Class: DatasetRecord::DarwinCore::Taxon

Inherits:

DatasetRecord::DarwinCore

Object
ActiveRecord::Base
ApplicationRecord
DatasetRecord
DatasetRecord::DarwinCore
DatasetRecord::DarwinCore::Taxon

show all

Defined in:: app/models/dataset_record/darwin_core/taxon.rb

Constant Summary collapse

KNOWN_KEYS_COMBINATIONS =

[
  %i{uninomial},
  %i{uninomial rank parent},
  %i{genus species},
  %i{genus species infraspecies},
  %i{genus subgenus species},
  %i{genus subgenus species infraspecies}
].freeze

PARSE_DETAILS_KEYS =

%i(uninomial genus species infraspecies).freeze

ORIGINAL_COMBINATION_RANKS =

{
  genus: 'TaxonNameRelationship::OriginalCombination::OriginalGenus',
  subgenus: 'TaxonNameRelationship::OriginalCombination::OriginalSubgenus',
  species: 'TaxonNameRelationship::OriginalCombination::OriginalSpecies',
  subspecies: 'TaxonNameRelationship::OriginalCombination::OriginalSubspecies',
  variety: 'TaxonNameRelationship::OriginalCombination::OriginalVariety',
  form: 'TaxonNameRelationship::OriginalCombination::OriginalForm'
}.freeze

Instance Attribute Summary

Attributes inherited from DatasetRecord

#metadata, #status

Instance Method Summary collapse

#create_parent_element_hash ⇒ Hash{Symbol => TaxonName} private

Create a hash of parents from checklist.
#data_field_changed(index, value) ⇒ Object private

TODO add restage button/trigger when relevant fields change.
#dependencies_imported?(taxon_id) ⇒ Boolean private

Check if all dependencies of a taxonID are imported.
#find_by_taxonID(taxon_id) ⇒ Object private
#get_original_combination ⇒ Object private
#get_parent ⇒ Object private
#get_taxon_name_from_taxon_id(taxon_id) ⇒ TaxonName private
#import(dwc_data_attributes = {}) ⇒ Object

rubocop:disable Metric/MethodLength.

Instance Method Details

#create_parent_element_hash ⇒ `Hash{Symbol => TaxonName}` (private)

Create a hash of parents from checklist

Returns:

(Hash{Symbol => TaxonName}) —

hash of ranks and TaxonNames of genus and species rank parents

# File 'app/models/dataset_record/darwin_core/taxon.rb', line 548

def create_parent_element_hash
  parent = get_parent

  # if parent is root, return empty hash
  return {} unless parent

  parents = [parent]

  while (next_parent = find_by_taxonID(parents[-1].metadata['parent']))
    parents << next_parent
  end

  # convert DatasetRecords into hash of rank, protonym pairs
  parent_elements = parents.to_h do |p|
    [
      # Key is rank (as set in checklist file)
      DatasetRecordField.where(dataset_record: p)
                        .at(get_field_mapping(:taxonRank))
        &.pick(:value)
        &.downcase&.to_sym,
      # value is Protonym
      TaxonName.find(p.metadata['imported_objects']['taxon_name']['id'])
    ]

  end

  parent_elements.filter! { |p_rank, _| ORIGINAL_COMBINATION_RANKS.has_key?(p_rank) }
  parent_elements
end

#data_field_changed(index, value) ⇒ `Object` (private)

TODO add restage button/trigger when relevant fields change. Changing an id here means recalculating dependencies

# File 'app/models/dataset_record/darwin_core/taxon.rb', line 631

def data_field_changed(index, value)
  # if index == get_field_mapping(:parentNameUsageID) && status == "NotReady"
  #   self.status = "Ready" if %w[Ready Imported].include? get_parent&.status
  # end
end

#dependencies_imported?(taxon_id) ⇒ `Boolean` (private)

Check if all dependencies of a taxonID are imported

Returns:

(Boolean)

