Class: Combination

Inherits:
TaxonName show all
Defined in:
app/models/combination.rb

Overview

A nomenclator name, composed of existing Protonyms. Each record reflects the subsequent use of two or more protonyms. Only the first use of a combination is stored here, subsequence uses of this combination are referenced in Citations.

A Combination has no name, it exists to group related Protonyms into an epithet.

They are applicable to genus group names and finer epithets.

All elements of the combination must be defined, nothing is assumed based on the relationship to the parent.

c = Combination.new
c.genus = a_protonym_genus
c.species = a_protonym_species
c.save # => true
c.genus_taxon_name_relationship  # => A instance of TaxonNameRelationship::Combination::Genus

# or

c = Combination.new(genus: genus_protonym, species: species_protonym)

Getters and setters for each of the APPLICABLE_RANKS are available:

`genus subgenus section subsection series subseries species subspecies variety subvariety form subform`
`genus_id subgenus_id section_id subsection_id series_id subseries_id species_id subspecies_id variety_id subvariety_id form_id subform_id`

You can do things like (notice mix/match of _id or not):

c = Combination.new(genus_id: @genus_protonym.id, subspecies: @some_species_group)
c.species_id = Protonym.find(some_species_id).id

or

c.species = Protonym.find(some_species_id)

Combinations are composed of TaxonNameRelationships. In those relationship the Combination#id is always the ‘object_taxon_name_id`, the individual Protonyms are stored in `subject_taxon_name_id`.

Constant Summary collapse

APPLICABLE_RANKS =

The ranks that can be used to build a Combination pointing to the corresponding TaxonNameRelationship type

%w{genus subgenus section subsection series subseries species subspecies variety subvariety form subform}.inject({}){|hsh,r|
  hsh[r] = "TaxonNameRelationship::Combination::#{r.capitalize}"; hsh;
}.freeze

Constants inherited from TaxonName

TaxonName::ALTERNATE_VALUES_FOR, TaxonName::COMBINATION_ELEMENTS, TaxonName::NOMEN_VALID, TaxonName::NOT_LATIN, TaxonName::NO_CACHED_MESSAGE, TaxonName::ROOT_NAME, TaxonName::SPECIES_EPITHET_RANKS

Constants included from SoftValidation

SoftValidation::ANCESTORS_WITH_SOFT_VALIDATIONS

Instance Attribute Summary collapse

Attributes inherited from TaxonName

#also_create_otu, #cached, #cached_author, #cached_author_year, #cached_classified_as, #cached_html, #cached_misspelling, #cached_original_combination, #cached_original_combination_html, #cached_primary_homonym, #cached_primary_homonym_alternative_spelling, #cached_secondary_homonym, #cached_secondary_homonym_alternative_spelling, #classifications, #etymology, #feminine_name, #masculine_name, #name, #neuter_name, #no_cached, #project_id, #rank_class, #related_relationships, #type, #verbatim_author, #verbatim_name, #year_of_publication

Class Method Summary collapse

Instance Method Summary collapse

Methods inherited from TaxonName

#all_taxon_name_relationships, #ancestor_at_rank, #ancestor_hash, #ancestor_protonyms, #ancestors_through_parents, #author_string, #cached_html_name_and_author_year, #cached_html_original_name_and_author_year, #cached_name_and_author_year, calculated_invalid, calculated_valid, #check_for_children, #check_new_parent_class, #check_new_rank_class, #classification_invalid_or_unavailable?, #classification_unavailable?, #classification_valid?, #clear_cached, #combination_list_all, #combination_list_self, #combined_statuses, #create_otu, #descendant_protonyms, #dwc_occurrences, #first_possible_invalid_taxan_name_relationship, #first_possible_valid_taxon_name, #first_possible_valid_taxon_name_relationship, #full_name, #full_name_array, #gbif_status_array, #gender_class, #gender_instance, #gender_name, #genderized_name, #get_author, #get_author_and_year, #get_cached_classified_as, #get_cached_misspelling, #get_full_name_html, #get_genus_species, #get_original_combination, #get_original_combination_html, #icn_author_and_year, #iczn_author_and_year, #is_ambiguously_invalid?, #is_candidatus?, #is_combination?, #is_fossil?, #is_genus_or_species_rank?, #is_hybrid?, #is_italicized?, #is_protonym?, #is_valid?, #list_of_invalid_taxon_names, #matrix_row_item, #merge_to, #minimum_invalidating_year, #minimum_years_valid, #name_in_gender, #name_is_misapplied?, #name_with_misspelling, #next_sibling, #nomeclatural_history, #nomenclature_date, #normalized_genus, #not_binominal?, not_leaves, #original_author_year, out_of_scope_combinations, #out_of_scope_combinations, #part_of_speech_class, #part_of_speech_instance, #part_of_speech_name, #previous_sibling, #rank, #rank_string, #reified_id, #related_taxon_names, #relationship_invalid?, #relationships, #reload, #safe_self_and_ancestors, select_optimized, #set_cached, #set_cached_author, #set_cached_author_columns, #set_cached_author_year, #set_cached_classified_as, #set_cached_is_valid, #set_cached_nomenclature_date, #set_cached_valid_taxon_name_id, #set_cached_warnings, sort_by_rank, #statuses_from_classifications, #statuses_from_relationships, #sv_conflicting_subordinate_taxa, #sv_fix_cached_names, #sv_fix_parent_is_valid_name, #sv_homotypic_synonyms, #sv_hybrid_name_relationships, #sv_incomplete_combination, #sv_missing_classifications, #sv_missing_confidence_level, #sv_missing_etymology, #sv_missing_original_publication, #sv_missing_relationships, #sv_not_synonym_of_self, #sv_parent_is_valid_name, #sv_parent_priority, #sv_potential_homonyms, #sv_primary_types, #sv_single_sub_taxon, #sv_species_gender_agreement, #sv_two_unresolved_alternative_synonyms, #sv_type_placement, #sv_validate_coordinated_names, #sv_validate_name, #sv_validate_parent_rank, #synonyms, #taxon_name_classification_minimum_invalidating_year, #taxon_name_classifications_for_statuses, #taxon_name_relationship_minimum_invalidating_year, #unavailable_or_invalid?, used_recently, used_recently_in_classifications, used_recently_in_relationships, #validate_parent_from_the_same_project, #validate_rank_class_class, #validate_root_name_is_root, #validate_source_type, with_taxon_name_relationship, #year_integer

Methods included from Shared::IsData

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

Methods included from TaxonName::MatrixHooks

#coordinate_observation_matrix_row_items, #in_scope_observation_matrix_row_items, #out_of_scope_observation_matrix_row_items

Methods included from Shared::MatrixHooks::Dynamic

#dynamic_add_to_matrix_column_items, #dynamic_add_to_matrix_row_items, #dynamic_cleanup_in_scope_column_items, #dynamic_cleanup_in_scope_row_items, #dynamic_cleanup_out_of_scope_column_items, #dynamic_cleanup_out_of_scope_row_items, #dynamic_column_items_in, #dynamic_column_items_out, #dynamic_inspect_matrices, #dynamic_remove_from_matrix_column_items, #dynamic_remove_from_matrix_row_items, #dynamic_row_items_in, #dynamic_row_items_out, #dynamic_synchronize_matrices, #dynamic_update_matrix_column_items?, #dynamic_update_matrix_row_items?, #in_scope_observation_matrix_column_items, #in_scope_observation_matrix_row_items, #out_of_scope_observation_matrix_column_items, #out_of_scope_observation_matrix_row_items, #prepare_matrix_items

Methods included from Shared::MatrixHooks::Member

#member_add_matrix_columns, #member_add_matrix_rows, #member_add_to_matrix_items, #member_of_new_matrix_column_items, #member_of_new_matrix_row_items, #member_of_old_matrix_column_items, #member_of_old_matrix_row_items, #member_remove_from_matrix_items, #member_remove_matrix_columns, #member_remove_matrix_rows, #member_synchronize_matrices, #member_update_matrix_items?

Methods included from Shared::QueryBatchUpdate

#query_update

Methods included from SoftValidation

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

Methods included from Shared::Labels

#labeled?

Methods included from Shared::HasPapertrail

#attribute_updated, #attribute_updater, #detect_version

Methods included from Shared::AlternateValues

#all_values_for, #alternate_valued?

Methods included from Shared::Confidences

#reject_confidences

Methods included from Shared::Citations

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

Methods included from Shared::Depictions

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

Methods included from Shared::Notes

#concatenated_notes_string, #reject_notes

Methods included from Shared::Identifiers

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

Methods included from Shared::Tags

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

Methods included from Shared::DataAttributes

#import_attributes, #internal_attributes, #keyword_value_hash, #reject_data_attributes

Methods included from Housekeeping

#has_polymorphic_relationship?

