not in the same monenclatural group (ICZN, ICN, ICNP, ICVCN') if subject_taxon_name.rank_class.try(:nomenclatural_code) != object_taxon_name.rank_class.try(:nomenclatural_code)
    end
  end

  def validate_subject_and_object_are_not_identical
    if !self.object_taxon_name_id.nil? && self.object_taxon_name == self.subject_taxon_name
      errors.add(:object_taxon_name_id, "#{self.object_taxon_name.try(:cached_html)} should not refer to itself") unless self.type =~ /OriginalCombination/
    end
  end

  def validate_object_must_equal_subject_for_uncertain_placement
    if self.object_taxon_name_id != self.subject_taxon_name.parent_id && self.type_name == 'TaxonNameRelationship::Iczn::Validating::UncertainPlacement'
      errors.add(:object_taxon_name_id, "The parent #{self.subject_taxon_name.parent.cached_html} and the Incertae Sedis placement (#{self.object_taxon_name.cached_html}) should match")
    end
  end

  def validate_subject_and_object_ranks
    tname = self.type_name

    if tname =~ /TaxonNameRelationship::(Icnp|Icn|Iczn|Icvcn)/ && tname != 'TaxonNameRelationship::Iczn::Validating::UncertainPlacement'
      rank_group = self.subject_taxon_name.rank_class.try(:parent)
      unless rank_group == self.object_taxon_name.rank_class.try(:parent)
        errors.add(:object_taxon_name_id, "Rank of related taxon should be in the #{rank_group.try(:rank_name)} rank group, not #{self.object_taxon_name.rank_class.try(:rank_name)}")
      end
    end

    if self.type_class.present? # only validate if it is set
      if object_taxon_name && object_taxon_name.rank_class
        if object_taxon_name.type == 'Protonym' || object_taxon_name.type == 'Hybrid'
          unless self.type_class.valid_object_ranks.include?(self.object_taxon_name.rank_string)
            errors.add(:object_taxon_name_id, "#{self.object_taxon_name.rank_class.rank_name.capitalize} rank of #{self.object_taxon_name.cached_html} is not compatible with the #{self.subject_status} relationship")
            errors.add(:type, "Relationship #{self.subject_status} is not compatible with the #{self.object_taxon_name.rank_class.rank_name} rank of #{self.object_taxon_name.cached_html}")
          end
        end
      end

      if subject_taxon_name && subject_taxon_name.rank_class
        if subject_taxon_name.type == 'Protonym' || subject_taxon_name.type == 'Hybrid'
          unless self.type_class.valid_subject_ranks.include?(self.subject_taxon_name.rank_string)
            soft_validations.add(:subject_taxon_name_id, "#{self.subject_taxon_name.rank_class.rank_name.capitalize} rank of #{self.subject_taxon_name.cached_html} is not compatible with the #{self.subject_status} relationship")
            soft_validations.add(:type, "Relationship #{self.subject_status} is not compatible with the #{self.subject_taxon_name.rank_class.rank_name} rank of #{self.subject_taxon_name.cached_html}")
          end
        end
      end
    end
  end

  ##### Protonym historically could be listed as a synonym to different taxa
  #def validate_uniqueness_of_synonym_subject
  #  if !self.type.nil? && /Synonym/.match(self.type_name) && !TaxonNameRelationship.where(subject_taxon_name_id: self.subject_taxon_name_id).with_type_contains('Synonym').not_self(self).empty?
  #    errors.add(:subject_taxon_name_id, 'Only one synonym relationship is allowed')
  #  end
  #end

  def validate_uniqueness_of_typification_object
    if /Typification/.match(self.type_name) && !TaxonNameRelationship.where(object_taxon_name_id: self.object_taxon_name_id).with_type_contains('Typification').not_self(self).empty?
      errors.add(:object_taxon_name_id, 'Only one Type designation relationship is allowed')
    end
  end

  def validate_rank_group
    if self.type =~ /Hybrid/ && self.subject_taxon_name && self.object_taxon_name
      if self.subject_taxon_name.rank_class.parent != self.object_taxon_name.rank_class.parent
        errors.add(:subject_taxon_name_id, "#{self.subject_taxon_name.rank_class.rank_name.capitalize} rank of #{self.subject_taxon_name.cached_html} is not compatible with the rank of hybrid (#{self.object_taxon_name.rank_class.rank_name})")
      end
    end
  end

  def validate_object_and_subject_both_protonyms
    if /TaxonNameRelationship::Combination::/.match(self.type)
      errors.add(:object_taxon_name_id, 'Not a Combination') if object_taxon_name.type != 'Combination'
    else
      errors.add(:object_taxon_name_id, 'Not a Protonym') if object_taxon_name.type == 'Combination'
    end
    errors.add(:subject_taxon_name_id, 'Not a Protonym') if subject_taxon_name.type == 'Combination' && self.type != 'TaxonNameRelationship::CurrentCombination'
  end

  def set_cached_names_for_taxon_names
    # !! only fire if subject_taxon_name changed
    return true unless subject_taxon_name_id_previously_changed? || destroyed?

