Module: CollectionObject::DwcExtensions

Extended by:
ActiveSupport::Concern
Includes:
TaxonworksExtensions
Included in:
CollectionObject, BiologicalCollectionObject
Defined in:
app/models/collection_object/dwc_extensions.rb

Defined Under Namespace

Modules: TaxonworksExtensions

Instance Method Summary collapse

Instance Method Details

TODO: likeley a helper



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# File 'app/models/collection_object/dwc_extensions.rb', line 213

def api_image_link(image)
  s = ENV['SERVER_NAME']
  if s.nil?
    s ||= 'http://127.0.0.1:3000'
  else
    s = 'https://' + s
  end

  s = s + '/api/v1/images/' + image.image_file_fingerprint # An experiment, use md5 as a proxy for id (also unique id)
end

#dwc_associated_media ⇒ Object

dwc.tdwg.org/terms/#dwc:associatedMedia



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# File 'app/models/collection_object/dwc_extensions.rb', line 203

def dwc_associated_media
  images.collect{|i| api_image_link(i) }.join(CollectionObject::DWC_DELIMITER).presence
end

#dwc_associated_taxa ⇒ Object

dwc.tdwg.org/terms/#dwc:associatedtaxa



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# File 'app/models/collection_object/dwc_extensions.rb', line 208

def dwc_associated_taxa
  dwc_internal_attribute_for(:collection_object, :associatedTaxa)
end

#dwc_caste ⇒ Object 



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# File 'app/models/collection_object/dwc_extensions.rb', line 335

def dwc_caste
  biocuration_classes.tagged_with_uri(::DWC_ATTRIBUTE_URIS[:caste])
     .pluck(:name)&.join(', ').presence #  TODO: Use delimeter!
end

#dwc_catalog_number ⇒ Object 



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# File 'app/models/collection_object/dwc_extensions.rb', line 522

def dwc_catalog_number
  catalog_number_cached # via delegation
end

#dwc_class ⇒ Object 



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# File 'app/models/collection_object/dwc_extensions.rb', line 418

def dwc_class
  taxonomy['class']
end

#dwc_collection_code ⇒ Object 



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# File 'app/models/collection_object/dwc_extensions.rb', line 518

def dwc_collection_code
  catalog_number_namespace&.verbatim_short_name || catalog_number_namespace&.short_name
end

#dwc_coordinate_uncertainty_in_meters ⇒ Object

TODO: extend to Georeferences when we understand how to describe spatial uncertainty



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# File 'app/models/collection_object/dwc_extensions.rb', line 259

def dwc_coordinate_uncertainty_in_meters
  if georeference_attributes[:coordinateUncertaintyInMeters]
    georeference_attributes[:coordinateUncertaintyInMeters]
  else
    collecting_event&.verbatim_geolocation_uncertainty
  end
end

#dwc_country ⇒ Object 



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# File 'app/models/collection_object/dwc_extensions.rb', line 531

def dwc_country
  v = try(:collecting_event).try(:geographic_names)
  v[:country] if v
end

#dwc_county ⇒ Object 



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# File 'app/models/collection_object/dwc_extensions.rb', line 541

def dwc_county
  v = try(:collecting_event).try(:geographic_names)
  v[:county] if v
end

#dwc_date_identified ⇒ Object

ISO 8601:2004(E).



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# File 'app/models/collection_object/dwc_extensions.rb', line 398

def dwc_date_identified
  current_taxon_determination&.date.presence
end

#dwc_day ⇒ Object 



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# File 'app/models/collection_object/dwc_extensions.rb', line 606

def dwc_day
  return unless collecting_event
  collecting_event.start_date_day.presence
end

#dwc_decimal_latitude ⇒ Object 



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# File 'app/models/collection_object/dwc_extensions.rb', line 550

def dwc_decimal_latitude
  georeference_attributes[:decimalLatitude]
end

#dwc_decimal_longitude ⇒ Object 



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# File 'app/models/collection_object/dwc_extensions.rb', line 554

def dwc_decimal_longitude
  georeference_attributes[:decimalLongitude]
end

#dwc_end_day_of_year ⇒ Object 



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# File 'app/models/collection_object/dwc_extensions.rb', line 616

def dwc_end_day_of_year
  return unless collecting_event
  collecting_event.end_day_of_year.presence
end

