Class: Protonym

Inherits:
TaxonName show all
Extended by:
SoftValidationExtensions::Klass
Includes:
Becomes, 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: Becomes, SoftValidationExtensions

Constant Summary collapse

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

Constants included from SoftValidationExtensions::Klass

SoftValidationExtensions::Klass::VALIDATIONS

Constants inherited from TaxonName

TaxonName::ALTERNATE_VALUES_FOR, TaxonName::COMBINATION_ELEMENTS, TaxonName::NOMEN_VALID, 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, #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, #etymology, #feminine_name, #masculine_name, #name, #neuter_name, #no_cached, #parent_id, #project_id, #rank_class, #taxonomy, #type, #verbatim_author, #verbatim_name, #year_of_publication

Class Method Summary collapse

Instance Method Summary collapse

Methods included from Becomes

#becomes_combination, #becomes_test_classifications, #becomes_test_for_original_genus, #becomes_test_for_original_relationships, #becomes_test_for_other_relationships, #becomes_test_for_relationship, #becomes_test_for_similarity, #convertable_to_combination?

Methods included from SoftValidationExtensions::Instance

#sv_author_is_not_required, #sv_extant_children, #sv_family_is_invalid, #sv_family_is_invalid_no_substitute, #sv_fix_add_nominotypical_sub, #sv_fix_author_is_not_required, #sv_fix_coordinated_names_author, #sv_fix_coordinated_names_etymology, #sv_fix_coordinated_names_gender, #sv_fix_coordinated_names_original_form, #sv_fix_coordinated_names_original_genus, #sv_fix_coordinated_names_original_species, #sv_fix_coordinated_names_original_subgenus, #sv_fix_coordinated_names_original_subspecies, #sv_fix_coordinated_names_original_variety, #sv_fix_coordinated_names_page, #sv_fix_coordinated_names_part_of_speech, #sv_fix_coordinated_names_roles, #sv_fix_coordinated_names_source, #sv_fix_coordinated_names_type_genus, #sv_fix_coordinated_names_type_species, #sv_fix_coordinated_names_type_species_type, #sv_fix_coordinated_names_type_specimen, #sv_fix_coordinated_names_year, #sv_fix_missing_otu, #sv_fix_misspelling_author_is_not_required, #sv_fix_misspelling_roles_are_not_required, #sv_fix_misspelling_year_is_not_required, #sv_fix_presence_of_combination, #sv_fix_type_placement1, #sv_fix_year_is_not_required, #sv_homotypic_synonyms, #sv_missing_etymology, #sv_missing_gender, #sv_missing_original_genus, #sv_missing_otu, #sv_missing_part_of_speech, #sv_missing_roles, #sv_missing_substitute_name, #sv_missing_type_genus, #sv_missing_type_species, #sv_misspelling_author_is_not_required, #sv_misspelling_roles_are_not_required, #sv_misspelling_year_is_not_required, #sv_original_combination_relationships, #sv_parent_priority, #sv_person_vs_year_of_publication, #sv_potential_family_homonyms, #sv_potential_genus_homonyms, #sv_potential_species_homonyms, #sv_potential_usage_duplicates, #sv_presence_of_combination, #sv_primary_types, #sv_primary_types_repository, #sv_protonym_to_combination, #sv_single_sub_taxon, #sv_source_not_older_then_description, #sv_species_gender_agreement, #sv_species_gender_agreement_not_required, #sv_type_placement, #sv_type_placement1, #sv_validate_coordinated_names_author, #sv_validate_coordinated_names_etymology, #sv_validate_coordinated_names_gender, #sv_validate_coordinated_names_original_form, #sv_validate_coordinated_names_original_genus, #sv_validate_coordinated_names_original_species, #sv_validate_coordinated_names_original_subgenus, #sv_validate_coordinated_names_original_subspecies, #sv_validate_coordinated_names_original_variety, #sv_validate_coordinated_names_page, #sv_validate_coordinated_names_part_of_speech, #sv_validate_coordinated_names_roles, #sv_validate_coordinated_names_source, #sv_validate_coordinated_names_type_genus, #sv_validate_coordinated_names_type_species, #sv_validate_coordinated_names_type_species_type, #sv_validate_coordinated_names_type_specimen, #sv_validate_coordinated_names_year, #sv_validate_name, #sv_validate_parent_rank, #sv_year_is_not_required

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_rank_class, #classification_invalid_or_unavailable?, #classification_unavailable?, #classification_valid?, #clear_cached, #combination_list_all, #combination_list_self, #combined_statuses, #descendant_protonyms, #descendants_at_rank, #first_possible_invalid_taxan_name_relationship, #first_possible_valid_taxon_name, #first_possible_valid_taxon_name_relationship, foo, #full_name_array, #full_name_hash, #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, #get_full_name_html, #icn_author_and_year, #iczn_author_and_year, #is_ambiguously_invalid?, #is_candidatus?, #is_combination?, #is_fossil?, #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, parent, #parent_is_set?, #part_of_speech_class, #part_of_speech_instance, #part_of_speech_name, #previous_sibling, #rank, #rank_string, #reified_id, #related_taxon_names, #relationship_invalid?, #safe_self_and_ancestors, select_optimized, #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_combination_duplicates, #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_one_root_per_project, #validate_parent_from_the_same_project, #validate_parent_is_set, #validate_source_type, with_taxon_name_relationship, #year_integer

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_syncronize_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_syncronize_matrices, #member_update_matrix_items?

Methods included from Shared::QueryBatchUpdate

#query_update

Methods included from Shared::IsData

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

Methods included from SoftValidation

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

Methods included from Shared::Labels

#labeled?

