Class: DatasetRecord::DarwinCore::Occurrence

Inherits:
DatasetRecord::DarwinCore show all
Defined in:
app/models/dataset_record/darwin_core/occurrence.rb

Overview

TODO: There are numerous very long methods here, we really need to break out logical chunks so that we can

a) better atomize and test the expecatations
b) interpret and document the behaviour of the importer

See app/javascript/vue/tasks/dwca_import/components/settings/Occurrences/OccurrenceSettings.vue for UI defined parameters

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 superfamily family subfamily tribe subtribe}.freeze
PARSE_DETAILS_KEYS = 
%i(uninomial genus species infraspecies).freeze
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_field_number
  ).to_set.freeze
}.freeze

Instance Attribute Summary

Attributes inherited from DatasetRecord

#metadata, #status

Instance Method Summary collapse

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

transaction_with_retry

Instance Method Details

#append_data_attribute(attributes, attribute) ⇒ Object (private) 



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# File 'app/models/dataset_record/darwin_core/occurrence.rb', line 1589

def append_data_attribute(attributes, attribute)
  predicate = Predicate.find_by(uri: attribute[:selector], project: self.project)
  predicate ||= Predicate.where(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:,
      value:,
      annotator_batch_mode: true
    }
  end
end

#append_dwc_attribute(attributes, predicate, value) ⇒ Object (private) 



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# File 'app/models/dataset_record/darwin_core/occurrence.rb', line 1680

def append_dwc_attribute(attributes, predicate, value)
  attributes << {
    type: 'InternalAttribute',
    predicate:,
    value:,
    annotator_batch_mode: true
  } if value
end

#append_dwc_attributes(dwc_attributes, target) ⇒ Object (private) 



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# File 'app/models/dataset_record/darwin_core/occurrence.rb', line 1689

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) 



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# File 'app/models/dataset_record/darwin_core/occurrence.rb', line 1566

def append_tag_attribute(tags, tag)
  value = get_field_value(tag[:field])
  return unless value

  keyword = Keyword.find_by(uri: tag[:selector], project: self.project)
  keyword ||= Keyword.where(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'
      tags.append({keyword:, annotator_batch_mode: true})
      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.

Parameters:

  • identifier_str (String)
  • namespace (Namespace) 


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# File 'app/models/dataset_record/darwin_core/occurrence.rb', line 624

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

#extract_event_identifier_params ⇒ Object 



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# File 'app/models/dataset_record/darwin_core/occurrence.rb', line 483

def extract_event_identifier_params()
  # TODO: Extract logic here for shorter main loop
end

#extract_field_number_identifier_params ⇒ Object 



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# File 'app/models/dataset_record/darwin_core/occurrence.rb', line 487

def extract_field_number_identifier_params()
  # TODO: Extract logic here for shorter main loop
end

#get_correct_spelling(protonym) ⇒ Object

Gets the correct spelling for a protonym, or returns the protonym if not a misspelling

Parameters:

  • protonym (Protonym) —

    the protonym to get correct spelling for



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# File 'app/models/dataset_record/darwin_core/occurrence.rb', line 1120

def get_correct_spelling(protonym)
  if protonym.is_protonym? && protonym.has_misspelling_relationship?
    return TaxonNameRelationship.where_subject_is_taxon_name(protonym)
                                .with_type_array(TAXON_NAME_RELATIONSHIP_NAMES_MISSPELLING_ONLY)
                                .first&.object_taxon_name
  end
  protonym
end

#get_integer_field_value(field_name) ⇒ Object (private) 



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# File 'app/models/dataset_record/darwin_core/occurrence.rb', line 518

def get_integer_field_value(field_name)
  value = get_field_value(field_name)

  if value.present?
    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 



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# File 'app/models/dataset_record/darwin_core/occurrence.rb', line 161

def import(dwc_data_attributes = {})
  super
  begin
    DatasetRecord.transaction(requires_new: true) do
      self.metadata.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(innermost_protonym))

