biodiversity 3.1.2 → 3.1.3

checksums.yaml

@@ -0,0 +1,7 @@
+---
+SHA1:
+  metadata.gz: c6dd51dda2a710e62e09554051bf9f26569e8f2c
+  data.tar.gz: 24d44fde0d6d582f485a45cfb0c809c22793aac3
+SHA512:
+  metadata.gz: 5e5505a4a8dd3980eac1f126886bb6d59840c2380149d0690666311445a3875f0693dd23b431d96e96736859e40fe4758e8e542e7cf11131cb83f4e3c36400b5
+  data.tar.gz: f33859933760acd98e440df9b059473f651eaa918d5cb799f855d506793d1877456d9bbf4eb42dc949676a2342b79086190b6faf8831ad05f2e39abbee0ff23a

data/.gitignore

@@ -0,0 +1,19 @@
+lib/biodiversity/parser/*rb
+*.sw?
+.DS_Store
+coverage
+rdoc
+pkg
+*.swp
+*.swo
+biodiversity*.gem
+*json
+*xml
+tmp
+.DS_Store
+spec/parser/test_data_new.txt
+t
+bin
+.bundle
+bundle_bin
+Gemfile.lock

data/.ruby-version

@@ -0,0 +1 @@
+2.0.0-p353

data/.travis.yml

@@ -1,7 +1,8 @@
 rvm:
-  - 1.9.3
-  - 2.0.0
-bundler_args: --without development
+  - 1.9.3-p448
+  - 2.0.0-p353
 branches:
   only:
       - master
+before_script:
+  - bundle exec rake tt

data/Gemfile

@@ -1,15 +1,3 @@
 source 'https://rubygems.org'
 
-gem 'rake',           '~> 10.0'
-gem 'treetop',        '~> 1.4'
-gem 'parallel',       '~> 0.6'
-gem 'unicode_utils',  '~> 1.4'
-
-group :development do
-  gem 'debugger',     '~> 1.5'
-  gem 'jeweler',      '~> 1.8'
-end
-
-group :test do
-  gem 'rspec',        '~> 2.13'
-end
+gemspec

data/Rakefile

@@ -1,12 +1,21 @@
-dir = File.dirname(__FILE__)
-require 'rubygems'
-require 'rake'
-#$LOAD_PATH.unshift(File.join(dir, 'vendor', 'rspec', 'lib'))
+require 'bundler'
+Bundler::GemHelper.install_tasks
+
+begin
+  Bundler.setup(:default, :development)
+rescue Bundler::BundlerError => e
+  $stderr.puts e.message
+  $stderr.puts 'Run `bundle install` to install missing gems'
+  exit e.status_code
+end
+
 require 'rspec/core'
 require 'rspec/core/rake_task'
+require 'rake/dsl_definition'
+require 'rake'
+require 'rspec'
+require 'rspec/core/rake_task'
 
-#Gem::manage_gems
-#require 'rake/gempackagetask'
 
 task :default => :spec
 
@@ -14,35 +23,8 @@ RSpec::Core::RakeTask.new do |t|
   t.pattern = 'spec/**/*spec.rb'
 end
 
-ruby_version = RUBY_VERSION.split('.')[0..1].join('').to_i
-
-
-begin
-  require 'jeweler'
-  Jeweler::Tasks.new do |gem|
-    gem.name = 'biodiversity'
-    #To delete ruby_version < 19 ? 'biodiversity' : 'biodiversity19'
-    gem.summary = 'Parser of scientific names'
-    gem.description = 'Tools for biodiversity informatics'
-    gem.email = 'dmozzherin@gmail.com'
-    gem.homepage = 'http://github.com/GlobalNamesArchitecture/biodiversity'
-    gem.authors = ['Dmitry Mozzherin']
-    gem.has_rdoc = false
-    gem.bindir = 'bin'
-    gem.executables = ['nnparse', 'parserver']
-    gem.add_dependency('treetop')
-    gem.add_dependency('parallel')
-    # gem.add_dependency('json') if ruby_version < 19
-    gem.add_development_dependency "rspec"
-    # gem is a Gem::Specification...
-    # see http://www.rubygems.org/read/chapter/20 for additional settings
-  end
-rescue LoadError
-  puts 'Jeweler (or a dependency) not available. ' +
-    'Install it with: sudo gem install jeweler'
-end
-
 task :tt do
+  dir = File.dirname(__FILE__)
   ['scientific_name_clean',
    'scientific_name_dirty',
    'scientific_name_canonical'].each do |f|