Methods included from Shared::HasPapertrail

#attribute_updated, #attribute_updater

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

#is_available ⇒ Boolean (readonly)

Returns memoize ‘#is_avaiable?`.

Returns:

  • (Boolean) —

    memoize ‘#is_avaiable?`



20
21
22
 
# File 'app/models/protonym.rb', line 20

def is_available
  @is_available
end

Class Method Details

.batch_move(params) ⇒ Hash

Returns:

  • (Hash) 


905
906
907
908
909
910
911
912
913
914
915
916
917
918
919
920
921
922
923
924
925
926
 
# File 'app/models/protonym.rb', line 905

def self.batch_move(params)
  return false if params[:parent_id].blank?

  a = Queries::TaxonName::Filter.new(params[:taxon_name_query]).all.where(type: 'Protonym')

  return false if a.count == 0

  moved = []
  unmoved = []

  begin
    a.each do |o|
      if o.update(parent_id: params[:parent_id] )
        moved.push o
      else
        unmoved.push o
      end
    end
  end

  return { moved:, unmoved:}
end

.batch_update(params) ⇒ Object 



933
934
935
936
937
938
939
940
941
942
943
 
# File 'app/models/protonym.rb', line 933

def self.batch_update(params)
  request = QueryBatchRequest.new(
    async_cutoff: params[:async_cutoff] || 50,
    klass: 'TaxonName',
    object_filter_params: params[:taxon_name_query],
    object_params: params[:taxon_name],
    preview: params[:preview],
  )

  query_batch_update(request)
end

.family_group_base(name_string) ⇒ Object 



156
157
158
159
 
# File 'app/models/protonym.rb', line 156

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

.family_group_name_at_rank(name_string, rank_string) ⇒ Object 



161
162
163
164
165
166
167
 
# File 'app/models/protonym.rb', line 161

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

.names_at_rank_group_for_collection_objects(rank: nil, collection_object_query: nil) ⇒ Object

!! Ensure collection_object_query is scoped to project

Parameters:

  • rank (defaults to: nil) —

    full String to match rank_class, like ‘%genusgroup%’ or ‘%::Family’ scope to names used in taxon determinations



172
173
174
175
176
177
178
179
180
181
182
183
184
185
 
# File 'app/models/protonym.rb', line 172

def self.names_at_rank_group_for_collection_objects(rank: nil, collection_object_query: nil)

  # Find all the names for the objects in question
  names = ::Queries::TaxonName::Filter.new(collection_object_query:).all

  s = 'WITH q_co_names AS (' + names.distinct.all.to_sql + ') ' +
    ::Protonym
    .joins('JOIN taxon_name_hierarchies tnh on tnh.ancestor_id = taxon_names.id')
    .joins('JOIN q_co_names as q_co1 on q_co1.id = tnh.descendant_id')
    .where('taxon_names.rank_class ilike ?', rank)
    .to_sql

  ::Protonym.from('(' + s + ') as taxon_names').distinct
end

.stub_root(project_id: nil, by: nil) ⇒ Protonym

Returns a name ready to become the root.

Returns:

  • (Protonym) —

    a name ready to become the root



152
153
154
 
# File 'app/models/protonym.rb', line 152

def self.stub_root(project_id: nil, by: nil)
  Protonym.new(name: 'Root', rank_class: 'NomenclaturalRank', parent_id: nil, project_id:, by:)
end

Instance Method Details

#all_generic_placements ⇒ Array of Strings

Returns genera where the species was placed.

Returns:

  • (Array of Strings) —

    genera where the species was placed



216
217
218
219
220
221
222
 
# File 'app/models/protonym.rb', line 216

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').try(:name)]).uniq
end

#ancestors_and_descendants ⇒ Array

Returns all descendant and ancestor protonyms for this Protonym.

Returns:

  • (Array) —

    all descendant and ancestor protonyms for this Protonym



333
334
335
 
# File 'app/models/protonym.rb', line 333

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

#build_original_combination_from_biodiversity(biodiversity_result, relationship_housekeeping = {}) ⇒ Boolean

TODO: likley belongs in lib/vendor/biodiversity.rb

Parameters:

  • biodiversity_result (Biodiversity.result)
  • relationship_housekeeping (Hash) (defaults to: {}) —

    like ‘22, created_by_id: 2`

Returns:

  • (Boolean) —

    Wraps set_original_combination with result from Biodiversity parse !!You must can optionally pre-calculate a disambiguated protonym if you wish to use one.



666
667
668
669
670
671
672
 
# File 'app/models/protonym.rb', line 666

def build_original_combination_from_biodiversity(biodiversity_result, relationship_housekeeping = {})
  br = biodiversity_result
  return false if br.nil?
  c = [br.disambiguated_combination, br.combination].first
  build_original_combinations(c, relationship_housekeeping)
  true
end

#build_original_combinations(combination, relationship_housekeeping) ⇒ Boolean

Parameters:

  • combination (Combination)
  • relationship_housekeeping (Hash) —

    like ‘22, created_by_id: 2` builds, but does not save, original relationships for all corresponding protonyms in a combination !! Replaces existing relationship without checking identify if they are there!

