lib/taxamatch_rb/base.rb
module Taxamatch
class Base
def initialize
@parser = Taxamatch::Atomizer.new
@dlm = DamerauLevenshtein
end
# takes two scientific names and returns true
# if names match and false if they don't
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
# takes two hashes of parsed scientific names, analyses them and
# returns back this function is useful when species strings are preparsed.
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
def match_uninomial(preparsed_1, preparsed_2)
match_genera(preparsed_1[:uninomial], preparsed_2[:uninomial])
end
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
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
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
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
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
end
end