Module: Shared::Dwc::CollectingEventExtensions

Extended by:
ActiveSupport::Concern
Included in:
CollectionObject::DwcExtensions, FieldOccurrence::DwcExtensions
Defined in:
app/models/concerns/shared/dwc/collecting_event_extensions.rb

Overview

Shared code for data classes that can be indexed/serialized as DwcOccurrence records

Instance Method Summary collapse

Instance Method Details

#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/concerns/shared/dwc/collecting_event_extensions.rb', line 92

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/concerns/shared/dwc/collecting_event_extensions.rb', line 218

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/concerns/shared/dwc/collecting_event_extensions.rb', line 228

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

#dwc_day ⇒ Object 



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# File 'app/models/concerns/shared/dwc/collecting_event_extensions.rb', line 291

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/concerns/shared/dwc/collecting_event_extensions.rb', line 237

def dwc_decimal_latitude
  georeference_attributes[:decimalLatitude]
end

#dwc_decimal_longitude ⇒ Object 



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# File 'app/models/concerns/shared/dwc/collecting_event_extensions.rb', line 241

def dwc_decimal_longitude
  georeference_attributes[:decimalLongitude]
end

#dwc_end_day_of_year ⇒ Object 



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# File 'app/models/concerns/shared/dwc/collecting_event_extensions.rb', line 301

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/concerns/shared/dwc/collecting_event_extensions.rb', line 266

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/concerns/shared/dwc/collecting_event_extensions.rb', line 114

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/concerns/shared/dwc/collecting_event_extensions.rb', line 59

def dwc_event_remarks
  collecting_event&.notes&.collect {|n| n.text}&.join(Export::Dwca::DELIMITER).presence
end

#dwc_event_time ⇒ Object 



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# File 'app/models/concerns/shared/dwc/collecting_event_extensions.rb', line 249

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_field_number ⇒ Object

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



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# File 'app/models/concerns/shared/dwc/collecting_event_extensions.rb', line 109

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/concerns/shared/dwc/collecting_event_extensions.rb', line 71

def dwc_footprint_wkt
  georeference_attributes[:footprintWKT]
end

#dwc_geodetic_datum ⇒ Object 



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# File 'app/models/concerns/shared/dwc/collecting_event_extensions.rb', line 83

def dwc_geodetic_datum
  georeference_attributes[:geodeticDatum]
end

#dwc_georeference_protocol ⇒ Object 



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# File 'app/models/concerns/shared/dwc/collecting_event_extensions.rb', line 306

def dwc_georeference_protocol
  georeference_attributes[:georeferenceProtocol]
end

#dwc_georeference_remarks ⇒ Object 



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# File 'app/models/concerns/shared/dwc/collecting_event_extensions.rb', line 67

def dwc_georeference_remarks
  georeference_attributes[:georeferenceRemarks]
end

#dwc_georeference_sources ⇒ Object 



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# File 'app/models/concerns/shared/dwc/collecting_event_extensions.rb', line 63

def dwc_georeference_sources
  georeference_attributes[:georeferenceSources]
end

#dwc_georeferenced_by ⇒ Object 



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# File 'app/models/concerns/shared/dwc/collecting_event_extensions.rb', line 75

def dwc_georeferenced_by
  georeference_attributes[:georeferencedBy]
end

#dwc_georeferenced_date ⇒ Object 



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# File 'app/models/concerns/shared/dwc/collecting_event_extensions.rb', line 79

def dwc_georeferenced_date
  georeference_attributes[:georeferencedDate]
end

#dwc_habitat ⇒ Object

Prioritize the curated AssertedEnvironments (ENVO terms) over the free-text verbatim_habitat, falling back to the latter when none have been asserted.



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# File 'app/models/concerns/shared/dwc/collecting_event_extensions.rb', line 180

def dwc_habitat
  return nil unless collecting_event

  collecting_event.asserted_environments.order(:position).pluck(:uri_label)
    .join(Export::Dwca::DELIMITER).presence || collecting_event.verbatim_habitat
end

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

TODO: hmm...



