Class: TaxonNameClassification
- Inherits:
-
ApplicationRecord
- Object
- ActiveRecord::Base
- ApplicationRecord
- TaxonNameClassification
- Includes:
- Housekeeping, Shared::Citations, Shared::IsData, Shared::Notes, SoftValidation
- Defined in:
- app/models/taxon_name_classification.rb
Overview
Defined Under Namespace
Classes: Icn, Icnp, Icvcn, Iczn, Latinized
Constant Summary
Constants included from SoftValidation
SoftValidation::ANCESTORS_WITH_SOFT_VALIDATIONS
Instance Attribute Summary collapse
-
#project_id ⇒ Integer
the project ID.
-
#taxon_name_id ⇒ Integer
The id of the TaxonName being classified.
-
#type ⇒ String
The type of classifiction (Rails STI).
Class Method Summary collapse
-
.annotates? ⇒ Boolean
endregion.
-
.applicable_ranks ⇒ Array of Strings of NomenclaturalRank names
nomenclatural ranks to which this class is applicable, that is, only TaxonNames of these NomenclaturalRanks may be classified as this class.
- .assignable ⇒ Object
-
.code_applicability_end_year ⇒ Integer
the last year of applicability for this class, defaults to 9999.
-
.code_applicability_start_year ⇒ Integer
the minimum year of applicability for this class, defaults to 1.
-
.collect_descendants_and_itself_to_s(*classes) ⇒ Object
private
!! using this strongly suggests something can be optimized, meomized etc.
-
.collect_descendants_to_s(*classes) ⇒ Object
private
!! using this strongly suggests something can be optimized, meomized etc.
- .collect_to_s(*args) ⇒ Object private
-
.disjoint_taxon_name_classes ⇒ Array of Strings of TaxonNameClassification names
the disjoint (inapplicable) TaxonNameClassifications for this class, that is, TaxonNames classified as this class can not be additionally classified under these classes.
-
.gbif_status ⇒ String?
If applicable, a DWC gbif status for this class.
- .label ⇒ Object
- .nomen_uri ⇒ Object
-
.parent ⇒ Object
Class this method calls Module#module_parent.
-
.possible_genus_endings ⇒ Array of Strings
the possible suffixes for a TaxonName name (genus) classified as this class, for example see Latinized::Gender::Masculine.
-
.possible_species_endings ⇒ Array of Strings
The possible suffixes for a TaxonName name (species) classified as this class, for example see Latinized::Gender::Masculine used to validate gender agreement of species name with a genus.
-
.questionable_species_endings ⇒ Array of Strings
The questionable suffixes for a TaxonName name classified as this class, for example see Latinized::Gender::Masculine.
Instance Method Summary collapse
- #annotated_object ⇒ Object
-
#classification_label ⇒ String
A humanized class name, with code appended to differentiate !! explored idea of LABEL in individual subclasses, use this if this doesn't work this is helper-esqe, but also useful in validation, so here for now.
-
#nomen_id ⇒ String
The NOMEN id for this classification.
- #nomenclature_code ⇒ Object
- #nomenclature_code_matches ⇒ Object private
- #set_cached ⇒ Object
-
#set_cached_names_for_taxon_names ⇒ Object
TODO: move these to individual classes?!.
- #sv_not_specific_classes ⇒ Object
-
#sv_proper_classification ⇒ Object
region Soft validation.
- #sv_proper_year ⇒ Object
- #sv_validate_disjoint_classes ⇒ Object
- #type_class ⇒ Object
- #type_class=(value) ⇒ Object
-
#type_name ⇒ String
The class name, “validated” against the known list of names.
- #validate_taxon_name_classification ⇒ Object private
-
#validate_uniqueness_of_latinized ⇒ Object
region Validation.
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::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 Shared::Notes
#concatenated_notes_string, #reject_notes
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 Housekeeping
#has_polymorphic_relationship?
Methods inherited from ApplicationRecord
Instance Attribute Details
#project_id ⇒ Integer
the project ID
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# File 'app/models/taxon_name_classification.rb', line 18 class TaxonNameClassification < ApplicationRecord include Housekeeping include Shared::Citations include Shared::Notes include Shared::IsData include SoftValidation belongs_to :taxon_name, inverse_of: :taxon_name_classifications before_validation :validate_taxon_name_classification before_validation :validate_uniqueness_of_latinized validates_presence_of :taxon_name validates_presence_of :type validates_uniqueness_of :taxon_name_id, scope: :type validate :nomenclature_code_matches scope :where_taxon_name, -> (taxon_name) {where(taxon_name_id: taxon_name)} scope :with_type_string, -> (base_string) {where('taxon_name_classifications.type LIKE ?', "#{base_string}" ) } scope :with_type_base, -> (base_string) {where('taxon_name_classifications.type LIKE ?', "#{base_string}%" ) } scope :with_type_array, -> (base_array) {where('taxon_name_classifications.type IN (?)', base_array ) } scope :with_type_contains, -> (base_string) {where('taxon_name_classifications.type LIKE ?', "%#{base_string}%" ) } soft_validate(:sv_proper_classification, set: :proper_classification, name: 'Applicable status', description: 'Check the status applicability.' ) soft_validate(:sv_proper_year, set: :proper_classification, name: 'Applicable protonym year', description: 'Check that the status is compatible with the year of publication of taxon.' ) soft_validate(:sv_validate_disjoint_classes, set: :validate_disjoint_classes, name: 'Conflicting status', description: 'Taxon has two conflicting statuses' ) soft_validate(:sv_not_specific_classes, set: :not_specific_classes, name: 'Not specific status', description: 'More specific statuses are preffered, for example: "Nomen nudum, no description" is better than "Nomen nudum".' ) after_save :set_cached after_destroy :set_cached def nomenclature_code return :iczn if type.match(/::Iczn/) return :icnp if type.match(/::Icnp/) return :icvcn if type.match(/::Icvcn/) return :icn if type.match(/::Icn/) return nil end def self.label name.demodulize.underscore.humanize.downcase.gsub(/\d+/, ' \0 ').squish end # @return class # this method calls Module#module_parent def self.parent self.module_parent end # @return [String] # the class name, "validated" against the known list of names def type_name r = self.type.to_s ::TAXON_NAME_CLASSIFICATION_NAMES.include?