biodiversity 0.5.14
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- data/.document +5 -0
- data/.gitignore +13 -0
- data/LICENSE +20 -0
- data/README.rdoc +44 -0
- data/Rakefile +43 -0
- data/VERSION +1 -0
- data/bin/nnparse +43 -0
- data/bin/parserver +14 -0
- data/biodiversity.gemspec +88 -0
- data/conf/environment.rb +3 -0
- data/lib/biodiversity.rb +9 -0
- data/lib/biodiversity/guid.rb +2 -0
- data/lib/biodiversity/guid/lsid.rb +18 -0
- data/lib/biodiversity/parser.rb +57 -0
- data/lib/biodiversity/parser/scientific_name_canonical.rb +462 -0
- data/lib/biodiversity/parser/scientific_name_canonical.treetop +111 -0
- data/lib/biodiversity/parser/scientific_name_clean.rb +5991 -0
- data/lib/biodiversity/parser/scientific_name_clean.treetop +1195 -0
- data/lib/biodiversity/parser/scientific_name_dirty.rb +1056 -0
- data/lib/biodiversity/parser/scientific_name_dirty.treetop +211 -0
- data/spec/biodiversity_spec.rb +0 -0
- data/spec/guid/lsid.spec.rb +12 -0
- data/spec/parser/scientific_name.spec.rb +35 -0
- data/spec/parser/scientific_name_canonical.spec.rb +27 -0
- data/spec/parser/scientific_name_clean.spec.rb +504 -0
- data/spec/parser/scientific_name_dirty.spec.rb +90 -0
- data/spec/parser/spec_helper.rb +69 -0
- data/spec/parser/test_data.txt +235 -0
- data/spec/spec_helper.rb +0 -0
- metadata +134 -0
data/.document
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data/.gitignore
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data/LICENSE
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Copyright (c) 2009 Dmitry Mozzherin
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Permission is hereby granted, free of charge, to any person obtaining
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a copy of this software and associated documentation files (the
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"Software"), to deal in the Software without restriction, including
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without limitation the rights to use, copy, modify, merge, publish,
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distribute, sublicense, and/or sell copies of the Software, and to
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permit persons to whom the Software is furnished to do so, subject to
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the following conditions:
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The above copyright notice and this permission notice shall be
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included in all copies or substantial portions of the Software.
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THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
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EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF
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MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
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NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE
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LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION
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OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION
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WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE.
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data/README.rdoc
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= Biodiversity
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Parses species scientific name and breaks it into elements.
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== Installation
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To install gem you need RubyGems >= 1.2.0
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$ gem sources -a http://gems.github.com (you only have to do this once)
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$ sudo gem install dimus-biodiversity
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== Example usage
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You can parse file with species names from command line. File should contain one scientific name per line
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nnparser file_with_names
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You can use it as a library
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require 'biodiversity'
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parser = ScientificNameParser.new
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# to parse a scientific name into a ruby hash
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parser.parse("Plantago major")
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#to get json representation
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parser.parse("Plantago").to_json
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#or
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parser.parse("Plantago")
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parser.all_json
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# to clean name up
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parser.parse(" Plantago major ")[:scientificName][:normalized]
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# to get only cleaned up latin part of the name
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parser.parse("Pseudocercospora dendrobii (H.C. Burnett) U. Braun & Crous 2003")[:scientificName][:canonical]
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# to get detailed information about elements of the name
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parser.parse("Pseudocercospora dendrobii (H.C. Burnett 1883) U. Braun & Crous 2003")[:scientificName][:details]
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# to resolve lsid and get back RDF file
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LsidResolver.resolve("urn:lsid:ubio.org:classificationbank:2232671")
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data/Rakefile
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dir = File.dirname(__FILE__)
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require 'rubygems'
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require 'rake'
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#$LOAD_PATH.unshift(File.join(dir, 'vendor', 'rspec', 'lib'))
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require 'spec/rake/spectask'
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#Gem::manage_gems
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#require 'rake/gempackagetask'
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task :default => :spec
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Spec::Rake::SpecTask.new do |t|
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t.pattern = 'spec/**/*spec.rb'
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end
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begin
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require 'jeweler'
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Jeweler::Tasks.new do |gem|
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gem.name = "biodiversity"
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gem.summary = 'Parser of scientific names'
