Module: Export::Coldp::Files::Name
- Defined in:
- lib/export/coldp/files/name.rb
Class Method Summary collapse
-
.add_original_combination(t, csv) ⇒ Object
Invalid Protonyms are rendered only as their original Combination.
-
.authorship_field(taxon_name, original) ⇒ Object
String.
- .code_field(taxon_name) ⇒ Object
- .generate(otu, reference_csv = nil) ⇒ Object
- .nom_status_field(taxon_name) ⇒ String?
- .remarks_field(taxon_name) ⇒ Object
Class Method Details
.add_original_combination(t, csv) ⇒ Object
Invalid Protonyms are rendered only as their original Combination
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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 (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.
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# File 'lib/export/coldp/files/name.rb', line 21 def self.(taxon_name, original) original ? taxon_name. : taxon_name. 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., # 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?
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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 |