Class: TaxonNameClassification

# File 'app/models/taxon_name_classification.rb', line 18

class TaxonNameClassification < ApplicationRecord
  include Housekeeping
  include Shared::BatchByFilterScope
  include Shared::Citations
  include Shared::Notes
  include Shared::IsData
  include SoftValidation

  belongs_to :taxon_name, inverse_of: :taxon_name_classifications

  before_validation :validate_taxon_name_classification
  before_validation :validate_uniqueness_of_latinized
  after_commit :set_cached

  validates_presence_of :taxon_name
  validates_presence_of :type
  validates_uniqueness_of :taxon_name_id, scope: [:type, :project_id]

  validate :nomenclature_code_matches

  scope :where_taxon_name, -> (taxon_name) {where(taxon_name_id: taxon_name)}
  scope :with_type_string, -> (base_string) {where('taxon_name_classifications.type LIKE ?', "#{base_string}" ) }
  scope :with_type_base, -> (base_string) {where('taxon_name_classifications.type LIKE ?', "#{base_string}%" ) }
  scope :with_type_array, -> (base_array) {where('taxon_name_classifications.type IN (?)', base_array ) }
  scope :with_type_contains, -> (base_string) {where('taxon_name_classifications.type LIKE ?', "%#{base_string}%" ) }

  soft_validate(:sv_proper_classification,
                set: :proper_classification,
                fix: :sv_fix_proper_classification,
                name: 'Applicable status',
                description: 'Check the status applicability.' )

  soft_validate(:sv_proper_year,
                set: :proper_classification,
                name: 'Applicable protonym year',
                description: 'Check that the status is compatible with the year of publication of taxon.' )

  soft_validate(:sv_validate_disjoint_classes,
                set: :validate_disjoint_classes,
                name: 'Conflicting status',
                description: 'Taxon has two conflicting statuses' )

  soft_validate(:sv_not_specific_classes,
                set: :not_specific_classes,
                name: 'Not specific status',
                description: 'More specific statuses are preffered, for example: "Nomen nudum, no description" is better than "Nomen nudum".' )

  def nomenclature_code
    return :iczn if type.match(/::Iczn/)
    return :icnp if type.match(/::Icnp/)
    return :icvcn if type.match(/::Icvcn/)
    return :icn if type.match(/::Icn/)
    return nil
  end

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

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

  # @return [String]
  #   the class name, "validated" against the known list of names
  def type_name
    r = self.type.to_s
    ::TAXON_NAME_CLASSIFICATION_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
    r = ::TAXON_NAME_CLASSIFICATION_NAMES.include?(r) ? r.safe_constantize : nil
  end

  # @return [String]
  #   a humanized class name, with code appended to differentiate
  #   !! explored idea of LABEL in individual subclasses, use this if this doesn't work
  #   this is helper-esqe, but also useful in validation, so here for now
  def classification_label
    return nil if type_name.nil?
    type_name.demodulize.underscore.humanize.downcase.gsub(/\d+/, ' \0 ').squish #+
      #(nomenclature_code ? " [#{nomenclature_code}]" : '')
  end

  # @return [String]
  #   the NOMEN id for this classification
  def nomen_id
    self.class::NOMEN_URI.split('/').last
  end

  # Attributes can be overridden in descendants

  # @return [Integer]
  # the minimum year of applicability for this class, defaults to 1
  def self.code_applicability_start_year
    1
  end

  # @return [Integer]
  # the last year of applicability for this class, defaults to 9999
  def self.code_applicability_end_year
    9999
  end

  # @return [Array of Strings of NomenclaturalRank names]
  # nomenclatural ranks to which this class is applicable, that is, only {TaxonName}s of these {NomenclaturalRank}s may be classified as this class
  def self.applicable_ranks
    []
  end

  # @return [Array of Strings of TaxonNameClassification names]
  # the disjoint (inapplicable) {TaxonNameClassification}s for this class, that is, {TaxonName}s classified as this class can not be additionally classified under these classes
  def self.disjoint_taxon_name_classes
    []
  end

  # @return [String, nil]
  #  if applicable, a DWC gbif status for this class
  def self.gbif_status
    nil
  end

  def self.assignable
    false
  end

 #def self.common
 #  false
 #end

  # @todo Perhaps not inherit these three meaxonNameClassificationsHelper::descendants_collection( TaxonNameClassification::Latinized )thods?

  # @return [Array of Strings]
  #   the possible suffixes for a {TaxonName} name (species) classified as this class, for example see {TaxonNameClassification::Latinized::Gender::Masculine}
  #   used to validate gender agreement of species name with a genus
  def self.possible_species_endings
    []
  end

  # @return [Array of Strings]
  #   the questionable suffixes for a {TaxonName} name classified as this class, for example see {TaxonNameClassification::Latinized::Gender::Masculine}
  def self.questionable_species_endings
    []
  end

  # @return [Array of Strings]
  # the possible suffixes for a {TaxonName} name (genus) classified as this class, for example see {TaxonNameClassification::Latinized::Gender::Masculine}
  def self.possible_genus_endings
    []
  end

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

  def set_cached
    set_cached_names_for_taxon_names
  end

  # TODO: move these to individual classes?!
  # Starting to move to individual classes
  #     Gender is sone
  def set_cached_names_for_taxon_names
    t = taxon_name
    return if t.destroyed?
    begin
      TaxonName.transaction_with_retry do
        if type_name =~ /(Fossil|Hybrid|Candidatus)/ # Break these out, they don't all apply to the same codes
          n = t.get_full_name
          t.update_columns(
            cached: n,
            cached_html: t.get_full_name_html(n),
            cached_original_combination: t.get_original_combination,
            cached_original_combination_html: t.get_original_combination_html
          )
        elsif type_name =~ /Latinized::PartOfSpeech/
          n = t.get_full_name
          t.update_columns(
              cached: n,
              cached_html: t.get_full_name_html(n),
              cached_original_combination: t.get_original_combination,
              cached_original_combination_html: t.get_original_combination_html
          )

          TaxonNameRelationship::OriginalCombination.where(subject_taxon_name: t).collect{|i| i.object_taxon_name}.uniq.each do |t1|
            t1.update_cached_original_combinations
          end

          TaxonNameRelationship::Combination.where(subject_taxon_name: t).collect{|i| i.object_taxon_name}.uniq.each do |t1|
            t1.update_column(:verbatim_name, t1.cached) if t1.verbatim_name.nil?
            n = t1.get_full_name
            t1.update_columns(
                cached: n,
                cached_html: t1.get_full_name_html(n)
            )
          end

        elsif type_name =~ /Latinized::Gender/
          # Handled in subclasses
          raise
        elsif TAXON_NAME_CLASS_NAMES_VALID.include?(type_name)
          vn = t.get_valid_taxon_name
          vn.update_columns(
            cached_valid_taxon_name_id: vn.id,
            cached_is_valid: !vn.unavailable_or_invalid?) # Do not change!
          vn.list_of_invalid_taxon_names.each do |s|
            s.update_columns(
              cached_valid_taxon_name_id: vn.id,
              cached_is_valid: false)
            s.combination_list_self.each do |c|
              c.update_columns(cached_valid_taxon_name_id: vn.id)
            end
          end
          t.combination_list_self.each do |c|
            c.update_columns(cached_valid_taxon_name_id: vn.id)
          end
        else
          t.update_columns(cached_is_valid: false)
        end

        if TAXON_NAME_CLASS_NAMES_UNAVAILABLE.include?( type_name )
          t.update_columns(
            cached_is_available: false
          )
        end
      end
    rescue ActiveRecord::RecordInvalid
      false
    end
    true
  end

  def validate_uniqueness_of_latinized
    true # moved to subclasses
  end

  def sv_proper_classification
    if TAXON_NAME_CLASSIFICATION_NAMES.include?(self.type)
      # self.type_class is a Class
      if not self.type_class.applicable_ranks.include?(self.taxon_name.rank_string)
        soft_validations.add(:type, "The status '#{self.classification_label}' is not applicable to the taxon #{self.taxon_name.cached_html} at the rank of #{self.taxon_name.rank_class.rank_name}", success_message: 'The status was deleted', failure_message:  'Fail to delete the status')
      end
    end
  end

  def sv_fix_proper_classification
    begin
      TaxonNameClassification.transaction do
        self.destroy
      end
      return true
    rescue
      return false
    end
  end

  def sv_proper_year
    y = self.taxon_name.year_of_publication
    if !y.nil? && (y > self.type_class.code_applicability_end_year || y < self.type_class.code_applicability_start_year)
      soft_validations.add(:type, "The status '#{self.classification_label}' is not applicable to the taxon #{self.taxon_name.cached_html} published in the year #{y}")
    end
  end

  def sv_validate_disjoint_classes
    classifications = TaxonNameClassification.where_taxon_name(self.taxon_name).not_self(self)
    classifications.each  do |i|
      soft_validations.add(:type, "The status  '#{self.classification_label}' conflicting with another status: '#{i.classification_label}'") if self.type_class.disjoint_taxon_name_classes.include?(i.type_name)
    end
  end

  def sv_not_specific_classes
    true # moved to subclasses
  end

  def self.annotates?
    true
  end

  def annotated_object
    taxon_name
  end

  # @param batch_response [BatchResponse]
  # @param query [ActiveRecord::Relation] TaxonName scope from the filter
  # @param hash_query [Hash] serialized filter params, used to re-run the query in async jobs
  # @param mode [Symbol, String] :set, :remove_gender (gender); :add_status, :remove_status (arbitrary status)
  # @param params [Hash] :type required for :set, :add_status, :remove_status;
  #   :citation (optional, :add_status only) a Hash with :source_id (required to attach), :pages, :is_original -
  #   attached to the status whether it was just created or already existed; tolerates (does not duplicate or
  #   error on) a citation with the same source, pages, and is_original already present on that status
  # @param async [Boolean]
  # @param project_id [Integer]
  # @param user_id [Integer]
  # @param called_from_async [Boolean] prevents re-dispatching when already inside a job
  # @return [BatchResponse]
  def self.process_batch_by_filter_scope(
    batch_response: nil, query: nil, hash_query: nil, mode: nil,
    params: nil, async: nil, project_id: nil, user_id: nil,
    called_from_async: false
  )
    async = false if called_from_async == true
    r = batch_response

    case mode.to_sym
    when :set # gender
      gender_type = params[:type]
      return r unless TAXON_NAME_CLASSIFICATIONS_FOR_GENDER.include?(gender_type)

