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
A NOMEN derived classfication (roughly, a status) for a TaxonName.
Defined Under Namespace
Classes: Icn, Icnp, Ictv, 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
TODO: helper method.
- .nomen_uri ⇒ Object
-
.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
after_save :set_cached_names_for_taxon_names after_destroy :set_cached_names_for_taxon_names.
- #nomenclature_code_matches ⇒ Object private
- #set_cached ⇒ Object
- #set_cached_names_for_taxon_names ⇒ Object
- #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_soft_validations, #soft_fixed?, #soft_valid?, #soft_validate, #soft_validated?, #soft_validations
Methods included from Housekeeping
#has_polymorphic_relationship?
Methods inherited from ApplicationRecord
Instance Attribute Details
#project_id ⇒ Integer
the project ID
18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80 81 82 83 84 85 86 87 88 89 90 91 92 93 94 95 96 97 98 99 100 101 102 103 104 105 106 107 108 109 110 111 112 113 114 115 116 117 118 119 120 121 122 123 124 125 126 127 128 129 130 131 132 133 134 135 136 137 138 139 140 141 142 143 144 145 146 147 148 149 150 151 152 153 154 155 156 157 158 159 160 161 162 163 164 165 166 167 168 169 170 171 172 173 174 175 176 177 178 179 180 181 182 183 184 185 186 187 188 189 190 191 192 193 194 195 196 197 198 199 200 201 202 203 204 205 206 207 208 209 210 211 212 213 214 215 216 217 218 219 220 221 222 223 224 225 226 227 228 229 230 231 232 233 234 235 236 237 238 239 240 241 242 243 244 245 246 247 248 249 250 251 252 253 254 255 256 257 258 259 260 261 262 263 264 265 266 267 268 269 270 271 272 273 274 275 276 277 278 279 280 281 282 283 284 285 286 287 288 289 290 291 292 293 294 295 296 297 298 299 300 301 302 303 304 305 306 307 308 309 310 311 312 313 314 315 316 317 318 319 320 321 322 323 324 325 326 327 328 329 330 331 332 333 334 335 336 337 338 339 340 341 342 343 344 345 346 347 348 349 350 351 352 353 354 355 356 357 358 359 |
# 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, presence: true validates_presence_of :type, presence: true 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('type LIKE ?', "#{base_string}" ) } scope :with_type_base, -> (base_string) {where('type LIKE ?', "#{base_string}%" ) } scope :with_type_array, -> (base_array) {where('type IN (?)', base_array ) } scope :with_type_contains, -> (base_string) {where('type LIKE ?', "%#{base_string}%" ) } soft_validate(:sv_proper_classification, set: :proper_classification, has_fix: false) soft_validate(:sv_proper_year, set: :proper_classification, has_fix: false) soft_validate(:sv_validate_disjoint_classes, set: :validate_disjoint_classes, has_fix: false) soft_validate(:sv_not_specific_classes, set: :not_specific_classes, has_fix: false) after_save :set_cached after_destroy :set_cached # after_save :set_cached_names_for_taxon_names # after_destroy :set_cached_names_for_taxon_names def nomenclature_code return :iczn if type.match(/::Iczn/) return :icnp if type.match(/::Icnp/) return :ictv if type.match(/::Ictv/) return :icn if type.match(/::Icn/) return nil end # TODO: helper method def self.label name.demodulize.underscore.humanize.downcase.gsub(/\d+/, ' \0 ').squish 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 def set_cached_names_for_taxon_names begin TaxonName.transaction_with_retry do t = taxon_name if type_name =~ /(Fossil|Hybrid|Candidatus)/ t.update_columns( cached: t.get_full_name, cached_html: t.get_full_name_html, cached_original_combination: t.get_original_combination, cached_original_combination_html: t.get_original_combination_html ) elsif type_name =~ /Latinized::Gender/ t.descendants.select{|t| t.id == t.cached_valid_taxon_name_id}.uniq.each do |t1| t1.update_columns( cached: t1.get_full_name, cached_html: t1.get_full_name_html ) end TaxonNameRelationship.where(type: 'TaxonNameRelationship::OriginalCombination::OriginalGenus', subject_taxon_name: t).collect{|i| i.object_taxon_name}.uniq.each do |t1| t1.update_cached_original_combinations end TaxonNameRelationship.where(type: 'TaxonNameRelationship::Combination::Genus', 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? t1.update_columns( cached: t1.get_full_name, cached_html: t1.get_full_name_html ) 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_column(:cached_valid_taxon_name_id, vn.id) # update self too! vn.list_of_invalid_taxon_names.each do |s| s.update_column(:cached_valid_taxon_name_id, vn.id) end t.combination_list_self.each do |c| c.update_column(:cached_valid_taxon_name_id, vn.id) end end end rescue ActiveRecord::RecordInvalid # should return false here, right? end # false # TODO: why false, success == true? end #region Validation def validate_uniqueness_of_latinized true # moved to subclasses # if /Latinized/.match(self.type_name) # lat = TaxonNameClassification.where(taxon_name_id: self.taxon_name_id).with_type_contains('Latinized').not_self(self) # unless lat.empty? # if /Gender/.match(lat.first.type_name) # errors.add(:taxon_name_id, 'The Gender is already selected') # elsif /PartOfSpeech/.match(lat.first.type_name) # errors.add(:taxon_name_id, 'The Part of speech is already selected') # end # end # end 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.type_class.