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gem.description = 'Tools for biodiversity informatics'
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gem.email = "dmozzherin@gmail.com"
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gem.homepage = "http://github.com/dimus/biodiversity"
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gem.authors = ["Dmitry Mozzherin"]
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gem.has_rdoc = false
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gem.bindir = 'bin'
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gem.executables = ['nnparse']
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gem.add_dependency('treetop')
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gem.add_dependency('json') if RUBY_VERSION.split(".")[0..1].join('').to_i < 19
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gem.add_development_dependency "rspec"
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# gem is a Gem::Specification... see http://www.rubygems.org/read/chapter/20 for additional settings
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end
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rescue LoadError
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puts "Jeweler (or a dependency) not available. Install it with: sudo gem install jeweler"
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end
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task :tt do
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system("tt #{dir}/lib/biodiversity/parser/scientific_name_clean.treetop")
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system("tt #{dir}/lib/biodiversity/parser/scientific_name_dirty.treetop")
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system("tt #{dir}/lib/biodiversity/parser/scientific_name_canonical.treetop")
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end
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data/VERSION
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1
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0.5.14
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data/bin/nnparse
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#!/usr/bin/env ruby
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require 'rubygems'
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gem 'dimus-biodiversity' rescue gem 'biodiversity' rescue nil
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$LOAD_PATH.unshift(File.expand_path(File.dirname(__FILE__) + "/../lib"))
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require 'biodiversity'
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require 'json'
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if ARGV.empty?
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puts "Usage:\n\nnnparse file_with_scientific_names [output_file]\n\ndefault output_file is parsed.json\n\n"
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exit
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end
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input = ARGV[0]
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output = ARGV[1] || 'parsed.json'
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ruby_min_version = RUBY_VERSION.split(".")[0..1].join('').to_i
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p = ScientificNameParser.new
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o = open(output, 'w')
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count = 0
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puts 'Parsing...'
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IO.foreach(input) do |line|
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count += 1
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puts("%s lines parsed" % count) if count % 10000 == 0
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name = line.gsub(/^[\d]*\s*/, '').strip
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begin
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if ruby_min_version < 19
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old_kcode = $KCODE
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$KCODE = 'NONE'
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end
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p.parse(name)
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parsed_data = p.parsed.all_json rescue {'parsed' => false, 'verbatim' => name, 'error' => 'Parser error'}.to_json
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if ruby_min_version < 19
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$KCODE = old_kcode
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end
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rescue
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parsed_data = {'parsed' => false, 'verbatim' => name, 'error' => 'Parser error'}.to_json
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end
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o.write parsed_data + "\n"
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end
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data/bin/parserver
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#!/usr/bin/env ruby
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require 'rubygems'
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require 'socket'
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require 'biodiversity' # Get sockets from stdlib
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parser = ScientificNameParser.new
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server = TCPServer.open(4334) # Socket to listen on port 4334
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loop do # Servers run forever
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client = server.accept # Wait for a client to connect
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while a = client.readline
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client.close if ['end','exit','q', '.'].include? a.strip
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client.puts parser.parse(a).to_json
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end
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end
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# Generated by jeweler
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# DO NOT EDIT THIS FILE DIRECTLY
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# Instead, edit Jeweler::Tasks in Rakefile, and run the gemspec command
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# -*- encoding: utf-8 -*-
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Gem::Specification.new do |s|
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s.name = %q{biodiversity}
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s.version = "0.5.14"
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s.required_rubygems_version = Gem::Requirement.new(">= 0") if s.respond_to? :required_rubygems_version=
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s.authors = ["Dmitry Mozzherin"]
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s.date = %q{2010-03-19}
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s.default_executable = %q{nnparse}
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s.description = %q{Tools for biodiversity informatics}
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s.email = %q{dmozzherin@gmail.com}
