Class: TaxonNameRelationship
- Inherits:
-
ApplicationRecord
- Object
- ActiveRecord::Base
- ApplicationRecord
- TaxonNameRelationship
- Includes:
- Housekeeping, Shared::Citations, Shared::DwcOccurrenceHooks, Shared::IsData, Shared::Notes, SoftValidation
- Defined in:
- app/models/taxon_name_relationship.rb
Overview
SourceClassifiedAs is not really Combination in the other sense
validate, that all the relationships in the table could be linked to relationships in classes (if those had changed)
Check if more than one species associated with the genus in the original paper
A NOMEN github.com/SpeciesFileGroup/nomen relationship between two Protonyms.
Unless otherwise noted relationships read left to right, and can be interpreted by inserting “of” after the class name.
For example the triple:
Subject: Aus aus - TaxonNameRelationship::Iczn::Invalidating::Synonym - Object: Bus bus
Can be read as:
aus synonym OF bus
Note that not all relationships are reflective. We can't say, for the example above we can't say
bus valid_name OF aus
Note that we can not say that all names that are subjects are valid, this is determined on a case by case basis.
TaxonNameRelationships have a domain (attributes on the subject) and range (attributes on the object). So if you use a relationship you may be asserting a TaxonNameClassification also exists for the subject or object.
Direct Known Subclasses
Combination, CurrentCombination, Hybrid, Icn, Icnp, Icvcn, Iczn, OriginalCombination, SourceClassifiedAs, Typification
Defined Under Namespace
Classes: Combination, CurrentCombination, Hybrid, Icn, Icnp, Icvcn, Iczn, OriginalCombination, SourceClassifiedAs, Typification
Constant Summary
Constants included from SoftValidation
SoftValidation::ANCESTORS_WITH_SOFT_VALIDATIONS
Instance Attribute Summary collapse
-
#no_cached ⇒ Boolean?
When true, cached values are not built.
-
#object_taxon_name_id ⇒ Integer
The object taxon name.
-
#project_id ⇒ Integer
the project ID.
-
#subject_taxon_name_id ⇒ Integer
The subject taxon name.
-
#type ⇒ String
The relationship/“predicate” between the subject and object taxon names.
Class Method Summary collapse
- .assignable ⇒ Object
- .collect_descendants_and_itself_to_s(*classes) ⇒ Object protected
- .collect_descendants_to_s(*classes) ⇒ Object protected
- .collect_to_s(*args) ⇒ Object protected
- .disjoint_object_classes ⇒ Object
- .disjoint_subject_classes ⇒ Object
-
.disjoint_taxon_name_relationships ⇒ Array of TaxonNameRelationships
If this relationships is set for the subject, then others in this array should not be used for that subject.
- .gbif_status_of_object ⇒ Object
- .gbif_status_of_subject ⇒ Object
-
.nomen_uri ⇒ String?
The NOMEN uri for this type.
-
.nomenclatural_priority ⇒ Symbol
Determine the relative age of subject and object :direct - subject is younger than object :reverse - object is younger than subject.
-
.parent ⇒ Object
Class this method calls Module#module_parent.
-
.required_taxon_name_relationships ⇒ Object
TODO: why isn’t this disjoint? disjoint relationships for the taxon as a object.
-
.valid_object_ranks ⇒ Array of NomenclatureRank
The valid ranks to which the object name can belong, set in subclasses.
-
.valid_subject_ranks ⇒ Array of NomenclatureRank
The valid ranks to which the subject name can belong, set in subclasses.
Instance Method Summary collapse
- #dwc_occurrences ⇒ Object
- #is_combination? ⇒ Boolean
- #is_invalidating? ⇒ Boolean protected
-
#nomenclature_date ⇒ Time
Effective date of publication, used to determine nomenclatural priorities !! Careful, if no date is present the current year is given, rather than nil, @proceps is this a safe inference?.
-
#object_properties ⇒ Array of TaxonNameClassification
The inferable TaxonNameClassification(s) added to the subject when this relationship is used !! Not implmented.
-
#object_status ⇒ String
The status inferred by the relationship to the object name.
-
#object_status_connector_to_subject ⇒ String
The connecting word in the relationship from the object name to subject name.
-
#object_status_tag ⇒ String
A readable fragement combining status and connector.
-
#set_cached_names_for_taxon_names ⇒ Object
protected
OriginalCombination has a replacement method.
- #subject_and_object_in_same_project ⇒ Object protected
- #subject_invalid_statuses ⇒ Object protected
-
#subject_properties ⇒ Array of TaxonNameClassification
The inferable TaxonNameClassification(s) added to the subject when this relationship is used !! Not implemented.
-
#subject_status ⇒ String
The status inferred by the relationship to the subject name.
-
#subject_status_connector_to_object ⇒ String
The connecting word in the relationship from the subject name to object name.
-
#subject_status_tag ⇒ String
A readable fragement combining status and connector.
- #sv_coordinated_taxa ⇒ Object protected
- #sv_coordinated_taxa_object ⇒ Object protected
- #sv_fix_combination_relationship ⇒ Object protected
- #sv_fix_coordinated_object_taxa ⇒ Object protected
- #sv_fix_coordinated_subject_taxa ⇒ Object protected
- #sv_fix_not_specific_relationship ⇒ Object protected
- #sv_fix_objective_synonym_relationship ⇒ Object protected
- #sv_fix_subject_parent_update ⇒ Object protected
- #sv_not_specific_relationship ⇒ Object protected
- #sv_objective_synonym_relationship ⇒ Object protected
- #sv_specific_relationship ⇒ Object protected
- #sv_synonym_linked_to_valid_name ⇒ Object protected
- #sv_synonym_relationship ⇒ Object protected
- #sv_validate_disjoint_object ⇒ Object protected
- #sv_validate_disjoint_relationships ⇒ Object protected
- #sv_validate_disjoint_subject ⇒ Object protected
- #sv_validate_priority ⇒ Object protected
- #sv_validate_required_relationships ⇒ Object protected
- #sv_validate_seniority ⇒ Object protected
- #type_class ⇒ Object
- #type_class=(value) ⇒ Object
-
#type_name ⇒ String?
The type of this relationship, IF the type is a valid name, else nil.
- #validate_object_and_subject_both_protonyms ⇒ Object protected
- #validate_object_must_equal_subject_for_uncertain_placement ⇒ Object protected
- #validate_rank_group ⇒ Object protected
- #validate_subject_and_object_are_not_identical ⇒ Object protected
- #validate_subject_and_object_ranks ⇒ Object protected
- #validate_subject_and_object_share_code ⇒ Object protected
- #validate_type ⇒ Object protected
-
#validate_uniqueness_of_typification_object ⇒ Object
protected
Protonym historically could be listed as a synonym to different taxa def validate_uniqueness_of_synonym_subject if !self.type.nil? && /Synonym/.match(self.type_name) && !TaxonNameRelationship.where(subject_taxon_name_id: self.subject_taxon_name_id).with_type_contains(‘Synonym’).not_self(self).empty? errors.add(:subject_taxon_name_id, ‘Only one synonym relationship is allowed’) end end.
Methods included from Shared::IsData
#errors_excepting, #full_error_messages_excepting, #identical, #is_community?, #is_destroyable?, #is_editable?, #is_in_use?, #is_in_users_projects?, #metamorphosize, #similar
Methods included from SoftValidation
#clear_soft_validations, #fix_for, #fix_soft_validations, #soft_fixed?, #soft_valid?, #soft_validate, #soft_validated?, #soft_validations, #soft_validators
Methods included from Shared::Notes
#concatenated_notes_string, #reject_notes
Methods included from Shared::Citations
#cited?, #mark_citations_for_destruction, #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
#no_cached ⇒ Boolean?
Returns When true, cached values are not built.
54 55 56 |
# File 'app/models/taxon_name_relationship.rb', line 54 def no_cached @no_cached end |
#object_taxon_name_id ⇒ Integer
Returns the object taxon name.
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# File 'app/models/taxon_name_relationship.rb', line 44 class TaxonNameRelationship < ApplicationRecord include Housekeeping include Shared::Citations include Shared::Notes include SoftValidation include Shared::DwcOccurrenceHooks include Shared::IsData # @return [Boolean, nil] # When true, cached values are not built attr_accessor :no_cached belongs_to :subject_taxon_name, class_name: 'TaxonName', inverse_of: :taxon_name_relationships # left side belongs_to :object_taxon_name, class_name: 'TaxonName', inverse_of: :related_taxon_name_relationships # right side # After commit only fires if there are changes to the record. after_commit :set_cached_names_for_taxon_names, unless: -> {self.no_cached } # TODO: remove, it's required by STI validates_presence_of :type, message: 'Relationship type should be specified' validates_presence_of :subject_taxon_name, message: 'Missing taxon name on the left side' validates_presence_of :object_taxon_name, message: 'Missing taxon name on the right side' validates_uniqueness_of :object_taxon_name_id, scope: [:type, :project_id], if: :is_combination? validates_uniqueness_of :object_taxon_name_id, scope: [:type, :subject_taxon_name_id, :project_id], unless: :is_combination? validate :validate_type, :validate_subject_and_object_are_not_identical validate :subject_and_object_in_same_project unless: -> {!subject_taxon_name || !object_taxon_name} do validate :validate_subject_and_object_share_code, :validate_uniqueness_of_typification_object, #:validate_uniqueness_of_synonym_subject, :validate_object_and_subject_both_protonyms, :validate_object_must_equal_subject_for_uncertain_placement, :validate_subject_and_object_ranks, :validate_rank_group end # TODO: isolate to an include file sensu protonym soft_validate( :sv_validate_required_relationships, set: :validate_required_relationships, name: 'Required relationships', description: 'Required relationships' ) soft_validate( :sv_validate_disjoint_relationships, set: :validate_disjoint_relationships, name: 'Conflicting relationships', description: 'Detect conflicting relationships' ) soft_validate( :sv_validate_disjoint_object, set: :validate_disjoint_object, name: 'Conflicting object taxon', description: 'Object taxon has a status conflicting with the relationship' ) soft_validate( :sv_validate_disjoint_subject, set: :validate_disjoint_subject, name: 'Conflicting subject taxon', description: 'Subject taxon has a status conflicting with the relationship' ) soft_validate( :sv_specific_relationship, set: :specific_relationship, name: 'validate relationship', description: 'Validate integrity of the relationship, for example, the year applicability range' ) soft_validate( :sv_objective_synonym_relationship, set: :objective_synonym_relationship, fix: :sv_fix_objective_synonym_relationship, name: 'Objective synonym relationship', description: 'Objective synonyms should have the same type' ) soft_validate( :sv_synonym_relationship, set: :synonym_relationship, name: 'Synonym relationship', description: 'Validate integrity of synonym relationship' ) soft_validate( :sv_not_specific_relationship, set: :not_specific_relationship, fix: :sv_fix_not_specific_relationship, name: 'Not specific relationship', description: 'More specific relationship is preferred, for example "Subjective synonym" instead of "Synonym".' ) soft_validate( :sv_synonym_linked_to_valid_name, set: :synonym_linked_to_valid_name, fix: :sv_fix_subject_parent_update, name: 'Synonym not linked to valid taxon', description: 'Synonyms should be linked to valid taxon.' ) soft_validate( :sv_validate_priority, set: :validate_priority, name: 'Priority validation', description: 'Junior synonym should be younger than senior synonym' ) soft_validate( :sv_validate_seniority, set: :validate_seniority, name: 'Seniority validation', description: 'Of two synonyms described in the same paper, one described at a higher rank has a priority' ) soft_validate( :sv_coordinated_taxa, set: :coordinated_taxa, fix: :sv_fix_coordinated_subject_taxa, name: 'Move relationship to coordinate taxon', description: 'Relationship should be moved to the lowest rank coordinate taxon (for example from species to nomynotypical subspecies). It could be updated automatically with the Fix.' ) soft_validate( :sv_coordinated_taxa_object, set: :coordinated_taxa, fix: :sv_fix_coordinated_object_taxa, name: 'Move object relationship to coordinate taxon', description: 'Relationship should be moved to the lowest rank coordinate object taxon (for example from species to nomynotypical subspecies). It could be updated automatically with the Fix.') scope :where_subject_is_taxon_name, -> (taxon_name) {where(subject_taxon_name_id: taxon_name)} scope :where_object_is_taxon_name, -> (taxon_name) {where(object_taxon_name_id: taxon_name)} scope :where_object_in_taxon_names, -> (taxon_name_array) {where('"taxon_name_relationships"."object_taxon_name_id" IN (?)', taxon_name_array)} scope :with_type_string, -> (type_string) { where(sanitize_sql_array(["taxon_name_relationships.type = '%s'", type_string])) } scope :with_type_base, -> (base_string) {where('"taxon_name_relationships"."type" LIKE ?', "#{base_string}%")} scope :with_type_contains, -> (base_string) {where('"taxon_name_relationships"."type" LIKE ?', "%#{base_string}%")} scope :with_two_type_bases, -> (base_string1, base_string2) { where('taxon_name_relationships.type LIKE ? OR taxon_name_relationships.type LIKE ?', "#{base_string1}%", "#{base_string2}%") } scope :homonym_or_suppressed, -> {where("taxon_name_relationships.type LIKE 'TaxonNameRelationship::Iczn::Invalidating::Homonym%' OR taxon_name_relationships.type LIKE 'TaxonNameRelationship::Iczn::Invalidating::Suppression::Total'") } scope :with_type_array, -> (base_array) {where('taxon_name_relationships.type IN (?)', base_array ) } def dwc_occurrences DwcOccurrence .joins("JOIN collection_objects co on dwc_occurrence_object_id = co.id AND dwc_occurrence_object_type = 'CollectionObject'") .joins("JOIN taxon_determinations td on co.id = td.taxon_determination_object_id AND td.taxon_determination_object_type = 'CollectionObject'") .joins("JOIN otus o on o.id = td.otu_id") .where(o: {taxon_name_id: [subject_taxon_name_id, object_taxon_name_id]}) .distinct end # @return [Array of TaxonNameClassification] # the inferable TaxonNameClassification(s) added to the subject when this relationship is used # !! Not implemented def subject_properties [] end # @return [Array of TaxonNameClassification] # the inferable TaxonNameClassification(s) added to the subject when this relationship is used # !! Not implmented def object_properties [] end # @return class # this method calls Module#module_parent def self.parent self.module_parent end # @return [Array of NomenclatureRank] # the valid ranks to which the subject name can belong, set in subclasses. (left side) def self.valid_subject_ranks [] end # @return [Array of NomenclatureRank] # the valid ranks to which the object name can belong, set in subclasses. (right side) def self.valid_object_ranks [] end # @return [Array of TaxonNameRelationships] # if this relationships is set for the subject, then others in this array should not be used for that subject def self.disjoint_taxon_name_relationships [] end # TODO: why isn't this disjoint? # disjoint relationships for the taxon as a object def self.required_taxon_name_relationships [] end def self.disjoint_subject_classes [] end def self.disjoint_object_classes [] end def self.gbif_status_of_subject nil end def self.gbif_status_of_object nil end def self.assignable false end # @return [Symbol] # determine the relative age of subject and object # :direct - subject is younger than object # :reverse - object is younger than subject def self.nomenclatural_priority nil end # @return [String] # the status inferred by the relationship to the object name def object_status self.type_name.demodulize.underscore.humanize.downcase.gsub(/\d+/, ' \0 ').squish end # @return [String] # the status inferred by the relationship to the subject name def subject_status self.type_name.demodulize.underscore.humanize.downcase.gsub(/\d+/, ' \0 ').squish end # @return [String] # the connecting word in the relationship from the subject name to object name def subject_status_connector_to_object ' of' end # @return [String] # the connecting word in the relationship from the object name to subject name def object_status_connector_to_subject ' of' end # @return [String] # a readable fragement combining status and connector def subject_status_tag subject_status + subject_status_connector_to_object end # @return [String] # a readable fragement combining status and connector def object_status_tag object_status + object_status_connector_to_subject end # @return [String, nil] # the type of this relationship, IF the type is a valid name, else nil def type_name r = self.type TAXON_NAME_RELATIONSHIP_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 TAXON_NAME_RELATIONSHIP_NAMES.include?