Methods inherited from ApplicationRecord

transaction_with_retry

Instance Attribute Details

#combination_verbatim_name ⇒ String

Use with caution, and sparingly! If the combination of values from Protonyms can not reflect the formulation of the combination as provided by the original author that string can be provided here. The verbatim value is not further parsed. It is only provided to clarify what the combination looked like when first published. The following recommendations are made:

1) The provided string should visually reflect as close as possible what was seen in the publication itself, including
capitalization, accented characters etc.
2) The full epithet (combination) should be provided, not just the differing component part (see 3 below).
3) Misspellings can be more acurately reflected by creating new Protonyms.

Example uses:

1) Jones 1915 publishes Aus aus. Smith 1920 uses, literally "Aus (Bus) Janes 1915".
   It is clear "Janes" is "Jones", therefor "Aus (Bus) Janes 1915" is provided as combination_verbatim_name.
2) Smith 1800 publishes Aus Jonesi (i.e. Aus jonesi). The combination_combination_verbatim name is used to
   provide the fact that Jonesi was capitalized.
3) "Aus brocen" is used for "Aus broken".  If the curators decide not to create a new protonym, perhaps because
   they feel "brocen" was a printing press error that left off the straight bit of the "k" then they should minimally
   include "Aus brocen" in this field, rather than just "brocen". An alternative is to create a new Protonym "brocen".
4) 'Aus (Aus)' was originally described in 1920.  "(Aus)" was used in a new combination alone as "Aus".  This is the only case
   in which combination may contain a single protonym.

Returns:

  • (String) 


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# File 'app/models/combination.rb', line 58

class Combination < TaxonName
  # The ranks that can be used to build a Combination pointing to the corresponding TaxonNameRelationship type
  APPLICABLE_RANKS = %w{genus subgenus section subsection series subseries species subspecies variety subvariety form subform}.inject({}){|hsh,r|
    hsh[r] = "TaxonNameRelationship::Combination::#{r.capitalize}"; hsh;
  }.freeze

  before_validation :set_parent

  # Before we set cached ensure we draw current data
  after_save :reset_protonyms_by_rank

  validate :validate_absence_of_subject_relationships

  # TODO: make access private
  attr_accessor :disable_combination_relationship_check

  # Memoize.
  attr_accessor :protonyms_by_rank

  # Overwritten here from TaxonName to allow for destroy
  has_many :related_taxon_name_relationships, class_name: 'TaxonNameRelationship',
    foreign_key: :object_taxon_name_id,
    inverse_of: :object_taxon_name,
    dependent: :destroy

  has_many :combination_relationships, -> {
    joins(:taxon_name_relationships)
    where("taxon_name_relationships.type LIKE 'TaxonNameRelationship::Combination::%'")
  }, class_name: 'TaxonNameRelationship',
  foreign_key: :object_taxon_name_id

  has_many :combination_taxon_names, through: :combination_relationships, source: :subject_taxon_name

  # Create syntactic helper methods
  TaxonNameRelationship.descendants.each do |d|
    if d.respond_to?(:assignment_method)
      if d.name.to_s =~ /TaxonNameRelationship::SourceClassifiedAs/
        relationship = "#{d.assignment_method}_relationship".to_sym
        has_one relationship, class_name: d.name.to_s, foreign_key: :subject_taxon_name_id
        has_one d.assignment_method.to_sym, through: relationship, source: :object_taxon_name
      end

      if d.name.to_s =~ /TaxonNameRelationship::Combination/ # |SourceClassifiedAs
        relationships = "#{d.assignment_method}_relationships".to_sym
        has_many relationships, -> {
          where('taxon_name_relationships.type LIKE ?', d.name + '%')
        }, class_name: 'TaxonNameRelationship', foreign_key: :subject_taxon_name_id
        has_many d.assignment_method.to_s.pluralize.to_sym, through: relationships, source: :object_taxon_name
      end
    end

    if d.respond_to?(:inverse_assignment_method)
      if d.name.to_s =~ /TaxonNameRelationship::SourceClassifiedAs/
        relationships = "#{d.inverse_assignment_method}_relationships".to_sym
        has_many relationships, -> {
          where('taxon_name_relationships.type LIKE ?', d.name + '%')
        }, class_name: 'TaxonNameRelationship', foreign_key: :object_taxon_name_id
        has_many d.inverse_assignment_method.to_s.pluralize.to_sym, through: relationships, source: :subject_taxon_name
      end

      if d.name.to_s =~ /TaxonNameRelationship::Combination/ # |SourceClassifiedAs
        relationship = "#{d.inverse_assignment_method}_relationship".to_sym
        has_one relationship, class_name: d.name.to_s, foreign_key: :object_taxon_name_id
        has_one d.inverse_assignment_method.to_sym, through: relationship, source: :subject_taxon_name
      end
    end
  end

  APPLICABLE_RANKS.keys.each do |rank|
    has_one "#{rank}_taxon_name_relationship".to_sym, -> {
      joins(:combination_relationships)
      where(taxon_name_relationships: {type: "TaxonNameRelationship::Combination::#{rank.capitalize}"}) },
    class_name: 'TaxonNameRelationship', foreign_key: :object_taxon_name_id, inverse_of: :object_taxon_name

    has_one rank.to_sym, -> {
      joins(:combination_relationships)
      where(taxon_name_relationships: {type: "TaxonNameRelationship::Combination::#{rank.capitalize}"})
    }, through: "#{rank}_taxon_name_relationship".to_sym, source: :subject_taxon_name

    accepts_nested_attributes_for rank.to_sym

    accepts_nested_attributes_for "#{rank}_taxon_name_relationship".to_sym, allow_destroy: true

    attr_accessor "#{rank}_id".to_sym
    method = "#{rank}_id"

    define_method(method) {
      if self.send(rank)
        self.send(rank).id
      else
        nil
      end
    }

    define_method("#{method}=") {|value|
      if value.present?
        if n = Protonym.find(value)
          self.send("#{rank}=", n)
        end
      end
    }
  end

  scope :with_protonym_at_rank, -> (rank, protonym) {
    includes(:combination_relationships).
    where('taxon_name_relationships.type = ? and taxon_name_relationships.subject_taxon_name_id = ?', rank, protonym).
    references(:combination_relationships)}

  validate :is_unique
  validate :does_not_exist_as_original_combination, unless: Proc.new {|a| a.errors.full_messages.include? 'Combination exists.' }
  validate :parent_is_properly_set , unless: Proc.new {|a| a.errors.full_messages.include? 'Combination exists.' }
  validate :composition, unless: Proc.new {|a| disable_combination_relationship_check == true || a.errors.full_messages.include?('Combination exists.') }
  validates :rank_class, absence: true

  soft_validate(
    :sv_redundant_verbatim_name,
    set: :cached,
    fix: :sv_fix_redundant_verbatim_name,
    name: 'Redundant verbatim name',
    description: 'Verbatim name is present but identical to computed name')


  soft_validate(
    :sv_combination_duplicates,
    set: :combination_duplicates,
    name: 'Duplicate combination',
    description: 'Combination is a duplicate' )

  soft_validate(
    :sv_year_of_publication_matches_source,
    set: :dates,
    name: 'Year of publication does not match the source',
    description: 'The published date of the combination is not the same as provided by the original publication' )

  soft_validate(
    :sv_year_of_publication_not_older_than_protonyms,
    set: :dates,
    name: 'Varbatim year in combination older than in protonyms',
    description: 'The varbatim year in combination is older than in protonyms in the combination' )

  soft_validate(
    :sv_source_not_older_than_protonyms,
    set: :dates,
    name: 'Combination older than protonyms',
    description: 'The combination is older than protonyms in the combination' )

  soft_validate(
    :sv_combination_linked_to_valid_name,
    set: :combination_linked_to_valid_name,
    fix: :sv_fix_combination_parent_update,
    name: 'Combination has valid parent',
    description: 'The combination should have the same parent as protonym' )

  soft_validate(
    :sv_author_and_year_is_not_required,
    set: :year_is_not_required,
    fix: :sv_fix_author_and_year_is_not_required,
    name: 'Verbatim author and year are not required',
    description: 'Verbatim author and year are not required. The Fix will delete both' )

  # @return [Protonym Scope]
  # @params protonym_ids [Hash] like `{genus: 4, species: 5}`
  #   the absence of _id in the keys in part reflects integration with Biodiversity gem
  #   AHA from http://stackoverflow.com/questions/28568205/rails-4-arel-join-on-subquery
  #   See also Descriptor::Gene
  def self.protonyms_matching_original_relationships(protonym_ids = {})
    protonym_ids.compact!
    return Protonym.none if !protonym_ids.keys.any?