#dwc_event_date ⇒ Object 



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# File 'app/models/collection_object/dwc_extensions.rb', line 583

def dwc_event_date
  return unless collecting_event

  %w{start_date end_date}
    .map { |d| %w{year month day}
    .map { |p| collecting_event["#{d}_#{p}"] }
    .map { |p| '%02d' % p if p } # At least two digits
    }
      .map { |d| d.compact.join('-') }
      .reject(&:blank?)
      .join('/').presence
end

#dwc_event_id ⇒ Object

TODO: Reconcile with eventID github.com/SpeciesFileGroup/taxonworks/issues/2852



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# File 'app/models/collection_object/dwc_extensions.rb', line 370

def dwc_event_id
  return nil unless collecting_event
  collecting_event.identifiers.where(type: 'Identifier::Local::Event').first&.cached
end

#dwc_event_remarks ⇒ Object 



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# File 'app/models/collection_object/dwc_extensions.rb', line 198

def dwc_event_remarks
  collecting_event&.notes&.collect {|n| n.text}&.join(CollectionObject::DWC_DELIMITER)
end

#dwc_event_time ⇒ Object 



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# File 'app/models/collection_object/dwc_extensions.rb', line 566

def dwc_event_time
  return unless collecting_event

  %w{start_time end_time}
    .map { |t| %w{hour minute second}
    .map { |p| collecting_event["#{t}_#{p}"] }
    .map { |p| '%02d' % p if p } # At least two digits
    }
      .map { |t| t.compact.join(':') }
      .reject(&:blank?)
      .join('/').presence
end

#dwc_family ⇒ Object

rs.tdwg.org/dwc/terms/family



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# File 'app/models/collection_object/dwc_extensions.rb', line 432

def dwc_family
  taxonomy['family']
end

#dwc_field_number ⇒ Object

There is no ‘otherEvent*ID`, prioritize formalized over verbatim TODO: Reconcile with eventID github.com/SpeciesFileGroup/taxonworks/issues/2852



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# File 'app/models/collection_object/dwc_extensions.rb', line 364

def dwc_field_number
  return nil unless collecting_event
  collecting_event.identifiers.where(type: 'Identifier::Local::TripCode').first&.cached || collecting_event.verbatim_trip_identifier
end

#dwc_footprint_wkt ⇒ Object 



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# File 'app/models/collection_object/dwc_extensions.rb', line 232

def dwc_footprint_wkt
  georeference_attributes[:footprintWKT]
end

#dwc_genus ⇒ Object

rs.tdwg.org/dwc/terms/genus



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# File 'app/models/collection_object/dwc_extensions.rb', line 452

def dwc_genus
  taxonomy['genus'] && taxonomy['genus'].compact.join(' ').presence
end

#dwc_geodetic_datum ⇒ Object 



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# File 'app/models/collection_object/dwc_extensions.rb', line 244

def dwc_geodetic_datum
  georeference_attributes[:geodeticDatum]
end

#dwc_georeference_protocol ⇒ Object 



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# File 'app/models/collection_object/dwc_extensions.rb', line 625

def dwc_georeference_protocol
  georeference_attributes[:georeferenceProtocol]
end

#dwc_georeference_remarks ⇒ Object 



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# File 'app/models/collection_object/dwc_extensions.rb', line 228

def dwc_georeference_remarks
  georeference_attributes[:georeferenceRemarks]
end

#dwc_georeference_sources ⇒ Object 



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# File 'app/models/collection_object/dwc_extensions.rb', line 224

def dwc_georeference_sources
  georeference_attributes[:georeferenceSources]
end

#dwc_georeferenced_by ⇒ Object 



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# File 'app/models/collection_object/dwc_extensions.rb', line 236

def dwc_georeferenced_by
  georeference_attributes[:georeferencedBy]
end

#dwc_georeferenced_date ⇒ Object

georeferenceDate technically could look at papertrail to see when geographic_area_id appeared