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.type_class.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.find_each do |i| soft_validations.add(:type, "The status '#{self.type_class.label}' conflicting with another status: '#{i.type_class.label}'") if self.type_class.disjoint_taxon_name_classes.include?(i.type_name) end end def sv_not_specific_classes true # moved to subclasses =begin case self.type_name when 'TaxonNameClassification::Iczn::Available' soft_validations.add(:type, 'Please specify if the name is Valid or Invalid') when 'TaxonNameClassification::Iczn::Unavailable' soft_validations.add(:type, 'Please specify the reasons for the name being Unavailable') when 'TaxonNameClassification::Iczn::Available::Invalid' soft_validations.add(:type, 'Although this status can be used, it is better to replace it with appropriate relationship (for example Synonym relationship)') when 'TaxonNameClassification::Iczn::Available::Invalid::Homonym' soft_validations.add(:type, 'Although this status can be used, it is better to replace it with with appropriate relationship (for example Primary Homonym)') when 'TaxonNameClassification::Iczn::Available::Valid' soft_validations.add(:type, 'This status should only be used when one or more conflicting invalidating relationships present in the database (for example, a taxon was used as a synonym in the past, but not now, and a synonym relationship is stored in the database for a historical record). Otherwise, this status should not be used. By default, any name which does not have invalidating relationship is a valid name') when 'TaxonNameClassification::Iczn::Unavailable::Suppressed' soft_validations.add(:type, 'Please specify the reasons for the name being Suppressed') when 'TaxonNameClassification::Iczn::Unavailable::Excluded' soft_validations.add(:type, 'Please specify the reasons for the name being Excluded') when 'TaxonNameClassification::Iczn::Unavailable::NomenNudum' soft_validations.add(:type, 'Please specify the reasons for the name being Nomen Nudum') when 'TaxonNameClassification::Iczn::Unavailable::NonBinomial' soft_validations.add(:type, 'Please specify the reasons for the name being Non Binomial') when 'TaxonNameClassification::Icn::EffectivelyPublished' soft_validations.add(:type, 'Please specify if the name is validly or Invalidly Published') when 'TaxonNameClassification::Icn::EffectivelyPublished::InvalidlyPublished' soft_validations.add(:type, 'Please specify the reasons for the name being Invalidly Published') when 'TaxonNameClassification::Icn::EffectivelyPublished::ValidlyPublished' soft_validations.add(:type, 'Please specify if the name is Legitimate or Illegitimate') when 'TaxonNameClassification::Icn::EffectivelyPublished::ValidlyPublished::Legitimate' soft_validations.add(:type, 'Please specify the reasons for the name being Legitimate') when 'TaxonNameClassification::Icn::EffectivelyPublished::ValidlyPublished::Illegitimate' soft_validations.add(:type, 'Please specify the reasons for the name being Illegitimate') when 'TaxonNameClassification::Icnp::EffectivelyPublished' soft_validations.add(:type, 'Please specify if the name is validly or Invalidly Published') when 'TaxonNameClassification::Icnp::EffectivelyPublished::InvalidlyPublished' soft_validations.add(:type, 'Please specify the reasons for the name being Invalidly Published') when 'TaxonNameClassification::Icnp::EffectivelyPublished::ValidlyPublished' soft_validations.add(:type, 'Please specify if the name is Legitimate or Illegitimate') when 'TaxonNameClassification::Icnp::EffectivelyPublished::ValidlyPublished::Legitimate' soft_validations.add(:type, 'Please specify the reasons for the name being Legitimate') # when 'TaxonNameClassification::Icn::EffectivelyPublished::ValidlyPublished::Illegitimate' # soft_validations.add(:type, 'Please specify the reasons for the name being Illegitimate') when 'TaxonNameClassification::Latinized::PartOfSpeech::Adjective' || 'TaxonNameClassification::Latinized::PartOfSpeech::Participle' t = taxon_name.name if !t.end_with?('us') && !t.end_with?('a') && !t.end_with?('um') && !t.end_with?('is') && !t.end_with?('e') && !t.end_with?('or') && !t.end_with?