Class: Protonym
- Inherits:
-
TaxonName
- Object
- ActiveRecord::Base
- ApplicationRecord
- TaxonName
- Protonym
- 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
-
#is_available ⇒ Boolean
readonly
Memoize ‘#is_avaiable?`.
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
- .batch_move(params) ⇒ Hash
- .batch_update(params) ⇒ Object
- .family_group_base(name_string) ⇒ Object
- .family_group_name_at_rank(name_string, rank_string) ⇒ Object
-
.names_at_rank_group_for_collection_objects(rank: nil, collection_object_query: nil) ⇒ Object
!! Ensure collection_object_query is scoped to project.
-
.stub_root(project_id: nil, by: nil) ⇒ Protonym
A name ready to become the root.
Instance Method Summary collapse
-
#all_generic_placements ⇒ Array of Strings
Genera where the species was placed.
-
#ancestors_and_descendants ⇒ Array
All descendant and ancestor protonyms for this Protonym.
-
#build_original_combination_from_biodiversity(biodiversity_result, relationship_housekeeping = {}) ⇒ Boolean
TODO: likley belongs in lib/vendor/biodiversity.rb.
- #build_original_combinations(combination, relationship_housekeeping) ⇒ Boolean
- #check_new_parent_class ⇒ Object protected
- #create_otu ⇒ Object protected
- #genus_suggested_gender ⇒ Object
-
#get_genus_species(genus_option, self_option) ⇒ nil, ...
This method is currently only used for setting cached_primary_homonym.
- #get_original_combination ⇒ Object
- #get_original_combination_html ⇒ Object
-
#get_primary_type ⇒ TypeMaterial, []
?!.
-
#get_valid_taxon_name ⇒ Protonym
The accepted “valid” version of this name in the present classification.
-
#has_alternate_original? ⇒ Boolean
Same as is_original_name?!.
-
#has_latinized_exceptions? ⇒ Boolean
Whether this name has one of the TaxonNameClassifications that except it from being tested as latinized.
- #has_misspelling_or_misapplication_relationship? ⇒ Boolean
-
#has_misspelling_relationship? ⇒ Boolean
Whether this name has one of the TaxonNameRelationships which justify wrong form of the name.
-
#has_same_primary_type(taxon2) ⇒ Boolean
!! TODO: Should not be possible- fix the incoming data.
- #is_available?(refresh = false) ⇒ Boolean
- #is_family_or_genus_or_species_rank? ⇒ Boolean
- #is_family_rank? ⇒ Boolean
- #is_genus_or_species_rank? ⇒ Boolean
- #is_genus_rank? ⇒ Boolean
- #is_higher_rank? ⇒ Boolean
- #is_latin? ⇒ Boolean
-
#is_original_name? ⇒ Boolean
Boolean.
- #is_species_rank? ⇒ Boolean
- #list_of_coordinated_names ⇒ Object
-
#lowest_rank_coordinated_taxon ⇒ Object
TODO, make back half of this raw SQL.
- #name_is_latinized ⇒ Object protected
- #name_is_valid_format ⇒ Object protected
- #name_with_alternative_spelling ⇒ Object
- #new_parent_taxon_name ⇒ Object protected
- #nominotypical_sub_of?(protonym) ⇒ boolean
-
#number_of_taxa_by_year ⇒ Object
temporary method to get a number of taxa described by year.
-
#original_combination_class_relationships ⇒ Object
return [Array] TaxonNameRelationship classes that are applicable to this name, as deterimined by Rank.
-
#original_combination_elements ⇒ Hash
{ genus: [“”, ‘Aus’ ], … form: [‘frm’, ‘aus’] }.
-
#original_combination_infraspecific_element(elements = nil, remove_sic = false) ⇒ [rank_name, name]?
Used in ColDP export.
-
#original_combination_relationships_and_stubs ⇒ Array
A relationships for each possible original combination relationship.
-
#original_name ⇒ String?
A monominal, as originally rendered, with parens if subgenus.
- #predict_three_forms ⇒ Object
-
#predicted_child_rank(child_string) ⇒ Object
taxon_name.predicted_children_rank(‘Cicadellidae’) >> NomenclaturalRank::Iczn::FamilyGroup::Family.
- #reduce_list_of_synonyms(list) ⇒ Object
- #set_cached ⇒ Object protected
- #set_cached_homonymy ⇒ Object protected
-
#set_cached_misspelling ⇒ Object
protected
all three in one update here.
- #set_cached_names_for_dependants ⇒ Object
- #set_cached_names_for_descendants ⇒ Object
- #set_cached_original_combination ⇒ Object protected
- #set_cached_original_combination_html ⇒ Object protected
- #set_cached_species_homonym ⇒ Object
- #species_questionable_ending(taxon_name_classification_class, tested_name) ⇒ Object
-
#sv_cached_names ⇒ Object
protected
!! This has to go.
-
#synonymize_with(protonym) ⇒ Object
A convenience method to make this name a low-level synonym of another.
- #update_cached_original_combinations ⇒ Object
- #validate_child_rank_is_equal_or_lower ⇒ Object protected
- #validate_parent_rank_is_higher ⇒ Object protected
- #validate_rank_class_class ⇒ Object protected
- #validate_same_nomenclatural_code ⇒ Object protected
- #verbatim_author_with_closed_parens_when_present ⇒ Object protected
- #verbatim_author_without_digits ⇒ Object protected
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
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
Methods included from Shared::HasPapertrail
#attribute_updated, #attribute_updater
Methods included from Shared::AlternateValues
#all_values_for, #alternate_valued?
Methods included from Shared::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
Instance Attribute Details
#is_available ⇒ Boolean (readonly)
Returns 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
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
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 |
Instance Method Details
#all_generic_placements ⇒ Array of Strings
Returns 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.
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
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
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
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 ?!.
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.
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?!
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.
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
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.
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
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
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
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
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
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
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
522 523 524 |
# File 'app/models/protonym.rb', line 522 def is_higher_rank? HIGHER_RANK_NAMES.include?(rank_string) end |
#is_latin? ⇒ 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.
527 528 529 |
# File 'app/models/protonym.rb', line 527 def is_original_name? =~ /\(/ ? false : true end |
#is_species_rank? ⇒ 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
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']
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.
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.
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.
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 = .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..to_s != 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 = [] combination_relationships = [] TaxonName.transaction_with_retry do if is_genus_or_species_rank? = 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') .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., 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., 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., 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., 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 != is_cached = false if != 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 if .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 =~ /\A\([^()]+\)\z|\A[^()]+\z/ end end |
#verbatim_author_without_digits ⇒ Object (protected)
961 962 963 |
# File 'app/models/protonym.rb', line 961 def errors.add(:verbatim_author, 'Verbatim author may not contain digits, a year may be present') if =~ /\d/ end |