    s  = Protonym.arel_table
    sr = TaxonNameRelationship.arel_table

    j = s.alias('j') # required for group/having purposes

    b = s.project(j[Arel.star]).from(j)
      .join(sr)
      .on(sr['object_taxon_name_id'].eq(j['id']))

    # Build an aliased join for each set of attributes
    protonym_ids.each do |rank, id|
      sr_a = sr.alias("b_#{rank}")
      b = b.join(sr_a).on(
        sr_a['object_taxon_name_id'].eq(j['id']),
        sr_a['type'].eq("TaxonNameRelationship::OriginalCombination::Original#{rank.capitalize}"),
        sr_a['subject_taxon_name_id'].eq(id)
      )
    end

    b = b.group(j['id']).having(sr['object_taxon_name_id'].count.eq(protonym_ids.count)).where(sr['type'].in(::COMBINATION_TAXON_NAME_RELATIONSHIP_NAMES))
    b = b.as('join_alias')

    Protonym.joins(Arel::Nodes::InnerJoin.new(b, Arel::Nodes::On.new(b['id'].eq(s['id']))))
  end

  # @return [Protonym Scope] hmmm- a Protonym class method?!
  #    Protonyms matching original relations, if name provided then name added as an additional check on verbatim match
  # @params name [String, nil] the non-htmlized version of the name, without author year
  def self.matching_protonyms(name = nil, **protonym_ids)
    q = nil
    if name.blank?
      q = protonyms_matching_original_relationships(protonym_ids)
    else
      q = protonyms_matching_original_relationships(protonym_ids).where('taxon_names.cached_original_combination = ?', name)
    end
    q
  end

  # @return [Scope]
  # @params keyword_args [Hash] like `{genus: 123, :species: 456}` (note no `_id` suffix)
  def self.find_by_protonym_ids(**keyword_args)
    keyword_args.compact!
    return Combination.none if keyword_args.empty?

    c = Combination.arel_table
    r = TaxonNameRelationship.arel_table

    a = c.alias('a_foo')

    b = c.project(a[Arel.star]).from(a)
      .join(r)
      .on(r['object_taxon_name_id'].eq(a['id']))

    s = []

    i = 0
    keyword_args.each do |rank, id|
      r_a = r.alias("foo_#{i}")
      b = b.join(r_a).on(
        r_a['object_taxon_name_id'].eq(a['id']),
        r_a['type'].eq(TAXON_NAME_RELATIONSHIP_COMBINATION_TYPES[rank]),
        r_a['subject_taxon_name_id'].eq(id)
      )
      i += 1
    end

    b = b.group(a['id']).having(r['object_taxon_name_id'].count.eq(keyword_args.keys.count))
    b = b.as('z_bar')

    Combination.joins(Arel::Nodes::InnerJoin.new(b, Arel::Nodes::On.new(b['id'].eq(c['id']))))
  end

  # @return [Combination, false]
  # @params keyword_args [Hash] like `{genus: 123, :species: 456}` (note no `_id` suffix)
  #    the matching Combination if it exists, otherwise false
  #    if name is provided then cached must match (i.e. verbatim_name if provided must also match)
  def self.match_exists?(name = nil, **keyword_args)
    if name.blank?
      a = find_by_protonym_ids(**keyword_args).first
    else
      a = find_by_protonym_ids(**keyword_args).where(cached: name).first
    end
    a ? a : false
  end

  # @return [Boolean]
  #   true if the finest level (typically species) currently has the same parent
  def is_current_placement?
    return false if protonyms.second_to_last.nil?
    protonyms.last.parent_id == protonyms.second_to_last.id
  end

  def get_full_name
    return verbatim_name if verbatim_name.present?
    full_name
  end

  # Is this used before persistence of the complete Combination?!
  # Overrides {TaxonName#full_name_hash}
  # @return [Hash]
  #
  #  Benchmark.measure { 1000.times do; Combination.find_by_id(ids.sample).full_name_hash; end}
  def full_name_hash
    gender = nil
    data = {}

    protonyms_by_rank.each do |rank, i|
      gender = i.gender_name if rank == 'genus'

      if ['genus', 'subgenus', 'species', 'subspecies'].include?(rank)
        data[rank] = [nil, i.name_with_misspelling(gender)]
      else
        data[rank] = [i.rank_class.abbreviation, i.name_with_misspelling(gender)]
      end
    end

    if data['genus'].nil?
      data['genus'] = [nil, '[GENUS NOT SPECIFIED]']
    end

    if data['species'].nil? && (!data['subspecies'].nil? || !data['variety'].nil? || !data['subvariety'].nil? || !data['form'].nil? || !data['subform'].nil?)
      data['species'] = [nil, '[SPECIES NOT SPECIFIED]']
    end

    if data['variety'].nil? && !data['subvariety'].nil?
      data['variety'] = [nil, '[VARIETY NOT SPECIFIED]']
    end

    if data['form'].nil? && !data['subform'].nil?
      data['form'] = [nil, '[FORM NOT SPECIFIED]']
    end

    data
  end

  # TODO: add higher classifcation here
  def combination_taxonomy
    d = full_name_hash
    protonyms_by_rank.to_a.first[1].ancestors.each do |a|
      d[a.rank] = a.name
    end

    d
  end

  def taxonomy(rebuild = false)
    if rebuild
      @taxonomy = combination_taxonomy
    else
      @taxonomy ||= combination_taxonomy
    end
  end

  # @return [Hash of {rank: Protonym}, nil]
  #  the component names for this combination, sorted in order
  #   _prior to it being saved_
  def protonyms_by_rank
    result = {}
    if persisted?
      ar = APPLICABLE_RANKS.values
      # nX fewer calls to database than send()
      @protonyms_by_rank ||= TaxonNameRelationship::Combination
        .where(object_taxon_name: self)
        .eager_load(:subject_taxon_name)
        .sort{|a,b| ar.index(a.type) <=> ar.index(b.type)}
        .inject({}) {|hsh,n| hsh[n.rank_name] = n.subject_taxon_name; hsh}
        .to_h
    else
      APPLICABLE_RANKS.keys.each do |rank|
        if protonym = send(rank.to_sym)
          result[rank] = protonym
        end
      end
      @protonyms_by_rank = result
    end

    @protonyms_by_rank
  end

  # @return [Array of TaxonNames, nil]
  #   return the component names for this combination prior to it being saved
  def protonyms_by_association
    APPLICABLE_RANKS.keys.collect{|r| self.send(r)}.compact
  end

  # @return [Array of TaxonName]
  #   pre-ordered by rank
  def protonyms
    return protonyms_by_association if new_record?
    combination_taxon_names.sort{|a,b| RANKS.index(a.rank_string) <=> RANKS.index(b.rank_string) }
  end

  # @return [Hash]
  #   like `{ genus: 1, species: 2 }`
  def protonym_ids_params
    protonyms_by_rank.inject({}) {|hsh, p| hsh.merge!( p[0].to_sym => p[1].id )}
  end

  # @return [Array of Integers]
  #   the collective years the protonyms were (nomenclaturaly) published on (ordered from genus to below)
  def publication_years
    description_years = protonyms.collect{|a| a.cached_nomenclature_date ? a.cached_nomenclature_date&.year : nil}.compact
  end

  # @return [Integer, nil]
  #   the earliest year (nomenclature) that a component Protonym was published on
  def earliest_protonym_year
    publication_years.sort.first
  end

  # return [Array of TaxonNameRelationship]
  #   classes that are applicable to this name, as deterimned by Rank
  def combination_class_relationships(rank_string)
    relations = []
    TaxonNameRelationship::Combination.descendants.each do |r|
      relations.push(r) if r.valid_object_ranks.include?(rank_string)
    end
    relations
  end

  # TODO: DEPRECATE this is likely not required in our new interfaces
  def combination_relationships_and_stubs(rank_string)
    display_order = [
      :combination_genus, :combination_subgenus, :combination_species, :combination_subspecies, :combination_variety, :combination_form
    ]

    defined_relations = combination_relationships.all
    created_already = defined_relations.collect{|a| a.class}
    new_relations = []

    combination_class_relationships(rank_string).each do |r|
      new_relations.push( r.new(object_taxon_name: self) ) if !created_already.include?(r)
    end