# File 'app/models/dataset_record/darwin_core/taxon.rb', line 615

def dependencies_imported?(taxon_id)
  dependency_taxon_ids = DatasetRecord::DarwinCore::Taxon.where(id: import_dataset.core_records_fields
                                                                                  .at(get_field_mapping(:taxonID))
                                                                                  .with_value(taxon_id.to_s)
                                                                                  .select(:dataset_record_id)
  ).pick(:metadata)['dependencies']

  DatasetRecord::DarwinCore::Taxon.where(id: import_dataset.core_records_fields
                                                           .at(get_field_mapping(:taxonID))
                                                           .with_values(dependency_taxon_ids.map { |d| d.to_s })
                                                           .select(:dataset_record_id)
  ).where(status: 'Imported').count == dependency_taxon_ids.length

end

#find_by_taxonID(taxon_id) ⇒ `Object` (private)

# File 'app/models/dataset_record/darwin_core/taxon.rb', line 597

def find_by_taxonID(taxon_id)
  DatasetRecord::DarwinCore::Taxon.where(id: import_dataset.core_records_fields
                                                           .at(get_field_mapping(:taxonID))
                                                           .with_value(taxon_id.to_s)
                                                           .select(:dataset_record_id)
  ).first
end

#get_original_combination ⇒ `Object` (private)

# File 'app/models/dataset_record/darwin_core/taxon.rb', line 588

def get_original_combination
  DatasetRecord::DarwinCore::Taxon.where(id: import_dataset.core_records_fields
                                                           .at(get_field_mapping(:taxonID))
                                                           .with_value(get_field_value(:originalNameUsageID))
                                                           .select(:dataset_record_id)
  ).first
end

#get_parent ⇒ `Object` (private)

# File 'app/models/dataset_record/darwin_core/taxon.rb', line 579

def get_parent
  DatasetRecord::DarwinCore::Taxon.where(id: import_dataset.core_records_fields
                                                           .at(get_field_mapping(:taxonID))
                                                           .with_value(get_field_value(:parentNameUsageID))
                                                           .select(:dataset_record_id)
  ).first
end

#get_taxon_name_from_taxon_id(taxon_id) ⇒ `TaxonName` (private)

Returns:

(TaxonName)

# File 'app/models/dataset_record/darwin_core/taxon.rb', line 606

def get_taxon_name_from_taxon_id(taxon_id)
  TaxonName.find(DatasetRecord::DarwinCore::Taxon.where(id: import_dataset.core_records_fields
                                                                          .at(get_field_mapping(:taxonID))
                                                                          .with_value(taxon_id.to_s)
                                                                          .select(:dataset_record_id)
  ).pick(:metadata)['imported_objects']['taxon_name']['id'])
end

#import(dwc_data_attributes = {}) ⇒ `Object`

rubocop:disable Metric/MethodLength

# File 'app/models/dataset_record/darwin_core/taxon.rb', line 26

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

      nomenclature_code = get_field_value('nomenclaturalCode')&.downcase&.to_sym || import_dataset.default_nomenclatural_code
      unless Ranks::CODES.include?(nomenclature_code)
        raise DarwinCore::InvalidData.new(
          { "nomenclaturalCode": ["Unrecognized nomenclatural code #{get_field_value('nomenclaturalCode')}"] }
        )
      end
      # parse_results_details = Biodiversity::Parser.parse(get_field_value('scientificName') || '')[:details]&.values&.first

      parse_results = Biodiversity::Parser.parse(get_field_value(:scientificName) || '')
      parse_results_details = parse_results[:details]
      parse_results_details = (parse_results_details.keys - PARSE_DETAILS_KEYS).empty? ? parse_results_details.values.first : nil if parse_results_details