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s.executables = ["nnparse"]
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s.extra_rdoc_files = [
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"LICENSE",
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"README.rdoc"
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]
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s.files = [
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".document",
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".gitignore",
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"LICENSE",
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"README.rdoc",
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"Rakefile",
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"VERSION",
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"bin/nnparse",
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"bin/parserver",
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"biodiversity.gemspec",
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"conf/environment.rb",
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"lib/biodiversity.rb",
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"lib/biodiversity/guid.rb",
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"lib/biodiversity/guid/lsid.rb",
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"lib/biodiversity/parser.rb",
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"lib/biodiversity/parser/scientific_name_canonical.rb",
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"lib/biodiversity/parser/scientific_name_canonical.treetop",
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"lib/biodiversity/parser/scientific_name_clean.rb",
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"lib/biodiversity/parser/scientific_name_clean.treetop",
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"lib/biodiversity/parser/scientific_name_dirty.rb",
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"lib/biodiversity/parser/scientific_name_dirty.treetop",
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"pkg/.gitignore",
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"spec/biodiversity_spec.rb",
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"spec/guid/lsid.spec.rb",
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"spec/parser/scientific_name.spec.rb",
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"spec/parser/scientific_name_canonical.spec.rb",
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"spec/parser/scientific_name_clean.spec.rb",
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"spec/parser/scientific_name_dirty.spec.rb",
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"spec/parser/spec_helper.rb",
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"spec/parser/test_data.txt",
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"spec/spec_helper.rb"
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]
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s.homepage = %q{http://github.com/dimus/biodiversity}
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s.rdoc_options = ["--charset=UTF-8"]
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s.require_paths = ["lib"]
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s.rubygems_version = %q{1.3.6}
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s.summary = %q{Parser of scientific names}
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s.test_files = [
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"spec/biodiversity_spec.rb",
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"spec/guid/lsid.spec.rb",
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"spec/parser/scientific_name.spec.rb",
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"spec/parser/scientific_name_canonical.spec.rb",
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"spec/parser/scientific_name_clean.spec.rb",
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"spec/parser/scientific_name_dirty.spec.rb",
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"spec/parser/spec_helper.rb",
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"spec/spec_helper.rb"
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]
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if s.respond_to? :specification_version then
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current_version = Gem::Specification::CURRENT_SPECIFICATION_VERSION
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s.specification_version = 3
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if Gem::Version.new(Gem::RubyGemsVersion) >= Gem::Version.new('1.2.0') then
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s.add_runtime_dependency(%q<treetop>, [">= 0"])
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s.add_runtime_dependency(%q<json>, [">= 0"])
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s.add_development_dependency(%q<rspec>, [">= 0"])
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else
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s.add_dependency(%q<treetop>, [">= 0"])
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s.add_dependency(%q<json>, [">= 0"])
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s.add_dependency(%q<rspec>, [">= 0"])
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end
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else
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s.add_dependency(%q<treetop>, [">= 0"])
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s.add_dependency(%q<json>, [">= 0"])
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s.add_dependency(%q<rspec>, [">= 0"])
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end
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end
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data/conf/environment.rb
ADDED
data/lib/biodiversity.rb
ADDED
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require 'rubygems'
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require 'treetop'
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dir = File.dirname(__FILE__)
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BIODIVERSITY_ROOT = File.join(dir, 'biodiversity')
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require File.join(dir, "/../conf/environment")
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require File.join(BIODIVERSITY_ROOT, "parser")
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require File.join(BIODIVERSITY_ROOT, "guid")
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require 'open-uri'
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class LsidResolver
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def self.resolve(lsid)
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http_get_rdf(lsid)
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end
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protected
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def self.http_get_rdf(lsid)
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rdf = ''
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open(LSID_RESOLVER_URL + lsid) do |f|
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f.each do |line|
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rdf += line if !line.strip.blank?