(r) ? r.safe_constantize : nil end # @return [String, nil] # the NOMEN uri for this type def self.nomen_uri const_defined?(:NOMEN_URI, false) ? self::NOMEN_URI : nil end # @return [Time] # effective date of publication, used to determine nomenclatural priorities # !! Careful, if no date is present the current year is given, rather than nil, @proceps is this a safe inference? def nomenclature_date self.source ? (self.source.cached_nomenclature_date ? self.source.cached_nomenclature_date.to_time : Time.current) : Time.current end def is_combination? !!/TaxonNameRelationship::(OriginalCombination|Combination)/.match(self.type.to_s) end protected def subject_and_object_in_same_project if subject_taxon_name && object_taxon_name if subject_taxon_name.project_id != object_taxon_name.project_id errors.add(:base, 'one name is not in the same project as the other') end end end def validate_type # TODO: Remove, handled by STI if type && !TAXON_NAME_RELATIONSHIP_NAMES.include?(type.to_s) errors.add(:type, "'#{type}' is not a valid taxon name relationship") elsif self.type_class && object_taxon_name.class.to_s == 'Protonym' && !self.type_class.valid_object_ranks.include?(object_taxon_name.rank_string) errors.add(:type, "'#{type}' is not a valid taxon name relationship") end if object_taxon_name.class.to_s == 'Protonym' || object_taxon_name.class.to_s == 'Hybrid' errors.add(:type, "'#{type}' is not a valid taxon name relationship") if /TaxonNameRelationship::Combination::/.match(self.type) end if object_taxon_name.class.to_s == 'Combination' errors.add(:type, "'#{type}' is not a valid taxon name relationship") unless /TaxonNameRelationship::Combination::/.match(self.type) end end # @todo validate, that all the relationships in the table could be linked to relationships in classes (if those had changed) def validate_subject_and_object_share_code if object_taxon_name.type == 'Protonym' && subject_taxon_name.type == 'Protonym' errors.add(:object_taxon_name_id, 'The related taxon is not in the same monenclatural group (ICZN, ICN, ICNP, ICVCN') if subject_taxon_name.rank_class.try(:nomenclatural_code) != object_taxon_name.rank_class.try(:nomenclatural_code) end end def validate_subject_and_object_are_not_identical if !self.object_taxon_name_id.nil? && self.object_taxon_name == self.subject_taxon_name errors.add(:object_taxon_name_id, "#{self.object_taxon_name.try(:cached_html)} should not refer to itself") unless self.type =~ /OriginalCombination/ end end def validate_object_must_equal_subject_for_uncertain_placement if self.object_taxon_name_id != self.subject_taxon_name.parent_id && self.type_name == 'TaxonNameRelationship::Iczn::Validating::UncertainPlacement' errors.add(:object_taxon_name_id, "The parent #{self.subject_taxon_name.parent.cached_html} and the Incertae Sedis placement (#{self.object_taxon_name.cached_html}) should match") end end def validate_subject_and_object_ranks tname = self.type_name if tname =~ /TaxonNameRelationship::(Icnp|Icn|Iczn|Icvcn)/ && tname != 'TaxonNameRelationship::Iczn::Validating::UncertainPlacement' rank_group = self.subject_taxon_name.rank_class.try(:parent) unless rank_group == self.object_taxon_name.rank_class.try(:parent) errors.add(:object_taxon_name_id, "Rank of related taxon should be in the #{rank_group.try(:rank_name)} rank group, not #{self.object_taxon_name.rank_class.try(:rank_name)}") end end if self.type_class.present? # only validate if it is set if object_taxon_name && object_taxon_name.rank_class if object_taxon_name.type == 'Protonym' || object_taxon_name.type == 'Hybrid' unless self.type_class.valid_object_ranks.include?(self.object_taxon_name.rank_string) errors.add(:object_taxon_name_id, "#{self.object_taxon_name.rank_class.rank_name.capitalize} rank of #{self.object_taxon_name.cached_html} is not compatible with the #{self.subject_status} relationship") errors.add(:type, "Relationship #{self.subject_status} is not compatible with the #{self.object_taxon_name.rank_class.rank_name} rank of #{self.object_taxon_name.cached_html}") end end end if subject_taxon_name && subject_taxon_name.rank_class if subject_taxon_name.type == 'Protonym' || subject_taxon_name.type == 'Hybrid' unless self.type_class.valid_subject_ranks.include?(self.subject_taxon_name.rank_string) soft_validations.add(:subject_taxon_name_id, "#{self.subject_taxon_name.rank_class.rank_name.capitalize} rank of #{self.subject_taxon_name.cached_html} is not compatible with the #{self.subject_status} relationship") soft_validations.add(:type, "Relationship #{self.subject_status} is not compatible with the #{self.subject_taxon_name.rank_class.rank_name} rank of #{self.subject_taxon_name.cached_html}") end end end end end ##### Protonym historically could be listed as a synonym to different taxa #def validate_uniqueness_of_synonym_subject # if !self.type.nil? && /Synonym/.match(self.type_name) && !TaxonNameRelationship.where(subject_taxon_name_id: self.subject_taxon_name_id).with_type_contains('Synonym').not_self(self).empty? # errors.add(:subject_taxon_name_id, 'Only one synonym relationship is allowed') # end #end def validate_uniqueness_of_typification_object if /Typification/.match(self.type_name) && !TaxonNameRelationship.where(object_taxon_name_id: self.object_taxon_name_id).with_type_contains('Typification').not_self(self).empty? errors.add(:object_taxon_name_id, 'Only one Type designation relationship is allowed') end end def validate_rank_group if self.type =~ /Hybrid/ && self.subject_taxon_name && self.object_taxon_name if self.subject_taxon_name.rank_class.parent != self.object_taxon_name.rank_class.parent errors.add(:subject_taxon_name_id, "#{self.subject_taxon_name.rank_class.rank_name.capitalize} rank of #{self.subject_taxon_name.cached_html} is not compatible with the rank of hybrid (#{self.object_taxon_name.rank_class.rank_name})") end end end def validate_object_and_subject_both_protonyms if /TaxonNameRelationship::Combination::/.match(self.type) errors.add(:object_taxon_name_id, 'Not a Combination') if object_taxon_name.type != 'Combination' else errors.add(:object_taxon_name_id, 'Not a Protonym') if object_taxon_name.type == 'Combination' end errors.add(:subject_taxon_name_id, 'Not a Protonym') if subject_taxon_name.type == 'Combination' && self.type != 'TaxonNameRelationship::CurrentCombination' end # OriginalCombination has a replacement method. def set_cached_names_for_taxon_names return true unless subject_taxon_name_id_previously_changed? || destroyed? # TODO: this should completely be replaced with Taxonname logic. TaxonName.transaction do # Why? if is_invalidating? t = subject_taxon_name if TAXON_NAME_RELATIONSHIP_NAMES_MISSPELLING_ONLY.include?(type_name) t.update_columns( cached_misspelling: true, cached_author_year: t., cached_nomenclature_date: t.nomenclature_date, cached_original_combination: t.get_original_combination, cached_original_combination_html: t.get_original_combination_html) end if type_name =~/Misapplication/ t.update_columns( cached_author_year: t., cached_nomenclature_date: t.nomenclature_date) end vn = t.get_valid_taxon_name # !! NO set cached should do this from TN side of things, # !! Not here n = t.get_full_name t.update_columns( cached: n, cached_html: t.get_full_name_html(n), # OK to force reload here, otherwise we need an exception in #set_cached cached_valid_taxon_name_id: vn.id, cached_is_valid: !t.unavailable_or_invalid?) t.combination_list_self.each do |c| c.update_column(:cached_valid_taxon_name_id, vn.id) end vn.list_of_invalid_taxon_names.each do |s| s.update_columns( cached_valid_taxon_name_id: vn.id, cached_is_valid: !s.unavailable_or_invalid?) s.combination_list_self.each do |c| c.update_column(:cached_valid_taxon_name_id, vn.id) end end end end true end def is_invalidating? TAXON_NAME_RELATIONSHIP_NAMES_INVALID.include?(type_name) end def sv_validate_required_relationships return true if self.subject_taxon_name.not_binominal? object_relationships = TaxonNameRelationship.where_object_is_taxon_name(self.object_taxon_name).not_self(self).collect{|r| r.type} required = self.type_class.required_taxon_name_relationships - object_relationships required.each do |r| soft_validations.add(:type, " Presence of #{self.subject_status} requires selection of #{r.demodulize.underscore.humanize.downcase}") end end def sv_validate_disjoint_relationships tname = self.type_name if tname =~ /TaxonNameRelationship::(Icnp|Icn|Iczn|Icvcn)/ && tname != 'TaxonNameRelationship::Iczn::Validating::UncertainPlacement' subject_relationships = TaxonNameRelationship.where_subject_is_taxon_name(self.subject_taxon_name).not_self(self) subject_relationships.each do |i| if self.type_class.disjoint_taxon_name_relationships.include?(i.type_name) soft_validations.add(:type, "#{self.subject_status.capitalize} relationship is conflicting with another relationship: '#{i.subject_status}'") end end end end def sv_validate_disjoint_object classifications = self.object_taxon_name.taxon_name_classifications.reload.map {|i| i.type_name} disjoint_object_classes = self.type_class.disjoint_object_classes compare = disjoint_object_classes & classifications compare.each do |i| c = i.demodulize.underscore.humanize.downcase soft_validations.add(:type, "#{self.subject_status.capitalize} relationship is conflicting with the taxon status: '#{c}'") soft_validations.add(:object_taxon_name_id, "#{self.object_taxon_name.cached_html} has a conflicting status: '#{c}'") end end def sv_validate_disjoint_subject classifications = self.subject_taxon_name.taxon_name_classifications.reload.map {|i| i.type_name} disjoint_subject_classes = self.type_class.disjoint_subject_classes compare = disjoint_subject_classes & classifications compare.each do |i| c = i.demodulize.underscore.humanize.downcase soft_validations.add(:type, "#{self.subject_status.capitalize} conflicting with the status: '#{c}'") soft_validations.add(:subject_taxon_name_id, "#{self.subject_taxon_name.cached_html} has a conflicting status: '#{c}'") end end def sv_specific_relationship true # all validations moved to subclasses end def sv_objective_synonym_relationship true # all validations moved to subclasses end def sv_fix_objective_synonym_relationship true # all validations moved to subclasses end def sv_synonym_relationship true # all validations moved to subclasses end def sv_not_specific_relationship true # all validations moved to subclasses end def sv_fix_not_specific_relationship true # all validations moved to subclasses end def sv_synonym_linked_to_valid_name #synonyms and misspellings should be linked to valid names if ::TAXON_NAME_RELATIONSHIP_NAMES_SYNONYM.include?(self.type_name) obj = self.object_taxon_name subj = self.subject_taxon_name if subj.rank_class.try(:nomenclatural_code) == :iczn && (obj.parent_id != subj.parent_id || obj.rank_class != subj.rank_class) && subj.cached_valid_taxon_name_id == obj.cached_valid_taxon_name_id soft_validations.add(:subject_taxon_name_id, "#{self.subject_status.capitalize} #{subj.} should have the same parent and rank with #{obj.}", success_message: 'The parent was updated', failure_message: 'The parent was not updated') end end end def sv_fix_subject_parent_update res = false if TAXON_NAME_RELATIONSHIP_NAMES_SYNONYM.include?(self.type_name) obj = self.object_taxon_name subj = self.subject_taxon_name unless obj.parent_id == subj.parent_id subj.parent_id = obj.parent_id subj.rank_class = obj.rank_class begin TaxonName.transaction do subj.save! res = true end rescue end end end res end def subject_invalid_statuses TAXON_NAME_CLASS_NAMES_UNAVAILABLE_AND_INVALID & self.subject_taxon_name.taxon_name_classifications.collect{|c| c.type_class.to_s} end def sv_validate_priority true # all validations moved to subclasses end def sv_validate_seniority true # all validations moved to subclasses end def sv_coordinated_taxa s = subject_taxon_name o = object_taxon_name s_new = s.lowest_rank_coordinated_taxon if s != s_new soft_validations.add(:subject_taxon_name_id, "Relationship should move from #{s.rank_class.rank_name} #{s.cached_html} to #{s_new.rank_class.rank_name} #{s_new.cached_html}", success_message: "Relationship moved to #{s_new.rank_class.rank_name}", failure_message: 'Failed to update relationship') end end def sv_coordinated_taxa_object s = subject_taxon_name o = object_taxon_name o_new = o.lowest_rank_coordinated_taxon if o != o_new soft_validations.add(:object_taxon_name_id, "Relationship should move from #{o.rank_class.rank_name} #{o.cached_html} to #{o_new.rank_class.rank_name} #{o_new.cached_html}", success_message: "Relationship moved to #{o_new.rank_class.rank_name}", failure_message: 'Failed to update relationship') end end def sv_fix_coordinated_subject_taxa s = subject_taxon_name s_new = s.lowest_rank_coordinated_taxon if s != s_new self.subject_taxon_name = s_new begin TaxonNameRelationship.transaction do self.save return true end rescue end end false end def sv_fix_coordinated_object_taxa o = self.object_taxon_name o_new = o.lowest_rank_coordinated_taxon if o != o_new self.object_taxon_name = o_new begin TaxonNameRelationship.transaction do self.save return true end rescue end end false end def sv_fix_combination_relationship s = self.subject_taxon_name list = s.list_of_coordinated_names + [s] if s.rank_string =~ /Species/ s_new = list.detect{|t| t.rank_class.rank_name == 'species'} elsif s.rank_string =~ /Genus/ s_new = list.detect{|t| t.rank_class.rank_name == 'genus'} else s_new = s end if s != s_new && !s.nil? self.subject_taxon_name = s_new begin TaxonNameRelationship.transaction do self.save return true end rescue end end false end def self.collect_to_s(*args) args.collect{|arg| arg.to_s} end def self.collect_descendants_to_s(*classes) ans = [] classes.each do |klass| ans += klass.descendants.collect{|k| k.to_s} end ans end def self.collect_descendants_and_itself_to_s(*classes) classes.collect{|k| k.to_s} + self.collect_descendants_to_s(*classes) end # Force loading all descendants as soon as this class is referenced Dir.glob("#{Rails.root.join("app/models/taxon_name_relationship/**/*.rb")}") .sort { |a, b| a.split('/').count <=> b.split('/').count } .map { |p| p.split('/app/models/').last.sub(/\.rb$/, '') } .map { |p| p.split('/') } .map { |c| c.map { |n| ActiveSupport::Inflector.camelize(n) } } .map { |c| c.join('::') }.map(&:constantize) end |
#project_id ⇒ Integer
the project ID
