Class: DatasetRecord::DarwinCore::Occurrence
- Inherits:
-
DatasetRecord::DarwinCore
- Object
- ActiveRecord::Base
- ApplicationRecord
- DatasetRecord
- DatasetRecord::DarwinCore
- DatasetRecord::DarwinCore::Occurrence
- Defined in:
- app/models/dataset_record/darwin_core/occurrence.rb
Defined Under Namespace
Classes: ImportProtonym
Constant Summary collapse
- DWC_CLASSIFICATION_TERMS =
genus, subgenus, specificEpithet and infraspecificEpithet are extracted from scientificName
%w{kingdom phylum class order family}
- PARSE_DETAILS_KEYS =
%i(uninomial genus species infraspecies)
- ACCEPTED_ATTRIBUTES =
{ :CollectionObject => %I( buffered_collecting_event buffered_determinations buffered_other_labels total ).to_set.freeze, :CollectingEvent => %I( document_label print_label verbatim_label field_notes formation group lithology max_ma maximum_elevation member min_ma minimum_elevation elevation_precision start_date_day start_date_month start_date_year end_date_day end_date_month end_date_year time_end_hour time_end_minute time_end_second time_start_hour time_start_minute time_start_second verbatim_collectors verbatim_date verbatim_datum verbatim_elevation verbatim_geolocation_uncertainty verbatim_habitat verbatim_latitude verbatim_locality verbatim_longitude verbatim_method verbatim_trip_identifier ).to_set.freeze }.freeze
Instance Attribute Summary
Attributes inherited from DatasetRecord
Instance Method Summary collapse
- #append_data_attribute(attributes, attribute) ⇒ Object private
- #append_dwc_attribute(attributes, predicate, value) ⇒ Object private
- #append_dwc_attributes(dwc_attributes, target) ⇒ Object private
- #append_tag_attribute(tags, tag) ⇒ Object private
-
#delete_namespace_prefix!(identifier_str, namespace) ⇒ Object
private
Remove the namespace short name and delimiter from start of string.
- #get_integer_field_value(field_name) ⇒ Object private
- #import(dwc_data_attributes = {}) ⇒ Object
- #parse_biocuration_group_field(group) ⇒ Object private
- #parse_biocuration_group_fields ⇒ Object private
- #parse_event_class ⇒ Object private
- #parse_identification_class ⇒ Object private
-
#parse_iso_date(field_name) ⇒ Array<OpenStruct>
private
Parse an iso date string from the specified column name.
- #parse_location_class ⇒ Object private
- #parse_occurrence_class ⇒ Object private
-
#parse_people(field_name) ⇒ Object
private
NOTE: Sometimes an identifier/collector happens to be a non-person (like “ANSP Orthopterist”).
- #parse_record_level_class ⇒ Object private
- #parse_taxon_class ⇒ Object private
- #parse_tw_collecting_event_attributes ⇒ Object private
- #parse_tw_collecting_event_data_attributes ⇒ Object private
- #parse_tw_collection_object_attributes ⇒ Object private
- #parse_tw_collection_object_data_attributes ⇒ Object private
- #term_value_changed(name, value) ⇒ Object private
Methods inherited from DatasetRecord::DarwinCore
#data_field_changed, #get_field_mapping, #get_field_value, #get_fields_mapping, #get_tw_biocuration_groups, #get_tw_data_attribute_fields_for, #get_tw_fields_for, #get_tw_tag_fields_for, #normalize_value!
Methods inherited from DatasetRecord
#create_fields, #data_field_changed, #data_fields, #dataset_record_fields, #destroy_fields, #field_db_attributes, #fields_db_attributes, #frozen_fields?, #get_data_field, #initialize_data_fields, #set_data_field, #update_fields
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 Housekeeping
#has_polymorphic_relationship?
Methods inherited from ApplicationRecord
Instance Method Details
#append_data_attribute(attributes, attribute) ⇒ Object (private)
1108 1109 1110 1111 1112 1113 1114 1115 1116 1117 1118 1119 1120 1121 1122 1123 |
# File 'app/models/dataset_record/darwin_core/occurrence.rb', line 1108 def append_data_attribute(attributes, attribute) predicate = Predicate.find_by(uri: attribute[:selector], project: self.project) predicate ||= Predicate.where(project: project).find_by( Predicate.arel_table[:name].matches(ApplicationRecord.sanitize_sql_like(attribute[:selector])) ) value = get_field_value(attribute[:field]) if value raise DarwinCore::InvalidData.new({ attribute[:field] => ["Predicate with #{attribute[:selector]} URI or name not found"] }) unless predicate attributes << { type: 'InternalAttribute', predicate: predicate, value: value } end end |
#append_dwc_attribute(attributes, predicate, value) ⇒ Object (private)
1198 1199 1200 1201 1202 1203 1204 |
# File 'app/models/dataset_record/darwin_core/occurrence.rb', line 1198 def append_dwc_attribute(attributes, predicate, value) attributes << { type: 'InternalAttribute', predicate: predicate, value: value } if value end |
#append_dwc_attributes(dwc_attributes, target) ⇒ Object (private)
1206 1207 1208 1209 1210 |
# File 'app/models/dataset_record/darwin_core/occurrence.rb', line 1206 def append_dwc_attributes(dwc_attributes, target) dwc_attributes.each do |field, predicate| append_dwc_attribute(target[:data_attributes_attributes], predicate, get_field_value(field)) end end |
#append_tag_attribute(tags, tag) ⇒ Object (private)
1085 1086 1087 1088 1089 1090 1091 1092 1093 1094 1095 1096 1097 1098 1099 1100 1101 1102 1103 1104 1105 1106 |
# File 'app/models/dataset_record/darwin_core/occurrence.rb', line 1085 def append_tag_attribute(, tag) value = get_field_value(tag[:field]) return unless value keyword = Keyword.find_by(uri: tag[:selector], project: self.project) keyword ||= Keyword.where(project: project).find_by( Keyword.arel_table[:name].matches(ApplicationRecord.sanitize_sql_like(tag[:selector])) ) if value raise DarwinCore::InvalidData.new({ tag[:field] => ["Tag with #{tag[:selector]} URI or name not found"] }) unless keyword if value.downcase == "true" || value == "1" .append({keyword: keyword}) return end unless value.downcase == "false" || value == "0" raise DarwinCore::InvalidData.new({ tag[:field] => ["Tag value must be \"true\" or \"1\" to apply, or blank, \"false\", or \"0\", to not apply"] }) end end end |
#delete_namespace_prefix!(identifier_str, namespace) ⇒ Object (private)
Remove the namespace short name and delimiter from start of string.