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end
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end
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rdf
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end
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end
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# encoding: UTF-8
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dir = File.dirname(__FILE__)
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require File.join(dir, *%w[parser scientific_name_clean])
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require File.join(dir, *%w[parser scientific_name_dirty])
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require File.join(dir, *%w[parser scientific_name_canonical])
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require 'rubygems'
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require 'json'
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class ScientificNameParser
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def initialize
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@verbatim = ''
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@clean = ScientificNameCleanParser.new
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@dirty = ScientificNameDirtyParser.new
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@canonical = ScientificNameCanonicalParser.new
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@parsed = nil
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end
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def parsed
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@parsed
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end
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def parse(a_string)
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@verbatim = a_string
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@parsed = @clean.parse(a_string) || @dirty.parse(a_string) || @canonical.parse(a_string) || {:verbatim => a_string}
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def @parsed.all
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parsed = self.class != Hash
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res = {:parsed => parsed}
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if parsed
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hybrid = self.hybrid rescue false
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res.merge!({
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:verbatim => self.text_value,
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:normalized => self.value,
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:canonical => self.canonical,
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:hybrid => hybrid,
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:details => self.details,
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:positions => self.pos
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})
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else
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res.merge!(self)
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end
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res = {:scientificName => res}
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res
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end
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def @parsed.pos_json