      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 record_number = get_field_value(:recordNumber)
        record_number_namespace = get_field_value('TW:Namespace:recordNumber')
        identifier_attributes = {
          identifier: record_number,
          project_id: Current.project_id
        }

        record_number_namespace = Namespace.find_by(Namespace.arel_table[:short_name].matches(record_number_namespace)) # Case insensitive match
        raise DarwinCore::InvalidData.new({ 'TW:Namespace:recordNumber' => ['Namespace not found'] }) unless record_number_namespace

        identifier_attributes[:namespace] = record_number_namespace
        identifier = Identifier::Local::RecordNumber
          .create_with(identifier_object: specimen, annotator_batch_mode: true)
          .find_or_create_by!(identifier_attributes)

        unless identifier.identifier_object == specimen
          raise DarwinCore::InvalidData.new({ 'recordNumber' => ['Is already in use'] })
        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, annotator_batch_mode: true)
          .find_or_create_by!(attributes[:catalog_number])

        # if desired, ensure that cached CO identifier will match verbatim catalogNumber
        # this ensures that DwC exported records will have identical catalogNumbers as when they were imported
        if self.import_dataset.require_catalog_number_match_verbatim? &&
          identifier.cached != get_field_value(:catalogNumber)

          error_message = "Computed catalog number #{identifier.cached} will not match verbatim #{get_field_value(:catalogNumber)}. "\
                          'Verify the mapped namespace and namespace delimiter are correct.'
          raise DarwinCore::InvalidData.new({'catalogNumber' => [error_message]})
        end

        object = identifier.identifier_object

        unless object == specimen
          unless record_number || self.import_dataset.containerize_dup_cat_no?
            raise DarwinCore::InvalidData.new({ 'catalogNumber' => ['Is already in use'] })
          end
          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),
        annotator_batch_mode: true
      ) 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]))


      #   There are 3 possible CE identifiers, each needs individual mapping
      #     eventID -> Identifier::Local::Event (with TW:Namespace:eventID)
      #     fieldNumber -> Identifier::Local::FieldNumber (with TW:Namespace:fieldNumber)
      #     TW::CollectingEvent::verbatim_field_number
      #
      event_id, field_number = get_field_value(:eventID), get_field_value(:fieldNumber)
      collecting_event_identifiers = []
      if event_id.present?
        event_id_namespace = get_field_value('TW:Namespace:eventID')

        # TODO: Shouldn't this be local?!
        identifier_type = Identifier::Global.descendants.detect { |c| c.name.downcase == event_id_namespace.downcase } if event_id_namespace

        identifier_attributes = {
          identifier: event_id,
          identifier_object_type: 'CollectingEvent',
          project_id: Current.project_id
        }

        if identifier_type.nil?
          identifier_type = Identifier::Local::Event # Note: This was TripCode.  This is a much better fit now, as EventID is a digital accession value.

          using_default_event_id = false
          if event_id_namespace.nil?
            event_id_namespace = import_dataset.get_event_id_namespace
            using_default_event_id = true
          else
            event_id_namespace = Namespace.find_by(Namespace.arel_table[:short_name].matches(event_id_namespace)) # Case insensitive match
            raise DarwinCore::InvalidData.new({ 'TW:Namespace:eventID' => ['Namespace not found'] }) unless event_id_namespace
          end

          identifier_attributes[:namespace] = event_id_namespace

          delete_namespace_prefix!(event_id, event_id_namespace)

          if !using_default_event_id && self.import_dataset.require_tripcode_match_verbatim?
            if (cached_identifier = Identifier::Local.build_cached_prefix(event_id_namespace) + event_id) != get_field_value(:eventID)
              error_message = "Computed Event #{cached_identifier} will not match verbatim #{get_field_value(:eventID)}. "\
                          'Verify the namespace delimiter is correct.' # TODO include link to namespace?
              raise DarwinCore::InvalidData.new({'eventID' => [error_message]})
            end
          end
        end