    TaxonName.transaction do
      if is_invalidating?
        t = subject_taxon_name

        if type_name =~/Misspelling/
          t.update_column(:cached_misspelling, t.get_cached_misspelling)
          t.update_columns(
              cached_author_year: t.get_author_and_year,
              cached_nomenclature_date: t.nomenclature_date,
              cached_original_combination: t.get_original_combination,
              cached_original_combination_html: t.get_original_combination_html)
        end

        if type_name =~/Misapplication/
          t.update_columns(
            cached_author_year: t.get_author_and_year,
            cached_nomenclature_date: t.nomenclature_date)
        end

        vn = t.get_valid_taxon_name

        # !! NO set cached should do this from TN side of things,
        # !! Not here

        n = t.get_full_name

        t.update_columns(
          cached: n,
          cached_html: t.get_full_name_html(n), # OK to force reload here, otherwise we need an exception in #set_cached
          cached_valid_taxon_name_id: vn.id,
          cached_is_valid: !t.unavailable_or_invalid?)

        t.combination_list_self.each do |c|
          c.update_column(:cached_valid_taxon_name_id, vn.id)
        end

        vn.list_of_invalid_taxon_names.each do |s|
          s.update_columns(
            cached_valid_taxon_name_id: vn.id,
            cached_is_valid: !s.unavailable_or_invalid?)

          s.combination_list_self.each do |c|
            c.update_column(:cached_valid_taxon_name_id, vn.id)
          end
        end

      end

    end

    true
  end

  def is_invalidating?
    TAXON_NAME_RELATIONSHIP_NAMES_INVALID.include?(type_name)
  end

  def sv_validate_required_relationships
    return true if self.subject_taxon_name.not_binominal?
    object_relationships = TaxonNameRelationship.where_object_is_taxon_name(self.object_taxon_name).not_self(self).collect{|r| r.type}
    required = self.type_class.required_taxon_name_relationships - object_relationships
    required.each do |r|
      soft_validations.add(:type, " Presence of #{self.subject_status} requires selection of #{r.demodulize.underscore.humanize.downcase}")
    end
  end

  def sv_validate_disjoint_relationships
    tname = self.type_name
    if tname =~ /TaxonNameRelationship::(Icnp|Icn|Iczn|Icvcn)/ && tname != 'TaxonNameRelationship::Iczn::Validating::UncertainPlacement'
      subject_relationships = TaxonNameRelationship.where_subject_is_taxon_name(self.subject_taxon_name).not_self(self)
      subject_relationships.each  do |i|
        if self.type_class.disjoint_taxon_name_relationships.include?(i.type_name)
          soft_validations.add(:type, "#{self.subject_status.capitalize} relationship is conflicting with another relationship: '#{i.subject_status}'")
        end
      end
    end
  end

  def sv_validate_disjoint_object
    classifications = self.object_taxon_name.taxon_name_classifications.reload.map {|i| i.type_name}
    disjoint_object_classes = self.type_class.disjoint_object_classes
    compare = disjoint_object_classes & classifications
    compare.each do |i|
      c = i.demodulize.underscore.humanize.downcase
      soft_validations.add(:type, "#{self.subject_status.capitalize} relationship is conflicting with the taxon status: '#{c}'")
      soft_validations.add(:object_taxon_name_id, "#{self.object_taxon_name.cached_html} has a conflicting status: '#{c}'")
    end
  end

  def sv_validate_disjoint_subject
    classifications = self.subject_taxon_name.taxon_name_classifications.reload.map {|i| i.type_name}
    disjoint_subject_classes = self.type_class.disjoint_subject_classes
    compare = disjoint_subject_classes & classifications
    compare.each do |i|
      c = i.demodulize.underscore.humanize.downcase
      soft_validations.add(:type, "#{self.subject_status.capitalize} conflicting with the status: '#{c}'")
      soft_validations.add(:subject_taxon_name_id, "#{self.subject_taxon_name.cached_html} has a conflicting status: '#{c}'")
    end
  end

  def sv_specific_relationship
    true # all validations moved to subclasses
  end

  def sv_objective_synonym_relationship
    true # all validations moved to subclasses
  end

  def sv_fix_objective_synonym_relationship
    true # all validations moved to subclasses
  end

  def sv_synonym_relationship
    true # all validations moved to subclasses
  end

  def sv_not_specific_relationship
    true # all validations moved to subclasses
  end

  def sv_fix_not_specific_relationship
    true # all validations moved to subclasses
  end

  def sv_synonym_linked_to_valid_name
    #synonyms and misspellings should be linked to valid names
    if ::TAXON_NAME_RELATIONSHIP_NAMES_SYNONYM.include?(self.type_name)
      obj = self.object_taxon_name
      subj = self.subject_taxon_name
      if subj.rank_class.try(:nomenclatural_code) == :iczn && (obj.parent_id != subj.parent_id || obj.rank_class != subj.rank_class) &&  subj.cached_valid_taxon_name_id == obj.cached_valid_taxon_name_id
        soft_validations.add(:subject_taxon_name_id, "#{self.subject_status.capitalize}  #{subj.cached_html_name_and_author_year} should have the same parent and rank with  #{obj.cached_html_name_and_author_year}",
                             success_message: 'The parent was updated', failure_message:  'The parent was not updated')
      end
    end
  end