data/bin/nnparse

@@ -1,24 +1,20 @@
 #!/usr/bin/env ruby
 # encoding: utf-8
-ruby_min_version = RUBY_VERSION.split(".")[0..1].join('').to_i
-if ruby_min_version < 19
-  require 'rubygems'
-  gem_name = 'biodiversity'
-else
-  gem_name = 'biodiversity19'
-end
-gem gem_name rescue nil
 
-$LOAD_PATH.unshift(File.expand_path(File.dirname(__FILE__) + "/../lib"))
 require 'biodiversity'
 require 'json'
 
 def parser_error(name)
-  {'scientificName' => {'parsed' => false, 'verbatim' => name,  'error' => 'Parser error'}}.to_json
+  { 'scientificName' => 
+    { 'parsed' => false, 
+      'verbatim' => name,  
+      'error' => 'Parser error' } }.to_json
 end
 
 if ARGV.empty?
-  puts "Usage:\n\nnnparse file_with_scientific_names [output_file]\n\ndefault output_file is parsed.json\n\n"
+  puts "Usage:\n\n" + 
+    "nnparse file_with_scientific_names [output_file]\n\n" + 
+    "default output_file is parsed.json\n\n"
   exit
 end
 
@@ -30,21 +26,14 @@ p = ScientificNameParser.new
 o = open(output, 'w')
 count = 0
 puts 'Parsing...'
-f = ruby_min_version < 19 ? open(input) : open(input, 'r:utf-8')
+f = open(input, 'r:utf-8')
 f.each do |line|
   count += 1
   puts("%s lines parsed" % count) if count % 10000 == 0
   name = line.gsub(/^[\d]*\s*/, '').strip
   begin
-    if ruby_min_version < 19
-      old_kcode = $KCODE
-      $KCODE = 'NONE'
-    end
     p.parse(name) 
     parsed_data = p.parsed.all_json rescue parser_error(name)
-    if ruby_min_version < 19
-      $KCODE = old_kcode
-    end
   rescue 
     parsed_data = parser_error(name)
   end

data/bin/parserver

@@ -1,8 +1,7 @@
 #!/usr/bin/env ruby
-require 'rubygems'
 require 'optparse'
 require 'socket'
-require 'biodiversity'          # Get sockets from stdlib
+require 'biodiversity'
 
 DEFAULT_PORT = 4334
 RUBY_VERSION_INT = RUBY_VERSION.split('.')[0..1].join('').to_i

data/biodiversity.gemspec

@@ -0,0 +1,28 @@
+$:.push File.expand_path("../lib", __FILE__)
+
+require 'biodiversity/version'
+
+Gem::Specification.new do |gem|
+  gem.name          = 'biodiversity'
+  gem.version       = Biodiversity::VERSION
+  gem.homepage      = 'https://github.com/GlobalNamesArchitecture/biodiversity'
+  gem.license       = 'MIT'
+  gem.summary       = %Q{Parser of scientific names}
+  gem.description   = %Q{Tools for biodiversity informatics}
+  gem.authors       = ['Dmitry Mozzherin']
+  gem.email         = 'dmozzherin@gmail.com'
+
+  gem.files         = `git ls-files`.split("\n")
+  gem.executables   = ['nnparse', 'parserver']
+  gem.require_paths = ['lib']
+
+  gem.add_runtime_dependency 'treetop', '~> 1.4'
+  gem.add_runtime_dependency 'parallel', '~> 0.7'
+  gem.add_runtime_dependency 'unicode_utils', '~> 1.4'
+
+  gem.add_development_dependency 'bundler', '~> 1.3'
+  gem.add_development_dependency 'rake', '~> 10.1'
+  gem.add_development_dependency 'rspec', '~> 2.14'
+  gem.add_development_dependency 'rr', '~> 1.1'
+  gem.add_development_dependency 'debugger', '~> 1.6'
+end

data/lib/biodiversity.rb

@@ -1,9 +1,15 @@
-require 'rubygems'
 require 'treetop'
+require 'json'
+require 'open-uri'
+require_relative 'biodiversity/version'
+require_relative 'biodiversity/parser'
+require_relative 'biodiversity/guid'
 