Returns:

  • (Boolean) 


679
680
681
682
683
684
685
686
687
688
689
690
691
692
 
# File 'app/models/protonym.rb', line 679

def build_original_combinations(combination, relationship_housekeeping)
  return false if combination.nil?
  combination.protonyms_by_rank.each do |rank, p|
    send("original_#{rank}=", p)
  end

  if !relationship_housekeeping.empty?
    combination.protonyms_by_rank.each do |rank, p|
      r = send("original_#{rank}_relationship")
      r.write_attributes(relationship_housekeeping)
    end
  end
  true
end

#check_new_parent_class ⇒ Object (protected) 



947
948
949
950
951
952
953
954
955
 
# File 'app/models/protonym.rb', line 947

def check_new_parent_class
  if is_protonym? && parent_id != parent_id_was && !parent_id_was.nil? && nomenclatural_code == :iczn
    if old_parent = TaxonName.find_by(id: parent_id_was)
      if (rank_name == 'subgenus' || rank_name == 'subspecies') && old_parent.name == name
        errors.add(:parent_id, "The nominotypical #{rank_name} #{name} can not be moved out of the nominal #{old_parent.rank_name}")
      end
    end
  end
end

#create_otu ⇒ Object (protected) 



976
977
978
 
# File 'app/models/protonym.rb', line 976

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

#genus_suggested_gender ⇒ Object 



642
643
644
645
646
647
648
649
650
 
# File 'app/models/protonym.rb', line 642

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

#get_genus_species(genus_option, self_option) ⇒ nil, ...

This method is currently only used for setting cached_primary_homonym

Returns:

  • (nil, false, String) —

    !! Why both?



291
292
293
294
295
296
297
298
299
300
301
302
303
304
305
306
307
308
309
310
311
312
313
314
315
316
317
318
 
# File 'app/models/protonym.rb', line 291

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

  if is_species_rank? # self.rank_string =~ /Species/
    if genus_option == :original
      genus = original_genus
    elsif genus_option == :current
      genus = ancestor_at_rank('genus')
    else
      return false
    end

    genus = genus.name if genus.present?
    return nil if genus.blank?
  end

  if self_option == :self
    name1 = name
  elsif self_option == :alternative
    name1 = name_with_alternative_spelling
  end

  return nil if genus.nil? && name1.nil? # <- hitting this because Genus is never set
  [genus, name1].compact.join(' ')
  # (genus.to_s + ' ' + name1.to_s).squish
end

#get_original_combination ⇒ Object 



694
695
696
697
698
699
700
701
702
703
704
705
706
707
708
709
710
 
# File 'app/models/protonym.rb', line 694

def get_original_combination
  return verbatim_name if !GENUS_AND_SPECIES_RANK_NAMES.include?(rank_string) && !verbatim_name.nil?
  e = original_combination_elements
  return nil if e.none?

  # Weird, why?
  # DD: in ICVCN the species name is "Potato spindle tuber viroid", the genus name is only used for classification...
  #
  # @proceps: then we should exclude or alter elements before we get to this point, not here, so that the renderer still works, exceptions at this point are bad
  # and this didn't do what you think it did, it's was returning an Array of two things
  return e[:species][1] if rank_class.to_s =~ /Icvcn/

  p = TaxonName::COMBINATION_ELEMENTS.inject([]){|ary, r| ary.push(e[r]) }

  s = p.flatten.compact.join(' ')
  (s.presence)
end

#get_original_combination_html ⇒ Object 



795
796
797
798
799
800
801
802
803
804
805
806
807
808
 
# File 'app/models/protonym.rb', line 795

def get_original_combination_html
  return  "\"<i>Candidatus</i> #{get_original_combination}\"" if is_candidatus?
  v = get_original_combination
  if v.present? && is_hybrid?
    w = v.split(' ')
    w[-1] = ('×' + w[-1]).gsub('×(', '(×').gsub(') [sic]', ' [sic])').gsub(') (sic)', ' (sic))')
    v = w.join(' ')
  end
  v = v.gsub(') [sic]', ' [sic])').gsub(') (sic)', ' (sic))') if v.present?

  v = Utilities::Italicize.taxon_name(v) if is_genus_or_species_rank?
  v = '† ' + v if v.present? && is_fossil?
  v
end

#get_primary_type ⇒ TypeMaterial, []

Returns ?!.

Returns:



338
339
340
341
342
343
344
345
346
347
348
349
 
# File 'app/models/protonym.rb', line 338

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

#get_valid_taxon_name ⇒ Protonym

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



275
276
277
278
279
280
281
282
283
284
285
286
 
# File 'app/models/protonym.rb', line 275

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

#has_alternate_original? ⇒ Boolean

Same as is_original_name?!

Returns:

  • (Boolean) 


498
499
500
 
# File 'app/models/protonym.rb', line 498

def has_alternate_original?
  cached_original_combination && (cached != cached_original_combination) ? true : false
end

#has_latinized_exceptions? ⇒ Boolean

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



468
469
470
471
472
473
474
475
476
477
478
479
480
 
# File 'app/models/protonym.rb', line 468

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?
  #    return true if rank_string =~ /Icnp/ && (name.start_with?('Candidatus ') || name.start_with?('Ca. '))

  return true if is_family_rank? && !family_group_name_form_relationship.nil?
  return true if is_family_rank? && !(taxon_name_relationships.collect{|i| i.type} & ::TAXON_NAME_RELATIONSHIP_NAMES_SYNONYM).empty?
  return true unless (taxon_name_classifications.collect{|i| i.type} & ::EXCEPTED_FORM_TAXON_NAME_CLASSIFICATIONS).empty?
  return true unless (taxon_name_relationships.collect{|i| i.type} & ::TAXON_NAME_RELATIONSHIP_NAMES_MISSPELLING).empty?
  false
end

#has_misspelling_or_misapplication_relationship? ⇒ Boolean

Returns:

  • (Boolean) 


493
494
495
 
# File 'app/models/protonym.rb', line 493

def has_misspelling_or_misapplication_relationship?
  taxon_name_relationships.with_type_array(TAXON_NAME_RELATIONSHIP_NAMES_MISSPELLING_AND_MISAPPLICATION).any?
end

#has_misspelling_relationship? ⇒ Boolean

Returns whether this name has one of the TaxonNameRelationships which justify wrong form of the name.