  def sv_fix_subject_parent_update
    res = false
    if TAXON_NAME_RELATIONSHIP_NAMES_SYNONYM.include?(self.type_name)
      obj = self.object_taxon_name
      subj = self.subject_taxon_name
      unless obj.parent_id == subj.parent_id
        subj.parent_id = obj.parent_id
        subj.rank_class = obj.rank_class
        begin
          TaxonName.transaction do
            subj.save!
            res = true
          end
        rescue
        end
      end
    end
    res
  end

  def subject_invalid_statuses
    TAXON_NAME_CLASS_NAMES_UNAVAILABLE_AND_INVALID & self.subject_taxon_name.taxon_name_classifications.collect{|c| c.type_class.to_s}
  end

  def sv_validate_priority
    true # all validations moved to subclasses
  end

  def sv_validate_seniority
    true # all validations moved to subclasses
  end

  def sv_coordinated_taxa
    s = subject_taxon_name
    o = object_taxon_name
    s_new = s.lowest_rank_coordinated_taxon
    if s != s_new
      soft_validations.add(:subject_taxon_name_id, "Relationship should move from #{s.rank_class.rank_name} #{s.cached_html} to #{s_new.rank_class.rank_name} #{s_new.cached_html}",
                           success_message: "Relationship moved to  #{s_new.rank_class.rank_name}", failure_message:  'Failed to update relationship')
    end
  end

  def sv_coordinated_taxa_object
    s = subject_taxon_name
    o = object_taxon_name
    o_new = o.lowest_rank_coordinated_taxon
    if o != o_new
      soft_validations.add(:object_taxon_name_id, "Relationship should move from #{o.rank_class.rank_name} #{o.cached_html} to #{o_new.rank_class.rank_name} #{o_new.cached_html}",
                           success_message: "Relationship moved to  #{o_new.rank_class.rank_name}", failure_message:  'Failed to update relationship')
    end
  end

  def sv_fix_coordinated_subject_taxa
    s = subject_taxon_name
    s_new = s.lowest_rank_coordinated_taxon
    if s != s_new
      self.subject_taxon_name = s_new
      begin
        TaxonNameRelationship.transaction do
          self.save
          return true
        end
      rescue
      end
    end
    false
  end

  def sv_fix_coordinated_object_taxa
    o = self.object_taxon_name
    o_new = o.lowest_rank_coordinated_taxon
    if o != o_new
      self.object_taxon_name = o_new
      begin
        TaxonNameRelationship.transaction do
          self.save
          return true
        end
      rescue
      end
    end
    false
  end

  def sv_fix_combination_relationship
    s = self.subject_taxon_name
    list = s.list_of_coordinated_names + [s]
    if s.rank_string =~ /Species/
      s_new = list.detect{|t| t.rank_class.rank_name == 'species'}
    elsif s.rank_string =~ /Genus/
      s_new = list.detect{|t| t.rank_class.rank_name == 'genus'}
    else
      s_new = s
    end
    if s != s_new && !s.nil?
      self.subject_taxon_name = s_new
      begin
        TaxonNameRelationship.transaction do
          self.save
          return true
        end
      rescue
      end
    end
    false
  end

  def self.collect_to_s(*args)
    args.collect{|arg| arg.to_s}
  end

  def self.collect_descendants_to_s(*classes)
    ans = []
    classes.each do |klass|
      ans += klass.descendants.collect{|k| k.to_s}
    end
    ans
  end

  def self.collect_descendants_and_itself_to_s(*classes)
    classes.collect{|k| k.to_s} + self.collect_descendants_to_s(*classes)
  end

  # Force loading all descendants as soon as this class is referenced
  Dir.glob("#{Rails.root.join("app/models/taxon_name_relationship/**/*.rb")}")
    .sort { |a, b| a.split('/').count <=> b.split('/').count }
    .map { |p| p.split('/app/models/').last.sub(/\.rb$/, '') }
    .map { |p| p.split('/') }
    .map { |c| c.map { |n| ActiveSupport::Inflector.camelize(n) } }
    .map { |c| c.join('::') }.map(&:constantize)
end

Class Method Details

.assignable ⇒ Object

# File 'app/models/taxon_name_relationship.rb', line 252

def self.assignable
  false
end

.collect_descendants_and_itself_to_s(*classes) ⇒ Object (protected)

# File 'app/models/taxon_name_relationship.rb', line 700

def self.collect_descendants_and_itself_to_s(*classes)
  classes.collect{|k| k.to_s} + self.collect_descendants_to_s(*classes)
end

.collect_descendants_to_s(*classes) ⇒ Object (protected)

# File 'app/models/taxon_name_relationship.rb', line 692

def self.collect_descendants_to_s(*classes)
  ans = []
  classes.each do |klass|
    ans += klass.descendants.collect{|k| k.to_s}
  end
  ans
end

.collect_to_s(*args) ⇒ Object (protected)

# File 'app/models/taxon_name_relationship.rb', line 688

def self.collect_to_s(*args)
  args.collect{|arg| arg.to_s}
end

.disjoint_object_classes ⇒ Object

# File 'app/models/taxon_name_relationship.rb', line 240

def self.disjoint_object_classes
  []
end

.disjoint_subject_classes ⇒ Object

# File 'app/models/taxon_name_relationship.rb', line 236

def self.disjoint_subject_classes
  []
end

.disjoint_taxon_name_relationships ⇒ Array of TaxonNameRelationships

Returns if this relationships is set for the subject, then others in this array should not be used for that subject.