('er') soft_validations.add(:type, 'Adjective or participle name should end with one of the ' \ 'following endings: -us, -a, -um, -is, -e, -er, -or') end end =end end #endregion def self.annotates? true end def annotated_object taxon_name end private def nomenclature_code_matches if taxon_name && type && nomenclature_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 != taxon_name.rank_class.nomenclatural_code 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
18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80 81 82 83 84 85 86 87 88 89 90 91 92 93 94 95 96 97 98 99 100 101 102 103 104 105 106 107 108 109 110 111 112 113 114 115 116 117 118 119 120 121 122 123 124 125 126 127 128 129 130 131 132 133 134 135 136 137 138 139 140 141 142 143 144 145 146 147 148 149 150 151 152 153 154 155 156 157 158 159 160 161 162 163 164 165 166 167 168 169 170 171 172 173 174 175 176 177 178 179 180 181 182 183 184 185 186 187 188 189 190 191 192 193 194 195 196 197 198 199 200 201 202 203 204 205 206 207 208 209 210 211 212 213 214 215 216 217 218 219 220 221 222 223 224 225 226 227 228 229 230 231 232 233 234 235 236 237 238 239 240 241 242 243 244 245 246 247 248 249 250 251 252 253 254 255 256 257 258 259 260 261 262 263 264 265 266 267 268 269 270 271 272 273 274 275 276 277 278 279 280 281 282 283 284 285 286 287 288 289 290 291 292 293 294 295 296 297 298 299 300 301 302 303 304 305 306 307 308 309 310 311 312 313 314 315 316 317 318 319 320 321 322 323 324 325 326 327 328 329 330 331 332 333 334 335 336 337 338 339 340 341 342 343 344 345 346 347 348 349 350 351 352 353 354 355 356 357 358 359 |
# 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, presence: true validates_presence_of :type, presence: true 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('type LIKE ?', "#{base_string}" ) } scope :with_type_base, -> (base_string) {where('type LIKE ?', "#{base_string}%" ) } scope :with_type_array, -> (base_array) {where('type IN (?)', base_array ) } scope :with_type_contains, -> (base_string) {where('type LIKE ?', "%#{base_string}%" ) } soft_validate(:sv_proper_classification, set: :proper_classification, has_fix: false) soft_validate(:sv_proper_year, set: :proper_classification, has_fix: false) soft_validate(:sv_validate_disjoint_classes, set: :validate_disjoint_classes, has_fix: false) soft_validate(:sv_not_specific_classes, set: :not_specific_classes, has_fix: false) after_save :set_cached after_destroy :set_cached # after_save :set_cached_names_for_taxon_names # after_destroy :set_cached_names_for_taxon_names def nomenclature_code return :iczn if type.match(/::Iczn/) return :icnp if type.match(/::Icnp/) return :ictv if type.match(/::Ictv/) return :icn if type.match(/::Icn/) return nil end # TODO: helper method def self.label name.demodulize.underscore.humanize.downcase.gsub(/\d+/, ' \0 ').squish 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 def set_cached_names_for_taxon_names begin TaxonName.transaction_with_retry do t = taxon_name if type_name =~ /(Fossil|Hybrid|Candidatus)/ t.update_columns( cached: t.get_full_name, cached_html: t.get_full_name_html, cached_original_combination: t.get_original_combination, cached_original_combination_html: t.get_original_combination_html ) elsif type_name =~ /Latinized::Gender/ t.descendants.select{|t| t.id == t.cached_valid_taxon_name_id}.uniq.each do |t1| t1.update_columns( cached: t1.get_full_name, cached_html: t1.get_full_name_html ) end TaxonNameRelationship.where(type: 'TaxonNameRelationship::OriginalCombination::OriginalGenus', subject_taxon_name: t).collect{|i| i.object_taxon_name}.uniq.each do |t1| t1.update_cached_original_combinations end TaxonNameRelationship.where(type: 'TaxonNameRelationship::Combination::Genus', 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? t1.update_columns( cached: t1.get_full_name, cached_html: t1.get_full_name_html ) 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_column(:cached_valid_taxon_name_id, vn.id) # update self too! vn.list_of_invalid_taxon_names.each do |s| s.update_column(:cached_valid_taxon_name_id, vn.id) end t.combination_list_self.each do |c| c.update_column(:cached_valid_taxon_name_id, vn.id) end end end rescue ActiveRecord::RecordInvalid # should return false here, right? end # false # TODO: why false, success == true? end #region Validation def validate_uniqueness_of_latinized true # moved to subclasses # if /Latinized/.match(self.type_name) # lat = TaxonNameClassification.where(taxon_name_id: self.taxon_name_id).with_type_contains('Latinized').not_self(self) # unless lat.empty? # if /Gender/.match(lat.first.type_name) # errors.add(:taxon_name_id, 'The Gender is already selected') # elsif /PartOfSpeech/.match(lat.first.type_name) # errors.add(:taxon_name_id, 'The Part of speech is already selected') # end # end # end 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.type_class.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.type_class.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.find_each do |i| soft_validations.add(:type, "The status '#{self.type_class.label}' conflicting with another status: '#{i.type_class.label}'") if self.type_class.disjoint_taxon_name_classes.include?