Class: Taxamatch::Base

Inherits:
Object
  • Object
show all
Defined in:
lib/taxamatch_rb/base.rb

Instance Method Summary collapse

Constructor Details

#initializeBase

Returns a new instance of Base



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# File 'lib/taxamatch_rb/base.rb', line 3

def initialize
  @parser = Taxamatch::Atomizer.new
  @dlm = DamerauLevenshtein
end

Instance Method Details

#match_authors(preparsed_1, preparsed_2) ⇒ Object



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# File 'lib/taxamatch_rb/base.rb', line 119

def match_authors(preparsed_1, preparsed_2)
  p1 = { normalized_authors: [], years: [] }
  p2 = { normalized_authors: [], years: [] }
  if preparsed_1[:infraspecies] || preparsed_2[:infraspecies]
    p1 = preparsed_1[:infraspecies].last if preparsed_1[:infraspecies]
    p2 = preparsed_2[:infraspecies].last if preparsed_2[:infraspecies]
  elsif preparsed_1[:species] || preparsed_2[:species]
    p1 = preparsed_1[:species] if preparsed_1[:species]
    p2 = preparsed_2[:species] if preparsed_2[:species]
  elsif preparsed_1[:uninomial] && preparsed_2[:uninomial]
    p1 = preparsed_1[:uninomial]
    p2 = preparsed_2[:uninomial]
  end
  au1 = p1[:normalized_authors]
  au2 = p2[:normalized_authors]
  yr1 = p1[:years]
  yr2 = p2[:years]
  return 0 if au1.empty? || au2.empty?
  score = Taxamatch::Authmatch.authmatch(au1, au2, yr1, yr2)
  score == 0 ? -1 : 1
end

#match_genera(genus1, genus2, opts = {}) ⇒ Object



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# File 'lib/taxamatch_rb/base.rb', line 67

def match_genera(genus1, genus2, opts = {})
  genus1_length = genus1[:normalized].size
  genus2_length = genus2[:normalized].size
  opts = { with_phonetic_match: true }.merge(opts)
  min_length = [genus1_length, genus2_length].min
  unless opts[:with_phonetic_match]
    genus1[:phonetized] = 'A'
    genus2[:phonetized] = 'B'
  end
  match = false
  ed = @dlm.distance(genus1[:normalized],
                     genus2[:normalized], 1, 3) #TODO put block = 2
  return { 'edit_distance' => ed,
    'phonetic_match' => false,
    'match' => false } if ed/min_length.to_f > 0.2
  return { 'edit_distance' => ed,
    'phonetic_match' => true,
    'match' => true } if genus1[:phonetized] == genus2[:phonetized]

  match = true if ed <= 3 && (min_length > ed * 2) &&
    (ed < 2 || genus1[0] == genus2[0])
  { 'edit_distance' => ed, 'match' => match, 'phonetic_match' => false }
end

#match_matches(genus_match, species_match, infraspecies_match = nil) ⇒ Object



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# File 'lib/taxamatch_rb/base.rb', line 141

def match_matches(genus_match, species_match, infraspecies_match = nil)
  match = species_match
  if infraspecies_match
    match['edit_distance'] += infraspecies_match['edit_distance']
    match['match'] &&= infraspecies_match['match']
    match['phonetic_match'] &&= infraspecies_match['phonetic_match']
  end
  match['edit_distance'] += genus_match['edit_distance']
  if match['edit_distance'] > (infraspecies_match ? 6 : 4)
    match['match'] = false
  end
  match['match'] &&= genus_match['match']
  match['phonetic_match'] &&= genus_match['phonetic_match']
  match
end