      if async && !called_from_async
        dispatch_batch_by_filter_scope_job(
          hash_query:, mode:, params:, project_id:, user_id:
        )
        return r
      end

      existing_by_taxon_name_id = TaxonNameClassification
        .with_type_array(TAXON_NAME_CLASSIFICATIONS_FOR_GENDER)
        .where(taxon_name: query)
        .index_by(&:taxon_name_id)

      query.find_each do |taxon_name|
        if existing = existing_by_taxon_name_id[taxon_name.id]
          if existing.type == gender_type
            # Already the requested gender - skip the update entirely rather
            # than trigger the expensive after_commit cascade (walks every
            # descendant taxon name to recompute cached spellings) for
            # nothing.
            r.updated.push existing.id
          elsif existing.update(type: gender_type)
            r.updated.push existing.id
          else
            r.not_updated.push taxon_name.id
            existing.errors.full_messages.each { |msg|
              r.validation_errors[msg] += 1
            }
          end
        else
          classification = TaxonNameClassification.create(
            taxon_name: taxon_name, type: gender_type
          )
          if classification.persisted?
            r.updated.push classification.id
          else
            r.not_updated.push taxon_name.id
            classification.errors.full_messages.each { |msg|
              r.validation_errors[msg] += 1
            }
          end
        end
      end

    when :remove_gender
      if async && !called_from_async
        dispatch_batch_by_filter_scope_job(
          hash_query:, mode:, params:, project_id:, user_id:
        )
        return r
      end

      destroy_classifications_for_batch(
        classifications: TaxonNameClassification.with_type_array(TAXON_NAME_CLASSIFICATIONS_FOR_GENDER),
        query:,
        batch_response: r
      )

    when :add_status
      status_type = params[:type]
      return r unless TAXON_NAME_CLASSIFICATION_NAMES.include?(status_type)

      if async && !called_from_async
        dispatch_batch_by_filter_scope_job(
          hash_query:, mode:, params:, project_id:, user_id:
        )
        return r
      end

      citation_params = params[:citation]&.symbolize_keys
      citation_source_id = citation_params && citation_params[:source_id]

      citation_source = citation_source_id && Source.find_by(id: citation_source_id)

      existing_by_taxon_name_id = TaxonNameClassification
        .where(type: status_type)
        .where(taxon_name: query)
        .index_by(&:taxon_name_id)

      # Disjoint types (e.g. Iczn::Fossil::Ichnotaxon is disjoint with its own
      # parent Iczn::Fossil) already satisfy this status; skip creating a
      # conflicting status rather than let the two coexist.
      disjoint_types = status_type.constantize.disjoint_taxon_name_classes

      conflicting_taxon_name_ids =
        if disjoint_types.empty?
          Set.new
        else
          TaxonNameClassification
            .where(type: disjoint_types)
            .where(taxon_name: query)
            .distinct
            .pluck(:taxon_name_id)
            .to_set
        end

      # Classifications that already carry the exact citation (same
      # source, pages, and is_original) being requested. This isn't just a
      # performance nicety: it's what distinguishes an identical repeat
      # (skipped and reported as updated) from a genuine conflict: same
      # source and pages but a different is_original (attempted, fails,
      # and is reported below with a message specific to that case).
      already_cited_classification_ids =
        if citation_source_id && existing_by_taxon_name_id.any?
          Citation.duplicate_citation_object_ids(
            citation_object_type: 'TaxonNameClassification',
            citation_object_ids: existing_by_taxon_name_id.values.map(&:id),
            source_id: citation_source_id,
            pages: citation_params[:pages],
            is_original: citation_params[:is_original]
          )
        else
          Set.new
        end

      query.find_each do |taxon_name|
        if (
          !existing_by_taxon_name_id.key?(taxon_name.id) &&
          conflicting_taxon_name_ids.include?(taxon_name.id)
        )
          r.not_updated.push taxon_name.id
          r.validation_errors['conflicts with an existing disjoint classification'] += 1
          next
        end

        classification = existing_by_taxon_name_id[taxon_name.id] ||
          TaxonNameClassification.create(taxon_name: taxon_name, type: status_type)

        unless classification.persisted?
          r.not_updated.push taxon_name.id
          classification.errors.full_messages.each { |msg|
            r.validation_errors[msg] += 1
          }
          next
        end

        if citation_source_id && !already_cited_classification_ids.include?(classification.id)
          citation = classification.citations.create(
            source: citation_source,
            pages: citation_params[:pages],
            is_original: citation_params[:is_original]
          )

          unless citation.persisted?
            r.not_updated.push taxon_name.id

            # An exact repeat was already ruled out above, so a source_id
            # conflict here can only mean a citation with this same source
            # and pages exists with a different is_original - Citation's
            # own validation doesn't know or care about is_original, it
            # only reports the source/pages conflict, so the more specific
            # wording is built here. The taxon name id is included (rather
            # than summarized by count, as validation_errors normally are)
            # since this needs manual review to resolve.
            if citation.errors[:source_id].any?
              r.validation_errors["citation already exists with a different 'original' flag for taxon name id #{taxon_name.id} - is_original was not changed"] += 1
            else # a second `is_original = true` citation, e.g.
              citation.errors.full_messages.each { |msg|
                r.validation_errors[msg] += 1
              }
            end

            next
          end
        end

        r.updated.push classification.id
      end

    when :remove_status
      status_type = params[:type]
      return r unless TAXON_NAME_CLASSIFICATION_NAMES.include?(status_type)

      if async && !called_from_async
        dispatch_batch_by_filter_scope_job(hash_query:, mode:, params:, project_id:, user_id:)
        return r
      end

      # Only the exact type selected: not its subclasses (e.g. removing
      # Iczn::Fossil leaves Iczn::Fossil::Ichnotaxon), and not
      # disjoint_taxon_name_classes, which is every *conflicting* status.
      destroy_classifications_for_batch(
        classifications: TaxonNameClassification.where(type: status_type),
        query:,
        batch_response: r
      )
    end

    r
  end

  # Destroys `classifications` belonging to taxon names in `query`.
  # Iterates every taxon name in the query (not just ones with a matching
  # classification) so updated/not_updated always account for the full
  # total_attempted. A taxon name with nothing to remove lands in
  # not_updated with no validation_errors entry; if a destroy were ever to
  # fail (nothing currently blocks one) it would also land in not_updated,
  # but with an error message - that's how the two would be told apart.
  def self.destroy_classifications_for_batch(classifications:, query:, batch_response:)
    existing_by_taxon_name_id = classifications
      .where(taxon_name: query)
      .includes(:taxon_name) # used by the set_cached callback
      .group_by(&:taxon_name_id)

    query.find_each do |taxon_name|
      found = existing_by_taxon_name_id[taxon_name.id] || []

      if found.empty?
        batch_response.not_updated.push taxon_name.id
        next
      end

      failed = found.reject do |c|
        c.destroy # destroy is necessary to update cached values
        c.destroyed?
      end

      if failed.empty?
        batch_response.updated.push nil
      else # never happens?
        batch_response.not_updated.push taxon_name.id
        failed.each { |c|
          c.errors.full_messages.each { |msg|
            batch_response.validation_errors[msg] += 1
          }
        }
      end
    end
  end

  def self.dispatch_batch_by_filter_scope_job(hash_query:, mode:, params:, project_id:, user_id:)
    BatchByFilterScopeJob.perform_later(
      klass: self.name,
      hash_query:,
      mode:,
      params:,
      project_id:,
      user_id:
    )
  end

 private

  def nomenclature_code_matches
    if taxon_name && type && nomenclature_code
      tn = taxon_name.is_combination? ? taxon_name.protonyms.last : taxon_name
      nc = tn.rank_class.nomenclatural_code
      if nomenclature_code != nc
        taxon_name_code = nc.nil? ? 'no' : "the #{nc}"
        errors.add(:taxon_name, "#{taxon_name.cached_html} belongs to #{taxon_name_code} nomenclatural code, but the status is from the #{nomenclature_code} nomenclatural code")
      end
    end
  end

  # TODO: unnecessary! Type handling will raise here
  def validate_taxon_name_classification
    errors.add(:type, 'Status not found') if !self.type.nil? and !TAXON_NAME_CLASSIFICATION_NAMES.include?(self.type.to_s)
  end

  # @todo move these to a shared library (see NomenclaturalRank too)
  def self.collect_to_s(*args)
    args.collect{|arg| arg.to_s}
  end

  # @todo move these to a shared library (see NomenclaturalRank too)
  # !! using this strongly suggests something can be optimized, meomized etc.
  def self.collect_descendants_to_s(*classes)
    ans = []
    classes.each do |klass|
      ans += klass.descendants.collect{|k| k.to_s}
    end
    ans
  end

  # @todo move these to a shared library (see NomenclaturalRank too)
  # !! using this strongly suggests something can be optimized, meomized etc.
  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}/app/models/taxon_name_classification/**/*.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

#taxon_name_id ⇒ `Integer`

Returns the id of the TaxonName being classified.

Returns:

(Integer) —
the id of the TaxonName being classified

# File 'app/models/taxon_name_classification.rb', line 18

class TaxonNameClassification < ApplicationRecord
  include Housekeeping
  include Shared::BatchByFilterScope
  include Shared::Citations
  include Shared::Notes
  include Shared::IsData
  include SoftValidation

  belongs_to :taxon_name, inverse_of: :taxon_name_classifications

  before_validation :validate_taxon_name_classification
  before_validation :validate_uniqueness_of_latinized
  after_commit :set_cached

  validates_presence_of :taxon_name
  validates_presence_of :type
  validates_uniqueness_of :taxon_name_id, scope: [:type, :project_id]

  validate :nomenclature_code_matches

  scope :where_taxon_name, -> (taxon_name) {where(taxon_name_id: taxon_name)}
  scope :with_type_string, -> (base_string) {where('taxon_name_classifications.type LIKE ?', "#{base_string}" ) }
  scope :with_type_base, -> (base_string) {where('taxon_name_classifications.type LIKE ?', "#{base_string}%" ) }
  scope :with_type_array, -> (base_array) {where('taxon_name_classifications.type IN (?)', base_array ) }
  scope :with_type_contains, -> (base_string) {where('taxon_name_classifications.type LIKE ?', "%#{base_string}%" ) }

  soft_validate(:sv_proper_classification,
                set: :proper_classification,
                fix: :sv_fix_proper_classification,
                name: 'Applicable status',
                description: 'Check the status applicability.' )

  soft_validate(:sv_proper_year,
                set: :proper_classification,
                name: 'Applicable protonym year',
                description: 'Check that the status is compatible with the year of publication of taxon.' )

  soft_validate(:sv_validate_disjoint_classes,
                set: :validate_disjoint_classes,
                name: 'Conflicting status',
                description: 'Taxon has two conflicting statuses' )

  soft_validate(:sv_not_specific_classes,
                set: :not_specific_classes,
                name: 'Not specific status',
                description: 'More specific statuses are preffered, for example: "Nomen nudum, no description" is better than "Nomen nudum".' )

  def nomenclature_code
    return :iczn if type.match(/::Iczn/)
    return :icnp if type.match(/::Icnp/)
    return :icvcn if type.match(/::Icvcn/)
    return :icn if type.match(/::Icn/)
    return nil
  end

