Class: Protonym

Inherits:
TaxonName show all
Extended by:
SoftValidationExtensions::Klass
Includes:
SoftValidationExtensions::Instance
Defined in:
app/models/protonym.rb

Overview

A monomial TaxonName, a record implies a first usage. This follows Pyle's concept almost exactly.

We inject a lot of relationship helper methods here, in this format.

subject                      object
Aus      original_genus of   bus
aus      type_species of     Bus

Defined Under Namespace

Modules: SoftValidationExtensions

Constant Summary

FAMILY_GROUP_ENDINGS =
%w{ini ina inae idae oidae odd ad oidea}

Constants included from SoftValidationExtensions::Klass

SoftValidationExtensions::Klass::VALIDATIONS

Constants inherited from TaxonName

TaxonName::ALTERNATE_VALUES_FOR, TaxonName::EXCEPTED_FORM_TAXON_NAME_CLASSIFICATIONS, TaxonName::NOT_LATIN, TaxonName::NO_CACHED_MESSAGE, TaxonName::SPECIES_EPITHET_RANKS

Constants included from SoftValidation

SoftValidation::ANCESTORS_WITH_SOFT_VALIDATIONS

Instance Attribute Summary

Attributes inherited from TaxonName

#also_create_otu, #cached, #cached_author_year, #cached_classified_as, #cached_higher_classification, #cached_html, #cached_misspelling, #cached_original_combination, #cached_primary_homonym, #cached_primary_homonym_alternative_spelling, #cached_secondary_homonym, #cached_secondary_homonym_alternative_spelling, #feminine_name, #masculine_name, #name, #neuter_name, #no_cached, #parent_id, #project_id, #rank_class, #type, #verbatim_author, #verbatim_name, #year_of_publication

Class Method Summary (collapse)

Instance Method Summary (collapse)

Methods included from SoftValidationExtensions::Instance

#sv_extant_children, #sv_fix_add_nominotypical_sub, #sv_fix_coordinated_names, #sv_homotypic_synonyms, #sv_missing_classifications, #sv_missing_relationships, #sv_original_combination_relationships, #sv_parent_priority, #sv_potential_homonyms, #sv_primary_types, #sv_single_sub_taxon, #sv_source_not_older_then_description, #sv_species_gender_agreement, #sv_type_placement, #sv_validate_coordinated_names, #sv_validate_parent_rank

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, #descendant_protonyms, #first_possible_valid_taxon_name, #first_possible_valid_taxon_name_relationship, #form_name_elements, #fossil?, #full_name_array, #full_name_hash, #gbif_status_array, #gender_class, #gender_instance, #gender_name, #genus_name_elements, #get_cached_classified_as, #get_cached_misspelling, #get_full_name, #get_full_name_html, #get_original_combination, #hybrid?, #icn_author_and_year, #iczn_author_and_year, #is_combination?, #is_protonym?, #is_valid?, #list_of_invalid_taxon_names, #name_in_gender, #name_is_missapplied?, #name_with_misspelling, #next_sibling, #nomenclature_date, #parent_is_set?, #part_of_speech_class, #part_of_speech_instance, #part_of_speech_name, #previous_sibling, #rank, #rank_string, #related_taxon_names, #relationship_invalid?, #safe_self_and_ancestors, #section_name_elements, #series_name_elements, #set_cached_author_year, #set_cached_classified_as, #set_cached_names_for_dependants_and_self, #set_type_if_empty, 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_combination_duplicates, #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_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?, #update_cached_original_combinations, #validate_one_root_per_project, #validate_parent_is_set, #validate_parent_rank_is_higher, #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?

Class Method Details

+ (Object) family_group_base(name_string)



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# File 'app/models/protonym.rb', line 259

def self.family_group_base(name_string)
  name_string.match(/(^.*)(ini|ina|inae|idae|oidae|odd|ad|oidea)$/)
  $1 || name_string
end

+ (Object) family_group_name_at_rank(name_string, rank_string)



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# File 'app/models/protonym.rb', line 264

def self.family_group_name_at_rank(name_string, rank_string)
  if name_string == family_group_base(name_string)
    name_string
  else
    family_group_base(name_string) + Ranks.lookup(:iczn, rank_string).constantize.try(:valid_name_ending).to_s
  end
end

