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

APPLICABLE_RANKS =

The ranks that can be used to build combinations. ! TODO: family group names

%w{family subfamily tribe subtribe genus subgenus section subsection
series subseries species subspecies variety subvariety form subform}.freeze

Constants inherited from TaxonName

TaxonName::ALTERNATE_VALUES_FOR, TaxonName::COMBINATION_ELEMENTS, TaxonName::EXCEPTED_FORM_TAXON_NAME_CLASSIFICATIONS, TaxonName::EXCEPTED_FORM_TAXON_NAME_RELATIONSHIPS, TaxonName::NOT_LATIN, TaxonName::NO_CACHED_MESSAGE, 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_classified_as, #no_cached

Class Method Summary (collapse)

Instance Method Summary (collapse)

Methods inherited from TaxonName

#all_taxon_name_relationships, #ancestor_at_rank, #ancestor_protonyms, #ancestors_through_parents, #author_string, #cached_html_name_and_author_year, #cached_name_and_author_year, #check_for_children, #check_new_parent_class, #check_new_rank_class, #classification_invalid_or_unavailable?, #classification_valid?, #combination_list_all, #combination_list_self, #combined_statuses, #create_new_combination_if_absent, #create_otu, #descendant_protonyms, #first_possible_valid_taxon_name, #first_possible_valid_taxon_name_relationship, #form_name_elements, #full_name_array, #gbif_status_array, #gender_class, #gender_instance, #gender_name, #genderized_name, #genus_name_elements, #get_cached_classified_as, #get_cached_misspelling, #get_full_name, #get_full_name_html, #get_genus_species, #get_original_combination, #get_original_combination_html, #icn_author_and_year, #iczn_author_and_year, #is_candidatus?, #is_combination?, #is_fossil?, #is_genus_or_species_rank?, #is_hybrid?, #is_italicized?, #is_protonym?, #is_valid?, #list_of_invalid_taxon_names, #name_in_gender, #name_is_missapplied?, #name_with_misspelling, #next_sibling, #nomenclature_date, #not_binomial?, #parent_is_set?, #part_of_speech_class, #part_of_speech_instance, #part_of_speech_name, #previous_sibling, #rank, #rank_class, #rank_class=, #rank_string, #related_taxon_names, #relationship_invalid?, #safe_self_and_ancestors, #section_name_elements, select_optimized, #series_name_elements, #set_cached, #set_cached_author_year, #set_cached_classified_as, #set_cached_valid_taxon_name_id, #set_cached_warnings, sort_by_rank, #species_group_name_elements, #species_name_elements, #statuses_from_classifications, #statuses_from_relationships, #subform_name_elements, #subgenus_name_elements, #subsection_name_elements, #subseries_name_elements, #subspecies_name_elements, #subvariety_name_elements, #superspecies_name_elements, #sv_cached_names, #sv_fix_cached_names, #sv_fix_missing_author, #sv_fix_missing_year, #sv_fix_parent_is_valid_name, #sv_homotypic_synonyms, #sv_hybrid_name_relationships, #sv_incomplete_combination, #sv_missing_classifications, #sv_missing_fields, #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_classifications_for_statuses, #unavailable_or_invalid?, used_recently, used_recently_in_classifications, used_recently_in_relationships, #validate_one_root_per_project, #validate_parent_from_the_same_project, #validate_parent_is_set, #validate_parent_rank_is_higher, #validate_rank_class_class, #validate_source_type, #variety_name_elements, with_taxon_name_relationship, #year_integer

Methods included from SoftValidation

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

Methods included from Housekeeping

#has_polymorphic_relationship?

Methods included from ActiverecordUtilities

#trim_attributes

Instance Attribute Details

- (String) combination_verbatim_name

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 combinations. ! TODO:  family group names 
  APPLICABLE_RANKS = %w{family subfamily tribe subtribe genus subgenus section subsection
                        series subseries species subspecies variety subvariety form subform}.freeze

  before_validation :set_parent

  # 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.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

    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

    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.blank?
        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| a.errors.full_messages.include? 'Combination exists.' }
  validates :rank_class, absence: true

  soft_validate(:sv_combination_duplicates, set: :combination_duplicates)
  soft_validate(:sv_year_of_publication_matches_source, set: :dates)
  soft_validate(:sv_year_of_publication_not_older_than_protonyms, set: :dates)
  soft_validate(:sv_source_not_older_than_protonyms, set: :dates)

  # @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) is currently has the same parent
  def is_current_placement?
    protonyms.last.parent_id == protonyms.second_to_last.id
  end

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

  # Overrides {TaxonName#full_name_hash}
  # @return [Hash]
  def full_name_hash
    gender = nil
    data   = {}
    protonyms_by_rank.each do |rank, name|
      gender = name.gender_name if rank == 'genus'
      method = "#{rank.gsub(/\s/, '_')}_name_elements"
      data[rank] = send(method, name, gender) if self.respond_to?(method)
    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

  # @return [Hash of {rank: Protonym}, nil]
  #   the component names for this combination prior to it being saved (used to return values prior to save)
  def protonyms_by_rank
    result = {}
    APPLICABLE_RANKS.each do |rank|
      if protonym = send(rank)
        result[rank] = protonym
      end
    end
    result
  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.nomenclature_date ? a.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 get_author_and_year
    ay = iczn_author_and_year
    ay.blank? ? nil : ay
  end

  # @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))

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

  protected

  # TODO: this is a TaxonName level validation, it doesn't belong here
  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) 
    soft_validations.add(:base, 'Combination is a duplicate') unless duplicate.empty?
  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