-dir = File.dirname(__FILE__)
+module Biodiversity
+  LSID_RESOLVER_URL = 'http://lsid.tdwg.org/' 
+
+  def self.version
+    VERSION
+  end
+end
 
-BIODIVERSITY_ROOT = File.join(dir, 'biodiversity')
-require File.join(dir, "/../conf/environment")
-require File.join(BIODIVERSITY_ROOT, "parser")
-require File.join(BIODIVERSITY_ROOT, "guid")

data/lib/biodiversity/guid.rb

@@ -1,2 +1 @@
-dir = File.dirname(__FILE__)
-require File.join(dir, *%w[guid lsid])
+require_relative 'guid/lsid'

data/lib/biodiversity/guid/lsid.rb

@@ -1,5 +1,3 @@
-require 'open-uri'
-
 class LsidResolver
   def self.resolve(lsid)
     http_get_rdf(lsid)
@@ -8,11 +6,11 @@ class LsidResolver
 protected
   def self.http_get_rdf(lsid)
     rdf = ''
-    open(LSID_RESOLVER_URL + lsid) do |f|
+    open(Biodiversity::LSID_RESOLVER_URL + lsid) do |f|
       f.each do |line|
         rdf += line if !line.strip.blank?
       end
     end
     rdf
   end
-end
+end

data/lib/biodiversity/parser.rb

@@ -1,10 +1,7 @@
 # encoding: UTF-8
-dir = File.dirname(__FILE__)
-require File.join(dir, *%w[parser scientific_name_clean])
-require File.join(dir, *%w[parser scientific_name_dirty])
-require File.join(dir, *%w[parser scientific_name_canonical])
-require 'rubygems'
-require 'json'
+require_relative 'parser/scientific_name_clean'
+require_relative 'parser/scientific_name_dirty'
+require_relative 'parser/scientific_name_canonical'
 
 module PreProcessor
   NOTES = /\s+(species\s+group|species\s+complex|group|author)\b.*$/i
@@ -108,10 +105,6 @@ end
 # end
 
 class ScientificNameParser
-  VERSION = open(File.join(File.dirname(__FILE__),
-                           '..',
-                           '..',
-                           'VERSION')).readline.strip
 
   FAILED_RESULT = ->(name) do
     { scientificName:
@@ -120,7 +113,7 @@ class ScientificNameParser
   end
 
   def self.version
-    VERSION
+    Biodiversity::VERSION
   end
 
   def self.fix_case(name_string)
@@ -213,7 +206,7 @@ class ScientificNameParser
     def @parsed.all(opts = {})
       canonical_with_rank = !!opts[:canonical_with_rank]
       parsed = self.class != Hash
-      res = { parsed: parsed, parser_version: ScientificNameParser::VERSION}
+      res = { parsed: parsed, parser_version: ScientificNameParser::version}
       if parsed
         hybrid = self.hybrid rescue false
         res.merge!({

data/lib/biodiversity/version.rb

@@ -0,0 +1,3 @@
+module Biodiversity
+  VERSION = '3.1.3'                                                              
+end 

data/spec/biodiversity_spec.rb

@@ -0,0 +1,9 @@
+require 'spec_helper'
+
+describe Biodiversity do
+  it 'should have version' do
+    version = Biodiversity::VERSION
+    version.should =~ /^\d+\.\d+\.\d+/
+    version.should == Biodiversity.version
+  end
+end

data/spec/guid/lsid.spec.rb

@@ -1,11 +1,9 @@
-dir = File.dirname("__FILE__")
-require 'rubygems'
-require File.expand_path(dir + "../../conf/environment")
-require File.expand_path(dir + "../../lib/biodiversity/guid")
+require_relative '../spec_helper'
 