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

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

  # @return [String]
  #   the class name, "validated" against the known list of names
  def type_name
    r = self.type.to_s
    ::TAXON_NAME_CLASSIFICATION_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
    r = ::TAXON_NAME_CLASSIFICATION_NAMES.include?(r) ? r.safe_constantize : nil
  end

  # @return [String]
  #   a humanized class name, with code appended to differentiate
  #   !! explored idea of LABEL in individual subclasses, use this if this doesn't work
  #   this is helper-esqe, but also useful in validation, so here for now
  def classification_label
    return nil if type_name.nil?
    type_name.demodulize.underscore.humanize.downcase.gsub(/\d+/, ' \0 ').squish #+
      #(nomenclature_code ? " [#{nomenclature_code}]" : '')
  end

  # @return [String]
  #   the NOMEN id for this classification
  def nomen_id
    self.class::NOMEN_URI.split('/').last
  end

  # Attributes can be overridden in descendants

  # @return [Integer]
  # the minimum year of applicability for this class, defaults to 1
  def self.code_applicability_start_year
    1
  end

  # @return [Integer]
  # the last year of applicability for this class, defaults to 9999
  def self.code_applicability_end_year
    9999
  end

  # @return [Array of Strings of NomenclaturalRank names]
  # nomenclatural ranks to which this class is applicable, that is, only {TaxonName}s of these {NomenclaturalRank}s may be classified as this class
  def self.applicable_ranks
    []
  end

  # @return [Array of Strings of TaxonNameClassification names]
  # the disjoint (inapplicable) {TaxonNameClassification}s for this class, that is, {TaxonName}s classified as this class can not be additionally classified under these classes
  def self.disjoint_taxon_name_classes
    []
  end

  # @return [String, nil]
  #  if applicable, a DWC gbif status for this class
  def self.gbif_status
    nil
  end

  def self.assignable
    false
  end

 #def self.common
 #  false
 #end

  # @todo Perhaps not inherit these three meaxonNameClassificationsHelper::descendants_collection( TaxonNameClassification::Latinized )thods?

  # @return [Array of Strings]
  #   the possible suffixes for a {TaxonName} name (species) classified as this class, for example see {TaxonNameClassification::Latinized::Gender::Masculine}
  #   used to validate gender agreement of species name with a genus
  def self.possible_species_endings
    []
  end

  # @return [Array of Strings]
  #   the questionable suffixes for a {TaxonName} name classified as this class, for example see {TaxonNameClassification::Latinized::Gender::Masculine}
  def self.questionable_species_endings
    []
  end

  # @return [Array of Strings]
  # the possible suffixes for a {TaxonName} name (genus) classified as this class, for example see {TaxonNameClassification::Latinized::Gender::Masculine}
  def self.possible_genus_endings
    []
  end

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

  def set_cached
    set_cached_names_for_taxon_names
  end

  # TODO: move these to individual classes?!
  # Starting to move to individual classes
  #     Gender is sone
  def set_cached_names_for_taxon_names
    t = taxon_name
    return if t.destroyed?
    begin
      TaxonName.transaction_with_retry do
        if type_name =~ /(Fossil|Hybrid|Candidatus)/ # Break these out, they don't all apply to the same codes
          n = t.get_full_name
          t.update_columns(
            cached: n,
            cached_html: t.get_full_name_html(n),
            cached_original_combination: t.get_original_combination,
            cached_original_combination_html: t.get_original_combination_html
          )
        elsif type_name =~ /Latinized::PartOfSpeech/
          n = t.get_full_name
          t.update_columns(
              cached: n,
              cached_html: t.get_full_name_html(n),
              cached_original_combination: t.get_original_combination,
              cached_original_combination_html: t.get_original_combination_html
          )

          TaxonNameRelationship::OriginalCombination.where(subject_taxon_name: t).collect{|i| i.object_taxon_name}.uniq.each do |t1|
            t1.update_cached_original_combinations
          end

          TaxonNameRelationship::Combination.where(subject_taxon_name: t).collect{|i| i.object_taxon_name}.uniq.each do |t1|
            t1.update_column(:verbatim_name, t1.cached) if t1.verbatim_name.nil?
            n = t1.get_full_name
            t1.update_columns(
                cached: n,
                cached_html: t1.get_full_name_html(n)
            )
          end

        elsif type_name =~ /Latinized::Gender/
          # Handled in subclasses
          raise
        elsif TAXON_NAME_CLASS_NAMES_VALID.include?(type_name)
          vn = t.get_valid_taxon_name
          vn.update_columns(
            cached_valid_taxon_name_id: vn.id,
            cached_is_valid: !vn.unavailable_or_invalid?) # Do not change!
          vn.list_of_invalid_taxon_names.each do |s|
            s.update_columns(
              cached_valid_taxon_name_id: vn.id,
              cached_is_valid: false)
            s.combination_list_self.each do |c|
              c.update_columns(cached_valid_taxon_name_id: vn.id)
            end
          end
          t.combination_list_self.each do |c|
            c.update_columns(cached_valid_taxon_name_id: vn.id)
          end
        else
          t.update_columns(cached_is_valid: false)
        end

        if TAXON_NAME_CLASS_NAMES_UNAVAILABLE.include?( type_name )
          t.update_columns(
            cached_is_available: false
          )
        end
      end
    rescue ActiveRecord::RecordInvalid
      false
    end
    true
  end

  def validate_uniqueness_of_latinized
    true # moved to subclasses
  end

  def sv_proper_classification
    if TAXON_NAME_CLASSIFICATION_NAMES.include?(self.type)
      # self.type_class is a Class
      if not self.type_class.applicable_ranks.include?(self.taxon_name.rank_string)
        soft_validations.add(:type, "The status '#{self.classification_label}' is not applicable to the taxon #{self.taxon_name.cached_html} at the rank of #{self.taxon_name.rank_class.rank_name}", success_message: 'The status was deleted', failure_message:  'Fail to delete the status')
      end
    end
  end

  def sv_fix_proper_classification
    begin
      TaxonNameClassification.transaction do
        self.destroy
      end
      return true
    rescue
      return false
    end
  end

  def sv_proper_year
    y = self.taxon_name.year_of_publication
    if !y.nil? && (y > self.type_class.code_applicability_end_year || y < self.type_class.code_applicability_start_year)
      soft_validations.add(:type, "The status '#{self.classification_label}' is not applicable to the taxon #{self.taxon_name.cached_html} published in the year #{y}")
    end
  end

  def sv_validate_disjoint_classes
    classifications = TaxonNameClassification.where_taxon_name(self.taxon_name).not_self(self)
    classifications.each  do |i|
      soft_validations.add(:type, "The status  '#{self.classification_label}' conflicting with another status: '#{i.classification_label}'") if self.type_class.disjoint_taxon_name_classes.include?(i.type_name)
    end
  end

  def sv_not_specific_classes
    true # moved to subclasses
  end

  def self.annotates?
    true
  end

  def annotated_object
    taxon_name
  end

  # @param batch_response [BatchResponse]
  # @param query [ActiveRecord::Relation] TaxonName scope from the filter
  # @param hash_query [Hash] serialized filter params, used to re-run the query in async jobs
  # @param mode [Symbol, String] :set, :remove_gender (gender); :add_status, :remove_status (arbitrary status)
  # @param params [Hash] :type required for :set, :add_status, :remove_status;
  #   :citation (optional, :add_status only) a Hash with :source_id (required to attach), :pages, :is_original -
  #   attached to the status whether it was just created or already existed; tolerates (does not duplicate or
  #   error on) a citation with the same source, pages, and is_original already present on that status
  # @param async [Boolean]
  # @param project_id [Integer]
  # @param user_id [Integer]
  # @param called_from_async [Boolean] prevents re-dispatching when already inside a job
  # @return [BatchResponse]
  def self.process_batch_by_filter_scope(
    batch_response: nil, query: nil, hash_query: nil, mode: nil,
    params: nil, async: nil, project_id: nil, user_id: nil,
    called_from_async: false
  )
    async = false if called_from_async == true
    r = batch_response

    case mode.to_sym
    when :set # gender
      gender_type = params[:type]
      return r unless TAXON_NAME_CLASSIFICATIONS_FOR_GENDER.include?(gender_type)

      if async && !called_from_async
        dispatch_batch_by_filter_scope_job(
          hash_query:, mode:, params:, project_id:, user_id:
        )
        return r
      end

      existing_by_taxon_name_id = TaxonNameClassification
        .with_type_array(TAXON_NAME_CLASSIFICATIONS_FOR_GENDER)
        .where(taxon_name: query)
        .index_by(&:taxon_name_id)

      query.find_each do |taxon_name|
        if existing = existing_by_taxon_name_id[taxon_name.id]
          if existing.type == gender_type
            # Already the requested gender - skip the update entirely rather
            # than trigger the expensive after_commit cascade (walks every
            # descendant taxon name to recompute cached spellings) for
            # nothing.
            r.updated.push existing.id
          elsif existing.update(type: gender_type)
            r.updated.push existing.id
          else
            r.not_updated.push taxon_name.id
            existing.errors.full_messages.each { |msg|
              r.validation_errors[msg] += 1
            }
          end
        else
          classification = TaxonNameClassification.create(
            taxon_name: taxon_name, type: gender_type
          )
          if classification.persisted?
            r.updated.push classification.id
          else
            r.not_updated.push taxon_name.id
            classification.errors.full_messages.each { |msg|
              r.validation_errors[msg] += 1
            }
          end
        end
      end

    when :remove_gender
      if async && !called_from_async
        dispatch_batch_by_filter_scope_job(
          hash_query:, mode:, params:, project_id:, user_id:
        )
        return r
      end

      destroy_classifications_for_batch(
        classifications: TaxonNameClassification.with_type_array(TAXON_NAME_CLASSIFICATIONS_FOR_GENDER),
        query:,
        batch_response: r
      )

    when :add_status
      status_type = params[:type]
      return r unless TAXON_NAME_CLASSIFICATION_NAMES.include?(status_type)

      if async && !called_from_async
        dispatch_batch_by_filter_scope_job(
          hash_query:, mode:, params:, project_id:, user_id:
        )
        return r
      end

      citation_params = params[:citation]&.symbolize_keys
      citation_source_id = citation_params && citation_params[:source_id]

      citation_source = citation_source_id && Source.find_by(id: citation_source_id)

      existing_by_taxon_name_id = TaxonNameClassification
        .where(type: status_type)
        .where(taxon_name: query)
        .index_by(&:taxon_name_id)