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# File 'app/models/taxon_name_relationship.rb', line 44 class TaxonNameRelationship < ApplicationRecord include Housekeeping include Shared::Citations include Shared::Notes include SoftValidation include Shared::DwcOccurrenceHooks include Shared::IsData # @return [Boolean, nil] # When true, cached values are not built attr_accessor :no_cached belongs_to :subject_taxon_name, class_name: 'TaxonName', inverse_of: :taxon_name_relationships # left side belongs_to :object_taxon_name, class_name: 'TaxonName', inverse_of: :related_taxon_name_relationships # right side # After commit only fires if there are changes to the record. after_commit :set_cached_names_for_taxon_names, unless: -> {self.no_cached } # TODO: remove, it's required by STI validates_presence_of :type, message: 'Relationship type should be specified' validates_presence_of :subject_taxon_name, message: 'Missing taxon name on the left side' validates_presence_of :object_taxon_name, message: 'Missing taxon name on the right side' validates_uniqueness_of :object_taxon_name_id, scope: [:type, :project_id], if: :is_combination? validates_uniqueness_of :object_taxon_name_id, scope: [:type, :subject_taxon_name_id, :project_id], unless: :is_combination? validate :validate_type, :validate_subject_and_object_are_not_identical validate :subject_and_object_in_same_project unless: -> {!subject_taxon_name || !object_taxon_name} do validate :validate_subject_and_object_share_code, :validate_uniqueness_of_typification_object, #:validate_uniqueness_of_synonym_subject, :validate_object_and_subject_both_protonyms, :validate_object_must_equal_subject_for_uncertain_placement, :validate_subject_and_object_ranks, :validate_rank_group end # TODO: isolate to an include file sensu protonym soft_validate( :sv_validate_required_relationships, set: :validate_required_relationships, name: 'Required relationships', description: 'Required relationships' ) soft_validate( :sv_validate_disjoint_relationships, set: :validate_disjoint_relationships, name: 'Conflicting relationships', description: 'Detect conflicting relationships' ) soft_validate( :sv_validate_disjoint_object, set: :validate_disjoint_object, name: 'Conflicting object taxon', description: 'Object taxon has a status conflicting with the relationship' ) soft_validate( :sv_validate_disjoint_subject, set: :validate_disjoint_subject, name: 'Conflicting subject taxon', description: 'Subject taxon has a status conflicting with the relationship' ) soft_validate( :sv_specific_relationship, set: :specific_relationship, name: 'validate relationship', description: 'Validate integrity of the relationship, for example, the year applicability range' ) soft_validate( :sv_objective_synonym_relationship, set: :objective_synonym_relationship, fix: :sv_fix_objective_synonym_relationship, name: 'Objective synonym relationship', description: 'Objective synonyms should have the same type' ) soft_validate( :sv_synonym_relationship, set: :synonym_relationship, name: 'Synonym relationship', description: 'Validate integrity of synonym relationship' ) soft_validate( :sv_not_specific_relationship, set: :not_specific_relationship, fix: :sv_fix_not_specific_relationship, name: 'Not specific relationship', description: 'More specific relationship is preferred, for example "Subjective synonym" instead of "Synonym".' ) soft_validate( :sv_synonym_linked_to_valid_name, set: :synonym_linked_to_valid_name, fix: :sv_fix_subject_parent_update, name: 'Synonym not linked to valid taxon', description: 'Synonyms should be linked to valid taxon.' ) soft_validate( :sv_validate_priority, set: :validate_priority, name: 'Priority validation', description: 'Junior synonym should be younger than senior synonym' ) soft_validate( :sv_validate_seniority, set: :validate_seniority, name: 'Seniority validation', description: 'Of two synonyms described in the same paper, one described at a higher rank has a priority' ) soft_validate( :sv_coordinated_taxa, set: :coordinated_taxa, fix: :sv_fix_coordinated_subject_taxa, name: 'Move relationship to coordinate taxon', description: 'Relationship should be moved to the lowest rank coordinate taxon (for example from species to nomynotypical subspecies). It could be updated automatically with the Fix.' ) soft_validate( :sv_coordinated_taxa_object, set: :coordinated_taxa, fix: :sv_fix_coordinated_object_taxa, name: 'Move object relationship to coordinate taxon', description: 'Relationship should be moved to the lowest rank coordinate object taxon (for example from species to nomynotypical subspecies). It could be updated automatically with the Fix.') scope :where_subject_is_taxon_name, -> (taxon_name) {where(subject_taxon_name_id: taxon_name)} scope :where_object_is_taxon_name, -> (taxon_name) {where(object_taxon_name_id: taxon_name)} scope :where_object_in_taxon_names, -> (taxon_name_array) {where('"taxon_name_relationships"."object_taxon_name_id" IN (?)', taxon_name_array)} scope :with_type_string, -> (type_string) { where(sanitize_sql_array(["taxon_name_relationships.type = '%s'", type_string])) } scope :with_type_base, -> (base_string) {where('"taxon_name_relationships"."type" LIKE ?', "#{base_string}%")} scope :with_type_contains, -> (base_string) {where('"taxon_name_relationships"."type" LIKE ?', "%#{base_string}%")} scope :with_two_type_bases, -> (base_string1, base_string2) { where('taxon_name_relationships.type LIKE ? OR taxon_name_relationships.type LIKE ?', "#{base_string1}%", "#{base_string2}%") } scope :homonym_or_suppressed, -> {where("taxon_name_relationships.type LIKE 'TaxonNameRelationship::Iczn::Invalidating::Homonym%' OR taxon_name_relationships.type LIKE 'TaxonNameRelationship::Iczn::Invalidating::Suppression::Total'") } scope :with_type_array, -> (base_array) {where('taxon_name_relationships.type IN (?)', base_array ) } def dwc_occurrences DwcOccurrence .joins("JOIN collection_objects co on dwc_occurrence_object_id = co.id AND dwc_occurrence_object_type = 'CollectionObject'") .joins("JOIN taxon_determinations td on co.id = td.taxon_determination_object_id AND td.taxon_determination_object_type = 'CollectionObject'") .joins("JOIN otus o on o.id = td.otu_id") .where(o: {taxon_name_id: [subject_taxon_name_id, object_taxon_name_id]}) .distinct end # @return [Array of TaxonNameClassification] # the inferable TaxonNameClassification(s) added to the subject when this relationship is used # !! Not implemented def subject_properties [] end # @return [Array of TaxonNameClassification] # the inferable TaxonNameClassification(s) added to the subject when this relationship is used # !! Not implmented def object_properties [] end # @return class # this method calls Module#module_parent def self.parent self.module_parent end # @return [Array of NomenclatureRank] # the valid ranks to which the subject name can belong, set in subclasses. (left side) def self.valid_subject_ranks [] end # @return [Array of NomenclatureRank] # the valid ranks to which the object name can belong, set in subclasses. (right side) def self.valid_object_ranks [] end # @return [Array of TaxonNameRelationships] # if this relationships is set for the subject, then others in this array should not be used for that subject def self.disjoint_taxon_name_relationships [] end # TODO: why isn't this disjoint? # disjoint relationships for the taxon as a object def self.required_taxon_name_relationships [] end def self.disjoint_subject_classes [] end def self.disjoint_object_classes [] end def self.gbif_status_of_subject nil end def self.gbif_status_of_object nil end def self.assignable false end # @return [Symbol] # determine the relative age of subject and object # :direct - subject is younger than object # :reverse - object is younger than subject def self.nomenclatural_priority nil end # @return [String] # the status inferred by the relationship to the object name def object_status self.type_name.demodulize.underscore.humanize.downcase.gsub(/\d+/, ' \0 ').squish end # @return [String] # the status inferred by the relationship to the subject name def subject_status self.type_name.demodulize.underscore.humanize.downcase.gsub(/\d+/, ' \0 ').squish end # @return [String] # the connecting word in the relationship from the subject name to object name def subject_status_connector_to_object ' of' end # @return [String] # the connecting word in the relationship from the object name to subject name def object_status_connector_to_subject ' of' end # @return [String] # a readable fragement combining status and connector def subject_status_tag subject_status + subject_status_connector_to_object end # @return [String] # a readable fragement combining status and connector def object_status_tag object_status + object_status_connector_to_subject end # @return [String, nil] # the type of this relationship, IF the type is a valid name, else nil def type_name r = self.type TAXON_NAME_RELATIONSHIP_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 TAXON_NAME_RELATIONSHIP_NAMES.include?(r) ? r.safe_constantize : nil end # @return [String, nil] # the NOMEN uri for this type def self.nomen_uri const_defined?(:NOMEN_URI, false) ? self::NOMEN_URI : nil end # @return [Time] # effective date of publication, used to determine nomenclatural priorities # !! Careful, if no date is present the current year is given, rather than nil, @proceps is this a safe inference? def nomenclature_date self.source ? (self.source.cached_nomenclature_date ? self.source.cached_nomenclature_date.to_time : Time.current) : Time.current end def is_combination? !!/TaxonNameRelationship::(OriginalCombination|Combination)/.match(self.type.to_s) end protected def subject_and_object_in_same_project if subject_taxon_name && object_taxon_name if subject_taxon_name.project_id != object_taxon_name.project_id errors.add(:base, 'one name is not in the same project as the other') end end end def validate_type # TODO: Remove, handled by STI if type && !TAXON_NAME_RELATIONSHIP_NAMES.include?(type.to_s) errors.add(:type, "'#{type}' is not a valid taxon name relationship") elsif self.type_class && object_taxon_name.class.to_s == 'Protonym' && !self.type_class.valid_object_ranks.include?(object_taxon_name.rank_string) errors.add(:type, "'#{type}' is not a valid taxon name relationship") end if object_taxon_name.class.to_s == 'Protonym' || object_taxon_name.class.to_s == 'Hybrid' errors.add(:type, "'#{type}' is not a valid taxon name relationship") if /TaxonNameRelationship::Combination::/.match(self.type) end if object_taxon_name.class.to_s == 'Combination' errors.add(:type, "'#{type}' is not a valid taxon name relationship") unless /TaxonNameRelationship::Combination::/.match(self.type) end end # @todo validate, that all the relationships in the table could be linked to relationships in classes (if those had changed) def validate_subject_and_object_share_code if object_taxon_name.type == 'Protonym' && subject_taxon_name.type == 'Protonym' errors.add(:object_taxon_name_id, 'The related taxon is not in the same monenclatural group (ICZN, ICN, ICNP, ICVCN') if subject_taxon_name.rank_class.try(:nomenclatural_code) != object_taxon_name.rank_class.try(:nomenclatural_code) end end def validate_subject_and_object_are_not_identical if !self.object_taxon_name_id.nil? && self.object_taxon_name == self.subject_taxon_name errors.add(:object_taxon_name_id, "#{self.object_taxon_name.try(:cached_html)} should not refer to itself") unless self.type =~ /OriginalCombination/ end end def validate_object_must_equal_subject_for_uncertain_placement if self.object_taxon_name_id != self.subject_taxon_name.parent_id && self.type_name == 'TaxonNameRelationship::Iczn::Validating::UncertainPlacement' errors.add(:object_taxon_name_id, "The parent #{self.subject_taxon_name.parent.cached_html} and the Incertae Sedis placement (#{self.object_taxon_name.cached_html}) should match") end end def validate_subject_and_object_ranks tname = self.type_name if tname =~ /TaxonNameRelationship::(Icnp|Icn|Iczn|Icvcn)/ && tname != 'TaxonNameRelationship::Iczn::Validating::UncertainPlacement' rank_group = self.subject_taxon_name.rank_class.try(:parent) unless rank_group == self.object_taxon_name.rank_class.try(:parent) errors.add(:object_taxon_name_id, "Rank of related taxon should be in the #{rank_group.try(:rank_name)} rank group, not #{self.object_taxon_name.rank_class.try(:rank_name)}") end end if self.type_class.present? # only validate if it is set if object_taxon_name && object_taxon_name.rank_class if object_taxon_name.type == 'Protonym' || object_taxon_name.type == 'Hybrid' unless self.type_class.valid_object_ranks.include?(self.object_taxon_name.rank_string) errors.add(:object_taxon_name_id, "#{self.object_taxon_name.rank_class.rank_name.capitalize} rank of #{self.object_taxon_name.cached_html} is not compatible with the #{self.subject_status} relationship") errors.add(:type, "Relationship #{self.subject_status} is not compatible with the #{self.object_taxon_name.rank_class.rank_name} rank of #{self.object_taxon_name.cached_html}") end end end if subject_taxon_name && subject_taxon_name.rank_class if subject_taxon_name.type == 'Protonym' || subject_taxon_name.type == 'Hybrid' unless self.type_class.valid_subject_ranks.include?(self.subject_taxon_name.rank_string) soft_validations.add(:subject_taxon_name_id, "#{self.subject_taxon_name.rank_class.rank_name.capitalize} rank of #{self.subject_taxon_name.cached_html} is not compatible with the #{self.subject_status} relationship") soft_validations.add(:type, "Relationship #{self.subject_status} is not compatible with the #{self.subject_taxon_name.rank_class.rank_name} rank of #{self.subject_taxon_name.cached_html}") end end end end end ##### Protonym historically could be listed as a synonym to different taxa #def validate_uniqueness_of_synonym_subject # if !self.type.nil? && /Synonym/.match(self.type_name) && !TaxonNameRelationship.where(subject_taxon_name_id: self.subject_taxon_name_id).with_type_contains('Synonym').not_self(self).empty? # errors.add(:subject_taxon_name_id, 'Only one synonym relationship is allowed') # end #end def validate_uniqueness_of_typification_object if /Typification/.match(self.type_name) && !TaxonNameRelationship.where(object_taxon_name_id: self.object_taxon_name_id).with_type_contains('Typification').not_self(self).empty? errors.add(:object_taxon_name_id, 'Only one Type designation relationship is allowed') end end def validate_rank_group if self.type =~ /Hybrid/ && self.subject_taxon_name && self.object_taxon_name if self.subject_taxon_name.rank_class.parent != self.object_taxon_name.rank_class.parent errors.add(:subject_taxon_name_id, "#{self.subject_taxon_name.rank_class.rank_name.capitalize} rank of #{self.subject_taxon_name.cached_html} is not compatible with the rank of hybrid (#{self.object_taxon_name.rank_class.rank_name})") end end end def validate_object_and_subject_both_protonyms if /TaxonNameRelationship::Combination::/.match(self.type) errors.add(:object_taxon_name_id, 'Not a Combination') if object_taxon_name.type != 'Combination' else errors.add(:object_taxon_name_id, 'Not a Protonym') if object_taxon_name.type == 'Combination' end errors.add(:subject_taxon_name_id, 'Not a Protonym') if subject_taxon_name.type == 'Combination' && self.type != 'TaxonNameRelationship::CurrentCombination' end # OriginalCombination has a replacement method. def set_cached_names_for_taxon_names return true unless subject_taxon_name_id_previously_changed? || destroyed? # TODO: this should completely be replaced with Taxonname logic. TaxonName.transaction do # Why? if is_invalidating? t = subject_taxon_name if TAXON_NAME_RELATIONSHIP_NAMES_MISSPELLING_ONLY.include?