taxamatch_rb 1.0.1 → 1.1.0

data/lib/taxamatch_rb.rb

@@ -1,176 +1,16 @@
-# encoding: UTF-8
-$:.unshift(File.dirname(__FILE__)) unless
-   $:.include?(File.dirname(__FILE__)) ||
-   $:.include?(File.expand_path(File.dirname(__FILE__)))
-# $:.unshift('taxamatch_rb')
-require 'damerau-levenshtein'
-require 'taxamatch_rb/atomizer'
-require 'taxamatch_rb/normalizer'
-require 'taxamatch_rb/phonetizer'
-require 'taxamatch_rb/authmatch'
-
-if RUBY_VERSION < '1.9.1'
-  raise 'IMPORTANT: Parsley-store gem  requires ruby >= 1.9.1'
+# encoding: utf-8
+require "taxamatch_rb/version"
+require "damerau-levenshtein"
+require "taxamatch_rb/base"
+require "taxamatch_rb/atomizer"
+require "taxamatch_rb/normalizer"
+require "taxamatch_rb/phonetizer"
+require "taxamatch_rb/authmatch"
+
+if RUBY_VERSION < "1.9.1"
+  fail "IMPORTANT: taxamatch_rb gem requires ruby >= 1.9.1"
 end
 
+# Taxamatch provides fuzzy comparison between two scientific names
 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) #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 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

data/taxamatch_rb.gemspec

@@ -1,62 +1,35 @@
-# Generated by jeweler
-# DO NOT EDIT THIS FILE DIRECTLY
-# Instead, edit Jeweler::Tasks in Rakefile, and run 'rake gemspec'
-# -*- encoding: utf-8 -*-
+# coding: utf-8
+lib = File.expand_path('../lib', __FILE__)
+$LOAD_PATH.unshift(lib) unless $LOAD_PATH.include?(lib)
+require 'taxamatch_rb/version'
 
-Gem::Specification.new do |s|
-  s.name = "taxamatch_rb"
-  s.version = "1.0.1"
+Gem::Specification.new do |gem|
+  gem.name          = "taxamatch_rb"
+  gem.version       = Taxamatch::VERSION
+  gem.authors       = ["Dmitry Mozzherin"]
+  gem.email         = ["dmozzherin@gmail.com"]
 
-  s.required_rubygems_version = Gem::Requirement.new(">= 0") if s.respond_to? :required_rubygems_version=
-  s.authors = ["Dmitry Mozzherin"]
-  s.date = "2013-06-17"
-  s.description = "This gem implements algorithm for fuzzy matching scientific names developed by Tony Rees"
-  s.email = "dmozzherin@gmail.com"
-  s.extra_rdoc_files = [
-    "LICENSE",
-    "README.md"
-  ]
-  s.files = [
-    "CHANGELOG",
-    "Gemfile",
-    "Gemfile.lock",
-    "LICENSE",
-    "Makefile",
-    "README.md",
-    "Rakefile",
-    "VERSION",
-    "lib/taxamatch_rb.rb",
-    "lib/taxamatch_rb/atomizer.rb",
-    "lib/taxamatch_rb/authmatch.rb",
-    "lib/taxamatch_rb/normalizer.rb",
-    "lib/taxamatch_rb/phonetizer.rb",
-    "spec/spec.opts",
-    "spec/spec_helper.rb",
-    "spec/taxamatch_rb_spec.rb",
-    "spec/taxamatch_test.txt",
-    "taxamatch_rb.gemspec"
-  ]
-  s.homepage = "http://github.com/GlobalNamesArchitecture/taxamatch_rb"
-  s.require_paths = ["lib"]
-  s.rubygems_version = "1.8.25"
-  s.summary = "Implementation of Tony Rees Taxamatch algorithms"
+  gem.summary       = %q{Fuzzy matching of scientific names}
+  gem.description   = "The purpose of Taxamatch gem is to facilitate fuzzy" \
+                      "comparison of two scientific name renderings to find" \
+                      "out if they actually point to the same scientific name."
+  gem.homepage      = "https://github.com/GlobalNamesArchitecture/taxamatch_rb"
+  gem.license       = "MIT"
 