    (new_relations + defined_relations).sort{|a,b|
      display_order.index(a.class.inverse_assignment_method) <=> display_order.index(b.class.inverse_assignment_method)
    }
  end

  def get_valid_taxon_name
    c = protonyms_by_rank
    return self if c.empty?
    c[c.keys.last].valid_taxon_name
  end

  def finest_protonym
    protonyms_by_rank.values.last
  end

  protected

  def reset_protonyms_by_rank
    @protonyms_by_rank = nil
  end

  def validate_absence_of_subject_relationships
    if TaxonNameRelationship.where(subject_taxon_name_id: self.id).where("type NOT LIKE 'TaxonNameRelationship::CurrentCombination'").any?
      errors.add(:base, 'This combination could not be used as a Subject in any TaxonNameRelationships.')
    end
  end

  def sv_redundant_verbatim_name
    if verbatim_name == full_name
      protonyms_by_rank.values.each do |t|
        return true unless t.has_latinized_classification?
      end
      soft_validations.add(:verbatim_name, 'Verbatim name is provided but not needed, it is the same as the computed value.')
    end
  end

  def sv_year_of_publication_matches_source
    source_year = source.nomenclature_year if source
    if year_of_publication && source_year
      soft_validations.add(:year_of_publication, 'The published date of the combination is not the same as provided by the original publication') if source_year != year_of_publication
    end
  end

  def sv_source_not_older_than_protonyms
    source_year = source.try(:nomenclature_year)
    target_year = earliest_protonym_year
    if source_year && target_year
      soft_validations.add(:base, "The publication date of combination (#{source_year}) is older than the original publication date of one of the name in the combination (#{target_year}") if source_year < target_year
    end
  end

  def sv_year_of_publication_not_older_than_protonyms
    if year_of_publication && earliest_protonym_year
      soft_validations.add(:year_of_publication,  "The publication date of combination (#{year_of_publication}) is older than the original publication date of one of the name in the combination (#{earliest_protonym_year}") if year_of_publication < earliest_protonym_year
    end
  end

  def sv_combination_duplicates
    duplicate = Combination.not_self(self).where(cached:, cached_author_year:, project_id: self.project_id)
    soft_validations.add(:base, 'Combination is a duplicate') unless duplicate.empty?
    if a = Combination.matching_protonyms(get_full_name, **protonym_ids_params)
      soft_validations.add(:base, "Combination exists as protonym(s) with matching original combination: #{a.all.pluck(:cached).join(', ')}.") if a.any?
    end
  end

  def sv_combination_linked_to_valid_name
    check = protonyms.first
    if parent_id && check && check.parent_id && parent_id != check.parent_id
      soft_validations.add(:base, "Combination #{cached_html_name_and_author_year} should have the same parent and rank with  #{check.cached_html_name_and_author_year}",
                           success_message: 'The parent was updated', failure_message:  'The parent was not updated')
    end
  end

  def sv_fix_combination_parent_update
    check = protonyms.first
    if parent_id && check && check.parent_id && parent_id != check.parent_id
      begin
        TaxonName.transaction do
          # update_column(:parent_id, check.parent_id) ## do not use this, it breaks the taxon_name_hierarchies
          parent_id = check.parent_id
          self.save
          return true
        end
      rescue
      end
    end
    false
  end

  def sv_cached_names
    is_cached = true
    is_cached = false if cached_author_year != get_author_and_year
    is_cached = false if cached_author != get_author

    if  is_cached && (
        cached_is_valid.nil? ||
        cached != get_full_name ||
        cached_html != get_full_name_html ||
        cached_nomenclature_date != nomenclature_date)
      is_cached = false
    end
    soft_validations.add(
      :base, 'Cached values should be updated',
      success_message: 'Cached values were updated',
      failure_message:  'Failed to update cached values') if !is_cached
  end

  def sv_author_and_year_is_not_required
    if !self.year_of_publication.nil? || !self.verbatim_author.nil?
      soft_validations.add(
        :base, 'Verbatim author and year of publication are not required, they both derive from the source',
        success_message: 'Verbatim author and year were deleted',
        failure_message: 'Failed to delete verbatim author and year')
    end
  end

  def sv_fix_author_and_year_is_not_required
    self.update_columns(year_of_publication: nil, verbatim_author: nil)
    return true
  end

  def sv_fix_redundant_verbatim_name
    self.update_columns(verbatim_name: nil)
    return true
  end

  def set_parent
    names = protonyms
    write_attribute(:parent_id, names.first.parent.id) if names.count > 0 && names.first.parent
  end

  # The parent of a Combination is the parent of the highest ranked protonym in that Combination
  def parent_is_properly_set
    check = protonyms.first
    if parent && check && check.parent
      errors.add(:base, 'Parent is not highest ranked name.') if parent != check.parent
    end
  end

  def composition
    c = protonyms.count

    if c == 0
      errors.add(:base, 'Combination includes no names.')
      return
    end

    protonyms.each do |p|
      if !p.is_genus_or_species_rank?
        errors.add(:base, 'Combination includes one or more non-species or genus group names.')
        return
      end
    end

    # There are more than one protonyms, which seem to be valid elements
    p = protonyms.last
    errors.add(:base, 'Combination includes only one name and that is name is not a genus name.') if c < 2 && p.is_species_rank?
    errors.add(:base, 'Combination includes more than two genus group names.') if c > 2 && p.is_genus_rank?
  end

  def is_unique
    if a = Combination.match_exists?(verbatim_name, **protonym_ids_params)
      errors.add(:base, 'Combination exists.') if a.id != id
    end
  end

  def does_not_exist_as_original_combination
    if a = Combination.matching_protonyms(get_full_name, **protonym_ids_params)
      errors.add(:base, "Combination exists as protonym(s) with matching original combination: #{a.all.pluck(:cached).join(', ')}.") if a.any?
    end
  end

end

#disable_combination_relationship_check ⇒ Object

TODO: make access private



72
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# File 'app/models/combination.rb', line 72

def disable_combination_relationship_check
  @disable_combination_relationship_check
end

#parent_id ⇒ Integer

the parent is the parent of the highest ranked component Protonym, it is automatically set i.e. it should never be assigned directly

Returns:

  • (Integer) 


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# File 'app/models/combination.rb', line 58

class Combination < TaxonName
  # The ranks that can be used to build a Combination pointing to the corresponding TaxonNameRelationship type
  APPLICABLE_RANKS = %w{genus subgenus section subsection series subseries species subspecies variety subvariety form subform}.inject({}){|hsh,r|
    hsh[r] = "TaxonNameRelationship::Combination::#{r.capitalize}"; hsh;
  }.freeze

  before_validation :set_parent

  # Before we set cached ensure we draw current data
  after_save :reset_protonyms_by_rank

  validate :validate_absence_of_subject_relationships

  # TODO: make access private
  attr_accessor :disable_combination_relationship_check

  # Memoize.
  attr_accessor :protonyms_by_rank

  # Overwritten here from TaxonName to allow for destroy
  has_many :related_taxon_name_relationships, class_name: 'TaxonNameRelationship',
    foreign_key: :object_taxon_name_id,
    inverse_of: :object_taxon_name,
    dependent: :destroy

  has_many :combination_relationships, -> {
    joins(:taxon_name_relationships)
    where("taxon_name_relationships.type LIKE 'TaxonNameRelationship::Combination::%'")
  }, class_name: 'TaxonNameRelationship',
  foreign_key: :object_taxon_name_id

  has_many :combination_taxon_names, through: :combination_relationships, source: :subject_taxon_name

  # Create syntactic helper methods
  TaxonNameRelationship.descendants.each do |d|
    if d.respond_to?(:assignment_method)
      if d.name.to_s =~ /TaxonNameRelationship::SourceClassifiedAs/
        relationship = "#{d.assignment_method}_relationship".to_sym
        has_one relationship, class_name: d.name.to_s, foreign_key: :subject_taxon_name_id
        has_one d.assignment_method.to_sym, through: relationship, source: :object_taxon_name
      end

      if d.name.to_s =~ /TaxonNameRelationship::Combination/ # |SourceClassifiedAs
        relationships = "#{d.assignment_method}_relationships".to_sym
        has_many relationships, -> {
          where('taxon_name_relationships.type LIKE ?', d.name + '%')
        }, class_name: 'TaxonNameRelationship', foreign_key: :subject_taxon_name_id
        has_many d.assignment_method.to_s.pluralize.to_sym, through: relationships, source: :object_taxon_name
      end
    end

    if d.respond_to?(:inverse_assignment_method)
      if d.name.to_s =~ /TaxonNameRelationship::SourceClassifiedAs/
        relationships = "#{d.inverse_assignment_method}_relationships".to_sym
        has_many relationships, -> {
          where('taxon_name_relationships.type LIKE ?', d.name + '%')
        }, class_name: 'TaxonNameRelationship', foreign_key: :object_taxon_name_id
        has_many d.inverse_assignment_method.to_s.pluralize.to_sym, through: relationships, source: :subject_taxon_name
      end

      if d.name.to_s =~ /TaxonNameRelationship::Combination/ # |SourceClassifiedAs
        relationship = "#{d.inverse_assignment_method}_relationship".to_sym
        has_one relationship, class_name: d.name.to_s, foreign_key: :object_taxon_name_id
        has_one d.inverse_assignment_method.to_sym, through: relationship, source: :subject_taxon_name
      end
    end
  end