(type_name) t.update_columns( cached_misspelling: true, cached_author_year: t., cached_nomenclature_date: t.nomenclature_date, cached_original_combination: t.get_original_combination, cached_original_combination_html: t.get_original_combination_html) end if type_name =~/Misapplication/ t.update_columns( cached_author_year: t., cached_nomenclature_date: t.nomenclature_date) end vn = t.get_valid_taxon_name # !! NO set cached should do this from TN side of things, # !! Not here n = t.get_full_name t.update_columns( cached: n, cached_html: t.get_full_name_html(n), # OK to force reload here, otherwise we need an exception in #set_cached cached_valid_taxon_name_id: vn.id, cached_is_valid: !t.unavailable_or_invalid?) t.combination_list_self.each do |c| c.update_column(:cached_valid_taxon_name_id, vn.id) end vn.list_of_invalid_taxon_names.each do |s| s.update_columns( cached_valid_taxon_name_id: vn.id, cached_is_valid: !s.unavailable_or_invalid?) s.combination_list_self.each do |c| c.update_column(:cached_valid_taxon_name_id, vn.id) end end end end true end def is_invalidating? TAXON_NAME_RELATIONSHIP_NAMES_INVALID.include?(type_name) end def sv_validate_required_relationships return true if self.subject_taxon_name.not_binominal? object_relationships = TaxonNameRelationship.where_object_is_taxon_name(self.object_taxon_name).not_self(self).collect{|r| r.type} required = self.type_class.required_taxon_name_relationships - object_relationships required.each do |r| soft_validations.add(:type, " Presence of #{self.subject_status} requires selection of #{r.demodulize.underscore.humanize.downcase}") end end def sv_validate_disjoint_relationships tname = self.type_name if tname =~ /TaxonNameRelationship::(Icnp|Icn|Iczn|Icvcn)/ && tname != 'TaxonNameRelationship::Iczn::Validating::UncertainPlacement' subject_relationships = TaxonNameRelationship.where_subject_is_taxon_name(self.subject_taxon_name).not_self(self) subject_relationships.each do |i| if self.type_class.disjoint_taxon_name_relationships.include?(i.type_name) soft_validations.add(:type, "#{self.subject_status.capitalize} relationship is conflicting with another relationship: '#{i.subject_status}'") end end end end def sv_validate_disjoint_object classifications = self.object_taxon_name.taxon_name_classifications.reload.map {|i| i.type_name} disjoint_object_classes = self.type_class.disjoint_object_classes compare = disjoint_object_classes & classifications compare.each do |i| c = i.demodulize.underscore.humanize.downcase soft_validations.add(:type, "#{self.subject_status.capitalize} relationship is conflicting with the taxon status: '#{c}'") soft_validations.add(:object_taxon_name_id, "#{self.object_taxon_name.cached_html} has a conflicting status: '#{c}'") end end def sv_validate_disjoint_subject classifications = self.subject_taxon_name.taxon_name_classifications.reload.map {|i| i.type_name} disjoint_subject_classes = self.type_class.disjoint_subject_classes compare = disjoint_subject_classes & classifications compare.each do |i| c = i.demodulize.underscore.humanize.downcase soft_validations.add(:type, "#{self.subject_status.capitalize} conflicting with the status: '#{c}'") soft_validations.add(:subject_taxon_name_id, "#{self.subject_taxon_name.cached_html} has a conflicting status: '#{c}'") end end def sv_specific_relationship true # all validations moved to subclasses end def sv_objective_synonym_relationship true # all validations moved to subclasses end def sv_fix_objective_synonym_relationship true # all validations moved to subclasses end def sv_synonym_relationship true # all validations moved to subclasses end def sv_not_specific_relationship true # all validations moved to subclasses end def sv_fix_not_specific_relationship true # all validations moved to subclasses end def sv_synonym_linked_to_valid_name #synonyms and misspellings should be linked to valid names if ::TAXON_NAME_RELATIONSHIP_NAMES_SYNONYM.include?(self.type_name) obj = self.object_taxon_name subj = self.subject_taxon_name if subj.rank_class.try(:nomenclatural_code) == :iczn && (obj.parent_id != subj.parent_id || obj.rank_class != subj.rank_class) && subj.cached_valid_taxon_name_id == obj.cached_valid_taxon_name_id soft_validations.add(:subject_taxon_name_id, "#{self.subject_status.capitalize} #{subj.} should have the same parent and rank with #{obj.}", success_message: 'The parent was updated', failure_message: 'The parent was not updated') end end end def sv_fix_subject_parent_update res = false if TAXON_NAME_RELATIONSHIP_NAMES_SYNONYM.include?(self.type_name) obj = self.object_taxon_name subj = self.subject_taxon_name unless obj.parent_id == subj.parent_id subj.parent_id = obj.parent_id subj.rank_class = obj.rank_class begin TaxonName.transaction do subj.save! res = true end rescue end end end res end def subject_invalid_statuses TAXON_NAME_CLASS_NAMES_UNAVAILABLE_AND_INVALID & self.subject_taxon_name.taxon_name_classifications.collect{|c| c.type_class.to_s} end def sv_validate_priority true # all validations moved to subclasses end def sv_validate_seniority true # all validations moved to subclasses end def sv_coordinated_taxa s = subject_taxon_name o = object_taxon_name s_new = s.lowest_rank_coordinated_taxon if s != s_new soft_validations.add(:subject_taxon_name_id, "Relationship should move from #{s.rank_class.rank_name} #{s.cached_html} to #{s_new.rank_class.rank_name} #{s_new.cached_html}", success_message: "Relationship moved to #{s_new.rank_class.rank_name}", failure_message: 'Failed to update relationship') end end def sv_coordinated_taxa_object s = subject_taxon_name o = object_taxon_name o_new = o.lowest_rank_coordinated_taxon if o != o_new soft_validations.add(:object_taxon_name_id, "Relationship should move from #{o.rank_class.rank_name} #{o.cached_html} to #{o_new.rank_class.rank_name} #{o_new.cached_html}", success_message: "Relationship moved to #{o_new.rank_class.rank_name}", failure_message: 'Failed to update relationship') end end def sv_fix_coordinated_subject_taxa s = subject_taxon_name s_new = s.lowest_rank_coordinated_taxon if s != s_new self.subject_taxon_name = s_new begin TaxonNameRelationship.transaction do self.save return true end rescue end end false end def sv_fix_coordinated_object_taxa o = self.object_taxon_name o_new = o.lowest_rank_coordinated_taxon if o != o_new self.object_taxon_name = o_new begin TaxonNameRelationship.transaction do self.save return true end rescue end end false end def sv_fix_combination_relationship s = self.subject_taxon_name list = s.list_of_coordinated_names + [s] if s.rank_string =~ /Species/ s_new = list.detect{|t| t.rank_class.rank_name == 'species'} elsif s.rank_string =~ /Genus/ s_new = list.detect{|t| t.rank_class.rank_name == 'genus'} else s_new = s end if s != s_new && !s.nil? self.subject_taxon_name = s_new begin TaxonNameRelationship.transaction do self.save return true end rescue end end false end def self.collect_to_s(*args) args.collect{|arg| arg.to_s} end def self.collect_descendants_to_s(*classes) ans = [] classes.each do |klass| ans += klass.descendants.collect{|k| k.to_s} end ans end def self.collect_descendants_and_itself_to_s(*classes) classes.collect{|k| k.to_s} + self.collect_descendants_to_s(*classes) end # Force loading all descendants as soon as this class is referenced Dir.glob("#{Rails.root.join("app/models/taxon_name_relationship/**/*.rb")}") .sort { |a, b| a.split('/').count <=> b.split('/').count } .map { |p| p.split('/app/models/').last.sub(/\.rb$/, '') } .map { |p| p.split('/') } .map { |c| c.map { |n| ActiveSupport::Inflector.camelize(n) } } .map { |c| c.join('::') }.map(&:constantize) end |
#subject_taxon_name_id ⇒ Integer
Returns the subject taxon name.
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# File 'app/models/taxon_name_relationship.rb', line 44 class TaxonNameRelationship < ApplicationRecord include Housekeeping include Shared::Citations include Shared::Notes include SoftValidation include Shared::DwcOccurrenceHooks include Shared::IsData # @return [Boolean, nil] # When true, cached values are not built attr_accessor :no_cached belongs_to :subject_taxon_name, class_name: 'TaxonName', inverse_of: :taxon_name_relationships # left side belongs_to :object_taxon_name, class_name: 'TaxonName', inverse_of: :related_taxon_name_relationships # right side # After commit only fires if there are changes to the record. after_commit :set_cached_names_for_taxon_names, unless: -> {self.no_cached } # TODO: remove, it's required by STI validates_presence_of :type, message: 'Relationship type should be specified' validates_presence_of :subject_taxon_name, message: 'Missing taxon name on the left side' validates_presence_of :object_taxon_name, message: 'Missing taxon name on the right side' validates_uniqueness_of :object_taxon_name_id, scope: [:type, :project_id], if: :is_combination? validates_uniqueness_of :object_taxon_name_id, scope: [:type, :subject_taxon_name_id, :project_id], unless: :is_combination? validate :validate_type, :validate_subject_and_object_are_not_identical validate :subject_and_object_in_same_project unless: -> {!subject_taxon_name || !object_taxon_name} do validate :validate_subject_and_object_share_code, :validate_uniqueness_of_typification_object, #:validate_uniqueness_of_synonym_subject, :validate_object_and_subject_both_protonyms, :validate_object_must_equal_subject_for_uncertain_placement, :validate_subject_and_object_ranks, :validate_rank_group end # TODO: isolate to an include file sensu protonym soft_validate( :sv_validate_required_relationships, set: :validate_required_relationships, name: 'Required relationships', description: 'Required relationships' ) soft_validate( :sv_validate_disjoint_relationships, set: :validate_disjoint_relationships, name: 'Conflicting relationships', description: 'Detect conflicting relationships' ) soft_validate( :sv_validate_disjoint_object, set: :validate_disjoint_object, name: 'Conflicting object taxon', description: 'Object taxon has a status conflicting with the relationship' ) soft_validate( :sv_validate_disjoint_subject, set: :validate_disjoint_subject, name: 'Conflicting subject taxon', description: 'Subject taxon has a status conflicting with the relationship' ) soft_validate( :sv_specific_relationship, set: :specific_relationship, name: 'validate relationship', description: 'Validate integrity of the relationship, for example, the year applicability range' ) soft_validate( :sv_objective_synonym_relationship, set: :objective_synonym_relationship, fix: :sv_fix_objective_synonym_relationship, name: 'Objective synonym relationship', description: 'Objective synonyms should have the same type' ) soft_validate( :sv_synonym_relationship, set: :synonym_relationship, name: 'Synonym relationship', description: 'Validate integrity of synonym relationship' ) soft_validate( :sv_not_specific_relationship, set: :not_specific_relationship, fix: :sv_fix_not_specific_relationship, name: 'Not specific relationship', description: 'More specific relationship is preferred, for example "Subjective synonym" instead of "Synonym".' ) soft_validate( :sv_synonym_linked_to_valid_name, set: :synonym_linked_to_valid_name, fix: :sv_fix_subject_parent_update, name: 'Synonym not linked to valid taxon', description: 'Synonyms should be linked to valid taxon.' ) soft_validate( :sv_validate_priority, set: :validate_priority, name: 'Priority validation', description: 'Junior synonym should be younger than senior synonym' ) soft_validate( :sv_validate_seniority, set: :validate_seniority, name: 'Seniority validation', description: 'Of two synonyms described in the same paper, one described at a higher rank has a priority' ) soft_validate( :sv_coordinated_taxa, set: :coordinated_taxa, fix: :sv_fix_coordinated_subject_taxa, name: 'Move relationship to coordinate taxon', description: 'Relationship should be moved to the lowest rank coordinate taxon (for example from species to nomynotypical subspecies). It could be updated automatically with the Fix.' ) soft_validate( :sv_coordinated_taxa_object, set: :coordinated_taxa, fix: :sv_fix_coordinated_object_taxa, name: 'Move object relationship to coordinate taxon', description: 'Relationship should be moved to the lowest rank coordinate object taxon (for example from species to nomynotypical subspecies). It could be updated automatically with the Fix.') scope :where_subject_is_taxon_name, -> (taxon_name) {where(subject_taxon_name_id: taxon_name)} scope :where_object_is_taxon_name, -> (taxon_name) {where(object_taxon_name_id: taxon_name)} scope :where_object_in_taxon_names, -> (taxon_name_array) {where('"taxon_name_relationships"."object_taxon_name_id" IN (?)', taxon_name_array)} scope :with_type_string, -> (type_string) { where(sanitize_sql_array(["taxon_name_relationships.type = '%s'", type_string])) } scope :with_type_base, -> (base_string) {where('"taxon_name_relationships"."type" LIKE ?', "#{base_string}%")} scope :with_type_contains, -> (base_string) {where('"taxon_name_relationships"."type" LIKE ?', "%#{base_string}%")} scope :with_two_type_bases, -> (base_string1, base_string2) { where('taxon_name_relationships.type LIKE ? OR taxon_name_relationships.type LIKE ?', "#{base_string1}%", "#{base_string2}%") } scope :homonym_or_suppressed, -> {where("taxon_name_relationships.type LIKE 'TaxonNameRelationship::Iczn::Invalidating::Homonym%' OR taxon_name_relationships.type LIKE 'TaxonNameRelationship::Iczn::Invalidating::Suppression::Total'") } scope :with_type_array, -> (base_array) {where('taxon_name_relationships.type IN (?)', base_array ) } def dwc_occurrences DwcOccurrence .joins("JOIN collection_objects co on dwc_occurrence_object_id = co.id AND dwc_occurrence_object_type = 'CollectionObject'") .joins("JOIN taxon_determinations td on co.id = td.taxon_determination_object_id AND td.taxon_determination_object_type = 'CollectionObject'") .joins("JOIN otus o on o.id = td.otu_id") .where(o: {taxon_name_id: [subject_taxon_name_id, object_taxon_name_id]}) .distinct end # @return [Array of TaxonNameClassification] # the inferable TaxonNameClassification(s) added to the subject when this relationship is used # !! Not implemented def subject_properties [] end # @return [Array of TaxonNameClassification] # the inferable TaxonNameClassification(s) added to the subject when this relationship is used # !! Not implmented def object_properties [] end # @return class # this method calls Module#module_parent def self.parent self.module_parent end # @return [Array of NomenclatureRank] # the valid ranks to which the subject name can belong, set in subclasses. (left side) def self.valid_subject_ranks [] end # @return [Array of NomenclatureRank] # the valid ranks to which the object name can belong, set in subclasses. (right side) def self.valid_object_ranks [] end # @return [Array of TaxonNameRelationships] # if this relationships is set for the subject, then others in this array should not be used for that subject def self.disjoint_taxon_name_relationships [] end # TODO: why isn't this disjoint? # disjoint relationships for the taxon as a object def self.required_taxon_name_relationships [] end def self.disjoint_subject_classes [] end def self.disjoint_object_classes [] end def self.gbif_status_of_subject nil end def self.gbif_status_of_object nil end def self.assignable false end # @return [Symbol] # determine the relative age of subject and object # :direct - subject is younger than object # :reverse - object is younger than subject def self.nomenclatural_priority nil end # @return [String] # the status inferred by the relationship to the object name def object_status self.type_name.demodulize.underscore.humanize.downcase.gsub(/\d+/, ' \0 ').squish end # @return [String] # the status inferred by the relationship to the subject name def subject_status self.type_name.demodulize.underscore.humanize.downcase.gsub(/\d+/, ' \0 ').squish end # @return [String] # the connecting word in the relationship from the subject name to object name def subject_status_connector_to_object ' of' end # @return [String] # the connecting word in the relationship from the object name to subject name def object_status_connector_to_subject ' of' end # @return [String] # a readable fragement combining status and connector def subject_status_tag subject_status + subject_status_connector_to_object end # @return [String] # a readable fragement combining status and connector def object_status_tag object_status + object_status_connector_to_subject end # @return [String, nil] # the type of this relationship, IF the type is a valid name, else nil def type_name r = self.type TAXON_NAME_RELATIONSHIP_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 TAXON_NAME_RELATIONSHIP_NAMES.include?