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# File 'app/models/concerns/shared/dwc/collecting_event_extensions.rb', line 120

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_locality ⇒ Object 



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# File 'app/models/concerns/shared/dwc/collecting_event_extensions.rb', line 233

def dwc_locality
  collecting_event.try(:verbatim_locality)
end

#dwc_maximum_depth_in_meters ⇒ Object 



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# File 'app/models/concerns/shared/dwc/collecting_event_extensions.rb', line 148

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/concerns/shared/dwc/collecting_event_extensions.rb', line 165

def dwc_maximum_elevation_in_meters
  collecting_event&.maximum_elevation
end

#dwc_minimum_depth_in_meters ⇒ Object 



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# File 'app/models/concerns/shared/dwc/collecting_event_extensions.rb', line 144

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/concerns/shared/dwc/collecting_event_extensions.rb', line 169

def dwc_minimum_elevation_in_meters
  collecting_event&.minimum_elevation
end

#dwc_month ⇒ Object 



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# File 'app/models/concerns/shared/dwc/collecting_event_extensions.rb', line 285

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_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/concerns/shared/dwc/collecting_event_extensions.rb', line 205

def dwc_recorded_by
  v = nil
  if collecting_event
    v = collecting_event.collectors
      .order('roles.position')
      .map(&:name)
      .join(Export::Dwca::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/concerns/shared/dwc/collecting_event_extensions.rb', line 189

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(Export::Dwca::DELIMITER)&.presence
  end
end

#dwc_sampling_protocol ⇒ Object

TODO: Reconcile with Protocol (capital P) assignments



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# File 'app/models/concerns/shared/dwc/collecting_event_extensions.rb', line 174

def dwc_sampling_protocol
  collecting_event&.verbatim_method
end

#dwc_start_day_of_year ⇒ Object 



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# File 'app/models/concerns/shared/dwc/collecting_event_extensions.rb', line 296

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/concerns/shared/dwc/collecting_event_extensions.rb', line 223

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

#dwc_verbatim_coordinates ⇒ Object 



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# File 'app/models/concerns/shared/dwc/collecting_event_extensions.rb', line 156

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/concerns/shared/dwc/collecting_event_extensions.rb', line 152

def dwc_verbatim_depth
  dwc_internal_attribute_for(:collecting_event, :verbatimDepth)
end

#dwc_verbatim_elevation ⇒ Object 



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# File 'app/models/concerns/shared/dwc/collecting_event_extensions.rb', line 161

def dwc_verbatim_elevation
  collecting_event&.verbatim_elevation
end

#dwc_verbatim_event_date ⇒ Object 



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# File 'app/models/concerns/shared/dwc/collecting_event_extensions.rb', line 262

def dwc_verbatim_event_date
  collecting_event&.verbatim_date
end

#dwc_verbatim_latitude ⇒ Object 



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# File 'app/models/concerns/shared/dwc/collecting_event_extensions.rb', line 100

def dwc_verbatim_latitude
  collecting_event&.verbatim_latitude
end

#dwc_verbatim_locality ⇒ Object 



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# File 'app/models/concerns/shared/dwc/collecting_event_extensions.rb', line 245

def dwc_verbatim_locality
  collecting_event.try(:verbatim_locality)
end

#dwc_verbatim_longitude ⇒ Object 



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# File 'app/models/concerns/shared/dwc/collecting_event_extensions.rb', line 104

def dwc_verbatim_longitude
  collecting_event&.verbatim_longitude
end

#dwc_verbatim_srs ⇒ Object 



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# File 'app/models/concerns/shared/dwc/collecting_event_extensions.rb', line 87

def dwc_verbatim_srs
  georeference_attributes[:dwcVerbatimSrs]
end

#dwc_water_body ⇒ Object 



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# File 'app/models/concerns/shared/dwc/collecting_event_extensions.rb', line 140

def dwc_water_body
  dwc_internal_attribute_for(:collecting_event, :waterBody)
end

#dwc_year ⇒ Object 



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# File 'app/models/concerns/shared/dwc/collecting_event_extensions.rb', line 280

def dwc_year
  return unless collecting_event
  collecting_event.start_date_year.presence
end

#set_georeference_attributes ⇒ Hash

TODO: Revisit

Returns:

  • (Hash) 


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# File 'app/models/concerns/shared/dwc/collecting_event_extensions.rb', line 24

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) if collecting_event.verbatim_latitude)

    h

  when :geographic_area
    h = collecting_event.geographic_area.dwc_georeference_attributes

    if collecting_event.geographic_area_id && (a = collecting_event.attribute_updater(:geographic_area_id))
      h[:georeferencedBy] = User.find_by(id: a)&.name # User might have been deleted if coming from PaperTrail versioning
    end

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

    h
  else
    {}
  end
end