(r) ? r : nil end def type_class=(value) write_attribute(:type, value.to_s) end def type_class r = read_attribute(:type).to_s r = ::TAXON_NAME_CLASSIFICATION_NAMES.include?(r) ? r.safe_constantize : nil end # @return [String] # a humanized class name, with code appended to differentiate # !! explored idea of LABEL in individual subclasses, use this if this doesn't work # this is helper-esqe, but also useful in validation, so here for now def classification_label return nil if type_name.nil? type_name.demodulize.underscore.humanize.downcase.gsub(/\d+/, ' \0 ').squish #+ #(nomenclature_code ? " [#{nomenclature_code}]" : '') end # @return [String] # the NOMEN id for this classification def nomen_id self.class::NOMEN_URI.split('/').last end # Attributes can be overridden in descendants # @return [Integer] # the minimum year of applicability for this class, defaults to 1 def self.code_applicability_start_year 1 end # @return [Integer] # the last year of applicability for this class, defaults to 9999 def self.code_applicability_end_year 9999 end # @return [Array of Strings of NomenclaturalRank names] # nomenclatural ranks to which this class is applicable, that is, only {TaxonName}s of these {NomenclaturalRank}s may be classified as this class def self.applicable_ranks [] end # @return [Array of Strings of TaxonNameClassification names] # the disjoint (inapplicable) {TaxonNameClassification}s for this class, that is, {TaxonName}s classified as this class can not be additionally classified under these classes def self.disjoint_taxon_name_classes [] end # @return [String, nil] # if applicable, a DWC gbif status for this class def self.gbif_status nil end def self.assignable false end #def self.common # false #end # @todo Perhaps not inherit these three meaxonNameClassificationsHelper::descendants_collection( TaxonNameClassification::Latinized )thods? # @return [Array of Strings] # the possible suffixes for a {TaxonName} name (species) classified as this class, for example see {TaxonNameClassification::Latinized::Gender::Masculine} # used to validate gender agreement of species name with a genus def self.possible_species_endings [] end # @return [Array of Strings] # the questionable suffixes for a {TaxonName} name classified as this class, for example see {TaxonNameClassification::Latinized::Gender::Masculine} def self.questionable_species_endings [] end # @return [Array of Strings] # the possible suffixes for a {TaxonName} name (genus) classified as this class, for example see {TaxonNameClassification::Latinized::Gender::Masculine} def self.possible_genus_endings [] end def self.nomen_uri const_defined?(:NOMEN_URI, false) ? self::NOMEN_URI : nil end def set_cached set_cached_names_for_taxon_names end # TODO: move these to individual classes?! def set_cached_names_for_taxon_names begin TaxonName.transaction_with_retry do t = taxon_name if type_name =~ /(Fossil|Hybrid|Candidatus)/ n = t.get_full_name t.update_columns( cached: n, cached_html: t.get_full_name_html(n), cached_original_combination: t.get_original_combination, cached_original_combination_html: t.get_original_combination_html ) elsif type_name =~ /Latinized::PartOfSpeech/ n = t.get_full_name t.update_columns( cached: n, cached_html: t.get_full_name_html(n), cached_original_combination: t.get_original_combination, cached_original_combination_html: t.get_original_combination_html ) TaxonNameRelationship::OriginalCombination.where(subject_taxon_name: t).collect{|i| i.object_taxon_name}.uniq.each do |t1| t1.update_cached_original_combinations end TaxonNameRelationship::Combination.where(subject_taxon_name: t).collect{|i| i.object_taxon_name}.uniq.each do |t1| t1.update_column(:verbatim_name, t1.cached) if t1.verbatim_name.nil? n = t1.get_full_name t1.update_columns( cached: n, cached_html: t1.get_full_name_html(n) ) end elsif type_name =~ /Latinized::Gender/ t.descendants.with_same_cached_valid_id.each do |t1| n = t1.get_full_name t1.update_columns( cached: n, cached_html: t1.get_full_name_html(n) ) end TaxonNameRelationship::OriginalCombination.where(subject_taxon_name: t).collect{|i| i.object_taxon_name}.uniq.each do |t1| t1.update_cached_original_combinations end TaxonNameRelationship::Combination.where(subject_taxon_name: t).collect{|i| i.object_taxon_name}.uniq.each do |t1| t1.update_column(:verbatim_name, t1.cached) if t1.verbatim_name.nil? n = t1.get_full_name t1.update_columns( cached: n, cached_html: t1.get_full_name_html(n) ) end elsif TAXON_NAME_CLASS_NAMES_VALID.include?(type_name) # TaxonName.where(cached_valid_taxon_name_id: t.cached_valid_taxon_name_id).each do |vn| # vn.update_column(:cached_valid_taxon_name_id, vn.get_valid_taxon_name.id) # update self too! # end vn = t.get_valid_taxon_name vn.update_columns( cached_valid_taxon_name_id: vn.id, cached_is_valid: !vn.unavailable_or_invalid?) # Do not change! vn.list_of_invalid_taxon_names.each do |s| s.update_columns( cached_valid_taxon_name_id: vn.id, cached_is_valid: false) s.combination_list_self.each do |c| c.update_columns(cached_valid_taxon_name_id: vn.id) end end t.combination_list_self.each do |c| c.update_columns(cached_valid_taxon_name_id: vn.id) end else t.update_columns(cached_is_valid: false) end end rescue ActiveRecord::RecordInvalid false end true end #region Validation def validate_uniqueness_of_latinized true # moved to subclasses end #endregion #region Soft validation def sv_proper_classification if TAXON_NAME_CLASSIFICATION_NAMES.include?(self.type) # self.type_class is a Class if not self.type_class.applicable_ranks.include?(self.taxon_name.rank_string) soft_validations.add(:type, "The status '#{self.classification_label}' is unapplicable to the taxon #{self.taxon_name.cached_html} at the rank of #{self.taxon_name.rank_class.rank_name}") end end end def sv_proper_year y = self.taxon_name.year_of_publication if !y.nil? && (y > self.type_class.code_applicability_end_year || y < self.type_class.code_applicability_start_year) soft_validations.add(:type, "The status '#{self.classification_label}' is unapplicable to the taxon #{self.taxon_name.cached_html} published in the year #{y}") end end def sv_validate_disjoint_classes classifications = TaxonNameClassification.where_taxon_name(self.taxon_name).not_self(self) classifications.each do |i| soft_validations.add(:type, "The status '#{self.classification_label}' conflicting with another status: '#{i.classification_label}'") if self.type_class.disjoint_taxon_name_classes.include?