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self.pos.to_json rescue ''
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end
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49
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+
|
50
|
+
def @parsed.all_json
|
51
|
+
self.all.to_json rescue ''
|
52
|
+
end
|
53
|
+
|
54
|
+
@parsed.all
|
55
|
+
end
|
56
|
+
end
|
57
|
+
|
@@ -0,0 +1,462 @@
|
|
1
|
+
# encoding: UTF-8
|
2
|
+
module ScientificNameCanonical
|
3
|
+
include Treetop::Runtime
|
4
|
+
|
5
|
+
def root
|
6
|
+
@root || :root
|
7
|
+
end
|
8
|
+
|
9
|
+
include ScientificNameClean
|
10
|
+
|
11
|
+
include ScientificNameDirty
|
12
|
+
|
13
|
+
module Root0
|
14
|
+
def hybrid
|
15
|
+
false
|
16
|
+
end
|
17
|
+
|
18
|
+
def details
|
19
|
+
[super]
|
20
|
+
end
|
21
|
+
end
|
22
|
+
|
23
|
+
module Root1
|
24
|
+
def hybrid
|
25
|
+
false
|
26
|
+
end
|
27
|
+
|
28
|
+
def details
|
29
|
+
[super]
|
30
|
+
end
|
31
|
+
end
|
32
|
+
|
33
|
+
def _nt_root
|
34
|
+
start_index = index
|
35
|
+
if node_cache[:root].has_key?(index)
|
36
|
+
cached = node_cache[:root][index]
|
37
|
+
@index = cached.interval.end if cached
|
38
|
+
return cached
|
39
|
+
end
|
40
|
+
|
41
|
+
i0 = index
|
42
|
+
r1 = _nt_multinomial_with_garbage
|
43
|
+
r1.extend(Root0)
|
44
|
+
if r1
|
45
|
+
r0 = r1
|
46
|
+
else
|
47
|
+
r2 = _nt_uninomial_with_garbage
|
48
|
+
r2.extend(Root1)
|
49
|
+
if r2
|
50
|
+
r0 = r2
|
51
|
+
else
|
52
|
+
@index = i0
|
53
|
+
r0 = nil
|
54
|
+
end
|
55
|
+
end
|
56
|
+
|
57
|
+
node_cache[:root][start_index] = r0
|
58
|
+
|
59
|
+
r0
|
60
|
+
end
|
61
|
+
|
62
|
+
module MultinomialWithGarbage0
|
63
|
+
def a
|
64
|
+
elements[0]
|
65
|
+
end
|
66
|
+
|
67
|
+
def space
|
68
|
+
elements[1]
|
69
|
+
end
|
70
|
+
|
71
|
+
def b
|
72
|
+
elements[2]
|
73
|
+
end
|
74
|
+
|
75
|
+
def space
|
76
|
+
elements[3]
|
77
|
+
end
|
78
|
+
|
79
|
+
def c
|
80
|
+
elements[4]
|
81
|
+
end
|
82
|
+
|
83
|
+
def garbage
|
84
|
+
elements[5]
|
85
|
+
end
|
86
|
+
end
|
87
|
+
|
88
|
+
module MultinomialWithGarbage1
|
89
|
+
def value
|
90
|
+
a.value + " " + b.value + " " + c.value
|
91
|
+
end
|
92
|
+
|
93
|
+
def canonical
|
94
|
+
a.canonical + " " + b.canonical + " " + c.canonical
|
95
|
+
end
|
96
|
+
|
97
|
+
def pos
|
98
|
+
a.pos.merge(b.pos).merge(c.pos)
|
99
|
+
end
|
100
|
+
|
101
|
+
def details
|
102
|
+
a.details.merge(b.details).merge(c.details)
|
103
|
+
end
|
104
|
+
end
|
105
|
+
|
106
|
+
module MultinomialWithGarbage2
|
107
|
+
def a
|
108
|
+
elements[0]
|
109
|
+
end
|
110
|
+
|
111
|
+
def space
|
112
|
+
elements[1]
|
113
|
+
end
|
114
|
+
|
115
|
+
def b
|
116
|
+
elements[2]
|
117
|
+
end
|
118
|
+
|
119
|
+
def garbage
|
120
|
+
elements[3]
|
121
|
+
end
|
122
|
+
end
|
123
|
+
|
124
|
+
module MultinomialWithGarbage3
|
125
|
+
def value
|
126
|
+
a.value + " " + b.value
|
127
|
+
end
|
128
|
+
|
129
|
+
def canonical
|
130
|
+
a.canonical + " " + b.canonical
|
131
|
+
end
|
132
|
+
|
133
|
+
def pos
|
134
|
+
a.pos.merge(b.pos)
|
135
|
+
end
|
136
|
+
|
137
|
+
def details
|
138
|
+
a.details.merge(b.details)
|
139
|
+
end
|
140
|
+
end
|
141
|
+
|
142
|
+
module MultinomialWithGarbage4
|
143
|
+
def a
|
144
|
+
elements[0]
|
145
|
+
end
|
146
|
+
|
147
|
+
def space
|
148
|
+
elements[1]
|
149
|
+
end
|
150
|
+
|
151
|
+
def b
|
152
|
+
elements[2]
|
153
|
+
end
|
154
|
+
|
155
|
+
def garbage
|
156
|
+
elements[3]
|
157
|
+
end
|
158
|
+
end
|
159
|
+
|
160
|
+
module MultinomialWithGarbage5
|
161
|
+
def value