        event_id_identifier = identifier_type.find_by(identifier_attributes)
        collecting_event = event_id_identifier&.identifier_object
        collecting_event_identifiers << {type: identifier_type, attributes: identifier_attributes}
      end

      if field_number.present?
        field_number_namespace = get_field_value('TW:Namespace:fieldNumber')

        identifier_attributes = {
          identifier: field_number,
          identifier_object_type: 'CollectingEvent',
          project_id: Current.project_id
        }

        field_number_namespace = Namespace.find_by(Namespace.arel_table[:short_name].matches(field_number_namespace)) # Case insensitive match
        raise DarwinCore::InvalidData.new({ 'TW:Namespace:fieldNumber' => ['Namespace not found'] }) unless field_number_namespace

        identifier_attributes[:namespace] = field_number_namespace

        field_number_identifier = Identifier::Local::FieldNumber.find_by(identifier_attributes)
        collecting_event ||= field_number_identifier&.identifier_object
        collecting_event_identifiers << {type: Identifier::Local::FieldNumber, attributes: identifier_attributes}
      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 field_number_identifier && event_id_identifier &&
          field_number_identifier.identifier_object != event_id_identifier.identifier_object
          raise DarwinCore::InvalidData.new({ 'eventID/fieldNumber' => ['eventId and fieldNumber refer to different collecting events'] })
        elsif (field_number_identifier && event_id) || (event_id_identifier && field_number)
          raise DarwinCore::InvalidData.new({ 'eventID/fieldNumber' => ['does not match previous definition of collecting event'] })
        end

        # if collecting_event.identifiers.where(type: Identifer::Local::FieldNumber)
        # 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
          current_tags = collecting_event.tags.pluck(:keyword_id).to_set

          new_tags = attributes[:collecting_event][:tags_attributes].reject { |t| current_tags.member?(t[:keyword].id) }

          # add tags if there were any new ones
          unless new_tags.empty?
            collecting_event.tags.build(new_tags)
            collecting_event.save!
          end
        end

        specimen.update!(collecting_event:)
      else
        collecting_event = CollectingEvent.create!({
          collection_objects: [specimen],
          no_dwc_occurrence: true,
          no_cached: true
        }.merge!(attributes[:collecting_event]))

        collecting_event_identifiers.each do |identifier|
          identifier[:type].create!({
            identifier_object: collecting_event,
            annotator_batch_mode: true
          }.merge!(identifier[:attributes]))
        end
        has_shape = self.import_dataset.metadata.dig('import_settings', 'require_geographic_area_has_shape')
        data_origin = self.import_dataset.metadata.dig('import_settings', 'geographic_area_data_origin')
        disable_recursive_search = self.import_dataset.metadata.dig('import_settings', 'require_geographic_area_exact_match')
        require_ga_found = self.import_dataset.metadata.dig('import_settings', 'require_geographic_area_exists')
        should_check_ga_exists = false
        location_hash = {}  # if requiring geographic area to exist, use hash of inputs for error message

        if collecting_event.verbatim_latitude && collecting_event.verbatim_longitude
          Georeference::VerbatimData.create!({
            collecting_event:,
            error_radius: get_field_value('coordinateUncertaintyInMeters'),
            no_cached: true
          }.merge(attributes[:georeference]))
        end

        county = get_field_value(:county)
        state_province = get_field_value(:stateProvince)
        country = get_field_value(:country)
        country_code = get_field_value(:countryCode)
        if country.blank? && country_code.present?
          if country_code.size == 2
            country = GeographicArea.find_by(iso_3166_a2: country_code, data_origin: 'country_names_and_code_elements').name
          elsif country_code.size == 3  # there are no GAs with alpha3 presently
            country = GeographicArea.find_by(iso_3166_a3: country_code, data_origin: 'country_names_and_code_elements').name
          end
        end

        location_levels = [county, state_province, country].compact

        if require_ga_found && location_levels.size > 0
          location_hash = {county:, state_province:, country:, country_code:}
          should_check_ga_exists = true
        end

