Class: Protonym
- Inherits:
-
TaxonName
- Object
- ActiveRecord::Base
- ApplicationRecord
- TaxonName
- Protonym
- Extended by:
- SoftValidationExtensions::Klass
- Includes:
- Becomes, Format, 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, Format, 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::ROOT_NAME, TaxonName::SPECIES_EPITHET_RANKS
Constants included from SoftValidation
SoftValidation::ANCESTORS_WITH_SOFT_VALIDATIONS
Instance Attribute Summary collapse
-
#_cached_build_state ⇒ Object
readonly
Hash !! Use only during building cached values.
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, #classifications, #etymology, #feminine_name, #masculine_name, #name, #neuter_name, #no_cached, #parent_id, #project_id, #rank_class, #related_relationships, #taxonomy, #type, #verbatim_author, #verbatim_name, #year_of_publication
Class Method Summary collapse
- .batch_move(params) ⇒ Hash
- .batch_update(params) ⇒ Object
-
.calculated_unavailable ⇒ Object
Note that Combinations are considered innaplicable, and are treated as unavailable for data-persistence purposes.
-
.family_group_base(name_string) ⇒ Object
TODO: Move to Utilities::Nomenclature, rename iczn_family_group_base.
-
.family_group_name_at_rank(name_string, rank_string) ⇒ Object
TODO: replace with @taxonomy.
-
.names_at_rank_group_for_collection_objects(rank: nil, collection_object_query: nil) ⇒ Object
TODO: feels like TaxonNames Filter f(n) !! 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
- #_initialize_cached_build_state ⇒ Object protected
-
#all_generic_placements ⇒ Array of Strings
TODO: Move to Homonym logic, it’s only used there.
-
#ancestors_and_descendants ⇒ Array
All descendant and ancestor protonyms for this Protonym.
-
#build_original_combination_from_biodiversity(biodiversity_result, relationship_housekeeping = {}) ⇒ Boolean
TODO: belongs in lib/vendor/biodiversity.rb.
- #build_original_combinations(combination, relationship_housekeeping) ⇒ Boolean
- #check_new_parent_class ⇒ 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_is_available ⇒ Object
Boolean See cached_is_available attribute in TaxonName.
-
#get_primary_type ⇒ TypeMaterial, []
?!.
-
#get_valid_taxon_name ⇒ Protonym
The accepted “valid” version of this name in the present classification.
- #has_alternate_original? ⇒ Boolean
-
#has_latinized_classification? ⇒ Boolean
Boolean.
-
#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.
- #has_unavailable_relationship? ⇒ 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
TODO: @proceps - define/describe this.
-
#lowest_rank_coordinated_taxon ⇒ Object
Protonym.
- #name_is_latinized ⇒ Object protected
- #name_is_valid_format ⇒ Object protected
-
#name_with_alternative_spelling ⇒ Object
TODO: refactor for Utilities::Nomenclature.
- #new_parent_taxon_name ⇒ Object protected
- #nominotypical_sub_of?(protonym) ⇒ boolean
-
#number_of_taxa_by_year ⇒ Object
TODO: Move to helper or lib/ 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_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.
-
#predicted_child_rank(child_string) ⇒ Object
taxon_name.predicted_children_rank(‘Cicadellidae’) >> NomenclaturalRank::Iczn::FamilyGroup::Family.
- #reduce_list_of_synonyms(list) ⇒ Object
-
#reload ⇒ Object
Reset memomized and utility variables on reload.
- #set_cached ⇒ Object protected
- #set_cached_homonymy ⇒ Object protected
-
#set_cached_misspelling ⇒ Object
protected
The only reason this is needed on this side is because of the verbatim_name checks, otherwise we could drive it from the TaxonNameRelationship creation.
- #set_cached_names_for_dependants ⇒ Object
-
#set_cached_names_for_descendants ⇒ Object
TODO: Are there are times where names are dependant and descendant? Original Genus is Genus, for example.