Returns:

• (Array of TaxonNameRelationships) —

  if this relationships is set for the subject, then others in this array should not be used for that subject

# File 'app/models/taxon_name_relationship.rb', line 226

def self.disjoint_taxon_name_relationships
  []
end

.gbif_status_of_object ⇒ Object

# File 'app/models/taxon_name_relationship.rb', line 248

def self.gbif_status_of_object
  nil
end

.gbif_status_of_subject ⇒ Object

# File 'app/models/taxon_name_relationship.rb', line 244

def self.gbif_status_of_subject
  nil
end

.nomen_uri ⇒ String^?

Returns the NOMEN uri for this type.

Returns:

• (String, nil) —

  the NOMEN uri for this type

# File 'app/models/taxon_name_relationship.rb', line 318

def self.nomen_uri
  const_defined?(:NOMEN_URI, false) ? self::NOMEN_URI : nil
end

.nomenclatural_priority ⇒ Symbol

Returns determine the relative age of subject and object :direct - subject is younger than object :reverse - object is younger than subject.

Returns:

• (Symbol) —

  determine the relative age of subject and object :direct - subject is younger than object :reverse - object is younger than subject

# File 'app/models/taxon_name_relationship.rb', line 260

def self.nomenclatural_priority
  nil
end

.parent ⇒ Object

Returns class this method calls Module#module_parent.

Returns:

• class this method calls Module#module_parent

# File 'app/models/taxon_name_relationship.rb', line 208

def self.parent
  self.module_parent
end

.required_taxon_name_relationships ⇒ Object

TODO: why isn’t this disjoint? disjoint relationships for the taxon as a object

# File 'app/models/taxon_name_relationship.rb', line 232

def self.required_taxon_name_relationships
  []
end

.valid_object_ranks ⇒ Array of NomenclatureRank

Returns the valid ranks to which the object name can belong, set in subclasses. (right side).

Returns:

• (Array of NomenclatureRank) —

  the valid ranks to which the object name can belong, set in subclasses. (right side)

# File 'app/models/taxon_name_relationship.rb', line 220

def self.valid_object_ranks
  []
end

.valid_subject_ranks ⇒ Array of NomenclatureRank

Returns the valid ranks to which the subject name can belong, set in subclasses. (left side).

Returns:

• (Array of NomenclatureRank) —

  the valid ranks to which the subject name can belong, set in subclasses. (left side)

# File 'app/models/taxon_name_relationship.rb', line 214

def self.valid_subject_ranks
  []
end

Instance Method Details

#dwc_occurrences ⇒ Object

# File 'app/models/taxon_name_relationship.rb', line 183

def dwc_occurrences
  DwcOccurrence
    .joins("JOIN collection_objects co on dwc_occurrence_object_id = co.id AND dwc_occurrence_object_type = 'CollectionObject'")
    .joins("JOIN taxon_determinations td on co.id = td.taxon_determination_object_id AND td.taxon_determination_object_type = 'CollectionObject'")
    .joins("JOIN otus o on o.id = td.otu_id")
    .where(o: {taxon_name_id: [subject_taxon_name_id, object_taxon_name_id]})
    .distinct
end

#is_combination? ⇒ Boolean

Returns:

• (Boolean)

# File 'app/models/taxon_name_relationship.rb', line 329

def is_combination?
  !!/TaxonNameRelationship::(OriginalCombination|Combination)/.match(self.type.to_s)
end

#is_invalidating? ⇒ Boolean (protected)

Returns:

• (Boolean)

# File 'app/models/taxon_name_relationship.rb', line 498

def is_invalidating?
  TAXON_NAME_RELATIONSHIP_NAMES_INVALID.include?(type_name)
end

#nomenclature_date ⇒ Time

Returns effective date of publication, used to determine nomenclatural priorities !! Careful, if no date is present the current year is given, rather than nil, @proceps is this a safe inference?.

Returns:

• (Time) —

  effective date of publication, used to determine nomenclatural priorities !! Careful, if no date is present the current year is given, rather than nil, @proceps is this a safe inference?

# File 'app/models/taxon_name_relationship.rb', line 325

def nomenclature_date
  self.source ? (self.source.cached_nomenclature_date ? self.source.cached_nomenclature_date.to_time : Time.current) : Time.current
end

#object_properties ⇒ Array of TaxonNameClassification

Returns the inferable TaxonNameClassification(s) added to the subject when this relationship is used !! Not implmented.

Returns:

• (Array of TaxonNameClassification) —

  the inferable TaxonNameClassification(s) added to the subject when this relationship is used !! Not implmented

# File 'app/models/taxon_name_relationship.rb', line 202

def object_properties
  []
end

#object_status ⇒ String

Returns the status inferred by the relationship to the object name.

Returns:

• (String) —

  the status inferred by the relationship to the object name

# File 'app/models/taxon_name_relationship.rb', line 266

def object_status
  self.type_name.demodulize.underscore.humanize.downcase.gsub(/\d+/, ' \0 ').squish
end

#object_status_connector_to_subject ⇒ String

Returns the connecting word in the relationship from the object name to subject name.