|
162
|
+
a.value + " " + b.value
|
163
|
+
end
|
164
|
+
|
165
|
+
def canonical
|
166
|
+
a.canonical + " " + b.canonical
|
167
|
+
end
|
168
|
+
|
169
|
+
def pos
|
170
|
+
a.pos.merge(b.pos)
|
171
|
+
end
|
172
|
+
|
173
|
+
def details
|
174
|
+
a.details.merge(b.details)
|
175
|
+
end
|
176
|
+
end
|
177
|
+
|
178
|
+
def _nt_multinomial_with_garbage
|
179
|
+
start_index = index
|
180
|
+
if node_cache[:multinomial_with_garbage].has_key?(index)
|
181
|
+
cached = node_cache[:multinomial_with_garbage][index]
|
182
|
+
@index = cached.interval.end if cached
|
183
|
+
return cached
|
184
|
+
end
|
185
|
+
|
186
|
+
i0 = index
|
187
|
+
i1, s1 = index, []
|
188
|
+
r2 = _nt_genus
|
189
|
+
s1 << r2
|
190
|
+
if r2
|
191
|
+
r3 = _nt_space
|
192
|
+
s1 << r3
|
193
|
+
if r3
|
194
|
+
r4 = _nt_subgenus
|
195
|
+
s1 << r4
|
196
|
+
if r4
|
197
|
+
r5 = _nt_space
|
198
|
+
s1 << r5
|
199
|
+
if r5
|
200
|
+
r6 = _nt_species
|
201
|
+
s1 << r6
|
202
|
+
if r6
|
203
|
+
r7 = _nt_garbage
|
204
|
+
s1 << r7
|
205
|
+
end
|
206
|
+
end
|
207
|
+
end
|
208
|
+
end
|
209
|
+
end
|
210
|
+
if s1.last
|
211
|
+
r1 = instantiate_node(SyntaxNode,input, i1...index, s1)
|
212
|
+
r1.extend(MultinomialWithGarbage0)
|
213
|
+
r1.extend(MultinomialWithGarbage1)
|
214
|
+
else
|
215
|
+
@index = i1
|
216
|
+
r1 = nil
|
217
|
+
end
|
218
|
+
if r1
|
219
|
+
r0 = r1
|
220
|
+
else
|
221
|
+
i8, s8 = index, []
|
222
|
+
r9 = _nt_genus
|
223
|
+
s8 << r9
|
224
|
+
if r9
|
225
|
+
r10 = _nt_space
|
226
|
+
s8 << r10
|
227
|
+
if r10
|
228
|
+
r11 = _nt_subgenus
|
229
|
+
s8 << r11
|
230
|
+
if r11
|
231
|
+
r12 = _nt_garbage
|
232
|
+
s8 << r12
|
233
|
+
end
|
234
|
+
end
|
235
|
+
end
|
236
|
+
if s8.last
|
237
|
+
r8 = instantiate_node(SyntaxNode,input, i8...index, s8)
|
238
|
+
r8.extend(MultinomialWithGarbage2)
|
239
|
+
r8.extend(MultinomialWithGarbage3)
|
240
|
+
else
|
241
|
+
@index = i8
|
242
|
+
r8 = nil
|
243
|
+
end
|
244
|
+
if r8
|
245
|
+
r0 = r8
|
246
|
+
else
|
247
|
+
i13, s13 = index, []
|
248
|
+
r14 = _nt_genus
|
249
|
+
s13 << r14
|
250
|
+
if r14
|
251
|
+
r15 = _nt_space
|
252
|
+
s13 << r15
|
253
|
+
if r15
|
254
|
+
r16 = _nt_species
|
255
|
+
s13 << r16
|
256
|
+
if r16
|
257
|
+
r17 = _nt_garbage
|
258
|
+
s13 << r17
|
259
|
+
end
|
260
|
+
end
|
261
|
+
end
|
262
|
+
if s13.last
|
263
|
+
r13 = instantiate_node(SyntaxNode,input, i13...index, s13)
|
264
|
+
r13.extend(MultinomialWithGarbage4)
|
265
|
+
r13.extend(MultinomialWithGarbage5)
|
266
|
+
else
|
267
|
+
@index = i13
|
268
|
+
r13 = nil
|
269
|
+
end
|
270
|
+
if r13
|
271
|
+
r0 = r13
|
272
|
+
else
|
273
|
+
@index = i0
|
274
|
+
r0 = nil
|
275
|
+
end
|
276
|
+
end
|
277
|
+
end
|
278
|
+
|
279
|
+
node_cache[:multinomial_with_garbage][start_index] = r0
|
280
|
+
|
281
|
+
r0
|
282
|
+
end
|
283
|
+
|
284
|
+
module UninomialWithGarbage0
|
285
|
+
def a
|
286
|
+
elements[0]
|
287
|
+
end
|
288
|
+
|
289
|
+
def b
|
290
|
+
elements[1]
|
291
|
+
end
|
292
|
+
end
|
293
|
+
|
294
|
+
module UninomialWithGarbage1
|
295
|
+
def value
|
296
|
+
a.value
|
297
|
+
end
|
298
|
+
|
299
|
+
def canonical
|
300
|
+
a.canonical
|
301
|
+
end
|
302
|
+
|
303
|
+
def pos
|
304
|
+
a.pos
|
305
|
+
end
|
306
|
+
|
307
|
+
def details
|
308
|
+
{:uninomial => a.details[:uninomial]}
|
309
|
+
end
|
310
|
+
end
|
311
|
+
|
312
|
+
def _nt_uninomial_with_garbage
|
313
|
+
start_index = index
|
314
|
+
if node_cache[:uninomial_with_garbage].has_key?(index)
|
315
|
+