- #set_cached_original_combination ⇒ Object protected
- #set_cached_original_combination_html ⇒ Object protected
- #set_cached_species_homonym ⇒ Object
-
#set_original_combination_cached_fields ⇒ Object
protected
All cached values that relate to an original combination should be referenced here so that they can be re-referenced indirectly from TaxonNameRelationships In particular those impacted by an OriginalCombination.
- #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 Format
#full_name_hash, #genderized_elements, #genderized_name, #get_full_name, #get_original_combination, #get_original_combination_html, #misspelling_tag, #name_in_gender, #original_combination_flat
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_duplicate_nomen_nudum, #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_infrasubspecific_status, #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, #create_otu, #descendant_protonyms, #dwc_occurrences, #first_possible_invalid_taxan_name_relationship, #first_possible_valid_taxon_name, #first_possible_valid_taxon_name_relationship, #full_name, #full_name_array, #gbif_status_array, #gender_class, #gender_instance, #get_author, #get_author_and_year, #get_cached_classified_as, #get_cached_misspelling, #get_full_name_html, #get_original_combination, #get_original_combination_html, #icn_author_and_year, #iczn_author_and_year, #is_ambiguously_invalid?, #is_available?, #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_from_biodiversity_result, #name_is_misapplied?, #next_sibling, #nomeclatural_history, #nomenclature_date, #normalized_genus, #not_binominal?, not_leaves, #original_author_year, out_of_scope_combinations, #out_of_scope_combinations, #part_of_speech_class, #part_of_speech_instance, #part_of_speech_name, #previous_sibling, #rank, rank_order, #rank_string, #reified_id, #related_taxon_names, #relationship_invalid?, #relationships, remove_authors, #safe_self_and_ancestors, select_optimized, #set_cached_author, #set_cached_author_columns, #set_cached_author_year, #set_cached_classified_as, #set_cached_is_available, #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_parent_from_the_same_project, #validate_root_name_is_root, #validate_source_type, with_taxon_name_relationship, #year_integer
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 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_synchronize_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_synchronize_matrices, #member_update_matrix_items?
Methods included from TaxonName::TextTree
#basionym_node, #synonym_nodes, #text_tree, #text_tree_nodes, #to_node
Methods included from Shared::QueryBatchUpdate
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, #detect_version
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
#_cached_build_state ⇒ Object (readonly)
Returns Hash !! Use only during building cached values. Idea !! is to store values used downstream in setting cached values.
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# File 'app/models/protonym.rb', line 27 def _cached_build_state @_cached_build_state end |
Class Method Details
.batch_move(params) ⇒ Hash
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# File 'app/models/protonym.rb', line 839 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
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# File 'app/models/protonym.rb', line 867 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 |
.calculated_unavailable ⇒ Object
Note that Combinations are considered innaplicable, and are treated as unavailable for data-persistence purposes.
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# File 'app/models/protonym.rb', line 208 def self.calculated_unavailable a = Protonym.joins(:taxon_name_relationships).where(taxon_name_relationships: {type: TAXON_NAME_RELATIONSHIP_NAMES_MISSPELLING_AND_MISAPPLICATION}) b = Protonym.joins(:taxon_name_classifications).where(taxon_name_classifications: {type: TAXON_NAME_CLASS_NAMES_UNAVAILABLE}) ::Queries.union(TaxonName, [a,b]) end |
.family_group_base(name_string) ⇒ Object
TODO: Move to Utilities::Nomenclature, rename iczn_family_group_base
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# File 'app/models/protonym.rb', line 173 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
TODO: replace with @taxonomy
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# File 'app/models/protonym.rb', line 179 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
TODO: feels like TaxonNames Filter f(n)
!! Ensure collection_object_query is scoped to project
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# File 'app/models/protonym.rb', line 191 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
#_initialize_cached_build_state ⇒ Object (protected)
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# File 'app/models/protonym.rb', line 1047 def _initialize_cached_build_state @_cached_build_state = {} end |
#all_generic_placements ⇒ Array of Strings
TODO: Move to Homonym logic, it’s only used there
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# File 'app/models/protonym.rb', line 243 def all_generic_placements valid_name = get_valid_taxon_name # TODO: depend on cached return nil unless valid_name.rank_string !=~/Species/ descendants_and_self = valid_name.descendants.unscope(:order) + [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.