Returns:

  • (Boolean) —

    whether this name has one of the TaxonNameRelationships which justify wrong form of the name



488
489
490
 
# File 'app/models/protonym.rb', line 488

def has_misspelling_relationship?
  taxon_name_relationships.with_type_array(TAXON_NAME_RELATIONSHIP_NAMES_MISSPELLING).any?
end

#has_same_primary_type(taxon2) ⇒ Boolean

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

Returns:

  • (Boolean) —

    true if taxon2 has the same primary type



426
427
428
429
430
431
432
433
434
435
 
# File 'app/models/protonym.rb', line 426

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

#is_available?(refresh = false) ⇒ Boolean

Returns:

  • (Boolean) 


264
265
266
267
268
269
270
271
 
# File 'app/models/protonym.rb', line 264

def is_available?(refresh = false)
  if !refresh
    @is_available ||= !has_misspelling_or_misapplication_relationship? && !classification_unavailable?
  else
    @is_available = !has_misspelling_or_misapplication_relationship? && !classification_unavailable?
  end
  @is_available
end

#is_family_or_genus_or_species_rank? ⇒ Boolean

Returns:

  • (Boolean) 


514
515
516
 
# File 'app/models/protonym.rb', line 514

def is_family_or_genus_or_species_rank?
  FAMILY_AND_GENUS_AND_SPECIES_RANK_NAMES.include?(rank_string)
end

#is_family_rank? ⇒ Boolean

Returns:

  • (Boolean) 


518
519
520
 
# File 'app/models/protonym.rb', line 518

def is_family_rank?
  FAMILY_RANK_NAMES.include?(rank_string)
end

#is_genus_or_species_rank? ⇒ Boolean

Returns:

  • (Boolean) 


510
511
512
 
# File 'app/models/protonym.rb', line 510

def is_genus_or_species_rank?
  GENUS_AND_SPECIES_RANK_NAMES.include?(rank_string)
end

#is_genus_rank? ⇒ Boolean

Returns:

  • (Boolean) 


506
507
508
 
# File 'app/models/protonym.rb', line 506

def is_genus_rank?
  GENUS_RANK_NAMES.include?(rank_string)
end

#is_higher_rank? ⇒ Boolean

Returns:

  • (Boolean) 


522
523
524
 
# File 'app/models/protonym.rb', line 522

def is_higher_rank?
  HIGHER_RANK_NAMES.include?(rank_string)
end

#is_latin? ⇒ Boolean

Returns:

  • (Boolean) 


482
483
484
 
# File 'app/models/protonym.rb', line 482

def is_latin?
  !NOT_LATIN.match(name) || has_latinized_exceptions? || rank_string =~ /Icvcn::Species/
end

#is_original_name? ⇒ Boolean

Returns Boolean.

Returns:

  • (Boolean) —

    Boolean



527
528
529
 
# File 'app/models/protonym.rb', line 527

def is_original_name?
  cached_author_year =~ /\(/ ? false : true
end

#is_species_rank? ⇒ Boolean

Returns:

  • (Boolean) 


502
503
504
 
# File 'app/models/protonym.rb', line 502

def is_species_rank?
  SPECIES_RANK_NAMES.include?(rank_string)
end

#list_of_coordinated_names ⇒ Object 



224
225
226
227
228
229
230
231
232
233
234
235
236
237
238
239
240
241
242
243
244
245
246
247
248
249
250
251
252
253
254
255
256
257
258
259
260
261
262
 
# File 'app/models/protonym.rb', line 224

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(rank_string)
      if !!search_rank
        if search_rank =~ /Family/
          if self.cached_is_valid
            z = Protonym.family_group_base(self.name)
            search_name = z.nil? ? nil : Protonym::FAMILY_GROUP_ENDINGS.collect{|i| z+i}
          else
            search_name = nil
          end
        else
          search_name = self.name
        end
      else
        search_name = nil
      end

      #  r = TaxonNameRelationship.where_subject_is_taxon_name(self).with_type_array(TAXON_NAME_RELATIONSHIP_NAMES_MISSPELLING)
      #  if !search_name.nil? && r.empty?
      if !search_name.nil? && is_available?
        list = Protonym
          .ancestors_and_descendants_of(self)
          .with_rank_class_including(search_rank)
          .where(name: search_name)
          .not_self(self)
          .that_is_valid
      else
        list = []
      end
    else
      list = [r.object_taxon_name]
    end
  end
  return list
end

#lowest_rank_coordinated_taxon ⇒ Object

TODO, make back half of this raw SQL



321
322
323
324
325
326
327
328
329
 
# File 'app/models/protonym.rb', line 321

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

#name_is_latinized ⇒ Object (protected) 



957
958
959
 
# File 'app/models/protonym.rb', line 957

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

#name_is_valid_format ⇒ Object (protected) 



972
973
974
 
# File 'app/models/protonym.rb', line 972

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

#name_with_alternative_spelling ⇒ Object 



544
545
546
547
548
549
550
551
552
553
554
555
556
557
558
559
560
561
562
563
564
565
566
567
568
569
570
571
572
573
574
575
576
577
578
579
580
581
582
583
584
585
586
587
588
589
590
591
592
593
594
595
596
597
598
599
600
 
# File 'app/models/protonym.rb', line 544

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$/ # -iana > -ana
    n = n.gsub('ae', 'e') if n =~ /^[a-z]*ae[a-z]+$/ # -ae-
    n = n.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

