# encoding: UTF-8 $:.unshift(File.dirname(__FILE__)) unless $:.include?(File.dirname(__FILE__)) || $:.include?(File.expand_path(File.dirname(__FILE__))) # $:.unshift('taxamatch_rb') require 'taxamatch_rb/damerau_levenshtein_mod' require 'taxamatch_rb/atomizer' require 'taxamatch_rb/normalizer' require 'taxamatch_rb/phonetizer' require 'taxamatch_rb/authmatch' raise "IMPORTANT: Parsley-store gem requires ruby >= 1.9.1" if RUBY_VERSION < "1.9.1" $KCODE='u' if RUBY_VERSION.split('.')[1].to_i < 9 module Taxamatch class Base def initialize @parser = Taxamatch::Atomizer.new @dlm = Taxamatch::DamerauLevenshteinMod.new 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 result = match_uninomial(preparsed_1, preparsed_2) if preparsed_1[:uninomial] && preparsed_2[:uninomial] result = match_multinomial(preparsed_1, preparsed_2) if preparsed_1[:genus] && preparsed_2[:genus] if result && result['match'] result['match'] = match_authors(preparsed_1, preparsed_2) == 0 ? 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) genus1_length = genus1[:normalized].size genus2_length = genus2[:normalized].size min_length = [genus1_length, genus2_length].min 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) sp1_length = sp1[:normalized].size sp2_length = sp2[:normalized].size min_length = [sp1_length, sp2_length].min 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) #TODO put block 4 return {'edit_distance' => ed, 'phonetic_match' => false, 'match' => false} if ed/min_length.to_f > 0.3334 #puts 's: %s, %s, %s' % [sp1[:normalized], sp2[:normalized], ed] 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) au1 = preparsed_1[:all_authors] au2 = preparsed_2[:all_authors] yr1 = preparsed_1[:all_years] yr2 = preparsed_2[:all_years] Taxamatch::Authmatch.authmatch(au1, au2, yr1, yr2) 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'] match['match'] = false if match['edit_distance'] > (infraspecies_match ? 6 : 4) match['match'] &&= genus_match['match'] match['phonetic_match'] &&= genus_match['phonetic_match'] match end end end