(i.type_name) end end def sv_not_specific_classes true # moved to subclasses end #endregion def self.annotates? true end def annotated_object taxon_name end private def nomenclature_code_matches if taxon_name && type && nomenclature_code tn = taxon_name.type == 'Combination' ? taxon_name.protonyms.last : taxon_name nc = tn.rank_class.nomenclatural_code errors.add(:taxon_name, "#{taxon_name.cached_html} belongs to #{taxon_name.rank_class.nomenclatural_code} nomenclatural code, but the status used from #{nomenclature_code} nomenclature code") if nomenclature_code != nc end end def validate_taxon_name_classification errors.add(:type, 'Status not found') if !self.type.nil? and !TAXON_NAME_CLASSIFICATION_NAMES.include?(self.type.to_s) end # @todo move these to a shared library (see NomenclaturalRank too) def self.collect_to_s(*args) args.collect{|arg| arg.to_s} end # @todo move these to a shared library (see NomenclaturalRank too) # !! using this strongly suggests something can be optimized, meomized etc. def self.collect_descendants_to_s(*classes) ans = [] classes.each do |klass| ans += klass.descendants.collect{|k| k.to_s} end ans end # @todo move these to a shared library (see NomenclaturalRank too) # !! using this strongly suggests something can be optimized, meomized etc. def self.collect_descendants_and_itself_to_s(*classes) classes.collect{|k| k.to_s} + self.collect_descendants_to_s(*classes) end end |
#taxon_name_id ⇒ Integer
Returns the id of the TaxonName being classified.
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# File 'app/models/taxon_name_classification.rb', line 18 class TaxonNameClassification < ApplicationRecord include Housekeeping include Shared::Citations include Shared::Notes include Shared::IsData include SoftValidation belongs_to :taxon_name, inverse_of: :taxon_name_classifications before_validation :validate_taxon_name_classification before_validation :validate_uniqueness_of_latinized validates_presence_of :taxon_name validates_presence_of :type validates_uniqueness_of :taxon_name_id, scope: :type validate :nomenclature_code_matches scope :where_taxon_name, -> (taxon_name) {where(taxon_name_id: taxon_name)} scope :with_type_string, -> (base_string) {where('taxon_name_classifications.type LIKE ?', "#{base_string}" ) } scope :with_type_base, -> (base_string) {where('taxon_name_classifications.type LIKE ?', "#{base_string}%" ) } scope :with_type_array, -> (base_array) {where('taxon_name_classifications.type IN (?)', base_array ) } scope :with_type_contains, -> (base_string) {where('taxon_name_classifications.type LIKE ?', "%#{base_string}%" ) } soft_validate(:sv_proper_classification, set: :proper_classification, name: 'Applicable status', description: 'Check the status applicability.' ) soft_validate(:sv_proper_year, set: :proper_classification, name: 'Applicable protonym year', description: 'Check that the status is compatible with the year of publication of taxon.' ) soft_validate(:sv_validate_disjoint_classes, set: :validate_disjoint_classes, name: 'Conflicting status', description: 'Taxon has two conflicting statuses' ) soft_validate(:sv_not_specific_classes, set: :not_specific_classes, name: 'Not specific status', description: 'More specific statuses are preffered, for example: "Nomen nudum, no description" is better than "Nomen nudum".' ) after_save :set_cached after_destroy :set_cached def nomenclature_code return :iczn if type.match(/::Iczn/) return :icnp if type.match(/::Icnp/) return :icvcn if type.match(/::Icvcn/) return :icn if type.match(/::Icn/) return nil end def self.label name.demodulize.underscore.humanize.downcase.gsub(/\d+/, ' \0 ').squish end # @return class # this method calls Module#module_parent def self.parent self.module_parent end # @return [String] # the class name, "validated" against the known list of names def type_name r = self.type.to_s ::TAXON_NAME_CLASSIFICATION_NAMES.include?(r) ? r : nil end def type_class=(value) write_attribute(:type, value.to_s) end def type_class r = read_attribute(:type).to_s r = ::TAXON_NAME_CLASSIFICATION_NAMES.include?(r) ? r.safe_constantize : nil end # @return [String] # a humanized class name, with code appended to differentiate # !! explored idea of LABEL in individual subclasses, use this if this doesn't work # this is helper-esqe, but also useful in validation, so here for now def classification_label return nil if type_name.nil? type_name.demodulize.underscore.humanize.downcase.gsub(/\d+/, ' \0 ').squish #+ #(nomenclature_code ? " [#{nomenclature_code}]" : '') end # @return [String] # the NOMEN id for this classification def nomen_id self.class::NOMEN_URI.split('/').last end # Attributes can be overridden in descendants # @return [Integer] # the minimum year of applicability for this class, defaults to 1 def self.code_applicability_start_year 1 end # @return [Integer] # the last year of applicability for this class, defaults to 9999 def self.code_applicability_end_year 9999 end # @return [Array of Strings of NomenclaturalRank names] # nomenclatural ranks to which this class is applicable, that is, only {TaxonName}s of these {NomenclaturalRank}s may be classified as this class def self.applicable_ranks [] end # @return [Array of Strings of TaxonNameClassification names] # the disjoint (inapplicable) {TaxonNameClassification}s for this class, that is, {TaxonName}s classified as this class can not be additionally classified under these classes def self.disjoint_taxon_name_classes [] end # @return [String, nil] # if applicable, a DWC gbif status for this class def self.gbif_status nil end def self.assignable false end #def self.common # false #end # @todo Perhaps not inherit these three meaxonNameClassificationsHelper::descendants_collection( TaxonNameClassification::Latinized )thods? # @return [Array of Strings] # the possible suffixes for a {TaxonName} name (species) classified as this class, for example see {TaxonNameClassification::Latinized::Gender::Masculine} # used to validate gender agreement of species name with a genus def self.possible_species_endings [] end # @return [Array of Strings] # the questionable suffixes for a {TaxonName} name classified as this class, for example see {TaxonNameClassification::Latinized::Gender::Masculine} def self.questionable_species_endings [] end # @return [Array of Strings] # the possible suffixes for a {TaxonName} name (genus) classified as this class, for example see {TaxonNameClassification::Latinized::Gender::Masculine} def self.possible_genus_endings [] end def self.nomen_uri const_defined?