  APPLICABLE_RANKS.keys.each do |rank|
    has_one "#{rank}_taxon_name_relationship".to_sym, -> {
      joins(:combination_relationships)
      where(taxon_name_relationships: {type: "TaxonNameRelationship::Combination::#{rank.capitalize}"}) },
    class_name: 'TaxonNameRelationship', foreign_key: :object_taxon_name_id, inverse_of: :object_taxon_name

    has_one rank.to_sym, -> {
      joins(:combination_relationships)
      where(taxon_name_relationships: {type: "TaxonNameRelationship::Combination::#{rank.capitalize}"})
    }, through: "#{rank}_taxon_name_relationship".to_sym, source: :subject_taxon_name

    accepts_nested_attributes_for rank.to_sym

    accepts_nested_attributes_for "#{rank}_taxon_name_relationship".to_sym, allow_destroy: true

    attr_accessor "#{rank}_id".to_sym
    method = "#{rank}_id"

    define_method(method) {
      if self.send(rank)
        self.send(rank).id
      else
        nil
      end
    }

    define_method("#{method}=") {|value|
      if value.present?
        if n = Protonym.find(value)
          self.send("#{rank}=", n)
        end
      end
    }
  end

  scope :with_protonym_at_rank, -> (rank, protonym) {
    includes(:combination_relationships).
    where('taxon_name_relationships.type = ? and taxon_name_relationships.subject_taxon_name_id = ?', rank, protonym).
    references(:combination_relationships)}

  validate :is_unique
  validate :does_not_exist_as_original_combination, unless: Proc.new {|a| a.errors.full_messages.include? 'Combination exists.' }
  validate :parent_is_properly_set , unless: Proc.new {|a| a.errors.full_messages.include? 'Combination exists.' }
  validate :composition, unless: Proc.new {|a| disable_combination_relationship_check == true || a.errors.full_messages.include?('Combination exists.') }
  validates :rank_class, absence: true

  soft_validate(
    :sv_redundant_verbatim_name,
    set: :cached,
    fix: :sv_fix_redundant_verbatim_name,
    name: 'Redundant verbatim name',
    description: 'Verbatim name is present but identical to computed name')


  soft_validate(
    :sv_combination_duplicates,
    set: :combination_duplicates,
    name: 'Duplicate combination',
    description: 'Combination is a duplicate' )

  soft_validate(
    :sv_year_of_publication_matches_source,
    set: :dates,
    name: 'Year of publication does not match the source',
    description: 'The published date of the combination is not the same as provided by the original publication' )

  soft_validate(
    :sv_year_of_publication_not_older_than_protonyms,
    set: :dates,
    name: 'Varbatim year in combination older than in protonyms',
    description: 'The varbatim year in combination is older than in protonyms in the combination' )

  soft_validate(
    :sv_source_not_older_than_protonyms,
    set: :dates,
    name: 'Combination older than protonyms',
    description: 'The combination is older than protonyms in the combination' )

  soft_validate(
    :sv_combination_linked_to_valid_name,
    set: :combination_linked_to_valid_name,
    fix: :sv_fix_combination_parent_update,
    name: 'Combination has valid parent',
    description: 'The combination should have the same parent as protonym' )

  soft_validate(
    :sv_author_and_year_is_not_required,
    set: :year_is_not_required,
    fix: :sv_fix_author_and_year_is_not_required,
    name: 'Verbatim author and year are not required',
    description: 'Verbatim author and year are not required. The Fix will delete both' )

  # @return [Protonym Scope]
  # @params protonym_ids [Hash] like `{genus: 4, species: 5}`
  #   the absence of _id in the keys in part reflects integration with Biodiversity gem
  #   AHA from http://stackoverflow.com/questions/28568205/rails-4-arel-join-on-subquery
  #   See also Descriptor::Gene
  def self.protonyms_matching_original_relationships(protonym_ids = {})
    protonym_ids.compact!
    return Protonym.none if !protonym_ids.keys.any?

    s  = Protonym.arel_table
    sr = TaxonNameRelationship.arel_table

    j = s.alias('j') # required for group/having purposes

    b = s.project(j[Arel.star]).from(j)
      .join(sr)
      .on(sr['object_taxon_name_id'].eq(j['id']))

    # Build an aliased join for each set of attributes
    protonym_ids.each do |rank, id|
      sr_a = sr.alias("b_#{rank}")
      b = b.join(sr_a).on(
        sr_a['object_taxon_name_id'].eq(j['id']),
        sr_a['type'].eq("TaxonNameRelationship::OriginalCombination::Original#{rank.capitalize}"),
        sr_a['subject_taxon_name_id'].eq(id)
      )
    end

    b = b.group(j['id']).having(sr['object_taxon_name_id'].count.eq(protonym_ids.count)).where(sr['type'].in(::COMBINATION_TAXON_NAME_RELATIONSHIP_NAMES))
    b = b.as('join_alias')

    Protonym.joins(Arel::Nodes::InnerJoin.new(b, Arel::Nodes::On.new(b['id'].eq(s['id']))))
  end

  # @return [Protonym Scope] hmmm- a Protonym class method?!
  #    Protonyms matching original relations, if name provided then name added as an additional check on verbatim match
  # @params name [String, nil] the non-htmlized version of the name, without author year
  def self.matching_protonyms(name = nil, **protonym_ids)
    q = nil
    if name.blank?
      q = protonyms_matching_original_relationships(protonym_ids)
    else
      q = protonyms_matching_original_relationships(protonym_ids).where('taxon_names.cached_original_combination = ?', name)
    end
    q
  end

  # @return [Scope]
  # @params keyword_args [Hash] like `{genus: 123, :species: 456}` (note no `_id` suffix)
  def self.find_by_protonym_ids(**keyword_args)
    keyword_args.compact!
    return Combination.none if keyword_args.empty?

    c = Combination.arel_table
    r = TaxonNameRelationship.arel_table

    a = c.alias('a_foo')

    b = c.project(a[Arel.star]).from(a)
      .join(r)
      .on(r['object_taxon_name_id'].eq(a['id']))

    s = []

    i = 0
    keyword_args.each do |rank, id|
      r_a = r.alias("foo_#{i}")
      b = b.join(r_a).on(
        r_a['object_taxon_name_id'].eq(a['id']),
        r_a['type'].eq(TAXON_NAME_RELATIONSHIP_COMBINATION_TYPES[rank]),
        r_a['subject_taxon_name_id'].eq(id)
      )
      i += 1
    end

    b = b.group(a['id']).having(r['object_taxon_name_id'].count.eq(keyword_args.keys.count))
    b = b.as('z_bar')

    Combination.joins(Arel::Nodes::InnerJoin.new(b, Arel::Nodes::On.new(b['id'].eq(c['id']))))
  end

  # @return [Combination, false]
  # @params keyword_args [Hash] like `{genus: 123, :species: 456}` (note no `_id` suffix)
  #    the matching Combination if it exists, otherwise false
  #    if name is provided then cached must match (i.e. verbatim_name if provided must also match)
  def self.match_exists?(name = nil, **keyword_args)
    if name.blank?
      a = find_by_protonym_ids(**keyword_args).first
    else
      a = find_by_protonym_ids(**keyword_args).where(cached: name).first
    end
    a ? a : false
  end

  # @return [Boolean]
  #   true if the finest level (typically species) currently has the same parent
  def is_current_placement?
    return false if protonyms.second_to_last.nil?
    protonyms.last.parent_id == protonyms.second_to_last.id
  end

  def get_full_name
    return verbatim_name if verbatim_name.present?
    full_name
  end

  # Is this used before persistence of the complete Combination?!
  # Overrides {TaxonName#full_name_hash}
  # @return [Hash]
  #
  #  Benchmark.measure { 1000.times do; Combination.find_by_id(ids.sample).full_name_hash; end}
  def full_name_hash
    gender = nil
    data = {}

    protonyms_by_rank.each do |rank, i|
      gender = i.gender_name if rank == 'genus'

      if ['genus', 'subgenus', 'species', 'subspecies'].include?(rank)
        data[rank] = [nil, i.name_with_misspelling(gender)]
      else
        data[rank] = [i.rank_class.abbreviation, i.name_with_misspelling(gender)]
      end
    end

    if data['genus'].nil?
      data['genus'] = [nil, '[GENUS NOT SPECIFIED]']
    end

    if data['species'].nil? && (!data['subspecies'].nil? || !data['variety'].nil? || !data['subvariety'].nil? || !data['form'].nil? || !data['subform'].nil?)
      data['species'] = [nil, '[SPECIES NOT SPECIFIED]']
    end

    if data['variety'].nil? && !data['subvariety'].nil?
      data['variety'] = [nil, '[VARIETY NOT SPECIFIED]']
    end

    if data['form'].nil? && !data['subform'].nil?
      data['form'] = [nil, '[FORM NOT SPECIFIED]']
    end

    data
  end

  # TODO: add higher classifcation here
  def combination_taxonomy
    d = full_name_hash
    protonyms_by_rank.to_a.first[1].ancestors.each do |a|
      d[a.rank] = a.name
    end

    d
  end

  def taxonomy(rebuild = false)
    if rebuild
      @taxonomy = combination_taxonomy
    else
      @taxonomy ||= combination_taxonomy
    end
  end