      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 (1..3).include?(parse_results[:quality]) && parse_results_details&.is_a?(Hash)

      raise 'UNKNOWN NAME DETAILS COMBINATION' unless KNOWN_KEYS_COMBINATIONS.include?(parse_results_details.keys - [:authorship])

      name_key = parse_results_details[:uninomial] ? :uninomial : (parse_results_details.keys - [:authorship]).last
      name_details = parse_results_details[name_key]

      name = name_details.kind_of?(Array) ? name_details.first[:value] : name_details

      authorship = parse_results_details.dig(:authorship, :normalized) || get_field_value('scientificNameAuthorship')

      author_name = nil
      year = nil

      # split authorship into name and year
      if authorship.present?
        if nomenclature_code == :iczn
          if (authorship_matchdata = authorship.match(/\(?(?<author>.+),? (?<year>\d{4})?\)?/))

            # regex will include comma, no easy way around it
            author_name = authorship_matchdata[:author].delete_suffix(',')
            year = authorship_matchdata[:year]

            # author name should be wrapped in parentheses if the verbatim authorship was
            if authorship.start_with?('(') and authorship.end_with?(')')
              author_name = '(' + author_name + ')'
            end
          end

        else
          # Fall back to simple name + date parsing if not iczn
          author_name = Utilities::Strings.verbatim_author(authorship)
          year = Utilities::Strings.year_of_publication(authorship)
        end
      end

      if year && (name_published_in_year = get_field_value('namePublishedInYear')) &&
        year != name_published_in_year
        raise DarwinCore::InvalidData.new(
          { "namePublishedInYear": ["parsed year from scientificName or scientificNameAuthorship (#{year}) "\
                                    "does not match namePublishedInYear (#{name_published_in_year})"]
          })
      end
      year ||= get_field_value('namePublishedInYear')

      # TODO validate that rank is a real rank, otherwise Combination will crash on find_or_initialize_by
      rank = get_field_value('taxonRank')
      is_hybrid = metadata['is_hybrid'] # TODO: NO...

      if metadata['parent'].nil?
        if self.import_dataset.use_existing_hierarchy?
          protonym_attributes = { name:, #
                                cached: get_field_value(:scientificName),
                                rank_class: Ranks.lookup(nomenclature_code, rank),
                                verbatim_author: author_name,
                                year_of_publication: year}
          potential_protonyms = TaxonName.where(protonym_attributes.merge({project:})) # merged project here so data is not leaked in error messages.

          if potential_protonyms.count == 1
            parent = potential_protonyms.first.parent
          elsif potential_protonyms.count > 1
            matching_protonyms = potential_protonyms.map { |proto| "[id: #{proto.id} #{proto.cached_html_name_and_author_year}]" }.join(', ')
            raise DarwinCore::InvalidData.new(
              { "parentNameUsageID": ["parent ID is blank, 'use existing taxon hierarchy' is enabled in settings, " \
                                        "and multiple TaxonNames matched #{protonym_attributes}: #{matching_protonyms}"] })
          else
            raise DarwinCore::InvalidData.new(
              { "parentNameUsageID": ["parent ID is blank, 'use existing taxon hierarchy' is enabled in settings, " \
                                        "and no TaxonNames matched #{protonym_attributes}"] })
          end
        else
          parent = project.root_taxon_name
        end
      else
        parent = TaxonName.find(get_parent.metadata['imported_objects']['taxon_name']['id'])
      end

      if metadata['type'] == 'protonym'

        # if the name is a synonym, we should use the valid taxon's rank and parent
        # I *think* it's ok to do the same for homonyms, since we could have case where homonym's parent is a synonym,
        # and it has been moved from species to subspecies rank.
        # we fetch parent from the source file when calculating original combination, so it's ok to modify it here.
        if metadata['has_external_accepted_name']
          valid_name = get_taxon_name_from_taxon_id(get_field_value(:acceptedNameUsageID))
          rank = valid_name.rank
          parent = valid_name.parent
        elsif parent.is_a? Combination # this can happen when the name is unavailable, it's not a synonym so it doesn't point to anything else
          parent = parent.finest_protonym
        end

        taxon_name = Protonym.find_or_initialize_by({
          name:,
          parent:,
          rank_class: Ranks.lookup(nomenclature_code, rank),
          # also_create_otu: false,
          verbatim_author: author_name,
          year_of_publication: year,
          project:
        })

