module Taxamatch # Matches name strings of scientific names class Base def initialize @parser = Taxamatch::Atomizer.new @dlm = DamerauLevenshtein end def taxamatch(str1, str2, return_boolean = true) preparsed_1 = @parser.parse(str1) preparsed_2 = @parser.parse(str2) match = taxamatch_preparsed(preparsed_1, preparsed_2) return_boolean ? (!!match && match["match"]) : match end def taxamatch_preparsed(preparsed_1, preparsed_2) result = nil if preparsed_1[:uninomial] && preparsed_2[:uninomial] result = match_uninomial(preparsed_1, preparsed_2) elsif 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) end result rescue StandardError nil 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) #TODO put block 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 true if au1.empty? || au2.empty? score = Taxamatch::Authmatch.authmatch(au1, au2, yr1, yr2) score == 0 ? false : true 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