If the namespace has a verbatim_short_name, that is removed instead of the short_name. The delimiter is only removed if the short_name was found in the identifier.
365 366 367 |
# File 'app/models/dataset_record/darwin_core/occurrence.rb', line 365 def delete_namespace_prefix!(identifier_str, namespace) identifier_str&.delete_prefix!(namespace.verbatim_short_name || namespace.short_name)&.delete_prefix!(namespace.delimiter || '') if namespace end |
#get_integer_field_value(field_name) ⇒ Object (private)
297 298 299 300 301 302 303 304 305 306 307 308 309 310 311 312 |
# File 'app/models/dataset_record/darwin_core/occurrence.rb', line 297 def get_integer_field_value(field_name) value = get_field_value(field_name) unless value.blank? begin raise unless /^\s*(?<integer>[+-]?\d+)\s*$/ =~ value value = integer.to_i rescue raise DarwinCore::InvalidData.new({ field_name => ["'#{value}' is not a valid integer value"] }) end else value = nil end value end |
#import(dwc_data_attributes = {}) ⇒ Object
87 88 89 90 91 92 93 94 95 96 97 98 99 100 101 102 103 104 105 106 107 108 109 110 111 112 113 114 115 116 117 118 119 120 121 122 123 124 125 126 127 128 129 130 131 132 133 134 135 136 137 138 139 140 141 142 143 144 145 146 147 148 149 150 151 152 153 154 155 156 157 158 159 160 161 162 163 164 165 166 167 168 169 170 171 172 173 174 175 176 177 178 179 180 181 182 183 184 185 186 187 188 189 190 191 192 193 194 195 196 197 198 199 200 201 202 203 204 205 206 207 208 209 210 211 212 213 214 215 216 217 218 219 220 221 222 223 224 225 226 227 228 229 230 231 232 233 234 235 236 237 238 239 240 241 242 243 244 245 246 247 248 249 250 251 252 253 254 255 256 257 258 259 260 261 262 263 264 265 266 267 268 269 270 271 272 273 |
# File 'app/models/dataset_record/darwin_core/occurrence.rb', line 87 def import(dwc_data_attributes = {}) super begin DatasetRecord.transaction(requires_new: true) do self..delete("error_data") names, origins = parse_taxon_class strategy = self.import_dataset.restrict_to_existing_nomenclature? ? ImportProtonym.match_existing : ImportProtonym.create_if_not_exists innermost_otu = nil innermost_protonym = names.inject(project.root_taxon_name) do |parent, name| otu_attributes = name.delete(:otu_attributes) unless name[:rank_class] || otu_attributes.present? name[:rank_class] = parent.predicted_child_rank(name[:name])&.to_s name.delete(:rank_class) unless name[:rank_class] && /::FamilyGroup::/ =~ name[:rank_class] end strategy.execute(origins, parent, name).tap do |protonym| innermost_otu = Otu.find_or_create_by!({taxon_name: protonym}.merge!(otu_attributes)) if otu_attributes end end attributes = parse_record_level_class record_level_biocuration_classifications = attributes.dig(:specimen, :biocuration_classifications) attributes.deep_merge!(parse_occurrence_class) attributes.deep_merge!(parse_event_class) attributes.deep_merge!(parse_location_class) attributes.deep_merge!(parse_identification_class) attributes.deep_merge!(parse_tw_collection_object_data_attributes) attributes.deep_merge!(parse_tw_collecting_event_data_attributes) attributes.deep_merge!(parse_tw_collection_object_attributes) attributes.deep_merge!(parse_tw_collecting_event_attributes) append_dwc_attributes(dwc_data_attributes['CollectionObject'], attributes[:specimen]) append_dwc_attributes(dwc_data_attributes['CollectingEvent'], attributes[:collecting_event]) Utilities::Hashes::set_unless_nil(attributes[:specimen], :biocuration_classifications, (parse_biocuration_group_fields.dig(:specimen, :biocuration_classifications) || []) + (record_level_biocuration_classifications || []) + (attributes.dig(:specimen, :biocuration_classifications) || []) ) specimen = Specimen.create!({ no_dwc_occurrence: true }.merge!(attributes[:specimen])) if attributes[:type_material] && (innermost_otu&.name).nil? type_material = TypeMaterial.new( { protonym: innermost_protonym, collection_object: specimen, }.merge!(attributes[:type_material])) # protoynm can be overwritten in type_materials hash if OC did not match scientific name / innermost_protonym if self.import_dataset.require_type_material_success? # raise error if validations fail and it cannot be imported type_material.save! else # Best effort only, import will proceed even if creating the type material fails type_material.save end end if attributes.dig(:catalog_number, :identifier) namespace = attributes.dig(:catalog_number, :namespace) delete_namespace_prefix!(attributes.dig(:catalog_number, :identifier), namespace) identifier = Identifier::Local::CatalogNumber .create_with(identifier_object: specimen) .find_or_create_by!(attributes[:catalog_number]) object = identifier.identifier_object unless object == specimen raise DarwinCore::InvalidData.new({ "catalogNumber" => ["Is already in use"] }) unless self.import_dataset.containerize_dup_cat_no? if object.is_a?(Container) object.add_container_items([specimen]) else identifier.update!( identifier_object: Container::Virtual.containerize([object, specimen]) ) end end end Identifier::Local::Import::Dwc.create!( namespace: import_dataset.get_core_record_identifier_namespace, identifier_object: specimen, identifier: get_field_value(:occurrenceID) ) unless get_field_value(:occurrenceID).nil? || import_dataset.get_core_record_identifier_namespace.nil? specimen.taxon_determinations.create!({ otu: innermost_otu || innermost_protonym.otus.find_by(name: nil) || innermost_protonym.otus.first # TODO: Might require select-and-confirm functionality }.merge(attributes[:taxon_determination])) event_id = get_field_value(:eventID) unless event_id.nil? namespace = get_field_value('TW:Namespace:eventID') identifier_type = Identifier::Global.descendants.detect { |c| c.name.downcase == namespace.downcase } if namespace identifier_attributes = { identifier: event_id, identifier_object_type: 'CollectingEvent', project_id: Current.project_id } if identifier_type.nil? identifier_type = Identifier::Local::TripCode # TODO: Or maybe Identifier::Local::Import? if namespace.nil? namespace = import_dataset.get_event_id_namespace else namespace = Namespace.find_by(Namespace.arel_table[:short_name].matches(namespace)) # Case insensitive match raise DarwinCore::InvalidData.new({ "TW:Namespace:eventID" => ["Namespace not found"] }) unless namespace end identifier_attributes[:namespace] = namespace delete_namespace_prefix!