Returns:

• (String) —

  the connecting word in the relationship from the object name to subject name

# File 'app/models/taxon_name_relationship.rb', line 284

def object_status_connector_to_subject
  ' of'
end

#object_status_tag ⇒ String

Returns a readable fragement combining status and connector.

Returns:

• (String) —

  a readable fragement combining status and connector

# File 'app/models/taxon_name_relationship.rb', line 296

def object_status_tag
  object_status + object_status_connector_to_subject
end

#set_cached_names_for_taxon_names ⇒ Object (protected)

# File 'app/models/taxon_name_relationship.rb', line 441

def set_cached_names_for_taxon_names
  # !! only fire if subject_taxon_name changed
  return true unless subject_taxon_name_id_previously_changed? || destroyed?

  TaxonName.transaction do
    if is_invalidating?
      t = subject_taxon_name

      if type_name =~/Misspelling/
        t.update_column(:cached_misspelling, t.get_cached_misspelling)
        t.update_columns(
            cached_author_year: t.get_author_and_year,
            cached_nomenclature_date: t.nomenclature_date,
            cached_original_combination: t.get_original_combination,
            cached_original_combination_html: t.get_original_combination_html)
      end

      if type_name =~/Misapplication/
        t.update_columns(
          cached_author_year: t.get_author_and_year,
          cached_nomenclature_date: t.nomenclature_date)
      end

      vn = t.get_valid_taxon_name

      # !! NO set cached should do this from TN side of things,
      # !! Not here

      n = t.get_full_name

      t.update_columns(
        cached: n,
        cached_html: t.get_full_name_html(n), # OK to force reload here, otherwise we need an exception in #set_cached
        cached_valid_taxon_name_id: vn.id,
        cached_is_valid: !t.unavailable_or_invalid?)

      t.combination_list_self.each do |c|
        c.update_column(:cached_valid_taxon_name_id, vn.id)
      end

      vn.list_of_invalid_taxon_names.each do |s|
        s.update_columns(
          cached_valid_taxon_name_id: vn.id,
          cached_is_valid: !s.unavailable_or_invalid?)

        s.combination_list_self.each do |c|
          c.update_column(:cached_valid_taxon_name_id, vn.id)
        end
      end

    end

  end

  true
end

#subject_and_object_in_same_project ⇒ Object (protected)

# File 'app/models/taxon_name_relationship.rb', line 335

def subject_and_object_in_same_project
  if subject_taxon_name && object_taxon_name
    if subject_taxon_name.project_id != object_taxon_name.project_id
      errors.add(:base, 'one name is not in the same project as the other')
    end
  end
end

#subject_invalid_statuses ⇒ Object (protected)

# File 'app/models/taxon_name_relationship.rb', line 601

def subject_invalid_statuses
  TAXON_NAME_CLASS_NAMES_UNAVAILABLE_AND_INVALID & self.subject_taxon_name.taxon_name_classifications.collect{|c| c.type_class.to_s}
end

#subject_properties ⇒ Array of TaxonNameClassification

Returns the inferable TaxonNameClassification(s) added to the subject when this relationship is used !! Not implemented.

Returns:

• (Array of TaxonNameClassification) —

  the inferable TaxonNameClassification(s) added to the subject when this relationship is used !! Not implemented

# File 'app/models/taxon_name_relationship.rb', line 195

def subject_properties
  []
end

#subject_status ⇒ String

Returns the status inferred by the relationship to the subject name.

Returns:

• (String) —

  the status inferred by the relationship to the subject name

# File 'app/models/taxon_name_relationship.rb', line 272

def subject_status
  self.type_name.demodulize.underscore.humanize.downcase.gsub(/\d+/, ' \0 ').squish
end

#subject_status_connector_to_object ⇒ String

Returns the connecting word in the relationship from the subject name to object name.

Returns:

• (String) —

  the connecting word in the relationship from the subject name to object name

# File 'app/models/taxon_name_relationship.rb', line 278

def subject_status_connector_to_object
  ' of'
end

#subject_status_tag ⇒ String

Returns a readable fragement combining status and connector.

Returns:

• (String) —

  a readable fragement combining status and connector

# File 'app/models/taxon_name_relationship.rb', line 290

def subject_status_tag
  subject_status + subject_status_connector_to_object
end

#sv_coordinated_taxa ⇒ Object (protected)

# File 'app/models/taxon_name_relationship.rb', line 613

def sv_coordinated_taxa
  s = subject_taxon_name
  o = object_taxon_name
  s_new = s.lowest_rank_coordinated_taxon
  if s != s_new
    soft_validations.add(:subject_taxon_name_id, "Relationship should move from #{s.rank_class.rank_name} #{s.cached_html} to #{s_new.rank_class.rank_name} #{s_new.cached_html}",
                         success_message: "Relationship moved to  #{s_new.rank_class.rank_name}", failure_message:  'Failed to update relationship')
  end
end

#sv_coordinated_taxa_object ⇒ Object (protected)

# File 'app/models/taxon_name_relationship.rb', line 623

def sv_coordinated_taxa_object
  s = subject_taxon_name
  o = object_taxon_name
  o_new = o.lowest_rank_coordinated_taxon
  if o != o_new
    soft_validations.add(:object_taxon_name_id, "Relationship should move from #{o.rank_class.rank_name} #{o.cached_html} to #{o_new.rank_class.rank_name} #{o_new.cached_html}",
                         success_message: "Relationship moved to  #{o_new.rank_class.rank_name}", failure_message:  'Failed to update relationship')
  end
end