Instance Method Details

- (Array of Strings) all_generic_placements

Returns genera where the species was placed

Returns:

  • (Array of Strings)

    genera where the species was placed



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# File 'app/models/protonym.rb', line 138

def all_generic_placements
  valid_name = get_valid_taxon_name
  return nil unless valid_name.rank_string !=~/Species/
  descendants_and_self = valid_name.descendants + [self] + self.combinations
  relationships        = TaxonNameRelationship.where_object_in_taxon_names(descendants_and_self).with_two_type_bases('TaxonNameRelationship::OriginalCombination::OriginalGenus', 'TaxonNameRelationship::Combination::Genus')
  (relationships.collect {|r| r.subject_taxon_name.name} + [self.ancestor_at_rank('genus').name]).uniq
end

- (Array) ancestors_and_descendants

Returns all descendant and ancestor protonyms for this Protonym

Returns:

  • (Array)

    all descendant and ancestor protonyms for this Protonym



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

def ancestors_and_descendants
  Protonym.ancestors_and_descendants_of(self).not_self(self).to_a
end

- (Object) create_otu (protected)



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# File 'app/models/protonym.rb', line 461

def create_otu
  Otu.create(by: self.creator, project: self.project, taxon_name_id: self.id)
end

- (Object) genus_suggested_gender

TODO: Why protected? What does it do?



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

def genus_suggested_gender
  return nil unless rank_string =~/Genus/
  TAXON_NAME_CLASSIFICATION_GENDER_CLASSES.each do |g|
    g.possible_genus_endings.each do |e|
      return g.name.demodulize.underscore.humanize.downcase if self.name =~ /^[a-zA-Z]*#{e}$/
    end
  end
  nil
end

- (String?) get_author_and_year

Returns a string, without parenthesis, that includes author and year

Returns:

  • (String, nil)

    a string, without parenthesis, that includes author and year



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

def get_author_and_year
  case self.rank_class.try(:nomenclatural_code)
    when :iczn
      ay = iczn_author_and_year
    when :icn
      ay = icn_author_and_year
    when :icnb
      ay = icn_author_and_year
    else
      ay = ([self.author_string] + [self.year_integer]).compact.join(' ')
  end
  ay.blank? ? nil : ay
end

- (Object) get_genus_species(genus_option, self_option)



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# File 'app/models/protonym.rb', line 216

def get_genus_species(genus_option, self_option)
  return nil if rank_class.nil?
  genus = nil
  name1 = nil


  if self.rank_string =~ /Species/
    if genus_option == :original
      genus = self.original_genus
    elsif genus_option == :current
      genus = self.ancestor_at_rank('genus')
    else
      return false
    end
    genus = genus.name unless genus.blank?
    return nil if genus.blank?
  end
  if self_option == :self
    name1 = self.name
  elsif self_option == :alternative
    name1 = name_with_alternative_spelling
  end

  return nil if genus.nil? && name1.nil?
  (genus.to_s + ' ' + name1.to_s).squish
end

- (TypeMaterial, []) get_primary_type

Returns ?!

Returns:



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# File 'app/models/protonym.rb', line 273

def get_primary_type
  return [] unless self.rank_class.parent.to_s =~ /Species/
  s = self.type_materials.syntypes
  p = self.type_materials.primary
  if s.empty? && p.count == 1
    p
  elsif p.empty? && !s.empty?
    s
  else
    []
  end
end

- (Protonym) get_valid_taxon_name

Returns the accepted “valid” version of this name in the present classification

Returns:

  • (Protonym)

    the accepted “valid” version of this name in the present classification



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

def get_valid_taxon_name
  v = first_possible_valid_taxon_name
  if v == self
    self
  elsif v.cached_valid_taxon_name_id == v.id
    v
  elsif !v.cached_valid_taxon_name_id.nil?
    v.valid_taxon_name
  else
    self
  end
end

- (Boolean) has_latinized_exceptions?

Returns whether this name has one of the TaxonNameClassifications that except it from being tested as latinized

Returns:

  • (Boolean)

    whether this name has one of the TaxonNameClassifications that except it from being tested as latinized



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# File 'app/models/protonym.rb', line 332

def has_latinized_exceptions?
  # The second half of this handles classifications in memory, as required to save a non-latinized name (i.e. don't tune it to .any?)
  # !((type == 'Protonym') && (taxon_name_classifications.collect{|t| t.type} & EXCEPTED_FORM_TAXON_NAME_CLASSIFICATIONS).empty?)