(r) ? r.safe_constantize : nil end # @return [String, nil] # the NOMEN uri for this type def self.nomen_uri const_defined?(:NOMEN_URI, false) ? self::NOMEN_URI : nil end # @return [Time] # effective date of publication, used to determine nomenclatural priorities # !! Careful, if no date is present the current year is given, rather than nil, @proceps is this a safe inference? def nomenclature_date self.source ? (self.source.cached_nomenclature_date ? self.source.cached_nomenclature_date.to_time : Time.current) : Time.current end def is_combination? !!/TaxonNameRelationship::(OriginalCombination|Combination)/.match(self.type.to_s) end protected def subject_and_object_in_same_project if subject_taxon_name && object_taxon_name if subject_taxon_name.project_id != object_taxon_name.project_id errors.add(:base, 'one name is not in the same project as the other') end end end def validate_type # TODO: Remove, handled by STI if type && !TAXON_NAME_RELATIONSHIP_NAMES.include?(type.to_s) errors.add(:type, "'#{type}' is not a valid taxon name relationship") elsif self.type_class && object_taxon_name.class.to_s == 'Protonym' && !self.type_class.valid_object_ranks.include?(object_taxon_name.rank_string) errors.add(:type, "'#{type}' is not a valid taxon name relationship") end if object_taxon_name.class.to_s == 'Protonym' || object_taxon_name.class.to_s == 'Hybrid' errors.add(:type, "'#{type}' is not a valid taxon name relationship") if /TaxonNameRelationship::Combination::/.match(self.type) end if object_taxon_name.class.to_s == 'Combination' errors.add(:type, "'#{type}' is not a valid taxon name relationship") unless /TaxonNameRelationship::Combination::/.match(self.type) end end # @todo validate, that all the relationships in the table could be linked to relationships in classes (if those had changed) def validate_subject_and_object_share_code if object_taxon_name.type == 'Protonym' && subject_taxon_name.type == 'Protonym' errors.add(:object_taxon_name_id, 'The related taxon is not in the same monenclatural group (ICZN, ICN, ICNP, ICVCN') if subject_taxon_name.rank_class.try(:nomenclatural_code) != object_taxon_name.rank_class.try(:nomenclatural_code) end end def validate_subject_and_object_are_not_identical if !self.object_taxon_name_id.nil? && self.object_taxon_name == self.subject_taxon_name errors.add(:object_taxon_name_id, "#{self.object_taxon_name.try(:cached_html)} should not refer to itself") unless self.type =~ /OriginalCombination/ end end def validate_object_must_equal_subject_for_uncertain_placement if self.object_taxon_name_id != self.subject_taxon_name.parent_id && self.type_name == 'TaxonNameRelationship::Iczn::Validating::UncertainPlacement' errors.add(:object_taxon_name_id, "The parent #{self.subject_taxon_name.parent.cached_html} and the Incertae Sedis placement (#{self.object_taxon_name.cached_html}) should match") end end def validate_subject_and_object_ranks tname = self.type_name if tname =~ /TaxonNameRelationship::(Icnp|Icn|Iczn|Icvcn)/ && tname != 'TaxonNameRelationship::Iczn::Validating::UncertainPlacement' rank_group = self.subject_taxon_name.rank_class.try(:parent) unless rank_group == self.object_taxon_name.rank_class.try(:parent) errors.add(:object_taxon_name_id, "Rank of related taxon should be in the #{rank_group.try(:rank_name)} rank group, not #{self.object_taxon_name.rank_class.try(:rank_name)}") end end if self.type_class.present? # only validate if it is set if object_taxon_name && object_taxon_name.rank_class if object_taxon_name.type == 'Protonym' || object_taxon_name.type == 'Hybrid' unless self.type_class.valid_object_ranks.include?(self.object_taxon_name.rank_string) errors.add(:object_taxon_name_id, "#{self.object_taxon_name.rank_class.rank_name.capitalize} rank of #{self.object_taxon_name.cached_html} is not compatible with the #{self.subject_status} relationship") errors.add(:type, "Relationship #{self.subject_status} is not compatible with the #{self.object_taxon_name.rank_class.rank_name} rank of #{self.object_taxon_name.cached_html}") end end end if subject_taxon_name && subject_taxon_name.rank_class if subject_taxon_name.type == 'Protonym' || subject_taxon_name.type == 'Hybrid' unless self.type_class.valid_subject_ranks.include?(self.subject_taxon_name.rank_string) soft_validations.add(:subject_taxon_name_id, "#{self.subject_taxon_name.rank_class.rank_name.capitalize} rank of #{self.subject_taxon_name.cached_html} is not compatible with the #{self.subject_status} relationship") soft_validations.add(:type, "Relationship #{self.subject_status} is not compatible with the #{self.subject_taxon_name.rank_class.rank_name} rank of #{self.subject_taxon_name.cached_html}") end end end end end ##### Protonym historically could be listed as a synonym to different taxa #def validate_uniqueness_of_synonym_subject # if !self.type.nil? && /Synonym/.match(self.type_name) && !TaxonNameRelationship.where(subject_taxon_name_id: self.subject_taxon_name_id).with_type_contains('Synonym').not_self(self).empty? # errors.add(:subject_taxon_name_id, 'Only one synonym relationship is allowed') # end #end def validate_uniqueness_of_typification_object if /Typification/.match(self.type_name) && !TaxonNameRelationship.where(object_taxon_name_id: self.object_taxon_name_id).with_type_contains('Typification').not_self(self).empty? errors.add(:object_taxon_name_id, 'Only one Type designation relationship is allowed') end end def validate_rank_group if self.type =~ /Hybrid/ && self.subject_taxon_name && self.object_taxon_name if self.subject_taxon_name.rank_class.parent != self.object_taxon_name.rank_class.parent errors.add(:subject_taxon_name_id, "#{self.subject_taxon_name.rank_class.rank_name.capitalize} rank of #{self.subject_taxon_name.cached_html} is not compatible with the rank of hybrid (#{self.object_taxon_name.rank_class.rank_name})") end end end def validate_object_and_subject_both_protonyms if /TaxonNameRelationship::Combination::/.match(self.type) errors.add(:object_taxon_name_id, 'Not a Combination') if object_taxon_name.type != 'Combination' else errors.add(:object_taxon_name_id, 'Not a Protonym') if object_taxon_name.type == 'Combination' end errors.add(:subject_taxon_name_id, 'Not a Protonym') if subject_taxon_name.type == 'Combination' && self.type != 'TaxonNameRelationship::CurrentCombination' end # OriginalCombination has a replacement method. def set_cached_names_for_taxon_names return true unless subject_taxon_name_id_previously_changed? || destroyed? # TODO: this should completely be replaced with Taxonname logic. TaxonName.transaction do # Why? if is_invalidating? t = subject_taxon_name if TAXON_NAME_RELATIONSHIP_NAMES_MISSPELLING_ONLY.include?(type_name) t.update_columns( cached_misspelling: true, cached_author_year: t., cached_nomenclature_date: t.nomenclature_date, cached_original_combination: t.get_original_combination, cached_original_combination_html: t.get_original_combination_html) end if type_name =~/Misapplication/ t.update_columns( cached_author_year: t., cached_nomenclature_date: t.nomenclature_date) end vn = t.get_valid_taxon_name # !! NO set cached should do this from TN side of things, # !! Not here n = t.get_full_name t.update_columns( cached: n, cached_html: t.get_full_name_html(n), # OK to force reload here, otherwise we need an exception in #set_cached cached_valid_taxon_name_id: vn.id, cached_is_valid: !t.unavailable_or_invalid?) t.combination_list_self.each do |c| c.update_column(:cached_valid_taxon_name_id, vn.id) end vn.list_of_invalid_taxon_names.each do |s| s.update_columns( cached_valid_taxon_name_id: vn.id, cached_is_valid: !s.unavailable_or_invalid?) s.combination_list_self.each do |c| c.update_column(:cached_valid_taxon_name_id, vn.id) end end end end true end def is_invalidating? TAXON_NAME_RELATIONSHIP_NAMES_INVALID.include?(type_name) end def sv_validate_required_relationships return true if self.subject_taxon_name.not_binominal? object_relationships = TaxonNameRelationship.where_object_is_taxon_name(self.object_taxon_name).not_self(self).collect{|r| r.type} required = self.type_class.required_taxon_name_relationships - object_relationships required.each do |r| soft_validations.add(:type, " Presence of #{self.subject_status} requires selection of #{r.demodulize.underscore.humanize.downcase}") end end def sv_validate_disjoint_relationships tname = self.type_name if tname =~ /TaxonNameRelationship::(Icnp|Icn|Iczn|Icvcn)/ && tname != 'TaxonNameRelationship::Iczn::Validating::UncertainPlacement' subject_relationships = TaxonNameRelationship.where_subject_is_taxon_name(self.subject_taxon_name).not_self(self) subject_relationships.each do |i| if self.type_class.disjoint_taxon_name_relationships.include?(i.type_name) soft_validations.add(:type, "#{self.subject_status.capitalize} relationship is conflicting with another relationship: '#{i.subject_status}'") end end end end def sv_validate_disjoint_object classifications = self.object_taxon_name.taxon_name_classifications.reload.map {|i| i.type_name} disjoint_object_classes = self.type_class.disjoint_object_classes compare = disjoint_object_classes & classifications compare.each do |i| c = i.demodulize.underscore.humanize.downcase soft_validations.add(:type, "#{self.subject_status.capitalize} relationship is conflicting with the taxon status: '#{c}'") soft_validations.add(:object_taxon_name_id, "#{self.object_taxon_name.cached_html} has a conflicting status: '#{c}'") end end def sv_validate_disjoint_subject classifications = self.subject_taxon_name.taxon_name_classifications.reload.map {|i| i.type_name} disjoint_subject_classes = self.type_class.disjoint_subject_classes compare = disjoint_subject_classes & classifications compare.each do |i| c = i.demodulize.underscore.humanize.downcase soft_validations.add(:type, "#{self.subject_status.capitalize} conflicting with the status: '#{c}'") soft_validations.add(:subject_taxon_name_id, "#{self.subject_taxon_name.cached_html} has a conflicting status: '#{c}'") end end def sv_specific_relationship true # all validations moved to subclasses end def sv_objective_synonym_relationship true # all validations moved to subclasses end def sv_fix_objective_synonym_relationship true # all validations moved to subclasses end def sv_synonym_relationship true # all validations moved to subclasses end def sv_not_specific_relationship true # all validations moved to subclasses end def sv_fix_not_specific_relationship true # all validations moved to subclasses end def sv_synonym_linked_to_valid_name #synonyms and misspellings should be linked to valid names if ::TAXON_NAME_RELATIONSHIP_NAMES_SYNONYM.include?(self.type_name) obj = self.object_taxon_name subj = self.subject_taxon_name if subj.rank_class.try(:nomenclatural_code) == :iczn && (obj.parent_id != subj.parent_id || obj.rank_class != subj.rank_class) && subj.cached_valid_taxon_name_id == obj.cached_valid_taxon_name_id soft_validations.add(:subject_taxon_name_id, "#{self.subject_status.capitalize} #{subj.} should have the same parent and rank with #{obj.}", success_message: 'The parent was updated', failure_message: 'The parent was not updated') end end end def sv_fix_subject_parent_update res = false if TAXON_NAME_RELATIONSHIP_NAMES_SYNONYM.include?(self.type_name) obj = self.object_taxon_name subj = self.subject_taxon_name unless obj.parent_id == subj.parent_id subj.parent_id = obj.parent_id subj.rank_class = obj.rank_class begin TaxonName.transaction do subj.save! res = true end rescue end end end res end def subject_invalid_statuses TAXON_NAME_CLASS_NAMES_UNAVAILABLE_AND_INVALID & self.subject_taxon_name.taxon_name_classifications.collect{|c| c.type_class.to_s} end def sv_validate_priority true # all validations moved to subclasses end def sv_validate_seniority true # all validations moved to subclasses end def sv_coordinated_taxa s = subject_taxon_name o = object_taxon_name s_new = s.lowest_rank_coordinated_taxon if s != s_new soft_validations.add(:subject_taxon_name_id, "Relationship should move from #{s.rank_class.rank_name} #{s.cached_html} to #{s_new.rank_class.rank_name} #{s_new.cached_html}", success_message: "Relationship moved to #{s_new.rank_class.rank_name}", failure_message: 'Failed to update relationship') end end def sv_coordinated_taxa_object s = subject_taxon_name o = object_taxon_name o_new = o.lowest_rank_coordinated_taxon if o != o_new soft_validations.add(:object_taxon_name_id, "Relationship should move from #{o.rank_class.rank_name} #{o.cached_html} to #{o_new.rank_class.rank_name} #{o_new.cached_html}", success_message: "Relationship moved to #{o_new.rank_class.rank_name}", failure_message: 'Failed to update relationship') end end def sv_fix_coordinated_subject_taxa s = subject_taxon_name s_new = s.lowest_rank_coordinated_taxon if s != s_new self.subject_taxon_name = s_new begin TaxonNameRelationship.transaction do self.save return true end rescue end end false end def sv_fix_coordinated_object_taxa o = self.object_taxon_name o_new = o.lowest_rank_coordinated_taxon if o != o_new self.object_taxon_name = o_new begin TaxonNameRelationship.transaction do self.save return true end rescue end end false end def sv_fix_combination_relationship s = self.subject_taxon_name list = s.list_of_coordinated_names + [s] if s.rank_string =~ /Species/ s_new = list.detect{|t| t.rank_class.rank_name == 'species'} elsif s.rank_string =~ /Genus/ s_new = list.detect{|t| t.rank_class.rank_name == 'genus'} else s_new = s end if s != s_new && !s.nil? self.subject_taxon_name = s_new begin TaxonNameRelationship.transaction do self.save return true end rescue end end false end def self.collect_to_s(*args) args.collect{|arg| arg.to_s} end def self.collect_descendants_to_s(*classes) ans = [] classes.each do |klass| ans += klass.descendants.collect{|k| k.to_s} end ans end def self.collect_descendants_and_itself_to_s(*classes) classes.collect{|k| k.to_s} + self.collect_descendants_to_s(*classes) end # Force loading all descendants as soon as this class is referenced Dir.glob("#{Rails.root.join("app/models/taxon_name_relationship/**/*.rb")}") .sort { |a, b| a.split('/').count <=> b.split('/').count } .map { |p| p.split('/app/models/').last.sub(/\.rb$/, '') } .map { |p| p.split('/') } .map { |c| c.map { |n| ActiveSupport::Inflector.camelize(n) } } .map { |c| c.join('::') }.map(&:constantize) end |
#type ⇒ String
Returns the relationship/“predicate” between the subject and object taxon names.