(event_id, namespace) end collecting_event = identifier_type.find_by(identifier_attributes)&.identifier_object end # TODO: If all attributes are equal assume it is the same event and share it with other specimens? (eventID is an alternate method to detect duplicates) if collecting_event # if tags have been specified to be added, update the collecting event if attributes[:collecting_event][:tags_attributes] # get list of preexisting tags, exclude them from update = collecting_event..pluck(:keyword_id).to_set = attributes[:collecting_event][:tags_attributes].reject { |t| .member?(t[:keyword].id) } # add tags if there were any new ones unless .empty? collecting_event..build() collecting_event.save! end end specimen.update!(collecting_event: collecting_event) else collecting_event = CollectingEvent.create!({ collection_objects: [specimen], no_dwc_occurrence: true }.merge!(attributes[:collecting_event])) identifier_type.create!({ identifier_object: collecting_event }.merge!(identifier_attributes)) unless identifier_attributes.nil? Georeference::VerbatimData.create!({ collecting_event: collecting_event, error_radius: get_field_value("coordinateUncertaintyInMeters"), no_cached: true }.merge(attributes[:georeference])) if collecting_event.verbatim_latitude && collecting_event.verbatim_longitude end DwcOccurrenceUpsertJob.perform_later(specimen) self.["imported_objects"] = { collection_object: { id: specimen.id } } self.status = "Imported" end rescue DarwinCore::InvalidData => invalid self.status = "Errored" self.["error_data"] = { messages: invalid.error_data } rescue ActiveRecord::RecordInvalid => invalid self.status = "Errored" self.["error_data"] = { messages: invalid.record.errors. } rescue StandardError => e raise if Rails.env.development? self.status = "Failed" self.["error_data"] = { exception: { message: e., backtrace: e.backtrace } } ensure save! end self end |
#parse_biocuration_group_field(group) ⇒ Object (private)
1135 1136 1137 1138 1139 1140 1141 1142 1143 1144 1145 1146 1147 1148 1149 1150 1151 1152 1153 1154 1155 1156 1157 1158 |
# File 'app/models/dataset_record/darwin_core/occurrence.rb', line 1135 def parse_biocuration_group_field(group) biocuration_group = BiocurationGroup.find_by(uri: group[:selector], project: self.project) biocuration_group ||= BiocurationGroup.where(project: project).find_by( BiocurationGroup.arel_table[:name].matches(ApplicationRecord.sanitize_sql_like(group[:selector])) ) value = get_field_value(group[:field]) if value raise DarwinCore::InvalidData.new({ group[:field] => ["Biocuration group with '#{group[:selector]}' URI or name not found"] }) unless biocuration_group biocuration_class = BiocurationClass.where(project: project).joins(:tags).merge( Tag.where(keyword: biocuration_group) ).find_by(uri: value) biocuration_class ||= BiocurationClass.where(project: project).joins(:tags).merge( Tag.where(keyword: biocuration_group) ).find_by( BiocurationClass.arel_table[:name].matches(ApplicationRecord.sanitize_sql_like(value)) ) raise DarwinCore::InvalidData.new({ group[:field] => ["Biocuration class with '#{value}' URI or name not found"] }) unless biocuration_class BiocurationClassification.new(biocuration_class: biocuration_class) end end |
#parse_biocuration_group_fields ⇒ Object (private)
1125 1126 1127 1128 1129 1130 1131 1132 1133 |
# File 'app/models/dataset_record/darwin_core/occurrence.rb', line 1125 def parse_biocuration_group_fields { specimen: { biocuration_classifications: get_tw_biocuration_groups .map { |g| parse_biocuration_group_field(g) } .reject(&:nil?) } } end |
#parse_event_class ⇒ Object (private)
549 550 551 552 553 554 555 556 557 558 559 560 561 562 563 564 565 566 567 568 569 570 571 572 573 574 575 576 577 578 579 580 581 582 583 584 585 586 587 588 589 590 591 592 593 594 595 596 597 598 599 600 601 602 603 604 605 606 607 608 609 610 611 612 613 614 615 616 617 618 619 620 621 622 623 624 625 626 627 628 629 630 631 632 633 634 635 636 637 638 639 640 641 642 643 644 645 646 647 648 649 650 651 652 653 654 655 656 |
# File 'app/models/dataset_record/darwin_core/occurrence.rb', line 549 def parse_event_class collecting_event = { } # eventID: [Mapped in import method] # parentEventID: [Not mapped] # fieldNumber: verbatim_trip_identifier Utilities::Hashes::set_unless_nil(collecting_event, :verbatim_trip_identifier, get_field_value(:fieldNumber)) start_date, end_date = parse_iso_date(:eventDate) year = get_integer_field_value(:year) month = get_integer_field_value(:month) day = get_integer_field_value(:day) startDayOfYear = get_integer_field_value(:startDayOfYear) raise DarwinCore::InvalidData.new({ "eventDate": ["Conflicting values. Please check year, month, and day match eventDate"] }) if start_date && (year && start_date.year != year || month && start_date.month != month || day && start_date.day != day) year ||= start_date&.year month ||= start_date&.month day ||= start_date&.day if startDayOfYear raise DarwinCore::InvalidData.new({ "startDayOfYear": ["Missing year value"] }) if year.nil? begin ordinal = Date.ordinal(year, startDayOfYear) rescue Date::Error raise DarwinCore::InvalidData.new({ "startDayOfYear": ["Out of range. Please also check year field"] }) end if month && ordinal.month != month || day && ordinal.day != day raise DarwinCore::InvalidData.new({ "startDayOfYear": ["Month and/or day of the event date do not match"] }) end month ||= ordinal.month day ||= ordinal.day end # eventDate | (year+month+day) | (year+startDayOfYear): start_date_* Utilities::Hashes::set_unless_nil(collecting_event, :start_date_year, year) Utilities::Hashes::set_unless_nil(collecting_event, :start_date_month, month) Utilities::Hashes::set_unless_nil(collecting_event, :start_date_day, day) # eventTime: time_start_* %r{^ (?