#new_parent_taxon_name ⇒ Object (protected) 



980
981
982
983
984
985
986
987
 
# File 'app/models/protonym.rb', line 980

def new_parent_taxon_name
  r = self.iczn_uncertain_placement_relationship
  if r.present?
    if self.parent != r.object_taxon_name
      errors.add(:parent_id, "Taxon has an 'Incertae sedis' relationship, which prevent the parent modifications, change the relationship to 'Source classified as' before updating the parent")
    end
  end
end

#nominotypical_sub_of?(protonym) ⇒ boolean

Returns:

  • (boolean) 


900
901
902
 
# File 'app/models/protonym.rb', line 900

def nominotypical_sub_of?(protonym)
  is_genus_or_species_rank? && parent == protonym && parent.name == protonym.name
end

#number_of_taxa_by_year ⇒ Object

temporary method to get a number of taxa described by year



395
396
397
398
399
400
401
402
403
404
405
406
407
408
409
410
411
412
413
414
415
416
417
418
419
420
421
 
# File 'app/models/protonym.rb', line 395

def number_of_taxa_by_year
  file_name = '/tmp/taxa_by_year' + '_' + Time.now.to_i.to_s + '.csv'
  a = {}
  descendants.find_each do |z|
    year = z.year_integer
    year = 0 if year.nil?
    a[year] = {valid: 0, synonyms: 0} unless a[year]
    if z.rank_string == 'NomenclaturalRank::Iczn::SpeciesGroup::Species'
      if z.cached_is_valid
        a[year][:valid] = a[year][:valid] += 1
      elsif TaxonNameRelationship.where_subject_is_taxon_name(z.id).with_type_array(::TAXON_NAME_RELATIONSHIP_NAMES_SYNONYM).any?
        a[year][:synonyms] = a[year][:synonyms] += 1
      end
    end
  end
  for i in 1758..Time.now.year do
    a[i] = {valid: 0, synonyms: 0} unless a[i]
  end
  b = a.sort.to_h
  CSV.open(file_name, 'w') do |csv|
    #CSV.generate do |csv|
    csv << ['year', 'valid species', 'synonyms']
    b.keys.each do |i|
      csv << [i, b[i][:valid], b[i][:synonyms]]
    end
  end
end

#original_combination_class_relationships ⇒ Object

return [Array]

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



439
440
441
442
443
444
445
 
# File 'app/models/protonym.rb', line 439

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

#original_combination_elements ⇒ Hash 

genus: ["", 'Aus' ],
...
form: ['frm', 'aus']

Returns:

  • (Hash) 


720
721
722
723
724
725
726
727
728
729
730
731
732
733
734
735
736
737
738
739
740
741
742
743
744
745
746
747
748
749
750
751
752
753
754
755
756
757
758
759
760
761
762
763
764
765
766
767
768
769
770
771
 
# File 'app/models/protonym.rb', line 720

def original_combination_elements
  elements = { }
  return elements if rank.blank?

  this_rank = rank.to_sym

  # Why this?
  #   We need to apply gender to "internal" names for original combinations, everything
  #   but the last name
  # DD: if we have subspecies, the species name should be used not in the original form,
  # but the form correlated with the present genus gender
  # TODO: get SQL based ordering for original_combination_relationships, hard coded

  # order the relationships
  r = original_combination_relationships.reload.sort{|a,b| ORIGINAL_COMBINATION_RANKS.index(a.type) <=> ORIGINAL_COMBINATION_RANKS.index(b.type) }

  # get gender from first
  gender = original_genus&.gender_name # r.first.subject_taxon_name.gender_name

  # Apply gender to everything but the last
  total = r.count - 1
  r.each_with_index do |j, i|
    if j.type =~ /enus/ || i == total
      g = nil
    else
      g = gender
    end
    elements.merge! j.combination_name(g) # this is like '{genus: [nil, 'Aus']}
  end

  # what is point of this? Do we get around this check by requiring self relationships? (species aus has species relationship to self)
  # DD: we do not require it, it is optional
  if !r.empty? && r.collect{|i| i.subject_taxon_name}.last.lowest_rank_coordinated_taxon.id != lowest_rank_coordinated_taxon.id
    if elements[this_rank].nil?
      elements[this_rank] = [nil, original_name]
    end
  end

  if elements.any?
    if !elements[:genus] && !not_binominal?
      if original_genus
        elements[:genus] = [nil, "[#{original_genus&.name}]"]
      else
        elements[:genus] = [nil, '[GENUS NOT SPECIFIED]']
      end
    end
    # If there is no :species, but some species group, add element
    elements[:species] = [nil, '[SPECIES NOT SPECIFIED]'] if !elements[:species] && ( [:subspecies, :variety, :form] & elements.keys ).size > 0
  end

  elements
end

#original_combination_infraspecific_element(elements = nil, remove_sic = false) ⇒ [rank_name, name]?

Returns Used in ColDP export.

Returns:

  • ([rank_name, name], nil) —

    Used in ColDP export



775
776
777
778
779
780
781
782
783
784
785
 
# File 'app/models/protonym.rb', line 775

def original_combination_infraspecific_element(elements = nil, remove_sic = false)
  elements ||= original_combination_elements

  elements = elements.each { |r, e| e.delete('[sic]') } if remove_sic

  # TODO: consider plants/other codes?
  [:form, :variety, :subspecies].each do |r|
    return [r.to_s, elements[r].last] if elements[r]
  end
  nil
end

#original_combination_relationships_and_stubs ⇒ Array

Returns A relationships for each possible original combination relationship.

