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

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

Overview

The names table includes

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

  • It contains strings that may be invalid or valid

Future considerations

- see bottom, should we parameterize a CSV row add, is it performat?, it
would let us DRY all csv << , but it's also not dry to parameterize.
Probably OK as is.

TODO:

- [ ] refactor ref additions so that they happen at the aggregate level
- [ ] resolve the `.length` issue, what the heck is that needed for [see comment from Tom]

Constant Summary collapse

MANIFEST = 
[
  :valid_higher_names,
  :valid_family_names,
  :core_names,
  :combination_names,
  :original_combination_names,

  :invalid_family_and_higher_names,
  :invalid_core_names,
  :invalid_original_combination_names,
]

Class Method Summary collapse

Class Method Details

.add_combination_names(otu, csv, project_members, reference_csv) ⇒ Object 



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# File 'lib/export/coldp/files/name.rb', line 555

def self.add_combination_names(otu, csv, project_members, reference_csv)
  names = combination_names(otu)
  names.length

  names.each do |row| # row is a Hash, not a ActiveRecord object

    # At this point all formatting (gender) is done
    elements = Combination.full_name_hash_from_row(row)

    # NOT POSSIBLE?! Combination can't have infraspecific in UI
    infraspecies, rank = Utilities::Nomenclature.infraspecies(elements)

    rank = elements.keys.last if rank.nil?

    #
    # TODO: this shouldn't be necessary with scoping of the EXISTS 1
    #
    # Decide whether or not to skip this Combination
    #   * Is it identical to the current placement?
    #      * Yes
    #         * Is the current placement an "inferred combination"?
    #             * Yes - include
    #             * No - skip
    #      * No - include
    #
    if (row[rank + "_cached"] == row['cached'])  # it is a dupe
      if  row[rank + '_cached_is_valid']         # it is valid
        ::Export::Coldp.skipped_combinations << row['id']
        next
      end
    end

    scientific_name = ::Utilities::Nomenclature.unmisspell_name(row['cached'])

    uninomial = scientific_name if rank == 'genus'

    csv << [
      row['id'],                                                          # ID
      nil,                                                                # basionymID
      scientific_name,                                                    # scientificName
      row['cached_author_year'],                                          # authorship
      rank,                                                               # rank
      uninomial,                                                          # uninomial   <- if genus group only (i.e. incomplete Combination)
      elements['genus']&.last,                                            # genus
      elements['subgenus']&.last,                                         # subgenus (no parens)
      elements['species']&.last,                                          # species
      infraspecies,                                                       # infraspecificEpithet
      row['source_id'],                                                   # publishedInID
      row['pages'],                                                       # publishedInPage
      row['cached_nomenclature_date']&.year,                              # publishedInYear
      code_field(row['reference_rank_class']),                            # code
      nil,                                                                # nomStatus (nil for Combination)
      nil,                                                                # etymology
      nil,                                                                # gender
      nil,                                                                # link (probably TW public or API)
      Export::Coldp.sanitize_remarks(row['id']),                          # remarks
      Export::Coldp.modified(row['updated_at']),                          # modified
      Export::Coldp.modified_by(row[:updated_by_id], project_members)     # modifiedBy
    ]
  end

  # TODO: CHECK THIS!!
  if reference_csv
    Source.with(names: names.where(citations: { is_original: true}))
      .joins('JOIN names n on n.source_id = sources.id')
      .find_each do |s|
        Export::Coldp::Files::Reference.add_reference_rows([s].compact, reference_csv, project_members)
      end
  end
end

.add_core_names(otu, csv, project_members, reference_csv) ⇒ Object 



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# File 'lib/export/coldp/files/name.rb', line 626

def self.add_core_names(otu, csv, project_members, reference_csv)
  names = core_names(otu)
  names.length

  names.find_each do |t|
    origin_citation = t.origin_citation

    # TODO: Is this needed for invalid names?
    #
    # Ugh, shame we need this. Our Protonyms are not Basionyms.
    #
    # If this name has a reified original combination (genus changed),
    # the basionym is the OC record, not this current placement record.
    if t.cached_original_combination.present? &&
        !t.cached_original_combination.include?('NOT SPECIFIED') &&
        t.cached != t.cached_original_combination
      scientific_name = ::Utilities::Nomenclature.unmisspell_name(t.cached_original_combination)
      basionym_id = ::Utilities::Nomenclature.reified_id(t.id, scientific_name)
    else
      basionym_id = t.id
    end

    uninomial = t.cached if t.rank == 'genus'