        # try to find geographic areas until no location levels are left
        geographic_areas = []
        if disable_recursive_search
          geographic_areas = GeographicArea.with_name_and_parent_names(location_levels).with_data_origin(data_origin).has_shape(has_shape)
        else
          while location_levels.size > 0 and geographic_areas.size == 0
            geographic_areas = GeographicArea.with_name_and_parent_names(location_levels).with_data_origin(data_origin).has_shape(has_shape)
            location_levels = location_levels.drop(1)
          end
        end

        if should_check_ga_exists && geographic_areas.size == 0
          levels = location_hash.to_a.filter{|_,v| !v.nil?}.map { |k,v| "#{k}:#{v}"}
          error_message = "GeographicArea with location levels #{levels.join(", ")} not found."
          raise DarwinCore::InvalidData.new({'country, stateProvince, county' => [error_message]})
        end

        collecting_event.geographic_area_id = geographic_areas[0].id if geographic_areas.size > 0
        collecting_event.save!
      end

      DwcOccurrenceUpsertJob.perform_later(specimen)

      self.metadata['imported_objects'] = { collection_object: { id: specimen.id } }
      self.status = 'Imported'
    end
  rescue DarwinCore::InvalidData => invalid
    self.status = 'Errored'
    self.metadata['error_data'] = { messages: invalid.error_data }
  rescue ActiveRecord::RecordInvalid => invalid
    self.status = 'Errored'
    self.metadata['error_data'] = {
      messages: invalid.record.errors.messages
    }
  rescue StandardError => e
    raise if Rails.env.development?
    self.status = 'Failed'
    self.metadata['error_data'] = {
      exception: {
        message: e.message,
        backtrace: e.backtrace
      }
    }
  ensure
    save!
  end

  self
end

#parse_biocuration_group_field(group) ⇒ Object (private) 



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# File 'app/models/dataset_record/darwin_core/occurrence.rb', line 1617

def parse_biocuration_group_field(group)
  biocuration_group = BiocurationGroup.find_by(uri: group[:selector], project: self.project)
  biocuration_group ||= BiocurationGroup.where(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:).joins(:tags).merge(
      Tag.where(keyword: biocuration_group)
    ).find_by(uri: value)
    biocuration_class ||= BiocurationClass.where(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:)
  end
end

#parse_biocuration_group_fields ⇒ Object (private) 



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# File 'app/models/dataset_record/darwin_core/occurrence.rb', line 1607

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)

rubocop:disable Metrics/MethodLength

Raises:



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# File 'app/models/dataset_record/darwin_core/occurrence.rb', line 857

def parse_event_class
  collecting_event = { }

  # eventID: [Mapped in import method]

  # parentEventID: [Not mapped]

  # fieldNumber: verbatim_field_number & Identifier::Local::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, annotator_batch_mode: true}]) if note

  { collecting_event: }
end

#parse_identification_class(taxon_protonym) ⇒ Object (private)

rubocop:enable Metric/MethodLength

Raises:



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# File 'app/models/dataset_record/darwin_core/occurrence.rb', line 1255

def parse_identification_class(taxon_protonym)
  taxon_determination = {}
  type_material = nil

  # identificationID: [Not mapped]

  # identificationQualifier: [Mapped 1:1 with otu name parse_taxon_class]

  # typeStatus: [Type material only if scientific name matches scientificName and type term is recognized by TW vocabulary]
  if (type_status = get_field_value(:typeStatus))
    type_material = parse_typestatus(type_status, taxon_protonym)
    if type_material.nil? && self.import_dataset.require_type_material_success?
      # generic error message, nothing more specific provided
      raise DarwinCore::InvalidData.new({ "typeStatus": ['Unprocessable typeStatus information'] })
    end
  end

  # identifiedBy: determiners of taxon determination
  determiners = nil
  if self.import_dataset.enable_organization_determiners?
    determiners = parse_organizations_and_people(:identifiedBy,
                                                 self.import_dataset.enable_organization_determiners_alt_name?)
  else
    determiners = parse_people(:identifiedBy)
  end
  unless determiners.nil?
    if determiners.first.is_a?(Person)
      taxon_determination[:determiners] = determiners
    elsif determiners.first.is_a?(Organization)
      taxon_determination[:determiners_organization] = determiners
    end
  end

  # 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, annotator_batch_mode: true}] if note

  {
    taxon_determination:,
    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.