        unless taxon_name.persisted?
          taxon_name.taxon_name_classifications.build(type: TaxonNameClassification::Icn::Hybrid) if is_hybrid
          taxon_name.data_attributes.build(import_predicate: 'DwC-A import metadata', type: 'ImportAttribute', value: {
            scientificName: get_field_value('scientificName'),
            scientificNameAuthorship: get_field_value('scientificNameAuthorship'),
            taxonRank: get_field_value('taxonRank'),
            metadata:
          })

        end

        # make OC relationships to OC ancestors
        # can't make original combination with Root or if matching pre-existing taxon name
        # Do not make original combination if we assumed the value.
        if metadata['parent'].present? && (metadata.fetch('create_original_combination', true) == true)

          # Loop through parents of original combination based on parentNameUsageID, not TW parent
          # this way we get the name as intended, not with any valid/current names
          original_combination_parents = [find_by_taxonID(get_original_combination.metadata['parent'])].compact

          # build list of parent DatasetRecords
          if original_combination_parents.size > 0
            while (next_parent = find_by_taxonID(original_combination_parents[-1]&.metadata['parent']))
              original_combination_parents << next_parent
            end
          end

          # in cases where the taxon original combination is subgenus of self eg Sima (Sima), the first parent of the list
          # should be dropped because it hasn't been imported yet
          original_combination_parents = original_combination_parents.drop_while {|p| p.status != 'Imported' }

          # convert DatasetRecords into list of Protonyms
          original_combination_parents.map! do |p|
            h = {}
            h[:protonym] = TaxonName.find(p.metadata['imported_objects']['taxon_name']['id'])
            h[:rank] = DatasetRecordField.where(dataset_record_id: p)
                                         .at(get_field_mapping(:taxonRank))
                                         .pick(:value)
                                         .downcase
            h
          end

          original_combination_parents.each do |ancestor|
            ancestor_protonym = ancestor[:protonym]
            ancestor_rank = ancestor[:rank]

            # If OC parent is combination, need to create relationship for lowest element
            if ancestor_protonym.is_a?(Combination)
              ancestor_protonym = ancestor[:protonym].finest_protonym
            end

            if (rank_in_type = ORIGINAL_COMBINATION_RANKS[ancestor_rank&.downcase&.to_sym])

              # if the subgenus is newer than taxon_name's authorship, skip it (the name must have been classified in the subgenus later)
              next if ancestor_rank&.downcase&.to_sym == :subgenus &&
                !ancestor_protonym.year_integer.nil? &&
                !taxon_name.year_integer.nil? &&
                ancestor_protonym.year_integer > taxon_name.year_integer

              taxon_name.save!
              TaxonNameRelationship.find_or_create_by!(type: rank_in_type, subject_taxon_name: ancestor_protonym, object_taxon_name: taxon_name)
            end
          end
        end

        # don't create OC relationship with self if OC was assumed, default to true for any datasets
        # created before this feature existed (since creating OC was always expected then)
        if metadata.fetch('create_original_combination', true)

          # when creating the OC record pointing to self,
          # can't assume OC rank is same as valid rank, need to look at OC row to find real rank
          # This is easier for the end-user than adding OC to protonym when importing the OC row,
          # but might be more complex to code

          # get OC dataset_record_id so we can pull the taxonRank from it.
          oc_dataset_record_id = import_dataset.core_records_fields
                                               .at(get_field_mapping(:taxonID))
                                               .with_value(get_field_value(:originalNameUsageID))
                                               .pick(:dataset_record_id)

          oc_protonym_rank = import_dataset.core_records_fields
                                           .where(dataset_record_id: oc_dataset_record_id)
                                           .at(get_field_mapping(:taxonRank))
                                           .pick(:value)
                                           .downcase.to_sym

          if ORIGINAL_COMBINATION_RANKS.has_key?(oc_protonym_rank)
            TaxonNameRelationship.create_with(subject_taxon_name: taxon_name).find_or_create_by!(
              type: ORIGINAL_COMBINATION_RANKS[oc_protonym_rank],
              object_taxon_name: taxon_name)