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# File 'app/models/collection_object/dwc_extensions.rb', line 254

def dwc_georeferenced_date
  georeference_attributes[:georeferencedDate]
end

#dwc_higher_classification ⇒ Object 



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# File 'app/models/collection_object/dwc_extensions.rb', line 402

def dwc_higher_classification
  v = taxonomy.values.collect{|a| a.kind_of?(Array) ? a.second : a}
  v.shift
  v.pop
  v.compact
  v.join(CollectionObject::DWC_DELIMITER).presence
end

#dwc_identification_remarks ⇒ Object

dwc.tdwg.org/list/#dwc_identificationRemarks



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# File 'app/models/collection_object/dwc_extensions.rb', line 194

def dwc_identification_remarks
  current_taxon_determination&.notes&.collect { |n| n.text }&.join(CollectionObject::DWC_DELIMITER)
end

#dwc_identified_by ⇒ Object 



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# File 'app/models/collection_object/dwc_extensions.rb', line 498

def dwc_identified_by
  # TaxonWorks allows for groups of determiners to collaborate on a single determination if they collectively came to a conclusion.
  current_taxon_determination&.determiners&.map(&:name)&.join(CollectionObject::DWC_DELIMITER).presence
end

#dwc_identified_by_id ⇒ Object 



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# File 'app/models/collection_object/dwc_extensions.rb', line 503

def dwc_identified_by_id
  # TaxonWorks allows for groups of determiners to collaborate on a single determination if they collectively came to a conclusion.
  current_taxon_determination&.determiners&.map(&:orcid)&.join(CollectionObject::DWC_DELIMITER).presence
end

#dwc_individual_count ⇒ Object

TODO: handle ranged lots



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# File 'app/models/collection_object/dwc_extensions.rb', line 527

def dwc_individual_count
  total
end

#dwc_infraspecific_epithet ⇒ Object 



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# File 'app/models/collection_object/dwc_extensions.rb', line 379

def dwc_infraspecific_epithet
  %w{variety form subspecies}.each do |n| # add more as observed
    return taxonomy[n].last if taxonomy[n]
  end
  nil
end

#dwc_institution_code ⇒ Object

we assert custody, NOT ownership



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# File 'app/models/collection_object/dwc_extensions.rb', line 509

def dwc_institution_code
  repository_acronym
end

#dwc_institution_id ⇒ Object

we assert custody, NOT ownership



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# File 'app/models/collection_object/dwc_extensions.rb', line 514

def dwc_institution_id
  repository_url
end

#dwc_internal_attribute_for(target = :collection_object, dwc_term_name) ⇒ Object 



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# File 'app/models/collection_object/dwc_extensions.rb', line 287

def dwc_internal_attribute_for(target = :collection_object, dwc_term_name)
  return nil if dwc_term_name.nil?

  case target
  when  :collecting_event
    return nil unless collecting_event
    collecting_event.internal_attributes.includes(:predicate)
      .where(
        controlled_vocabulary_terms: {uri: ::DWC_ATTRIBUTE_URIS[dwc_term_name.to_sym] })
      .pluck(:value)&.join(', ').presence
  when :collection_object
    internal_attributes.includes(:predicate)
      .where(
        controlled_vocabulary_terms: {uri: ::DWC_ATTRIBUTE_URIS[dwc_term_name.to_sym] })
      .pluck(:value)&.join(', ').presence
  else
    nil
  end
end

#dwc_kingdom ⇒ Object 



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# File 'app/models/collection_object/dwc_extensions.rb', line 410

def dwc_kingdom
  taxonomy['kingdom']
end

#dwc_life_stage ⇒ Object

TODO: consider CVT attributes with Predicates linked to URIs



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# File 'app/models/collection_object/dwc_extensions.rb', line 324

def dwc_life_stage
  biocuration_classes.tagged_with_uri(::DWC_ATTRIBUTE_URIS[:lifeStage])
    .pluck(:name)&.join(', ').presence # `.presence` is a Rails extension
end