 describe LsidResolver do
-  it "should return RFD document from lsid" do
-    lsid = "urn:lsid:ubio.org:classificationbank:2232671"
-    LsidResolver.resolve(lsid).class.should == "".class
+  it 'should return RFD document from lsid' do
+    lsid = 'urn:lsid:ubio.org:classificationbank:2232671'
+    stub(LsidResolver).resolve(lsid) {''}
+    LsidResolver.resolve(lsid).class.should == String
   end
 end

data/spec/parser/scientific_name_canonical_spec.rb

@@ -0,0 +1,37 @@
+# encoding: UTF-8
+require_relative '../spec_helper'
+
+describe ScientificNameCanonical do
+  before(:all) do
+    set_parser(ScientificNameCanonicalParser.new)
+  end
+
+  it 'should parse names with valid name part and unparseable rest' do
+    [
+      ['Morea ssjjlajajaj324$33 234243242','Morea', 
+       [{:uninomial=>{:string=>"Morea"}}], {0=>["uninomial", 5]}],
+      ['Morea (Morea) Burt 2342343242 23424322342 23424234', 
+       'Morea (Morea)', [{:genus=>{:string=>"Morea"}, 
+                          :infragenus=>{:string=>"Morea"}}], 
+       {0=>["genus", 5], 7=>["infragenus", 12]}],      
+      ['Morea (Morea) burtius 2342343242 23424322342 23424234', 
+       'Morea (Morea) burtius', [{:genus=>{:string=>"Morea"}, 
+                                  :infragenus=>{:string=>"Morea"}, 
+                                  :species=>{:string=>"burtius"}}], 
+       {0=>["genus", 5], 7=>["infragenus", 12], 14=>["species", 21]}],
+      ['Moraea spathulata ( (L. f. Klatt','Moraea spathulata',
+       [{:genus=>{:string=>"Moraea"}, :species=>{:string=>"spathulata"}}], 
+       {0=>["genus", 6], 7=>["species", 17]} ],
+      ['Verpericola megasoma ""Dall" Pils.','Verpericola megasoma',
+       [{:genus=>{:string=>"Verpericola"}, :species=>{:string=>"megasoma"}}], 
+       {0=>["genus", 11], 12=>["species", 20]}] 
+    ].each do |n|
+      parse(n[0]).should_not be_nil
+      value(n[0]).should == n[1]
+      details(n[0]).should == n[2]
+      pos(n[0]).should == n[3]
+      parse(n[0]).hybrid.should be_false
+    end
+  end  
+  
+end

data/spec/parser/{scientific_name_clean.spec.rb → scientific_name_clean_spec.rb}

@@ -1,6 +1,5 @@
 # encoding: UTF-8
-dir = File.dirname("__FILE__")
-require File.expand_path(dir + '../../spec/parser/spec_helper')
+require_relative '../spec_helper'
 
 
 describe ScientificNameClean do
@@ -20,19 +19,36 @@ describe ScientificNameClean do
   it 'should parse uninomial with author and year' do
     sn = 'Pseudocercospora Speg.'
     parse(sn).should_not be_nil
-    details(sn).should == [{:uninomial=>{:string=>"Pseudocercospora", :authorship=>"Speg.", :basionymAuthorTeam=>{:authorTeam=>"Speg.", :author=>["Speg."]}}}]
+    details(sn).should == [{:uninomial=>
+                            {:string=>"Pseudocercospora", 
+                             :authorship=>"Speg.", 
+                             :basionymAuthorTeam=>
+                          {:authorTeam=>"Speg.", :author=>["Speg."]}}}]
     pos(sn).should == {0=>["uninomial", 16], 17=>["author_word", 22]}
     sn = 'Pseudocercospora Spegazzini, 1910'
     parse(sn).should_not be_nil
     value(sn).should == 'Pseudocercospora Spegazzini 1910'
-    details(sn).should == [{:uninomial=>{:string=>"Pseudocercospora", :authorship=>"Spegazzini, 1910", :basionymAuthorTeam=>{:authorTeam=>"Spegazzini", :author=>["Spegazzini"], :year=>"1910"}}}]
-    pos(sn).should == {0=>["uninomial", 16], 17=>["author_word", 27], 29=>["year", 33]}
+    details(sn).should == [{:uninomial=>
+                            {:string=>"Pseudocercospora", 
+                             :authorship=>"Spegazzini, 1910", 
+                             :basionymAuthorTeam=>
+                            {:authorTeam=>"Spegazzini", 
+                             :author=>["Spegazzini"], :year=>"1910"}}}]
+    pos(sn).should == {0=>["uninomial", 16], 
+                       17=>["author_word", 27], 29=>["year", 33]}
   end
 