-  if s.respond_to? :specification_version then
-    s.specification_version = 3
+  gem.files         = `git ls-files -z`.split("\x0").
+                      reject { |f| f.match(%r{^(test|spec|features)/}) }
+  gem.bindir        = "exe"
+  gem.executables   = gem.files.grep(%r{^exe/}) { |f| File.basename(f) }
+  gem.require_paths = ["lib"]
 
-    if Gem::Version.new(Gem::VERSION) >= Gem::Version.new('1.2.0') then
-      s.add_runtime_dependency(%q<biodiversity>, ["~> 3.1.0"])
-      s.add_runtime_dependency(%q<damerau-levenshtein>, ["~> 0.5.4"])
-      s.add_runtime_dependency(%q<json>, ["~> 1.7.7"])
-    else
-      s.add_dependency(%q<biodiversity>, ["~> 3.1.0"])
-      s.add_dependency(%q<damerau-levenshtein>, ["~> 0.5.4"])
-      s.add_dependency(%q<json>, ["~> 1.7.7"])
-    end
-  else
-    s.add_dependency(%q<biodiversity>, ["~> 3.1.0"])
-    s.add_dependency(%q<damerau-levenshtein>, ["~> 0.5.4"])
-    s.add_dependency(%q<json>, ["~> 1.7.7"])
-  end
-end
+  gem.add_runtime_dependency "biodiversity", "~> 3.1"
+  gem.add_runtime_dependency "damerau-levenshtein", "~> 1.0"
+  gem.add_runtime_dependency "json", "~> 1.8"
 
+  gem.add_development_dependency "bundler", "~> 1.6"
+  gem.add_development_dependency "rake", "~> 10.4"
+  gem.add_development_dependency "rspec", "~> 3.2"
+  gem.add_development_dependency "cucumber", "~> 2.0"
+  gem.add_development_dependency "coveralls", "~> 0.8"
+  gem.add_development_dependency "rubocop", "~> 0.30"
+end