(:NOMEN_URI, false) ? self::NOMEN_URI : nil end def set_cached set_cached_names_for_taxon_names end # TODO: move these to individual classes?! def set_cached_names_for_taxon_names begin TaxonName.transaction_with_retry do t = taxon_name if type_name =~ /(Fossil|Hybrid|Candidatus)/ n = t.get_full_name t.update_columns( cached: n, cached_html: t.get_full_name_html(n), cached_original_combination: t.get_original_combination, cached_original_combination_html: t.get_original_combination_html ) elsif type_name =~ /Latinized::PartOfSpeech/ n = t.get_full_name t.update_columns( cached: n, cached_html: t.get_full_name_html(n), cached_original_combination: t.get_original_combination, cached_original_combination_html: t.get_original_combination_html ) TaxonNameRelationship::OriginalCombination.where(subject_taxon_name: t).collect{|i| i.object_taxon_name}.uniq.each do |t1| t1.update_cached_original_combinations end TaxonNameRelationship::Combination.where(subject_taxon_name: t).collect{|i| i.object_taxon_name}.uniq.each do |t1| t1.update_column(:verbatim_name, t1.cached) if t1.verbatim_name.nil? n = t1.get_full_name t1.update_columns( cached: n, cached_html: t1.get_full_name_html(n) ) end elsif type_name =~ /Latinized::Gender/ t.descendants.with_same_cached_valid_id.each do |t1| n = t1.get_full_name t1.update_columns( cached: n, cached_html: t1.get_full_name_html(n) ) end TaxonNameRelationship::OriginalCombination.where(subject_taxon_name: t).collect{|i| i.object_taxon_name}.uniq.each do |t1| t1.update_cached_original_combinations end TaxonNameRelationship::Combination.where(subject_taxon_name: t).collect{|i| i.object_taxon_name}.uniq.each do |t1| t1.update_column(:verbatim_name, t1.cached) if t1.verbatim_name.nil? n = t1.get_full_name t1.update_columns( cached: n, cached_html: t1.get_full_name_html(n) ) end elsif TAXON_NAME_CLASS_NAMES_VALID.include?(type_name) # TaxonName.where(cached_valid_taxon_name_id: t.cached_valid_taxon_name_id).each do |vn| # vn.update_column(:cached_valid_taxon_name_id, vn.get_valid_taxon_name.id) # update self too! # end vn = t.get_valid_taxon_name vn.update_columns( cached_valid_taxon_name_id: vn.id, cached_is_valid: !vn.unavailable_or_invalid?) # Do not change! vn.list_of_invalid_taxon_names.each do |s| s.update_columns( cached_valid_taxon_name_id: vn.id, cached_is_valid: false) s.combination_list_self.each do |c| c.update_columns(cached_valid_taxon_name_id: vn.id) end end t.combination_list_self.each do |c| c.update_columns(cached_valid_taxon_name_id: vn.id) end else t.update_columns(cached_is_valid: false) end end rescue ActiveRecord::RecordInvalid false end true end #region Validation def validate_uniqueness_of_latinized true # moved to subclasses end #endregion #region Soft validation def sv_proper_classification if TAXON_NAME_CLASSIFICATION_NAMES.include?(self.type) # self.type_class is a Class if not self.type_class.applicable_ranks.include?(self.taxon_name.rank_string) soft_validations.add(:type, "The status '#{self.classification_label}' is unapplicable to the taxon #{self.taxon_name.cached_html} at the rank of #{self.taxon_name.rank_class.rank_name}") end end end def sv_proper_year y = self.taxon_name.year_of_publication if !y.nil? && (y > self.type_class.code_applicability_end_year || y < self.type_class.code_applicability_start_year) soft_validations.add(:type, "The status '#{self.classification_label}' is unapplicable to the taxon #{self.taxon_name.cached_html} published in the year #{y}") end end def sv_validate_disjoint_classes classifications = TaxonNameClassification.where_taxon_name(self.taxon_name).not_self(self) classifications.each do |i| soft_validations.add(:type, "The status '#{self.classification_label}' conflicting with another status: '#{i.classification_label}'") if self.type_class.disjoint_taxon_name_classes.include?(i.type_name) end end def sv_not_specific_classes true # moved to subclasses end #endregion def self.annotates? true end def annotated_object taxon_name end private def nomenclature_code_matches if taxon_name && type && nomenclature_code tn = taxon_name.type == 'Combination' ? taxon_name.protonyms.last : taxon_name nc = tn.rank_class.nomenclatural_code errors.add(:taxon_name, "#{taxon_name.cached_html} belongs to #{taxon_name.rank_class.nomenclatural_code} nomenclatural code, but the status used from #{nomenclature_code} nomenclature code") if nomenclature_code != nc end end def validate_taxon_name_classification errors.add(:type, 'Status not found') if !self.type.nil? and !TAXON_NAME_CLASSIFICATION_NAMES.include?(self.type.to_s) end # @todo move these to a shared library (see NomenclaturalRank too) def self.collect_to_s(*args) args.collect{|arg| arg.to_s} end # @todo move these to a shared library (see NomenclaturalRank too) # !! using this strongly suggests something can be optimized, meomized etc. def self.collect_descendants_to_s(*classes) ans = [] classes.each do |klass| ans += klass.descendants.collect{|k| k.to_s} end ans end # @todo move these to a shared library (see NomenclaturalRank too) # !! using this strongly suggests something can be optimized, meomized etc. def self.collect_descendants_and_itself_to_s(*classes) classes.collect{|k| k.to_s} + self.collect_descendants_to_s(*classes) end end |
#type ⇒ String
Returns the type of classifiction (Rails STI).
