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

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

Overview

The names table includes

  • All names strings, even if hanging (= not attached to OTUs/Taxa)

Class Method Summary collapse

Class Method Details

.add_original_combination(t, csv, origin_citation, name_remarks_vocab_id) ⇒ 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 61

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

  infraspecific_element = t.original_combination_infraspecific_element(e)

  rank = nil
  if infraspecific_element
    rank = infraspecific_element.first
    rank = 'forma' if rank == 'form' # CoL preferred string
  else
    [:subspecies, :species, :subgenus, :genus].each do |r|
      if e[r]
        rank = r
        break
      end
    end
  end

  id = t.reified_id
  basionym_id = t.has_misspelling_relationship? ? t.valid_taxon_name.reified_id : id # => t.reified_id
  # case 1 - original combination difference
  # case 2 - misspelling (same combination)

  genus, subgenus, species = nil, nil, nil

  uninomial = nil

  if rank == :genus
    uninomial = e[:genus][1]

  else
    if e[:genus]
      if e[:genus][1] =~ /NOT SPECIFIED/
        genus = nil
      else
        genus = e[:genus][1]
      end
    end

    if e[:subgenus]
      if e[:subgenus][1] =~ /NOT SPECIFIED/
        subgenus = nil
      else
        subgenus = e[:subgenus][1]&.gsub(/[\)\(]/, '')
      end
    end

    if e[:species]
      if e[:species][1] =~ /NOT SPECIFIED/
        species = nil
      else
        species = e[:species][1]
      end
    end

  end

  csv << [
    id,                                                        # ID
    basionym_id,                                               # basionymID
    clean_sic(t.cached_original_combination),                  # scientificName
    authorship_field(t, true),                                 # authorship
    rank,                                                      # rank
    uninomial,                                                 # uninomial
    genus,                                                     # genus
    subgenus,                                                  # subgenus (no parens)
    species,                                                   # species
    infraspecific_element ? infraspecific_element.last : nil,  # infraspecificEpithet
    origin_citation&.source_id,                                # referenceID    |
    origin_citation&.pages,                                    # publishedInPage  | !! All origin citations get added to reference_csv via the main loop, not here
    t.year_of_publication,                                     # publishedInYear  |
    true,                                                      # original
    code_field(t),                                             # code
    nil,                                                       # status https://api.checklistbank.org/vocab/nomStatus
    nil,                                                       # link (probably TW public or API)
    remarks(t, name_remarks_vocab_id),                         # remarks
  ]
end

.authorship_field(taxon_name, original) ⇒ Object

Returns String.

Returns:

  • String



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

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

.clean_sic(name) ⇒ Object 



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# File 'lib/export/coldp/files/name.rb', line 140

def self.clean_sic(name)
  name&.gsub(/\s+\[sic\]/, '') # TODO: remove `&` once cached_original_combination is re-indexed
end

.code_field(taxon_name) ⇒ Object 



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# File 'lib/export/coldp/files/name.rb', line 7

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 146

def self.generate(otu, reference_csv = nil)
   name_total = 0
  CSV.generate(col_sep: "\t") do |csv|
    csv << %w{
      ID
      basionymID
      scientificName
      authorship
      rank
      uninomial
      genus
      infragenericEpithet
      specificEpithet
      infraspecificEpithet
      referenceID
      publishedInPage
      publishedInYear
      original
      code
      status
      link
      remarks
    }

    Current.project_id = otu.project_id
    name_remarks_vocab_id = Predicate.find_by(uri: 'https://github.com/catalogueoflife/coldp#Name.remarks',
                                              project_id: Current.project_id)&.id

    otu.taxon_name.self_and_descendants.that_is_valid
      .pluck(:id, :cached)
      .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)

      name_total += 1

      TaxonName
        .where(cached_valid_taxon_name_id: name[0]) # == .historical_taxon_names
        .where.not("(taxon_names.type = 'Combination' AND taxon_names.cached = ?)", name[1]) # This eliminates Combinations that are identical to the current placement.
        .find_each do |t|

        origin_citation = t.origin_citation

        original = Export::Coldp.original_field(t) # Protonym, no parens

        basionym_id = t.reified_id

        is_genus_species = t.is_genus_or_species_rank?

        # TODO: Subgenus as Genus combination may break this
        is_col_uninomial = !t.is_combination? && ((t.rank == 'genus') || !is_genus_species)

        higher = !t.is_combination? && !is_genus_species

        # TODO: consider faster ways to check for misspellings
        name_string = clean_sic(t.cached) # if higher and misspelling, then it's in name too

        uninomial = nil
        generic_epithet, infrageneric_epithet, specific_epithet, infraspecific_epithet = nil, nil, nil, nil

        if !is_col_uninomial
          elements = t.full_name_hash

          generic_epithet = clean_sic(elements['genus']&.last)
          infrageneric_epithet = clean_sic(elements['subgenus']&.last)
          specific_epithet = clean_sic(elements['species']&.last)
          infraspecific_epithet = clean_sic(elements['subspecies']&.last)
        else
          uninomial = name_string
        end

        # TODO: Combinations don't have rank BUT CoL importer can interpret, so we're OK here for now
        rank = t.rank

        # Set is: no original combination OR (valid or invalid higher, valid lower, past combinations)
        if t.cached_original_combination.blank? || higher || t.is_valid? || t.is_combination?
          csv << [
            t.id,                                     # ID
            basionym_id,                              # basionymID
            name_string,                              # scientificName  # should just be t.cached
            t.cached_author_year,                     # authorship
            rank,                                     # rank
            uninomial,                                # uninomial   <- if genus here
            generic_epithet,                          # genus and below - IIF species or lower
            infrageneric_epithet,                     # infragenericEpithet
            specific_epithet,                         # specificEpithet
            infraspecific_epithet,                    # infraspecificEpithet
            origin_citation&.source_id,               # publishedInID
            origin_citation&.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(t, name_remarks_vocab_id),        # remarks
          ]
        end

        # Here we truly want no higher
        if !t.cached_original_combination.blank? && (is_genus_species && !t.is_combination? && (!t.is_valid? || t.has_alternate_original?))
          name_total += 1
          add_original_combination(t, csv, origin_citation, name_remarks_vocab_id)
        end

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

.nom_status_field(taxon_name) ⇒ String?

api.checklistbank.org/vocab/nomStatus

Returns:

  • (String, nil) 


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# File 'lib/export/coldp/files/name.rb', line 37

def self.nom_status_field(taxon_name)
  case taxon_name.type
  when 'Combination'
    nil # This is *not* 'chresonym' sensu CoL (which is this: [correct: 'Aus bus Smith 1920', chresonym: 'Aus bus Jones 1922'])
  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

      # We should also infer status from TaxonNameRelationship and be more specific, but if CoL doesn't
      # use NOMEN this won't mean much
      #
      # Note: We supply `nil` when relationship is used here because it is declared in synonym table.
      # Note: This means that the *type* of synonym is lost (e.g. Misspelling)

      c ? c.class::NOMEN_URI : nil
    end
  end
end

.remarks(name, name_remarks_vocab_id) ⇒ Object 



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# File 'lib/export/coldp/files/name.rb', line 20

def self.remarks(name, name_remarks_vocab_id)
  if name.data_attributes.where(controlled_vocabulary_term_id: name_remarks_vocab_id).any?
    name.data_attributes.where(controlled_vocabulary_term_id: name_remarks_vocab_id).pluck(:value).join('|')
  else
    nil
  end
end