#sv_fix_combination_relationship ⇒ Object (protected)

# File 'app/models/taxon_name_relationship.rb', line 665

def sv_fix_combination_relationship
  s = self.subject_taxon_name
  list = s.list_of_coordinated_names + [s]
  if s.rank_string =~ /Species/
    s_new = list.detect{|t| t.rank_class.rank_name == 'species'}
  elsif s.rank_string =~ /Genus/
    s_new = list.detect{|t| t.rank_class.rank_name == 'genus'}
  else
    s_new = s
  end
  if s != s_new && !s.nil?
    self.subject_taxon_name = s_new
    begin
      TaxonNameRelationship.transaction do
        self.save
        return true
      end
    rescue
    end
  end
  false
end

#sv_fix_coordinated_object_taxa ⇒ Object (protected)

# File 'app/models/taxon_name_relationship.rb', line 649

def sv_fix_coordinated_object_taxa
  o = self.object_taxon_name
  o_new = o.lowest_rank_coordinated_taxon
  if o != o_new
    self.object_taxon_name = o_new
    begin
      TaxonNameRelationship.transaction do
        self.save
        return true
      end
    rescue
    end
  end
  false
end

#sv_fix_coordinated_subject_taxa ⇒ Object (protected)

# File 'app/models/taxon_name_relationship.rb', line 633

def sv_fix_coordinated_subject_taxa
  s = subject_taxon_name
  s_new = s.lowest_rank_coordinated_taxon
  if s != s_new
    self.subject_taxon_name = s_new
    begin
      TaxonNameRelationship.transaction do
        self.save
        return true
      end
    rescue
    end
  end
  false
end

#sv_fix_not_specific_relationship ⇒ Object (protected)

# File 'app/models/taxon_name_relationship.rb', line 565

def sv_fix_not_specific_relationship
  true # all validations moved to subclasses
end

#sv_fix_objective_synonym_relationship ⇒ Object (protected)

# File 'app/models/taxon_name_relationship.rb', line 553

def sv_fix_objective_synonym_relationship
  true # all validations moved to subclasses
end

#sv_fix_subject_parent_update ⇒ Object (protected)

# File 'app/models/taxon_name_relationship.rb', line 581

def sv_fix_subject_parent_update
  res = false
  if TAXON_NAME_RELATIONSHIP_NAMES_SYNONYM.include?(self.type_name)
    obj = self.object_taxon_name
    subj = self.subject_taxon_name
    unless obj.parent_id == subj.parent_id
      subj.parent_id = obj.parent_id
      subj.rank_class = obj.rank_class
      begin
        TaxonName.transaction do
          subj.save!
          res = true
        end
      rescue
      end
    end
  end
  res
end

#sv_not_specific_relationship ⇒ Object (protected)

# File 'app/models/taxon_name_relationship.rb', line 561

def sv_not_specific_relationship
  true # all validations moved to subclasses
end

#sv_objective_synonym_relationship ⇒ Object (protected)

# File 'app/models/taxon_name_relationship.rb', line 549

def sv_objective_synonym_relationship
  true # all validations moved to subclasses
end

#sv_specific_relationship ⇒ Object (protected)

# File 'app/models/taxon_name_relationship.rb', line 545

def sv_specific_relationship
  true # all validations moved to subclasses
end

#sv_synonym_linked_to_valid_name ⇒ Object (protected)

# File 'app/models/taxon_name_relationship.rb', line 569

def sv_synonym_linked_to_valid_name
  #synonyms and misspellings should be linked to valid names
  if ::TAXON_NAME_RELATIONSHIP_NAMES_SYNONYM.include?(self.type_name)
    obj = self.object_taxon_name
    subj = self.subject_taxon_name
    if subj.rank_class.try(:nomenclatural_code) == :iczn && (obj.parent_id != subj.parent_id || obj.rank_class != subj.rank_class) &&  subj.cached_valid_taxon_name_id == obj.cached_valid_taxon_name_id
      soft_validations.add(:subject_taxon_name_id, "#{self.subject_status.capitalize}  #{subj.cached_html_name_and_author_year} should have the same parent and rank with  #{obj.cached_html_name_and_author_year}",
                           success_message: 'The parent was updated', failure_message:  'The parent was not updated')
    end
  end
end

#sv_synonym_relationship ⇒ Object (protected)

# File 'app/models/taxon_name_relationship.rb', line 557

def sv_synonym_relationship
  true # all validations moved to subclasses
end

#sv_validate_disjoint_object ⇒ Object (protected)

# File 'app/models/taxon_name_relationship.rb', line 523

def sv_validate_disjoint_object
  classifications = self.object_taxon_name.taxon_name_classifications.reload.map {|i| i.type_name}
  disjoint_object_classes = self.type_class.disjoint_object_classes
  compare = disjoint_object_classes & classifications
  compare.each do |i|
    c = i.demodulize.underscore.humanize.downcase
    soft_validations.add(:type, "#{self.subject_status.capitalize} relationship is conflicting with the taxon status: '#{c}'")
    soft_validations.add(:object_taxon_name_id, "#{self.object_taxon_name.cached_html} has a conflicting status: '#{c}'")
  end
end