(i.type_name) end end def sv_not_specific_classes true # moved to subclasses =begin case self.type_name when 'TaxonNameClassification::Iczn::Available' soft_validations.add(:type, 'Please specify if the name is Valid or Invalid') when 'TaxonNameClassification::Iczn::Unavailable' soft_validations.add(:type, 'Please specify the reasons for the name being Unavailable') when 'TaxonNameClassification::Iczn::Available::Invalid' soft_validations.add(:type, 'Although this status can be used, it is better to replace it with appropriate relationship (for example Synonym relationship)') when 'TaxonNameClassification::Iczn::Available::Invalid::Homonym' soft_validations.add(:type, 'Although this status can be used, it is better to replace it with with appropriate relationship (for example Primary Homonym)') when 'TaxonNameClassification::Iczn::Available::Valid' soft_validations.add(:type, 'This status should only be used when one or more conflicting invalidating relationships present in the database (for example, a taxon was used as a synonym in the past, but not now, and a synonym relationship is stored in the database for a historical record). Otherwise, this status should not be used. By default, any name which does not have invalidating relationship is a valid name') when 'TaxonNameClassification::Iczn::Unavailable::Suppressed' soft_validations.add(:type, 'Please specify the reasons for the name being Suppressed') when 'TaxonNameClassification::Iczn::Unavailable::Excluded' soft_validations.add(:type, 'Please specify the reasons for the name being Excluded') when 'TaxonNameClassification::Iczn::Unavailable::NomenNudum' soft_validations.add(:type, 'Please specify the reasons for the name being Nomen Nudum') when 'TaxonNameClassification::Iczn::Unavailable::NonBinomial' soft_validations.add(:type, 'Please specify the reasons for the name being Non Binomial') when 'TaxonNameClassification::Icn::EffectivelyPublished' soft_validations.add(:type, 'Please specify if the name is validly or Invalidly Published') when 'TaxonNameClassification::Icn::EffectivelyPublished::InvalidlyPublished' soft_validations.add(:type, 'Please specify the reasons for the name being Invalidly Published') when 'TaxonNameClassification::Icn::EffectivelyPublished::ValidlyPublished' soft_validations.add(:type, 'Please specify if the name is Legitimate or Illegitimate') when 'TaxonNameClassification::Icn::EffectivelyPublished::ValidlyPublished::Legitimate' soft_validations.add(:type, 'Please specify the reasons for the name being Legitimate') when 'TaxonNameClassification::Icn::EffectivelyPublished::ValidlyPublished::Illegitimate' soft_validations.add(:type, 'Please specify the reasons for the name being Illegitimate') when 'TaxonNameClassification::Icnp::EffectivelyPublished' soft_validations.add(:type, 'Please specify if the name is validly or Invalidly Published') when 'TaxonNameClassification::Icnp::EffectivelyPublished::InvalidlyPublished' soft_validations.add(:type, 'Please specify the reasons for the name being Invalidly Published') when 'TaxonNameClassification::Icnp::EffectivelyPublished::ValidlyPublished' soft_validations.add(:type, 'Please specify if the name is Legitimate or Illegitimate') when 'TaxonNameClassification::Icnp::EffectivelyPublished::ValidlyPublished::Legitimate' soft_validations.add(:type, 'Please specify the reasons for the name being Legitimate') # when 'TaxonNameClassification::Icn::EffectivelyPublished::ValidlyPublished::Illegitimate' # soft_validations.add(:type, 'Please specify the reasons for the name being Illegitimate') when 'TaxonNameClassification::Latinized::PartOfSpeech::Adjective' || 'TaxonNameClassification::Latinized::PartOfSpeech::Participle' t = taxon_name.name if !t.end_with?('us') && !t.end_with?('a') && !t.end_with?('um') && !t.end_with?('is') && !t.end_with?('e') && !t.end_with?('or') && !t.end_with?('er') soft_validations.add(:type, 'Adjective or participle name should end with one of the ' \ 'following endings: -us, -a, -um, -is, -e, -er, -or') end end =end end #endregion def self.annotates? true end def annotated_object taxon_name end private def nomenclature_code_matches if taxon_name && type && nomenclature_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 != taxon_name.rank_class.nomenclatural_code 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)
18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80 81 82 83 84 85 86 87 88 89 90 91 92 93 94 95 96 97 98 99 100 101 102 103 104 105 106 107 108 109 110 111 112 113 114 115 116 117 118 119 120 121 122 123 124 125 126 127 128 129 130 131 132 133 134 135 136 137 138 139 140 141 142 143 144 145 146 147 148 149 150 151 152 153 154 155 156 157 158 159 160 161 162 163 164 165 166 167 168 169 170 171 172 173 174 175 176 177 178 179 180 181 182 183 184 185 186 187 188 189 190 191 192 193 194 195 196 197 198 199 200 201 202 203 204 205 206 207 208 209 210 211 212 213 214 215 216 217 218 219 220 221 222 223 224 225 226 227 228 229 230 231 232 233 234 235 236 237 238 239 240 241 242 243 244 245 246 247 248 249 250 251 252 253 254 255 256 257 258 259 260 261 262 263 264 265 266 267 268 269 270 271 272 273 274 275 276 277 278 279 280 281 282 283 284 285 286 287 288 289 290 291 292 293 294 295 296 297 298 299 300 301 302 303 304 305 306 307 308 309 310 311 312 313 314 315 316 317 318 319 320 321 322 323 324 325 326 327 328 329 330 331 332 333 334 335 336 337 338 339 340 341 342 343 344 345 346 347 348 349 350 351 352 353 354 355 356 357 358 359 |
