Module: Export::CSV::Dwc::Extension::Checklist::Reference

Defined in:
lib/export/csv/dwc/extension/checklist/reference.rb

Overview

CSV for References/Literature extension (for checklist archives) See http://rs.gbif.org/extension/gbif/1.0/references.xml

Note: Using only DwcOccurrence data, we can only populate bibliographicCitation. Other fields (title, author, date, identifier, etc.) would require accessing the source objects directly.

Constant Summary collapse

GBIF =

Alias for brevity

Export::Dwca::GbifProfile::Reference
CHECKLIST_FIELDS =

Fields used in checklist exports (subset of full GBIF profile). !! Only including fields that can be populated from DwcOccurrence data, which only includes Asserted Distribution data on references.

[
  :id, # Required for DwC-A star joins (taxonID, an OTU UUID)
  :bibliographicCitation
].freeze
HEADERS = 
CHECKLIST_FIELDS
HEADERS_NAMESPACES = 
CHECKLIST_FIELDS.map do |field|
  field == :id ? '' : GBIF::NAMESPACES[field]
end.freeze

Class Method Summary collapse

Class Method Details

.csv(scope, taxon_name_id_to_taxon_id, accepted_name_mode:) ⇒ String

Generate CSV for references extension using only DwcOccurrence data.

Parameters:

  • scope (ActiveRecord::Relation) —

    DwcOccurrence records

  • taxon_name_id_to_taxon_id (Hash) —

    taxon_name_id => OTU UUID (used as dwc:taxonID in the checklist core)

  • accepted_name_mode (String) —

    checklist synonym handling mode

Returns:

  • (String) —

    CSV content



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# File 'lib/export/csv/dwc/extension/checklist/reference.rb', line 32

def self.csv(scope, taxon_name_id_to_taxon_id, accepted_name_mode:)
  tbl = []
  tbl[0] = HEADERS
  seen_rows = {}

  ad_scope = scope
    .where(dwc_occurrence_object_type: 'AssertedDistribution')
    .where.not(associatedReferences: [nil, ''])

  otu_to_taxon_name_id = ad_scope
    .joins('JOIN otus ON otus.id = dwc_occurrences.otu_id')
    .joins('JOIN taxon_names ON taxon_names.id = otus.taxon_name_id')
    .pluck(
      Arel.sql('dwc_occurrences.otu_id'),
      Arel.sql(
        if accepted_name_mode == ::Export::Dwca::Checklist::Data::ACCEPTED_NAME_USAGE_ID
          'taxon_names.id'
        else
          'COALESCE(taxon_names.cached_valid_taxon_name_id, taxon_names.id)'
        end
      )
    )
    .to_h

  ad_scope.find_each do |dwc_occ|
    taxon_name_id = otu_to_taxon_name_id[dwc_occ.otu_id]
    next unless taxon_name_id

    taxon_id = taxon_name_id_to_taxon_id[taxon_name_id]
    next unless taxon_id

    references_str = dwc_occ.associatedReferences

    citations = references_str.split(Export::Dwca::DELIMITER).map(&:strip).reject(&:blank?)

    citations.each do |citation|
      row_key = [taxon_id, citation]
      next if seen_rows[row_key]

      row = [
        taxon_id,
        citation
      ]

      tbl << row
      seen_rows[row_key] = true
    end
  end

  ::Export::Dwca.output_csv(tbl)
end