#sv_validate_disjoint_relationships ⇒ Object (protected)

# File 'app/models/taxon_name_relationship.rb', line 511

def sv_validate_disjoint_relationships
  tname = self.type_name
  if tname =~ /TaxonNameRelationship::(Icnp|Icn|Iczn|Icvcn)/ && tname != 'TaxonNameRelationship::Iczn::Validating::UncertainPlacement'
    subject_relationships = TaxonNameRelationship.where_subject_is_taxon_name(self.subject_taxon_name).not_self(self)
    subject_relationships.each  do |i|
      if self.type_class.disjoint_taxon_name_relationships.include?(i.type_name)
        soft_validations.add(:type, "#{self.subject_status.capitalize} relationship is conflicting with another relationship: '#{i.subject_status}'")
      end
    end
  end
end

#sv_validate_disjoint_subject ⇒ Object (protected)

# File 'app/models/taxon_name_relationship.rb', line 534

def sv_validate_disjoint_subject
  classifications = self.subject_taxon_name.taxon_name_classifications.reload.map {|i| i.type_name}
  disjoint_subject_classes = self.type_class.disjoint_subject_classes
  compare = disjoint_subject_classes & classifications
  compare.each do |i|
    c = i.demodulize.underscore.humanize.downcase
    soft_validations.add(:type, "#{self.subject_status.capitalize} conflicting with the status: '#{c}'")
    soft_validations.add(:subject_taxon_name_id, "#{self.subject_taxon_name.cached_html} has a conflicting status: '#{c}'")
  end
end

#sv_validate_priority ⇒ Object (protected)

# File 'app/models/taxon_name_relationship.rb', line 605

def sv_validate_priority
  true # all validations moved to subclasses
end

#sv_validate_required_relationships ⇒ Object (protected)

# File 'app/models/taxon_name_relationship.rb', line 502

def sv_validate_required_relationships
  return true if self.subject_taxon_name.not_binominal?
  object_relationships = TaxonNameRelationship.where_object_is_taxon_name(self.object_taxon_name).not_self(self).collect{|r| r.type}
  required = self.type_class.required_taxon_name_relationships - object_relationships
  required.each do |r|
    soft_validations.add(:type, " Presence of #{self.subject_status} requires selection of #{r.demodulize.underscore.humanize.downcase}")
  end
end

#sv_validate_seniority ⇒ Object (protected)

# File 'app/models/taxon_name_relationship.rb', line 609

def sv_validate_seniority
  true # all validations moved to subclasses
end

#type_class ⇒ Object

# File 'app/models/taxon_name_relationship.rb', line 311

def type_class
  r = read_attribute(:type).to_s
  TAXON_NAME_RELATIONSHIP_NAMES.include?(r) ? r.safe_constantize : nil
end

#type_class=(value) ⇒ Object

# File 'app/models/taxon_name_relationship.rb', line 307

def type_class=(value)
  write_attribute(:type, value.to_s)
end

#type_name ⇒ String^?

Returns the type of this relationship, IF the type is a valid name, else nil.

Returns:

• (String, nil) —

  the type of this relationship, IF the type is a valid name, else nil

# File 'app/models/taxon_name_relationship.rb', line 302

def type_name
  r = self.type
  TAXON_NAME_RELATIONSHIP_NAMES.include?(r) ? r : nil
end

#validate_object_and_subject_both_protonyms ⇒ Object (protected)

# File 'app/models/taxon_name_relationship.rb', line 432

def validate_object_and_subject_both_protonyms
  if /TaxonNameRelationship::Combination::/.match(self.type)
    errors.add(:object_taxon_name_id, 'Not a Combination') if object_taxon_name.type != 'Combination'
  else
    errors.add(:object_taxon_name_id, 'Not a Protonym') if object_taxon_name.type == 'Combination'
  end
  errors.add(:subject_taxon_name_id, 'Not a Protonym') if subject_taxon_name.type == 'Combination' && self.type != 'TaxonNameRelationship::CurrentCombination'
end

#validate_object_must_equal_subject_for_uncertain_placement ⇒ Object (protected)

# File 'app/models/taxon_name_relationship.rb', line 374

def validate_object_must_equal_subject_for_uncertain_placement
  if self.object_taxon_name_id != self.subject_taxon_name.parent_id && self.type_name == 'TaxonNameRelationship::Iczn::Validating::UncertainPlacement'
    errors.add(:object_taxon_name_id, "The parent #{self.subject_taxon_name.parent.cached_html} and the Incertae Sedis placement (#{self.object_taxon_name.cached_html}) should match")
  end
end

#validate_rank_group ⇒ Object (protected)

# File 'app/models/taxon_name_relationship.rb', line 424

def validate_rank_group
  if self.type =~ /Hybrid/ && self.subject_taxon_name && self.object_taxon_name
    if self.subject_taxon_name.rank_class.parent != self.object_taxon_name.rank_class.parent
      errors.add(:subject_taxon_name_id, "#{self.subject_taxon_name.rank_class.rank_name.capitalize} rank of #{self.subject_taxon_name.cached_html} is not compatible with the rank of hybrid (#{self.object_taxon_name.rank_class.rank_name})")
    end
  end
end

