Class: Autoselect::TaxonName::ColAncestryComparator

Inherits:
Object
  • Object
show all
Defined in:
lib/autoselect/taxon_name/col_ancestry_comparator.rb

Overview

Diffs TaxonWorks' real ancestor chain for a matched "anchor" TaxonName against Catalogue of Life's classification for the same lineage, producing one unified, kingdom-first row list.

CoL gives ranks as plain names (e.g. 'family'), so each TaxonWorks rank_class is converted to its plain name (via RANKS_LOOKUP) to see whether two rows are at the same rank.

To decide which of two different ranks is more specific, both names are looked up under one code. When CoL gives a code, the TaxonWorks chain is already in it, so that code is used; otherwise the anchor's own code is.

Instance Method Summary collapse

Constructor Details

#initialize(tw_chain:, col_chain:, col_code: nil) ⇒ ColAncestryComparator

Returns a new instance of ColAncestryComparator.

Parameters:

  • tw_chain (Array<TaxonName>) —

    kingdom-first, the anchor and its real ancestors (excluding the project root / non-taxonomic node)

  • col_chain (Array<Hash>) —

    kingdom-first, CoL's classification up to and including the anchor's own rank; each hash has :col_name, :rank (human rank name, e.g. 'family'), :col_id, :dataset_id, :col_authorship, :above_genus_group, :rank_unknown

  • col_code (String, nil) (defaults to: nil) —

    CoL nomenclatural code ('zoological', 'botanical', …)



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# File 'lib/autoselect/taxon_name/col_ancestry_comparator.rb', line 24

def initialize(tw_chain:, col_chain:, col_code: nil)
  @tw_chain = tw_chain
  @col_chain = col_chain
  @rank_code =
    if ::Vendor::Colrapi::COL_CODE_LOOKUP_MAP.key?(col_code)
      col_code
    else
      anchor_col_code
    end
end

Instance Method Details

#anchor_col_code ⇒ String? (private)

Returns the anchor's nomenclatural code as a CoL code string, e.g. 'botanical'; nil leaves col_rank_sort on its zoological default.

Returns:

  • (String, nil) —

    the anchor's nomenclatural code as a CoL code string, e.g. 'botanical'; nil leaves col_rank_sort on its zoological default



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# File 'lib/autoselect/taxon_name/col_ancestry_comparator.rb', line 85

def anchor_col_code
  code = @tw_chain.last&.rank_class&.nomenclatural_code
  ::Vendor::Colrapi::COL_CODE_TO_NOMENCLATURE_CODE.key(code)
end

#call ⇒ Array<Hash>

Returns kingdom-first, each row tagged :match => 'exact' | 'none' (CoL-only, to be created) | 'extra' (TaxonWorks-only) | 'conflict' (same rank, different name — the actual disagreement).

Returns:

  • (Array<Hash>) —

    kingdom-first, each row tagged :match => 'exact' | 'none' (CoL-only, to be created) | 'extra' (TaxonWorks-only) | 'conflict' (same rank, different name — the actual disagreement)



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# File 'lib/autoselect/taxon_name/col_ancestry_comparator.rb', line 39

def call
  result = []
  tw_i = @tw_chain.length - 1
  col_i = @col_chain.length - 1

  while tw_i >= 0 && col_i >= 0
    tw_entry = @tw_chain[tw_i]
    col_entry = @col_chain[col_i]
    tw_rank_name = rank_name_for(tw_entry.rank_class)

    if tw_rank_name == col_entry[:rank]
      result.unshift(matched_row(tw_entry, col_entry, tw_rank_name))
      tw_i -= 1
      col_i -= 1
    elsif more_specific?(tw_entry, col_entry[:rank])
      result.unshift(extra_row(tw_entry, tw_rank_name))
      tw_i -= 1
    else
      result.unshift(none_row(col_entry))
      col_i -= 1
    end
  end

  while tw_i >= 0
    entry = @tw_chain[tw_i]
    result.unshift(extra_row(entry, rank_name_for(entry.rank_class)))
    tw_i -= 1
  end

  while col_i >= 0
    result.unshift(none_row(@col_chain[col_i]))
    col_i -= 1
  end

  result
end

#extra_row(tw_entry, rank_name) ⇒ Object (private) 



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# File 'lib/autoselect/taxon_name/col_ancestry_comparator.rb', line 123

def extra_row(tw_entry, rank_name)
  {
    rank: rank_name,
    col_name: nil,
    col_id: nil,
    dataset_id: nil,
    col_authorship: nil,
    taxonworks_id: tw_entry.id,
    taxonworks_name: tw_entry.cached,
    match: 'extra'
  }
end

#matched_row(tw_entry, col_entry, rank_name) ⇒ Object (private) 



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# File 'lib/autoselect/taxon_name/col_ancestry_comparator.rb', line 105

def matched_row(tw_entry, col_entry, rank_name)
  # Compared by key, not raw name - see Vendor::Colrapi::NameTranslation.
  translation = ::Vendor::Colrapi::NameTranslation
  exact = translation.taxonworks_name_keys(tw_entry)[:current] ==
    translation.col_name_key(col_entry[:col_name], col_entry[:rank])

  {
    rank: rank_name,
    col_name: col_entry[:col_name],
    col_id: col_entry[:col_id],
    dataset_id: col_entry[:dataset_id],
    col_authorship: col_entry[:col_authorship],
    taxonworks_id: tw_entry.id,
    taxonworks_name: tw_entry.cached,
    match: exact ? 'exact' : 'conflict'
  }
end

#more_specific?(tw_entry, col_rank_name) ⇒ Boolean (private)

The TaxonWorks chain is always in @rank_code's code (see the class comment), so tw_entry's own rank_class indexes RANK_SORT directly; only CoL's rank name can fail to resolve under that code.

Returns:

  • (Boolean) —

    true when tw_entry's rank is narrower (more specific) than col_rank_name, i.e. TaxonWorks' pointer hasn't reached CoL's rank yet. An unresolvable CoL rank is treated as not-more-specific, so CoL's side advances and the row shows up as 'none'.



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# File 'lib/autoselect/taxon_name/col_ancestry_comparator.rb', line 98

def more_specific?(tw_entry, col_rank_name)
  col_sort = ::Vendor::Colrapi.col_rank_sort(col_rank_name, @rank_code)
  return false if col_sort.nil?

  ::RANK_SORT[tw_entry.rank_class.to_s] > col_sort
end

#none_row(col_entry) ⇒ Object (private) 



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# File 'lib/autoselect/taxon_name/col_ancestry_comparator.rb', line 136

def none_row(col_entry)
  {
    rank: col_entry[:rank],
    col_name: col_entry[:col_name],
    col_id: col_entry[:col_id],
    dataset_id: col_entry[:dataset_id],
    col_authorship: col_entry[:col_authorship],
    above_genus_group: col_entry[:above_genus_group],
    rank_unknown: col_entry[:rank_unknown],
    taxonworks_id: nil,
    taxonworks_name: nil,
    match: 'none'
  }
end

#rank_name_for(rank_class) ⇒ Object (private) 



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# File 'lib/autoselect/taxon_name/col_ancestry_comparator.rb', line 78

def rank_name_for(rank_class)
  ::RANKS_LOOKUP[rank_class.to_s]
end