  # Is faster than above?
  if type == 'Protonym'
    taxon_name_classifications.each do |tc| # ! find_each
      return true if TaxonName::EXCEPTED_FORM_TAXON_NAME_CLASSIFICATIONS.include?(tc.type)
    end
  end
  false
end

- (Boolean) has_same_primary_type(taxon2)

!! TODO: Should not be possible- fix the incoming data

Returns:

  • (Boolean)

    true if taxon2 has the same primary type



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# File 'app/models/protonym.rb', line 289

def has_same_primary_type(taxon2)
  return true unless rank_class.parent.to_s =~ /Species/

  taxon1_types = get_primary_type.sort_by{|i| i.id}
  taxon2_types = taxon2.get_primary_type.sort_by{|i| i.id}
  return true if taxon1_types.empty? && taxon2_types.empty? # both are empty !! If they are both empty then they don't have the same type, the have no types  !!
  return false if taxon1_types.empty? || taxon2_types.empty? # one is empty

  taxon1_types.map(&:biological_object_id) == taxon2_types.map(&:biological_object_id) # collect{|i| i.biological_object_id}
end

- (Boolean) is_family_rank?

Returns:

  • (Boolean)


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# File 'app/models/protonym.rb', line 357

def is_family_rank?
  FAMILY_RANK_NAMES.include?(rank_string)
end

- (boolean) is_fossil?

Returns:

  • (boolean)


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

def is_fossil?
  taxon_name_classifications.with_type_contains('::Fossil').any?
end

- (Boolean) is_genus_rank?

Returns:

  • (Boolean)


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# File 'app/models/protonym.rb', line 353

def is_genus_rank?
  GENUS_RANK_NAMES.include?(rank_string)
end

- (Boolean) is_latin?

Returns:

  • (Boolean)


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# File 'app/models/protonym.rb', line 345

def is_latin?
  !NOT_LATIN.match(name) || has_latinized_exceptions?
end

- (Boolean) is_species_rank?

Returns:

  • (Boolean)


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# File 'app/models/protonym.rb', line 349

def is_species_rank?
  SPECIES_RANK_NAMES.include?(rank_string)
end

- (Object) list_of_coordinated_names



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# File 'app/models/protonym.rb', line 151

def list_of_coordinated_names
  list = []
  if self.rank_string
    r = self.iczn_set_as_incorrect_original_spelling_of_relationship
    if r.blank?
      search_rank = NomenclaturalRank::Iczn.group_base(self.rank_string)
      if !!search_rank
        if search_rank =~ /Family/
          z = Protonym.family_group_base(self.name)
          search_name = z.nil? ? nil : Protonym::FAMILY_GROUP_ENDINGS.collect{|i| z+i}
        else
          search_name = self.name
        end
      else
        search_name = nil
      end

      unless search_name.nil?
        list = Protonym.ancestors_and_descendants_of(self).not_self(self).
          with_rank_class_including(search_rank).
          # TODO @proceps Rails 5.0 makes this scope fail, for reasons I have not yet investigated. @tuckerjd
          # with_name_in_array(search_name).
          where('name in (?)', search_name).
          as_subject_without_taxon_name_relationship_base('TaxonNameRelationship::Iczn::Invalidating::Synonym')
      else
        list = []
      end
    else
      list = [r.object_taxon_name]
    end
  end
  return list
end

- (Object) lowest_rank_coordinated_taxon



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# File 'app/models/protonym.rb', line 243

def lowest_rank_coordinated_taxon
  list = [self] + list_of_coordinated_names
  if list.count == 1
    self
  else
    parents = list.collect{|i| i.parent.id}
    list.detect{|t| !parents.include?(t.id)}
  end
end

- (Object) name_is_latinized (protected)



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# File 'app/models/protonym.rb', line 453

def name_is_latinized
  errors.add(:name, 'Name must be latinized, no digits or spaces allowed') if !is_latin?
end

- (Object) name_is_valid_format (protected)