#validate_subject_and_object_are_not_identical ⇒ Object (protected)

# File 'app/models/taxon_name_relationship.rb', line 368

def validate_subject_and_object_are_not_identical
  if !self.object_taxon_name_id.nil? && self.object_taxon_name == self.subject_taxon_name
    errors.add(:object_taxon_name_id, "#{self.object_taxon_name.try(:cached_html)} should not refer to itself") unless self.type =~ /OriginalCombination/
  end
end

#validate_subject_and_object_ranks ⇒ Object (protected)

# File 'app/models/taxon_name_relationship.rb', line 380

def validate_subject_and_object_ranks
  tname = self.type_name

  if tname =~ /TaxonNameRelationship::(Icnp|Icn|Iczn|Icvcn)/ && tname != 'TaxonNameRelationship::Iczn::Validating::UncertainPlacement'
    rank_group = self.subject_taxon_name.rank_class.try(:parent)
    unless rank_group == self.object_taxon_name.rank_class.try(:parent)
      errors.add(:object_taxon_name_id, "Rank of related taxon should be in the #{rank_group.try(:rank_name)} rank group, not #{self.object_taxon_name.rank_class.try(:rank_name)}")
    end
  end

  if self.type_class.present? # only validate if it is set
    if object_taxon_name && object_taxon_name.rank_class
      if object_taxon_name.type == 'Protonym' || object_taxon_name.type == 'Hybrid'
        unless self.type_class.valid_object_ranks.include?(self.object_taxon_name.rank_string)
          errors.add(:object_taxon_name_id, "#{self.object_taxon_name.rank_class.rank_name.capitalize} rank of #{self.object_taxon_name.cached_html} is not compatible with the #{self.subject_status} relationship")
          errors.add(:type, "Relationship #{self.subject_status} is not compatible with the #{self.object_taxon_name.rank_class.rank_name} rank of #{self.object_taxon_name.cached_html}")
        end
      end
    end

    if subject_taxon_name && subject_taxon_name.rank_class
      if subject_taxon_name.type == 'Protonym' || subject_taxon_name.type == 'Hybrid'
        unless self.type_class.valid_subject_ranks.include?(self.subject_taxon_name.rank_string)
          soft_validations.add(:subject_taxon_name_id, "#{self.subject_taxon_name.rank_class.rank_name.capitalize} rank of #{self.subject_taxon_name.cached_html} is not compatible with the #{self.subject_status} relationship")
          soft_validations.add(:type, "Relationship #{self.subject_status} is not compatible with the #{self.subject_taxon_name.rank_class.rank_name} rank of #{self.subject_taxon_name.cached_html}")
        end
      end
    end
  end
end

#validate_subject_and_object_share_code ⇒ Object (protected)

TODO:

validate, that all the relationships in the table could be linked to relationships in classes (if those had changed)

# File 'app/models/taxon_name_relationship.rb', line 362

def validate_subject_and_object_share_code
  if object_taxon_name.type  == 'Protonym' && subject_taxon_name.type == 'Protonym'
    errors.add(:object_taxon_name_id, 'The related taxon is not in the same monenclatural group (ICZN, ICN, ICNP, ICVCN') if subject_taxon_name.rank_class.try(:nomenclatural_code) != object_taxon_name.rank_class.try(:nomenclatural_code)
  end
end

#validate_type ⇒ Object (protected)

# File 'app/models/taxon_name_relationship.rb', line 343

def validate_type
  # TODO: Remove, handled by STI
  if type && !TAXON_NAME_RELATIONSHIP_NAMES.include?(type.to_s)
    errors.add(:type, "'#{type}' is not a valid taxon name relationship")
  elsif self.type_class && object_taxon_name.class.to_s == 'Protonym' && !self.type_class.valid_object_ranks.include?(object_taxon_name.rank_string)
    errors.add(:type, "'#{type}' is not a valid taxon name relationship")
  end

  if object_taxon_name.class.to_s == 'Protonym' || object_taxon_name.class.to_s == 'Hybrid'
    errors.add(:type, "'#{type}' is not a valid taxon name relationship") if /TaxonNameRelationship::Combination::/.match(self.type)
  end

  if object_taxon_name.class.to_s == 'Combination'
    errors.add(:type, "'#{type}' is not a valid taxon name relationship") unless /TaxonNameRelationship::Combination::/.match(self.type)
  end
end

#validate_uniqueness_of_typification_object ⇒ Object (protected)

Protonym historically could be listed as a synonym to different taxa def validate_uniqueness_of_synonym_subject

if !self.type.nil? && /Synonym/.match(self.type_name) && !TaxonNameRelationship.where(subject_taxon_name_id: self.subject_taxon_name_id).with_type_contains('Synonym').not_self(self).empty?
  errors.add(:subject_taxon_name_id, 'Only one synonym relationship is allowed')
end

end

# File 'app/models/taxon_name_relationship.rb', line 418

def validate_uniqueness_of_typification_object
  if /Typification/.match(self.type_name) && !TaxonNameRelationship.where(object_taxon_name_id: self.object_taxon_name_id).with_type_contains('Typification').not_self(self).empty?
    errors.add(:object_taxon_name_id, 'Only one Type designation relationship is allowed')
  end
end