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# File 'app/models/taxon_name_classification.rb', line 18 class TaxonNameClassification < ApplicationRecord include Housekeeping include Shared::Citations include Shared::Notes include Shared::IsData include SoftValidation belongs_to :taxon_name, inverse_of: :taxon_name_classifications before_validation :validate_taxon_name_classification before_validation :validate_uniqueness_of_latinized validates_presence_of :taxon_name validates_presence_of :type validates_uniqueness_of :taxon_name_id, scope: :type validate :nomenclature_code_matches scope :where_taxon_name, -> (taxon_name) {where(taxon_name_id: taxon_name)} scope :with_type_string, -> (base_string) {where('taxon_name_classifications.type LIKE ?', "#{base_string}" ) } scope :with_type_base, -> (base_string) {where('taxon_name_classifications.type LIKE ?', "#{base_string}%" ) } scope :with_type_array, -> (base_array) {where('taxon_name_classifications.type IN (?)', base_array ) } scope :with_type_contains, -> (base_string) {where('taxon_name_classifications.type LIKE ?', "%#{base_string}%" ) } soft_validate(:sv_proper_classification, set: :proper_classification, name: 'Applicable status', description: 'Check the status applicability.' ) soft_validate(:sv_proper_year, set: :proper_classification, name: 'Applicable protonym year', description: 'Check that the status is compatible with the year of publication of taxon.' ) soft_validate(:sv_validate_disjoint_classes, set: :validate_disjoint_classes, name: 'Conflicting status', description: 'Taxon has two conflicting statuses' ) soft_validate(:sv_not_specific_classes, set: :not_specific_classes, name: 'Not specific status', description: 'More specific statuses are preffered, for example: "Nomen nudum, no description" is better than "Nomen nudum".' ) after_save :set_cached after_destroy :set_cached def nomenclature_code return :iczn if type.match(/::Iczn/) return :icnp if type.match(/::Icnp/) return :icvcn if type.match(/::Icvcn/) return :icn if type.match(/::Icn/) return nil end def self.label name.demodulize.underscore.humanize.downcase.gsub(/\d+/, ' \0 ').squish end # @return class # this method calls Module#module_parent def self.parent self.module_parent end # @return [String] # the class name, "validated" against the known list of names def type_name r = self.type.to_s ::TAXON_NAME_CLASSIFICATION_NAMES.include?(r) ? r : nil end def type_class=(value) write_attribute(:type, value.to_s) end def type_class r = read_attribute(:type).to_s r = ::TAXON_NAME_CLASSIFICATION_NAMES.include?(r) ? r.safe_constantize : nil end # @return [String] # a humanized class name, with code appended to differentiate # !! explored idea of LABEL in individual subclasses, use this if this doesn't work # this is helper-esqe, but also useful in validation, so here for now def classification_label return nil if type_name.nil? type_name.demodulize.underscore.humanize.downcase.gsub(/\d+/, ' \0 ').squish #+ #(nomenclature_code ? " [#{nomenclature_code}]" : '') end # @return [String] # the NOMEN id for this classification def nomen_id self.class::NOMEN_URI.split('/').last end # Attributes can be overridden in descendants # @return [Integer] # the minimum year of applicability for this class, defaults to 1 def self.code_applicability_start_year 1 end # @return [Integer] # the last year of applicability for this class, defaults to 9999 def self.code_applicability_end_year 9999 end # @return [Array of Strings of NomenclaturalRank names] # nomenclatural ranks to which this class is applicable, that is, only {TaxonName}s of these {NomenclaturalRank}s may be classified as this class def self.applicable_ranks [] end # @return [Array of Strings of TaxonNameClassification names] # the disjoint (inapplicable) {TaxonNameClassification}s for this class, that is, {TaxonName}s classified as this class can not be additionally classified under these classes def self.disjoint_taxon_name_classes [] end # @return [String, nil] # if applicable, a DWC gbif status for this class def self.gbif_status nil end def self.assignable false end #def self.common # false #end # @todo Perhaps not inherit these three meaxonNameClassificationsHelper::descendants_collection( TaxonNameClassification::Latinized )thods? # @return [Array of Strings] # the possible suffixes for a {TaxonName} name (species) classified as this class, for example see {TaxonNameClassification::Latinized::Gender::Masculine} # used to validate gender agreement of species name with a genus def self.possible_species_endings [] end # @return [Array of Strings] # the questionable suffixes for a {TaxonName} name classified as this class, for example see {TaxonNameClassification::Latinized::Gender::Masculine} def self.questionable_species_endings [] end # @return [Array of Strings] # the possible suffixes for a {TaxonName} name (genus) classified as this class, for example see {TaxonNameClassification::Latinized::Gender::Masculine} def self.possible_genus_endings [] end def self.nomen_uri const_defined?