metadata

@@ -1,116 +1,192 @@
 --- !ruby/object:Gem::Specification
 name: taxamatch_rb
 version: !ruby/object:Gem::Version
-  version: 1.0.1
-  prerelease: 
+  version: 1.1.0
 platform: ruby
 authors:
 - Dmitry Mozzherin
 autorequire: 
-bindir: bin
+bindir: exe
 cert_chain: []
-date: 2013-06-17 00:00:00.000000000 Z
+date: 2015-04-21 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: biodiversity
   requirement: !ruby/object:Gem::Requirement
-    none: false
     requirements:
-    - - ~>
+    - - "~>"
       - !ruby/object:Gem::Version
-        version: 3.1.0
+        version: '3.1'
   type: :runtime
   prerelease: false
   version_requirements: !ruby/object:Gem::Requirement
-    none: false
     requirements:
-    - - ~>
+    - - "~>"
       - !ruby/object:Gem::Version
-        version: 3.1.0
+        version: '3.1'
 - !ruby/object:Gem::Dependency
   name: damerau-levenshtein
   requirement: !ruby/object:Gem::Requirement
-    none: false
     requirements:
-    - - ~>
+    - - "~>"
       - !ruby/object:Gem::Version
-        version: 0.5.4
+        version: '1.0'
   type: :runtime
   prerelease: false
   version_requirements: !ruby/object:Gem::Requirement
-    none: false
     requirements:
-    - - ~>
+    - - "~>"
       - !ruby/object:Gem::Version
-        version: 0.5.4
+        version: '1.0'
 - !ruby/object:Gem::Dependency
   name: json
   requirement: !ruby/object:Gem::Requirement
-    none: false
     requirements:
-    - - ~>
+    - - "~>"
       - !ruby/object:Gem::Version
-        version: 1.7.7
+        version: '1.8'
   type: :runtime
   prerelease: false
   version_requirements: !ruby/object:Gem::Requirement
-    none: false
     requirements:
-    - - ~>
+    - - "~>"
       - !ruby/object:Gem::Version
-        version: 1.7.7
-description: This gem implements algorithm for fuzzy matching scientific names developed
-  by Tony Rees
-email: dmozzherin@gmail.com
+        version: '1.8'
+- !ruby/object:Gem::Dependency
+  name: bundler
+  requirement: !ruby/object:Gem::Requirement
+    requirements:
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: '1.6'
+  type: :development
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    requirements:
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: '1.6'
+- !ruby/object:Gem::Dependency
+  name: rake
+  requirement: !ruby/object:Gem::Requirement
+    requirements:
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: '10.4'
+  type: :development
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    requirements:
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: '10.4'
+- !ruby/object:Gem::Dependency
+  name: rspec
+  requirement: !ruby/object:Gem::Requirement
+    requirements:
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: '3.2'
+  type: :development
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    requirements:
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: '3.2'
+- !ruby/object:Gem::Dependency
+  name: cucumber
+  requirement: !ruby/object:Gem::Requirement
+    requirements:
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: '2.0'
+  type: :development
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    requirements:
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: '2.0'
+- !ruby/object:Gem::Dependency
+  name: coveralls
+  requirement: !ruby/object:Gem::Requirement
+    requirements:
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: '0.8'
+  type: :development
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    requirements:
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: '0.8'
+- !ruby/object:Gem::Dependency
+  name: rubocop
+  requirement: !ruby/object:Gem::Requirement
+    requirements:
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: '0.30'
+  type: :development
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    requirements:
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: '0.30'
+description: The purpose of Taxamatch gem is to facilitate fuzzycomparison of two
+  scientific name renderings to findout if they actually point to the same scientific
+  name.
+email:
+- dmozzherin@gmail.com
 executables: []
 extensions: []
-extra_rdoc_files:
-- LICENSE
-- README.md
+extra_rdoc_files: []
 files:
+- ".gitignore"
+- ".rspec"
+- ".rubocop.yml"
+- ".travis.yml"
 - CHANGELOG
+- CODE_OF_CONDUCT.md
 - Gemfile
-- Gemfile.lock
-- LICENSE
-- Makefile
+- LICENSE.txt
 - README.md
 - Rakefile
-- VERSION
+- bin/console
+- bin/setup
 - lib/taxamatch_rb.rb
 - lib/taxamatch_rb/atomizer.rb
 - lib/taxamatch_rb/authmatch.rb
+- lib/taxamatch_rb/base.rb
 - lib/taxamatch_rb/normalizer.rb
 - lib/taxamatch_rb/phonetizer.rb
-- spec/spec.opts
-- spec/spec_helper.rb
-- spec/taxamatch_rb_spec.rb
-- spec/taxamatch_test.txt
+- lib/taxamatch_rb/version.rb
 - taxamatch_rb.gemspec
-homepage: http://github.com/GlobalNamesArchitecture/taxamatch_rb
-licenses: []
+homepage: https://github.com/GlobalNamesArchitecture/taxamatch_rb
+licenses:
+- MIT
+metadata: {}
 post_install_message: 
 rdoc_options: []
 require_paths:
 - lib
 required_ruby_version: !ruby/object:Gem::Requirement
-  none: false
   requirements:
-  - - ! '>='
+  - - ">="
     - !ruby/object:Gem::Version
       version: '0'
-      segments:
-      - 0
-      hash: 1177825761849915556
 required_rubygems_version: !ruby/object:Gem::Requirement
-  none: false
   requirements:
-  - - ! '>='
+  - - ">="
     - !ruby/object:Gem::Version
       version: '0'
 requirements: []
 rubyforge_project: 
-rubygems_version: 1.8.25
+rubygems_version: 2.4.5
 signing_key: 
-specification_version: 3
-summary: Implementation of Tony Rees Taxamatch algorithms
+specification_version: 4
+summary: Fuzzy matching of scientific names
 test_files: []

