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
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
Attributes inherited from TaxonName
#also_create_otu, #cached_classified_as, #foo, #no_cached
Class Method Summary collapse
- .family_group_base(name_string) ⇒ Object
- .family_group_name_at_rank(name_string, rank_string) ⇒ Object
- .names_at_rank_group_for_collection_objects(rank = 'speciesgroup') ⇒ Object
-
.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
Wraps set_original_combination with result from Biodiversity parse !!You must can optionally pre-calculate a disambiguated protonym if you wish to use one.
- #build_original_combinations(combination, relationship_housekeeping) ⇒ Boolean
-
#check_new_parent_class ⇒ Object
protected
TODO: move to Protonym.
- #create_otu ⇒ Object protected
- #genus_suggested_gender ⇒ Object
-
#get_author_and_year ⇒ String?
TODO: not true, has parens?! a string, without parenthesis, that includes author and year.
-
#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_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? ⇒ Boolean
- #is_family_rank? ⇒ Boolean
- #is_genus_or_species_rank? ⇒ Boolean
- #is_genus_rank? ⇒ Boolean
- #is_higher_rank? ⇒ Boolean
- #is_homonym_or_suppressed? ⇒ Boolean
- #is_latin? ⇒ Boolean
-
#is_original_name? ⇒ Boolean
Boolean could also be determined by parens in cached_author year.
- #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
-
#original_combination_class_relationships ⇒ Object
return [Array] TaxonNameRelationship classes that are applicable to this name, as deterimined by Rank.
-
#original_combination_elements ⇒ Object
{ genus: [“”, 'Aus' ], … form: ['frm', 'aus'] }.
- #original_combination_infraspecific_element(elements = nil) ⇒ [rank_name, name]?
-
#original_combination_relationships_and_stubs ⇒ Array
A relationships for each possible original combination relationship.
-
#original_name ⇒ String?
A monomial, as originally rendered, with parens if subgenus.
-
#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_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
Validate whether cached names need to be rebuilt.
- #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
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_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_part_of_speach, #sv_fix_coordinated_names_source, #sv_fix_coordinated_names_type_genus, #sv_fix_coordinated_names_type_species, #sv_fix_coordinated_names_type_species_type, #sv_fix_coordinated_names_type_specimen, #sv_fix_coordinated_names_year, #sv_fix_misspelling_author_is_not_required, #sv_fix_misspelling_roles_are_not_required, #sv_fix_misspelling_year_is_not_required, #sv_fix_year_is_not_required, #sv_homotypic_synonyms, #sv_missing_author, #sv_missing_etymology, #sv_missing_gender, #sv_missing_original_genus, #sv_missing_part_of_speach, #sv_missing_roles, #sv_missing_substitute_name, #sv_missing_type_genus, #sv_missing_type_species, #sv_missing_year, #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_potential_family_homonyms, #sv_potential_genus_homonyms, #sv_potential_species_homonyms, #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_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_part_of_speach, #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_parent_rank, #sv_year_is_not_required
Methods inherited from TaxonName
#all_taxon_name_relationships, #ancestor_at_rank, #ancestor_hash, #ancestor_protonyms, #ancestors_through_parents, #author_string, #cached_author, #cached_html_name_and_author_year, #cached_name_and_author_year, #cached_year, #check_for_children, #check_new_rank_class, #classification_invalid_or_unavailable?, #classification_valid?, #clear_cached, #combination_list_all, #combination_list_self, #combined_statuses, #descendant_protonyms, #descendants_at_rank, #first_possible_valid_taxon_name, #first_possible_valid_taxon_name_relationship, foo, #full_name_array, #full_name_hash, #gbif_status_array, #gender_class, #gender_instance, #gender_name, #genderized_name, #get_cached_classified_as, #get_cached_misspelling, #get_full_name, #get_full_name_html, #icn_author_and_year, #iczn_author_and_year, #is_candidatus?, #is_combination?, #is_fossil?, #is_hybrid?, #is_italicized?, #is_protonym?, #is_valid?, #list_of_invalid_taxon_names, #matrix_row_item, #name_in_gender, #name_is_misapplied?, #name_with_misspelling, #next_sibling, #nomenclature_date, #normalized_genus, #not_binomial?, not_leaves, #original_author_year, parent, #parent_is_set?, #part_of_speech_class, #part_of_speech_instance, #part_of_speech_name, #previous_sibling, #rank, #rank_class, #rank_class=, #rank_string, #reified_id, #related_taxon_names, #relationship_invalid?, #safe_self_and_ancestors, select_optimized, #set_cached_author_year, #set_cached_classified_as, #set_cached_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_missing_author, #sv_fix_missing_year, #sv_fix_parent_is_valid_name, #sv_homotypic_synonyms, #sv_hybrid_name_relationships, #sv_incomplete_combination, #sv_missing_author, #sv_missing_classifications, #sv_missing_confidence_level, #sv_missing_etymology, #sv_missing_original_publication, #sv_missing_relationships, #sv_missing_year, #sv_not_synonym_of_self, #sv_parent_is_valid_name, #sv_parent_priority, #sv_potential_homonyms, #sv_primary_types, #sv_single_sub_taxon, #sv_species_gender_agreement, #sv_two_unresolved_alternative_synonyms, #sv_type_placement, #sv_validate_coordinated_names, #sv_validate_name, #sv_validate_parent_rank, #synonyms, #taxon_name_classifications_for_statuses, #unavailable_or_invalid?, used_recently, used_recently_in_classifications, used_recently_in_relationships, #validate_one_root_per_project, #validate_parent_from_the_same_project, #validate_parent_is_set, #validate_source_type, with_taxon_name_relationship, #year_integer
Methods included from TaxonName::MatrixHooks
#coordinate_observation_matrix_row_items, #in_scope_observation_matrix_row_items, #out_of_scope_observation_matrix_row_items
Methods included from Shared::MatrixHooks::Dynamic
#dynamic_add_to_matrix_column_items, #dynamic_add_to_matrix_row_items, #dynamic_cleanup_in_scope_column_items, #dynamic_cleanup_in_scope_row_items, #dynamic_cleanup_out_of_scope_column_items, #dynamic_cleanup_out_of_scope_row_items, #dynamic_column_items_in, #dynamic_column_items_out, #dynamic_inspect_matrices, #dynamic_remove_from_matrix_column_items, #dynamic_remove_from_matrix_row_items, #dynamic_row_items_in, #dynamic_row_items_out, #dynamic_syncronize_matrices, #dynamic_update_matrix_column_items?, #dynamic_update_matrix_row_items?, #in_scope_observation_matrix_column_items, #in_scope_observation_matrix_row_items, #out_of_scope_observation_matrix_column_items, #out_of_scope_observation_matrix_row_items, #prepare_matrix_items
Methods included from Shared::MatrixHooks::Member
#member_add_matrix_columns, #member_add_matrix_rows, #member_add_to_matrix_items, #member_of_new_matrix_column_items, #member_of_new_matrix_row_items, #member_of_old_matrix_column_items, #member_of_old_matrix_row_items, #member_remove_from_matrix_items, #member_remove_matrix_columns, #member_remove_matrix_rows, #member_syncronize_matrices, #member_update_matrix_items?
Methods included from Shared::IsData
#errors_excepting, #full_error_messages_excepting, #identical, #is_community?, #is_destroyable?, #is_editable?, #is_in_use?, #is_in_users_projects?, #metamorphosize, #similar
Methods included from SoftValidation
#clear_soft_validations, #fix_soft_validations, #soft_fixed?, #soft_valid?, #soft_validate, #soft_validated?, #soft_validations
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
#identified?, #next_by_identifier, #previous_by_identifier, #reject_identifiers
Methods included from Shared::Tags
#reject_tags, #tag_with, #tagged?, #tagged_with?
Methods included from Shared::HasRoles
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
Class Method Details
.family_group_base(name_string) ⇒ Object
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# File 'app/models/protonym.rb', line 147 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
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# File 'app/models/protonym.rb', line 152 def self.family_group_name_at_rank(name_string, rank_string) if name_string == family_group_base(name_string) name_string else family_group_base(name_string) + Ranks.lookup(:iczn, rank_string).constantize.try(:valid_name_ending).to_s end end |
.names_at_rank_group_for_collection_objects(rank = 'speciesgroup') ⇒ Object
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# File 'app/models/protonym.rb', line 162 def self.names_at_rank_group_for_collection_objects(rank = 'speciesgroup') h = ::TaxonNameHierarchy.arel_table t = ::TaxonName.arel_table t1 = ::TaxonName.arel_table.alias('tndet') d = ::TaxonDetermination.arel_table o = ::Otu.arel_table q = t.join(h, Arel::Nodes::InnerJoin).on( t[:id].eq(h[:ancestor_id]) ).join(t1, Arel::Nodes::InnerJoin).on( h[:descendant_id].eq(t1[:id]) ).join(o, Arel::Nodes::InnerJoin).on( t1[:id].eq(o[:id]) ).join(d, Arel::Nodes::InnerJoin).on( o[:id].eq(d[:otu_id]) ) joins(q.join_sources).where(t[:rank_class].matches('%' + rank + '%').to_sql).distinct end |
.stub_root(project_id: nil, by: nil) ⇒ Protonym
Returns a name ready to become the root.