<start_hour>\d+)(:(?<start_minute>\d+))?(:(?<start_second>\d+))? (/(?<end_hour>\d+))?(:(?<end_minute>\d+))?(:(?<end_second>\d+))? $}x =~ get_field_value(:eventTime) Utilities::Hashes::set_unless_nil(collecting_event, :time_start_hour, start_hour) Utilities::Hashes::set_unless_nil(collecting_event, :time_start_minute, start_minute) Utilities::Hashes::set_unless_nil(collecting_event, :time_start_second, start_second) Utilities::Hashes::set_unless_nil(collecting_event, :time_end_hour, end_hour) Utilities::Hashes::set_unless_nil(collecting_event, :time_end_minute, end_minute) Utilities::Hashes::set_unless_nil(collecting_event, :time_end_second, end_second) endDayOfYear = get_integer_field_value(:endDayOfYear) if endDayOfYear raise DarwinCore::InvalidData.new({ "endDayOfYear": ["Missing year value"] }) if year.nil? begin ordinal = Date.ordinal(year, endDayOfYear) rescue Date::Error raise DarwinCore::InvalidData.new({ "endDayOfYear": ["Out of range. Please also check year field"] }) end month = ordinal.month day = ordinal.day raise DarwinCore::InvalidData.new({ "eventDate": ["Conflicting values. Please check year and endDayOfYear match eventDate"] }) if end_date && (year && end_date.year != year || month && end_date.month != month || day && end_date.day != day) else year = end_date&.year month = end_date&.month day = end_date&.day end Utilities::Hashes::set_unless_nil(collecting_event, :end_date_year, year) Utilities::Hashes::set_unless_nil(collecting_event, :end_date_month, month) Utilities::Hashes::set_unless_nil(collecting_event, :end_date_day, day) # verbatimEventDate: verbatim_date Utilities::Hashes::set_unless_nil(collecting_event, :verbatim_date, get_field_value(:verbatimEventDate)) # habitat: verbatim_habitat Utilities::Hashes::set_unless_nil(collecting_event, :verbatim_habitat, get_field_value(:habitat)) # samplingProtocol: verbatim_method Utilities::Hashes::set_unless_nil(collecting_event, :verbatim_method, get_field_value(:samplingProtocol)) # sampleSizeValue: [Not mapped] # sampleSizeUnit: [Not mapped] # samplingEffort: [Not mapped] # fieldNotes: field_notes Utilities::Hashes::set_unless_nil(collecting_event, :field_notes, get_field_value(:fieldNotes)) # eventRemarks: [collecting event note] note = get_field_value(:eventRemarks) Utilities::Hashes::set_unless_nil(collecting_event, :notes_attributes, [{text: note}]) if note { collecting_event: collecting_event } end |
#parse_identification_class ⇒ Object (private)
791 792 793 794 795 796 797 798 799 800 801 802 803 804 805 806 807 808 809 810 811 812 813 814 815 816 817 818 819 820 821 822 823 824 825 826 827 828 829 830 831 832 833 834 835 836 837 838 839 840 841 842 843 844 845 846 847 848 849 850 |
# File 'app/models/dataset_record/darwin_core/occurrence.rb', line 791 def parse_identification_class taxon_determination = {} type_material = nil # identificationID: [Not mapped] # identificationQualifier: [Mapped as part of otu name in parse_taxon_class] # typeStatus: [Type material only if scientific name matches scientificName and type term is recognized by TW vocabulary] type_status = get_field_value(:typeStatus) type_status_parsed = type_status&.match(/^(?<type>\w+)$/i) || type_status&.match(/(?<type>\w+)(\s+OF\s+(?<scientificName>.*))/i) scientific_name = get_field_value(:scientificName)&.gsub(/\s+/, ' ') type_scientific_name = (type_status_parsed&.[](:scientificName)&.gsub(/\s+/, ' ') rescue nil) || scientific_name if type_status_parsed && scientific_name && type_scientific_name.present? # if type_scientific_name matches the current name of the occurrence, use that if type_scientific_name&.delete_prefix!(scientific_name)&.match(/^\W*$/) type_material = { type_type: type_status_parsed[:type].downcase } elsif (original_combination_protonym = Protonym.find_by(cached_original_combination: type_scientific_name, project_id: self.project_id)) type_material = { type_type: type_status_parsed[:type].downcase, protonym: original_combination_protonym } end end if type_status && type_material.nil? raise DarwinCore::InvalidData.new({ "typeStatus": ["Unprocessable typeStatus information"] }) if self.import_dataset.require_type_material_success? end # identifiedBy: determiners of taxon determination Utilities::Hashes::set_unless_nil(taxon_determination, :determiners, parse_people(:identifiedBy)) # dateIdentified: {year,month,day}_made of taxon determination start_date, end_date = parse_iso_date(:dateIdentified) raise DarwinCore::InvalidData.new({ "dateIdentified": ["Date range for taxon determination is not supported."] }) if end_date if start_date Utilities::Hashes::set_unless_nil(taxon_determination, :year_made, start_date.year) Utilities::Hashes::set_unless_nil(taxon_determination, :month_made, start_date.month) Utilities::Hashes::set_unless_nil(taxon_determination, :day_made, start_date.day) end # identificationReferences: [Not mapped. Can they be imported as citations without breaking semantics?] # identificationVerificationStatus: [Not mapped] # identificationRemarks: Note for taxon determination note = get_field_value(:identificationRemarks) taxon_determination[:notes_attributes] = [{text: note}] if note { taxon_determination: taxon_determination, type_material: type_material } end |
#parse_iso_date(field_name) ⇒ Array<OpenStruct> (private)
Parse an iso date string from the specified column name
The date may be a single date, or an interval of two dates separated by a slash. The second date may omit higher-order elements that are the same as the first date. See en.wikipedia.org/wiki/ISO_8601#Time_intervals for more information.