            # detect if current name rank is genus and original combination is with self at subgenus level, eg Aus (Aus)
            # if so, generate OC relationship with genus (since oc_protonym_rank will be subgenus)
            if oc_protonym_rank == :subgenus && get_field_value('taxonRank').downcase == 'genus' &&
              (get_original_combination&.metadata['parent'] == get_field_value('taxonID'))
              TaxonNameRelationship.create_with(subject_taxon_name: taxon_name).find_or_create_by!(
                type: ORIGINAL_COMBINATION_RANKS[:genus],
                object_taxon_name: taxon_name)
            end
          end
        end

        # if taxonomicStatus is a synonym or homonym, create the relationship to acceptedNameUsageID
        if metadata['has_external_accepted_name']
          valid_name = get_taxon_name_from_taxon_id(get_field_value(:acceptedNameUsageID))

          synonym_classes = {
            iczn: {
              synonym: 'TaxonNameRelationship::Iczn::Invalidating::Synonym',
              homonym: 'TaxonNameRelationship::Iczn::Invalidating::Synonym::Objective::ReplacedHomonym',
              misspelling: 'TaxonNameRelationship::Iczn::Invalidating::Usage::Misspelling',
              'original misspelling':  'TaxonNameRelationship::Iczn::Invalidating::Usage::IncorrectOriginalSpelling',

              # invalid can be either a relationship or classification, depending on if 'has_external_accepted_name' is true or not
              invalid: 'TaxonNameRelationship::Iczn::Invalidating'
            },
            # TODO support other nomenclatural codes
            # icnp: {
            #   synonym: "TaxonNameRelationship::Icnp::Unaccepting::Synonym",
            #   homonym: "TaxonNameRelationship::Icnp::Unaccepting::Homonym"
            # },
            # icn: {
            #   synonym: "TaxonNameRelationship::Icn::Unaccepting::Synonym",
            #   homonym: "TaxonNameRelationship::Icn::Unaccepting::Homonym"
            # }
          }.freeze

          if (status = get_field_value(:taxonomicStatus)&.downcase)

            # workaround to handle cases where Protonym is a synonym, but row marked as synonym has different rank/parent
            # so we use a row that does as the protonym instead. That row could have some other status, but
            # we know it's a synonym.
            if metadata['is_synonym']
              status = :synonym
            end

            type = synonym_classes[nomenclature_code][status.to_sym]


            raise DarwinCore::InvalidData.new(
              { "taxonomicStatus": ['acceptedNameUsageID refers to a different protonym, ' \
                "but status #{status} did not match synonym, homonym, invalid, misspelling or original misspelling."] }) if type.nil?

            taxon_name.taxon_name_relationships.find_or_initialize_by(object_taxon_name: valid_name, type:)

            if status.to_s == 'synonym'
              # if synonym and not same rank as valid, and not original combination,
              # create a combination with the old parent and rank

              if (old_rank = get_field_value('taxonRank').downcase) != rank.downcase &&
                metadata['original_combination'] != get_field_value('taxonID') &&
                ORIGINAL_COMBINATION_RANKS.has_key?(old_rank.downcase.to_sym)

                # save taxon so we can create a combination
                taxon_name.save!

                # stolen from combination handling portion of code
                parent_elements = create_parent_element_hash.transform_values {|v| v.is_a?(Combination) ? v.finest_protonym : v}

                combination_attributes = { **parent_elements }
                combination_attributes[old_rank.downcase] = taxon_name if old_rank

                # Can't use find_or_initialize_by because of dynamic parameters, causes query to fail because ranks are not columns in db
                # => PG::UndefinedTable: ERROR:  missing FROM-clause entry for table "genus"
                # LINE 1: ..."taxon_names" WHERE "taxon_names"."type" = $1 AND "genus"."i...