Parameters:

  • field_name (String) —

    The column name to get the date string from

Returns:

  • (Array<OpenStruct>) —

    A list of one or two date structs (with year, month, day, hour, minute, second values)

Raises:



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# File 'app/models/dataset_record/darwin_core/occurrence.rb', line 601

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)

rubocop:enable Metrics/MethodLength



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# File 'app/models/dataset_record/darwin_core/occurrence.rb', line 967

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:).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:,
        value: georeferenced_by,
        annotator_batch_mode: true
      )
    ]
  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, annotator_batch_mode: true}] if note

  {
    collecting_event:,
    georeference:
  }
end

#parse_occurrence_class ⇒ Object (private)

rubocop:enable Metrics/MethodLength



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# File 'app/models/dataset_record/darwin_core/occurrence.rb', line 760

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: [Mapped in import method]

  # 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, annotator_batch_mode: true}]) if note

  res
end

#parse_organizations_and_people(field_name, search_alt_name = false) ⇒ Array<Organization, Person::Unvetted>? (private)

Search for an Organization by name or alternate name in the given field. If no organization found, find or create a Person::Unvetted, scoped to the import_dataset

Parameters:

  • field_name (String, Symbol) —

    Field name (column) to parse for people in

  • search_alt_name (Boolean) (defaults to: false) —

    Search by alternate_name in addition to name

Returns:



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# File 'app/models/dataset_record/darwin_core/occurrence.rb', line 542

def parse_organizations_and_people(field_name, search_alt_name = false)
  org_name = get_field_value(field_name)
  possible_organizations = Organization.where(name: org_name)
  if search_alt_name
    possible_organizations = possible_organizations.or(Organization.where(alternate_name: org_name))
  end
  if possible_organizations.exists?
    if possible_organizations.count == 1
      return [possible_organizations.first]

    elsif possible_organizations.count > 1
      matching_orgs = possible_organizations.map do |o|
        str = "[id:#{o.id} #{o.name}"
        if o.alternate_name.present?
          str << " (AKA: #{o.alternate_name})"
        end
        str << ']'
      end.join(', ')
      # TODO how should the user disambiguate which organization they are referring to?
      raise DarwinCore::InvalidData.new({ field_name => ["Multiple organizations matched name or alternate name '#{org_name}': #{matching_orgs}"] })
    end
  end

  parse_people(field_name)
end

#parse_people(field_name) ⇒ Array<Person::Unvetted>? (private)

Parse for names in a given field and find or create one or more Person::Unvetted (scoped to the import dataset).

Parameters:

  • field_name (String, Symbol) —

    Field name (column) to parse for people in

Returns:



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# File 'app/models/dataset_record/darwin_core/occurrence.rb', line 571

def parse_people(field_name)
  #noinspection RubyMismatchedReturnType
  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, annotator_batch_mode: true)]
      }))
    end
  end
end

#parse_record_level_class ⇒ Object (private)

rubocop:disable Metrics/MethodLength

Raises:



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# File 'app/models/dataset_record/darwin_core/occurrence.rb', line 630

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 = nil
    error_messages = []

    if institution_code.starts_with?('http://') || institution_code.starts_with?('https://')
      url_repositories = Repository.where(url: institution_code)
      if url_repositories.count == 1
        repository = url_repositories.first
      elsif url_repositories.count > 1
        error_messages << "Multiple repositories with url #{institution_code} found"
      else
        error_messages << "No repositories with url #{institution_code} found"
      end
    end

    unless repository
      acronym_repositories = Repository.where(acronym: institution_code)
      if acronym_repositories.count == 1
        repository = acronym_repositories.first
      elsif acronym_repositories.count > 1
        error_messages << "Multiple repositories with acronym #{institution_code} found."
      else
        error_messages << "No repositories with acronym #{institution_code} found."
      end
    end