   it "should parse uninomials with uninomial ranks" do
     sn = "Epacridaceae trib. Archerieae Crayn & Quinn"
     parse(sn).should_not be_nil
-    details(sn).should == [{:uninomial=>{:string=>"Epacridaceae"}, :rank_uninomials=>"trib.", :uninomial2=>{:string=>"Archerieae", :authorship=>"Crayn & Quinn", :basionymAuthorTeam=>{:authorTeam=>"Crayn & Quinn", :author=>["Crayn", "Quinn"]}}}]
+    details(sn).should == [{:uninomial=>
+                            {:string=>"Epacridaceae"}, 
+                              :rank_uninomials=>"trib.", 
+                              :uninomial2=>{:string=>"Archerieae", 
+                                            :authorship=>"Crayn & Quinn", 
+                                            :basionymAuthorTeam=>
+                            {:authorTeam=>"Crayn & Quinn", 
+                             :author=>["Crayn", "Quinn"]}}}]
   end
 
   it 'should parse names with a valid 2 letter genus' do
@@ -65,7 +81,9 @@ describe ScientificNameClean do
     parse(sn).should_not be_nil
     value(sn).should == 'Pseudocercospora dendrobii'
     canonical(sn).should == 'Pseudocercospora dendrobii'
-    details(sn).should == [{:genus=>{:string=>"Pseudocercospora"}, :species=>{:string=>"dendrobii"}}]
+    details(sn).should == [{:genus=>
+                            {:string=>"Pseudocercospora"}, 
+                              :species=>{:string=>"dendrobii"}}]
     pos(sn).should == {0=>["genus", 16], 21=>["species", 30]}
   end
 
@@ -76,7 +94,9 @@ describe ScientificNameClean do
     sn = 'Ps.    dendrobii'
     parse(sn).should_not be_nil
     value(sn).should == 'Ps. dendrobii'
-    details(sn).should == [{:genus=>{:string=>"Ps."}, :species=>{:string=>"dendrobii"}}]
+    details(sn).should == [{:genus=>
+                            {:string=>"Ps."}, 
+                              :species=>{:string=>"dendrobii"}}]
   end
 
 
@@ -87,8 +107,16 @@ describe ScientificNameClean do
     sn = "Platypus bicaudatulus Schedl, 1935h"
     parse(sn).should_not be_nil
     value(sn).should == "Platypus bicaudatulus Schedl 1935"
-    details(sn).should == [{:genus=>{:string=>"Platypus"}, :species=>{:string=>"bicaudatulus", :authorship=>"Schedl, 1935h", :basionymAuthorTeam=>{:authorTeam=>"Schedl", :author=>["Schedl"], :year=>"1935"}}}]
-    pos(sn).should == {0=>["genus", 8], 9=>["species", 21], 22=>["author_word", 28], 30=>["year", 35]}
+    details(sn).should == [{:genus=>
+                            {:string=>"Platypus"}, 
+                              :species=>{:string=>"bicaudatulus", 
+                                         :authorship=>"Schedl, 1935h", 
+                                         :basionymAuthorTeam=>
+                            {:authorTeam=>"Schedl", :author=>["Schedl"], 
+                             :year=>"1935"}}}]
+    pos(sn).should == {0=>["genus", 8],
+                       9=>["species", 21], 22=>["author_word", 28], 
+                       30=>["year", 35]}
     parse("Platypus bicaudatulus Schedl, 1935B").should_not be_nil
     sn = "Platypus bicaudatulus Schedl (1935h)"
     parse(sn).should_not be_nil