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# File 'app/models/taxon_name_relationship.rb', line 44 class TaxonNameRelationship < ApplicationRecord include Housekeeping include Shared::Citations include Shared::Notes include SoftValidation include Shared::DwcOccurrenceHooks include Shared::IsData # @return [Boolean, nil] # When true, cached values are not built attr_accessor :no_cached belongs_to :subject_taxon_name, class_name: 'TaxonName', inverse_of: :taxon_name_relationships # left side belongs_to :object_taxon_name, class_name: 'TaxonName', inverse_of: :related_taxon_name_relationships # right side # After commit only fires if there are changes to the record. after_commit :set_cached_names_for_taxon_names, unless: -> {self.no_cached } # TODO: remove, it's required by STI validates_presence_of :type, message: 'Relationship type should be specified' validates_presence_of :subject_taxon_name, message: 'Missing taxon name on the left side' validates_presence_of :object_taxon_name, message: 'Missing taxon name on the right side' validates_uniqueness_of :object_taxon_name_id, scope: [:type, :project_id], if: :is_combination? validates_uniqueness_of :object_taxon_name_id, scope: [:type, :subject_taxon_name_id, :project_id], unless: :is_combination? validate :validate_type, :validate_subject_and_object_are_not_identical validate :subject_and_object_in_same_project unless: -> {!subject_taxon_name || !object_taxon_name} do validate :validate_subject_and_object_share_code, :validate_uniqueness_of_typification_object, #:validate_uniqueness_of_synonym_subject, :validate_object_and_subject_both_protonyms, :validate_object_must_equal_subject_for_uncertain_placement, :validate_subject_and_object_ranks, :validate_rank_group end # TODO: isolate to an include file sensu protonym soft_validate( :sv_validate_required_relationships, set: :validate_required_relationships, name: 'Required relationships', description: 'Required relationships' ) soft_validate( :sv_validate_disjoint_relationships, set: :validate_disjoint_relationships, name: 'Conflicting relationships', description: 'Detect conflicting relationships' ) soft_validate( :sv_validate_disjoint_object, set: :validate_disjoint_object, name: 'Conflicting object taxon', description: 'Object taxon has a status conflicting with the relationship' ) soft_validate( :sv_validate_disjoint_subject, set: :validate_disjoint_subject, name: 'Conflicting subject taxon', description: 'Subject taxon has a status conflicting with the relationship' ) soft_validate( :sv_specific_relationship, set: :specific_relationship, name: 'validate relationship', description: 'Validate integrity of the relationship, for example, the year applicability range' ) soft_validate( :sv_objective_synonym_relationship, set: :objective_synonym_relationship, fix: :sv_fix_objective_synonym_relationship, name: 'Objective synonym relationship', description: 'Objective synonyms should have the same type' ) soft_validate( :sv_synonym_relationship, set: :synonym_relationship, name: 'Synonym relationship', description: 'Validate integrity of synonym relationship' ) soft_validate( :sv_not_specific_relationship, set: :not_specific_relationship, fix: :sv_fix_not_specific_relationship, name: 'Not specific relationship', description: 'More specific relationship is preferred, for example "Subjective synonym" instead of "Synonym".' ) soft_validate( :sv_synonym_linked_to_valid_name, set: :synonym_linked_to_valid_name, fix: :sv_fix_subject_parent_update, name: 'Synonym not linked to valid taxon', description: 'Synonyms should be linked to valid taxon.' ) soft_validate( :sv_validate_priority, set: :validate_priority, name: 'Priority validation', description: 'Junior synonym should be younger than senior synonym' ) soft_validate( :sv_validate_seniority, set: :validate_seniority, name: 'Seniority validation', description: 'Of two synonyms described in the same paper, one described at a higher rank has a priority' ) soft_validate( :sv_coordinated_taxa, set: :coordinated_taxa, fix: :sv_fix_coordinated_subject_taxa, name: 'Move relationship to coordinate taxon', description: 'Relationship should be moved to the lowest rank coordinate taxon (for example from species to nomynotypical subspecies). It could be updated automatically with the Fix.' ) soft_validate( :sv_coordinated_taxa_object, set: :coordinated_taxa, fix: :sv_fix_coordinated_object_taxa, name: 'Move object relationship to coordinate taxon', description: 'Relationship should be moved to the lowest rank coordinate object taxon (for example from species to nomynotypical subspecies). It could be updated automatically with the Fix.') scope :where_subject_is_taxon_name, -> (taxon_name) {where(subject_taxon_name_id: taxon_name)} scope :where_object_is_taxon_name, -> (taxon_name) {where(object_taxon_name_id: taxon_name)} scope :where_object_in_taxon_names, -> (taxon_name_array) {where('"taxon_name_relationships"."object_taxon_name_id" IN (?)', taxon_name_array)} scope :with_type_string, -> (type_string) { where(sanitize_sql_array(["taxon_name_relationships.type = '%s'", type_string])) } scope :with_type_base, -> (base_string) {where('"taxon_name_relationships"."type" LIKE ?', "#{base_string}%")} scope :with_type_contains, -> (base_string) {where('"taxon_name_relationships"."type" LIKE ?', "%#{base_string}%")} scope :with_two_type_bases, -> (base_string1, base_string2) { where('taxon_name_relationships.type LIKE ? OR taxon_name_relationships.type LIKE ?', "#{base_string1}%", "#{base_string2}%") } scope :homonym_or_suppressed, -> {where("taxon_name_relationships.type LIKE 'TaxonNameRelationship::Iczn::Invalidating::Homonym%' OR taxon_name_relationships.type LIKE 'TaxonNameRelationship::Iczn::Invalidating::Suppression::Total'") } scope :with_type_array, -> (base_array) {where('taxon_name_relationships.type IN (?)', base_array ) } def dwc_occurrences DwcOccurrence .joins("JOIN collection_objects co on dwc_occurrence_object_id = co.id AND dwc_occurrence_object_type = 'CollectionObject'") .joins("JOIN taxon_determinations td on co.id = td.taxon_determination_object_id AND td.taxon_determination_object_type = 'CollectionObject'") .joins("JOIN otus o on o.id = td.otu_id") .where(o: {taxon_name_id: [subject_taxon_name_id, object_taxon_name_id]}) .distinct end # @return [Array of TaxonNameClassification] # the inferable TaxonNameClassification(s) added to the subject when this relationship is used # !! Not implemented def subject_properties [] end # @return [Array of TaxonNameClassification] # the inferable TaxonNameClassification(s) added to the subject when this relationship is used # !! Not implmented def object_properties [] end # @return class # this method calls Module#module_parent def self.parent self.module_parent end # @return [Array of NomenclatureRank] # the valid ranks to which the subject name can belong, set in subclasses. (left side) def self.valid_subject_ranks [] end # @return [Array of NomenclatureRank] # the valid ranks to which the object name can belong, set in subclasses. (right side) def self.valid_object_ranks [] end # @return [Array of TaxonNameRelationships] # if this relationships is set for the subject, then others in this array should not be used for that subject def self.disjoint_taxon_name_relationships [] end # TODO: why isn't this disjoint? # disjoint relationships for the taxon as a object def self.required_taxon_name_relationships [] end def self.disjoint_subject_classes [] end def self.disjoint_object_classes [] end def self.gbif_status_of_subject nil end def self.gbif_status_of_object nil end def self.assignable false end # @return [Symbol] # determine the relative age of subject and object # :direct - subject is younger than object # :reverse - object is younger than subject def self.nomenclatural_priority nil end # @return [String] # the status inferred by the relationship to the object name def object_status self.type_name.demodulize.underscore.humanize.downcase.gsub(/\d+/, ' \0 ').squish end # @return [String] # the status inferred by the relationship to the subject name def subject_status self.type_name.demodulize.underscore.humanize.downcase.gsub(/\d+/, ' \0 ').squish end # @return [String] # the connecting word in the relationship from the subject name to object name def subject_status_connector_to_object ' of' end # @return [String] # the connecting word in the relationship from the object name to subject name def object_status_connector_to_subject ' of' end # @return [String] # a readable fragement combining status and connector def subject_status_tag subject_status + subject_status_connector_to_object end # @return [String] # a readable fragement combining status and connector def object_status_tag object_status + object_status_connector_to_subject end # @return [String, nil] # the type of this relationship, IF the type is a valid name, else nil def type_name r = self.type TAXON_NAME_RELATIONSHIP_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 TAXON_NAME_RELATIONSHIP_NAMES.include?(r) ? r.safe_constantize : nil end # @return [String, nil] # the NOMEN uri for this type def self.nomen_uri const_defined?(:NOMEN_URI, false) ? self::NOMEN_URI : nil end # @return [Time] # effective date of publication, used to determine nomenclatural priorities # !! Careful, if no date is present the current year is given, rather than nil, @proceps is this a safe inference? def nomenclature_date self.source ? (self.source.cached_nomenclature_date ? self.source.cached_nomenclature_date.to_time : Time.current) : Time.current end def is_combination? !!/TaxonNameRelationship::(OriginalCombination|Combination)/.match(self.type.to_s) end protected def subject_and_object_in_same_project if subject_taxon_name && object_taxon_name if subject_taxon_name.project_id != object_taxon_name.project_id errors.add(:base, 'one name is not in the same project as the other') end end end def validate_type # TODO: Remove, handled by STI if type && !TAXON_NAME_RELATIONSHIP_NAMES.include?(type.to_s) errors.add(:type, "'#{type}' is not a valid taxon name relationship") elsif self.type_class && object_taxon_name.class.to_s == 'Protonym' && !self.type_class.valid_object_ranks.include?(object_taxon_name.rank_string) errors.add(:type, "'#{type}' is not a valid taxon name relationship") end if object_taxon_name.class.to_s == 'Protonym' || object_taxon_name.class.to_s == 'Hybrid' errors.add(:type, "'#{type}' is not a valid taxon name relationship") if /TaxonNameRelationship::Combination::/.match(self.type) end if object_taxon_name.class.to_s == 'Combination' errors.add(:type, "'#{type}' is not a valid taxon name relationship") unless /TaxonNameRelationship::Combination::/.match(self.type) end end # @todo validate, that all the relationships in the table could be linked to relationships in classes (if those had changed) def validate_subject_and_object_share_code if object_taxon_name.type == 'Protonym' && subject_taxon_name.type == 'Protonym' errors.add(:object_taxon_name_id, 'The related taxon is not in the same monenclatural group (ICZN, ICN, ICNP, ICVCN') if subject_taxon_name.rank_class.try(:nomenclatural_code) != object_taxon_name.rank_class.try(:nomenclatural_code) end end def validate_subject_and_object_are_not_identical if !self.object_taxon_name_id.nil? && self.object_taxon_name == self.subject_taxon_name errors.add(:object_taxon_name_id, "#{self.object_taxon_name.try(:cached_html)} should not refer to itself") unless self.type =~ /OriginalCombination/ end end def validate_object_must_equal_subject_for_uncertain_placement if self.object_taxon_name_id != self.subject_taxon_name.parent_id && self.type_name == 'TaxonNameRelationship::Iczn::Validating::UncertainPlacement' errors.add(:object_taxon_name_id, "The parent #{self.subject_taxon_name.parent.cached_html} and the Incertae Sedis placement (#{self.object_taxon_name.cached_html}) should match") end end def validate_subject_and_object_ranks tname = self.type_name if tname =~ /TaxonNameRelationship::(Icnp|Icn|Iczn|Icvcn)/ && tname != 'TaxonNameRelationship::Iczn::Validating::UncertainPlacement' rank_group = self.subject_taxon_name.rank_class.try(:parent) unless rank_group == self.object_taxon_name.rank_class.try(:parent) errors.add(:object_taxon_name_id, "Rank of related taxon should be in the #{rank_group.try(:rank_name)} rank group, not #{self.object_taxon_name.rank_class.try(:rank_name)}") end end if self.type_class.present? # only validate if it is set if object_taxon_name && object_taxon_name.rank_class if object_taxon_name.type == 'Protonym' || object_taxon_name.type == 'Hybrid' unless self.type_class.valid_object_ranks.include?(self.object_taxon_name.rank_string) errors.add(:object_taxon_name_id, "#{self.object_taxon_name.rank_class.rank_name.capitalize} rank of #{self.object_taxon_name.cached_html} is not compatible with the #{self.subject_status} relationship") errors.add(:type, "Relationship #{self.subject_status} is not compatible with the #{self.object_taxon_name.rank_class.rank_name} rank of #{self.object_taxon_name.cached_html}") end end end if subject_taxon_name && subject_taxon_name.rank_class if subject_taxon_name.type == 'Protonym' || subject_taxon_name.type == 'Hybrid' unless self.type_class.valid_subject_ranks.include?(self.subject_taxon_name.rank_string) soft_validations.add(:subject_taxon_name_id, "#{self.subject_taxon_name.rank_class.rank_name.capitalize} rank of #{self.subject_taxon_name.cached_html} is not compatible with the #{self.subject_status} relationship") soft_validations.add(:type, "Relationship #{self.subject_status} is not compatible with the #{self.subject_taxon_name.rank_class.rank_name} rank of #{self.subject_taxon_name.cached_html}") end end end end end ##### Protonym historically could be listed as a synonym to different taxa #def validate_uniqueness_of_synonym_subject # if !self.type.nil? && /Synonym/.match(self.type_name) && !TaxonNameRelationship.where(subject_taxon_name_id: self.subject_taxon_name_id).with_type_contains('Synonym').not_self(self).empty? # errors.add(:subject_taxon_name_id, 'Only one synonym relationship is allowed') # end #end def validate_uniqueness_of_typification_object if /Typification/.match(self.type_name) && !TaxonNameRelationship.where(object_taxon_name_id: self.object_taxon_name_id).with_type_contains('Typification').not_self(self).empty? errors.add(:object_taxon_name_id, 'Only one Type designation relationship is allowed') end end def validate_rank_group if self.type =~ /Hybrid/ && self.subject_taxon_name && self.object_taxon_name if self.subject_taxon_name.rank_class.parent != self.object_taxon_name.rank_class.parent errors.add(:subject_taxon_name_id, "#{self.subject_taxon_name.rank_class.rank_name.capitalize} rank of #{self.subject_taxon_name.cached_html} is not compatible with the rank of hybrid (#{self.object_taxon_name.rank_class.rank_name})") end end end def validate_object_and_subject_both_protonyms if /TaxonNameRelationship::Combination::/.match(self.type) errors.add(:object_taxon_name_id, 'Not a Combination') if object_taxon_name.type != 'Combination' else errors.add(:object_taxon_name_id, 'Not a Protonym') if object_taxon_name.type == 'Combination' end errors.add(:subject_taxon_name_id, 'Not a Protonym') if subject_taxon_name.type == 'Combination' && self.type != 'TaxonNameRelationship::CurrentCombination' end # OriginalCombination has a replacement method. def set_cached_names_for_taxon_names return true unless subject_taxon_name_id_previously_changed? || destroyed? # TODO: this should completely be replaced with Taxonname logic. TaxonName.transaction do # Why? if is_invalidating? t = subject_taxon_name if TAXON_NAME_RELATIONSHIP_NAMES_MISSPELLING_ONLY.include?(type_name) t.update_columns( cached_misspelling: true, cached_author_year: t., cached_nomenclature_date: t.nomenclature_date, cached_original_combination: t.get_original_combination, cached_original_combination_html: t.get_original_combination_html) end if type_name =~/Misapplication/ t.update_columns( cached_author_year: t., cached_nomenclature_date: t.nomenclature_date) end vn = t.get_valid_taxon_name # !! NO set cached should do this from TN side of things, # !! Not here n = t.get_full_name t.update_columns( cached: n, cached_html: t.get_full_name_html(n), # OK to force reload here, otherwise we need an exception in #set_cached cached_valid_taxon_name_id: vn.id, cached_is_valid: !t.unavailable_or_invalid?) t.combination_list_self.each do |c| c.update_column(:cached_valid_taxon_name_id, vn.id) end vn.list_of_invalid_taxon_names.each do |s| s.update_columns( cached_valid_taxon_name_id: vn.id, cached_is_valid: !s.unavailable_or_invalid?) s.combination_list_self.each do |c| c.update_column(:cached_valid_taxon_name_id, vn.id) end end end end true end def is_invalidating? TAXON_NAME_RELATIONSHIP_NAMES_INVALID.include?