    # TODO: Spammed the || in align_gender, may need checking
    # Future- resolve in SQL perhaps, though not very expensive here
    species = align_gender(t, :species)
    infraspecies = align_gender(t, :infraspecies)

    csv << [
      t.id,                                                               # ID
      basionym_id,                                                        # basionymID
      t.cached,                                                           # scientificName  # should just be t.cached
      t.cached_author_year,                                               # authorship
      t.rank,                                                             # rank
      uninomial,                                                          # uninomial   <- if genus here
      t.genus,                                                            # genus and below - IIF species or lower # TODO: confirm this is OK now
      t.subgenus,                                                         # infragenericEpithet (subgenus)
      species,                                                            # specificEpithet
      infraspecies,                                                       # infraspecificEpithet
      origin_citation&.source_id,                                         # publishedInID
      origin_citation&.pages,                                             # publishedInPage
      t.cached_nomenclature_date&.year,                                   # publishedInYear
      code_field(t.rank_class.name),                                      # code
      ::TaxonName::NOMEN_VALID[t.rank_class.name.to_sym],                 # nomStatus # TODO: untested
      nil,                                                                # etymology
      nil,                                                                # gender
      nil,                                                                # link (probably TW public or API)
      Export::Coldp.sanitize_remarks(t.id),                               # remarks
      Export::Coldp.modified(t[:updated_at]),                             # modified
      Export::Coldp.modified_by(t[:updated_by_id], project_members)       # modifiedBy
    ]

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

.add_invalid_core_names(otu, csv, project_members, reference_csv) ⇒ Object 



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# File 'lib/export/coldp/files/name.rb', line 725

def self.add_invalid_core_names(otu, csv, project_members, reference_csv)
  names = invalid_core_names(otu)

  classification_status = taxon_name_classification_status(names)
  relationship_status = taxon_name_relationship_status(names)

  names.length # !! TODO: without this the result is truncated, why!?

  names.find_each do |t|

    origin_citation = t.origin_citation

    scientific_name = t.cached_misspelling ? ::Utilities::Nomenclature.unmisspell_name(t.cached) : t.cached

    uninomial = scientific_name if t.rank == 'genus'

    nom_status = nomenclatural_status(t.id, classification_status, relationship_status)

    csv << [
      t.id,                                                               # ID
      nil,                                                                # basionymID
      scientific_name,                                                    # scientificName  # should just be t.cached
      t.cached_author_year,                                               # authorship
      t.rank,                                                             # rank
      uninomial,                                                          # uninomial   <- if genus here
      t.genus,                                                            # genus and below - IIF species or lower
      t.subgenus,                                                         # infragenericEpithet (subgenus)
      t.species,                                                          # specificEpithet
      t.infraspecies,                                                     # infraspecificEpithet
      origin_citation&.source_id,                                         # publishedInID
      origin_citation&.pages,                                             # publishedInPage
      t.cached_nomenclature_date&.year,                                   # publishedInYear
      code_field(t.rank_class.name),                                      # code
      nom_status,                                                         # nomStatus
      nil,                                                                # etymology
      nil,                                                                # gender
      nil,                                                                # link (probably TW public or API)
      Export::Coldp.sanitize_remarks(t.id),                               # remarks
      Export::Coldp.modified(t[:updated_at]),                             # modified
      Export::Coldp.modified_by(t[:updated_by_id], project_members)       # modifiedBy
    ]

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

.add_invalid_family_and_higher_names(otu, csv, project_members, reference_csv) ⇒ Object 



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# File 'lib/export/coldp/files/name.rb', line 683

def self.add_invalid_family_and_higher_names(otu, csv, project_members, reference_csv)

  names = invalid_family_and_higher_names(otu)

  classification_status = taxon_name_classification_status(names)
  relationship_status = taxon_name_relationship_status(names)

  names.length # !! TODO: without this the result is truncated, why!?