  # @return [Hash of {rank: Protonym}, nil]
  #  the component names for this combination, sorted in order
  #   _prior to it being saved_
  def protonyms_by_rank
    result = {}
    if persisted?
      ar = APPLICABLE_RANKS.values
      # nX fewer calls to database than send()
      @protonyms_by_rank ||= TaxonNameRelationship::Combination
        .where(object_taxon_name: self)
        .eager_load(:subject_taxon_name)
        .sort{|a,b| ar.index(a.type) <=> ar.index(b.type)}
        .inject({}) {|hsh,n| hsh[n.rank_name] = n.subject_taxon_name; hsh}
        .to_h
    else
      APPLICABLE_RANKS.keys.each do |rank|
        if protonym = send(rank.to_sym)
          result[rank] = protonym
        end
      end
      @protonyms_by_rank = result
    end

    @protonyms_by_rank
  end

  # @return [Array of TaxonNames, nil]
  #   return the component names for this combination prior to it being saved
  def protonyms_by_association
    APPLICABLE_RANKS.keys.collect{|r| self.send(r)}.compact
  end

  # @return [Array of TaxonName]
  #   pre-ordered by rank
  def protonyms
    return protonyms_by_association if new_record?
    combination_taxon_names.sort{|a,b| RANKS.index(a.rank_string) <=> RANKS.index(b.rank_string) }
  end

  # @return [Hash]
  #   like `{ genus: 1, species: 2 }`
  def protonym_ids_params
    protonyms_by_rank.inject({}) {|hsh, p| hsh.merge!( p[0].to_sym => p[1].id )}
  end

  # @return [Array of Integers]
  #   the collective years the protonyms were (nomenclaturaly) published on (ordered from genus to below)
  def publication_years
    description_years = protonyms.collect{|a| a.cached_nomenclature_date ? a.cached_nomenclature_date&.year : nil}.compact
  end

  # @return [Integer, nil]
  #   the earliest year (nomenclature) that a component Protonym was published on
  def earliest_protonym_year
    publication_years.sort.first
  end

  # return [Array of TaxonNameRelationship]
  #   classes that are applicable to this name, as deterimned by Rank
  def combination_class_relationships(rank_string)
    relations = []
    TaxonNameRelationship::Combination.descendants.each do |r|
      relations.push(r) if r.valid_object_ranks.include?(rank_string)
    end
    relations
  end

  # TODO: DEPRECATE this is likely not required in our new interfaces
  def combination_relationships_and_stubs(rank_string)
    display_order = [
      :combination_genus, :combination_subgenus, :combination_species, :combination_subspecies, :combination_variety, :combination_form
    ]

    defined_relations = combination_relationships.all
    created_already = defined_relations.collect{|a| a.class}
    new_relations = []

    combination_class_relationships(rank_string).each do |r|
      new_relations.push( r.new(object_taxon_name: self) ) if !created_already.include?(r)
    end

    (new_relations + defined_relations).sort{|a,b|
      display_order.index(a.class.inverse_assignment_method) <=> display_order.index(b.class.inverse_assignment_method)
    }
  end

  def get_valid_taxon_name
    c = protonyms_by_rank
    return self if c.empty?
    c[c.keys.last].valid_taxon_name
  end

  def finest_protonym
    protonyms_by_rank.values.last
  end

  protected

  def reset_protonyms_by_rank
    @protonyms_by_rank = nil
  end

  def validate_absence_of_subject_relationships
    if TaxonNameRelationship.where(subject_taxon_name_id: self.id).where("type NOT LIKE 'TaxonNameRelationship::CurrentCombination'").any?
      errors.add(:base, 'This combination could not be used as a Subject in any TaxonNameRelationships.')
    end
  end

  def sv_redundant_verbatim_name
    if verbatim_name == full_name
      protonyms_by_rank.values.each do |t|
        return true unless t.has_latinized_classification?
      end
      soft_validations.add(:verbatim_name, 'Verbatim name is provided but not needed, it is the same as the computed value.')
    end
  end

  def sv_year_of_publication_matches_source
    source_year = source.nomenclature_year if source
    if year_of_publication && source_year
      soft_validations.add(:year_of_publication, 'The published date of the combination is not the same as provided by the original publication') if source_year != year_of_publication
    end
  end

  def sv_source_not_older_than_protonyms
    source_year = source.try(:nomenclature_year)
    target_year = earliest_protonym_year
    if source_year && target_year
      soft_validations.add(:base, "The publication date of combination (#{source_year}) is older than the original publication date of one of the name in the combination (#{target_year}") if source_year < target_year
    end
  end

  def sv_year_of_publication_not_older_than_protonyms
    if year_of_publication && earliest_protonym_year
      soft_validations.add(:year_of_publication,  "The publication date of combination (#{year_of_publication}) is older than the original publication date of one of the name in the combination (#{earliest_protonym_year}") if year_of_publication < earliest_protonym_year
    end
  end

  def sv_combination_duplicates
    duplicate = Combination.not_self(self).where(cached:, cached_author_year:, project_id: self.project_id)
    soft_validations.add(:base, 'Combination is a duplicate') unless duplicate.empty?
    if a = Combination.matching_protonyms(get_full_name, **protonym_ids_params)
      soft_validations.add(:base, "Combination exists as protonym(s) with matching original combination: #{a.all.pluck(:cached).join(', ')}.") if a.any?
    end
  end

  def sv_combination_linked_to_valid_name
    check = protonyms.first
    if parent_id && check && check.parent_id && parent_id != check.parent_id
      soft_validations.add(:base, "Combination #{cached_html_name_and_author_year} should have the same parent and rank with  #{check.cached_html_name_and_author_year}",
                           success_message: 'The parent was updated', failure_message:  'The parent was not updated')
    end
  end

  def sv_fix_combination_parent_update
    check = protonyms.first
    if parent_id && check && check.parent_id && parent_id != check.parent_id
      begin
        TaxonName.transaction do
          # update_column(:parent_id, check.parent_id) ## do not use this, it breaks the taxon_name_hierarchies
          parent_id = check.parent_id
          self.save
          return true
        end
      rescue
      end
    end
    false
  end

  def sv_cached_names
    is_cached = true
    is_cached = false if cached_author_year != get_author_and_year
    is_cached = false if cached_author != get_author

    if  is_cached && (
        cached_is_valid.nil? ||
        cached != get_full_name ||
        cached_html != get_full_name_html ||
        cached_nomenclature_date != nomenclature_date)
      is_cached = false
    end
    soft_validations.add(
      :base, 'Cached values should be updated',
      success_message: 'Cached values were updated',
      failure_message:  'Failed to update cached values') if !is_cached
  end

  def sv_author_and_year_is_not_required
    if !self.year_of_publication.nil? || !self.verbatim_author.nil?
      soft_validations.add(
        :base, 'Verbatim author and year of publication are not required, they both derive from the source',
        success_message: 'Verbatim author and year were deleted',
        failure_message: 'Failed to delete verbatim author and year')
    end
  end

  def sv_fix_author_and_year_is_not_required
    self.update_columns(year_of_publication: nil, verbatim_author: nil)
    return true
  end

  def sv_fix_redundant_verbatim_name
    self.update_columns(verbatim_name: nil)
    return true
  end

  def set_parent
    names = protonyms
    write_attribute(:parent_id, names.first.parent.id) if names.count > 0 && names.first.parent
  end

  # The parent of a Combination is the parent of the highest ranked protonym in that Combination
  def parent_is_properly_set
    check = protonyms.first
    if parent && check && check.parent
      errors.add(:base, 'Parent is not highest ranked name.') if parent != check.parent
    end
  end

  def composition
    c = protonyms.count

    if c == 0
      errors.add(:base, 'Combination includes no names.')
      return
    end

    protonyms.each do |p|
      if !p.is_genus_or_species_rank?
        errors.add(:base, 'Combination includes one or more non-species or genus group names.')
        return
      end
    end

    # There are more than one protonyms, which seem to be valid elements
    p = protonyms.last
    errors.add(:base, 'Combination includes only one name and that is name is not a genus name.') if c < 2 && p.is_species_rank?
    errors.add(:base, 'Combination includes more than two genus group names.') if c > 2 && p.is_genus_rank?
  end

  def is_unique
    if a = Combination.match_exists?(verbatim_name, **protonym_ids_params)
      errors.add(:base, 'Combination exists.') if a.id != id
    end
  end

  def does_not_exist_as_original_combination
    if a = Combination.matching_protonyms(get_full_name, **protonym_ids_params)
      errors.add(:base, "Combination exists as protonym(s) with matching original combination: #{a.all.pluck(:cached).join(', ')}.") if a.any?
    end
  end

end

#protonyms_by_rank ⇒ Hash of {rank: Protonym}?