    # 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)))
      if repository_results.count == 1
        repository = repository_results.first
      elsif repository_results.count > 1
        error_messages << "Multiple repositories match the name #{institution_code}."
      else
        error_messages << "No repositories match the name #{institution_code}"
      end

      unless repository
        if error_messages
          error_messages.unshift("Could not disambiguate repository name '#{institution_code}'.")
        else
          error_messages.unshift("Unknown #{institution_code} repository. If valid please register it using '#{institution_code}' as acronym or name.")
        end
        raise DarwinCore::InvalidData.new({ "institutionCode": error_messages })
      end
    end
    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
  if namespace = get_field_value('TW:Namespace:catalogNumber')
    namespace = Namespace.find_by(Namespace.arel_table[:short_name].matches(namespace)) # Case insensitive match
    raise DarwinCore::InvalidData.new({ 'TW:Namespace:catalogNumber' => ['Namespace not found'] }) unless namespace
  else
    namespace_id = self.import_dataset.get_catalog_number_namespace(institution_code, get_field_value(:collectionCode))
    namespace = Namespace.find(namespace_id) if namespace_id
  end
  if namespace
    Utilities::Hashes::set_unless_nil(res[:catalog_number], :namespace, namespace)
    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)
  basis = basis.downcase.camelize if basis&.include? '_' # Reformat GBIF occurrence download basis of records (e.g., PRESERVED_SPECIMEN to PreservedSpecimen)
  if 'FossilSpecimen'.casecmp(basis) == 0
    fossil_biocuration = BiocurationClass.where(project:).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)

rubocop:disable Metric/MethodLength

Raises:



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# File 'app/models/dataset_record/darwin_core/occurrence.rb', line 1315

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

  # superfamily: [Superfamily protonym]
  origins[
    {rank_class: Ranks.lookup(code, 'superfamily'), name: get_field_value(:superfamily)}.tap { |h| names << h }.object_id
  ] = :superfamily

  # family: [Family protonym]
  origins[
    {rank_class: Ranks.lookup(code, 'family'), name: get_field_value(:family)}.tap { |h| names << h }.object_id
  ] = :family

  # subfamily: [Subfamily protonym]
  origins[
    {rank_class: Ranks.lookup(code, 'subfamily'), name: get_field_value(:subfamily)}.tap { |h| names << h }.object_id
  ] = :subfamily

  # tribe: [Tribe protonym]
  origins[
    {rank_class: Ranks.lookup(code, 'tribe'), name: get_field_value(:tribe)}.tap { |h| names << h }.object_id
  ] = :tribe

  # subtribe: [Subtribe protonym]
  origins[
    {rank_class: Ranks.lookup(code, 'subtribe'), name: get_field_value(:subtribe)}.tap { |h| names << h }.object_id
  ] = :subtribe

  # 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
  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&.is_a?(Hash)

  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? # TODO: Probably don't need otu_name check, rank matches the taxon name, NOT the OTU concept when identificationQualifier is used
    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)
  otu_names << ident_qualifier 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:}
  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
    author_name, year = Utilities::Strings.parse_authorship(get_field_value('scientificNameAuthorship'))

    names.last&.merge!({ verbatim_author: author_name, 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) 



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# File 'app/models/dataset_record/darwin_core/occurrence.rb', line 1661

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) 



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# File 'app/models/dataset_record/darwin_core/occurrence.rb', line 1546

def parse_tw_collecting_event_data_attributes
  attributes = []
  tags = []

  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(tags, tag)
  end

  {
    collecting_event: {
      data_attributes_attributes: attributes,
      tags_attributes: tags
    }
  }
end