(type_name) end def sv_validate_required_relationships return true if self.subject_taxon_name.not_binominal? object_relationships = TaxonNameRelationship.where_object_is_taxon_name(self.object_taxon_name).not_self(self).collect{|r| r.type} required = self.type_class.required_taxon_name_relationships - object_relationships required.each do |r| soft_validations.add(:type, " Presence of #{self.subject_status} requires selection of #{r.demodulize.underscore.humanize.downcase}") end end def sv_validate_disjoint_relationships tname = self.type_name if tname =~ /TaxonNameRelationship::(Icnp|Icn|Iczn|Icvcn)/ && tname != 'TaxonNameRelationship::Iczn::Validating::UncertainPlacement' subject_relationships = TaxonNameRelationship.where_subject_is_taxon_name(self.subject_taxon_name).not_self(self) subject_relationships.each do |i| if self.type_class.disjoint_taxon_name_relationships.include?(i.type_name) soft_validations.add(:type, "#{self.subject_status.capitalize} relationship is conflicting with another relationship: '#{i.subject_status}'") end end end end def sv_validate_disjoint_object classifications = self.object_taxon_name.taxon_name_classifications.reload.map {|i| i.type_name} disjoint_object_classes = self.type_class.disjoint_object_classes compare = disjoint_object_classes & classifications compare.each do |i| c = i.demodulize.underscore.humanize.downcase soft_validations.add(:type, "#{self.subject_status.capitalize} relationship is conflicting with the taxon status: '#{c}'") soft_validations.add(:object_taxon_name_id, "#{self.object_taxon_name.cached_html} has a conflicting status: '#{c}'") end end def sv_validate_disjoint_subject classifications = self.subject_taxon_name.taxon_name_classifications.reload.map {|i| i.type_name} disjoint_subject_classes = self.type_class.disjoint_subject_classes compare = disjoint_subject_classes & classifications compare.each do |i| c = i.demodulize.underscore.humanize.downcase soft_validations.add(:type, "#{self.subject_status.capitalize} conflicting with the status: '#{c}'") soft_validations.add(:subject_taxon_name_id, "#{self.subject_taxon_name.cached_html} has a conflicting status: '#{c}'") end end def sv_specific_relationship true # all validations moved to subclasses end def sv_objective_synonym_relationship true # all validations moved to subclasses end def sv_fix_objective_synonym_relationship true # all validations moved to subclasses end def sv_synonym_relationship true # all validations moved to subclasses end def sv_not_specific_relationship true # all validations moved to subclasses end def sv_fix_not_specific_relationship true # all validations moved to subclasses end def sv_synonym_linked_to_valid_name #synonyms and misspellings should be linked to valid names if ::TAXON_NAME_RELATIONSHIP_NAMES_SYNONYM.include?(self.type_name) obj = self.object_taxon_name subj = self.subject_taxon_name if subj.rank_class.try(:nomenclatural_code) == :iczn && (obj.parent_id != subj.parent_id || obj.rank_class != subj.rank_class) && subj.cached_valid_taxon_name_id == obj.cached_valid_taxon_name_id soft_validations.add(:subject_taxon_name_id, "#{self.subject_status.capitalize} #{subj.} should have the same parent and rank with #{obj.}", success_message: 'The parent was updated', failure_message: 'The parent was not updated') end end end def sv_fix_subject_parent_update res = false if TAXON_NAME_RELATIONSHIP_NAMES_SYNONYM.include?(self.type_name) obj = self.object_taxon_name subj = self.subject_taxon_name unless obj.parent_id == subj.parent_id subj.parent_id = obj.parent_id subj.rank_class = obj.rank_class begin TaxonName.transaction do subj.save! res = true end rescue end end end res end def subject_invalid_statuses TAXON_NAME_CLASS_NAMES_UNAVAILABLE_AND_INVALID & self.subject_taxon_name.taxon_name_classifications.collect{|c| c.type_class.to_s} end def sv_validate_priority true # all validations moved to subclasses end def sv_validate_seniority true # all validations moved to subclasses end def sv_coordinated_taxa s = subject_taxon_name o = object_taxon_name s_new = s.lowest_rank_coordinated_taxon if s != s_new soft_validations.add(:subject_taxon_name_id, "Relationship should move from #{s.rank_class.rank_name} #{s.cached_html} to #{s_new.rank_class.rank_name} #{s_new.cached_html}", success_message: "Relationship moved to #{s_new.rank_class.rank_name}", failure_message: 'Failed to update relationship') end end def sv_coordinated_taxa_object s = subject_taxon_name o = object_taxon_name o_new = o.lowest_rank_coordinated_taxon if o != o_new soft_validations.add(:object_taxon_name_id, "Relationship should move from #{o.rank_class.rank_name} #{o.cached_html} to #{o_new.rank_class.rank_name} #{o_new.cached_html}", success_message: "Relationship moved to #{o_new.rank_class.rank_name}", failure_message: 'Failed to update relationship') end end def sv_fix_coordinated_subject_taxa s = subject_taxon_name s_new = s.lowest_rank_coordinated_taxon if s != s_new self.subject_taxon_name = s_new begin TaxonNameRelationship.transaction do self.save return true end rescue end end false end def sv_fix_coordinated_object_taxa o = self.object_taxon_name o_new = o.lowest_rank_coordinated_taxon if o != o_new self.object_taxon_name = o_new begin TaxonNameRelationship.transaction do self.save return true end rescue end end false end def sv_fix_combination_relationship s = self.subject_taxon_name list = s.list_of_coordinated_names + [s] if s.rank_string =~ /Species/ s_new = list.detect{|t| t.rank_class.rank_name == 'species'} elsif s.rank_string =~ /Genus/ s_new = list.detect{|t| t.rank_class.rank_name == 'genus'} else s_new = s end if s != s_new && !s.nil? self.subject_taxon_name = s_new begin TaxonNameRelationship.transaction do self.save return true end rescue end end false end def self.collect_to_s(*args) args.collect{|arg| arg.to_s} end def self.collect_descendants_to_s(*classes) ans = [] classes.each do |klass| ans += klass.descendants.collect{|k| k.to_s} end ans end def self.collect_descendants_and_itself_to_s(*classes) classes.collect{|k| k.to_s} + self.collect_descendants_to_s(*classes) end # Force loading all descendants as soon as this class is referenced Dir.glob("#{Rails.root.join("app/models/taxon_name_relationship/**/*.rb")}") .sort { |a, b| a.split('/').count <=> b.split('/').count } .map { |p| p.split('/app/models/').last.sub(/\.rb$/, '') } .map { |p| p.split('/') } .map { |c| c.map { |n| ActiveSupport::Inflector.camelize(n) } } .map { |c| c.join('::') }.map(&:constantize) end |
Class Method Details
.assignable ⇒ Object
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# File 'app/models/taxon_name_relationship.rb', line 251 def self.assignable false end |
.collect_descendants_and_itself_to_s(*classes) ⇒ Object (protected)
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# File 'app/models/taxon_name_relationship.rb', line 698 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 (protected)
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# File 'app/models/taxon_name_relationship.rb', line 690 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 (protected)
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# File 'app/models/taxon_name_relationship.rb', line 686 def self.collect_to_s(*args) args.collect{|arg| arg.to_s} end |
.disjoint_object_classes ⇒ Object
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# File 'app/models/taxon_name_relationship.rb', line 239 def self.disjoint_object_classes [] end |
.disjoint_subject_classes ⇒ Object
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# File 'app/models/taxon_name_relationship.rb', line 235 def self.disjoint_subject_classes [] end |
.disjoint_taxon_name_relationships ⇒ Array of TaxonNameRelationships
Returns if this relationships is set for the subject, then others in this array should not be used for that subject.
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# File 'app/models/taxon_name_relationship.rb', line 225 def self.disjoint_taxon_name_relationships [] end |
.gbif_status_of_object ⇒ Object
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# File 'app/models/taxon_name_relationship.rb', line 247 def self.gbif_status_of_object nil end |
.gbif_status_of_subject ⇒ Object
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# File 'app/models/taxon_name_relationship.rb', line 243 def self.gbif_status_of_subject nil end |
.nomen_uri ⇒ String?
Returns the NOMEN uri for this type.
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# File 'app/models/taxon_name_relationship.rb', line 317 def self.nomen_uri const_defined?(:NOMEN_URI, false) ? self::NOMEN_URI : nil end |
.nomenclatural_priority ⇒ Symbol
Returns determine the relative age of subject and object :direct - subject is younger than object :reverse - object is younger than subject.
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# File 'app/models/taxon_name_relationship.rb', line 259 def self.nomenclatural_priority nil end |
.parent ⇒ Object
Returns class this method calls Module#module_parent.
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# File 'app/models/taxon_name_relationship.rb', line 207 def self.parent self.module_parent end |
.required_taxon_name_relationships ⇒ Object
TODO: why isn’t this disjoint? disjoint relationships for the taxon as a object
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# File 'app/models/taxon_name_relationship.rb', line 231 def self.required_taxon_name_relationships [] end |
.valid_object_ranks ⇒ Array of NomenclatureRank
Returns the valid ranks to which the object name can belong, set in subclasses. (right side).
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# File 'app/models/taxon_name_relationship.rb', line 219 def self.valid_object_ranks [] end |
.valid_subject_ranks ⇒ Array of NomenclatureRank
Returns the valid ranks to which the subject name can belong, set in subclasses. (left side).
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# File 'app/models/taxon_name_relationship.rb', line 213 def self.valid_subject_ranks [] end |
Instance Method Details
#dwc_occurrences ⇒ Object
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# File 'app/models/taxon_name_relationship.rb', line 182 def dwc_occurrences DwcOccurrence .joins("JOIN collection_objects co on dwc_occurrence_object_id = co.id AND dwc_occurrence_object_type = 'CollectionObject'") .joins("JOIN taxon_determinations td on co.id = td.taxon_determination_object_id AND td.taxon_determination_object_type = 'CollectionObject'") .joins("JOIN otus o on o.id = td.otu_id") .where(o: {taxon_name_id: [subject_taxon_name_id, object_taxon_name_id]}) .distinct end |
#is_combination? ⇒ Boolean
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# File 'app/models/taxon_name_relationship.rb', line 328 def is_combination? !!/TaxonNameRelationship::(OriginalCombination|Combination)/.match(self.type.to_s) end |
#is_invalidating? ⇒ Boolean (protected)
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# File 'app/models/taxon_name_relationship.rb', line 496 def is_invalidating? TAXON_NAME_RELATIONSHIP_NAMES_INVALID.include?(type_name) end |
#nomenclature_date ⇒ Time
Returns effective date of publication, used to determine nomenclatural priorities !! Careful, if no date is present the current year is given, rather than nil, @proceps is this a safe inference?.
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# File 'app/models/taxon_name_relationship.rb', line 324 def nomenclature_date self.source ? (self.source.cached_nomenclature_date ? self.source.cached_nomenclature_date.to_time : Time.current) : Time.current end |
#object_properties ⇒ Array of TaxonNameClassification
Returns the inferable TaxonNameClassification(s) added to the subject when this relationship is used !! Not implmented.
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# File 'app/models/taxon_name_relationship.rb', line 201 def object_properties [] end |
#object_status ⇒ String
Returns the status inferred by the relationship to the object name.
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# File 'app/models/taxon_name_relationship.rb', line 265 def object_status self.type_name.demodulize.underscore.humanize.downcase.gsub(/\d+/, ' \0 ').squish end |
#object_status_connector_to_subject ⇒ String
Returns the connecting word in the relationship from the object name to subject name.
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# File 'app/models/taxon_name_relationship.rb', line 283 def object_status_connector_to_subject ' of' end |
#object_status_tag ⇒ String
Returns a readable fragement combining status and connector.
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# File 'app/models/taxon_name_relationship.rb', line 295 def object_status_tag object_status + object_status_connector_to_subject end |
#set_cached_names_for_taxon_names ⇒ Object (protected)
OriginalCombination has a replacement method.
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# File 'app/models/taxon_name_relationship.rb', line 441 def set_cached_names_for_taxon_names return true unless subject_taxon_name_id_previously_changed? || destroyed? # TODO: this should completely be replaced with Taxonname logic. TaxonName.transaction do # Why? if is_invalidating? t = subject_taxon_name if TAXON_NAME_RELATIONSHIP_NAMES_MISSPELLING_ONLY.include?(type_name) t.update_columns( cached_misspelling: true, cached_author_year: t., cached_nomenclature_date: t.nomenclature_date, cached_original_combination: t.get_original_combination, cached_original_combination_html: t.get_original_combination_html) end if type_name =~/Misapplication/ t.update_columns( cached_author_year: t., cached_nomenclature_date: t.nomenclature_date) end vn = t.get_valid_taxon_name # !! NO set cached should do this from TN side of things, # !! Not here n = t.get_full_name t.update_columns( cached: n, cached_html: t.get_full_name_html(n), # OK to force reload here, otherwise we need an exception in #set_cached cached_valid_taxon_name_id: vn.id, cached_is_valid: !t.unavailable_or_invalid?) t.combination_list_self.each do |c| c.update_column(:cached_valid_taxon_name_id, vn.id) end vn.list_of_invalid_taxon_names.each do |s| s.update_columns( cached_valid_taxon_name_id: vn.id, cached_is_valid: !s.unavailable_or_invalid?) s.combination_list_self.each do |c| c.update_column(:cached_valid_taxon_name_id, vn.id) end end end end true end |
#subject_and_object_in_same_project ⇒ Object (protected)
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# File 'app/models/taxon_name_relationship.rb', line 334 def subject_and_object_in_same_project if subject_taxon_name && object_taxon_name if subject_taxon_name.project_id != object_taxon_name.project_id errors.add(:base, 'one name is not in the same project as the other') end end end |
#subject_invalid_statuses ⇒ Object (protected)
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# File 'app/models/taxon_name_relationship.rb', line 599 def subject_invalid_statuses TAXON_NAME_CLASS_NAMES_UNAVAILABLE_AND_INVALID & self.subject_taxon_name.taxon_name_classifications.collect{|c| c.type_class.to_s} end |
#subject_properties ⇒ Array of TaxonNameClassification
Returns the inferable TaxonNameClassification(s) added to the subject when this relationship is used !! Not implemented.
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# File 'app/models/taxon_name_relationship.rb', line 194 def subject_properties [] end |
#subject_status ⇒ String
Returns the status inferred by the relationship to the subject name.
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# File 'app/models/taxon_name_relationship.rb', line 271 def subject_status self.type_name.demodulize.underscore.humanize.downcase.gsub(/\d+/, ' \0 ').squish end |
#subject_status_connector_to_object ⇒ String
Returns the connecting word in the relationship from the subject name to object name.
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# File 'app/models/taxon_name_relationship.rb', line 277 def subject_status_connector_to_object ' of' end |
#subject_status_tag ⇒ String
Returns a readable fragement combining status and connector.
