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_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, #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_misspelling_author_is_not_required, #sv_fix_misspelling_otu, #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_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_author, #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_valid?, #clear_cached, #combination_list_all, #combination_list_self, #combined_statuses, #descendant_protonyms, #descendants_at_rank, #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_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, #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_year, #set_cached_classified_as, #set_cached_is_valid, #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_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_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::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::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

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_availableBoolean (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

.family_group_base(name_string) ⇒ Object



154
155
156
157
# File 'app/models/protonym.rb', line 154

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



159
160
161
162
163
164
165
# File 'app/models/protonym.rb', line 159

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 = 'speciesgroup') ⇒ Object

Parameters:

  • rank ('speciesgroup' or 'genusgroup' or 'family') (defaults to: 'speciesgroup')

    scope to names used in taxon determinations



169
170
171
172
173
174
175
176
177
178
179
180
181
182
183
184
185
186
187
# File 'app/models/protonym.rb', line 169

def self.names_at_rank_group_for_collection_objects(rank = 'speciesgroup')
  h = ::TaxonNameHierarchy.arel_table
  t = ::TaxonName.arel_table
  t1 = ::TaxonName.arel_table.alias('tndet')
  d = ::TaxonDetermination.arel_table
  o = ::Otu.arel_table

  q = t.join(h, Arel::Nodes::InnerJoin).on(
    t[:id].eq(h[:ancestor_id])
  ).join(t1, Arel::Nodes::InnerJoin).on(
    h[:descendant_id].eq(t1[:id])
  ).join(o, Arel::Nodes::InnerJoin).on(
    t1[:id].eq(o[:id])
  ).join(d, Arel::Nodes::InnerJoin).on(
    o[:id].eq(d[:otu_id])
  )

  joins(q.join_sources).where(t[:rank_class].matches('%' + rank + '%').to_sql).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



150
151
152
# File 'app/models/protonym.rb', line 150

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

Instance Method Details

#all_generic_placementsArray of Strings

Returns genera where the species was placed.

Returns:

  • (Array of Strings)

    genera where the species was placed



218
219
220
221
222
223
224
# File 'app/models/protonym.rb', line 218

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_descendantsArray

Returns all descendant and ancestor protonyms for this Protonym.

Returns:

  • (Array)

    all descendant and ancestor protonyms for this Protonym



335
336
337
# File 'app/models/protonym.rb', line 335

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.



658
659
660
661
662
663
664
# File 'app/models/protonym.rb', line 658

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)


671
672
673
674
675
676
677
678
679
680
681
682
683
684
# File 'app/models/protonym.rb', line 671

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_classObject (protected)



891
892
893
894
895
896
897
898
899
# File 'app/models/protonym.rb', line 891

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_otuObject (protected)



920
921
922
# File 'app/models/protonym.rb', line 920

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

#genus_suggested_genderObject



634
635
636
637
638
639
640
641
642
# File 'app/models/protonym.rb', line 634

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?



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
319
320
# File 'app/models/protonym.rb', line 293

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 unless genus.blank?
    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_combinationObject



686
687
688
689
690
691
692
693
694
695
696
697
698
699
700
701
702
# File 'app/models/protonym.rb', line 686

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.blank? ? nil : s
end

#get_original_combination_htmlObject



785
786
787
788
789
790
791
792
793
794
795
796
797
798
# File 'app/models/protonym.rb', line 785

def get_original_combination_html
  return  "\"<i>Candidatus</i> #{get_original_combination}\"" if is_candidatus?
  v = get_original_combination
  if !v.blank? && 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.blank?

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

#get_primary_typeTypeMaterial, []

Returns ?!.

Returns:



340
341
342
343
344
345
346
347
348
349
350
351
# File 'app/models/protonym.rb', line 340

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_nameProtonym

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



277
278
279
280
281
282
283
284
285
286
287
288
# File 'app/models/protonym.rb', line 277

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)


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

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



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

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? && !(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_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



427
428
429
430
431
432
433
434
435
436
# File 'app/models/protonym.rb', line 427

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)


266
267
268
269
270
271
272
273
# File 'app/models/protonym.rb', line 266

def is_available?(refresh = false)
  if !refresh
    @is_available ||= !has_misspelling_relationship? && !name_is_misapplied? && !classification_invalid_or_unavailable?
  else
    @is_available = !has_misspelling_relationship? && !name_is_misapplied? && !classification_invalid_or_unavailable?
  end
  @is_available
end

#is_family_or_genus_or_species_rank?Boolean

Returns:

  • (Boolean)


509
510
511
# File 'app/models/protonym.rb', line 509

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)


513
514
515
# File 'app/models/protonym.rb', line 513

def is_family_rank?
  FAMILY_RANK_NAMES.include?(rank_string)
end

#is_genus_or_species_rank?Boolean

Returns:

  • (Boolean)


505
506
507
# File 'app/models/protonym.rb', line 505

def is_genus_or_species_rank?
  GENUS_AND_SPECIES_RANK_NAMES.include?(rank_string)
end

#is_genus_rank?Boolean

Returns:

  • (Boolean)


501
502
503
# File 'app/models/protonym.rb', line 501

def is_genus_rank?
  GENUS_RANK_NAMES.include?(rank_string)
end

#is_higher_rank?Boolean

Returns:

  • (Boolean)


517
518
519
# File 'app/models/protonym.rb', line 517

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?
end

#is_original_name?Boolean

Returns Boolean could also be determined by parens in cached_author year.