cached = node_cache[:uninomial_with_garbage][index]
|
316
|
+
@index = cached.interval.end if cached
|
317
|
+
return cached
|
318
|
+
end
|
319
|
+
|
320
|
+
i0, s0 = index, []
|
321
|
+
r1 = _nt_uninomial_epitheton
|
322
|
+
s0 << r1
|
323
|
+
if r1
|
324
|
+
r2 = _nt_garbage
|
325
|
+
s0 << r2
|
326
|
+
end
|
327
|
+
if s0.last
|
328
|
+
r0 = instantiate_node(SyntaxNode,input, i0...index, s0)
|
329
|
+
r0.extend(UninomialWithGarbage0)
|
330
|
+
r0.extend(UninomialWithGarbage1)
|
331
|
+
else
|
332
|
+
@index = i0
|
333
|
+
r0 = nil
|
334
|
+
end
|
335
|
+
|
336
|
+
node_cache[:uninomial_with_garbage][start_index] = r0
|
337
|
+
|
338
|
+
r0
|
339
|
+
end
|
340
|
+
|
341
|
+
module Garbage0
|
342
|
+
def space
|
343
|
+
elements[0]
|
344
|
+
end
|
345
|
+
|
346
|
+
def space
|
347
|
+
elements[2]
|
348
|
+
end
|
349
|
+
|
350
|
+
end
|
351
|
+
|
352
|
+
module Garbage1
|
353
|
+
def space_hard
|
354
|
+
elements[0]
|
355
|
+
end
|
356
|
+
|
357
|
+
end
|
358
|
+
|
359
|
+
def _nt_garbage
|
360
|
+
start_index = index
|
361
|
+
if node_cache[:garbage].has_key?(index)
|
362
|
+
cached = node_cache[:garbage][index]
|
363
|
+
@index = cached.interval.end if cached
|
364
|
+
return cached
|
365
|
+
end
|
366
|
+
|
367
|
+
i0 = index
|
368
|
+
i1, s1 = index, []
|
369
|
+
r2 = _nt_space
|
370
|
+
s1 << r2
|
371
|
+
if r2
|
372
|
+
if has_terminal?('\G["\',.]', true, index)
|
373
|
+
r3 = instantiate_node(SyntaxNode,input, index...(index + 1))
|
374
|
+
@index += 1
|
375
|
+
else
|
376
|
+
r3 = nil
|
377
|
+
end
|
378
|
+
s1 << r3
|
379
|
+
if r3
|
380
|
+
r4 = _nt_space
|
381
|
+
s1 << r4
|
382
|
+
if r4
|
383
|
+
s5, i5 = [], index
|
384
|
+
loop do
|
385
|
+
if has_terminal?('\G[^щ]', true, index)
|
386
|
+
r6 = instantiate_node(SyntaxNode,input, index...(index + 1))
|
387
|
+
@index += 1
|
388
|
+
else
|
389
|
+
r6 = nil
|
390
|
+
end
|
391
|
+
if r6
|
392
|
+
s5 << r6
|
393
|
+
else
|
394
|
+
break
|
395
|
+
end
|
396
|
+
end
|
397
|
+
r5 = instantiate_node(SyntaxNode,input, i5...index, s5)
|
398
|
+
s1 << r5
|
399
|
+
end
|
400
|
+
end
|
401
|
+
end
|
402
|
+
if s1.last
|
403
|
+
r1 = instantiate_node(SyntaxNode,input, i1...index, s1)
|
404
|
+
r1.extend(Garbage0)
|
405
|
+
else
|
406
|
+
@index = i1
|
407
|
+
r1 = nil
|
408
|
+
end
|
409
|
+
if r1
|
410
|
+
r0 = r1
|
411
|
+
else
|
412
|
+
i7, s7 = index, []
|
413
|
+
r8 = _nt_space_hard
|
414
|
+
s7 << r8
|
415
|
+
if r8
|
416
|
+
s9, i9 = [], index
|
417
|
+
loop do
|
418
|
+
if has_terminal?('\G[^ш]', true, index)
|
419
|
+
r10 = instantiate_node(SyntaxNode,input, index...(index + 1))
|
420
|
+
@index += 1
|
421
|
+
else
|
422
|
+
r10 = nil
|
423
|
+
end
|
424
|
+
if r10
|
425
|
+
s9 << r10
|
426
|
+
else
|
427
|
+
break
|
428
|
+
end
|
429
|
+
end
|
430
|
+
if s9.empty?
|
431
|
+
@index = i9
|
432
|
+
r9 = nil
|
433
|
+
else
|
434
|
+
r9 = instantiate_node(SyntaxNode,input, i9...index, s9)
|
435
|
+
end
|
436
|
+
s7 << r9
|
437
|
+
end
|
438
|
+
if s7.last
|
439
|
+
r7 = instantiate_node(SyntaxNode,input, i7...index, s7)
|
440
|
+
r7.extend(Garbage1)
|
441
|
+
else
|
442
|
+
@index = i7
|
443
|
+
r7 = nil
|
444
|
+
end
|
445
|
+
if r7
|
446
|
+
r0 = r7
|
447
|
+
else
|
448
|
+
@index = i0
|
449
|
+
r0 = nil
|
450
|
+
end
|
451
|
+
end
|
452
|
+
|
453
|
+
node_cache[:garbage][start_index] = r0
|
454
|
+
|
455
|
+
r0
|
456
|
+
end
|
457
|
+
|
458
|
+
end
|
459
|
+
|
460
|
+
class ScientificNameCanonicalParser < Treetop::Runtime::CompiledParser
|
461
|
+
include ScientificNameCanonical
|
462
|
+
end
|