# 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, presence: true validates_presence_of :type, presence: true 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('type LIKE ?', "#{base_string}" ) } scope :with_type_base, -> (base_string) {where('type LIKE ?', "#{base_string}%" ) } scope :with_type_array, -> (base_array) {where('type IN (?)', base_array ) } scope :with_type_contains, -> (base_string) {where('type LIKE ?', "%#{base_string}%" ) } soft_validate(:sv_proper_classification, set: :proper_classification, has_fix: false) soft_validate(:sv_proper_year, set: :proper_classification, has_fix: false) soft_validate(:sv_validate_disjoint_classes, set: :validate_disjoint_classes, has_fix: false) soft_validate(:sv_not_specific_classes, set: :not_specific_classes, has_fix: false) after_save :set_cached after_destroy :set_cached # after_save :set_cached_names_for_taxon_names # after_destroy :set_cached_names_for_taxon_names def nomenclature_code return :iczn if type.match(/::Iczn/) return :icnp if type.match(/::Icnp/) return :ictv if type.match(/::Ictv/) return :icn if type.match(/::Icn/) return nil end # TODO: helper method def self.label name.demodulize.underscore.humanize.downcase.gsub(/\d+/, ' \0 ').squish 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 def set_cached_names_for_taxon_names begin TaxonName.transaction_with_retry do t = taxon_name if type_name =~ /(Fossil|Hybrid|Candidatus)/ t.update_columns( cached: t.get_full_name, cached_html: t.get_full_name_html, cached_original_combination: t.get_original_combination, cached_original_combination_html: t.get_original_combination_html ) elsif type_name =~ /Latinized::Gender/ t.descendants.select{|t| t.id == t.cached_valid_taxon_name_id}.uniq.each do |t1| t1.update_columns( cached: t1.get_full_name, cached_html: t1.get_full_name_html ) end TaxonNameRelationship.where(type: 'TaxonNameRelationship::OriginalCombination::OriginalGenus', subject_taxon_name: t).collect{|i| i.object_taxon_name}.uniq.each do |t1| t1.update_cached_original_combinations end TaxonNameRelationship.where(type: 'TaxonNameRelationship::Combination::Genus', 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? t1.update_columns( cached: t1.get_full_name, cached_html: t1.get_full_name_html ) 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_column(:cached_valid_taxon_name_id, vn.id) # update self too! vn.list_of_invalid_taxon_names.each do |s| s.update_column(:cached_valid_taxon_name_id, vn.id) end t.combination_list_self.each do |c| c.update_column(:cached_valid_taxon_name_id, vn.id) end end end rescue ActiveRecord::RecordInvalid # should return false here, right? end # false # TODO: why false, success == true? end #region Validation def validate_uniqueness_of_latinized true # moved to subclasses # if /Latinized/.match(self.type_name) # lat = TaxonNameClassification.where(taxon_name_id: self.taxon_name_id).with_type_contains('Latinized').not_self(self) # unless lat.empty? # if /Gender/.match(lat.first.type_name) # errors.add(:taxon_name_id, 'The Gender is already selected') # elsif /PartOfSpeech/.match(lat.first.type_name) # errors.add(:taxon_name_id, 'The Part of speech is already selected') # end # end # end 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.type_class.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.type_class.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.find_each do |i| soft_validations.add(:type, "The status '#{self.type_class.label}' conflicting with another status: '#{i.type_class.label}'") if self.type_class.disjoint_taxon_name_classes.include?(i.type_name) end end def sv_not_specific_classes true # moved to subclasses =begin case self.type_name when 'TaxonNameClassification::Iczn::Available' soft_validations.add(:type, 'Please specify if the name is Valid or Invalid') when 'TaxonNameClassification::Iczn::Unavailable' soft_validations.add(:type, 'Please specify the reasons for the name being Unavailable') when 'TaxonNameClassification::Iczn::Available::Invalid' soft_validations.add(:type, 'Although this status can be used, it is better to replace it with appropriate relationship (for example Synonym relationship)') when 'TaxonNameClassification::Iczn::Available::Invalid::Homonym' soft_validations.add(:type, 'Although this status can be used, it is better to replace it with with appropriate relationship (for example