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# File 'app/models/protonym.rb', line 457

def name_is_valid_format
  rank_class.validate_name_format(self) if rank_class && rank_class.respond_to?(:validate_name_format) && !has_latinized_exceptions?
end

- (Object) name_with_alternative_spelling



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# File 'app/models/protonym.rb', line 393

def name_with_alternative_spelling
  if rank_class.nil? || nomenclatural_code != :iczn
    # rank_string =~ /::Icn::/ # self.class != Protonym
    return nil
  elsif is_species_rank? # rank_string =~ /Species/
    n = name.squish # remove extra spaces and line brakes
    n = n.split(' ').last
    n = n[0..-4] + 'ae' if n =~ /^[a-z]*iae$/ # -iae > -ae in the end of word
    n = n[0..-6] + 'orum' if n =~ /^[a-z]*iorum$/ # -iorum > -orum
    n = n[0..-6] + 'arum' if n =~ /^[a-z]*iarum$/ # -iarum > -arum
    n = n[0..-3] + 'a' if n =~ /^[a-z]*um$/ # -um > -a
    n = n[0..-3] + 'a' if n =~ /^[a-z]*us$/ # -us > -a
    n = n[0..-3] + 'e' if n =~ /^[a-z]*is$/ # -is > -e
    n = n[0..-3] + 'ra' if n =~ /^[a-z]*er$/ # -er > -ra
    n = n[0..-7] + 'ensis' if n =~ /^[a-z]*iensis$/ # -iensis > -ensis
    n = n[0..-5] + 'ana' if n =~ /^[a-z]*iana$/ # -iana > -ana
    n = n.gsub('ae', 'e').
          gsub('oe', 'e').
          gsub('ai', 'i').
          gsub('ei', 'i').
          gsub('ej', 'i').
          gsub('ii', 'i').
          gsub('ij', 'i').
          gsub('jj', 'i').
          gsub('j', 'i').
          gsub('y', 'i').
          gsub('v', 'u').
          gsub('rh', 'r').
          gsub('th', 't').
          gsub('k', 'c').
          gsub('ch', 'c').
          gsub('tt', 't').
          gsub('bb', 'b').
          gsub('rr', 'r').
          gsub('nn', 'n').
          gsub('mm', 'm').
          gsub('pp', 'p').
          gsub('ss', 's').
          gsub('ff', 'f').
          gsub('ll', 'l').
          gsub('ct', 't').
          gsub('ph', 'f').
          gsub('-', '')
    n = n[0, 3] + n[3..-4].gsub('o', 'i') + n[-3, 3] if n.length > 6 # connecting vowel in the middle of the word (nigrocinctus vs. nigricinctus)
  elsif rank_string =~ /Family/
    n_base = Protonym.family_group_base(self.name)
    if n_base.nil? || n_base == self.name
      n = self.name
    else
      n = n_base + 'idae'
    end
  else
    n = self.name.squish
  end

  return n
end

- (Object) new_parent_taxon_name (protected)

region Validation



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# File 'app/models/protonym.rb', line 467

def new_parent_taxon_name
  r = self.iczn_uncertain_placement_relationship
  unless r.blank?
    if self.parent != r.object_taxon_name
      errors.add(:parent_id, "Taxon has a relationship 'incertae sedis' - delete the relationship before changing the parent")
    end
  end
end

- (Object) original_combination_class_relationships

return [Array of TaxonNameRelationship]

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


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

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

- (Object) original_combination_relationships_and_stubs



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# File 'app/models/protonym.rb', line 310

def original_combination_relationships_and_stubs
  # TODO: figure out where to really put this, likely in one big sort
  display_order = [
    :original_genus, :original_subgenus, :original_species, :original_subspecies, :original_variety, :original_form
  ]

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

  original_combination_class_relationships.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) reduce_list_of_synonyms(list)



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# File 'app/models/protonym.rb', line 381

def reduce_list_of_synonyms(list)
  return [] if list.empty?
  list1 = list.select{|s| s.id == s.lowest_rank_coordinated_taxon.id}
  unless list1.empty?
    date1 = self.nomenclature_date
    unless date1.nil?
      list1.reject!{|s| date1 < (s.year_of_publication ? s.nomenclature_date : Time.utc(1))}
    end
  end
  list1
end