#dwc_locality ⇒ Object 



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# File 'app/models/collection_object/dwc_extensions.rb', line 546

def dwc_locality
  collecting_event.try(:verbatim_locality)
end

#dwc_maximum_depth_in_meters ⇒ Object 



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# File 'app/models/collection_object/dwc_extensions.rb', line 315

def dwc_maximum_depth_in_meters
  dwc_internal_attribute_for(:collecting_event, :maximumDepthInMeters)
end

#dwc_maximum_elevation_in_meters ⇒ Object 



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# File 'app/models/collection_object/dwc_extensions.rb', line 349

def dwc_maximum_elevation_in_meters
  collecting_event&.maximum_elevation
end

#dwc_minimum_depth_in_meters ⇒ Object 



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# File 'app/models/collection_object/dwc_extensions.rb', line 311

def dwc_minimum_depth_in_meters
  dwc_internal_attribute_for(:collecting_event, :minimumDepthInMeters)
end

#dwc_minimum_elevation_in_meters ⇒ Object 



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# File 'app/models/collection_object/dwc_extensions.rb', line 353

def dwc_minimum_elevation_in_meters
  collecting_event&.minimum_elevation
end

#dwc_month ⇒ Object 



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# File 'app/models/collection_object/dwc_extensions.rb', line 601

def dwc_month
  return unless collecting_event
  collecting_event.start_date_month.presence
end

#dwc_nomenclatural_code ⇒ Object 



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# File 'app/models/collection_object/dwc_extensions.rb', line 562

def dwc_nomenclatural_code
  current_otu.try(:taxon_name).try(:nomenclatural_code)
end

#dwc_occurrence_remarks ⇒ Object

dwc.tdwg.org/list/#dwc_georeferenceRemarks



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# File 'app/models/collection_object/dwc_extensions.rb', line 189

def dwc_occurrence_remarks
  notes.collect{|n| n.text}&.join(CollectionObject::DWC_DELIMITER)
end

#dwc_occurrence_status ⇒ Object 



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# File 'app/models/collection_object/dwc_extensions.rb', line 184

def dwc_occurrence_status
  'present'
end

#dwc_order ⇒ Object 



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# File 'app/models/collection_object/dwc_extensions.rb', line 422

def dwc_order
  taxonomy['order']
end

#dwc_other_catalog_numbers ⇒ Object 



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# File 'app/models/collection_object/dwc_extensions.rb', line 275

def dwc_other_catalog_numbers
  i = identifiers.where.not('type ilike ?', 'Identifier::Global::Uuid%').order(:position).to_a
  i.shift
  i.map(&:cached).join(CollectionObject::DWC_DELIMITER).presence
end

#dwc_phylum ⇒ Object 



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# File 'app/models/collection_object/dwc_extensions.rb', line 414

def dwc_phylum
  taxonomy['phylum']
end

#dwc_preparations ⇒ Object 



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# File 'app/models/collection_object/dwc_extensions.rb', line 621

def dwc_preparations
  preparation_type_name
end

#dwc_previous_identifications ⇒ Object 



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# File 'app/models/collection_object/dwc_extensions.rb', line 281

def dwc_previous_identifications
  a = taxon_determinations.order(:position).to_a
  a.shift
  a.collect{|d| ApplicationController.helpers.label_for_taxon_determination(d)}.join(CollectionObject::DWC_DELIMITER).presence
end

#dwc_recorded_by ⇒ Object

Definition: A list (concatenated and separated) of names of people, groups, or organizations responsible for recording the original Occurrence. The primary collector or observer, especially one who applies a personal identifier (recordNumber), should be listed first.

This was interpreted as collectors (in the field in this context), not those who recorded other aspects of the data.