  names.find_each do |t|
    origin_citation = t.origin_citation

    nom_status = nomenclatural_status(t.id, classification_status, relationship_status)

    csv << [
      t.id,                                                             # ID
      nil,                                                              # basionymID
      t.name,                                                           # scientificName
      t.cached_author_year,                                             # authorship
      t.rank,                                                           # rank
      t.name,                                                           # uninomial
      nil,                                                              # genus and below - IIF species or lower
      nil,                                                              # infragenericEpithet (subgenus)
      nil,                                                              # specificEpithet
      nil,                                                              # infraspecificEpithet
      origin_citation&.source_id,                                       # publishedInID
      origin_citation&.pages,                                           # publishedInPage
      t.cached_nomenclature_date&.year,                                 # publishedInYear
      code_field(t.rank_class.name),                                    # code
      nom_status,                                                       # nomStatus
      nil,                                                              # etymology
      nil,                                                              # gender
      nil,                                                              # link (probably TW public or API)
      Export::Coldp.sanitize_remarks(t.id),                             # remarks
      Export::Coldp.modified(t[:updated_at]),                           # modified
      Export::Coldp.modified_by(t[:updated_by_id], project_members)     # modifiedBy
    ]

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

.add_invalid_original_combination_names(otu, csv, project_members, reference_csv) ⇒ Object

May have to split out misspellings from other invalid names to handle parens



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# File 'lib/export/coldp/files/name.rb', line 326

def self.add_invalid_original_combination_names(otu, csv, project_members, reference_csv)

  # !!
  # !! Remember, the names here are loaded with values FROM THEIR ORIGINAL COMBINATIONS
  # !!
  names = invalid_original_combination_names(otu)
  names.length

  names.find_each do |row|

    # At this point all formatting (gender) is done
    elements = Protonym.original_combination_full_name_hash_from_flat(row)

    infraspecies, rank = Utilities::Nomenclature.infraspecies(elements)
    rank = 'forma' if rank == 'form' # CoL preferred string

    # Hmm- why needed?
    rank = elements.keys.last if rank.nil? # Note that this depends on order of Hash creation

    # Generic names can also be misspelled so, just process everything, don't bother checking the flag
    scientific_name = ::Utilities::Nomenclature.unmisspell_name(row['cached_original_combination'])

    # TODO: resolve/verify needed
    uninomial = scientific_name if rank == 'genus'

    # !! Ideally we de-reify these names in the query with (cached != cached_original_combination)
    # !! SO that we know these *must* be reified
    # !! We are reifying *without* "[sic]" in the string
    id = ::Utilities::Nomenclature.reified_id(row['id'], scientific_name)

    # By definition - for invalid names, the basionym points to itself (the reified original combination)
    basionym_id = id

    # A major brain-@#$@#.
    # Original combinations of misspelled names
    # CAN have parenthesis in their rendering
    # if the original genus is different
    # THAN THE GENUS OF THE PROPERLY SPELLED VERSION OF THE NAME

    # Remember, 'genus' is `original_genus`, so
    # by the fact that synonyms are under the same parent
    # as that of the valid name we are comparing the
    # placement of the properly spelled version of the name.

    author_year = row['cached_author_year']
    author_year = author_year&.delete('()') if strip_parens_for_author_year?(row)

    # !!
    # !! Here we accomodate, somehwat crudely, that original combinations will infer the rank of
    # !! of a species protonym without specifically assining an original species relationship.
    # !!
    # !! Curators can avoid this ambiguity by assigning the full original combination.
    # !!
    if rank == 'genus' && row.rank != 'genus'
      rank = row.rank
    end

    csv << [
      id,                                                                 # ID
      basionym_id,                                                        # basionymID
      scientific_name,                                                    # scientificName
      author_year,                                                        # authorship
      rank,                                                               # rank
      uninomial,                                                          # uninomial
      elements['genus']&.last,                                            # genus
      elements['subgenus']&.last,                                         # subgenus (no parens)
      elements['species']&.last,                                          # species
      infraspecies,                                                       # infraspecificEpithet
      row['source_id'],                                                   # referenceID
      row['pages'],                                                       # publishedInPage
      row['cached_nomenclature_date']&.year,                              # publishedInYear - OK
      code_field(row['reference_rank_class']),                            # code
      nil,                                                                # status https://api.checklistbank.org/vocab/nomStatus
      nil,                                                                # etymology
      nil,                                                                # gender
      nil,                                                                # link (probably TW public or API)
      nil,                                                                # remarks (we have no way to capture this in TW)
      Export::Coldp.modified(row[:updated_at]),                           # modified
      Export::Coldp.modified_by(row[:updated_by_id], project_members)     # modifiedBy
    ]

    # !! We do not need to add a reference here because it is the same as the corresponding Protonym id
  end
end

.add_original_combination_names(otu, csv, project_members, reference_csv) ⇒ Object 