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# File 'app/models/taxon_name_relationship.rb', line 289 def subject_status_tag subject_status + subject_status_connector_to_object end |
#sv_coordinated_taxa ⇒ Object (protected)
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# File 'app/models/taxon_name_relationship.rb', line 611 def sv_coordinated_taxa s = subject_taxon_name o = object_taxon_name s_new = s.lowest_rank_coordinated_taxon if s != s_new soft_validations.add(:subject_taxon_name_id, "Relationship should move from #{s.rank_class.rank_name} #{s.cached_html} to #{s_new.rank_class.rank_name} #{s_new.cached_html}", success_message: "Relationship moved to #{s_new.rank_class.rank_name}", failure_message: 'Failed to update relationship') end end |
#sv_coordinated_taxa_object ⇒ Object (protected)
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# File 'app/models/taxon_name_relationship.rb', line 621 def sv_coordinated_taxa_object s = subject_taxon_name o = object_taxon_name o_new = o.lowest_rank_coordinated_taxon if o != o_new soft_validations.add(:object_taxon_name_id, "Relationship should move from #{o.rank_class.rank_name} #{o.cached_html} to #{o_new.rank_class.rank_name} #{o_new.cached_html}", success_message: "Relationship moved to #{o_new.rank_class.rank_name}", failure_message: 'Failed to update relationship') end end |
#sv_fix_combination_relationship ⇒ Object (protected)
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# File 'app/models/taxon_name_relationship.rb', line 663 def sv_fix_combination_relationship s = self.subject_taxon_name list = s.list_of_coordinated_names + [s] if s.rank_string =~ /Species/ s_new = list.detect{|t| t.rank_class.rank_name == 'species'} elsif s.rank_string =~ /Genus/ s_new = list.detect{|t| t.rank_class.rank_name == 'genus'} else s_new = s end if s != s_new && !s.nil? self.subject_taxon_name = s_new begin TaxonNameRelationship.transaction do self.save return true end rescue end end false end |
#sv_fix_coordinated_object_taxa ⇒ Object (protected)
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# File 'app/models/taxon_name_relationship.rb', line 647 def sv_fix_coordinated_object_taxa o = self.object_taxon_name o_new = o.lowest_rank_coordinated_taxon if o != o_new self.object_taxon_name = o_new begin TaxonNameRelationship.transaction do self.save return true end rescue end end false end |
#sv_fix_coordinated_subject_taxa ⇒ Object (protected)
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# File 'app/models/taxon_name_relationship.rb', line 631 def sv_fix_coordinated_subject_taxa s = subject_taxon_name s_new = s.lowest_rank_coordinated_taxon if s != s_new self.subject_taxon_name = s_new begin TaxonNameRelationship.transaction do self.save return true end rescue end end false end |
#sv_fix_not_specific_relationship ⇒ Object (protected)
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# File 'app/models/taxon_name_relationship.rb', line 563 def sv_fix_not_specific_relationship true # all validations moved to subclasses end |
#sv_fix_objective_synonym_relationship ⇒ Object (protected)
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# File 'app/models/taxon_name_relationship.rb', line 551 def sv_fix_objective_synonym_relationship true # all validations moved to subclasses end |
#sv_fix_subject_parent_update ⇒ Object (protected)
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# File 'app/models/taxon_name_relationship.rb', line 579 def sv_fix_subject_parent_update res = false if TAXON_NAME_RELATIONSHIP_NAMES_SYNONYM.include?(self.type_name) obj = self.object_taxon_name subj = self.subject_taxon_name unless obj.parent_id == subj.parent_id subj.parent_id = obj.parent_id subj.rank_class = obj.rank_class begin TaxonName.transaction do subj.save! res = true end rescue end end end res end |
#sv_not_specific_relationship ⇒ Object (protected)
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# File 'app/models/taxon_name_relationship.rb', line 559 def sv_not_specific_relationship true # all validations moved to subclasses end |
#sv_objective_synonym_relationship ⇒ Object (protected)
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# File 'app/models/taxon_name_relationship.rb', line 547 def sv_objective_synonym_relationship true # all validations moved to subclasses end |
#sv_specific_relationship ⇒ Object (protected)
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# File 'app/models/taxon_name_relationship.rb', line 543 def sv_specific_relationship true # all validations moved to subclasses end |
#sv_synonym_linked_to_valid_name ⇒ Object (protected)
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# File 'app/models/taxon_name_relationship.rb', line 567 def sv_synonym_linked_to_valid_name #synonyms and misspellings should be linked to valid names if ::TAXON_NAME_RELATIONSHIP_NAMES_SYNONYM.include?(self.type_name) obj = self.object_taxon_name subj = self.subject_taxon_name if subj.rank_class.try(:nomenclatural_code) == :iczn && (obj.parent_id != subj.parent_id || obj.rank_class != subj.rank_class) && subj.cached_valid_taxon_name_id == obj.cached_valid_taxon_name_id soft_validations.add(:subject_taxon_name_id, "#{self.subject_status.capitalize} #{subj.} should have the same parent and rank with #{obj.}", success_message: 'The parent was updated', failure_message: 'The parent was not updated') end end end |
#sv_synonym_relationship ⇒ Object (protected)
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# File 'app/models/taxon_name_relationship.rb', line 555 def sv_synonym_relationship true # all validations moved to subclasses end |
#sv_validate_disjoint_object ⇒ Object (protected)
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# File 'app/models/taxon_name_relationship.rb', line 521 def sv_validate_disjoint_object classifications = self.object_taxon_name.taxon_name_classifications.reload.map {|i| i.type_name} disjoint_object_classes = self.type_class.disjoint_object_classes compare = disjoint_object_classes & classifications compare.each do |i| c = i.demodulize.underscore.humanize.downcase soft_validations.add(:type, "#{self.subject_status.capitalize} relationship is conflicting with the taxon status: '#{c}'") soft_validations.add(:object_taxon_name_id, "#{self.object_taxon_name.cached_html} has a conflicting status: '#{c}'") end end |
#sv_validate_disjoint_relationships ⇒ Object (protected)
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# File 'app/models/taxon_name_relationship.rb', line 509 def sv_validate_disjoint_relationships tname = self.type_name if tname =~ /TaxonNameRelationship::(Icnp|Icn|Iczn|Icvcn)/ && tname != 'TaxonNameRelationship::Iczn::Validating::UncertainPlacement' subject_relationships = TaxonNameRelationship.where_subject_is_taxon_name(self.subject_taxon_name).not_self(self) subject_relationships.each do |i| if self.type_class.disjoint_taxon_name_relationships.include?(i.type_name) soft_validations.add(:type, "#{self.subject_status.capitalize} relationship is conflicting with another relationship: '#{i.subject_status}'") end end end end |
#sv_validate_disjoint_subject ⇒ Object (protected)
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# File 'app/models/taxon_name_relationship.rb', line 532 def sv_validate_disjoint_subject classifications = self.subject_taxon_name.taxon_name_classifications.reload.map {|i| i.type_name} disjoint_subject_classes = self.type_class.disjoint_subject_classes compare = disjoint_subject_classes & classifications compare.each do |i| c = i.demodulize.underscore.humanize.downcase soft_validations.add(:type, "#{self.subject_status.capitalize} conflicting with the status: '#{c}'") soft_validations.add(:subject_taxon_name_id, "#{self.subject_taxon_name.cached_html} has a conflicting status: '#{c}'") end end |
#sv_validate_priority ⇒ Object (protected)
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# File 'app/models/taxon_name_relationship.rb', line 603 def sv_validate_priority true # all validations moved to subclasses end |
#sv_validate_required_relationships ⇒ Object (protected)
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# File 'app/models/taxon_name_relationship.rb', line 500 def sv_validate_required_relationships return true if self.subject_taxon_name.not_binominal? object_relationships = TaxonNameRelationship.where_object_is_taxon_name(self.object_taxon_name).not_self(self).collect{|r| r.type} required = self.type_class.required_taxon_name_relationships - object_relationships required.each do |r| soft_validations.add(:type, " Presence of #{self.subject_status} requires selection of #{r.demodulize.underscore.humanize.downcase}") end end |
#sv_validate_seniority ⇒ Object (protected)
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# File 'app/models/taxon_name_relationship.rb', line 607 def sv_validate_seniority true # all validations moved to subclasses end |
#type_class ⇒ Object
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# File 'app/models/taxon_name_relationship.rb', line 310 def type_class r = read_attribute(:type).to_s TAXON_NAME_RELATIONSHIP_NAMES.include?(r) ? r.safe_constantize : nil end |
#type_class=(value) ⇒ Object
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# File 'app/models/taxon_name_relationship.rb', line 306 def type_class=(value) write_attribute(:type, value.to_s) end |
#type_name ⇒ String?
Returns the type of this relationship, IF the type is a valid name, else nil.
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# File 'app/models/taxon_name_relationship.rb', line 301 def type_name r = self.type TAXON_NAME_RELATIONSHIP_NAMES.include?(r) ? r : nil end |
#validate_object_and_subject_both_protonyms ⇒ Object (protected)
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# File 'app/models/taxon_name_relationship.rb', line 431 def validate_object_and_subject_both_protonyms if /TaxonNameRelationship::Combination::/.match(self.type) errors.add(:object_taxon_name_id, 'Not a Combination') if object_taxon_name.type != 'Combination' else errors.add(:object_taxon_name_id, 'Not a Protonym') if object_taxon_name.type == 'Combination' end errors.add(:subject_taxon_name_id, 'Not a Protonym') if subject_taxon_name.type == 'Combination' && self.type != 'TaxonNameRelationship::CurrentCombination' end |
#validate_object_must_equal_subject_for_uncertain_placement ⇒ Object (protected)
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# File 'app/models/taxon_name_relationship.rb', line 373 def validate_object_must_equal_subject_for_uncertain_placement if self.object_taxon_name_id != self.subject_taxon_name.parent_id && self.type_name == 'TaxonNameRelationship::Iczn::Validating::UncertainPlacement' errors.add(:object_taxon_name_id, "The parent #{self.subject_taxon_name.parent.cached_html} and the Incertae Sedis placement (#{self.object_taxon_name.cached_html}) should match") end end |
#validate_rank_group ⇒ Object (protected)
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# File 'app/models/taxon_name_relationship.rb', line 423 def validate_rank_group if self.type =~ /Hybrid/ && self.subject_taxon_name && self.object_taxon_name if self.subject_taxon_name.rank_class.parent != self.object_taxon_name.rank_class.parent errors.add(:subject_taxon_name_id, "#{self.subject_taxon_name.rank_class.rank_name.capitalize} rank of #{self.subject_taxon_name.cached_html} is not compatible with the rank of hybrid (#{self.object_taxon_name.rank_class.rank_name})") end end end |
#validate_subject_and_object_are_not_identical ⇒ Object (protected)
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# File 'app/models/taxon_name_relationship.rb', line 367 def validate_subject_and_object_are_not_identical if !self.object_taxon_name_id.nil? && self.object_taxon_name == self.subject_taxon_name errors.add(:object_taxon_name_id, "#{self.object_taxon_name.try(:cached_html)} should not refer to itself") unless self.type =~ /OriginalCombination/ end end |
#validate_subject_and_object_ranks ⇒ Object (protected)
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# File 'app/models/taxon_name_relationship.rb', line 379 def validate_subject_and_object_ranks tname = self.type_name if tname =~ /TaxonNameRelationship::(Icnp|Icn|Iczn|Icvcn)/ && tname != 'TaxonNameRelationship::Iczn::Validating::UncertainPlacement' rank_group = self.subject_taxon_name.rank_class.try(:parent) unless rank_group == self.object_taxon_name.rank_class.try(:parent) errors.add(:object_taxon_name_id, "Rank of related taxon should be in the #{rank_group.try(:rank_name)} rank group, not #{self.object_taxon_name.rank_class.try(:rank_name)}") end end if self.type_class.present? # only validate if it is set if object_taxon_name && object_taxon_name.rank_class if object_taxon_name.type == 'Protonym' || object_taxon_name.type == 'Hybrid' unless self.type_class.valid_object_ranks.include?(self.object_taxon_name.rank_string) errors.add(:object_taxon_name_id, "#{self.object_taxon_name.rank_class.rank_name.capitalize} rank of #{self.object_taxon_name.cached_html} is not compatible with the #{self.subject_status} relationship") errors.add(:type, "Relationship #{self.subject_status} is not compatible with the #{self.object_taxon_name.rank_class.rank_name} rank of #{self.object_taxon_name.cached_html}") end end end if subject_taxon_name && subject_taxon_name.rank_class if subject_taxon_name.type == 'Protonym' || subject_taxon_name.type == 'Hybrid' unless self.type_class.valid_subject_ranks.include?(self.subject_taxon_name.rank_string) soft_validations.add(:subject_taxon_name_id, "#{self.subject_taxon_name.rank_class.rank_name.capitalize} rank of #{self.subject_taxon_name.cached_html} is not compatible with the #{self.subject_status} relationship") soft_validations.add(:type, "Relationship #{self.subject_status} is not compatible with the #{self.subject_taxon_name.rank_class.rank_name} rank of #{self.subject_taxon_name.cached_html}") end end end end end |
#validate_subject_and_object_share_code ⇒ Object (protected)
validate, that all the relationships in the table could be linked to relationships in classes (if those had changed)
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# File 'app/models/taxon_name_relationship.rb', line 361 def validate_subject_and_object_share_code if object_taxon_name.type == 'Protonym' && subject_taxon_name.type == 'Protonym' errors.add(:object_taxon_name_id, 'The related taxon is not in the same monenclatural group (ICZN, ICN, ICNP, ICVCN') if subject_taxon_name.rank_class.try(:nomenclatural_code) != object_taxon_name.rank_class.try(:nomenclatural_code) end end |
#validate_type ⇒ Object (protected)
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# File 'app/models/taxon_name_relationship.rb', line 342 def validate_type # TODO: Remove, handled by STI if type && !TAXON_NAME_RELATIONSHIP_NAMES.include?(type.to_s) errors.add(:type, "'#{type}' is not a valid taxon name relationship") elsif self.type_class && object_taxon_name.class.to_s == 'Protonym' && !self.type_class.valid_object_ranks.include?(object_taxon_name.rank_string) errors.add(:type, "'#{type}' is not a valid taxon name relationship") end if object_taxon_name.class.to_s == 'Protonym' || object_taxon_name.class.to_s == 'Hybrid' errors.add(:type, "'#{type}' is not a valid taxon name relationship") if /TaxonNameRelationship::Combination::/.match(self.type) end if object_taxon_name.class.to_s == 'Combination' errors.add(:type, "'#{type}' is not a valid taxon name relationship") unless /TaxonNameRelationship::Combination::/.match(self.type) end end |
#validate_uniqueness_of_typification_object ⇒ Object (protected)
Protonym historically could be listed as a synonym to different taxa def validate_uniqueness_of_synonym_subject
if !self.type.nil? && /Synonym/.match(self.type_name) && !TaxonNameRelationship.where(subject_taxon_name_id: self.subject_taxon_name_id).with_type_contains('Synonym').not_self(self).empty?
errors.add(:subject_taxon_name_id, 'Only one synonym relationship is allowed')
end
end
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# File 'app/models/taxon_name_relationship.rb', line 417 def validate_uniqueness_of_typification_object if /Typification/.match(self.type_name) && !TaxonNameRelationship.where(object_taxon_name_id: self.object_taxon_name_id).with_type_contains('Typification').not_self(self).empty? errors.add(:object_taxon_name_id, 'Only one Type designation relationship is allowed') end end |