      # Disjoint types (e.g. Iczn::Fossil::Ichnotaxon is disjoint with its own
      # parent Iczn::Fossil) already satisfy this status; skip creating a
      # conflicting status rather than let the two coexist.
      disjoint_types = status_type.constantize.disjoint_taxon_name_classes

      conflicting_taxon_name_ids =
        if disjoint_types.empty?
          Set.new
        else
          TaxonNameClassification
            .where(type: disjoint_types)
            .where(taxon_name: query)
            .distinct
            .pluck(:taxon_name_id)
            .to_set
        end

      # Classifications that already carry the exact citation (same
      # source, pages, and is_original) being requested. This isn't just a
      # performance nicety: it's what distinguishes an identical repeat
      # (skipped and reported as updated) from a genuine conflict: same
      # source and pages but a different is_original (attempted, fails,
      # and is reported below with a message specific to that case).
      already_cited_classification_ids =
        if citation_source_id && existing_by_taxon_name_id.any?
          Citation.duplicate_citation_object_ids(
            citation_object_type: 'TaxonNameClassification',
            citation_object_ids: existing_by_taxon_name_id.values.map(&:id),
            source_id: citation_source_id,
            pages: citation_params[:pages],
            is_original: citation_params[:is_original]
          )
        else
          Set.new
        end

      query.find_each do |taxon_name|
        if (
          !existing_by_taxon_name_id.key?(taxon_name.id) &&
          conflicting_taxon_name_ids.include?(taxon_name.id)
        )
          r.not_updated.push taxon_name.id
          r.validation_errors['conflicts with an existing disjoint classification'] += 1
          next
        end

        classification = existing_by_taxon_name_id[taxon_name.id] ||
          TaxonNameClassification.create(taxon_name: taxon_name, type: status_type)

        unless classification.persisted?
          r.not_updated.push taxon_name.id
          classification.errors.full_messages.each { |msg|
            r.validation_errors[msg] += 1
          }
          next
        end

        if citation_source_id && !already_cited_classification_ids.include?(classification.id)
          citation = classification.citations.create(
            source: citation_source,
            pages: citation_params[:pages],
            is_original: citation_params[:is_original]
          )

          unless citation.persisted?
            r.not_updated.push taxon_name.id

            # An exact repeat was already ruled out above, so a source_id
            # conflict here can only mean a citation with this same source
            # and pages exists with a different is_original - Citation's
            # own validation doesn't know or care about is_original, it
            # only reports the source/pages conflict, so the more specific
            # wording is built here. The taxon name id is included (rather
            # than summarized by count, as validation_errors normally are)
            # since this needs manual review to resolve.
            if citation.errors[:source_id].any?
              r.validation_errors["citation already exists with a different 'original' flag for taxon name id #{taxon_name.id} - is_original was not changed"] += 1
            else # a second `is_original = true` citation, e.g.
              citation.errors.full_messages.each { |msg|
                r.validation_errors[msg] += 1
              }
            end

            next
          end
        end

        r.updated.push classification.id
      end

    when :remove_status
      status_type = params[:type]
      return r unless TAXON_NAME_CLASSIFICATION_NAMES.include?(status_type)

      if async && !called_from_async
        dispatch_batch_by_filter_scope_job(hash_query:, mode:, params:, project_id:, user_id:)
        return r
      end

      # Only the exact type selected: not its subclasses (e.g. removing
      # Iczn::Fossil leaves Iczn::Fossil::Ichnotaxon), and not
      # disjoint_taxon_name_classes, which is every *conflicting* status.
      destroy_classifications_for_batch(
        classifications: TaxonNameClassification.where(type: status_type),
        query:,
        batch_response: r
      )
    end

    r
  end

  # Destroys `classifications` belonging to taxon names in `query`.
  # Iterates every taxon name in the query (not just ones with a matching
  # classification) so updated/not_updated always account for the full
  # total_attempted. A taxon name with nothing to remove lands in
  # not_updated with no validation_errors entry; if a destroy were ever to
  # fail (nothing currently blocks one) it would also land in not_updated,
  # but with an error message - that's how the two would be told apart.
  def self.destroy_classifications_for_batch(classifications:, query:, batch_response:)
    existing_by_taxon_name_id = classifications
      .where(taxon_name: query)
      .includes(:taxon_name) # used by the set_cached callback
      .group_by(&:taxon_name_id)

    query.find_each do |taxon_name|
      found = existing_by_taxon_name_id[taxon_name.id] || []

      if found.empty?
        batch_response.not_updated.push taxon_name.id
        next
      end

      failed = found.reject do |c|
        c.destroy # destroy is necessary to update cached values
        c.destroyed?
      end

      if failed.empty?
        batch_response.updated.push nil
      else # never happens?
        batch_response.not_updated.push taxon_name.id
        failed.each { |c|
          c.errors.full_messages.each { |msg|
            batch_response.validation_errors[msg] += 1
          }
        }
      end
    end
  end

  def self.dispatch_batch_by_filter_scope_job(hash_query:, mode:, params:, project_id:, user_id:)
    BatchByFilterScopeJob.perform_later(
      klass: self.name,
      hash_query:,
      mode:,
      params:,
      project_id:,
      user_id:
    )
  end

 private

  def nomenclature_code_matches
    if taxon_name && type && nomenclature_code
      tn = taxon_name.is_combination? ? taxon_name.protonyms.last : taxon_name
      nc = tn.rank_class.nomenclatural_code
      if nomenclature_code != nc
        taxon_name_code = nc.nil? ? 'no' : "the #{nc}"
        errors.add(:taxon_name, "#{taxon_name.cached_html} belongs to #{taxon_name_code} nomenclatural code, but the status is from the #{nomenclature_code} nomenclatural code")
      end
    end
  end

  # TODO: unnecessary! Type handling will raise here
  def validate_taxon_name_classification
    errors.add(:type, 'Status not found') if !self.type.nil? and !TAXON_NAME_CLASSIFICATION_NAMES.include?(self.type.to_s)
  end

  # @todo move these to a shared library (see NomenclaturalRank too)
  def self.collect_to_s(*args)
    args.collect{|arg| arg.to_s}
  end

  # @todo move these to a shared library (see NomenclaturalRank too)
  # !! using this strongly suggests something can be optimized, meomized etc.
  def self.collect_descendants_to_s(*classes)
    ans = []
    classes.each do |klass|
      ans += klass.descendants.collect{|k| k.to_s}
    end
    ans
  end

  # @todo move these to a shared library (see NomenclaturalRank too)
  # !! using this strongly suggests something can be optimized, meomized etc.
  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}/app/models/taxon_name_classification/**/*.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 type of classifiction (Rails STI).

Returns:

(String) —
the type of classifiction (Rails STI)

# File 'app/models/taxon_name_classification.rb', line 18

class TaxonNameClassification < ApplicationRecord
  include Housekeeping
  include Shared::BatchByFilterScope
  include Shared::Citations
  include Shared::Notes
  include Shared::IsData
  include SoftValidation

  belongs_to :taxon_name, inverse_of: :taxon_name_classifications

  before_validation :validate_taxon_name_classification
  before_validation :validate_uniqueness_of_latinized
  after_commit :set_cached

  validates_presence_of :taxon_name
  validates_presence_of :type
  validates_uniqueness_of :taxon_name_id, scope: [:type, :project_id]

  validate :nomenclature_code_matches

  scope :where_taxon_name, -> (taxon_name) {where(taxon_name_id: taxon_name)}
  scope :with_type_string, -> (base_string) {where('taxon_name_classifications.type LIKE ?', "#{base_string}" ) }
  scope :with_type_base, -> (base_string) {where('taxon_name_classifications.type LIKE ?', "#{base_string}%" ) }
  scope :with_type_array, -> (base_array) {where('taxon_name_classifications.type IN (?)', base_array ) }
  scope :with_type_contains, -> (base_string) {where('taxon_name_classifications.type LIKE ?', "%#{base_string}%" ) }

  soft_validate(:sv_proper_classification,
                set: :proper_classification,
                fix: :sv_fix_proper_classification,
                name: 'Applicable status',
                description: 'Check the status applicability.' )

  soft_validate(:sv_proper_year,
                set: :proper_classification,
                name: 'Applicable protonym year',
                description: 'Check that the status is compatible with the year of publication of taxon.' )

  soft_validate(:sv_validate_disjoint_classes,
                set: :validate_disjoint_classes,
                name: 'Conflicting status',
                description: 'Taxon has two conflicting statuses' )

  soft_validate(:sv_not_specific_classes,
                set: :not_specific_classes,
                name: 'Not specific status',
                description: 'More specific statuses are preffered, for example: "Nomen nudum, no description" is better than "Nomen nudum".' )

  def nomenclature_code
    return :iczn if type.match(/::Iczn/)
    return :icnp if type.match(/::Icnp/)
    return :icvcn if type.match(/::Icvcn/)
    return :icn if type.match(/::Icn/)
    return nil
  end

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

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

  # @return [String]
  #   the class name, "validated" against the known list of names
  def type_name
    r = self.type.to_s
    ::TAXON_NAME_CLASSIFICATION_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
    r = ::TAXON_NAME_CLASSIFICATION_NAMES.include?(r) ? r.safe_constantize : nil
  end

  # @return [String]
  #   a humanized class name, with code appended to differentiate
  #   !! explored idea of LABEL in individual subclasses, use this if this doesn't work
  #   this is helper-esqe, but also useful in validation, so here for now
  def classification_label
    return nil if type_name.nil?
    type_name.demodulize.underscore.humanize.downcase.gsub(/\d+/, ' \0 ').squish #+
      #(nomenclature_code ? " [#{nomenclature_code}]" : '')
  end

  # @return [String]
  #   the NOMEN id for this classification
  def nomen_id
    self.class::NOMEN_URI.split('/').last
  end

  # Attributes can be overridden in descendants

  # @return [Integer]
  # the minimum year of applicability for this class, defaults to 1
  def self.code_applicability_start_year
    1
  end

  # @return [Integer]
  # the last year of applicability for this class, defaults to 9999
  def self.code_applicability_end_year
    9999
  end

  # @return [Array of Strings of NomenclaturalRank names]
  # nomenclatural ranks to which this class is applicable, that is, only {TaxonName}s of these {NomenclaturalRank}s may be classified as this class
  def self.applicable_ranks
    []
  end

  # @return [Array of Strings of TaxonNameClassification names]
  # the disjoint (inapplicable) {TaxonNameClassification}s for this class, that is, {TaxonName}s classified as this class can not be additionally classified under these classes
  def self.disjoint_taxon_name_classes
    []
  end

  # @return [String, nil]
  #  if applicable, a DWC gbif status for this class
  def self.gbif_status
    nil
  end

  def self.assignable
    false
  end

 #def self.common
 #  false
 #end

  # @todo Perhaps not inherit these three meaxonNameClassificationsHelper::descendants_collection( TaxonNameClassification::Latinized )thods?