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# File 'app/models/collection_object/dwc_extensions.rb', line 472

def dwc_recorded_by
  v = nil
  if collecting_event
    v = collecting_event.collectors
      .order('roles.position')
      .map(&:name)
      .join(CollectionObject::DWC_DELIMITER)
      .presence
    v = collecting_event.verbatim_collectors.presence if v.blank?
  end
  v
end

#dwc_recorded_by_id ⇒ Object

See dwc_recorded_by TODO: Expand to any GlobalIdentifier



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# File 'app/models/collection_object/dwc_extensions.rb', line 487

def dwc_recorded_by_id
  if collecting_event
    collecting_event.collectors
      .order('roles.position')
      .map(&:orcid)
      .compact
      .join(CollectionObject::DWC_DELIMITER)
      .presence
  end
end

#dwc_sampling_protocol ⇒ Object

TODO: Reconcile with Protocol (capital P) assignments



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# File 'app/models/collection_object/dwc_extensions.rb', line 358

def dwc_sampling_protocol
  collecting_event&.verbatim_method
end

#dwc_scientific_name ⇒ Object 



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# File 'app/models/collection_object/dwc_extensions.rb', line 461

def dwc_scientific_name
  current_taxon_name.try(:cached_name_and_author_year)
end

#dwc_sex ⇒ Object

TODO: consider CVT attributes with Predicates linked to URIs



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# File 'app/models/collection_object/dwc_extensions.rb', line 330

def dwc_sex
  biocuration_classes.tagged_with_uri(::DWC_ATTRIBUTE_URIS[:sex])
    .pluck(:name)&.join(', ').presence # TODO: Use delimeter!
end

#dwc_specific_epithet ⇒ Object

rs.tdwg.org/dwc/terms/species



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# File 'app/models/collection_object/dwc_extensions.rb', line 457

def dwc_specific_epithet
  taxonomy['species'] && taxonomy['species'].compact.join(' ').presence
end

#dwc_start_day_of_year ⇒ Object 



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# File 'app/models/collection_object/dwc_extensions.rb', line 611

def dwc_start_day_of_year
  return unless collecting_event
  collecting_event.start_day_of_year.presence
end

#dwc_state_province ⇒ Object 



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# File 'app/models/collection_object/dwc_extensions.rb', line 536

def dwc_state_province
  v = try(:collecting_event).try(:geographic_names)
  v[:state] if v
end

#dwc_subfamily ⇒ Object

rs.tdwg.org/dwc/terms/subfamily



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# File 'app/models/collection_object/dwc_extensions.rb', line 437

def dwc_subfamily
  taxonomy['subfamily']
end

#dwc_subtribe ⇒ Object

rs.tdwg.org/dwc/terms/subtribe



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# File 'app/models/collection_object/dwc_extensions.rb', line 447

def dwc_subtribe
  taxonomy['subtribe']
end

#dwc_superfamily ⇒ Object

rs.tdwg.org/dwc/terms/superfamily



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# File 'app/models/collection_object/dwc_extensions.rb', line 427

def dwc_superfamily
  taxonomy['superfamily']
end

#dwc_taxon_name_authorship ⇒ Object 



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# File 'app/models/collection_object/dwc_extensions.rb', line 465

def dwc_taxon_name_authorship
  current_taxon_name.try(:cached_author_year)
end

#dwc_taxon_rank ⇒ Object 



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# File 'app/models/collection_object/dwc_extensions.rb', line 386

def dwc_taxon_rank
  current_taxon_name&.rank
end

#dwc_tribe ⇒ Object

rs.tdwg.org/dwc/terms/tribe



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# File 'app/models/collection_object/dwc_extensions.rb', line 442

def dwc_tribe
  taxonomy['tribe']
end

#dwc_type_status ⇒ Object

holotype of Ctenomys sociabilis. Pearson O. P., and M. I. Christie. 1985. Historia Natural, 5(37):388, holotype of Pinus abies | holotype of Picea abies



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# File 'app/models/collection_object/dwc_extensions.rb', line 391

def dwc_type_status
  type_materials.all.collect{|t|
    ApplicationController.helpers.label_for_type_material(t)
  }.join(CollectionObject::DWC_DELIMITER).presence
end

#dwc_verbatim_coordinates ⇒ Object 



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# File 'app/models/collection_object/dwc_extensions.rb', line 340

def dwc_verbatim_coordinates
  return nil unless collecting_event
  [collecting_event.verbatim_latitude, collecting_event.verbatim_longitude].compact.join(' ').presence
end