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# File 'lib/export/coldp/files/name.rb', line 418

def self.add_original_combination_names(otu, csv, project_members, reference_csv)
  names = original_combination_names(otu)
  names.length

  names.find_each do |row|
    # At this point all formatting (gender) is done
    elements = Protonym.original_combination_full_name_hash_from_flat(row)

    infraspecies, rank = Utilities::Nomenclature.infraspecies(elements)
    rank = 'forma' if rank == 'form' # CoL preferred string

    # Hmm- why needed?
    rank = elements.keys.last if rank.nil? # Note that this depends on order of Hash creation

    scientific_name = ::Utilities::Nomenclature.unmisspell_name(row['cached_original_combination'])

    # TODO: resolve/verify needed
    uninomial = scientific_name if rank == 'genus'

    # !! Ideally we de-reify these names in the query with (cached != cached_original_combination)
    # !! So that we know these *must* be reified
    # !! We are reifieing *without* "[sic]" in the string
    id = ::Utilities::Nomenclature.reified_id(row['id'], scientific_name)

    # The reified OC IS the original combination/basionym, so it points to itself
    basionym_id = id

    # !!
    # !! Here we accomodate, somehwat crudely, that original combinations will infer the rank of
    # !! of a species protonym without specifically assining an original species relationship.
    # !!
    # !! Curators can avoid this ambiguity by assigning the full original combination.
    # !!
    if rank == 'genus' && row.rank != 'genus'
      rank = row.rank
    end

    csv << [
      id,                                                                 # ID
      basionym_id,                                                        # basionymID
      scientific_name,                                                    # scientificName
      row['cached_author_year']&.gsub(/[\(\)]/, ''),                      # authorship  # TODO <- stripping author/year here
      rank,                                                               # rank
      uninomial,                                                          # uninomial
      elements['genus']&.last,                                            # genus
      elements['subgenus']&.last,                                         # subgenus (no parens)
      elements['species']&.last,                                          # species
      infraspecies,                                                       # infraspecificEpithet
      row['source_id'],                                                   # referenceID
      row['pages'],                                                       # publishedInPage
      row['cached_nomenclature_date']&.year,                              # publishedInYear - OK
      code_field(row['reference_rank_class']),                            # code
      nil,                                                                # status https://api.checklistbank.org/vocab/nomStatus
      nil,                                                                # etymology
      nil,                                                                # gender
      nil,                                                                # link (probably TW public or API)
      nil,                                                                # remarks (we have no way to capture this in TW)
      Export::Coldp.modified(row[:updated_at]),                           # modified
      Export::Coldp.modified_by(row[:updated_by_id], project_members)     # modifiedBy
    ]

    # !! We do not need to add a reference here because it is the same as the corresponding Protonym id
  end
end

.add_valid_family_names(otu, csv, project_members, reference_csv) ⇒ Object 



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# File 'lib/export/coldp/files/name.rb', line 483

def self.add_valid_family_names(otu, csv, project_members, reference_csv)
  names = valid_family_names(otu)
  names.length

  names.find_each do |t|
    origin_citation = t.origin_citation
    csv << [
      t.id,                                                               # ID
      nil,                                                                # basionymID
      t.cached,                                                           # scientificName  # should just be t.cached
      t.cached_author_year,                                               # authorship
      t.rank,                                                             # rank
      t.cached,                                                           # uninomial
      nil,                                                                # genus and below - IIF species or lower
      nil,                                                                # infragenericEpithet (subgenus)
      nil,                                                                # specificEpithet
      nil,                                                                # infraspecificEpithet
      origin_citation&.source_id,                                         # publishedInID
      origin_citation&.pages,                                             # publishedInPage
      t.cached_nomenclature_date&.year,                                   # publishedInYear
      code_field(t.rank_class.name),                                      # code
      ::TaxonName::NOMEN_VALID[t.rank_class.name.to_sym],                 # nomStatus
      nil,                                                                # etymology
      nil,                                                                # gender
      nil,                                                                # link (probably TW public or API)
      Export::Coldp.sanitize_remarks(t.id),                               # remarks
      Export::Coldp.modified(t[:updated_at]),                             # modified
      Export::Coldp.modified_by(t[:updated_by_id], project_members)       # modifiedBy
    ]

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

.add_valid_higher_names(otu, csv, project_members, reference_csv) ⇒ Object

TODO: could select less, don’t need ‘cached’, just name?