344 345 346 347 348 349 350 351 352 353 354 355 356 357 |
# File 'app/models/dataset_record/darwin_core/occurrence.rb', line 344 def parse_iso_date(field_name) value = get_field_value(field_name) return nil if value.nil? result = Utilities::Dates.parse_iso_date_str(value) raise DarwinCore::InvalidData.new( { "#{field_name}": ["Invalid date. Please make sure it conforms to ISO 8601 date format (yyyy-mm-ddThh:mm:ss). If expressing interval separate result with '/'. Examples: 1972-05; 1983-10-25; 2020-09-22T15:30; 2020-11-30/2020-12-04"] } ) if result.nil? result end |
#parse_location_class ⇒ Object (private)
658 659 660 661 662 663 664 665 666 667 668 669 670 671 672 673 674 675 676 677 678 679 680 681 682 683 684 685 686 687 688 689 690 691 692 693 694 695 696 697 698 699 700 701 702 703 704 705 706 707 708 709 710 711 712 713 714 715 716 717 718 719 720 721 722 723 724 725 726 727 728 729 730 731 732 733 734 735 736 737 738 739 740 741 742 743 744 745 746 747 748 749 750 751 752 753 754 755 756 757 758 759 760 761 762 763 764 765 766 767 768 769 770 771 772 773 774 775 776 777 778 779 780 781 782 783 784 785 786 787 788 789 |
# File 'app/models/dataset_record/darwin_core/occurrence.rb', line 658 def parse_location_class collecting_event = {} georeference = {} # locationID: [Not mapped] # higherGeographyID: [Not mapped] # higherGeography: [Not mapped] # continent: [Not mapped] # waterBody: [Not mapped] # islandGroup: [Not mapped] # island: [Not mapped] # country: [Not mapped] # countryCode: [Not mapped] # stateProvince: [Not mapped] # county: [Not mapped] # municipality: [Not mapped] # locality: [Not mapped] # verbatimLocality: [verbatim_locality] Utilities::Hashes::set_unless_nil(collecting_event, :verbatim_locality, get_field_value(:verbatimLocality)) # minimumElevationInMeters: [Not mapped] Utilities::Hashes::set_unless_nil(collecting_event, :minimum_elevation, get_field_value(:minimumElevationInMeters)) # maximumElevationInMeters: [Not mapped] Utilities::Hashes::set_unless_nil(collecting_event, :maximum_elevation, get_field_value(:maximumElevationInMeters)) # verbatimElevation: [Not mapped] Utilities::Hashes::set_unless_nil(collecting_event, :verbatim_elevation, get_field_value(:verbatimElevation)) # minimumDepthInMeters: [Not mapped. REVISIT] # maximumDepthInMeters: [Not mapped. REVISIT] # verbatimDepth: [Not mapped. REVISIT] # minimumDistanceAboveSurfaceInMeters: [Not mapped] # maximumDistanceAboveSurfaceInMeters: [Not mapped] # locationAccordingTo: [Not mapped. REVISIT] # locationRemarks: [Not mapped. REVISIT] # decimalLatitude: [verbatim_latitude] Utilities::Hashes::set_unless_nil(collecting_event, :verbatim_latitude, get_field_value(:decimalLatitude)) # decimalLongitude: [verbatim_longitude] Utilities::Hashes::set_unless_nil(collecting_event, :verbatim_longitude, get_field_value(:decimalLongitude)) # geodeticDatum: [verbatim_datum] Utilities::Hashes::set_unless_nil(collecting_event, :verbatim_datum, get_field_value(:geodeticDatum)) # coordinateUncertaintyInMeters: [verbatim_geolocation_uncertainty] uncertainty = get_field_value(:coordinateUncertaintyInMeters) unless uncertainty.nil? || uncertainty =~ /\A[+-]?\d+\z/ raise DarwinCore::InvalidData.new({ "coordinateUncertaintyInMeters": ["Non-integer value"] }) end Utilities::Hashes::set_unless_nil(collecting_event, :verbatim_geolocation_uncertainty, uncertainty&.send(:+, 'm')) # coordinatePrecision: [Not mapped. Fail import if claimed precision is incorrect? Round to precision?] # pointRadiusSpatialFit: [Not mapped] # verbatimCoordinates: [Not mapped] # verbatimLatitude: [Not mapped] # verbatimLongitude: [Not mapped] # verbatimCoordinateSystem: [Not mapped] # verbatimSRS: [Not mapped] # footprintWKT: [Not mapped] # footprintSRS: [Not mapped] # footprintSpatialFit: [Not mapped] # georeferencedBy: [Not mapped] if georeferenced_by = get_field_value(:georeferencedBy) predicate_base_props = {uri: 'http://rs.tdwg.org/dwc/terms/georeferencedBy', project: self.project} predicate = Predicate.find_by(predicate_base_props) predicate ||= Predicate.where(project: project).find_by( Predicate.arel_table[:name].matches('georeferencedBy') ) predicate ||= Predicate.create!(predicate_base_props.merge( { name: 'georeferencedBy', definition: 'A list (concatenated and separated) of names of people, groups, or organizations who determined the georeference (spatial representation) for the Location.' }) ) georeference[:data_attributes] = [ InternalAttribute.new( type: 'InternalAttribute', predicate: predicate, value: georeferenced_by ) ] end # georeferencedDate: [Not mapped] # georeferenceProtocol: [Not mapped] # georeferenceSources: [Not mapped. REVISIT] # georeferenceVerificationStatus: [Not mapped] # georeferenceRemarks: [georeference note] note = get_field_value(:georeferenceRemarks) georeference[:notes_attributes] = [{text: note}] if note { collecting_event: collecting_event, georeference: georeference } end |
#parse_occurrence_class ⇒ Object (private)
454 455 456 457 458 459 460 461 462 463 464 465 466 467 468 469 470 471 472 473 474 475 476 477 478 479 480 481 482 483 484 485 486 487 488 489 490 491 492 493 494 495 496 497 498 499 500 501 502 503 504 505 506 507 508 509 510 511 512 513 514 515 516 517 518 519 520 521 522 523 524 525 526 527 528 529 530 531 532 533 534 535 536 537 538 539 540 541 542 543 544 545 546 547 |