#parse_tw_collection_object_attributes ⇒ Object (private) 



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# File 'app/models/dataset_record/darwin_core/occurrence.rb', line 1642

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)

rubocop:disable Metric/MethodLength



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# File 'app/models/dataset_record/darwin_core/occurrence.rb', line 1526

def parse_tw_collection_object_data_attributes
  attributes = []
  tags = []

  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(tags, tag)
  end

  {
    specimen: {
      data_attributes_attributes: attributes,
      tags_attributes: tags
    }
  }
end

#parse_typestatus(type_status, taxon_protonym) ⇒ Hash{Symbol=>String, TaxonName}? (private)

Parameters:

  • type_status (String)
  • taxon_protonym (Protonym)

Returns:

Raises:



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# File 'app/models/dataset_record/darwin_core/occurrence.rb', line 1106

def parse_typestatus(type_status, taxon_protonym)
  type_material = nil
  type_status_parsed = type_status&.match(/^(?<type>\w+)$/i) || type_status&.match(/(?<type>\w+)(\s+OF\s+(?<scientificName>.*))/i)
  # only nil if non-alphanumeric entry, or multiple words not matching "\w+ of \w+"
  raise DarwinCore::InvalidData.new({ "typeStatus": ['Unprocessable typeStatus information'] }) unless type_status_parsed && type_status_parsed[:type]
  type_type = type_status_parsed[:type].downcase

  code = get_field_value(:nomenclaturalCode)&.downcase&.to_sym || import_dataset.default_nomenclatural_code
  unless TypeMaterial::legal_type_type(code, type_type)
    raise DarwinCore::InvalidData.new({ "typeStatus": ['could not extract legal type from typeStatus'] })
  end

  # Gets the correct spelling for a protonym, or returns the protonym if not a misspelling
  # @param [Protonym] protonym the protonym to get correct spelling for
  def get_correct_spelling(protonym)
    if protonym.is_protonym? && protonym.has_misspelling_relationship?
      return TaxonNameRelationship.where_subject_is_taxon_name(protonym)
                                  .with_type_array(TAXON_NAME_RELATIONSHIP_NAMES_MISSPELLING_ONLY)
                                  .first&.object_taxon_name
    end
    protonym
  end

  scientific_name = get_field_value(:scientificName)&.gsub(/\s+/, ' ')

  # Run the name through the biodiversity parser to remove authorship info
  parse_results = Biodiversity::Parser.parse((type_status_parsed&.[](:scientificName)&.gsub(/\s+/, ' ') rescue nil) || '')

  type_author_name, type_year = nil
  # Only use biodiversity parsed name if it has very high confidence
  if parse_results[:quality] == 1
    type_scientific_name = parse_results.dig(:canonical, :simple)
    # Save authorship info for narrowing down potential protonyms
    type_author_name, type_year = Utilities::Strings.parse_authorship(parse_results.dig(:authorship, :normalized))
  end

  # if typeStatus is single word, assume the user wants the specimen name as the type name
  type_scientific_name ||= scientific_name

  if scientific_name && type_scientific_name.present?
    # list of messages to help user debug why matching failed
    error_messages = []

    # if type_scientific_name matches the current name of the occurrence, use that
    if type_scientific_name.delete_prefix(scientific_name)&.match(/^\W*$/)
      return {
        type_type:
      }
    end

    name_pattern = "^#{type_scientific_name.split.map { |n| "#{n}(?: \\[sic\\])?" }.join(" ")}$"
    original_combination_protonyms = Protonym.where('cached_original_combination ~ :pat', pat: name_pattern)
                                             .where(project_id: self.project_id)

    if original_combination_protonyms.count == 1
      oc_protonym = original_combination_protonyms.first
      return {
        type_type:,
        protonym: get_correct_spelling(oc_protonym)
      }
    elsif original_combination_protonyms.count > 1
      potential_protonym_strings = original_combination_protonyms.map { |proto|
        "[id: #{proto.id} #{proto.cached_original_combination_html}]"
      }.join(', ')
      error_messages << "Multiple matches found for name #{type_scientific_name}}: #{potential_protonym_strings}"
    else
      error_messages << 'Could not find exact original combination match for typeStatus'
    end