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# File 'lib/export/coldp/files/name.rb', line 518

def self.add_valid_higher_names(otu, csv, project_members, reference_csv)
  names = valid_higher_names(otu)

  names.length
  names.find_each do |t|

    # TODO: isolate/refine
    origin_citation = t.origin_citation

    csv << [
      t.id,                                                               # ID
      nil,                                                                # basionymID
      t.cached,                                                           # scientificName  # should just be t.name?
      t.cached_author_year,                                               # authorship
      t.rank,                                                             # rank
      t.cached,                                                           # uninomial
      nil,                                                                # genus and below - IIF species or lower
      nil,                                                                # infragenericEpithet (subgenus)
      nil,                                                                # specificEpithet
      nil,                                                                # infraspecificEpithet
      origin_citation&.source_id,                                         # publishedInID
      origin_citation&.pages,                                             # publishedInPage
      t.cached_nomenclature_date&.year,                                   # publishedInYear
      code_field(t.rank_class.name),                                      # code
      ::TaxonName::NOMEN_VALID[t.rank_class.name.to_sym],                 # nomStatus
      nil,                                                                # etymology
      nil,                                                                # gender
      nil,                                                                # link (probably TW public or API)
      Export::Coldp.sanitize_remarks(t.id),                               # remarks
      Export::Coldp.modified(t[:updated_at]),                             # modified
      Export::Coldp.modified_by(t[:updated_by_id], project_members)       # modifiedBy
    ]

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

.align_gender(core_name, rank = :species) ⇒ Object

Return, based on the gender of the genus, the element at the rank requested. Note infraspecies is a “fake” rank that is combined data here. This is in part because CoL only handles trinomials.

Parameters:

  • rank (defaults to: :species) —

    • the element of the name requested



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# File 'lib/export/coldp/files/name.rb', line 124

def self.align_gender(core_name, rank = :species)
  if g = core_name.genus_gender # there is a name at this rank and we can work with the gender

    case core_name.rank
    when 'species'
      case rank
      when :species
        core_name.send( (g + '_name').to_sym ) || core_name.species
      else
        nil
      end
    when 'subspecies', 'form', 'variety' # See compression in core_names, may be an issue
      case rank
      when :species
        core_name.send( "species_#{g}_name".to_sym ) || core_name.species
      when :infraspecies
        core_name.send( (g + '_name').to_sym ) || core_name.infraspecies
      end
    end
  end
end

.code_field(rank_class) ⇒ Object 



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# File 'lib/export/coldp/files/name.rb', line 79

def self.code_field(rank_class)
  return 'ICZN' if rank_class =~ /Iczn/
  return 'ICNP' if rank_class =~ /Icnp/
  return 'ICVCN' if rank_class =~ /Icvcn/
  return 'ICN' if rank_class =~ /Icn/
  nil
end

.combination_names(otu) ⇒ Object

Combinations

 See also self.core_names
- Potential TODO: a-typical verbatim_names (though perhaps OK)
  - If not OK, then simply provide verbatim_name *without* genus, subgenus, species fields



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# File 'lib/export/coldp/files/name.rb', line 236

def self.combination_names(otu)
  a = otu.taxon_name.self_and_descendants.unscope(:order).select(:id)

  b = Combination
    .where('taxon_names.verbatim_name is null OR taxon_names.verbatim_name = taxon_names.cached') # !! verbatim_name when present is used in cached?! if so this isn't correct!
    .flattened
    .with(project_scope: a)
    .complete
    .joins('JOIN project_scope ps on ps.id = taxon_names.cached_valid_taxon_name_id')           # Combinations that point to any of "a"
    .where("NOT EXISTS( SELECT 1 from taxon_names tnc WHERE tnc.type = 'Protonym' AND tnc.cached = taxon_names.cached )") # No Combinations identical to Protonyms
end

.core_names(otu) ⇒ Object

Core names are:

- Protonyms
- Valid
- Genus or species group

They are NOT

- "inferred combinations" - We have consciously excluded inferred combinations (sensu Browse TaxonNames) from the result set.

If you wish to include an inferred combination then you must create an equivalent (subsequent) Combination.



