Class: DatasetRecord::DarwinCore::Occurrence

Inherits:
DatasetRecord::DarwinCore show all
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

#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 1413

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,
      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 1504

def append_dwc_attribute(attributes, predicate, value)
  attributes << {
    type: 'InternalAttribute',
    predicate: predicate,
    value: 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 1513

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 1390

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: 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: 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 507

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_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 988

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 403

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 



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# File 'app/models/dataset_record/darwin_core/occurrence.rb', line 121

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 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
          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),
        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]))

      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?

          using_default_event_id = false
          if namespace.nil?
            namespace = import_dataset.get_event_id_namespace
            using_default_event_id = true
          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)

          if !using_default_event_id && self.import_dataset.require_tripcode_match_verbatim?
            if (cached_identifier = Identifier::Local.build_cached_prefix(namespace) + event_id) != get_field_value(:eventID)
              error_message = "Computed TripCode #{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

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

        identifier_type.create!({
          identifier_object: collecting_event,
          annotator_batch_mode: true
        }.merge!(identifier_attributes)) unless identifier_attributes.nil?

        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: 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: county, state_province: state_province, country: country, country_code: 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.to_s}:#{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 1441

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) 



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# File 'app/models/dataset_record/darwin_core/occurrence.rb', line 1431

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)

Raises:



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# File 'app/models/dataset_record/darwin_core/occurrence.rb', line 728

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, annotator_batch_mode: true}]) if note

  { collecting_event: collecting_event }
end

#parse_identification_class(taxon_protonym) ⇒ Object (private)

Raises:



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# File 'app/models/dataset_record/darwin_core/occurrence.rb', line 1095

def parse_identification_class(taxon_protonym)
  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]
  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: 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.

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 486

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) 



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# File 'app/models/dataset_record/darwin_core/occurrence.rb', line 837

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,
        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: collecting_event,
    georeference: georeference
  }
end

#parse_occurrence_class ⇒ Object (private) 



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# File 'app/models/dataset_record/darwin_core/occurrence.rb', line 633

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, 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 427

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}"
        unless o.alternate_name.blank?
          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 456

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)

Raises:



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# File 'app/models/dataset_record/darwin_core/occurrence.rb', line 511

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
  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)
  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.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)

Raises:



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# File 'app/models/dataset_record/darwin_core/occurrence.rb', line 1153

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

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

  # 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
    author_name, year = Utilities::Strings.parse_authorship(get_field_value("scientificNameAuthorship"))

    names.last&.merge!({ cached_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 1485

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 1370

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 1466

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) 



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# File 'app/models/dataset_record/darwin_core/occurrence.rb', line 1350

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:

  • (Hash{Symbol=>String, TaxonName}, nil)

Raises:



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# File 'app/models/dataset_record/darwin_core/occurrence.rb', line 974

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+/, ' ')

  # if typeStatus is single word, assume the user wants the specimen name as the type name
  type_scientific_name = (type_status_parsed&.[](:scientificName)&.gsub(/\s+/, ' ') rescue nil) || 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: 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: 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
      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: 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 wildcard_original_protonym.count == 1
        return {
          type_type: 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 383

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.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