(:NOMEN_URI, false) ? self::NOMEN_URI : nil end def set_cached set_cached_names_for_taxon_names end # TODO: move these to individual classes?! def set_cached_names_for_taxon_names begin TaxonName.transaction_with_retry do t = taxon_name if type_name =~ /(Fossil|Hybrid|Candidatus)/ n = t.get_full_name t.update_columns( cached: n, cached_html: t.get_full_name_html(n), cached_original_combination: t.get_original_combination, cached_original_combination_html: t.get_original_combination_html ) elsif type_name =~ /Latinized::PartOfSpeech/ n = t.get_full_name t.update_columns( cached: n, cached_html: t.get_full_name_html(n), cached_original_combination: t.get_original_combination, cached_original_combination_html: t.get_original_combination_html ) TaxonNameRelationship::OriginalCombination.where(subject_taxon_name: t).collect{|i| i.object_taxon_name}.uniq.each do |t1| t1.update_cached_original_combinations end TaxonNameRelationship::Combination.where(subject_taxon_name: t).collect{|i| i.object_taxon_name}.uniq.each do |t1| t1.update_column(:verbatim_name, t1.cached) if t1.verbatim_name.nil? n = t1.get_full_name t1.update_columns( cached: n, cached_html: t1.get_full_name_html(n) ) end elsif type_name =~ /Latinized::Gender/ t.descendants.with_same_cached_valid_id.each do |t1| n = t1.get_full_name t1.update_columns( cached: n, cached_html: t1.get_full_name_html(n) ) end TaxonNameRelationship::OriginalCombination.where(subject_taxon_name: t).collect{|i| i.object_taxon_name}.uniq.each do |t1| t1.update_cached_original_combinations end TaxonNameRelationship::Combination.where(subject_taxon_name: t).collect{|i| i.object_taxon_name}.uniq.each do |t1| t1.update_column(:verbatim_name, t1.cached) if t1.verbatim_name.nil? n = t1.get_full_name t1.update_columns( cached: n, cached_html: t1.get_full_name_html(n) ) end elsif TAXON_NAME_CLASS_NAMES_VALID.include?(type_name) # TaxonName.where(cached_valid_taxon_name_id: t.cached_valid_taxon_name_id).each do |vn| # vn.update_column(:cached_valid_taxon_name_id, vn.get_valid_taxon_name.id) # update self too! # end vn = t.get_valid_taxon_name vn.update_columns( cached_valid_taxon_name_id: vn.id, cached_is_valid: !vn.unavailable_or_invalid?) # Do not change! vn.list_of_invalid_taxon_names.each do |s| s.update_columns( cached_valid_taxon_name_id: vn.id, cached_is_valid: false) s.combination_list_self.each do |c| c.update_columns(cached_valid_taxon_name_id: vn.id) end end t.combination_list_self.each do |c| c.update_columns(cached_valid_taxon_name_id: vn.id) end else t.update_columns(cached_is_valid: false) end end rescue ActiveRecord::RecordInvalid false end true end #region Validation def validate_uniqueness_of_latinized true # moved to subclasses end #endregion #region Soft validation def sv_proper_classification if TAXON_NAME_CLASSIFICATION_NAMES.include?(self.type) # self.type_class is a Class if not self.type_class.applicable_ranks.include?(self.taxon_name.rank_string) soft_validations.add(:type, "The status '#{self.classification_label}' is unapplicable to the taxon #{self.taxon_name.cached_html} at the rank of #{self.taxon_name.rank_class.rank_name}") end end end def sv_proper_year y = self.taxon_name.year_of_publication if !y.nil? && (y > self.type_class.code_applicability_end_year || y < self.type_class.code_applicability_start_year) soft_validations.add(:type, "The status '#{self.classification_label}' is unapplicable to the taxon #{self.taxon_name.cached_html} published in the year #{y}") end end def sv_validate_disjoint_classes classifications = TaxonNameClassification.where_taxon_name(self.taxon_name).not_self(self) classifications.each do |i| soft_validations.add(:type, "The status '#{self.classification_label}' conflicting with another status: '#{i.classification_label}'") if self.type_class.disjoint_taxon_name_classes.include?(i.type_name) end end def sv_not_specific_classes true # moved to subclasses end #endregion def self.annotates? true end def annotated_object taxon_name end private def nomenclature_code_matches if taxon_name && type && nomenclature_code tn = taxon_name.type == 'Combination' ? taxon_name.protonyms.last : taxon_name nc = tn.rank_class.nomenclatural_code errors.add(:taxon_name, "#{taxon_name.cached_html} belongs to #{taxon_name.rank_class.nomenclatural_code} nomenclatural code, but the status used from #{nomenclature_code} nomenclature code") if nomenclature_code != nc end end def validate_taxon_name_classification errors.add(:type, 'Status not found') if !self.type.nil? and !TAXON_NAME_CLASSIFICATION_NAMES.include?(self.type.to_s) end # @todo move these to a shared library (see NomenclaturalRank too) def self.collect_to_s(*args) args.collect{|arg| arg.to_s} end # @todo move these to a shared library (see NomenclaturalRank too) # !! using this strongly suggests something can be optimized, meomized etc. def self.collect_descendants_to_s(*classes) ans = [] classes.each do |klass| ans += klass.descendants.collect{|k| k.to_s} end ans end # @todo move these to a shared library (see NomenclaturalRank too) # !! using this strongly suggests something can be optimized, meomized etc. def self.collect_descendants_and_itself_to_s(*classes) classes.collect{|k| k.to_s} + self.collect_descendants_to_s(*classes) end end |
Class Method Details
.annotates? ⇒ Boolean
endregion
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# File 'app/models/taxon_name_classification.rb', line 306 def self.annotates? true end |
.applicable_ranks ⇒ Array of Strings of NomenclaturalRank names
nomenclatural ranks to which this class is applicable, that is, only TaxonNames of these NomenclaturalRanks may be classified as this class
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# File 'app/models/taxon_name_classification.rb', line 130 def self.applicable_ranks [] end |
.assignable ⇒ Object
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# File 'app/models/taxon_name_classification.rb', line 146 def self.assignable false end |
.code_applicability_end_year ⇒ Integer
the last year of applicability for this class, defaults to 9999
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# File 'app/models/taxon_name_classification.rb', line 124 def self.code_applicability_end_year 9999 end |
.code_applicability_start_year ⇒ Integer
the minimum year of applicability for this class, defaults to 1
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# File 'app/models/taxon_name_classification.rb', line 118 def self.code_applicability_start_year 1 end |
.collect_descendants_and_itself_to_s(*classes) ⇒ Object (private)
move these to a shared library (see NomenclaturalRank too)
!! using this strongly suggests something can be optimized, meomized etc.