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# File 'lib/export/coldp/files/name.rb', line 166

def self.core_names(otu)

  # TODO: adding .that_is_valid increases names, why? Are we hitting duplicates?
  a = otu.taxon_name.self_and_descendants.unscope(:order).select(:id)

  # b sets up the query that aggregates the different ranks in one row
  b = ::Protonym.is_species_or_genus_group.with(valid_scope: a)
    .where(cached_is_valid: true)
    .joins('JOIN valid_scope on valid_scope.id = taxon_names.cached_valid_taxon_name_id')

  select = 'taxon_names.id,'
  select << ::NomenclaturalRank.rank_expansion_sql(ranks: %w{genus subgenus species}, nomenclatural_code: otu.taxon_name.nomenclatural_code)

  # We group some ranks here
  # TODO: This doesn't likely actually work in the case of subspecies + <some other rank> ?
  select << ", MAX(CASE WHEN parent.rank_class LIKE \'%::Subspecies\' OR parent.rank_class LIKE \'%::Variety\' OR parent.rank_class LIKE \'%::Form\' THEN parent.name END) AS infraspecies"

  b = b.select(select)
    .joins('INNER JOIN taxon_name_hierarchies ON taxon_names.id = taxon_name_hierarchies.descendant_id')
    .joins('LEFT JOIN taxon_names AS parent ON parent.id = taxon_name_hierarchies.ancestor_id')
    .group('taxon_names.id')

  c = ::TaxonName.with(n: b)
    .joins('JOIN n on n.id = taxon_names.id')
    .joins('JOIN taxon_names parent_name on parent_name.id = taxon_names.parent_id')
    .where(cached_is_valid: true)
    .eager_load(origin_citation: [:source])
    .select('taxon_names.*, parent_name.name parent_name, n.genus, n.subgenus, n.species, n.infraspecies, n.genus_gender, n.species_masculine_name, n.species_neuter_name, n.species_feminine_name')
end

.generate(otu, project_members, reference_csv = nil) ⇒ Object 



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# File 'lib/export/coldp/files/name.rb', line 30

def self.generate(otu, project_members, reference_csv = nil)
  name_total = 0

  # We should not be setting this here !!
  project_id = otu.project_id

  # TODO: scope this to name_remarks, keep internal
  if predicate_id = Predicate.find_by(
      uri: 'https://github.com/catalogueoflife/coldp#Name.remarks',
      project_id:)&.id

    ::Export::Coldp.remarks = ::Export::Coldp.get_remarks(otu.taxon_name.self_and_descendants, predicate_id)
  end

  # genderAgreement boolean is ultimately derivable from TaxonNameClassification::Gender

  output = ::CSV.generate(col_sep: "\t") do |csv|
    csv << %w{
      ID
      basionymID
      scientificName
      authorship
      rank
      uninomial
      genus
      infragenericEpithet
      specificEpithet
      infraspecificEpithet
      referenceID
      publishedInPage
      publishedInYear
      code
      status
      etymology
      gender
      link
      remarks
      modified
      modifiedBy
    }

    MANIFEST.each do |m|
      send( ('add_' + m.to_s).to_sym, otu, csv, project_members, reference_csv)
    end

    true
  end
end

.invalid_core_names(otu) ⇒ Object 



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# File 'lib/export/coldp/files/name.rb', line 196

def self.invalid_core_names(otu)
  a = otu.taxon_name.self_and_descendants.unscope(:order).select(:id)

  b = ::Protonym
    .with(valid_scope: a)
    .joins('JOIN valid_scope on valid_scope.id = taxon_names.cached_valid_taxon_name_id')
    .is_species_or_genus_group
    .where(cached_is_valid: false)
    .where('((taxon_names.cached = taxon_names.cached_original_combination) OR (taxon_names.cached_original_combination IS NULL))')
    .and(TaxonName.where.not("taxon_names.rank_class like '%::Iczn::Family%' AND taxon_names.cached_is_valid = FALSE"))
    .where(not_misapplication_sql)

  select = 'taxon_names.id,'
  select << ::NomenclaturalRank.rank_expansion_sql(ranks: %w{genus subgenus species}, nomenclatural_code: otu.taxon_name.nomenclatural_code)