  # @return [Array of Strings]
  #   the possible suffixes for a {TaxonName} name (species) classified as this class, for example see {TaxonNameClassification::Latinized::Gender::Masculine}
  #   used to validate gender agreement of species name with a genus
  def self.possible_species_endings
    []
  end

  # @return [Array of Strings]
  #   the questionable suffixes for a {TaxonName} name classified as this class, for example see {TaxonNameClassification::Latinized::Gender::Masculine}
  def self.questionable_species_endings
    []
  end

  # @return [Array of Strings]
  # the possible suffixes for a {TaxonName} name (genus) classified as this class, for example see {TaxonNameClassification::Latinized::Gender::Masculine}
  def self.possible_genus_endings
    []
  end

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

  def set_cached
    set_cached_names_for_taxon_names
  end

  # TODO: move these to individual classes?!
  # Starting to move to individual classes
  #     Gender is sone
  def set_cached_names_for_taxon_names
    t = taxon_name
    return if t.destroyed?
    begin
      TaxonName.transaction_with_retry do
        if type_name =~ /(Fossil|Hybrid|Candidatus)/ # Break these out, they don't all apply to the same codes
          n = t.get_full_name
          t.update_columns(
            cached: n,
            cached_html: t.get_full_name_html(n),
            cached_original_combination: t.get_original_combination,
            cached_original_combination_html: t.get_original_combination_html
          )
        elsif type_name =~ /Latinized::PartOfSpeech/
          n = t.get_full_name
          t.update_columns(
              cached: n,
              cached_html: t.get_full_name_html(n),
              cached_original_combination: t.get_original_combination,
              cached_original_combination_html: t.get_original_combination_html
          )

          TaxonNameRelationship::OriginalCombination.where(subject_taxon_name: t).collect{|i| i.object_taxon_name}.uniq.each do |t1|
            t1.update_cached_original_combinations
          end

          TaxonNameRelationship::Combination.where(subject_taxon_name: t).collect{|i| i.object_taxon_name}.uniq.each do |t1|
            t1.update_column(:verbatim_name, t1.cached) if t1.verbatim_name.nil?
            n = t1.get_full_name
            t1.update_columns(
                cached: n,
                cached_html: t1.get_full_name_html(n)
            )
          end

        elsif type_name =~ /Latinized::Gender/
          # Handled in subclasses
          raise
        elsif TAXON_NAME_CLASS_NAMES_VALID.include?(type_name)
          vn = t.get_valid_taxon_name
          vn.update_columns(
            cached_valid_taxon_name_id: vn.id,
            cached_is_valid: !vn.unavailable_or_invalid?) # Do not change!
          vn.list_of_invalid_taxon_names.each do |s|
            s.update_columns(
              cached_valid_taxon_name_id: vn.id,
              cached_is_valid: false)
            s.combination_list_self.each do |c|
              c.update_columns(cached_valid_taxon_name_id: vn.id)
            end
          end
          t.combination_list_self.each do |c|
            c.update_columns(cached_valid_taxon_name_id: vn.id)
          end
        else
          t.update_columns(cached_is_valid: false)
        end

        if TAXON_NAME_CLASS_NAMES_UNAVAILABLE.include?( type_name )
          t.update_columns(
            cached_is_available: false
          )
        end
      end
    rescue ActiveRecord::RecordInvalid
      false
    end
    true
  end

  def validate_uniqueness_of_latinized
    true # moved to subclasses
  end

  def sv_proper_classification
    if TAXON_NAME_CLASSIFICATION_NAMES.include?(self.type)
      # self.type_class is a Class
      if not self.type_class.applicable_ranks.include?(self.taxon_name.rank_string)
        soft_validations.add(:type, "The status '#{self.classification_label}' is not applicable to the taxon #{self.taxon_name.cached_html} at the rank of #{self.taxon_name.rank_class.rank_name}", success_message: 'The status was deleted', failure_message:  'Fail to delete the status')
      end
    end
  end

  def sv_fix_proper_classification
    begin
      TaxonNameClassification.transaction do
        self.destroy
      end
      return true
    rescue
      return false
    end
  end

  def sv_proper_year
    y = self.taxon_name.year_of_publication
    if !y.nil? && (y > self.type_class.code_applicability_end_year || y < self.type_class.code_applicability_start_year)
      soft_validations.add(:type, "The status '#{self.classification_label}' is not applicable to the taxon #{self.taxon_name.cached_html} published in the year #{y}")
    end
  end

  def sv_validate_disjoint_classes
    classifications = TaxonNameClassification.where_taxon_name(self.taxon_name).not_self(self)
    classifications.each  do |i|
      soft_validations.add(:type, "The status  '#{self.classification_label}' conflicting with another status: '#{i.classification_label}'") if self.type_class.disjoint_taxon_name_classes.include?(i.type_name)
    end
  end

  def sv_not_specific_classes
    true # moved to subclasses
  end

  def self.annotates?
    true
  end

  def annotated_object
    taxon_name
  end

  # @param batch_response [BatchResponse]
  # @param query [ActiveRecord::Relation] TaxonName scope from the filter
  # @param hash_query [Hash] serialized filter params, used to re-run the query in async jobs
  # @param mode [Symbol, String] :set, :remove_gender (gender); :add_status, :remove_status (arbitrary status)
  # @param params [Hash] :type required for :set, :add_status, :remove_status;
  #   :citation (optional, :add_status only) a Hash with :source_id (required to attach), :pages, :is_original -
  #   attached to the status whether it was just created or already existed; tolerates (does not duplicate or
  #   error on) a citation with the same source, pages, and is_original already present on that status
  # @param async [Boolean]
  # @param project_id [Integer]
  # @param user_id [Integer]
  # @param called_from_async [Boolean] prevents re-dispatching when already inside a job
  # @return [BatchResponse]
  def self.process_batch_by_filter_scope(
    batch_response: nil, query: nil, hash_query: nil, mode: nil,
    params: nil, async: nil, project_id: nil, user_id: nil,
    called_from_async: false
  )
    async = false if called_from_async == true
    r = batch_response

    case mode.to_sym
    when :set # gender
      gender_type = params[:type]
      return r unless TAXON_NAME_CLASSIFICATIONS_FOR_GENDER.include?(gender_type)

      if async && !called_from_async
        dispatch_batch_by_filter_scope_job(
          hash_query:, mode:, params:, project_id:, user_id:
        )
        return r
      end

      existing_by_taxon_name_id = TaxonNameClassification
        .with_type_array(TAXON_NAME_CLASSIFICATIONS_FOR_GENDER)
        .where(taxon_name: query)
        .index_by(&:taxon_name_id)

      query.find_each do |taxon_name|
        if existing = existing_by_taxon_name_id[taxon_name.id]
          if existing.type == gender_type
            # Already the requested gender - skip the update entirely rather
            # than trigger the expensive after_commit cascade (walks every
            # descendant taxon name to recompute cached spellings) for
            # nothing.
            r.updated.push existing.id
          elsif existing.update(type: gender_type)
            r.updated.push existing.id
          else
            r.not_updated.push taxon_name.id
            existing.errors.full_messages.each { |msg|
              r.validation_errors[msg] += 1
            }
          end
        else
          classification = TaxonNameClassification.create(
            taxon_name: taxon_name, type: gender_type
          )
          if classification.persisted?
            r.updated.push classification.id
          else
            r.not_updated.push taxon_name.id
            classification.errors.full_messages.each { |msg|
              r.validation_errors[msg] += 1
            }
          end
        end
      end

    when :remove_gender
      if async && !called_from_async
        dispatch_batch_by_filter_scope_job(
          hash_query:, mode:, params:, project_id:, user_id:
        )
        return r
      end

      destroy_classifications_for_batch(
        classifications: TaxonNameClassification.with_type_array(TAXON_NAME_CLASSIFICATIONS_FOR_GENDER),
        query:,
        batch_response: r
      )

    when :add_status
      status_type = params[:type]
      return r unless TAXON_NAME_CLASSIFICATION_NAMES.include?(status_type)

      if async && !called_from_async
        dispatch_batch_by_filter_scope_job(
          hash_query:, mode:, params:, project_id:, user_id:
        )
        return r
      end

      citation_params = params[:citation]&.symbolize_keys
      citation_source_id = citation_params && citation_params[:source_id]

      citation_source = citation_source_id && Source.find_by(id: citation_source_id)

      existing_by_taxon_name_id = TaxonNameClassification
        .where(type: status_type)
        .where(taxon_name: query)
        .index_by(&:taxon_name_id)

      # Disjoint types (e.g. Iczn::Fossil::Ichnotaxon is disjoint with its own
      # parent Iczn::Fossil) already satisfy this status; skip creating a
      # conflicting status rather than let the two coexist.
      disjoint_types = status_type.constantize.disjoint_taxon_name_classes

      conflicting_taxon_name_ids =
        if disjoint_types.empty?
          Set.new
        else
          TaxonNameClassification
            .where(type: disjoint_types)
            .where(taxon_name: query)
            .distinct
            .pluck(:taxon_name_id)
            .to_set
        end