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# File 'app/models/taxon_name_classification.rb', line 346 def self.collect_descendants_and_itself_to_s(*classes) classes.collect{|k| k.to_s} + self.collect_descendants_to_s(*classes) end |
.collect_descendants_to_s(*classes) ⇒ Object (private)
move these to a shared library (see NomenclaturalRank too)
!! using this strongly suggests something can be optimized, meomized etc.
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# File 'app/models/taxon_name_classification.rb', line 336 def self.collect_descendants_to_s(*classes) ans = [] classes.each do |klass| ans += klass.descendants.collect{|k| k.to_s} end ans end |
.collect_to_s(*args) ⇒ Object (private)
move these to a shared library (see NomenclaturalRank too)
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# File 'app/models/taxon_name_classification.rb', line 330 def self.collect_to_s(*args) args.collect{|arg| arg.to_s} end |
.disjoint_taxon_name_classes ⇒ Array of Strings of TaxonNameClassification names
the disjoint (inapplicable) TaxonNameClassifications for this class, that is, TaxonNames classified as this class can not be additionally classified under these classes
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# File 'app/models/taxon_name_classification.rb', line 136 def self.disjoint_taxon_name_classes [] end |
.gbif_status ⇒ String?
Returns if applicable, a DWC gbif status for this class.
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# File 'app/models/taxon_name_classification.rb', line 142 def self.gbif_status nil end |
.label ⇒ Object
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# File 'app/models/taxon_name_classification.rb', line 72 def self.label name.demodulize.underscore.humanize.downcase.gsub(/\d+/, ' \0 ').squish end |
.nomen_uri ⇒ Object
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# File 'app/models/taxon_name_classification.rb', line 175 def self.nomen_uri const_defined?(:NOMEN_URI, false) ? self::NOMEN_URI : nil end |
.parent ⇒ Object
Returns class this method calls Module#module_parent.
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# File 'app/models/taxon_name_classification.rb', line 78 def self.parent self.module_parent end |
.possible_genus_endings ⇒ Array of Strings
the possible suffixes for a TaxonName name (genus) classified as this class, for example see TaxonNameClassification::Latinized::Gender::Masculine
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# File 'app/models/taxon_name_classification.rb', line 171 def self.possible_genus_endings [] end |
.possible_species_endings ⇒ Array of Strings
Returns the possible suffixes for a TaxonName name (species) classified as this class, for example see TaxonNameClassification::Latinized::Gender::Masculine used to validate gender agreement of species name with a genus.
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# File 'app/models/taxon_name_classification.rb', line 159 def self.possible_species_endings [] end |
.questionable_species_endings ⇒ Array of Strings
Returns the questionable suffixes for a TaxonName name classified as this class, for example see TaxonNameClassification::Latinized::Gender::Masculine.
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# File 'app/models/taxon_name_classification.rb', line 165 def self.questionable_species_endings [] end |
Instance Method Details
#annotated_object ⇒ Object
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# File 'app/models/taxon_name_classification.rb', line 310 def annotated_object taxon_name end |
#classification_label ⇒ String
Returns a humanized class name, with code appended to differentiate !! explored idea of LABEL in individual subclasses, use this if this doesn't work this is helper-esqe, but also useful in validation, so here for now.
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# File 'app/models/taxon_name_classification.rb', line 102 def classification_label return nil if type_name.nil? type_name.demodulize.underscore.humanize.downcase.gsub(/\d+/, ' \0 ').squish #+ #(nomenclature_code ? " [#{nomenclature_code}]" : '') end |
#nomen_id ⇒ String
Returns the NOMEN id for this classification.
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# File 'app/models/taxon_name_classification.rb', line 110 def nomen_id self.class::NOMEN_URI.split('/').last end |
#nomenclature_code ⇒ Object
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# File 'app/models/taxon_name_classification.rb', line 64 def nomenclature_code return :iczn if type.match(/::Iczn/) return :icnp if type.match(/::Icnp/) return :icvcn if type.match(/::Icvcn/) return :icn if type.match(/::Icn/) return nil end |
#nomenclature_code_matches ⇒ Object (private)
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# File 'app/models/taxon_name_classification.rb', line 316 def nomenclature_code_matches if taxon_name && type && nomenclature_code tn = taxon_name.type == 'Combination' ? taxon_name.protonyms.last : taxon_name nc = tn.rank_class.nomenclatural_code errors.add(:taxon_name, "#{taxon_name.cached_html} belongs to #{taxon_name.rank_class.nomenclatural_code} nomenclatural code, but the status used from #{nomenclature_code} nomenclature code") if nomenclature_code != nc end end |
#set_cached ⇒ Object
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# File 'app/models/taxon_name_classification.rb', line 179 def set_cached set_cached_names_for_taxon_names end |
#set_cached_names_for_taxon_names ⇒ Object
TODO: move these to individual classes?!