  # We group some ranks here
  # TODO: This doesn't likely actually work in the case of subspecies + <some other rank> ?
  select << ", MAX(CASE WHEN parent.rank_class LIKE \'%::Subspecies\' OR parent.rank_class LIKE \'%::Variety\' OR parent.rank_class LIKE \'%::Form\' THEN parent.name END) AS infraspecies"

  b = b

  b = b.select(select)
    .joins('INNER JOIN taxon_name_hierarchies ON taxon_names.id = taxon_name_hierarchies.descendant_id')
    .joins('LEFT JOIN taxon_names AS parent ON parent.id = taxon_name_hierarchies.ancestor_id')
    .group('taxon_names.id')
    .eager_load(origin_citation: [:source])

  c = ::TaxonName.with(n: b)
    .joins('JOIN n on n.id = taxon_names.id')
    .joins('JOIN taxon_names parent_name on parent_name.id = taxon_names.parent_id')
    .where(cached_is_valid: false) # redundant
    .eager_load(origin_citation: [:source])
    .select('taxon_names.*, parent_name.name parent_name, n.genus, n.subgenus, n.species, n.infraspecies')
end

.invalid_family_and_higher_names(otu) ⇒ Object

Invalid family/higher names



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# File 'lib/export/coldp/files/name.rb', line 271

def self.invalid_family_and_higher_names(otu)
  a = otu.taxon_name.self_and_descendants
    .where(
      type: 'Protonym',
      rank_class: FAMILY_RANK_NAMES + HIGHER_RANK_NAMES,
      cached_is_valid: false)
    .unscope(:order)
    .eager_load(origin_citation: [:source]) # TODO, just source_id, and pages
    .select(:id, :name, :type, :cached_author_year, :cached_nomenclature_date, :rank_class, :cached_is_valid, :cached_valid_taxon_name_id, :updated_at, :updated_by_id) # cached has sic
end

.invalid_original_combination_names(otu) ⇒ Object

Invalid original combinations are:

- Species or genus group names
- invalid names (not valid)
- names with original combinations set
- names where cached != original_combination, i.e. it needs re-ification

These are the original combinations for invalid protonyms that need reified IDs



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# File 'lib/export/coldp/files/name.rb', line 309

def self.invalid_original_combination_names(otu)
  a = otu.taxon_name.self_and_descendants.unscope(:order).select(:id)

  b = Protonym
    .original_combination_specified
    .original_combinations_flattened
    .with(valid_scope: a)
    .where(cached_is_valid: false)
    .where('taxon_names.cached != taxon_names.cached_original_combination') # Only reified!!
    .where(not_misapplication_sql)
    .joins('JOIN valid_scope on valid_scope.id = taxon_names.cached_valid_taxon_name_id')
end

.nomenclatural_status(taxon_name_id, classification_status = [], relationship_status = []) ⇒ Object

Parameters:

  • classification_status (defaults to: []) —

    Array

  • relationship_status (defaults to: []) —

    Array



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# File 'lib/export/coldp/files/name.rb', line 148

def self.nomenclatural_status(taxon_name_id, classification_status = [], relationship_status = [])
  # Always prefer  a classification, regardless of age
  a = classification_status.bsearch{|i| i['taxon_name_id'] >= taxon_name_id}
  return a['type'].safe_constantize::NOMEN_URI if !a.blank? && a['taxon_name_id'] == taxon_name_id # binary is first >=
  b = relationship_status.bsearch{|i| i['subject_taxon_name_id'] >= taxon_name_id}
  return nil if b.blank? || b['subject_taxon_name_id'] != taxon_name_id
  return b['type'].safe_constantize::NOMEN_URI unless b.blank?
  nil
end

.not_misapplication_sql ⇒ Object

Misapplications are not nomenclatural acts and should be excluded from the export. Returns a SQL fragment that excludes names with a Misapplication relationship.



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# File 'lib/export/coldp/files/name.rb', line 773

def self.not_misapplication_sql
  misapplication_types = %w[
    TaxonNameRelationship::Iczn::Invalidating::Misapplication
    TaxonNameRelationship::Icn::Unaccepting::Misapplication
    TaxonNameRelationship::Icnp::Unaccepting::Misapplication
  ]

  "NOT EXISTS (SELECT 1 FROM taxon_name_relationships tnr
    WHERE tnr.subject_taxon_name_id = taxon_names.id
    AND tnr.type IN (#{misapplication_types.map { |t| "'#{t}'" }.join(',')}))"
end

.original_combination_names(otu) ⇒ Object

Valid original combinations are:

- species or genus group names
- valid names
- names with original combinations set
- names where cached != original_combination, i.e. it needs re-ification

As a test these should parse correctly in the Biodiversity wrapper as of 4/8/2025.



