Module: CollectionObject::DwcExtensions

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

Defined Under Namespace

Modules: TaxonworksExtensions

Constant Summary

Constants included from Shared::IsDwcOccurrence

Shared::IsDwcOccurrence::DWC_DELIMITER, Shared::IsDwcOccurrence::VIEW_EXCLUSIONS

Instance Method Summary collapse

Methods included from Shared::IsDwcOccurrence

#dwc_occurrence_attribute_values, #dwc_occurrence_attributes, #dwc_occurrence_id, #get_dwc_occurrence, #set_dwc_occurrence

Instance Method Details

TODO: likeley a helper



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# File 'app/models/collection_object/dwc_extensions.rb', line 156

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 146

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 151

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 244

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 177

def dwc_catalog_number
  catalog_number_cached # via delegation
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 169

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

#dwc_event_time ⇒ Object 



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# File 'app/models/collection_object/dwc_extensions.rb', line 286

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_higher_classification ⇒ Object 



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# File 'app/models/collection_object/dwc_extensions.rb', line 260

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_individual_count ⇒ Object

TODO: handle ranged lots



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# File 'app/models/collection_object/dwc_extensions.rb', line 282

def dwc_individual_count
  total
end

#dwc_institution_code ⇒ Object

we assert custody, NOT ownership



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

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 276

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

TODO: duplicated in CE extension



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

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_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 233

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

#dwc_occurrence_remarks ⇒ Object

dwc.tdwg.org/list/#dwc_georeferenceRemarks



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# File 'app/models/collection_object/dwc_extensions.rb', line 141

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 136

def dwc_occurrence_status
  'present'
end

#dwc_other_catalog_numbers ⇒ Object 



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# File 'app/models/collection_object/dwc_extensions.rb', line 181

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_preparations ⇒ Object 



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# File 'app/models/collection_object/dwc_extensions.rb', line 299

def dwc_preparations
  preparation_type_name
end

#dwc_record_number ⇒ Object 



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# File 'app/models/collection_object/dwc_extensions.rb', line 173

def dwc_record_number
  record_number_cached # via delegation
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 239

def dwc_sex
  biocuration_classes.tagged_with_uri(::DWC_ATTRIBUTE_URIS[:sex])
    .pluck(:name)&.join(', ').presence # TODO: Use delimeter!
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 254

def dwc_type_status
  type_materials.all.collect{|t|
    ApplicationController.helpers.label_for_type_material(t)
  }.join(CollectionObject::DWC_DELIMITER).presence
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 130

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

#is_fossil? ⇒ Boolean

Returns:

  • (Boolean) 


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# File 'app/models/collection_object/dwc_extensions.rb', line 249

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