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# File 'app/models/taxon_name_classification.rb', line 184 def set_cached_names_for_taxon_names begin TaxonName.transaction_with_retry do t = taxon_name if type_name =~ /(Fossil|Hybrid|Candidatus)/ n = t.get_full_name t.update_columns( cached: n, cached_html: t.get_full_name_html(n), cached_original_combination: t.get_original_combination, cached_original_combination_html: t.get_original_combination_html ) elsif type_name =~ /Latinized::PartOfSpeech/ n = t.get_full_name t.update_columns( cached: n, cached_html: t.get_full_name_html(n), cached_original_combination: t.get_original_combination, cached_original_combination_html: t.get_original_combination_html ) TaxonNameRelationship::OriginalCombination.where(subject_taxon_name: t).collect{|i| i.object_taxon_name}.uniq.each do |t1| t1.update_cached_original_combinations end TaxonNameRelationship::Combination.where(subject_taxon_name: t).collect{|i| i.object_taxon_name}.uniq.each do |t1| t1.update_column(:verbatim_name, t1.cached) if t1.verbatim_name.nil? n = t1.get_full_name t1.update_columns( cached: n, cached_html: t1.get_full_name_html(n) ) end elsif type_name =~ /Latinized::Gender/ t.descendants.with_same_cached_valid_id.each do |t1| n = t1.get_full_name t1.update_columns( cached: n, cached_html: t1.get_full_name_html(n) ) end TaxonNameRelationship::OriginalCombination.where(subject_taxon_name: t).collect{|i| i.object_taxon_name}.uniq.each do |t1| t1.update_cached_original_combinations end TaxonNameRelationship::Combination.where(subject_taxon_name: t).collect{|i| i.object_taxon_name}.uniq.each do |t1| t1.update_column(:verbatim_name, t1.cached) if t1.verbatim_name.nil? n = t1.get_full_name t1.update_columns( cached: n, cached_html: t1.get_full_name_html(n) ) end elsif TAXON_NAME_CLASS_NAMES_VALID.include?(type_name) # TaxonName.where(cached_valid_taxon_name_id: t.cached_valid_taxon_name_id).each do |vn| # vn.update_column(:cached_valid_taxon_name_id, vn.get_valid_taxon_name.id) # update self too! # end vn = t.get_valid_taxon_name vn.update_columns( cached_valid_taxon_name_id: vn.id, cached_is_valid: !vn.unavailable_or_invalid?) # Do not change! vn.list_of_invalid_taxon_names.each do |s| s.update_columns( cached_valid_taxon_name_id: vn.id, cached_is_valid: false) s.combination_list_self.each do |c| c.update_columns(cached_valid_taxon_name_id: vn.id) end end t.combination_list_self.each do |c| c.update_columns(cached_valid_taxon_name_id: vn.id) end else t.update_columns(cached_is_valid: false) end end rescue ActiveRecord::RecordInvalid false end true end |
#sv_not_specific_classes ⇒ Object
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# File 'app/models/taxon_name_classification.rb', line 300 def sv_not_specific_classes true # moved to subclasses end |
#sv_proper_classification ⇒ Object
region Soft validation
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# File 'app/models/taxon_name_classification.rb', line 277 def sv_proper_classification if TAXON_NAME_CLASSIFICATION_NAMES.include?(self.type) # self.type_class is a Class if not self.type_class.applicable_ranks.include?(self.taxon_name.rank_string) soft_validations.add(:type, "The status '#{self.classification_label}' is unapplicable to the taxon #{self.taxon_name.cached_html} at the rank of #{self.taxon_name.rank_class.rank_name}") end end end |
#sv_proper_year ⇒ Object
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# File 'app/models/taxon_name_classification.rb', line 286 def sv_proper_year y = self.taxon_name.year_of_publication if !y.nil? && (y > self.type_class.code_applicability_end_year || y < self.type_class.code_applicability_start_year) soft_validations.add(:type, "The status '#{self.classification_label}' is unapplicable to the taxon #{self.taxon_name.cached_html} published in the year #{y}") end end |
#sv_validate_disjoint_classes ⇒ Object
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# File 'app/models/taxon_name_classification.rb', line 293 def sv_validate_disjoint_classes classifications = TaxonNameClassification.where_taxon_name(self.taxon_name).not_self(self) classifications.each do |i| soft_validations.add(:type, "The status '#{self.classification_label}' conflicting with another status: '#{i.classification_label}'") if self.type_class.disjoint_taxon_name_classes.include?(i.type_name) end end |
#type_class ⇒ Object
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# File 'app/models/taxon_name_classification.rb', line 93 def type_class r = read_attribute(:type).to_s r = ::TAXON_NAME_CLASSIFICATION_NAMES.include?(r) ? r.safe_constantize : nil end |
#type_class=(value) ⇒ Object
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# File 'app/models/taxon_name_classification.rb', line 89 def type_class=(value) write_attribute(:type, value.to_s) end |
#type_name ⇒ String
Returns the class name, “validated” against the known list of names.
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# File 'app/models/taxon_name_classification.rb', line 84 def type_name r = self.type.to_s ::TAXON_NAME_CLASSIFICATION_NAMES.include?(r) ? r : nil end |
#validate_taxon_name_classification ⇒ Object (private)
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# File 'app/models/taxon_name_classification.rb', line 324 def validate_taxon_name_classification errors.add(:type, 'Status not found') if !self.type.nil? and !TAXON_NAME_CLASSIFICATION_NAMES.include?(self.type.to_s) end |
#validate_uniqueness_of_latinized ⇒ Object
region Validation
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# File 'app/models/taxon_name_classification.rb', line 269 def validate_uniqueness_of_latinized true # moved to subclasses end |