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# File 'app/models/protonym.rb', line 375 def ancestors_and_descendants Protonym.ancestors_and_descendants_of(self).not_self(self).unscope(:order).to_a end |
#build_original_combination_from_biodiversity(biodiversity_result, relationship_housekeeping = {}) ⇒ Boolean
TODO: belongs in lib/vendor/biodiversity.rb
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# File 'app/models/protonym.rb', line 674 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
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# File 'app/models/protonym.rb', line 687 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 unless relationship_housekeeping.blank? 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)
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# File 'app/models/protonym.rb', line 881 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 |
#genus_suggested_gender ⇒ Object
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# File 'app/models/protonym.rb', line 650 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.
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# File 'app/models/protonym.rb', line 333 def get_genus_species(genus_option, self_option) return nil if rank_class.nil? || rank_class.to_s == 'NomenclaturalRank' genus = nil name1 = nil if is_species_rank? if genus_option == :original genus = original_genus elsif genus_option == :current genus = ancestor_at_rank('genus') # @taxonomy 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(' ') end |
#get_is_available ⇒ Object
Returns Boolean See cached_is_available attribute in TaxonName.
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# File 'app/models/protonym.rb', line 310 def get_is_available !has_unavailable_relationship? && !classification_unavailable? end |
#get_primary_type ⇒ TypeMaterial, []
Returns ?!.
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# File 'app/models/protonym.rb', line 453 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.
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# File 'app/models/protonym.rb', line 316 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
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# File 'app/models/protonym.rb', line 540 def has_alternate_original? cached_original_combination && (cached != cached_original_combination) ? true : false end |
#has_latinized_classification? ⇒ Boolean
Returns Boolean.
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# File 'app/models/protonym.rb', line 574 def has_latinized_classification? TaxonNameClassification.where_taxon_name(self).where(type: LATINIZED_TAXON_NAME_CLASSIFICATION_NAMES).any? end |
#has_latinized_exceptions? ⇒ Boolean
Returns whether this name has one of the TaxonNameClassifications that except it from being tested as latinized.
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# File 'app/models/protonym.rb', line 511 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
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# File 'app/models/protonym.rb', line 299 def has_misspelling_or_misapplication_relationship? # TODO: Looping the constant and meomizing the taxon_name_relationships prevents another query taxon_name_relationships.where(type: 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.
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# File 'app/models/protonym.rb', line 531 def has_misspelling_relationship? # taxon_name_relationships.with_type_array(TAXON_NAME_RELATIONSHIP_NAMES_MISSPELLING).any? if cached_misspelling || cached_original_combination_html.to_s.include?('[sic]') return true else return false end end |
#has_same_primary_type(taxon2) ⇒ Boolean
!! TODO: Should not be possible- fix the incoming data
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# File 'app/models/protonym.rb', line 469 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, they 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 |
#has_unavailable_relationship? ⇒ Boolean
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# File 'app/models/protonym.rb', line 304 def has_unavailable_relationship? taxon_name_relationships.where(type: TAXON_NAME_RELATIONSHIP_UNAVAILABLE).any? end |
#is_family_or_genus_or_species_rank? ⇒ Boolean
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# File 'app/models/protonym.rb', line 556 def is_family_or_genus_or_species_rank? FAMILY_AND_GENUS_AND_SPECIES_RANK_NAMES.include?(rank_string) end |
#is_family_rank? ⇒ Boolean
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# File 'app/models/protonym.rb', line 560 def is_family_rank? FAMILY_RANK_NAMES.include?(rank_string) end |
#is_genus_or_species_rank? ⇒ Boolean
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# File 'app/models/protonym.rb', line 552 def is_genus_or_species_rank? GENUS_AND_SPECIES_RANK_NAMES.include?(rank_string) end |
#is_genus_rank? ⇒ Boolean
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# File 'app/models/protonym.rb', line 548 def is_genus_rank? GENUS_RANK_NAMES.include?(rank_string) end |
#is_higher_rank? ⇒ Boolean
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# File 'app/models/protonym.rb', line 564 def is_higher_rank? HIGHER_RANK_NAMES.include?(rank_string) end |
#is_latin? ⇒ Boolean
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# File 'app/models/protonym.rb', line 525 def is_latin? !NOT_LATIN.match(name) || has_latinized_exceptions? || rank_string =~ /Icvcn::Species/ end |
#is_original_name? ⇒ Boolean
Returns Boolean.