Returns:

  • (Array) —

    A relationships for each possible original combination relationship



449
450
451
452
453
454
455
456
457
458
459
460
461
462
463
464
 
# File 'app/models/protonym.rb', line 449

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_subvariety, :original_form, :original_subform ]

  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

#original_name ⇒ String?

Returns a monominal, as originally rendered, with parens if subgenus.

Returns:

  • (String, nil) —

    a monominal, as originally rendered, with parens if subgenus



789
790
791
792
793
 
# File 'app/models/protonym.rb', line 789

def original_name
  n = verbatim_name.nil? ? name_with_misspelling(nil) : verbatim_name
  n = "(#{n})" if n && rank_name == 'subgenus'
  n
end

#predict_three_forms ⇒ Object 



602
603
604
605
606
607
608
609
610
611
612
613
614
615
616
617
618
619
620
621
622
623
624
625
626
627
628
629
630
631
632
633
634
635
636
637
638
639
640
 
# File 'app/models/protonym.rb', line 602

def predict_three_forms
  exception = LATIN_ADJECTIVES[name]

  return exception unless exception.nil?
  m_name, f_name, n_name = nil, nil, nil
  case name
  when /(color|coloris)$/
    m_name, f_name, n_name = name, name, name
  when /is$/
    m_name, f_name, n_name = name, name, name[0..-3] + 'e'
  when /e$/
    m_name, f_name, n_name = name[0..-2] + 'is', name[0..-2] + 'is', name
  when /us$/
    m_name, f_name, n_name = name, name[0..-3] + 'a', name[0..-3] + 'um'
  when /(niger|integer)$/
    m_name, f_name, n_name = name, name[0..-3] + 'ra', name[0..-3] + 'rum'
  when /(fer|ger)$/
    m_name, f_name, n_name = name, name + 'a', name + 'um'
  when /er$/
    m_name, f_name, n_name = name, name[0..-3] + 'ra', name[0..-3] + 'rum'
  when /(ferum|gerum)$/
    m_name, f_name, n_name = name[0..-3], name[0..-3] + 'a', name
  when /(gera|fera)$/
    m_name, f_name, n_name = name[0..-2], name, name[0..-2] + 'um'
  when /(brum|frum|grum)$/
    m_name, f_name, n_name = name[0..-4] + 'er', name[0..-3] + 'a', name
  when /(bra|gra|fra)$/
    m_name, f_name, n_name = name[0..-3] + 'er', name, name[0..-2] + 'um'
  when /(um)$/
    m_name, f_name, n_name = name[0..-3] + 'us', name[0..-3] + 'a', name
  when /a$/
    m_name, f_name, n_name = name[0..-2] + 'us', name, name[0..-2] + 'um'
  when /(nor|ior|jor)$/
    m_name, f_name, n_name = name, name, name[0..-3] + 'us'
  else
    m_name, f_name, n_name = name, name, name
  end
  {masculine_name: m_name, feminine_name: f_name, neuter_name: n_name}
end

#predicted_child_rank(child_string) ⇒ Object

taxon_name.predicted_children_rank(‘Cicadellidae’) >> NomenclaturalRank::Iczn::FamilyGroup::Family



352
353
354
355
356
357
358
359
360
361
362
363
364
365
366
367
368
369
370
371
372
373
374
375
376
377
378
379
380
381
382
383
384
385
386
387
388
389
390
391
392
 
# File 'app/models/protonym.rb', line 352

def predicted_child_rank(child_string)
  return nil if child_string.blank?
  parent_rank = rank_class.to_s
  parent_rank_name = rank_name
  ncode = nomenclatural_code

  return nil if ncode.nil? # Happens with some names like "Root"

  if child_string == child_string.downcase
    if !is_species_rank?
      r = Ranks.lookup(ncode, 'species')
    elsif parent_rank_name == 'species'
      r = Ranks.lookup(ncode, 'subspecies')
    elsif parent_rank_name == 'subspecies'
      r = Ranks.lookup(ncode, 'variety')
    elsif parent_rank_name == 'variety'
      r = Ranks.lookup(ncode, 'form')
    elsif parent_rank_name == 'form'
      r = Ranks.lookup(ncode, 'subform')
    else
      return nil
    end
  elsif child_string == child_string.capitalize
    if rank_name == 'genus'
      r = Ranks.lookup(ncode, 'subgenus')
    else
      Ranks.lookup(ncode, 'family').constantize.valid_parents.each do |r1|
        r2 = r1.constantize
        if r2.valid_name_ending.present? && child_string.end_with?(r2.valid_name_ending) && r2.typical_use && RANKS.index(r1) > RANKS.index(parent_rank)
          r = r1
          break
        end
      end
      r = Ranks.lookup(ncode, 'genus') if r.nil?
    end
  else
    return nil
  end
  return nil if r.nil?
  r.constantize
end

#reduce_list_of_synonyms(list) ⇒ Object 



531
532
533
534
535
536
537
538
539
540
541
542
 
# File 'app/models/protonym.rb', line 531

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

#set_cached ⇒ Object (protected) 



1058
1059
1060
1061
1062
1063
1064
1065
1066
1067
1068
1069
1070
1071
 
# File 'app/models/protonym.rb', line 1058

def set_cached
  old_cached_html = cached_html.to_s
  old_cached_author_year = cached_author_year.to_s

  super
  set_cached_original_combination
  set_cached_original_combination_html
  set_cached_homonymy
  set_cached_species_homonym if is_species_rank?
  set_cached_misspelling
  tn = TaxonName.find(id)
  set_cached_names_for_descendants if tn.cached_html != old_cached_html
  set_cached_names_for_dependants if tn.cached_html.to_s != old_cached_html || tn.cached_author_year.to_s != old_cached_author_year
end