      # Classifications that already carry the exact citation (same
      # source, pages, and is_original) being requested. This isn't just a
      # performance nicety: it's what distinguishes an identical repeat
      # (skipped and reported as updated) from a genuine conflict: same
      # source and pages but a different is_original (attempted, fails,
      # and is reported below with a message specific to that case).
      already_cited_classification_ids =
        if citation_source_id && existing_by_taxon_name_id.any?
          Citation.duplicate_citation_object_ids(
            citation_object_type: 'TaxonNameClassification',
            citation_object_ids: existing_by_taxon_name_id.values.map(&:id),
            source_id: citation_source_id,
            pages: citation_params[:pages],
            is_original: citation_params[:is_original]
          )
        else
          Set.new
        end

      query.find_each do |taxon_name|
        if (
          !existing_by_taxon_name_id.key?(taxon_name.id) &&
          conflicting_taxon_name_ids.include?(taxon_name.id)
        )
          r.not_updated.push taxon_name.id
          r.validation_errors['conflicts with an existing disjoint classification'] += 1
          next
        end

        classification = existing_by_taxon_name_id[taxon_name.id] ||
          TaxonNameClassification.create(taxon_name: taxon_name, type: status_type)

        unless classification.persisted?
          r.not_updated.push taxon_name.id
          classification.errors.full_messages.each { |msg|
            r.validation_errors[msg] += 1
          }
          next
        end

        if citation_source_id && !already_cited_classification_ids.include?(classification.id)
          citation = classification.citations.create(
            source: citation_source,
            pages: citation_params[:pages],
            is_original: citation_params[:is_original]
          )

          unless citation.persisted?
            r.not_updated.push taxon_name.id

            # An exact repeat was already ruled out above, so a source_id
            # conflict here can only mean a citation with this same source
            # and pages exists with a different is_original - Citation's
            # own validation doesn't know or care about is_original, it
            # only reports the source/pages conflict, so the more specific
            # wording is built here. The taxon name id is included (rather
            # than summarized by count, as validation_errors normally are)
            # since this needs manual review to resolve.
            if citation.errors[:source_id].any?
              r.validation_errors["citation already exists with a different 'original' flag for taxon name id #{taxon_name.id} - is_original was not changed"] += 1
            else # a second `is_original = true` citation, e.g.
              citation.errors.full_messages.each { |msg|
                r.validation_errors[msg] += 1
              }
            end

            next
          end
        end

        r.updated.push classification.id
      end

    when :remove_status
      status_type = params[:type]
      return r unless TAXON_NAME_CLASSIFICATION_NAMES.include?(status_type)

      if async && !called_from_async
        dispatch_batch_by_filter_scope_job(hash_query:, mode:, params:, project_id:, user_id:)
        return r
      end

      # Only the exact type selected: not its subclasses (e.g. removing
      # Iczn::Fossil leaves Iczn::Fossil::Ichnotaxon), and not
      # disjoint_taxon_name_classes, which is every *conflicting* status.
      destroy_classifications_for_batch(
        classifications: TaxonNameClassification.where(type: status_type),
        query:,
        batch_response: r
      )
    end

    r
  end

  # Destroys `classifications` belonging to taxon names in `query`.
  # Iterates every taxon name in the query (not just ones with a matching
  # classification) so updated/not_updated always account for the full
  # total_attempted. A taxon name with nothing to remove lands in
  # not_updated with no validation_errors entry; if a destroy were ever to
  # fail (nothing currently blocks one) it would also land in not_updated,
  # but with an error message - that's how the two would be told apart.
  def self.destroy_classifications_for_batch(classifications:, query:, batch_response:)
    existing_by_taxon_name_id = classifications
      .where(taxon_name: query)
      .includes(:taxon_name) # used by the set_cached callback
      .group_by(&:taxon_name_id)

    query.find_each do |taxon_name|
      found = existing_by_taxon_name_id[taxon_name.id] || []

      if found.empty?
        batch_response.not_updated.push taxon_name.id
        next
      end

      failed = found.reject do |c|
        c.destroy # destroy is necessary to update cached values
        c.destroyed?
      end

      if failed.empty?
        batch_response.updated.push nil
      else # never happens?
        batch_response.not_updated.push taxon_name.id
        failed.each { |c|
          c.errors.full_messages.each { |msg|
            batch_response.validation_errors[msg] += 1
          }
        }
      end
    end
  end

  def self.dispatch_batch_by_filter_scope_job(hash_query:, mode:, params:, project_id:, user_id:)
    BatchByFilterScopeJob.perform_later(
      klass: self.name,
      hash_query:,
      mode:,
      params:,
      project_id:,
      user_id:
    )
  end

 private

  def nomenclature_code_matches
    if taxon_name && type && nomenclature_code
      tn = taxon_name.is_combination? ? taxon_name.protonyms.last : taxon_name
      nc = tn.rank_class.nomenclatural_code
      if nomenclature_code != nc
        taxon_name_code = nc.nil? ? 'no' : "the #{nc}"
        errors.add(:taxon_name, "#{taxon_name.cached_html} belongs to #{taxon_name_code} nomenclatural code, but the status is from the #{nomenclature_code} nomenclatural code")
      end
    end
  end

  # TODO: unnecessary! Type handling will raise here
  def validate_taxon_name_classification
    errors.add(:type, 'Status not found') if !self.type.nil? and !TAXON_NAME_CLASSIFICATION_NAMES.include?(self.type.to_s)
  end

  # @todo move these to a shared library (see NomenclaturalRank too)
  def self.collect_to_s(*args)
    args.collect{|arg| arg.to_s}
  end

  # @todo move these to a shared library (see NomenclaturalRank too)
  # !! using this strongly suggests something can be optimized, meomized etc.
  def self.collect_descendants_to_s(*classes)
    ans = []
    classes.each do |klass|
      ans += klass.descendants.collect{|k| k.to_s}
    end
    ans
  end

  # @todo move these to a shared library (see NomenclaturalRank too)
  # !! using this strongly suggests something can be optimized, meomized etc.
  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}/app/models/taxon_name_classification/**/*.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

.annotates? ⇒ `Boolean`

Returns:

(Boolean)



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# File 'app/models/taxon_name_classification.rb', line 299

def self.annotates?
  true
end

.applicable_ranks ⇒ `Array of Strings of NomenclaturalRank names`

nomenclatural ranks to which this class is applicable, that is, only TaxonNames of these NomenclaturalRanks may be classified as this class

Returns:

(Array of Strings of NomenclaturalRank names)



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# File 'app/models/taxon_name_classification.rb', line 131

def self.applicable_ranks
  []
end

.assignable ⇒ `Object`



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# File 'app/models/taxon_name_classification.rb', line 147

def self.assignable
  false
end

.code_applicability_end_year ⇒ `Integer`

the last year of applicability for this class, defaults to 9999

Returns:

(Integer)



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# File 'app/models/taxon_name_classification.rb', line 125

def self.code_applicability_end_year
  9999
end

.code_applicability_start_year ⇒ `Integer`

the minimum year of applicability for this class, defaults to 1

Returns:

(Integer)



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# File 'app/models/taxon_name_classification.rb', line 119

def self.code_applicability_start_year
  1
end

.collect_descendants_and_itself_to_s(*classes) ⇒ `Object`

TODO:

move these to a shared library (see NomenclaturalRank too)

!! using this strongly suggests something can be optimized, meomized etc.



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# File 'app/models/taxon_name_classification.rb', line 608

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`

TODO:

move these to a shared library (see NomenclaturalRank too)

!! using this strongly suggests something can be optimized, meomized etc.

# File 'app/models/taxon_name_classification.rb', line 598

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`

TODO:

move these to a shared library (see NomenclaturalRank too)



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# File 'app/models/taxon_name_classification.rb', line 592

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

.destroy_classifications_for_batch(classifications:, query:, batch_response:) ⇒ `Object`

Destroys classifications belonging to taxon names in query. Iterates every taxon name in the query (not just ones with a matching classification) so updated/not_updated always account for the full total_attempted. A taxon name with nothing to remove lands in not_updated with no validation_errors entry; if a destroy were ever to fail (nothing currently blocks one) it would also land in not_updated, but with an error message - that's how the two would be told apart.

# File 'app/models/taxon_name_classification.rb', line 530

def self.destroy_classifications_for_batch(classifications:, query:, batch_response:)
  existing_by_taxon_name_id = classifications
    .where(taxon_name: query)
    .includes(:taxon_name) # used by the set_cached callback
    .group_by(&:taxon_name_id)

  query.find_each do |taxon_name|
    found = existing_by_taxon_name_id[taxon_name.id] || []

    if found.empty?
      batch_response.not_updated.push taxon_name.id
      next
    end

    failed = found.reject do |c|
      c.destroy # destroy is necessary to update cached values
      c.destroyed?
    end

    if failed.empty?
      batch_response.updated.push nil
    else # never happens?
      batch_response.not_updated.push taxon_name.id
      failed.each { |c|
        c.errors.full_messages.each { |msg|
          batch_response.validation_errors[msg] += 1
        }
      }
    end
  end
end

.disjoint_taxon_name_classes ⇒ `Array of Strings of TaxonNameClassification names`

the disjoint (inapplicable) TaxonNameClassifications for this class, that is, TaxonNames classified as this class can not be additionally classified under these classes

Returns:

(Array of Strings of TaxonNameClassification names)



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# File 'app/models/taxon_name_classification.rb', line 137

def self.disjoint_taxon_name_classes
  []
end

.dispatch_batch_by_filter_scope_job(hash_query:, mode:, params:, project_id:, user_id:) ⇒ `Object`

# File 'app/models/taxon_name_classification.rb', line 562

def self.dispatch_batch_by_filter_scope_job(hash_query:, mode:, params:, project_id:, user_id:)
  BatchByFilterScopeJob.perform_later(
    klass: self.name,
    hash_query:,
    mode:,
    params:,
    project_id:,
    user_id:
  )
end

.gbif_status ⇒ `String`^?

Returns if applicable, a DWC gbif status for this class.

Returns:

(String, nil) —
if applicable, a DWC gbif status for this class



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# File 'app/models/taxon_name_classification.rb', line 143

def self.gbif_status
  nil
end

.label ⇒ `Object`



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# File 'app/models/taxon_name_classification.rb', line 73

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

.nomen_uri ⇒ `Object`



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# File 'app/models/taxon_name_classification.rb', line 176

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

.parent ⇒ `Object`

Returns class this method calls Module#module_parent.

Returns:

class this method calls Module#module_parent



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# File 'app/models/taxon_name_classification.rb', line 79

def self.parent
  self.module_parent
end

.possible_genus_endings ⇒ `Array of Strings`

the possible suffixes for a TaxonName name (genus) classified as this class, for example see TaxonNameClassification::Latinized::Gender::Masculine

Returns:

(Array of Strings)



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# File 'app/models/taxon_name_classification.rb', line 172

def self.possible_genus_endings
  []
end

.possible_species_endings ⇒ `Array of Strings`

Returns the possible suffixes for a TaxonName name (species) classified as this class, for example see TaxonNameClassification::Latinized::Gender::Masculine used to validate gender agreement of species name with a genus.