                taxon_combination_name = Combination.matching_protonyms(**combination_attributes.transform_values { |v| v.id }).first
                taxon_combination_name = Combination.create!(combination_attributes) if taxon_combination_name.nil?
              end
            end

            # Add homonym status (if applicable)
            if status == 'homonym'
              taxon_name.taxon_name_classifications.find_or_initialize_by(type: 'TaxonNameClassification::Iczn::Available::Invalid::Homonym')
            end

          else
            raise DarwinCore::InvalidData.new({ "taxonomicStatus": ['No taxonomic status, but acceptedNameUsageID has different protonym'] })
          end

          # if taxonomicStatus is a homonym, invalid, unavailable, excluded, create the status
          # if it's incertae sedis, create the relationship
          # TODO why have an OR with nil? shouldn't the first condition check that?
        elsif get_field_value(:taxonomicStatus) != 'valid' || get_field_value(:taxonomicStatus).nil?
          status_types = {
            invalid: 'TaxonNameClassification::Iczn::Available::Invalid',
            unavailable: 'TaxonNameClassification::Iczn::Unavailable',
            excluded: 'TaxonNameClassification::Iczn::Unavailable::Excluded',
            'nomen nudum': 'TaxonNameClassification::Iczn::Unavailable::NomenNudum',
            ichnotaxon: 'TaxonNameClassification::Iczn::Fossil::Ichnotaxon',
            fossil: 'TaxonNameClassification::Iczn::Fossil',
            'nomen dubium': 'TaxonNameClassification::Iczn::Available::Valid::NomenDubium'
          }.freeze

          if (status = get_field_value(:taxonomicStatus)&.downcase)

            # if name in incertae sedis, attach to finest level known (usually parent) and add TaxonNameRelationship
            if status == 'incertae sedis'

              # if user has provided a `TW:TaxonNameRelationship:incertae_sedis_in_rank` field, use that to determine
              # which rank of parent should be used for I.S. relationship
              if (verbatim_is_rank = get_field_value('TW:TaxonNameRelationship:incertae_sedis_in_rank'))
                # must save here so that `ancestor_at_rank` works
                # (otherwise could use `ancestors_through_parents` and check rank manually)
                taxon_name.save
                incertae_sedis_parent = taxon_name.ancestor_at_rank(verbatim_is_rank.downcase)

                if incertae_sedis_parent.nil?
                  available_parent_ranks = taxon_name.ancestors.map { |a| "#{a.rank}: #{a.name}" }.join(', ')
                  raise DarwinCore::InvalidData.new({ "TW:TaxonNameRelationship:incertae_sedis_in_rank":
                                                        ["Taxon #{taxon_name.name} does not have a parent at rank #{verbatim_is_rank}.
                                                          Available ancestors are #{available_parent_ranks}.".squish] })
                end

                # Parent should be same as incertae sedis object_taxon
                # Supplying a parent taxonID with a different rank than the incertae sedis parent
                # will an original combination relationship with the old parent, which
                # the ui will render as [Aus] bus, (where the incertae sedis parent is Cus)
                taxon_name.parent = incertae_sedis_parent

              else
                # if parent has uncertain placement in rank, taxon's parent should be changed to whichever taxon the parent's UncertainRelationship is with
                incertae_sedis_parent = parent.iczn_uncertain_placement
                # if parent doesn't have uncertain placement, make relationship with family or subfamily (FamilyGroup)
                incertae_sedis_parent ||= taxon_name.ancestors.with_base_of_rank_class('NomenclaturalRank::Iczn::FamilyGroup').first

                # Parent should be same as incertae sedis object_taxon
                taxon_name.parent = incertae_sedis_parent
              end

              taxon_name.taxon_name_relationships.find_or_initialize_by(
                object_taxon_name: incertae_sedis_parent,
                type: 'TaxonNameRelationship::Iczn::Validating::UncertainPlacement')

            else
              type = status_types[status.to_sym]

              raise DarwinCore::InvalidData.new(
                { "taxonomicStatus": ["Couldn't find a status that matched #{status}.",
                                      "Possible statuses: [#{status_types.keys.join(", ")}]"] }) if type.nil?