#dwc_verbatim_depth ⇒ Object 



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# File 'app/models/collection_object/dwc_extensions.rb', line 319

def dwc_verbatim_depth
  dwc_internal_attribute_for(:collecting_event, :verbatimDepth)
end

#dwc_verbatim_elevation ⇒ Object 



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# File 'app/models/collection_object/dwc_extensions.rb', line 345

def dwc_verbatim_elevation
  collecting_event&.verbatim_elevation
end

#dwc_verbatim_event_date ⇒ Object 



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# File 'app/models/collection_object/dwc_extensions.rb', line 579

def dwc_verbatim_event_date
  collecting_event&.verbatim_date
end

#dwc_verbatim_habitat ⇒ Object 



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# File 'app/models/collection_object/dwc_extensions.rb', line 375

def dwc_verbatim_habitat
  collecting_event&.verbatim_habitat
end

#dwc_verbatim_label ⇒ Object

use buffered if any if not check CE verbatim_label



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# File 'app/models/collection_object/dwc_extensions.rb', line 178

def dwc_verbatim_label
  b = [buffered_collecting_event, buffered_determinations, buffered_other_labels].compact
  return  b.join("\n\n") if b.present?
  collecting_event&.verbatim_label.presence
end

#dwc_verbatim_latitude ⇒ Object 



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# File 'app/models/collection_object/dwc_extensions.rb', line 267

def dwc_verbatim_latitude
  collecting_event&.verbatim_latitude
end

#dwc_verbatim_locality ⇒ Object 



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# File 'app/models/collection_object/dwc_extensions.rb', line 558

def dwc_verbatim_locality
  collecting_event.try(:verbatim_locality)
end

#dwc_verbatim_longitude ⇒ Object 



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# File 'app/models/collection_object/dwc_extensions.rb', line 271

def dwc_verbatim_longitude
  collecting_event&.verbatim_longitude
end

#dwc_verbatim_srs ⇒ Object 



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# File 'app/models/collection_object/dwc_extensions.rb', line 248

def dwc_verbatim_srs
  georeference_attributes[:dwcVerbatimSrs]
end

#dwc_water_body ⇒ Object 



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# File 'app/models/collection_object/dwc_extensions.rb', line 307

def dwc_water_body
  dwc_internal_attribute_for(:collecting_event, :waterBody)
end

#dwc_year ⇒ Object 



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# File 'app/models/collection_object/dwc_extensions.rb', line 596

def dwc_year
  return unless collecting_event
  collecting_event.start_date_year.presence
end

#is_fossil? ⇒ Boolean

Returns:

  • (Boolean) 


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# File 'app/models/collection_object/dwc_extensions.rb', line 172

def is_fossil?
  biocuration_classes.where(uri: DWC_FOSSIL_URI).any?
end

#set_georeference_attributes ⇒ Hash

Returns:

  • (Hash) 


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# File 'app/models/collection_object/dwc_extensions.rb', line 138

def set_georeference_attributes
  case collecting_event&.dwc_georeference_source
  when :georeference
    collecting_event.preferred_georeference.dwc_georeference_attributes
  when :verbatim
    h = collecting_event.dwc_georeference_attributes

    # Our interpretation is now that georeferencedBy is the person who "computed" the
    # values, not transcribed the values.
    #
    #     if a = collecting_event&.attribute_updater(:verbatim_latitude)
    #       h[:georeferencedBy] = User.find(a).name
    #     end

    # verbatim_longitude could technically be different, but...
    h[:georeferencedDate] = collecting_event&.attribute_updated(:verbatim_latitude)

    h

  when :geographic_area
    h = collecting_event.geographic_area.dwc_georeference_attributes
    if a = collecting_event&.attribute_updater(:geographic_area_id)
      h[:georeferencedBy] = User.find(a).name
    end

    h[:georeferencedDate] = collecting_event&.attribute_updated(:geographic_area_id)

    h
  else
    {}
  end
end