Returns:

  • (Boolean)

    Boolean could also be determined by parens in cached_author year



523
524
525
# File 'app/models/protonym.rb', line 523

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

#is_species_rank?Boolean

Returns:

  • (Boolean)


497
498
499
# File 'app/models/protonym.rb', line 497

def is_species_rank?
  SPECIES_RANK_NAMES.include?(rank_string)
end

#list_of_coordinated_namesObject



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
263
264
# File 'app/models/protonym.rb', line 226

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_taxonObject

TODO, make back half of this raw SQL



323
324
325
326
327
328
329
330
331
# File 'app/models/protonym.rb', line 323

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_latinizedObject (protected)



901
902
903
# File 'app/models/protonym.rb', line 901

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

#name_is_valid_formatObject (protected)



916
917
918
# File 'app/models/protonym.rb', line 916

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_spellingObject



540
541
542
543
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
# File 'app/models/protonym.rb', line 540

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

#new_parent_taxon_nameObject (protected)



924
925
926
927
928
929
930
931
# File 'app/models/protonym.rb', line 924

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 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)


885
886
887
# File 'app/models/protonym.rb', line 885

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

#number_of_taxa_by_yearObject

temporary method to get a number of taxa described by year



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
422
# File 'app/models/protonym.rb', line 396

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_relationshipsObject

return [Array]

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


440
441
442
443
444
445
446
# File 'app/models/protonym.rb', line 440

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_elementsHash

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

Returns:

  • (Hash)


712
713
714
715
716
717
718
719
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
# File 'app/models/protonym.rb', line 712

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) ⇒ [rank_name, name]?

Returns Used in ColDP export.

Returns:

  • ([rank_name, name], nil)

    Used in ColDP export



767
768
769
770
771
772
773
774
775
# File 'app/models/protonym.rb', line 767

def original_combination_infraspecific_element(elements = nil)
  elements ||= original_combination_elements

  # 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_stubsArray

Returns A relationships for each possible original combination relationship.

Returns:

  • (Array)

    A relationships for each possible original combination relationship



450
451
452
453
454
455
456
457
458
459
460
461
462
463
464
465
# File 'app/models/protonym.rb', line 450

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_nameString?

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

Returns:

  • (String, nil)

    a monominal, as originally rendered, with parens if subgenus



779
780
781
782
783
# File 'app/models/protonym.rb', line 779

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

#predict_three_formsObject



598
599
600
601
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
# File 'app/models/protonym.rb', line 598

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 /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



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
393
# File 'app/models/protonym.rb', line 354

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.blank? && 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
  r.constantize
end

#reduce_list_of_synonyms(list) ⇒ Object



527
528
529
530
531
532
533
534
535
536
537
538
# File 'app/models/protonym.rb', line 527

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.nomenclature_date
    unless date1.nil?
      list1.reject!{|s| date1 < (s.year_of_publication ? s.nomenclature_date : Time.utc(1))}
    end
  end
  list1
end

#set_cachedObject (protected)



989
990
991
992
993
994
995
996
997
# File 'app/models/protonym.rb', line 989

def set_cached
  super
  set_cached_names_for_dependants
  set_cached_original_combination
  set_cached_original_combination_html
  set_cached_homonymy
  set_cached_species_homonym if is_species_rank?
  set_cached_misspelling
end

#set_cached_homonymyObject (protected)



999
1000
1001
1002
1003
1004
# File 'app/models/protonym.rb', line 999

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_misspellingObject (protected)

all three in one update here



1007
1008
1009
# File 'app/models/protonym.rb', line 1007

def set_cached_misspelling
  update_column(:cached_misspelling, get_cached_misspelling)
end

#set_cached_names_for_dependantsObject



815
816
817
818
819
820
821
822
823
824
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
851
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
# File 'app/models/protonym.rb', line 815

def set_cached_names_for_dependants
  dependants = []
  related_through_original_combination_relationships = []
  combination_relationships = []

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

   #  dependants.push(self) # combination does hit here

    # Combination can hit here
    classified_as_relationships = TaxonNameRelationship.where_object_is_taxon_name(self).with_type_contains('SourceClassifiedAs')

    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

    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_original_combinationObject (protected)



1011
1012
1013
# File 'app/models/protonym.rb', line 1011

def set_cached_original_combination
  update_column(:cached_original_combination, get_original_combination)
end

#set_cached_original_combination_htmlObject (protected)



1015
1016
1017
# File 'app/models/protonym.rb', line 1015

def set_cached_original_combination_html
  update_column(:cached_original_combination_html, get_original_combination_html)
end

#set_cached_species_homonymObject



808
809
810
811
812
813
# File 'app/models/protonym.rb', line 808

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



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

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_namesObject (protected)

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.



963
964
965
966
967
968
969
970
971
972
973
974
975
976
977
978
979
980
981
982
983
984
985
986
987
# File 'app/models/protonym.rb', line 963

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

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)



192
193
194
195
196
197
198
199
200
201
202
203
204
205
206
207
208
209
210
211
212
213
# File 'app/models/protonym.rb', line 192

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_combinationsObject



800
801
802
803
804
805
806
# File 'app/models/protonym.rb', line 800

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_lowerObject (protected)



937
938
939
940
941
942
943
944
945
946
947
948
949
950
# File 'app/models/protonym.rb', line 937

def validate_child_rank_is_equal_or_lower
  if parent && !rank_class.blank? && 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_higherObject (protected)



952
953
954
955
956
957
958
# File 'app/models/protonym.rb', line 952

def validate_parent_rank_is_higher
  if parent && !rank_class.blank? && rank_string != 'NomenclaturalRank'
    if RANKS.index(rank_string) <= RANKS.index(parent.rank_string)
      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_classObject (protected)



933
934
935
# File 'app/models/protonym.rb', line 933

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

#verbatim_author_with_closed_parens_when_presentObject (protected)



909
910
911
912
913
914
# File 'app/models/protonym.rb', line 909

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_digitsObject (protected)



905
906
907
# File 'app/models/protonym.rb', line 905

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