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# File 'app/models/protonym.rb', line 143 def self.stub_root(project_id: nil, by: nil) Protonym.new(name: 'Root', rank_class: 'NomenclaturalRank', parent_id: nil, project_id: project_id, by: by) end |
Instance Method Details
#all_generic_placements ⇒ Array of Strings
Returns genera where the species was placed.
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# File 'app/models/protonym.rb', line 184 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.
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# File 'app/models/protonym.rb', line 310 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
Returns Wraps set_original_combination with result from Biodiversity parse !!You must can optionally pre-calculate a disambiguated protonym if you wish to use one.
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# File 'app/models/protonym.rb', line 600 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 613 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)
TODO: move to Protonym
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# File 'app/models/protonym.rb', line 825 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)
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# File 'app/models/protonym.rb', line 843 def create_otu Otu.create(by: self.creator, project: self.project, taxon_name_id: self.id) end |
#genus_suggested_gender ⇒ Object
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# File 'app/models/protonym.rb', line 577 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_author_and_year ⇒ String?
TODO: not true, has parens?!
a string, without parenthesis, that includes author and year
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# File 'app/models/protonym.rb', line 248 def # times_called case rank_class.try(:nomenclatural_code) when :iczn ay = when :icvcn ay = when :icnp ay = when :icn ay = else ay = ([] + [year_integer]).compact.join(' ') end ay.blank? ? nil : ay 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 268 def get_genus_species(genus_option, self_option) return nil if rank_class.nil? genus = nil name1 = nil if is_species_rank? # self.rank_string =~ /Species/ if genus_option == :original genus = original_genus elsif genus_option == :current genus = ancestor_at_rank('genus') else return false end genus = genus.name unless genus.blank? return nil if genus.blank? end if self_option == :self name1 = name elsif self_option == :alternative name1 = name_with_alternative_spelling end return nil if genus.nil? && name1.nil? # <- hitting this because Genus is never set [genus, name1].compact.join(' ') # (genus.to_s + ' ' + name1.to_s).squish end |
#get_original_combination ⇒ Object
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# File 'app/models/protonym.rb', line 628 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 ICTV the species name is "Potato spindle tuber viroid", the genus name is only used for classification... # # @proceps: then we should exclude or alter elements before we get to this point, not here, so that the renderer still works, exceptions at this point are bad # and this didn't do what you think it did, it's was returning an Array of two things return e[:species][1] if rank_class.to_s =~ /Icvcn/ p = TaxonName::COMBINATION_ELEMENTS.inject([]){|ary, r| ary.push(e[r]) } s = p.flatten.compact.join(' ') s.blank? ? nil : s end |
#get_original_combination_html ⇒ Object
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# File 'app/models/protonym.rb', line 725 def get_original_combination_html return "\"<i>Candidatus</i> #{get_original_combination}\"" if is_candidatus? v = get_original_combination if !v.blank? && is_hybrid? w = v.split(' ') w[-1] = ('×' + w[-1]).gsub('×(', '(×').gsub(') [sic]', ' [sic])').gsub(') (sic)', ' (sic))') v = w.join(' ') end v = v.gsub(') [sic]', ' [sic])').gsub(') (sic)', ' (sic))') if !v.blank? v = Utilities::Italicize.taxon_name(v) v = '† ' + v if !v.blank? && is_fossil? v end |
#get_primary_type ⇒ TypeMaterial, []
Returns ?!.
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# File 'app/models/protonym.rb', line 315 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 232 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?!
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# File 'app/models/protonym.rb', line 476 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.