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# File 'app/models/protonym.rb', line 569 def is_original_name? =~ /\(/ ? false : true end |
#is_species_rank? ⇒ Boolean
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# File 'app/models/protonym.rb', line 544 def is_species_rank? SPECIES_RANK_NAMES.include?(rank_string) end |
#list_of_coordinated_names ⇒ Object
TODO: @proceps - define/describe this
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# File 'app/models/protonym.rb', line 254 def list_of_coordinated_names list = [] if self.rank_string ## All Protonym must have this. if cached_misspelling list = [ self.iczn_set_as_incorrect_original_spelling_of_relationship&.object_taxon_name ].compact else search_rank = NomenclaturalRank::Iczn.group_base(rank_string) if !!search_rank # how can this not hit? if search_rank =~ /Family/ if cached_is_valid z = Protonym.family_group_base(name) search_name = z.nil? ? nil : Protonym::FAMILY_GROUP_ENDINGS.collect{|i| z+i} # ! array 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.blank? && cached_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 .unscope(:order) else list = [] end end end list end |
#lowest_rank_coordinated_taxon ⇒ Object
Returns Protonym.
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# File 'app/models/protonym.rb', line 363 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)
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# File 'app/models/protonym.rb', line 891 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)
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# File 'app/models/protonym.rb', line 906 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
TODO: refactor for Utilities::Nomenclature
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# File 'app/models/protonym.rb', line 592 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)
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# File 'app/models/protonym.rb', line 910 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
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# File 'app/models/protonym.rb', line 834 def nominotypical_sub_of?(protonym) is_genus_or_species_rank? && parent == protonym && parent.name == protonym.name end |
#number_of_taxa_by_year ⇒ Object
TODO: Move to helper or lib/ temporary method to get a number of taxa described by year
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# File 'app/models/protonym.rb', line 424 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).where(type: ::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
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# File 'app/models/protonym.rb', line 482 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_infraspecific_element(elements = nil, remove_sic = false) ⇒ [rank_name, name]?
Returns Used in ColDP export.
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# File 'app/models/protonym.rb', line 706 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.
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# File 'app/models/protonym.rb', line 492 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 |
#predicted_child_rank(child_string) ⇒ Object
taxon_name.predicted_children_rank(‘Cicadellidae’) >> NomenclaturalRank::Iczn::FamilyGroup::Family
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# File 'app/models/protonym.rb', line 380 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
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# File 'app/models/protonym.rb', line 578 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 |
#reload ⇒ Object
Reset memomized and utility variables on reload.
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# File 'app/models/protonym.rb', line 159 def reload(*) super.tap do @_initialize_cached_build_state = {} @original_combination_elements = nil end end |
#set_cached ⇒ Object (protected)
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# File 'app/models/protonym.rb', line 996 def set_cached return true if destroyed? = .to_s # why to_s? old_cached = cached.to_s # why to_s? super if parent_id || parent # Don't do this for Root!! set_original_combination_cached_fields set_cached_homonymy set_cached_species_homonym if is_species_rank? set_cached_misspelling # Here we start to calculate off of what was previously set tn = TaxonName.find(id) # Why not "reload" (maybe OK with re-initialize) set_cached_names_for_descendants if tn.cached != old_cached set_cached_names_for_dependants if tn.cached.to_s != old_cached || tn..to_s != end true end |
#set_cached_homonymy ⇒ Object (protected)
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# File 'app/models/protonym.rb', line 1017 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)
The only reason this is needed on this side is because of the verbatim_name checks, otherwise we could drive it from the TaxonNameRelationship creation.
