Module: Export::Coldp::Files::Name

Defined in:
lib/export/coldp/files/name.rb

Class Method Summary collapse

Class Method Details

.add_original_combination(t, csv) ⇒ Object

Invalid Protonyms are rendered only as their original Combination

Parameters:

  • t (Protonym) —

    only place that var./frm can be handled.



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# File 'lib/export/coldp/files/name.rb', line 46

def self.add_original_combination(t, csv)
  e = t.original_combination_elements

  infraspecific_element = t.original_combination_infraspecific_element(e)
  rank = infraspecific_element ? infraspecific_element.first : t.rank

  id = t.reified_id

  csv << [
    id,                                                                                     # ID
    id,                                                                                     # basionymID, always nil, this is the original
    t.cached_original_combination,                                                          # scientificName
    authorship_field(t, true),                                                              # authorship
    rank,                                                                                   # rank
    nil,                                                                                    # uninomial
    (e[:genus]&.last =~ /NOT SPECIFIED/) ? nil : e[:genus]&.last,                           # genus
    (e[:subgenus]&.last =~ /NOT SPECIFIED/) ? nil : e[:subgenus]&.last&.gsub(/[\)\(]/, ''), # subgenus (no parens) # TODO - optimize to not have to strip these
    (e[:species]&.last =~ /NOT SPECIFIED/) ? nil : e[:species]&.last,                       # species
    infraspecific_element ? infraspecific_element.last : nil,                           # infraspecificEpithet
    nil,                                                                                # publishedInID   |
    nil,                                                                                # publishedInPage |-- Decisions is that these add to Synonym table
    nil,                                                                                # publishedInYear |
    true,                                                                               # original
    code_field(t),                                                                      # code
    nil,                                                                                # status https://api.catalogue.life/vocab/nomStatus
    nil,                                                                                # link (probably TW public or API)
    remarks_field(t),                                                                   # remarks
  ]
end

.authorship_field(taxon_name, original) ⇒ Object

Returns String.

Returns:

  • String



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# File 'lib/export/coldp/files/name.rb', line 21

def self.authorship_field(taxon_name, original)
  original ? taxon_name.original_author_year : taxon_name.cached_author_year
end

.code_field(taxon_name) ⇒ Object 



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# File 'lib/export/coldp/files/name.rb', line 3

def self.code_field(taxon_name)
  case taxon_name.nomenclatural_code
  when :iczn
    'ICZN'
  when :icn
    'ICN'
  when :icnp
    'ICNP'
  when :icvcn
    'ICVCN'
  end
end

.generate(otu, reference_csv = nil) ⇒ Object 



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# File 'lib/export/coldp/files/name.rb', line 78

def self.generate(otu, reference_csv = nil)
  CSV.generate(col_sep: "\t") do |csv|
    csv << %w{
      ID
      basionymID
      scientificName
      authorship
      rank
      uninomial
      genus
      infragenericEpithet
      specificEpithet
      infraspecificEpithet
      publishedInID
      publishedInPage
      publishedInYear
      original
      code
      status
      link
      remarks
    }

    # why we getting double
    unique = {}

    otu.taxon_name.self_and_descendants.each do |name|

      # TODO: handle > quadranomial names (e.g. super species like `Bus (Dus aus aus) aus eus var. fus`
      # Proposal is to exclude names of a specific ranks see taxon.rb
      #
      # Need the next highest valid parent not in this list!!
      # %w{
      #   NomenclaturalRank::Iczn::SpeciesGroup::Supersuperspecies
      #   NomenclaturalRank::Iczn::SpeciesGroup::Superspecies
      # }
      #
      # infragenericEpithet needs to handle subsection (NomenclaturalRank::Icn::GenusGroup::Subsection)

      if name.is_valid?
        data = ::Catalog::Nomenclature::Entry.new(name)

        data.names.each do |t|
          source = t.source

          original = Export::Coldp.original_field(t) # Protonym, no parens
          higher = !t.is_combination? && !t.is_species_rank?

          elements = t.full_name_hash if !higher

          basionym_id = t.reified_id

          # higher, valid, combination and not added
          if higher || t.is_valid? || t.is_combination? # && unique[basionym_id].nil?
            # unique[basionym_id] = true
            csv << [
              t.id,                                               # ID
              basionym_id,                                        # basionymID
              t.cached,                                           # scientificName
              t.cached_author_year,                               # authorship
              t.rank,                                             # rank
              (higher ? t.cached : nil),                          # uninomial
              (higher ? nil : elements['genus']&.last),           # genus and below - IIF species or lower
              (higher ? nil : elements['subgenus']&.last),        # infragenericEpithet
              (higher ? nil : elements['species']&.last),         # specificEpithet
              (higher ? nil : elements['subspecies']&.last),      # infraspecificEpithet
              source&.id,                                         # publishedInID
              source&.pages,                                      # publishedInPage
              t.year_of_publication,                              # publishedInYear
              original,                                           # original
              code_field(t),                                      # code
              nom_status_field(t),                                # nomStatus
              nil,                                                # link (probably TW public or API)
              remarks_field(t),                                   # remarks
            ]
          end

          if (!higher && !t.is_combination? && (!t.is_valid? || t.has_alternate_original?)) && unique[basionym_id].nil?
            unique[basionym_id] = true
            add_original_combination(t, csv)
          end

          Export::Coldp::Files::Reference.add_reference_rows([source].compact, reference_csv) if reference_csv && source
        end
      end
    end
  end
end

.nom_status_field(taxon_name) ⇒ String?

api.catalogue.life/vocab/nomStatus

Returns:

  • (String, nil) 


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# File 'lib/export/coldp/files/name.rb', line 29

def self.nom_status_field(taxon_name)
  case taxon_name.type
  when 'Combination'
    'chresonym' # TODO: remove this for updated semantics
  else
    if taxon_name.is_valid?
      ::TaxonName::NOMEN_VALID[taxon_name.nomenclatural_code]
    else
      c = taxon_name.taxon_name_classifications_for_statuses.order_by_youngest_source_first.first
      c ? c.class::NOMEN_URI : nil # We should also infer status from TaxonNameRelationship see
    end
  end
end

.remarks_field(taxon_name) ⇒ Object 



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# File 'lib/export/coldp/files/name.rb', line 16

def self.remarks_field(taxon_name)
  Utilities::Strings.nil_squish_strip(taxon_name.notes.collect{|n| n.text}.join('; ')) # remarks - !! check for tabs
end