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# File 'app/models/protonym.rb', line 446 def has_latinized_exceptions? # The second half of this handles classifications in memory, as required to save a non-latinized name (i.e. don't tune it to .any?) # !((type == 'Protonym') && (taxon_name_classifications.collect{|t| t.type} & EXCEPTED_FORM_TAXON_NAME_CLASSIFICATIONS).empty?) # Is faster than above? # return true if rank_string =~ /Icnp/ && (name.start_with?('Candidatus ') || name.start_with?('Ca. ')) return true if is_family_rank? && !(taxon_name_relationships.collect{|i| i.type} & TAXON_NAME_RELATIONSHIP_NAMES_SYNONYM).empty? return true unless (taxon_name_classifications.collect{|i| i.type} & EXCEPTED_FORM_TAXON_NAME_CLASSIFICATIONS).empty? return true unless (taxon_name_relationships.collect{|i| i.type} & TAXON_NAME_RELATIONSHIP_NAMES_MISSPELLING).empty? false end |
#has_misspelling_relationship? ⇒ Boolean
Returns whether this name has one of the TaxonNameRelationships which justify wrong form of the name.
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# File 'app/models/protonym.rb', line 468 def has_misspelling_relationship? taxon_name_relationships.each do |tr| return true if TAXON_NAME_RELATIONSHIP_NAMES_MISSPELLING.include?(tr.type) end false 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 404 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? ⇒ Boolean
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# File 'app/models/protonym.rb', line 226 def is_available? !has_misspelling_relationship? && !name_is_misapplied? && !classification_invalid_or_unavailable? end |
#is_family_rank? ⇒ Boolean
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# File 'app/models/protonym.rb', line 492 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 488 def is_genus_or_species_rank? is_species_rank? || is_genus_rank? end |
#is_genus_rank? ⇒ Boolean
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# File 'app/models/protonym.rb', line 484 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 496 def is_higher_rank? HIGHER_RANK_NAMES.include?(rank_string) end |
#is_homonym_or_suppressed? ⇒ Boolean
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# File 'app/models/protonym.rb', line 463 def is_homonym_or_suppressed? end |
#is_latin? ⇒ Boolean
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# File 'app/models/protonym.rb', line 459 def is_latin? !NOT_LATIN.match(name) || has_latinized_exceptions? end |
#is_original_name? ⇒ Boolean
Returns Boolean could also be determined by parens in cached_author year.
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# File 'app/models/protonym.rb', line 502 def is_original_name? =~ /\(/ ? false : true end |
#is_species_rank? ⇒ Boolean
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# File 'app/models/protonym.rb', line 480 def is_species_rank? SPECIES_RANK_NAMES.include?(rank_string) end |
#list_of_coordinated_names ⇒ Object
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# File 'app/models/protonym.rb', line 192 def list_of_coordinated_names list = [] if self.rank_string r = self.iczn_set_as_incorrect_original_spelling_of_relationship if r.blank? search_rank = NomenclaturalRank::Iczn.group_base(self.rank_string) if !!search_rank if search_rank =~ /Family/ z = Protonym.that_is_valid.family_group_base(self.name) search_name = z.nil? ? nil : Protonym::FAMILY_GROUP_ENDINGS.collect{|i| z+i} else search_name = self.name end else search_name = nil end r = TaxonNameRelationship.where_subject_is_taxon_name(self).with_type_array(TAXON_NAME_RELATIONSHIP_NAMES_MISSPELLING) if !search_name.nil? && r.empty? list = Protonym.ancestors_and_descendants_of(self).not_self(self). with_rank_class_including(search_rank). where('name in (?)', search_name). as_subject_without_taxon_name_relationship_array(TAXON_NAME_RELATIONSHIP_NAMES_SYNONYM) #as_subject_without_taxon_name_relationship_base('TaxonNameRelationship::Iczn::Invalidating::Synonym'). else list = [] end else list = [r.object_taxon_name] end end return list end |
#lowest_rank_coordinated_taxon ⇒ Object
TODO, make back half of this raw SQL