data/Gemfile.lock

@@ -1,86 +0,0 @@
-GEM
-  remote: https://rubygems.org/
-  specs:
-    activesupport (3.2.13)
-      i18n (= 0.6.1)
-      multi_json (~> 1.0)
-    biodiversity (3.1.0)
-      parallel
-      parallel (~> 0.6)
-      rake (~> 10.0)
-      treetop
-      treetop (~> 1.4)
-      unicode_utils (~> 1.4)
-    builder (3.2.0)
-    columnize (0.3.6)
-    cucumber (1.3.1)
-      builder (>= 2.1.2)
-      diff-lcs (>= 1.1.3)
-      gherkin (~> 2.12.0)
-      multi_json (~> 1.3)
-    damerau-levenshtein (0.5.4)
-    debugger (1.5.0)
-      columnize (>= 0.3.1)
-      debugger-linecache (~> 1.2.0)
-      debugger-ruby_core_source (~> 1.2.0)
-    debugger-linecache (1.2.0)
-    debugger-ruby_core_source (1.2.0)
-    diff-lcs (1.2.4)
-    gherkin (2.12.0)
-      multi_json (~> 1.3)
-    git (1.2.5)
-    i18n (0.6.1)
-    jeweler (1.8.4)
-      bundler (~> 1.0)
-      git (>= 1.2.5)
-      rake
-      rdoc
-    json (1.7.7)
-    metaclass (0.0.1)
-    mocha (0.13.3)
-      metaclass (~> 0.0.1)
-    multi_json (1.7.3)
-    parallel (0.7.0)
-    polyglot (0.3.3)
-    rake (10.0.4)
-    rake-compiler (0.8.3)
-      rake
-    rdoc (4.0.1)
-      json (~> 1.4)
-    rspec (2.13.0)
-      rspec-core (~> 2.13.0)
-      rspec-expectations (~> 2.13.0)
-      rspec-mocks (~> 2.13.0)
-    rspec-core (2.13.1)
-    rspec-expectations (2.13.0)
-      diff-lcs (>= 1.1.3, < 2.0)
-    rspec-mocks (2.13.1)
-    ruby-prof (0.13.0)
-    shoulda (3.5.0)
-      shoulda-context (~> 1.0, >= 1.0.1)
-      shoulda-matchers (>= 1.4.1, < 3.0)
-    shoulda-context (1.1.1)
-    shoulda-matchers (2.1.0)
-      activesupport (>= 3.0.0)
-    treetop (1.4.14)
-      polyglot
-      polyglot (>= 0.3.1)
-    unicode_utils (1.4.0)
-
-PLATFORMS
-  ruby
-
-DEPENDENCIES
-  biodiversity (~> 3.1.0)
-  bundler (~> 1.3)
-  cucumber (~> 1.3)
-  damerau-levenshtein (~> 0.5.4)
-  debugger (~> 1.5)
-  jeweler (~> 1.8)
-  json (~> 1.7.7)
-  mocha (~> 0.13)
-  rake (~> 10.0)
-  rake-compiler (~> 0.8)
-  rspec (~> 2.13)
-  ruby-prof (~> 0.13)
-  shoulda (~> 3.5)

data/LICENSE

@@ -1,20 +0,0 @@
-Copyright (c) 2009-2013 Marine Biological Laboratory
-
-Permission is hereby granted, free of charge, to any person obtaining
-a copy of this software and associated documentation files (the
-"Software"), to deal in the Software without restriction, including
-without limitation the rights to use, copy, modify, merge, publish,
-distribute, sublicense, and/or sell copies of the Software, and to
-permit persons to whom the Software is furnished to do so, subject to
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