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 214

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 204

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 209

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 428

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 296

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 498

def dwc_class
  taxonomy['class']
end

#dwc_collection_code ⇒ Object

TODO: optimize by finding all relevant identifiers in one query, then looping through them



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# File 'app/models/collection_object/dwc_extensions.rb', line 288

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 260

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 581

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 591

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 277

def dwc_date_identified
  target_taxon_determination&.date.presence
end

#dwc_day ⇒ Object 



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# File 'app/models/collection_object/dwc_extensions.rb', line 658

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 600

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 604

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 668

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 633

def dwc_event_date
  return unless collecting_event
  return if collecting_event.start_date_year.blank? # don't need to check end, it requires start in model

  %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 



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# File 'app/models/collection_object/dwc_extensions.rb', line 326

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

#dwc_event_remarks ⇒ Object 



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# File 'app/models/collection_object/dwc_extensions.rb', line 199

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

#dwc_event_time ⇒ Object 



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

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 512

def dwc_family
  taxonomy['family']
end

#dwc_field_number ⇒ Object

Prioritize the formalized version of the identifier for data-sharing purposes



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# File 'app/models/collection_object/dwc_extensions.rb', line 321

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

#dwc_footprint_wkt ⇒ Object 



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# File 'app/models/collection_object/dwc_extensions.rb', line 233

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 532

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 245

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 677

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 229

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 225

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 237

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 255

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 482

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 347

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

#dwc_identified_by ⇒ Object 



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

def dwc_identified_by
  # TaxonWorks allows for groups of determiners to collaborate on a single determination if they collectively came to a conclusion.
  target_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 306

def dwc_identified_by_id
  # TaxonWorks allows for groups of determiners to collaborate on a single determination if they collectively came to a conclusion.
  if target_taxon_determination
    target_taxon_determination&.determiners
      .joins(:identifiers)
      .where(identifiers: {type: ['Identifier::Global::Orcid', 'Identifier::Global::Wikidata']})
      .select('identifiers.identifier_object_id, identifiers.cached')
      .unscope(:order)
      .distinct
      .pluck('identifiers.cached')
      .join(CollectionObject::DWC_DELIMITER)&.presence
  end
end

#dwc_individual_count ⇒ Object

TODO: handle ranged lots



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# File 'app/models/collection_object/dwc_extensions.rb', line 577

def dwc_individual_count
  total
end

#dwc_infraspecific_epithet ⇒ Object 



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# File 'app/models/collection_object/dwc_extensions.rb', line 464

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 566

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 571

def dwc_institution_id
  # TODO: identifiers on Repositories
  repository_url || repository_institutional_LSID
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 357

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 490

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 417

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 596

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 385

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 446

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 381

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 450

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 652

def dwc_month
  return unless collecting_event
  return if collecting_event.start_date_month.present? && collecting_event.end_date_month.present?
  collecting_event.start_date_month.presence
end

#dwc_nomenclatural_code ⇒ Object 



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# File 'app/models/collection_object/dwc_extensions.rb', line 612

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 195

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

#dwc_occurrence_status ⇒ Object 



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# File 'app/models/collection_object/dwc_extensions.rb', line 190

def dwc_occurrence_status
  'present'
end

#dwc_order ⇒ Object 



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# File 'app/models/collection_object/dwc_extensions.rb', line 502

def dwc_order
  taxonomy['order']
end

#dwc_other_catalog_numbers ⇒ Object 



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# File 'app/models/collection_object/dwc_extensions.rb', line 300

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 494

def dwc_phylum
  taxonomy['phylum']
end

#dwc_preparations ⇒ Object 



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# File 'app/models/collection_object/dwc_extensions.rb', line 673

def dwc_preparations
  preparation_type_name
end

#dwc_previous_identifications ⇒ Object 



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# File 'app/models/collection_object/dwc_extensions.rb', line 351

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_record_number ⇒ Object 



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# File 'app/models/collection_object/dwc_extensions.rb', line 292

def dwc_record_number
  record_number_cached # via delegation
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 552

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 333

def dwc_recorded_by_id
  if collecting_event
    collecting_event.collectors
      .joins(:identifiers)
      .where(identifiers: {type: ['Identifier::Global::Orcid', 'Identifier::Global::Wikidata']})
      .select('identifiers.identifier_object_id, identifiers.cached')
      .unscope(:order)
      .distinct
      .pluck('identifiers.cached')
      .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 455

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 541

def dwc_scientific_name
  target_taxon_name&.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 423

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 537

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 663

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 586

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 517

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 527

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 507

def dwc_superfamily
  taxonomy['superfamily']
end

#dwc_taxon_name_authorship ⇒ Object 



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# File 'app/models/collection_object/dwc_extensions.rb', line 545

def dwc_taxon_name_authorship
  target_taxon_name&.cached_author_year
end

#dwc_taxon_rank ⇒ Object 



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# File 'app/models/collection_object/dwc_extensions.rb', line 471

def dwc_taxon_rank
  target_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 522

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 476

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 437

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 389

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 442

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 629

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 460

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 184

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 268

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 608

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 272

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 249

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 377

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 647

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 433

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 149

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