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# File 'app/models/protonym.rb', line 298 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 835 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 839 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
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# File 'app/models/protonym.rb', line 519 def name_with_alternative_spelling if rank_class.nil? || nomenclatural_code != :iczn # rank_string =~ /::Icn::/ # self.class != Protonym return nil elsif is_species_rank? # rank_string =~ /Species/ n = name.squish # remove extra spaces and line brakes n = n.split(' ').last n = n[0..-4] + 'ae' if n =~ /^[a-z]*iae$/ # -iae > -ae in the end of word n = n[0..-6] + 'orum' if n =~ /^[a-z]*iorum$/ # -iorum > -orum n = n[0..-6] + 'arum' if n =~ /^[a-z]*iarum$/ # -iarum > -arum n = n[0..-3] + 'a' if n =~ /^[a-z]*um$/ # -um > -a n = n[0..-3] + 'a' if n =~ /^[a-z]*us$/ # -us > -a n = n[0..-3] + 'e' if n =~ /^[a-z]*is$/ # -is > -e n = n[0..-3] + 'ra' if n =~ /^[a-z]*er$/ # -er > -ra n = n[0..-7] + 'ensis' if n =~ /^[a-z]*iensis$/ # -iensis > -ensis n = n[0..-5] + 'ana' if n =~ /^[a-z]*iana$/ # -iana > -ana n = n.gsub('ae', 'e'). gsub('oe', 'e'). gsub('ai', 'i'). gsub('ei', 'i'). gsub('ej', 'i'). gsub('ii', 'i'). gsub('ij', 'i'). gsub('jj', 'i'). gsub('j', 'i'). gsub('y', 'i'). gsub('v', 'u'). gsub('rh', 'r'). gsub('th', 't'). gsub('k', 'c'). gsub('ch', 'c'). gsub('tt', 't'). gsub('bb', 'b'). gsub('rr', 'r'). gsub('nn', 'n'). gsub('mm', 'm'). gsub('pp', 'p'). gsub('ss', 's'). gsub('ff', 'f'). gsub('ll', 'l'). gsub('ct', 't'). gsub('ph', 'f'). gsub('-', '') n = n[0, 3] + n[3..-4].gsub('o', 'i') + n[-3, 3] if n.length > 6 # connecting vowel in the middle of the word (nigrocinctus vs. nigricinctus) elsif rank_string =~ /Family/ n_base = Protonym.family_group_base(self.name) if n_base.nil? || n_base == self.name n = self.name else n = n_base + 'idae' end else n = self.name.squish end return n end |
#new_parent_taxon_name ⇒ Object (protected)
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# File 'app/models/protonym.rb', line 847 def new_parent_taxon_name r = self.iczn_uncertain_placement_relationship unless r.blank? if self.parent != r.object_taxon_name errors.add(:parent_id, "Taxon has a relationship 'incertae sedis' - delete the relationship before changing the parent") end end end |
#nominotypical_sub_of?(protonym) ⇒ boolean
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# File 'app/models/protonym.rb', line 818 def nominotypical_sub_of?(protonym) is_genus_or_species_rank? && parent == protonym && parent.name == protonym.name end |
#number_of_taxa_by_year ⇒ Object
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# File 'app/models/protonym.rb', line 375 def number_of_taxa_by_year 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.id == z.cached_valid_taxon_name_id 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.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 417 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 ⇒ Object
genus: ["", 'Aus' ],
...
form: ['frm', 'aus']
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# File 'app/models/protonym.rb', line 653 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) 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] = [original_name] end end if elements.any? if !elements[:genus] && !not_binomial? if original_genus elements[:genus] = "[#{original_genus&.name}]" else elements[:genus] = '[GENUS NOT SPECIFIED]' end end # If there is no :species, but some species group, add element elements[:species] = '[SPECIES NOT SPECIFIED]' if !elements[:species] && ( [:subspecies, :variety, :form] & elements.keys ).size > 0 end elements end |
#original_combination_infraspecific_element(elements = nil) ⇒ [rank_name, name]?
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# File 'app/models/protonym.rb', line 707 def original_combination_infraspecific_element(elements = nil) elements ||= original_combination_elements # TODO: consider plants/other codes? [:form, :variety, :subspecies].each do |r| return [r.to_s, original_combination_elements[r].last] if original_combination_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 427 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 monomial, as originally rendered, with parens if subgenus.