# File 'app/models/dataset_record/darwin_core/occurrence.rb', line 454 def parse_occurrence_class res = { catalog_number: {}, specimen: {}, collecting_event: {} } # occurrenceID: [Mapped in import method] # catalogNumber: [catalog_number.identifier] Utilities::Hashes::set_unless_nil(res[:catalog_number], :identifier, get_field_value(:catalogNumber)) # recordNumber: [Not mapped] # recordedBy: [collecting_event.collectors and collecting_event.verbatim_collectors] Utilities::Hashes::set_unless_nil(res[:collecting_event], :collectors, (parse_people(:recordedBy) rescue nil)) Utilities::Hashes::set_unless_nil(res[:collecting_event], :verbatim_collectors, get_field_value(:recordedBy)) # individualCount: [specimen.total] Utilities::Hashes::set_unless_nil(res[:specimen], :total, get_field_value(:individualCount) || 1) # organismQuantity: [Not mapped. Check relation with invidivialCount] # organismQuantityType: [Not mapped. Check relation with invidivialCount] # sex: [Find or create by name inside Sex biocuration Group] TODO: Think of duplicates (with and without URI) sex = get_field_value(:sex) if sex raise DarwinCore::InvalidData.new({ "sex": ["Only single-word controlled vocabulary supported at this time."] }) if sex =~ /\s/ group = BiocurationGroup.find_by(project_id: Current.project_id, uri: DWC_ATTRIBUTE_URIS[:sex]) group ||= BiocurationGroup.where(project_id: Current.project_id).where('name ILIKE ?', 'sex').first group ||= BiocurationGroup.create!( name: 'Sex', definition: 'The sex of the individual(s) [CREATED FROM DWC-A IMPORT]', uri: DWC_ATTRIBUTE_URIS[:sex] ) # TODO: BiocurationGroup.biocuration_classes not returning AR relation sex_biocuration = group.biocuration_classes.detect { |c| c.name.casecmp(sex) == 0 } unless sex_biocuration sex_biocuration = BiocurationClass.create!(name: sex, definition: "#{sex} individual(s) [CREATED FROM DWC-A IMPORT]") Tag.create!(keyword: group, tag_object: sex_biocuration) else sex = sex_biocuration end Utilities::Hashes::set_unless_nil(res[:specimen], :biocuration_classifications, [BiocurationClassification.new(biocuration_class: sex_biocuration)]) end # lifeStage: [Not mapped] # reproductiveCondition: [Not mapped] # behavior: [Not mapped] # establishmentMeans: [Not mapped] # degreeOfEstablishment [Not mapped] # pathway [Not mapped] # occurrenceStatus: [Not mapped] # preparations: [Match PreparationType by name (case insensitive)] preparation_name = get_field_value(:preparations) if preparation_name preparation_type = PreparationType.find_by(PreparationType.arel_table[:name].matches(preparation_name)) raise DarwinCore::InvalidData.new({ "preparations": ["Unknown preparation \"#{preparation_name}\". If it is correct please add it to preparation types and retry."] }) unless preparation_type Utilities::Hashes::set_unless_nil(res[:specimen], :preparation_type, preparation_type) end Utilities::Hashes::delete_nil_and_empty_hash_values(res) # disposition: [Not mapped] # associatedMedia: [Not mapped] # associatedReferences: [Not mapped] # associatedSequences: [Not mapped] # associatedTaxa: [Not mapped] # otherCatalogNumbers: [Not mapped] # occurrenceRemarks: [specimen note] note = get_field_value(:occurrenceRemarks) Utilities::Hashes::set_unless_nil(res[:specimen], :notes_attributes, [{text: note}]) if note res end |
#parse_people(field_name) ⇒ Object (private)
NOTE: Sometimes an identifier/collector happens to be a non-person (like “ANSP Orthopterist”). Does TW (will) have something for this? Currently imported as an Unvetted Person.
315 316 317 318 319 320 321 322 323 324 325 326 327 328 329 330 331 332 333 334 |
# File 'app/models/dataset_record/darwin_core/occurrence.rb', line 315 def parse_people(field_name) Person.transaction(requires_new: true) do DwcAgent.parse(get_field_value(field_name)).map! { |n| DwcAgent.clean(n) }.map! do |name| attributes = { last_name: [name[:particle], name[:family]].compact.join(" "), first_name: name[:given], suffix: name[:suffix], prefix: name[:title] || name[:appellation] } # self.import_dataset.derived_people.merge(Person.where(attributes)).first || # TODO: Doesn't work, fails to detect Person subclasses. Why (besides explanation in Shared::OriginRelationship)? Person.where(attributes).joins(:related_origin_relationships).merge( OriginRelationship.where(old_object: self.import_dataset) ).first || Person::Unvetted.create!(attributes.merge({ related_origin_relationships: [OriginRelationship.new(old_object: self.import_dataset)] })) end end end |
#parse_record_level_class ⇒ Object (private)
369 370 371 372 373 374 375 376 377 378 379 380 381 382 383 384 385 386 387 388 389 390 391 392 393 394 395 396 397 398 399 400 401 402 403 404 405 406 407 408 409 410 411 412 413 414 415 416 417 418 419 420 421 422 423 424 425 426 427 428 429 430 431 432 433 434 435 436 437 438 439 440 441 442 443 444 445 446 447 448 449 450 451 452 |
# File 'app/models/dataset_record/darwin_core/occurrence.rb', line 369 def parse_record_level_class res = { specimen: {}, catalog_number: {} } # type: [Check it is 'PhysicalObject'] type = get_field_value(:type) || 'PhysicalObject' raise DarwinCore::InvalidData.new({ 'type' => ["Only 'PhysicalObject' or empty allowed"] }) if type != 'PhysicalObject' # modified: [Not mapped] # language: [Not mapped] # license: [Not mapped. Possible with Attribution model? To which object(s)?] # rightsHolder: [Not mapped. Same questions as license but using roles] # accessRights: [Not mapped. Related to license] # bibliographicCitation: [Not mapped] # references: [Not mapped] # institutionID: [Not mapped. Review] # collectionID: [Not mapped. Review] # datasetID: [Not mapped] # institutionCode: [repository.acronym] # TODO: Use mappings like with namespaces here as well? (Although probably attempt guessing) institution_code = get_field_value(:institutionCode) if institution_code repository = Repository.find_by(acronym: institution_code) # Some repositories may not have acronyms, in that case search by name as well unless repository repository_results = Repository.where(Repository.arel_table['name'].matches(Repository.sanitize_sql_like(institution_code))) raise DarwinCore::InvalidData.new({ "institutionCode": ["Multiple repositories match the name #{institution_code}. Please use the acronym instead."] }) if repository_results.count > 1 repository = repository_results.first end raise DarwinCore::InvalidData.new({ "institutionCode": ["Unknown #{institution_code} repository. If valid please register it using '#{institution_code}' as acronym or name."] }) unless repository Utilities::Hashes::set_unless_nil(res[:specimen], :repository, repository) end # collectionCode: [catalog_number.namespace] # collection_code = get_field_value(:collectionCode) # Utilities::Hashes::set_unless_nil(res[:catalog_number], :namespace, Namespace.create_with({ # name: "#{institution_code}-#{collection_code} [CREATED FROM DWC-A IMPORT IN #{project.name} PROJECT]", # delimiter: '-' # }).find_or_create_by!