Returns:

(Array of Strings) —
the possible suffixes for a TaxonName name (species) classified as this class, for example see TaxonNameClassification::Latinized::Gender::Masculine used to validate gender agreement of species name with a genus



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# File 'app/models/taxon_name_classification.rb', line 160

def self.possible_species_endings
  []
end

.process_batch_by_filter_scope(batch_response: nil, query: nil, hash_query: nil, mode: nil, params: nil, async: nil, project_id: nil, user_id: nil, called_from_async: false) ⇒ `BatchResponse`

Parameters:

batch_response (BatchResponse) (defaults to: nil)
query (ActiveRecord::Relation) (defaults to: nil) —
TaxonName scope from the filter
hash_query (Hash) (defaults to: nil) —
serialized filter params, used to re-run the query in async jobs
mode (Symbol, String) (defaults to: nil) —
:set, :remove_gender (gender); :add_status, :remove_status (arbitrary status)
params (Hash) (defaults to: nil) —
:type required for :set, :add_status, :remove_status; :citation (optional, :add_status only) a Hash with :source_id (required to attach), :pages, :is_original - attached to the status whether it was just created or already existed; tolerates (does not duplicate or error on) a citation with the same source, pages, and is_original already present on that status
async (Boolean) (defaults to: nil)
project_id (Integer) (defaults to: nil)
user_id (Integer) (defaults to: nil)
called_from_async (Boolean) (defaults to: false) —
prevents re-dispatching when already inside a job

Returns:

(BatchResponse)

# File 'app/models/taxon_name_classification.rb', line 320

def self.process_batch_by_filter_scope(
  batch_response: nil, query: nil, hash_query: nil, mode: nil,
  params: nil, async: nil, project_id: nil, user_id: nil,
  called_from_async: false
)
  async = false if called_from_async == true
  r = batch_response

  case mode.to_sym
  when :set # gender
    gender_type = params[:type]
    return r unless TAXON_NAME_CLASSIFICATIONS_FOR_GENDER.include?(gender_type)

    if async && !called_from_async
      dispatch_batch_by_filter_scope_job(
        hash_query:, mode:, params:, project_id:, user_id:
      )
      return r
    end

    existing_by_taxon_name_id = TaxonNameClassification
      .with_type_array(TAXON_NAME_CLASSIFICATIONS_FOR_GENDER)
      .where(taxon_name: query)
      .index_by(&:taxon_name_id)

    query.find_each do |taxon_name|
      if existing = existing_by_taxon_name_id[taxon_name.id]
        if existing.type == gender_type
          # Already the requested gender - skip the update entirely rather
          # than trigger the expensive after_commit cascade (walks every
          # descendant taxon name to recompute cached spellings) for
          # nothing.
          r.updated.push existing.id
        elsif existing.update(type: gender_type)
          r.updated.push existing.id
        else
          r.not_updated.push taxon_name.id
          existing.errors.full_messages.each { |msg|
            r.validation_errors[msg] += 1
          }
        end
      else
        classification = TaxonNameClassification.create(
          taxon_name: taxon_name, type: gender_type
        )
        if classification.persisted?
          r.updated.push classification.id
        else
          r.not_updated.push taxon_name.id
          classification.errors.full_messages.each { |msg|
            r.validation_errors[msg] += 1
          }
        end
      end
    end

  when :remove_gender
    if async && !called_from_async
      dispatch_batch_by_filter_scope_job(
        hash_query:, mode:, params:, project_id:, user_id:
      )
      return r
    end

    destroy_classifications_for_batch(
      classifications: TaxonNameClassification.with_type_array(TAXON_NAME_CLASSIFICATIONS_FOR_GENDER),
      query:,
      batch_response: r
    )

  when :add_status
    status_type = params[:type]
    return r unless TAXON_NAME_CLASSIFICATION_NAMES.include?(status_type)

    if async && !called_from_async
      dispatch_batch_by_filter_scope_job(
        hash_query:, mode:, params:, project_id:, user_id:
      )
      return r
    end

    citation_params = params[:citation]&.symbolize_keys
    citation_source_id = citation_params && citation_params[:source_id]

    citation_source = citation_source_id && Source.find_by(id: citation_source_id)

    existing_by_taxon_name_id = TaxonNameClassification
      .where(type: status_type)
      .where(taxon_name: query)
      .index_by(&:taxon_name_id)

    # Disjoint types (e.g. Iczn::Fossil::Ichnotaxon is disjoint with its own
    # parent Iczn::Fossil) already satisfy this status; skip creating a
    # conflicting status rather than let the two coexist.
    disjoint_types = status_type.constantize.disjoint_taxon_name_classes

    conflicting_taxon_name_ids =
      if disjoint_types.empty?
        Set.new
      else
        TaxonNameClassification
          .where(type: disjoint_types)
          .where(taxon_name: query)
          .distinct
          .pluck(:taxon_name_id)
          .to_set
      end

    # Classifications that already carry the exact citation (same
    # source, pages, and is_original) being requested. This isn't just a
    # performance nicety: it's what distinguishes an identical repeat
    # (skipped and reported as updated) from a genuine conflict: same
    # source and pages but a different is_original (attempted, fails,
    # and is reported below with a message specific to that case).
    already_cited_classification_ids =
      if citation_source_id && existing_by_taxon_name_id.any?
        Citation.duplicate_citation_object_ids(
          citation_object_type: 'TaxonNameClassification',
          citation_object_ids: existing_by_taxon_name_id.values.map(&:id),
          source_id: citation_source_id,
          pages: citation_params[:pages],
          is_original: citation_params[:is_original]
        )
      else
        Set.new
      end

    query.find_each do |taxon_name|
      if (
        !existing_by_taxon_name_id.key?(taxon_name.id) &&
        conflicting_taxon_name_ids.include?(taxon_name.id)
      )
        r.not_updated.push taxon_name.id
        r.validation_errors['conflicts with an existing disjoint classification'] += 1
        next
      end

      classification = existing_by_taxon_name_id[taxon_name.id] ||
        TaxonNameClassification.create(taxon_name: taxon_name, type: status_type)

      unless classification.persisted?
        r.not_updated.push taxon_name.id
        classification.errors.full_messages.each { |msg|
          r.validation_errors[msg] += 1
        }
        next
      end

      if citation_source_id && !already_cited_classification_ids.include?(classification.id)
        citation = classification.citations.create(
          source: citation_source,
          pages: citation_params[:pages],
          is_original: citation_params[:is_original]
        )

        unless citation.persisted?
          r.not_updated.push taxon_name.id

          # An exact repeat was already ruled out above, so a source_id
          # conflict here can only mean a citation with this same source
          # and pages exists with a different is_original - Citation's
          # own validation doesn't know or care about is_original, it
          # only reports the source/pages conflict, so the more specific
          # wording is built here. The taxon name id is included (rather
          # than summarized by count, as validation_errors normally are)
          # since this needs manual review to resolve.
          if citation.errors[:source_id].any?
            r.validation_errors["citation already exists with a different 'original' flag for taxon name id #{taxon_name.id} - is_original was not changed"] += 1
          else # a second `is_original = true` citation, e.g.
            citation.errors.full_messages.each { |msg|
              r.validation_errors[msg] += 1
            }
          end

          next
        end
      end

      r.updated.push classification.id
    end

  when :remove_status
    status_type = params[:type]
    return r unless TAXON_NAME_CLASSIFICATION_NAMES.include?(status_type)

    if async && !called_from_async
      dispatch_batch_by_filter_scope_job(hash_query:, mode:, params:, project_id:, user_id:)
      return r
    end

    # Only the exact type selected: not its subclasses (e.g. removing
    # Iczn::Fossil leaves Iczn::Fossil::Ichnotaxon), and not
    # disjoint_taxon_name_classes, which is every *conflicting* status.
    destroy_classifications_for_batch(
      classifications: TaxonNameClassification.where(type: status_type),
      query:,
      batch_response: r
    )
  end

  r
end

.questionable_species_endings ⇒ `Array of Strings`

Returns the questionable suffixes for a TaxonName name classified as this class, for example see TaxonNameClassification::Latinized::Gender::Masculine.

Returns:

(Array of Strings) —
the questionable suffixes for a TaxonName name classified as this class, for example see TaxonNameClassification::Latinized::Gender::Masculine



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# File 'app/models/taxon_name_classification.rb', line 166

def self.questionable_species_endings
  []
end

Instance Method Details

#annotated_object ⇒ `Object`



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# File 'app/models/taxon_name_classification.rb', line 303

def annotated_object
  taxon_name
end

#classification_label ⇒ `String`

Returns a humanized class name, with code appended to differentiate !! explored idea of LABEL in individual subclasses, use this if this doesn't work this is helper-esqe, but also useful in validation, so here for now.

Returns:

(String) —
a humanized class name, with code appended to differentiate !! explored idea of LABEL in individual subclasses, use this if this doesn't work this is helper-esqe, but also useful in validation, so here for now

# File 'app/models/taxon_name_classification.rb', line 103

def classification_label
  return nil if type_name.nil?
  type_name.demodulize.underscore.humanize.downcase.gsub(/\d+/, ' \0 ').squish #+
    #(nomenclature_code ? " [#{nomenclature_code}]" : '')
end

#nomen_id ⇒ `String`

Returns the NOMEN id for this classification.