- (Integer) parent_id

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 combinations. ! TODO:  family group names 
  APPLICABLE_RANKS = %w{family subfamily tribe subtribe genus subgenus section subsection
                        series subseries species subspecies variety subvariety form subform}.freeze

  before_validation :set_parent

  # 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.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

    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

    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.blank?
        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| a.errors.full_messages.include? 'Combination exists.' }
  validates :rank_class, absence: true

  soft_validate(:sv_combination_duplicates, set: :combination_duplicates)
  soft_validate(:sv_year_of_publication_matches_source, set: :dates)
  soft_validate(:sv_year_of_publication_not_older_than_protonyms, set: :dates)
  soft_validate(:sv_source_not_older_than_protonyms, set: :dates)

  # @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) is currently has the same parent
  def is_current_placement?
    protonyms.last.parent_id == protonyms.second_to_last.id
  end

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

  # Overrides {TaxonName#full_name_hash}
  # @return [Hash]
  def full_name_hash
    gender = nil
    data   = {}
    protonyms_by_rank.each do |rank, name|
      gender = name.gender_name if rank == 'genus'
      method = "#{rank.gsub(/\s/, '_')}_name_elements"
      data[rank] = send(method, name, gender) if self.respond_to?(method)
    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

  # @return [Hash of {rank: Protonym}, nil]
  #   the component names for this combination prior to it being saved (used to return values prior to save)
  def protonyms_by_rank
    result = {}
    APPLICABLE_RANKS.each do |rank|
      if protonym = send(rank)
        result[rank] = protonym
      end
    end
    result
  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.nomenclature_date ? a.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 get_author_and_year
    ay = iczn_author_and_year
    ay.blank? ? nil : ay
  end

  # @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))

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

  protected

  # TODO: this is a TaxonName level validation, it doesn't belong here
  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) 
    soft_validations.add(:base, 'Combination is a duplicate') unless duplicate.empty?
  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

Class Method Details

+ (Scope) find_by_protonym_ids(**keyword_args)

Returns:

  • (Scope)


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

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

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

Returns:



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

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

+ (Protonym Scope) matching_protonyms(name = nil, **protonym_ids)

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 360

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

+ (Protonym Scope) protonyms_matching_original_relationships(protonym_ids = {})

Returns:



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# File 'app/models/combination.rb', line 327

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))

  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

- (Object) combination_class_relationships(rank_string)

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 284

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

- (Object) combination_relationships_and_stubs(rank_string)

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



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# File 'app/models/combination.rb', line 293

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

- (Object) composition (protected)



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

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

- (Object) does_not_exist_as_original_combination (protected)



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# File 'app/models/combination.rb', line 445

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

- (Integer?) earliest_protonym_year

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 278

def earliest_protonym_year
  publication_years.sort.first
end

- (Hash) full_name_hash

Returns:

  • (Hash)


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# File 'app/models/combination.rb', line 234

def full_name_hash
  gender = nil
  data   = {}
  protonyms_by_rank.each do |rank, name|
    gender = name.gender_name if rank == 'genus'
    method = "#{rank.gsub(/\s/, '_')}_name_elements"
    data[rank] = send(method, name, gender) if self.respond_to?(method)
  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

- (Object) get_author_and_year



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# File 'app/models/combination.rb', line 317

def get_author_and_year
  ay = iczn_author_and_year
  ay.blank? ? nil : ay
end

- (Object) get_valid_taxon_name



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

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

- (Boolean) is_current_placement?

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

Returns:

  • (Boolean)

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



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# File 'app/models/combination.rb', line 213

def is_current_placement?
  protonyms.last.parent_id == protonyms.second_to_last.id
end

- (Object) is_unique (protected)



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

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

- (Object) parent_is_properly_set (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 411

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

- (Hash) protonym_ids_params

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

Returns:

  • (Hash)

    like `{ genus: 1, species: 2 }`



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# File 'app/models/combination.rb', line 228

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

- (Array of TaxonName) protonyms

Returns pre-ordered by rank

Returns:

  • (Array of TaxonName)

    pre-ordered by rank



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# File 'app/models/combination.rb', line 219

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

- (Array of TaxonNames?) protonyms_by_association

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 372

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

- (Hash of {rank: Protonym}?) protonyms_by_rank

Returns the component names for this combination prior to it being saved (used to return values prior to save)

Returns:

  • (Hash of {rank: Protonym}, nil)

    the component names for this combination prior to it being saved (used to return values prior to save)



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

def protonyms_by_rank
  result = {}
  APPLICABLE_RANKS.each do |rank|
    if protonym = send(rank)
      result[rank] = protonym
    end
  end
  result
end

- (Array of Integers) publication_years

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 272

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

- (Object) set_parent (protected)



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# File 'app/models/combination.rb', line 405

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

- (Object) sv_combination_duplicates (protected)



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# File 'app/models/combination.rb', line 400

def sv_combination_duplicates
  duplicate = Combination.not_self(self).where(cached: cached) 
  soft_validations.add(:base, 'Combination is a duplicate') unless duplicate.empty?
end

- (Object) sv_source_not_older_than_protonyms (protected)



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# File 'app/models/combination.rb', line 386

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

- (Object) sv_year_of_publication_matches_source (protected)

TODO: this is a TaxonName level validation, it doesn't belong here



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# File 'app/models/combination.rb', line 379

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

- (Object) sv_year_of_publication_not_older_than_protonyms (protected)



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# File 'app/models/combination.rb', line 394

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