(short_name: "#{institution_code}-#{collection_code}")) if collection_code namespace_id = self.import_dataset.get_catalog_number_namespace(institution_code, get_field_value(:collectionCode)) if namespace_id Utilities::Hashes::set_unless_nil(res[:catalog_number], :namespace, Namespace.find(namespace_id)) Utilities::Hashes::set_unless_nil(res[:catalog_number], :project, self.project) end # datasetName: [Not mapped] # ownerInstitutionCode: [Not mapped] # basisOfRecord: [Check it is 'PreservedSpecimen', 'FossilSpecimen'] basis = get_field_value(:basisOfRecord) if 'FossilSpecimen'.casecmp(basis) == 0 fossil_biocuration = BiocurationClass.find_by(uri: DWC_FOSSIL_URI) raise DarwinCore::InvalidData.new( { 'basisOfRecord' => ["Biocuration class #{DWC_FOSSIL_URI} is not present in project"] } ) if fossil_biocuration.nil? Utilities::Hashes::set_unless_nil(res[:specimen], :biocuration_classifications, [BiocurationClassification.new(biocuration_class: fossil_biocuration)]) else raise DarwinCore::InvalidData.new( { 'basisOfRecord' => ["Only 'PreservedSpecimen', 'FossilSpecimen' or blank is allowed."] } ) unless basis.nil? || 'PreservedSpecimen'.casecmp(basis) == 0 end # informationWithheld: [Not mapped] # dataGeneralizations: [Not mapped] # dynamicProperties: [Not mapped. Could be ImportAttribute?] Utilities::Hashes::delete_nil_and_empty_hash_values(res) end |
#parse_taxon_class ⇒ Object (private)
852 853 854 855 856 857 858 859 860 861 862 863 864 865 866 867 868 869 870 871 872 873 874 875 876 877 878 879 880 881 882 883 884 885 886 887 888 889 890 891 892 893 894 895 896 897 898 899 900 901 902 903 904 905 906 907 908 909 910 911 912 913 914 915 916 917 918 919 920 921 922 923 924 925 926 927 928 929 930 931 932 933 934 935 936 937 938 939 940 941 942 943 944 945 946 947 948 949 950 951 952 953 954 955 956 957 958 959 960 961 962 963 964 965 966 967 968 969 970 971 972 973 974 975 976 977 978 979 980 981 982 983 984 985 986 987 988 989 990 991 992 993 994 995 996 997 998 999 1000 1001 1002 1003 1004 1005 1006 1007 1008 1009 1010 1011 1012 1013 1014 1015 1016 1017 1018 1019 1020 1021 1022 1023 1024 1025 1026 1027 1028 1029 1030 1031 1032 1033 1034 1035 1036 1037 1038 1039 1040 1041 1042 1043 |
# File 'app/models/dataset_record/darwin_core/occurrence.rb', line 852 def parse_taxon_class names = [] otu_names = [] origins = {} # taxonID: [Not mapped. Usually alias of core id] # scientificNameID: [Not mapped. Could be mapped with type detection into LSID identifier or global ID] # acceptedNameUsageID: [N/A for occurrences] # parentNameUsageID: [N/A for occurrences] # originalNameUsageID: [N/A for occurrences] # nameAccordingToID: [Not mapped] # namePublishedInID: [Not mapped] # taxonConceptID: [Not mapped] # acceptedNameUsage: [Not mapped. Review] # parentNameUsage: [N/A for occurrences] # originalNameUsage: [Not mapped. Review] # nameAccordingTo: [Not mapped] # namePublishedIn: [Not mapped] # namePublishedInYear: [Not mapped] # nomenclaturalCode: [Selects nomenclature code to pick ranks from] code = get_field_value(:nomenclaturalCode)&.downcase&.to_sym || import_dataset.default_nomenclatural_code unless Ranks::CODES.include?(code) raise DarwinCore::InvalidData.new( { "nomenclaturalCode": ["Unrecognized nomenclatural code #{get_field_value(:nomenclaturalCode)}"] } ) end # kingdom: [Kingdom protonym] origins[ {rank_class: Ranks.lookup(code, "kingdom"), name: get_field_value(:kingdom)}.tap { |h| names << h }.object_id ] = :kingdom # phylum: [Phylum protonym] origins[ {rank_class: Ranks.lookup(code, "phylum"), name: get_field_value(:phylum)}.tap { |h| names << h }.object_id ] = :phylum # class: [Class protonym] origins[ {rank_class: Ranks.lookup(code, "class"), name: get_field_value(:class)}.tap { |h| names << h }.object_id ] = :class # order: [Order protonym] origins[ {rank_class: Ranks.lookup(code, "order"), name: get_field_value(:order)}.tap { |h| names << h }.object_id ] = :order # family: [Family protonym] origins[ {rank_class: Ranks.lookup(code, "family"), name: get_field_value(:family)}.tap { |h| names << h }.object_id ] = :family # genus: [Not mapped, extracted from scientificName instead] # subgenus: [Not mapped, extracted from scientificName instead] # specificEpithet: [Not mapped, extracted from scientificName instead] # infraspecificEpithet: [Not mapped, extracted from scientificName instead] # scientificName: [Parsed with biodiversity and mapped into several protonyms] parse_results = Biodiversity::Parser.parse(get_field_value(:scientificName) || "") parse_details = parse_results[:details] parse_details = (parse_details&.keys - PARSE_DETAILS_KEYS).empty? ? parse_details.values.first : nil if parse_details unless (1..3).include?(parse_results[:quality]) && parse_details parse_details = parse_results[:details]&.values&.first otu_names << get_field_value(:scientificName) end raise DarwinCore::InvalidData.new({ "scientificName": parse_results[:qualityWarnings] ? parse_results[:qualityWarnings].map { |q| q[:warning] } : ["Unable to parse scientific name. Please make sure it is correctly spelled."] }) unless parse_details unless parse_details[:uninomial] origins[ {rank_class: Ranks.lookup(code, "genus"), name: parse_details[:genus]}.tap { |h| names << h }.object_id ] = :scientificName origins[ {rank_class: Ranks.lookup(code, "subgenus"), name: parse_details[:subgenus]}.tap { |h| names << h }.object_id ] = :scientificName origins[ {rank_class: Ranks.lookup(code, "species"), name: parse_details[:species]}.tap { |h| names << h }.object_id ] = :scientificName origins[ {rank_class: Ranks.lookup(code, "subspecies"), name: parse_details[:infraspecies]&.map{ |d| d.dig(:value) }&.join(' ') }.tap { |h| names << h }.object_id ] = :scientificName else if parse_details[:parent] origins[ {rank_class: Ranks.lookup(code, "genus"), name: parse_details[:parent]}.tap { |h| names << h }.object_id ] = :scientificName origins[ { rank_class: /subgen/ =~ parse_details[:rank] ? Ranks.lookup(code, "subgenus") : nil, name: parse_details[:uninomial] }.tap { |h| names << h }.object_id ] = :scientificName elsif get_field_value(:genus) == parse_details[:uninomial] origins[ {rank_class: Ranks.lookup(code, "genus"), name: parse_details[:uninomial]}.tap { |h| names << h }.object_id ] = :scientificName elsif names.reverse.detect { |n| n[:name] }&.dig(:name) != parse_details[:uninomial] origins[ {rank_class: nil, name: parse_details[:uninomial]}.tap { |h| names << h }.object_id ] = :scientificName end end names.reject! { |v| v[:name].nil? } # taxonRank: [Rank of innermost protonym] rank = get_field_value(:taxonRank) if rank && otu_names.empty? names.last[:rank_class] = Ranks.lookup(code, rank) raise DarwinCore::InvalidData.new({ "taxonRank": ["Unknown #{code.upcase} rank #{rank}"] }) unless names.last[:rank_class] end ident_qualifier = get_field_value(:identificationQualifier) if ident_qualifier =~ /^cf[\.\s]/ otu_names << ident_qualifier else otu_names << "#{get_field_value(:scientificName)} #{ident_qualifier}" end unless ident_qualifier.nil? names.last&.merge!({otu_attributes: {name: otu_names.join(' ')}}) unless otu_names.empty? # higherClassification: [Several protonyms with ranks determined automatically when possible. Classification lower or at genus level is ignored and extracted from scientificName instead] higherClassification = ['|', ':', ';', ','].inject([]) do |names, separator| break names if names.size > 1 get_field_value(:higherClassification)&.split(separator) || [] end.map! do |name| normalize_value!(name) {rank_class: nil, name: name} end curr = 0 names.each do |name| idx = higherClassification[curr..].index { |n| n[:name] == name[:name] } if idx higherClassification[curr+idx] = name curr += idx + 1 end end idx = higherClassification.index { |n| n[:rank_class] == Ranks.lookup(code, "genus") } higherClassification = higherClassification.slice(0, idx) if idx curr = 0 higherClassification.each do |name| if name[:rank_class] curr = names.index(name) + 1 else names.insert(curr, name) origins[name.object_id] = :higherClassification curr += 1 end end # verbatimTaxonRank: [Not mapped] # scientificNameAuthorship: [verbatim_author of innermost protonym] begin , year = Utilities::Strings.(get_field_value("scientificNameAuthorship")) names.last&.merge!({ verbatim_author: , year_of_publication: year }) end # vernacularName: [Not mapped] # taxonomicStatus: [Not mapped. Review] # nomenclaturalStatus: [Not mapped. Review] # taxonRemarks: [Not mapped] [names, origins] end |
#parse_tw_collecting_event_attributes ⇒ Object (private)
1179 1180 1181 1182 1183 1184 1185 1186 1187 1188 1189 1190 1191 1192 1193 1194 1195 1196 |
# File 'app/models/dataset_record/darwin_core/occurrence.rb', line 1179 def parse_tw_collecting_event_attributes attributes = {} get_tw_fields_for('CollectingEvent').each do |attribute| value = get_field_value(attribute[:field]) if value if !ACCEPTED_ATTRIBUTES[:CollectingEvent].include?(attribute[:name]) raise DarwinCore::InvalidData.new({ attribute[:field] => ["#{attribute[:name]} is not a valid CollectingEvent attribute"] }) end attributes[attribute[:name]] = value end end { collecting_event: attributes } end |
#parse_tw_collecting_event_data_attributes ⇒ Object (private)
1065 1066 1067 1068 1069 1070 1071 1072 1073 1074 1075 1076 1077 1078 1079 1080 1081 1082 1083 |
# File 'app/models/dataset_record/darwin_core/occurrence.rb', line 1065 def parse_tw_collecting_event_data_attributes attributes = [] = [] get_tw_data_attribute_fields_for('CollectingEvent').each do |attribute| append_data_attribute(attributes, attribute) end get_tw_tag_fields_for('CollectingEvent').each do |tag| append_tag_attribute(, tag) end { collecting_event: { data_attributes_attributes: attributes, tags_attributes: } } end |
#parse_tw_collection_object_attributes ⇒ Object (private)
1160 1161 1162 1163 1164 1165 1166 1167 1168 1169 1170 1171 1172 1173 1174 1175 1176 1177 |
# File 'app/models/dataset_record/darwin_core/occurrence.rb', line 1160 def parse_tw_collection_object_attributes attributes = {} get_tw_fields_for('CollectionObject').each do |attribute| value = get_field_value(attribute[:field]) if value if !ACCEPTED_ATTRIBUTES[:CollectionObject].include?(attribute[:name]) raise DarwinCore::InvalidData.new({ attribute[:field] => ["#{attribute[:name]} is not a valid CollectionObject attribute"] }) end attributes[attribute[:name]] = value end end { specimen: attributes } end |
#parse_tw_collection_object_data_attributes ⇒ Object (private)
1045 1046 1047 1048 1049 1050 1051 1052 1053 1054 1055 1056 1057 1058 1059 1060 1061 1062 1063 |
# File 'app/models/dataset_record/darwin_core/occurrence.rb', line 1045 def parse_tw_collection_object_data_attributes attributes = [] = [] get_tw_data_attribute_fields_for('CollectionObject').each do |attribute| append_data_attribute(attributes, attribute) end get_tw_tag_fields_for('CollectionObject').each do |tag| append_tag_attribute(, tag) end { specimen: { data_attributes_attributes: attributes, tags_attributes: } } end |
#term_value_changed(name, value) ⇒ Object (private)
277 278 279 280 281 282 283 284 285 286 287 288 289 290 291 292 293 294 295 |
# File 'app/models/dataset_record/darwin_core/occurrence.rb', line 277 def term_value_changed(name, value) if ['institutioncode', 'collectioncode', 'catalognumber', 'basisofrecord'].include?(name.downcase) and self.status != 'Imported' ready = get_field_value('catalogNumber').blank? ready ||= !!self.import_dataset.get_catalog_number_namespace(get_field_value('institutionCode'), get_field_value('collectionCode')) self..delete("error_data") if ready self.status = 'Ready' else self.status = 'NotReady' self.["error_data"] = { messages: { catalogNumber: ["Record cannot be imported until namespace is set, see \"Settings\"."] } } end self.import_dataset.add_catalog_number_namespace(get_field_value('institutionCode'), get_field_value('collectionCode')) self.import_dataset.add_catalog_number_collection_code_namespace(get_field_value('collectionCode')) self.save! end end |