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# File 'lib/export/coldp/files/name.rb', line 290

def self.original_combination_names(otu)
  a = core_names(otu)

  b = Protonym
    .original_combination_specified
    .original_combinations_flattened # !! This is excluding things that are not full specified for species group names
    .with(project_scope: a)
    .where('taxon_names.cached != taxon_names.cached_original_combination') # Only reified!!
    .joins('JOIN project_scope ps on ps.id = taxon_names.id')
end

.strip_parens_for_author_year?(row) ⇒ Boolean

Returns:

  • (Boolean) 


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# File 'lib/export/coldp/files/name.rb', line 411

def self.strip_parens_for_author_year?(row)
  return true unless row['cached_misspelling']
  return true if row['genus'].nil?

  row['cached'] =~ /\A#{Regexp.escape(row['genus'])}\b/
end

.taxon_name_classification_status(scope) ⇒ Object 



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# File 'lib/export/coldp/files/name.rb', line 87

def self.taxon_name_classification_status(scope)
  c = TaxonNameClassification.with(invalid_names: scope.select('taxon_names.id invalid_id'))
    .joins('JOIN invalid_names ON invalid_names.invalid_id = taxon_name_classifications.taxon_name_id')
    .joins("LEFT JOIN citations c on c.citation_object_id = taxon_name_classifications.id and c.citation_object_type = 'TaxonNameClassification'")
    .joins('LEFT JOIN sources s on s.id = c.source_id')
    .select('taxon_name_classifications.taxon_name_id, s.cached_nomenclature_date,
            MAX(taxon_name_classifications.type) AS type,
            MAX(s.cached_nomenclature_date) as date')
    .group('taxon_name_classifications.taxon_name_id, s.cached_nomenclature_date, taxon_name_classifications.type')
    .order('taxon_name_classifications.taxon_name_id, s.cached_nomenclature_date')

  ApplicationRecord.connection.execute(c.to_sql).to_a
end

.taxon_name_relationship_status(scope) ⇒ Object 



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# File 'lib/export/coldp/files/name.rb', line 101

def self.taxon_name_relationship_status(scope)
  c = TaxonNameRelationship.with(invalid_names: scope.select('taxon_names.id invalid_id'))
    .joins('JOIN invalid_names ON invalid_names.invalid_id = taxon_name_relationships.subject_taxon_name_id')
    .joins("LEFT JOIN citations c on c.citation_object_id = taxon_name_relationships.id and c.citation_object_type = 'TaxonNameClassification'")
    .joins('LEFT JOIN sources s on s.id = c.source_id')
    .where('taxon_name_relationships.object_taxon_name_id = invalid_names.cached_valid_taxon_name_id')
    .where(taxon_name_relationships: {type: TAXON_NAME_RELATIONSHIP_NAMES_SYNONYM})
    .select('taxon_name_relationships.subject_taxon_name_id, s.cached_nomenclature_date,
            MAX(taxon_name_relationships.type) AS type,
            MAX(s.cached_nomenclature_date) as date')
    .group('taxon_name_relationships.subject_taxon_name_id, s.cached_nomenclature_date, taxon_name_relationships.type')
    .order('taxon_name_relationships.subject_taxon_name_id, s.cached_nomenclature_date')

  ApplicationRecord.connection.execute(c.to_sql).to_a
end

.valid_family_names(otu) ⇒ Object

Valid family names are:

- valid family group names



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# File 'lib/export/coldp/files/name.rb', line 262

def self.valid_family_names(otu)
  a = otu.taxon_name.self_and_descendants
    .where(rank_class: FAMILY_RANK_NAMES, cached_is_valid: true)
    .unscope(:order)
    .eager_load(origin_citation: [:source]) # TODO, just source_id, and pages
    .select(:id, :cached, :type, :cached_author_year, :cached_nomenclature_date, :rank_class, :updated_at, :updated_by_id)
end

.valid_higher_names(otu) ⇒ Object

Higher names are:

- valid higher names

Notes

- candidate for merging with valid_family_names



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# File 'lib/export/coldp/files/name.rb', line 252

def self.valid_higher_names(otu)
  a = otu.taxon_name.self_and_descendants
    .where(rank_class: HIGHER_RANK_NAMES, cached_is_valid: true)
    .unscope(:order)
    .eager_load(origin_citation: [:source]) # TODO, just source_id, and pages
    .select(:id, :cached, :type, :cached_author_year, :cached_nomenclature_date, :rank_class, :updated_at, :updated_by_id)
end