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# File 'app/models/protonym.rb', line 719 def original_name n = verbatim_name.nil? ? name_with_misspelling(nil) : verbatim_name n = "(#{n})" if n && rank_name == 'subgenus' n 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 329 def predicted_child_rank(child_string) return nil if child_string.blank? parent_rank = rank_class.to_s parent_rank_name = rank_name ncode = nomenclatural_code return nil if ncode.nil? # Happens with some names like "Root" if child_string == child_string.downcase if !is_species_rank? r = Ranks.lookup(ncode, 'species') elsif parent_rank_name == 'species' r = Ranks.lookup(ncode, 'subspecies') elsif parent_rank_name == 'subspecies' r = Ranks.lookup(ncode, 'variety') elsif parent_rank_name == 'variety' r = Ranks.lookup(ncode, 'form') elsif parent_rank_name == 'form' r = Ranks.lookup(ncode, 'subform') else return nil end elsif child_string == child_string.capitalize if rank_name == 'genus' r = Ranks.lookup(ncode, 'subgenus') else Ranks.lookup(ncode, 'family').constantize.valid_parents.each do |r1| r2 = r1.constantize if !r2.valid_name_ending.blank? && child_string.end_with?(r2.valid_name_ending) && RANKS.index(r1) > RANKS.index(parent_rank) r = r1 break end end r = Ranks.lookup(ncode, 'genus') if r.nil? end else return nil # RANKS.index(rank_string) <= RANKS.index(parent.rank_string) # Ranks.lookup(:iczn, 'species') # .valid_name_ending #FAMILY_AND_ABOVE_RANK_NAMES end r.constantize end |
#reduce_list_of_synonyms(list) ⇒ Object
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# File 'app/models/protonym.rb', line 506 def reduce_list_of_synonyms(list) return [] if list.empty? list1 = list.select{|s| s.id == s.lowest_rank_coordinated_taxon.id} list1.reject!{|s| self.cached_valid_taxon_name_id == s.cached_valid_taxon_name_id} unless list1.empty? unless list1.empty? date1 = self.nomenclature_date unless date1.nil? list1.reject!{|s| date1 < (s.year_of_publication ? s.nomenclature_date : Time.utc(1))} end end list1 end |
#set_cached ⇒ Object (protected)
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# File 'app/models/protonym.rb', line 893 def set_cached super set_cached_names_for_dependants set_cached_original_combination set_cached_original_combination_html set_cached_homonymy set_cached_species_homonym if is_species_rank? set_cached_misspelling end |
#set_cached_homonymy ⇒ Object (protected)
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# File 'app/models/protonym.rb', line 903 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
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# File 'app/models/protonym.rb', line 911 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 755 def set_cached_names_for_dependants dependants = [] = [] combination_relationships = [] TaxonName.transaction_with_retry do if is_genus_or_species_rank? dependants = Protonym.unscoped.descendants_of(self).to_a = TaxonNameRelationship.where_subject_is_taxon_name(self).with_type_contains('OriginalCombination') combination_relationships = TaxonNameRelationship.where_subject_is_taxon_name(self).with_type_contains('::Combination') end # dependants.push(self) # combination does hit here # Combination can hit here classified_as_relationships = TaxonNameRelationship.where_object_is_taxon_name(self).with_type_contains('SourceClassifiedAs') dependants.each do |i| columns_to_update = { cached: i.get_full_name, cached_html: i.get_full_name_html, cached_author_year: i. } 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 .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| j.update_columns( cached: j.get_full_name, cached_html: j.get_full_name_html, cached_author_year: j.) 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| i.update_columns( cached: i.get_full_name, cached_html: i.get_full_name_html, cached_author_year: i.) 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.) end end end |
#set_cached_original_combination ⇒ Object (protected)
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# File 'app/models/protonym.rb', line 915 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 919 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 748 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
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# File 'app/models/protonym.rb', line 587 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)
Validate whether cached names need to be rebuilt.
TODO: this is kind of pointless, we generate all the values need for cached, names, at that point the cached values should just be persisted The logic here also duplicates the tracking needed for building cached names.
Refactor this to single methods, one each to validate cached name?
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# File 'app/models/protonym.rb', line 934 def sv_cached_names is_cached = true is_cached = false if != if is_cached && 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_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', fix: :sv_fix_cached_names, success_message: 'Cached values were updated' ) if !is_cached end |
#update_cached_original_combinations ⇒ Object
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# File 'app/models/protonym.rb', line 740 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)
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# File 'app/models/protonym.rb', line 870 def validate_child_rank_is_equal_or_lower if parent && !rank_class.blank? && rank_string != 'NomenclaturalRank' if rank_class_changed? a = children.where(type: 'Protonym').pluck(:rank_class) v = RANKS.index(rank_string) a.each do |b| if v >= RANKS.index(b) errors.add(:rank_class, "The rank of this taxon (#{rank_name}) should be higher than the ranks of children") break end end end end end |
#validate_parent_rank_is_higher ⇒ Object (protected)
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# File 'app/models/protonym.rb', line 885 def validate_parent_rank_is_higher if parent && !rank_class.blank? && rank_string != 'NomenclaturalRank' if RANKS.index(rank_string) <= RANKS.index(parent.rank_string) errors.add(:parent_id, "The parent rank (#{parent.rank_class.rank_name}) is not higher than the rank (#{rank_name}) of this taxon") end end end |
#validate_rank_class_class ⇒ Object (protected)
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# File 'app/models/protonym.rb', line 866 def validate_rank_class_class errors.add(:rank_class, 'Rank not found') unless RANKS.include?(rank_string) end |