Primary Homonym)') when 'TaxonNameClassification::Iczn::Available::Valid' soft_validations.add(:type, 'This status should only be used when one or more conflicting invalidating relationships present in the database (for example, a taxon was used as a synonym in the past, but not now, and a synonym relationship is stored in the database for a historical record). Otherwise, this status should not be used. By default, any name which does not have invalidating relationship is a valid name') when 'TaxonNameClassification::Iczn::Unavailable::Suppressed' soft_validations.add(:type, 'Please specify the reasons for the name being Suppressed') when 'TaxonNameClassification::Iczn::Unavailable::Excluded' soft_validations.add(:type, 'Please specify the reasons for the name being Excluded') when 'TaxonNameClassification::Iczn::Unavailable::NomenNudum' soft_validations.add(:type, 'Please specify the reasons for the name being Nomen Nudum') when 'TaxonNameClassification::Iczn::Unavailable::NonBinomial' soft_validations.add(:type, 'Please specify the reasons for the name being Non Binomial') when 'TaxonNameClassification::Icn::EffectivelyPublished' soft_validations.add(:type, 'Please specify if the name is validly or Invalidly Published') when 'TaxonNameClassification::Icn::EffectivelyPublished::InvalidlyPublished' soft_validations.add(:type, 'Please specify the reasons for the name being Invalidly Published') when 'TaxonNameClassification::Icn::EffectivelyPublished::ValidlyPublished' soft_validations.add(:type, 'Please specify if the name is Legitimate or Illegitimate') when 'TaxonNameClassification::Icn::EffectivelyPublished::ValidlyPublished::Legitimate' soft_validations.add(:type, 'Please specify the reasons for the name being Legitimate') when 'TaxonNameClassification::Icn::EffectivelyPublished::ValidlyPublished::Illegitimate' soft_validations.add(:type, 'Please specify the reasons for the name being Illegitimate') when 'TaxonNameClassification::Icnp::EffectivelyPublished' soft_validations.add(:type, 'Please specify if the name is validly or Invalidly Published') when 'TaxonNameClassification::Icnp::EffectivelyPublished::InvalidlyPublished' soft_validations.add(:type, 'Please specify the reasons for the name being Invalidly Published') when 'TaxonNameClassification::Icnp::EffectivelyPublished::ValidlyPublished' soft_validations.add(:type, 'Please specify if the name is Legitimate or Illegitimate') when 'TaxonNameClassification::Icnp::EffectivelyPublished::ValidlyPublished::Legitimate' soft_validations.add(:type, 'Please specify the reasons for the name being Legitimate') # when 'TaxonNameClassification::Icn::EffectivelyPublished::ValidlyPublished::Illegitimate' # soft_validations.add(:type, 'Please specify the reasons for the name being Illegitimate') when 'TaxonNameClassification::Latinized::PartOfSpeech::Adjective' || 'TaxonNameClassification::Latinized::PartOfSpeech::Participle' t = taxon_name.name if !t.end_with?('us') && !t.end_with?('a') && !t.end_with?('um') && !t.end_with?('is') && !t.end_with?('e') && !t.end_with?('or') && !t.end_with?('er') soft_validations.add(:type, 'Adjective or participle name should end with one of the ' \ 'following endings: -us, -a, -um, -is, -e, -er, -or') end end =end end #endregion def self.annotates? true end def annotated_object taxon_name end private def nomenclature_code_matches if taxon_name && type && nomenclature_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 != taxon_name.rank_class.nomenclatural_code 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
317 318 319 |
# File 'app/models/taxon_name_classification.rb', line 317 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
112 113 114 |
# File 'app/models/taxon_name_classification.rb', line 112 def self.applicable_ranks [] end |
.assignable ⇒ Object
128 129 130 |
# File 'app/models/taxon_name_classification.rb', line 128 def self.assignable false end |
.code_applicability_end_year ⇒ Integer
the last year of applicability for this class, defaults to 9999
106 107 108 |
# File 'app/models/taxon_name_classification.rb', line 106 def self.code_applicability_end_year 9999 end |
.code_applicability_start_year ⇒ Integer
the minimum year of applicability for this class, defaults to 1
100 101 102 |
# File 'app/models/taxon_name_classification.rb', line 100 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.
355 356 357 |
# File 'app/models/taxon_name_classification.rb', line 355 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.
345 346 347 348 349 350 351 |
# File 'app/models/taxon_name_classification.rb', line 345 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)
339 340 341 |
# File 'app/models/taxon_name_classification.rb', line 339 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
118 119 120 |
# File 'app/models/taxon_name_classification.rb', line 118 def self.disjoint_taxon_name_classes [] end |
.gbif_status ⇒ String?