              taxon_name.taxon_name_classifications.find_or_initialize_by(type:)
            end
          end
        end

        # Taxon status might not be "fossil" if synonym, homonym, incertae sedis, etc.
        if get_field_value('TW:TaxonNameClassification:Iczn:Fossil')
          taxon_name.taxon_name_classifications.find_or_initialize_by(type: 'TaxonNameClassification::Iczn::Fossil')
        end

        # add gender or part of speech classification if given
        if (gender = get_field_value('TW:TaxonNameClassification:Latinized:Gender'))
          gender_types = {
            masculine: 'TaxonNameClassification::Latinized::Gender::Masculine',
            feminine: 'TaxonNameClassification::Latinized::Gender::Feminine',
            neuter: 'TaxonNameClassification::Latinized::Gender::Neuter'
          }.freeze

          gender_classification = gender_types[gender.downcase.to_sym]

          raise DarwinCore::InvalidData.new({ "TW:TaxonNameClassification:Latinized:Gender": ["Gender #{gender.downcase} is not one of: masculine, feminine, neuter."] }) if gender_classification.nil?

          taxon_name.taxon_name_classifications.find_or_initialize_by(type: gender_classification)

        elsif (part_of_speech = get_field_value('TW:TaxonNameClassification:Latinized:PartOfSpeech'))
          parts_of_speech_types = {
            adjective: 'TaxonNameClassification::Latinized::PartOfSpeech::Adjective',
            participle: 'TaxonNameClassification::Latinized::PartOfSpeech::Participle',
            'noun in apposition': 'TaxonNameClassification::Latinized::PartOfSpeech::NounInApposition',
            'noun in genitive case': 'TaxonNameClassification::Latinized::PartOfSpeech::NounInGenitiveCase'
          }.freeze

          part_of_speech_classification = parts_of_speech_types[part_of_speech.downcase.to_sym]

          raise DarwinCore::InvalidData.new({ "TW:TaxonNameClassification:Latinized:": ["PartOfSpeech #{part_of_speech.downcase} is not one of: adjective, participle, noun in apposition, noun in genitive case."] }) if part_of_speech_classification.nil?

          taxon_name.taxon_name_classifications.find_or_initialize_by(type: part_of_speech_classification)

          # if taxon has different original combination conjugation, and genus has gender, use OC name.
          # It will be conjugated correctly with new genus and the original combination will use the correct conjugation

          if oc_dataset_record_id != self.id &&
            taxon_name.is_species_rank? &&
            taxon_name.ancestor_at_rank('genus').gender_name

            oc_name = import_dataset.core_records_fields
                          .where(dataset_record_id: oc_dataset_record_id)
                          .at(get_field_mapping(:scientificName))
                          .pick(:value)

            finest_oc_name = oc_name.split.last

            # check if OC name is conjugated differently, then see if current name can be conjugated into oc name
            if finest_oc_name != name and taxon_name.predict_three_forms.values.include?(finest_oc_name)
              taxon_name.name = finest_oc_name
            end
          end
        end

      elsif metadata['type'] == 'combination'

        # get protonym from staging metadata
        protonym_record = find_by_taxonID(metadata['protonym_taxon_id'])
        # current_name_record = find_by_taxonID(get_field_value(:originalNameUsageID))

        current_name = Protonym.find(protonym_record.metadata['imported_objects']['taxon_name']['id'])

        # because Combination uses named arguments, we need to get the ranks of the parent names to create the combination
        if parent.is_a?(Combination)
          parent_elements = parent.combination_taxon_names.index_by { |protonym| protonym.rank }

        else
          # parent is a protonym, look at parents in checklist to build combination
          parent_elements = create_parent_element_hash
        end

        combination_attributes = { **parent_elements }
        combination_attributes[rank.downcase] = current_name if rank