Returns:

(String) —
the NOMEN id for this classification



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

def nomen_id
  self.class::NOMEN_URI.split('/').last
end

#nomenclature_code ⇒ `Object`

# File 'app/models/taxon_name_classification.rb', line 65

def nomenclature_code
  return :iczn if type.match(/::Iczn/)
  return :icnp if type.match(/::Icnp/)
  return :icvcn if type.match(/::Icvcn/)
  return :icn if type.match(/::Icn/)
  return nil
end

#nomenclature_code_matches ⇒ `Object` (private)

# File 'app/models/taxon_name_classification.rb', line 575

def nomenclature_code_matches
  if taxon_name && type && nomenclature_code
    tn = taxon_name.is_combination? ? taxon_name.protonyms.last : taxon_name
    nc = tn.rank_class.nomenclatural_code
    if nomenclature_code != nc
      taxon_name_code = nc.nil? ? 'no' : "the #{nc}"
      errors.add(:taxon_name, "#{taxon_name.cached_html} belongs to #{taxon_name_code} nomenclatural code, but the status is from the #{nomenclature_code} nomenclatural code")
    end
  end
end

#set_cached ⇒ `Object`



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# File 'app/models/taxon_name_classification.rb', line 180

def set_cached
  set_cached_names_for_taxon_names
end

#set_cached_names_for_taxon_names ⇒ `Object`

TODO: move these to individual classes?! Starting to move to individual classes Gender is sone

# File 'app/models/taxon_name_classification.rb', line 187

def set_cached_names_for_taxon_names
  t = taxon_name
  return if t.destroyed?
  begin
    TaxonName.transaction_with_retry do
      if type_name =~ /(Fossil|Hybrid|Candidatus)/ # Break these out, they don't all apply to the same codes
        n = t.get_full_name
        t.update_columns(
          cached: n,
          cached_html: t.get_full_name_html(n),
          cached_original_combination: t.get_original_combination,
          cached_original_combination_html: t.get_original_combination_html
        )
      elsif type_name =~ /Latinized::PartOfSpeech/
        n = t.get_full_name
        t.update_columns(
            cached: n,
            cached_html: t.get_full_name_html(n),
            cached_original_combination: t.get_original_combination,
            cached_original_combination_html: t.get_original_combination_html
        )

        TaxonNameRelationship::OriginalCombination.where(subject_taxon_name: t).collect{|i| i.object_taxon_name}.uniq.each do |t1|
          t1.update_cached_original_combinations
        end

        TaxonNameRelationship::Combination.where(subject_taxon_name: t).collect{|i| i.object_taxon_name}.uniq.each do |t1|
          t1.update_column(:verbatim_name, t1.cached) if t1.verbatim_name.nil?
          n = t1.get_full_name
          t1.update_columns(
              cached: n,
              cached_html: t1.get_full_name_html(n)
          )
        end

      elsif type_name =~ /Latinized::Gender/
        # Handled in subclasses
        raise
      elsif TAXON_NAME_CLASS_NAMES_VALID.include?(type_name)
        vn = t.get_valid_taxon_name
        vn.update_columns(
          cached_valid_taxon_name_id: vn.id,
          cached_is_valid: !vn.unavailable_or_invalid?) # Do not change!
        vn.list_of_invalid_taxon_names.each do |s|
          s.update_columns(
            cached_valid_taxon_name_id: vn.id,
            cached_is_valid: false)
          s.combination_list_self.each do |c|
            c.update_columns(cached_valid_taxon_name_id: vn.id)
          end
        end
        t.combination_list_self.each do |c|
          c.update_columns(cached_valid_taxon_name_id: vn.id)
        end
      else
        t.update_columns(cached_is_valid: false)
      end

      if TAXON_NAME_CLASS_NAMES_UNAVAILABLE.include?( type_name )
        t.update_columns(
          cached_is_available: false
        )
      end
    end
  rescue ActiveRecord::RecordInvalid
    false
  end
  true
end

#sv_fix_proper_classification ⇒ `Object`

# File 'app/models/taxon_name_classification.rb', line 270

def sv_fix_proper_classification
  begin
    TaxonNameClassification.transaction do
      self.destroy
    end
    return true
  rescue
    return false
  end
end

#sv_not_specific_classes ⇒ `Object`



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# File 'app/models/taxon_name_classification.rb', line 295

def sv_not_specific_classes
  true # moved to subclasses
end

#sv_proper_classification ⇒ `Object`

# File 'app/models/taxon_name_classification.rb', line 261

def sv_proper_classification
  if TAXON_NAME_CLASSIFICATION_NAMES.include?(self.type)
    # self.type_class is a Class
    if not self.type_class.applicable_ranks.include?(self.taxon_name.rank_string)
      soft_validations.add(:type, "The status '#{self.classification_label}' is not applicable to the taxon #{self.taxon_name.cached_html} at the rank of #{self.taxon_name.rank_class.rank_name}", success_message: 'The status was deleted', failure_message:  'Fail to delete the status')
    end
  end
end

#sv_proper_year ⇒ `Object`

# File 'app/models/taxon_name_classification.rb', line 281

def sv_proper_year
  y = self.taxon_name.year_of_publication
  if !y.nil? && (y > self.type_class.code_applicability_end_year || y < self.type_class.code_applicability_start_year)
    soft_validations.add(:type, "The status '#{self.classification_label}' is not applicable to the taxon #{self.taxon_name.cached_html} published in the year #{y}")
  end
end

#sv_validate_disjoint_classes ⇒ `Object`

# File 'app/models/taxon_name_classification.rb', line 288

def sv_validate_disjoint_classes
  classifications = TaxonNameClassification.where_taxon_name(self.taxon_name).not_self(self)
  classifications.each  do |i|
    soft_validations.add(:type, "The status  '#{self.classification_label}' conflicting with another status: '#{i.classification_label}'") if self.type_class.disjoint_taxon_name_classes.include?(i.type_name)
  end
end

#type_class ⇒ `Object`

# File 'app/models/taxon_name_classification.rb', line 94

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

#type_class=(value) ⇒ `Object`



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# File 'app/models/taxon_name_classification.rb', line 90

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

#type_name ⇒ `String`

Returns the class name, "validated" against the known list of names.

Returns:

(String) —
the class name, "validated" against the known list of names

# File 'app/models/taxon_name_classification.rb', line 85

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

#validate_taxon_name_classification ⇒ `Object` (private)

TODO: unnecessary! Type handling will raise here



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# File 'app/models/taxon_name_classification.rb', line 587

def validate_taxon_name_classification
  errors.add(:type, 'Status not found') if !self.type.nil? and !TAXON_NAME_CLASSIFICATION_NAMES.include?(self.type.to_s)
end

#validate_uniqueness_of_latinized ⇒ `Object`



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# File 'app/models/taxon_name_classification.rb', line 257

def validate_uniqueness_of_latinized
  true # moved to subclasses
end

Class: TaxonNameClassification

Overview

Direct Known Subclasses

Defined Under Namespace

Constant Summary

Constants included from SoftValidation

Instance Attribute Summary collapse

Class Method Summary collapse

Instance Method Summary collapse

Methods included from SoftValidation

Methods included from Shared::IsData

Methods included from Shared::Notes

Methods included from Shared::Citations

Methods included from Housekeeping

Methods inherited from ApplicationRecord

Instance Attribute Details

#project_id ⇒ Integer

#taxon_name_id ⇒ Integer

#type ⇒ String

Class Method Details

.annotates? ⇒ Boolean

.applicable_ranks ⇒ Array of Strings of NomenclaturalRank names

.assignable ⇒ Object

.code_applicability_end_year ⇒ Integer

.code_applicability_start_year ⇒ Integer

.collect_descendants_and_itself_to_s(*classes) ⇒ Object

.collect_descendants_to_s(*classes) ⇒ Object

.collect_to_s(*args) ⇒ Object

.destroy_classifications_for_batch(classifications:, query:, batch_response:) ⇒ Object

.disjoint_taxon_name_classes ⇒ Array of Strings of TaxonNameClassification names

.dispatch_batch_by_filter_scope_job(hash_query:, mode:, params:, project_id:, user_id:) ⇒ Object

.gbif_status ⇒ String?

.label ⇒ Object

.nomen_uri ⇒ Object

.parent ⇒ Object

.possible_genus_endings ⇒ Array of Strings

.possible_species_endings ⇒ Array of Strings

.process_batch_by_filter_scope(batch_response: nil, query: nil, hash_query: nil, mode: nil, params: nil, async: nil, project_id: nil, user_id: nil, called_from_async: false) ⇒ BatchResponse

.questionable_species_endings ⇒ Array of Strings

Instance Method Details

#annotated_object ⇒ Object

#classification_label ⇒ String

#nomen_id ⇒ String

#nomenclature_code ⇒ Object

#nomenclature_code_matches ⇒ Object (private)

#set_cached ⇒ Object

#set_cached_names_for_taxon_names ⇒ Object

#sv_fix_proper_classification ⇒ Object

#sv_not_specific_classes ⇒ Object

#sv_proper_classification ⇒ Object

#sv_proper_year ⇒ Object

#sv_validate_disjoint_classes ⇒ Object

#type_class ⇒ Object

#type_class=(value) ⇒ Object

#type_name ⇒ String

#validate_taxon_name_classification ⇒ Object (private)

#validate_uniqueness_of_latinized ⇒ Object

#project_id ⇒ `Integer`

#taxon_name_id ⇒ `Integer`

#type ⇒ `String`

.annotates? ⇒ `Boolean`

.applicable_ranks ⇒ `Array of Strings of NomenclaturalRank names`

.assignable ⇒ `Object`

.code_applicability_end_year ⇒ `Integer`

.code_applicability_start_year ⇒ `Integer`

.collect_descendants_and_itself_to_s(*classes) ⇒ `Object`

.collect_descendants_to_s(*classes) ⇒ `Object`

.collect_to_s(*args) ⇒ `Object`

.destroy_classifications_for_batch(classifications:, query:, batch_response:) ⇒ `Object`

.disjoint_taxon_name_classes ⇒ `Array of Strings of TaxonNameClassification names`

.dispatch_batch_by_filter_scope_job(hash_query:, mode:, params:, project_id:, user_id:) ⇒ `Object`

.gbif_status ⇒ `String`^?

.label ⇒ `Object`

.nomen_uri ⇒ `Object`

.parent ⇒ `Object`

.possible_genus_endings ⇒ `Array of Strings`

.possible_species_endings ⇒ `Array of Strings`

.process_batch_by_filter_scope(batch_response: nil, query: nil, hash_query: nil, mode: nil, params: nil, async: nil, project_id: nil, user_id: nil, called_from_async: false) ⇒ `BatchResponse`

.questionable_species_endings ⇒ `Array of Strings`

#annotated_object ⇒ `Object`

#classification_label ⇒ `String`

#nomen_id ⇒ `String`

#nomenclature_code ⇒ `Object`

#nomenclature_code_matches ⇒ `Object` (private)

#set_cached ⇒ `Object`

#set_cached_names_for_taxon_names ⇒ `Object`

#sv_fix_proper_classification ⇒ `Object`

#sv_not_specific_classes ⇒ `Object`

#sv_proper_classification ⇒ `Object`

#sv_proper_year ⇒ `Object`

#sv_validate_disjoint_classes ⇒ `Object`

#type_class ⇒ `Object`

#type_class=(value) ⇒ `Object`

#type_name ⇒ `String`

#validate_taxon_name_classification ⇒ `Object` (private)

#validate_uniqueness_of_latinized ⇒ `Object`