Returns if applicable, a DWC gbif status for this class
124 125 126 |
# File 'app/models/taxon_name_classification.rb', line 124 def self.gbif_status nil end |
.label ⇒ Object
TODO: helper method
60 61 62 |
# File 'app/models/taxon_name_classification.rb', line 60 def self.label name.demodulize.underscore.humanize.downcase.gsub(/\d+/, ' \0 ').squish end |
.nomen_uri ⇒ Object
157 158 159 |
# File 'app/models/taxon_name_classification.rb', line 157 def self.nomen_uri const_defined?(:NOMEN_URI, false) ? self::NOMEN_URI : nil 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
153 154 155 |
# File 'app/models/taxon_name_classification.rb', line 153 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
141 142 143 |
# File 'app/models/taxon_name_classification.rb', line 141 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
147 148 149 |
# File 'app/models/taxon_name_classification.rb', line 147 def self.questionable_species_endings [] end |
Instance Method Details
#annotated_object ⇒ Object
321 322 323 |
# File 'app/models/taxon_name_classification.rb', line 321 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
84 85 86 87 88 |
# File 'app/models/taxon_name_classification.rb', line 84 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
92 93 94 |
# File 'app/models/taxon_name_classification.rb', line 92 def nomen_id self.class::NOMEN_URI.split('/').last end |
#nomenclature_code ⇒ Object
after_save :set_cached_names_for_taxon_names after_destroy :set_cached_names_for_taxon_names
51 52 53 54 55 56 57 |
# File 'app/models/taxon_name_classification.rb', line 51 def nomenclature_code return :iczn if type.match(/::Iczn/) return :icnp if type.match(/::Icnp/) return :ictv if type.match(/::Ictv/) return :icn if type.match(/::Icn/) return nil end |
#nomenclature_code_matches ⇒ Object (private)
327 328 329 330 331 |
# File 'app/models/taxon_name_classification.rb', line 327 def nomenclature_code_matches if taxon_name && type && nomenclature_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 != taxon_name.rank_class.nomenclatural_code end end |
#set_cached ⇒ Object
161 162 163 |
# File 'app/models/taxon_name_classification.rb', line 161 def set_cached set_cached_names_for_taxon_names end |
#set_cached_names_for_taxon_names ⇒ Object
165 166 167 168 169 170 171 172 173 174 175 176 177 178 179 180 181 182 183 184 185 186 187 188 189 190 191 192 193 194 195 196 197 198 199 200 201 202 203 204 205 206 207 208 209 210 211 212 |
# File 'app/models/taxon_name_classification.rb', line 165 def set_cached_names_for_taxon_names begin TaxonName.transaction_with_retry do t = taxon_name if type_name =~ /(Fossil|Hybrid|Candidatus)/ t.update_columns( cached: t.get_full_name, cached_html: t.get_full_name_html, cached_original_combination: t.get_original_combination, cached_original_combination_html: t.get_original_combination_html ) elsif type_name =~ /Latinized::Gender/ t.descendants.select{|t| t.id == t.cached_valid_taxon_name_id}.uniq.each do |t1| t1.update_columns( cached: t1.get_full_name, cached_html: t1.get_full_name_html ) end TaxonNameRelationship.where(type: 'TaxonNameRelationship::OriginalCombination::OriginalGenus', subject_taxon_name: t).collect{|i| i.object_taxon_name}.uniq.each do |t1| t1.update_cached_original_combinations end TaxonNameRelationship.where(type: 'TaxonNameRelationship::Combination::Genus', 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? t1.update_columns( cached: t1.get_full_name, cached_html: t1.get_full_name_html ) 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_column(:cached_valid_taxon_name_id, vn.id) # update self too! vn.list_of_invalid_taxon_names.each do |s| s.update_column(:cached_valid_taxon_name_id, vn.id) end t.combination_list_self.each do |c| c.update_column(:cached_valid_taxon_name_id, vn.id) end end end rescue ActiveRecord::RecordInvalid # should return false here, right? end # false # TODO: why false, success == true? end |
#sv_not_specific_classes ⇒ Object
256 257 258 259 260 261 262 263 264 265 266 267 268 269 270 271 272 273 274 275 276 277 278 279 280 281 282 283 284 285 286 287 288 289 290 291 292 293 294 295 296 297 298 299 300 301 302 303 304 305 306 307 308 309 310 311 312 313 |
# File 'app/models/taxon_name_classification.rb', line 256 def sv_not_specific_classes true # moved to subclasses =begin case self.type_name when 'TaxonNameClassification::Iczn::Available' soft_validations.add(:type, 'Please specify if the name is Valid or Invalid') when 'TaxonNameClassification::Iczn::Unavailable' soft_validations.add(:type, 'Please specify the reasons for the name being Unavailable') when 'TaxonNameClassification::Iczn::Available::Invalid' soft_validations.add(:type, 'Although this status can be used, it is better to replace it with appropriate relationship (for example Synonym relationship)') when 'TaxonNameClassification::Iczn::Available::Invalid::Homonym' soft_validations.add(:type, 'Although this status can be used, it is better to replace it with with appropriate relationship (for example Primary Homonym)') when 'TaxonNameClassification::Iczn::Available::Valid' soft_validations.add(:type, 'This status should only be used when one or more conflicting invalidating relationships present in the database (for example, a