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# File 'app/models/protonym.rb', line 1027 def set_cached_misspelling update_column(:cached_misspelling, get_cached_misspelling) end |
#set_cached_names_for_dependants ⇒ Object
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# File 'app/models/protonym.rb', line 770 def set_cached_names_for_dependants = [] combination_relationships = [] all_names = [] # This transaction makes it difficult to re-use cached fields to derive other =cached fields, # thus the existence of some cachine attributes in TaxonName. 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 # byebug if name == 'Dus' classified_as_relationships = TaxonNameRelationship.where_object_is_taxon_name(self).with_type_contains('SourceClassifiedAs') .collect{|i| i.object_taxon_name}.uniq.each do |i| all_names.push i i.reload # byebug if name == 'Dus' i.update_cached_original_combinations end # Update values in Combinations combination_relationships.collect{|i| i.object_taxon_name}.uniq.each do |j| all_names.push j n = j.get_full_name j.update_columns( cached: n, cached_html: j.get_full_name_html(n), cached_author_year: j., # !! Only if it changed? cached_nomenclature_date: j.nomenclature_date) # !! Only if it changed? 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| all_names.push 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).where(type: TAXON_NAME_RELATIONSHIP_NAMES_MISSPELLING_AND_MISAPPLICATION) misspelling_relationships.collect{|i| i.subject_taxon_name}.uniq.each do |i| all_names.push i i.update_columns( cached_author_year: i., cached_nomenclature_date: i.nomenclature_date) end # byebug if all_names.uniq.size != all_names.size || all_names.size > 1 end end |
#set_cached_names_for_descendants ⇒ Object
TODO: Are there are times where names are dependant and descendant?
Original Genus is Genus, for example
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# File 'app/models/protonym.rb', line 742 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)
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# File 'app/models/protonym.rb', line 1031 def set_cached_original_combination update_column(:cached_original_combination, get_original_combination) end |
#set_cached_original_combination_html ⇒ Object (protected)
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# File 'app/models/protonym.rb', line 1035 def set_cached_original_combination_html update_column(:cached_original_combination_html, get_original_combination_html) end |
#set_cached_species_homonym ⇒ Object
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# File 'app/models/protonym.rb', line 732 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 |
#set_original_combination_cached_fields ⇒ Object (protected)
All cached values that relate to an original combination should be referenced here so that they can be re-referenced indirectly from TaxonNameRelationships In particular those impacted by an OriginalCombination.
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# File 'app/models/protonym.rb', line 1042 def set_original_combination_cached_fields set_cached_original_combination set_cached_original_combination_html end |
#species_questionable_ending(taxon_name_classification_class, tested_name) ⇒ Object
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# File 'app/models/protonym.rb', line 660 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.
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# File 'app/models/protonym.rb', line 960 def sv_cached_names # this cannot be moved to soft_validation_extensions is_cached = true is_cached = false if != is_cached = false if != n = get_full_name # TODO: missing `cached_gender` # TODO: missing `cached` ?! # Right side values should call methods that calculate from the db if is_cached && ( cached_valid_taxon_name_id != get_valid_taxon_name.id || cached_is_valid != !unavailable_or_invalid? || cached_is_available != get_is_available || cached_html != get_full_name_html(n) || 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') unless 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)
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# File 'app/models/protonym.rb', line 218 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
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# File 'app/models/protonym.rb', line 718 def update_cached_original_combinations # if @pp # @pp += 1 # else # @pp = 1 # end 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)) # puts Rainbow(@pp).orange.bold end |
#validate_child_rank_is_equal_or_lower ⇒ Object (protected)
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# File 'app/models/protonym.rb', line 923 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)
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# File 'app/models/protonym.rb', line 938 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)
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# File 'app/models/protonym.rb', line 919 def validate_rank_class_class errors.add(:rank_class, 'Rank not found') unless RANKS.include?(rank_string) end |
#validate_same_nomenclatural_code ⇒ Object (protected)
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# File 'app/models/protonym.rb', line 946 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)
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# File 'app/models/protonym.rb', line 899 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)
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# File 'app/models/protonym.rb', line 895 def errors.add(:verbatim_author, 'Verbatim author may not contain digits, a year may be present') if =~ /\d/ end |