Returns the component names for this combination, sorted in order

_prior to it being saved_.

Returns:

  • (Hash of {rank: Protonym}, nil) —

    the component names for this combination, sorted in order

    _prior to it being saved_



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# File 'app/models/combination.rb', line 75

def protonyms_by_rank
  @protonyms_by_rank
end

Class Method Details

.find_by_protonym_ids(**keyword_args) ⇒ Scope

Returns:

  • (Scope) 


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# File 'app/models/combination.rb', line 267

def self.find_by_protonym_ids(**keyword_args)
  keyword_args.compact!
  return Combination.none if keyword_args.empty?

  c = Combination.arel_table
  r = TaxonNameRelationship.arel_table

  a = c.alias('a_foo')

  b = c.project(a[Arel.star]).from(a)
    .join(r)
    .on(r['object_taxon_name_id'].eq(a['id']))

  s = []

  i = 0
  keyword_args.each do |rank, id|
    r_a = r.alias("foo_#{i}")
    b = b.join(r_a).on(
      r_a['object_taxon_name_id'].eq(a['id']),
      r_a['type'].eq(TAXON_NAME_RELATIONSHIP_COMBINATION_TYPES[rank]),
      r_a['subject_taxon_name_id'].eq(id)
    )
    i += 1
  end

  b = b.group(a['id']).having(r['object_taxon_name_id'].count.eq(keyword_args.keys.count))
  b = b.as('z_bar')

  Combination.joins(Arel::Nodes::InnerJoin.new(b, Arel::Nodes::On.new(b['id'].eq(c['id']))))
end

.match_exists?(name = nil, **keyword_args) ⇒ Combination, false

Returns:



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

def self.match_exists?(name = nil, **keyword_args)
  if name.blank?
    a = find_by_protonym_ids(**keyword_args).first
  else
    a = find_by_protonym_ids(**keyword_args).where(cached: name).first
  end
  a ? a : false
end

.matching_protonyms(name = nil, **protonym_ids) ⇒ Protonym Scope

Returns hmmm- a Protonym class method?! Protonyms matching original relations, if name provided then name added as an additional check on verbatim match.

Returns:

  • (Protonym Scope) —

    hmmm- a Protonym class method?! Protonyms matching original relations, if name provided then name added as an additional check on verbatim match



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# File 'app/models/combination.rb', line 255

def self.matching_protonyms(name = nil, **protonym_ids)
  q = nil
  if name.blank?
    q = protonyms_matching_original_relationships(protonym_ids)
  else
    q = protonyms_matching_original_relationships(protonym_ids).where('taxon_names.cached_original_combination = ?', name)
  end
  q
end

.protonyms_matching_original_relationships(protonym_ids = {}) ⇒ Protonym Scope

Returns:



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# File 'app/models/combination.rb', line 223

def self.protonyms_matching_original_relationships(protonym_ids = {})
  protonym_ids.compact!
  return Protonym.none if !protonym_ids.keys.any?

  s  = Protonym.arel_table
  sr = TaxonNameRelationship.arel_table

  j = s.alias('j') # required for group/having purposes

  b = s.project(j[Arel.star]).from(j)
    .join(sr)
    .on(sr['object_taxon_name_id'].eq(j['id']))

  # Build an aliased join for each set of attributes
  protonym_ids.each do |rank, id|
    sr_a = sr.alias("b_#{rank}")
    b = b.join(sr_a).on(
      sr_a['object_taxon_name_id'].eq(j['id']),
      sr_a['type'].eq("TaxonNameRelationship::OriginalCombination::Original#{rank.capitalize}"),
      sr_a['subject_taxon_name_id'].eq(id)
    )
  end

  b = b.group(j['id']).having(sr['object_taxon_name_id'].count.eq(protonym_ids.count)).where(sr['type'].in(::COMBINATION_TAXON_NAME_RELATIONSHIP_NAMES))
  b = b.as('join_alias')

  Protonym.joins(Arel::Nodes::InnerJoin.new(b, Arel::Nodes::On.new(b['id'].eq(s['id']))))
end

Instance Method Details

#combination_class_relationships(rank_string) ⇒ Object

return [Array of TaxonNameRelationship]

classes that are applicable to this name, as deterimned by Rank



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# File 'app/models/combination.rb', line 439

def combination_class_relationships(rank_string)
  relations = []
  TaxonNameRelationship::Combination.descendants.each do |r|
    relations.push(r) if r.valid_object_ranks.include?(rank_string)
  end
  relations
end

#combination_relationships_and_stubs(rank_string) ⇒ Object

TODO: DEPRECATE this is likely not required in our new interfaces



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# File 'app/models/combination.rb', line 448

def combination_relationships_and_stubs(rank_string)
  display_order = [
    :combination_genus, :combination_subgenus, :combination_species, :combination_subspecies, :combination_variety, :combination_form
  ]

  defined_relations = combination_relationships.all
  created_already = defined_relations.collect{|a| a.class}
  new_relations = []

  combination_class_relationships(rank_string).each do |r|
    new_relations.push( r.new(object_taxon_name: self) ) if !created_already.include?(r)
  end

  (new_relations + defined_relations).sort{|a,b|
    display_order.index(a.class.inverse_assignment_method) <=> display_order.index(b.class.inverse_assignment_method)
  }
end

#combination_taxonomy ⇒ Object

TODO: add higher classifcation here



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# File 'app/models/combination.rb', line 363

def combination_taxonomy
  d = full_name_hash
  protonyms_by_rank.to_a.first[1].ancestors.each do |a|
    d[a.rank] = a.name
  end

  d
end

#composition ⇒ Object (protected) 



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# File 'app/models/combination.rb', line 600

def composition
  c = protonyms.count

  if c == 0
    errors.add(:base, 'Combination includes no names.')
    return
  end

  protonyms.each do |p|
    if !p.is_genus_or_species_rank?
      errors.add(:base, 'Combination includes one or more non-species or genus group names.')
      return
    end
  end

  # There are more than one protonyms, which seem to be valid elements
  p = protonyms.last
  errors.add(:base, 'Combination includes only one name and that is name is not a genus name.') if c < 2 && p.is_species_rank?
  errors.add(:base, 'Combination includes more than two genus group names.') if c > 2 && p.is_genus_rank?
end

#does_not_exist_as_original_combination ⇒ Object (protected) 



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# File 'app/models/combination.rb', line 627

def does_not_exist_as_original_combination
  if a = Combination.matching_protonyms(get_full_name, **protonym_ids_params)
    errors.add(:base, "Combination exists as protonym(s) with matching original combination: #{a.all.pluck(:cached).join(', ')}.") if a.any?
  end
end

#earliest_protonym_year ⇒ Integer?

Returns the earliest year (nomenclature) that a component Protonym was published on.

Returns:

  • (Integer, nil) —

    the earliest year (nomenclature) that a component Protonym was published on



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# File 'app/models/combination.rb', line 433

def earliest_protonym_year
  publication_years.sort.first
end

#finest_protonym ⇒ Object 



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# File 'app/models/combination.rb', line 472

def finest_protonym
  protonyms_by_rank.values.last
end

#full_name_hash ⇒ Hash

Is this used before persistence of the complete Combination?! Overrides TaxonName#full_name_hash

Returns:

  • (Hash) —

    Benchmark.measure { 1000.times do; Combination.find_by_id(ids.sample).full_name_hash; end}



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

def full_name_hash
  gender = nil
  data = {}

  protonyms_by_rank.each do |rank, i|
    gender = i.gender_name if rank == 'genus'

    if ['genus', 'subgenus', 'species', 'subspecies'].include?(rank)
      data[rank] = [nil, i.name_with_misspelling(gender)]
    else
      data[rank] = [i.rank_class.abbreviation, i.name_with_misspelling(gender)]
    end
  end

  if data['genus'].nil?
    data['genus'] = [nil, '[GENUS NOT SPECIFIED]']
  end

  if data['species'].nil? && (!data['subspecies'].nil? || !data['variety'].nil? || !data['subvariety'].nil? || !data['form'].nil? || !data['subform'].nil?)
    data['species'] = [nil, '[SPECIES NOT SPECIFIED]']
  end

  if data['variety'].nil? && !data['subvariety'].nil?
    data['variety'] = [nil, '[VARIETY NOT SPECIFIED]']
  end

  if data['form'].nil? && !data['subform'].nil?
    data['form'] = [nil, '[FORM NOT SPECIFIED]']
  end

  data
end

#get_full_name ⇒ Object 



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# File 'app/models/combination.rb', line 319

def get_full_name
  return verbatim_name if verbatim_name.present?
  full_name
end

#get_valid_taxon_name ⇒ Object 



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# File 'app/models/combination.rb', line 466

def get_valid_taxon_name
  c = protonyms_by_rank
  return self if c.empty?
  c[c.keys.last].valid_taxon_name
end

#is_current_placement? ⇒ Boolean

Returns true if the finest level (typically species) currently has the same parent.