#set_cached_homonymy ⇒ Object (protected) 



1073
1074
1075
1076
1077
1078
 
# File 'app/models/protonym.rb', line 1073

def set_cached_homonymy
  update_columns(
    cached_primary_homonym: get_genus_species(:original, :self),
    cached_primary_homonym_alternative_spelling: get_genus_species(:original, :alternative)
  )
end

#set_cached_misspelling ⇒ Object (protected)

all three in one update here



1081
1082
1083
 
# File 'app/models/protonym.rb', line 1081

def set_cached_misspelling
  update_column(:cached_misspelling, get_cached_misspelling)
end

#set_cached_names_for_dependants ⇒ Object 



852
853
854
855
856
857
858
859
860
861
862
863
864
865
866
867
868
869
870
871
872
873
874
875
876
877
878
879
880
881
882
883
884
885
886
887
888
889
890
891
892
893
894
895
896
897
 
# File 'app/models/protonym.rb', line 852

def set_cached_names_for_dependants
  related_through_original_combination_relationships = []
  combination_relationships = []

  TaxonName.transaction_with_retry do
    if is_genus_or_species_rank?
      related_through_original_combination_relationships = TaxonNameRelationship.where_subject_is_taxon_name(self).with_type_contains('OriginalCombination')
      combination_relationships = TaxonNameRelationship.where_subject_is_taxon_name(self).with_type_contains('::Combination')
    end

    classified_as_relationships = TaxonNameRelationship.where_object_is_taxon_name(self).with_type_contains('SourceClassifiedAs')

    related_through_original_combination_relationships.collect{|i| i.object_taxon_name}.uniq.each do |i|
      i.update_cached_original_combinations
    end

    # Update values in Combinations
    combination_relationships.collect{|i| i.object_taxon_name}.uniq.each do |j|
      n = j.get_full_name
      j.update_columns(
        cached: n,
        cached_html: j.get_full_name_html(n),
        cached_author_year: j.get_author_and_year,
        cached_nomenclature_date: j.nomenclature_date)
    end

    classified_as_relationships.collect{|i| i.subject_taxon_name}.uniq.each do |i|
      i.update_column(:cached_classified_as, i.get_cached_classified_as)
    end

    classified_as_relationships.collect{|i| i.object_taxon_name}.uniq.each do |i|
      n = i.get_full_name
      i.update_columns(
        cached: n,
        cached_html: i.get_full_name_html(n),
        cached_author_year: i.get_author_and_year,
        cached_nomenclature_date: i.nomenclature_date)
    end

    misspelling_relationships = TaxonNameRelationship.where_object_is_taxon_name(self).with_type_array(TAXON_NAME_RELATIONSHIP_NAMES_MISSPELLING_AND_MISAPPLICATION)
    misspelling_relationships.collect{|i| i.subject_taxon_name}.uniq.each do |i|
      i.update_columns(cached_author_year: i.get_author_and_year,
                       cached_nomenclature_date: i.nomenclature_date)
    end
  end
end

#set_cached_names_for_descendants ⇒ Object 



825
826
827
828
829
830
831
832
833
834
835
836
837
838
839
840
841
842
843
844
845
846
847
848
849
850
 
# File 'app/models/protonym.rb', line 825

def set_cached_names_for_descendants
  dependants = []

  TaxonName.transaction_with_retry do
    if is_genus_or_species_rank?
      dependants = Protonym.unscoped.descendants_of(self).to_a
    end

    dependants.each do |i|
      n = i.get_full_name
      columns_to_update = {
        cached: n,
        cached_html: i.get_full_name_html(n),
        cached_author_year: i.get_author_and_year,
        cached_nomenclature_date: i.nomenclature_date
      }

      if i.is_species_rank?
        columns_to_update[:cached_secondary_homonym] = i.get_genus_species(:current, :self)
        columns_to_update[:cached_secondary_homonym_alternative_spelling] = i.get_genus_species(:current, :alternative)
      end

      i.update_columns(columns_to_update)
    end
  end
end

#set_cached_original_combination ⇒ Object (protected) 



1085
1086
1087
 
# File 'app/models/protonym.rb', line 1085

def set_cached_original_combination
  update_column(:cached_original_combination, get_original_combination)
end

#set_cached_original_combination_html ⇒ Object (protected) 



1089
1090
1091
 
# File 'app/models/protonym.rb', line 1089

def set_cached_original_combination_html
  update_column(:cached_original_combination_html, get_original_combination_html)
end

#set_cached_species_homonym ⇒ Object 



818
819
820
821
822
823
 
# File 'app/models/protonym.rb', line 818

def set_cached_species_homonym
  update_columns(
    cached_secondary_homonym: get_genus_species(:current, :self),
    cached_secondary_homonym_alternative_spelling: get_genus_species(:current, :alternative)
  )
end

#species_questionable_ending(taxon_name_classification_class, tested_name) ⇒ Object 



652
653
654
655
656
657
658
 
# File 'app/models/protonym.rb', line 652

def species_questionable_ending(taxon_name_classification_class, tested_name)
  return nil unless is_species_rank?
  taxon_name_classification_class.questionable_species_endings.each do |e|
    return e if tested_name =~ /^[a-z]*#{e}$/
  end
  nil
end

#sv_cached_names ⇒ Object (protected)

!! This has to go. A single method is meaningless to the user and to developers. Which cached is the problem it the problem? We simply can’t tell what went wrong in this case.

This is a very expensive soft validation, it should be fragemented into individual parts likely. It should also not be necessary by default our code should be good enough to handle these issues in the long run. DD: rules for cached tend to evolve, what was good in the past, may not be true today MJY: If the meaning of cached changes then it should be removed, not changed.