taxon was used as a synonym in the past, but not now, and a synonym relationship is stored in the database for a historical record). Otherwise, this status should not be used. By default, any name which does not have invalidating relationship is a valid name') when 'TaxonNameClassification::Iczn::Unavailable::Suppressed' soft_validations.add(:type, 'Please specify the reasons for the name being Suppressed') when 'TaxonNameClassification::Iczn::Unavailable::Excluded' soft_validations.add(:type, 'Please specify the reasons for the name being Excluded') when 'TaxonNameClassification::Iczn::Unavailable::NomenNudum' soft_validations.add(:type, 'Please specify the reasons for the name being Nomen Nudum') when 'TaxonNameClassification::Iczn::Unavailable::NonBinomial' soft_validations.add(:type, 'Please specify the reasons for the name being Non Binomial') when 'TaxonNameClassification::Icn::EffectivelyPublished' soft_validations.add(:type, 'Please specify if the name is validly or Invalidly Published') when 'TaxonNameClassification::Icn::EffectivelyPublished::InvalidlyPublished' soft_validations.add(:type, 'Please specify the reasons for the name being Invalidly Published') when 'TaxonNameClassification::Icn::EffectivelyPublished::ValidlyPublished' soft_validations.add(:type, 'Please specify if the name is Legitimate or Illegitimate') when 'TaxonNameClassification::Icn::EffectivelyPublished::ValidlyPublished::Legitimate' soft_validations.add(:type, 'Please specify the reasons for the name being Legitimate') when 'TaxonNameClassification::Icn::EffectivelyPublished::ValidlyPublished::Illegitimate' soft_validations.add(:type, 'Please specify the reasons for the name being Illegitimate') when 'TaxonNameClassification::Icnp::EffectivelyPublished' soft_validations.add(:type, 'Please specify if the name is validly or Invalidly Published') when 'TaxonNameClassification::Icnp::EffectivelyPublished::InvalidlyPublished' soft_validations.add(:type, 'Please specify the reasons for the name being Invalidly Published') when 'TaxonNameClassification::Icnp::EffectivelyPublished::ValidlyPublished' soft_validations.add(:type, 'Please specify if the name is Legitimate or Illegitimate') when 'TaxonNameClassification::Icnp::EffectivelyPublished::ValidlyPublished::Legitimate' soft_validations.add(:type, 'Please specify the reasons for the name being Legitimate') # when 'TaxonNameClassification::Icn::EffectivelyPublished::ValidlyPublished::Illegitimate' # soft_validations.add(:type, 'Please specify the reasons for the name being Illegitimate') when 'TaxonNameClassification::Latinized::PartOfSpeech::Adjective' || 'TaxonNameClassification::Latinized::PartOfSpeech::Participle' t = taxon_name.name if !t.end_with?('us') && !t.end_with?('a') && !t.end_with?('um') && !t.end_with?('is') && !t.end_with?('e') && !t.end_with?('or') && !t.end_with?('er') soft_validations.add(:type, 'Adjective or participle name should end with one of the ' \ 'following endings: -us, -a, -um, -is, -e, -er, -or') end end =end end |
#sv_proper_classification ⇒ Object
region Soft validation
233 234 235 236 237 238 239 240 |
# File 'app/models/taxon_name_classification.rb', line 233 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.type_class.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
242 243 244 245 246 247 |
# File 'app/models/taxon_name_classification.rb', line 242 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.type_class.label}' is unapplicable to the taxon #{self.taxon_name.cached_html} published in the year #{y}") end end |
#sv_validate_disjoint_classes ⇒ Object
249 250 251 252 253 254 |
# File 'app/models/taxon_name_classification.rb', line 249 def sv_validate_disjoint_classes classifications = TaxonNameClassification.where_taxon_name(self.taxon_name).not_self(self) classifications.find_each do |i| soft_validations.add(:type, "The status '#{self.type_class.label}' conflicting with another status: '#{i.type_class.label}'") if self.type_class.disjoint_taxon_name_classes.include?(i.type_name) end end |
#type_class ⇒ Object
75 76 77 78 |
# File 'app/models/taxon_name_classification.rb', line 75 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
71 72 73 |
# File 'app/models/taxon_name_classification.rb', line 71 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
66 67 68 69 |
# File 'app/models/taxon_name_classification.rb', line 66 def type_name r = self.type.to_s ::TAXON_NAME_CLASSIFICATION_NAMES.include?(r) ? r : nil end |
#validate_taxon_name_classification ⇒ Object (private)
333 334 335 |
# File 'app/models/taxon_name_classification.rb', line 333 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
215 216 217 218 219 220 221 222 223 224 225 226 227 |
# File 'app/models/taxon_name_classification.rb', line 215 def validate_uniqueness_of_latinized true # moved to subclasses # if /Latinized/.match(self.type_name) # lat = TaxonNameClassification.where(taxon_name_id: self.taxon_name_id).with_type_contains('Latinized').not_self(self) # unless lat.empty? # if /Gender/.match(lat.first.type_name) # errors.add(:taxon_name_id, 'The Gender is already selected') # elsif /PartOfSpeech/.match(lat.first.type_name) # errors.add(:taxon_name_id, 'The Part of speech is already selected') # end # end # end end |