Returns:

  • (Boolean) —

    true if the finest level (typically species) currently has the same parent



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# File 'app/models/combination.rb', line 314

def is_current_placement?
  return false if protonyms.second_to_last.nil?
  protonyms.last.parent_id == protonyms.second_to_last.id
end

#is_unique ⇒ Object (protected) 



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# File 'app/models/combination.rb', line 621

def is_unique
  if a = Combination.match_exists?(verbatim_name, **protonym_ids_params)
    errors.add(:base, 'Combination exists.') if a.id != id
  end
end

#parent_is_properly_set ⇒ Object (protected)

The parent of a Combination is the parent of the highest ranked protonym in that Combination



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# File 'app/models/combination.rb', line 593

def parent_is_properly_set
  check = protonyms.first
  if parent && check && check.parent
    errors.add(:base, 'Parent is not highest ranked name.') if parent != check.parent
  end
end

#protonym_ids_params ⇒ Hash

Returns like ‘{ genus: 1, species: 2 }`.

Returns:

  • (Hash) —

    like ‘{ genus: 1, species: 2 }`



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# File 'app/models/combination.rb', line 421

def protonym_ids_params
  protonyms_by_rank.inject({}) {|hsh, p| hsh.merge!( p[0].to_sym => p[1].id )}
end

#protonyms ⇒ Array of TaxonName

Returns pre-ordered by rank.

Returns:

  • (Array of TaxonName) —

    pre-ordered by rank



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# File 'app/models/combination.rb', line 414

def protonyms
  return protonyms_by_association if new_record?
  combination_taxon_names.sort{|a,b| RANKS.index(a.rank_string) <=> RANKS.index(b.rank_string) }
end

#protonyms_by_association ⇒ Array of TaxonNames?

Return the component names for this combination prior to it being saved

Returns:

  • (Array of TaxonNames, nil) —

    return the component names for this combination prior to it being saved



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# File 'app/models/combination.rb', line 408

def protonyms_by_association
  APPLICABLE_RANKS.keys.collect{|r| self.send(r)}.compact
end

#publication_years ⇒ Array of Integers

Returns the collective years the protonyms were (nomenclaturaly) published on (ordered from genus to below).

Returns:

  • (Array of Integers) —

    the collective years the protonyms were (nomenclaturaly) published on (ordered from genus to below)



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# File 'app/models/combination.rb', line 427

def publication_years
  description_years = protonyms.collect{|a| a.cached_nomenclature_date ? a.cached_nomenclature_date&.year : nil}.compact
end

#reset_protonyms_by_rank ⇒ Object (protected) 



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# File 'app/models/combination.rb', line 478

def reset_protonyms_by_rank
  @protonyms_by_rank = nil
end

#set_parent ⇒ Object (protected) 



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

def set_parent
  names = protonyms
  write_attribute(:parent_id, names.first.parent.id) if names.count > 0 && names.first.parent
end

#sv_author_and_year_is_not_required ⇒ Object (protected) 



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# File 'app/models/combination.rb', line 568

def sv_author_and_year_is_not_required
  if !self.year_of_publication.nil? || !self.verbatim_author.nil?
    soft_validations.add(
      :base, 'Verbatim author and year of publication are not required, they both derive from the source',
      success_message: 'Verbatim author and year were deleted',
      failure_message: 'Failed to delete verbatim author and year')
  end
end

#sv_cached_names ⇒ Object (protected) 



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# File 'app/models/combination.rb', line 550

def sv_cached_names
  is_cached = true
  is_cached = false if cached_author_year != get_author_and_year
  is_cached = false if cached_author != get_author

  if  is_cached && (
      cached_is_valid.nil? ||
      cached != get_full_name ||
      cached_html != get_full_name_html ||
      cached_nomenclature_date != nomenclature_date)
    is_cached = false
  end
  soft_validations.add(
    :base, 'Cached values should be updated',
    success_message: 'Cached values were updated',
    failure_message:  'Failed to update cached values') if !is_cached
end

#sv_combination_duplicates ⇒ Object (protected) 



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# File 'app/models/combination.rb', line 518

def sv_combination_duplicates
  duplicate = Combination.not_self(self).where(cached:, cached_author_year:, project_id: self.project_id)
  soft_validations.add(:base, 'Combination is a duplicate') unless duplicate.empty?
  if a = Combination.matching_protonyms(get_full_name, **protonym_ids_params)
    soft_validations.add(:base, "Combination exists as protonym(s) with matching original combination: #{a.all.pluck(:cached).join(', ')}.") if a.any?
  end
end

#sv_combination_linked_to_valid_name ⇒ Object (protected) 



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# File 'app/models/combination.rb', line 526

def sv_combination_linked_to_valid_name
  check = protonyms.first
  if parent_id && check && check.parent_id && parent_id != check.parent_id
    soft_validations.add(:base, "Combination #{cached_html_name_and_author_year} should have the same parent and rank with  #{check.cached_html_name_and_author_year}",
                         success_message: 'The parent was updated', failure_message:  'The parent was not updated')
  end
end

#sv_fix_author_and_year_is_not_required ⇒ Object (protected) 



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# File 'app/models/combination.rb', line 577

def sv_fix_author_and_year_is_not_required
  self.update_columns(year_of_publication: nil, verbatim_author: nil)
  return true
end

#sv_fix_combination_parent_update ⇒ Object (protected) 



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

def sv_fix_combination_parent_update
  check = protonyms.first
  if parent_id && check && check.parent_id && parent_id != check.parent_id
    begin
      TaxonName.transaction do
        # update_column(:parent_id, check.parent_id) ## do not use this, it breaks the taxon_name_hierarchies
        parent_id = check.parent_id
        self.save
        return true
      end
    rescue
    end
  end
  false
end

#sv_fix_redundant_verbatim_name ⇒ Object (protected) 



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# File 'app/models/combination.rb', line 582

def sv_fix_redundant_verbatim_name
  self.update_columns(verbatim_name: nil)
  return true
end

#sv_redundant_verbatim_name ⇒ Object (protected) 



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# File 'app/models/combination.rb', line 488

def sv_redundant_verbatim_name
  if verbatim_name == full_name
    protonyms_by_rank.values.each do |t|
      return true unless t.has_latinized_classification?
    end
    soft_validations.add(:verbatim_name, 'Verbatim name is provided but not needed, it is the same as the computed value.')
  end
end

#sv_source_not_older_than_protonyms ⇒ Object (protected) 



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# File 'app/models/combination.rb', line 504

def sv_source_not_older_than_protonyms
  source_year = source.try(:nomenclature_year)
  target_year = earliest_protonym_year
  if source_year && target_year
    soft_validations.add(:base, "The publication date of combination (#{source_year}) is older than the original publication date of one of the name in the combination (#{target_year}") if source_year < target_year
  end
end

#sv_year_of_publication_matches_source ⇒ Object (protected) 



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# File 'app/models/combination.rb', line 497

def sv_year_of_publication_matches_source
  source_year = source.nomenclature_year if source
  if year_of_publication && source_year
    soft_validations.add(:year_of_publication, 'The published date of the combination is not the same as provided by the original publication') if source_year != year_of_publication
  end
end

#sv_year_of_publication_not_older_than_protonyms ⇒ Object (protected) 



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# File 'app/models/combination.rb', line 512

def sv_year_of_publication_not_older_than_protonyms
  if year_of_publication && earliest_protonym_year
    soft_validations.add(:year_of_publication,  "The publication date of combination (#{year_of_publication}) is older than the original publication date of one of the name in the combination (#{earliest_protonym_year}") if year_of_publication < earliest_protonym_year
  end
end

#taxonomy(rebuild = false) ⇒ Object 



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# File 'app/models/combination.rb', line 372

def taxonomy(rebuild = false)
  if rebuild
    @taxonomy = combination_taxonomy
  else
    @taxonomy ||= combination_taxonomy
  end
end

#validate_absence_of_subject_relationships ⇒ Object (protected) 



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# File 'app/models/combination.rb', line 482

def validate_absence_of_subject_relationships
  if TaxonNameRelationship.where(subject_taxon_name_id: self.id).where("type NOT LIKE 'TaxonNameRelationship::CurrentCombination'").any?
    errors.add(:base, 'This combination could not be used as a Subject in any TaxonNameRelationships.')
  end
end