1030
1031
1032
1033
1034
1035
1036
1037
1038
1039
1040
1041
1042
1043
1044
1045
1046
1047
1048
1049
1050
1051
1052
1053
1054
1055
1056
 
# File 'app/models/protonym.rb', line 1030

def sv_cached_names # this cannot be moved to soft_validation_extensions
  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_valid_taxon_name_id != get_valid_taxon_name.id ||
    cached_is_valid != !unavailable_or_invalid? || # Do not change this, we want the calculated value.
    cached_html != get_full_name_html ||
    cached_misspelling != get_cached_misspelling ||
    cached_original_combination != get_original_combination ||
    cached_original_combination_html != get_original_combination_html ||
    cached_primary_homonym != get_genus_species(:original, :self) ||
    cached_nomenclature_date != nomenclature_date ||
    cached_primary_homonym_alternative_spelling != get_genus_species(:original, :alternative) ||
    rank_string =~ /Species/ &&
    (cached_secondary_homonym != get_genus_species(:current, :self) ||
     cached_secondary_homonym_alternative_spelling != get_genus_species(:current, :alternative)))
  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

#synonymize_with(protonym) ⇒ Object

A convenience method to make this name a low-level synonym of another. Presently limited in scope to names that share rank (not rank group)



190
191
192
193
194
195
196
197
198
199
200
201
202
203
204
205
206
207
208
209
210
211
 
# File 'app/models/protonym.rb', line 190

def synonymize_with(protonym)
  return false if protonym.nil?
  return false if protonym.rank_class.to_s != rank_class.to_s

  begin
    case nomenclatural_code
    when  :iczn
      TaxonNameRelationship::Iczn::Invalidating::Synonym.create!(subject_taxon_name: self, object_taxon_name: protonym)
    when :icn
      TaxonNameRelationship::Icn::Unaccepting::Synonym.create!(subject_taxon_name: self, object_taxon_name: protonym)
    when :icnp
      TaxonNameRelationship::Icnp::Unaccepting::Synonym.create!(subject_taxon_name: self, object_taxon_name: protonym)
    when :icvnc
      TaxonNameRelationship::Icnp::Unaccepting::SupressedSynony.create!(subject_taxon_name: self, object_taxon_name: protonym)
    else
      return false
    end
  rescue ActiveRecord::RecordInvalid
    return false
  end

end

#update_cached_original_combinations ⇒ Object 



810
811
812
813
814
815
816
 
# File 'app/models/protonym.rb', line 810

def update_cached_original_combinations
  update_columns(
    cached_original_combination: get_original_combination,
    cached_original_combination_html: get_original_combination_html,
    cached_primary_homonym: get_genus_species(:original, :self),
    cached_primary_homonym_alternative_spelling: get_genus_species(:original, :alternative))
end

#validate_child_rank_is_equal_or_lower ⇒ Object (protected) 



993
994
995
996
997
998
999
1000
1001
1002
1003
1004
1005
1006
 
# File 'app/models/protonym.rb', line 993

def validate_child_rank_is_equal_or_lower
  if parent && rank_class.present? && rank_string != 'NomenclaturalRank'
    if rank_class_changed?
      a = children.where(type: 'Protonym').pluck(:rank_class)
      v = RANKS.index(rank_string)
      a.each do |b|
        if v >= RANKS.index(b)
          errors.add(:rank_class, "The rank of this taxon (#{rank_name}) should be higher than the ranks of children")
          break
        end
      end
    end
  end
end

#validate_parent_rank_is_higher ⇒ Object (protected) 



1008
1009
1010
1011
1012
1013
1014
 
# File 'app/models/protonym.rb', line 1008

def validate_parent_rank_is_higher
  if parent && rank_class.present? && rank_string != 'NomenclaturalRank'
    if RANKS.index(rank_string).to_i <= RANKS.index(parent.rank_string).to_i
      errors.add(:parent_id, "The parent rank (#{parent.rank_class.rank_name}) is not higher than the rank (#{rank_name}) of this taxon")
    end
  end
end

#validate_rank_class_class ⇒ Object (protected) 



989
990
991
 
# File 'app/models/protonym.rb', line 989

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

#validate_same_nomenclatural_code ⇒ Object (protected) 



1016
1017
1018
1019
1020
 
# File 'app/models/protonym.rb', line 1016

def validate_same_nomenclatural_code
  if parent&.nomenclatural_code && nomenclatural_code != parent.nomenclatural_code
    errors.add(:rank_class, "The parent nomenclatural code (#{parent.nomenclatural_code.to_s.upcase}) is not matching to the nomenclatural code (#{nomenclatural_code.to_s.upcase}) of this taxon")
  end
end

#verbatim_author_with_closed_parens_when_present ⇒ Object (protected) 



965
966
967
968
969
970
 
# File 'app/models/protonym.rb', line 965

def verbatim_author_with_closed_parens_when_present
  if verbatim_author.present? and nomenclatural_code != :icn  # workaround until basyonim field exists
    # Regex matches two possible, both params, or no params at start/end
    errors.add(:verbatim_author, 'Verbatim author is missing a parenthesis') unless verbatim_author =~ /\A\([^()]+\)\z|\A[^()]+\z/
  end
end

#verbatim_author_without_digits ⇒ Object (protected) 



961
962
963
 
# File 'app/models/protonym.rb', line 961

def verbatim_author_without_digits
  errors.add(:verbatim_author, 'Verbatim author may not contain digits, a year may be present') if verbatim_author =~ /\d/
end