#match_multinomial(preparsed_1, preparsed_2) ⇒ Object



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# File 'lib/taxamatch_rb/base.rb', line 38

def match_multinomial(preparsed_1, preparsed_2)
  gen_match = match_genera(preparsed_1[:genus], preparsed_2[:genus])
  sp_match = match_species(preparsed_1[:species], preparsed_2[:species])
  total_length = preparsed_1[:genus][:string].size +
    preparsed_2[:genus][:string].size +
    preparsed_1[:species][:string].size +
    preparsed_2[:species][:string].size
  if preparsed_1[:infraspecies] && preparsed_2[:infraspecies]
    infrasp_match = match_species(preparsed_1[:infraspecies][0],
                                  preparsed_2[:infraspecies][0])
    total_length += preparsed_1[:infraspecies][0][:string].size +
      preparsed_2[:infraspecies][0][:string].size
    match_hash = match_matches(gen_match, sp_match, infrasp_match)
  elsif (preparsed_1[:infraspecies] && !preparsed_2[:infraspecies]) ||
    (!preparsed_1[:infraspecies] && preparsed_2[:infraspecies])
    match_hash = { 'match' => false,
      'edit_distance' => 5,
      'phonetic_match' => false }
    total_length += preparsed_1[:infraspecies] ?
      preparsed_1[:infraspecies][0][:string].size :
      preparsed_2[:infraspecies][0][:string].size
  else
    match_hash = match_matches(gen_match, sp_match)
  end
  match_hash.merge({ 'score' =>
                   (1 - match_hash['edit_distance']/(total_length/2)) })
  match_hash
end

#match_species(sp1, sp2, opts = {}) ⇒ Object



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# File 'lib/taxamatch_rb/base.rb', line 91

def match_species(sp1, sp2, opts = {})
  sp1_length = sp1[:normalized].size
  sp2_length = sp2[:normalized].size
  opts = { with_phonetic_match: true }.merge(opts)
  min_length = [sp1_length, sp2_length].min
  unless opts[:with_phonetic_match]
    sp1[:phonetized] = 'A'
    sp2[:phonetized] = 'B'
  end
  sp1[:phonetized] = Taxamatch::Phonetizer.normalize_ending sp1[:phonetized]
  sp2[:phonetized] = Taxamatch::Phonetizer.normalize_ending sp2[:phonetized]
  match = false
  ed = @dlm.distance(sp1[:normalized],
                     sp2[:normalized], 1, 4)
  return { 'edit_distance' => ed,
    'phonetic_match' => false,
    'match' => false } if ed/min_length.to_f > 0.3334
  return {'edit_distance' => ed,
    'phonetic_match' => true,
    'match' => true} if sp1[:phonetized] == sp2[:phonetized]

  match = true if ed <= 4 &&
    (min_length >= ed * 2) &&
    (ed < 2 || sp1[:normalized][0] == sp2[:normalized][0]) &&
    (ed < 4 || sp1[:normalized][0...3] == sp2[:normalized][0...3])
  { 'edit_distance' => ed, 'match' => match, 'phonetic_match' => false }
end

#match_uninomial(preparsed_1, preparsed_2) ⇒ Object



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# File 'lib/taxamatch_rb/base.rb', line 34

def match_uninomial(preparsed_1, preparsed_2)
  match_genera(preparsed_1[:uninomial], preparsed_2[:uninomial])
end

#taxamatch(str1, str2, return_boolean = true) ⇒ Object

takes two scientific names and returns true if names match and false if they don't



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# File 'lib/taxamatch_rb/base.rb', line 10

def taxamatch(str1, str2, return_boolean = true)
  preparsed_1 = @parser.parse(str1)
  preparsed_2 = @parser.parse(str2)
  match = taxamatch_preparsed(preparsed_1, preparsed_2) rescue nil
  return_boolean ? (!!match && match['match']) : match
end

#taxamatch_preparsed(preparsed_1, preparsed_2) ⇒ Object

takes two hashes of parsed scientific names, analyses them and returns back this function is useful when species strings are preparsed.



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# File 'lib/taxamatch_rb/base.rb', line 19

def taxamatch_preparsed(preparsed_1, preparsed_2)
  result = nil
  if preparsed_1[:uninomial] && preparsed_2[:uninomial]
    result =  match_uninomial(preparsed_1, preparsed_2)
  end
  if preparsed_1[:genus] && preparsed_2[:genus]
    result =  match_multinomial(preparsed_1, preparsed_2)
  end
  if result && result['match']
    result['match'] = match_authors(preparsed_1, preparsed_2) == -1 ?
      false : true
  end
  return result
end