- (Object) set_cached (protected)



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# File 'app/models/protonym.rb', line 499

def set_cached
  self.cached = get_full_name
end

- (Object) set_cached_html (protected)



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# File 'app/models/protonym.rb', line 503

def set_cached_html
  self.cached_html = get_full_name_html
end

- (Object) set_cached_misspelling (protected)



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# File 'app/models/protonym.rb', line 507

def set_cached_misspelling
  self.cached_misspelling = get_cached_misspelling
end

- (Object) set_cached_names (protected)



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# File 'app/models/protonym.rb', line 483

def set_cached_names
  super
  if self.errors.empty? && !self.no_cached

    # set_cached_higher_classification
    set_primary_homonym
    set_primary_homonym_alternative_spelling

    if rank_string =~ /Species/
      set_secondary_homonym
      set_secondary_homonym_alternative_spelling
    end
    set_cached_misspelling
  end
end

- (Object) set_cached_original_combination (protected)



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# File 'app/models/protonym.rb', line 532

def set_cached_original_combination
  self.cached_original_combination = get_original_combination
end

- (Object) set_cached_valid_taxon_name_id (protected)



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# File 'app/models/protonym.rb', line 536

def set_cached_valid_taxon_name_id
  begin
    TaxonName.transaction do
      self.update_column(:cached_valid_taxon_name_id, self.get_valid_taxon_name.id)
      #self.valid_taxon_name = get_valid_taxon_name
    end
  rescue
  end
end

- (Object) set_primary_homonym (protected)

Deprecated def set_cached_higher_classification

self.cached_higher_classification = get_higher_classification

end



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# File 'app/models/protonym.rb', line 516

def set_primary_homonym
  self.cached_primary_homonym = get_genus_species(:original, :self)
end

- (Object) set_primary_homonym_alternative_spelling (protected)



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# File 'app/models/protonym.rb', line 520

def set_primary_homonym_alternative_spelling
  self.cached_primary_homonym_alternative_spelling = get_genus_species(:original, :alternative)
end

- (Object) set_secondary_homonym (protected)



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# File 'app/models/protonym.rb', line 524

def set_secondary_homonym
  self.cached_secondary_homonym = get_genus_species(:current, :self)
end

- (Object) set_secondary_homonym_alternative_spelling (protected)



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# File 'app/models/protonym.rb', line 528

def set_secondary_homonym_alternative_spelling
  self.cached_secondary_homonym_alternative_spelling = get_genus_species(:current, :alternative)
end

- (Object) species_questionable_ending(g, n)

TODO: why protected?



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# File 'app/models/protonym.rb', line 373

def species_questionable_ending(g, n)
  return nil unless rank_string =~ /Species/
  g.questionable_species_endings.each do |e|
    return e if n =~ /^[a-z]*#{e}$/
  end
  nil
end

- (Object) sv_cached_names (protected)

Update cached values when a related taxon changes (e.g. new genus, or new original genus) Combination caching is handled in Combination



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

def sv_cached_names
  # if updated, update also set_cached_names
  # if type == 'Protonym'
  is_cached = true
  is_cached = false if self.cached_author_year != get_author_and_year

  if is_cached # don't run the tests if it's already false # self.class == Protonym
    if self.cached_html != get_full_name_html ||
        self.cached_misspelling != get_cached_misspelling ||
        self.cached_original_combination != get_original_combination ||
        #          self.cached_higher_classification != get_higher_classification ||
        self.cached_primary_homonym != get_genus_species(:original, :self) ||
        self.cached_primary_homonym_alternative_spelling != get_genus_species(:original, :alternative) ||
        self.rank_string =~ /Species/ && (self.cached_secondary_homonym != get_genus_species(:current, :self) || self.cached_secondary_homonym_alternative_spelling != get_genus_species(:current, :alternative))
      is_cached = false
    end
  end

  soft_validations.add(
    :base, 'Cached values should be updated',
    fix: :sv_fix_cached_names, success_message: 'Cached values were updated'
  ) if !is_cached
  # end
end

- (Object) validate_rank_class_class (protected)



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# File 'app/models/protonym.rb', line 476

def validate_rank_class_class
  errors.add(:rank_class, 'Rank not found') unless RANKS.include?(rank_string)
end