    # See if name matches a synonym of taxon name (ie any name linked to current taxon name)
    synonyms = taxon_protonym.synonyms
    matching_synonyms = Set[]
    synonyms.each do |s|
      possible_names = [s.cached, s.cached_original_combination].compact.to_set
      # Try excluding subgenus
      possible_names += possible_names.map {|n| n.sub(/\(\w+\) /, '')}
      # Check for misspellings
      possible_names += possible_names.map { |n| n.gsub(' [sic]', '') }
      if possible_names.include?(type_scientific_name)
        if s.is_combination?
          matching_synonyms << s.finest_protonym
        else
          matching_synonyms << s
        end
      end
    end

    matching_synonyms = matching_synonyms.map { |s| get_correct_spelling(s) }.uniq

    if matching_synonyms.count == 1
      return {
        type_type:,
        protonym: matching_synonyms.first
      }
    elsif matching_synonyms.count > 1
      synonym_strings = matching_synonyms.map { |proto| "[id: #{proto.id} #{proto.cached_original_combination_html}]" }.join(', ')
      error_messages << "Multiple synonym matches found for name #{type_scientific_name}}: #{synonym_strings}"
    end

    # Try wildcard match on subgenus if not present
    type_name_elements = type_scientific_name.split
    if type_name_elements.length > 1 && type_name_elements[1].first != '(' && type_name_elements[1].last != ')'
      type_name_elements.map! { |s| Regexp.escape(s) }
      # append subgenus wildcard to genus string
      type_name_elements[0] << '( \(\w+\))?'
      name_pattern = "^#{type_name_elements.join(" ")}$"

      wildcard_original_protonym = Protonym.where('cached_original_combination ~ :pat', pat: name_pattern)
                                           .or(Protonym.where('cached ~ :pat', pat: name_pattern))
                                           .where(project_id: self.project_id)

      if type_author_name.present?
        cached_author = type_author_name
        if cached_author.starts_with?('(') && cached_author.end_with?(')')
          cached_author.delete_prefix!('(').delete_suffix!(')')
        end
        wildcard_original_protonym = wildcard_original_protonym.where(cached_author:)
      end

      if type_year.present?
        wildcard_original_protonym = wildcard_original_protonym.where(year_of_publication: type_year)
      end

      if wildcard_original_protonym.count == 1
        return {
          type_type:,
          protonym: get_correct_spelling(wildcard_original_protonym.first)
        }
      elsif wildcard_original_protonym.count > 1
        matching_protonyms = wildcard_original_protonym.map { |p| "[id: #{p.id} #{p.cached_html_original_name_and_author_year}]" }
                                                       .join(', ')
        error_messages << "Multiple names returned in wildcard search: #{matching_protonyms}"
      else
        error_messages << 'No names returned in subgenus wildcard search'
      end
    end

    # report errors
    if error_messages
      error_messages.unshift "Could not identify or disambiguate name #{type_scientific_name}."
      raise DarwinCore::InvalidData.new({ "typeStatus": error_messages })
    end

  end
  type_material
end

#term_value_changed(name, value) ⇒ Object (private) 



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# File 'app/models/dataset_record/darwin_core/occurrence.rb', line 496

def term_value_changed(name, value)
  if ['institutioncode', 'collectioncode', 'catalognumber', 'basisofrecord'].include?(name.downcase) and self.status != 'Imported'
    ready = get_field_value('catalogNumber').blank? || get_field_value('TW:Namespaces:catalogNumber').present?
    ready ||= !!self.import_dataset.get_catalog_number_namespace(get_field_value('institutionCode'), get_field_value('collectionCode'))

    self.metadata.delete('error_data')
    if ready
      self.status = 'Ready'
    else
      self.status = 'NotReady'
      self.metadata['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