        # Can't use find_or_initialize_by because of dynamic parameters, causes query to fail because ranks are not columns in db
        # => PG::UndefinedTable: ERROR:  missing FROM-clause entry for table "genus"
        # LINE 1: ..."taxon_names" WHERE "taxon_names"."type" = $1 AND "genus"."i...

        taxon_name = Combination.matching_protonyms(**combination_attributes.transform_values { |v| v.id }).first
        taxon_name = Combination.new(combination_attributes) if taxon_name.nil?

      else
        raise DarwinCore::InvalidData.new({ "originalNameUsageID": ['Could not determine if name is protonym or combination'] })
      end

      if taxon_name.save
        # TODO add relationships and combinations to this hash
        self.metadata[:imported_objects] = { taxon_name: { id: taxon_name.id } }
        self.status = 'Imported'
      else
        self.status = 'Errored'

        # if error exist with taxon_name_relationships, add their errors under the main attribute (:taxon_name_relationships)
        # eg:
        #   original error: {:taxon_name_relationships=>["is invalid"]}
        #   TNR error: [{:object_taxon_name_id=>["The parent Miomyrmecini and the Incertae Sedis placement (Dolichoderinae) should match"]}]
        #   resulting message: {:taxon_name_relationships=>["is invalid", "The parent Miomyrmecini and the Incertae Sedis placement (Dolichoderinae) should match"]}
        # TODO expand to other relationships, like classifications
        if taxon_name.errors.messages[:taxon_name_relationships]
          # skip relationships with no errors
          errored_relationships = taxon_name.taxon_name_relationships.reject { |r| r.errors.empty? }

          # add error messages to taxon_name.errors[:taxon_name_relationships]
          errored_relationships.each { |r| r.errors.map { |error| taxon_name.errors.add(:taxon_name_relationships, message: error.message) } }
        end

        self.metadata[:error_data] = {
          messages: taxon_name.errors.messages
        }
      end

      save!

      if self.status == 'Imported'
        # loop over dependants, see if all other dependencies are met, if so mark them as ready
        metadata['dependants'].each do |dependant_taxonID|
          if dependencies_imported?(dependant_taxonID)
            DatasetRecord::DarwinCore::Taxon.where(status: 'NotReady',
                                                   id: import_dataset.core_records_fields
                                                                     .at(get_field_mapping(:taxonID))
                                                                     .where(value: dependant_taxonID)
                                                                     .select(:dataset_record_id)
            ).first&.update!(status: 'Ready')
          end
        end
      end
    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[:exception_data] = {
      message: e.message,
      backtrace: e.backtrace
    }
  ensure
    save!
  end

  self
end

Class: DatasetRecord::DarwinCore::Taxon

Constant Summary collapse

Instance Attribute Summary

Attributes inherited from DatasetRecord

Instance Method Summary collapse

Methods inherited from DatasetRecord::DarwinCore

Methods inherited from DatasetRecord

Methods included from Shared::IsData

Methods included from Housekeeping

Methods inherited from ApplicationRecord

Instance Method Details

#create_parent_element_hash ⇒ Hash{Symbol => TaxonName} (private)

#data_field_changed(index, value) ⇒ Object (private)

#dependencies_imported?(taxon_id) ⇒ Boolean (private)

#find_by_taxonID(taxon_id) ⇒ Object (private)

#get_original_combination ⇒ Object (private)

#get_parent ⇒ Object (private)

#get_taxon_name_from_taxon_id(taxon_id) ⇒ TaxonName (private)

#import(dwc_data_attributes = {}) ⇒ Object

#create_parent_element_hash ⇒ `Hash{Symbol => TaxonName}` (private)

#data_field_changed(index, value) ⇒ `Object` (private)

#dependencies_imported?(taxon_id) ⇒ `Boolean` (private)

#find_by_taxonID(taxon_id) ⇒ `Object` (private)

#get_original_combination ⇒ `Object` (private)

#get_parent ⇒ `Object` (private)

#get_taxon_name_from_taxon_id(taxon_id) ⇒ `TaxonName` (private)

#import(dwc_data_attributes = {}) ⇒ `Object`