data/spec/parser/{scientific_name_dirty.spec.rb → scientific_name_dirty_spec.rb}

@@ -1,6 +1,5 @@
 # encoding: UTF-8
-dir = File.dirname("__FILE__")
-require File.expand_path(dir + '../../spec/parser/spec_helper')
+require_relative '../spec_helper'
 
 describe ScientificNameDirty do
   before(:all) do
@@ -15,7 +14,13 @@ describe ScientificNameDirty do
     sn = "Eichornia crassipes ( (Martius) ) Solms-Laub."
     parse(sn).should_not be_nil
     value(sn).should == "Eichornia crassipes (Martius) Solms-Laub."
-    details(sn).should == [{:genus=>{:string=>"Eichornia"}, :species=>{:string=>"crassipes", :authorship=>"( (Martius) ) Solms-Laub.", :combinationAuthorTeam=>{:authorTeam=>"Solms-Laub.", :author=>["Solms-Laub."]}, :basionymAuthorTeam=>{:authorTeam=>"Martius", :author=>["Martius"]}}}]
+    details(sn).should == [{:genus=>{:string=>"Eichornia"}, 
+      :species=>{:string=>"crassipes", 
+      :authorship=>"( (Martius) ) Solms-Laub.", 
+      :combinationAuthorTeam=>{:authorTeam=>"Solms-Laub.", 
+        :author=>["Solms-Laub."]}, 
+        :basionymAuthorTeam=>{:authorTeam=>"Martius", 
+          :author=>["Martius"]}}}]
     pos(sn).should == {0=>["genus", 9], 10=>["species", 19], 23=>["author_word", 30], 34=>["author_word", 45]} 
   end
   

data/spec/parser/{scientific_name.spec.rb → scientific_name_spec.rb}

@@ -1,8 +1,7 @@
 # encoding: utf-8
+
 #NOTE: this spec needs compiled treetop files.
-dir = File.dirname("__FILE__")
-require File.expand_path(dir + '../../spec/parser/spec_helper')
-require File.expand_path(dir + '../../lib/biodiversity/parser')
+require_relative '../spec_helper'
 
 describe ScientificNameParser do
   before(:all) do
@@ -15,10 +14,10 @@ describe ScientificNameParser do
 
   it 'should ScientificNameParser::fix_case' do
     names = [
-      ["QUERCUS ALBA", "Quercus alba"],
-      ["QUERCUS (QUERCUS) ALBA", "Quercus (Quercus) alba"],
-      ["QÜERCUS", "Qüercus"],
-      ["PARDOSA MOéSTA", "Pardosa moésta"],
+      ['QUERCUS ALBA', 'Quercus alba'],
+      ['QUERCUS (QUERCUS) ALBA', 'Quercus (Quercus) alba'],
+      ['QÜERCUS', 'Qüercus'],
+      ['PARDOSA MOéSTA', 'Pardosa moésta'],
     ]
     names.each do |name, capitalization|
       ScientificNameParser::fix_case(name).should == capitalization
@@ -34,7 +33,7 @@ describe ScientificNameParser do
 
   # it 'should generate new test_file' do
   #   new_test = open(File.expand_path(dir +
-  #                    "../../spec/parser/test_data_new.txt"),'w')
+  #                    '../../spec/parser/test_data_new.txt'),'w')
   #   read_test_file do |y|
   #     if y[:comment]
   #       new_test.write y[:comment]
@@ -52,20 +51,20 @@ describe ScientificNameParser do
       '"parser_version":"test_version","verbatim":"ddd sljlkj 3223452432"}}'
   end
 
-  it "should show version when the flag :show_version set to true" do
+  it 'should show version when the flag :show_version set to true' do
     parse('Homo sapiens')[:scientificName][:parser_version].should_not be_nil
   end
 
-  it "should show version for not spelled names" do
+  it 'should show version for not spelled names' do
     parse('not_a_name')[:scientificName][:parser_version].should_not be_nil
   end
 
-  it "should generate version for viruses" do
+  it 'should generate version for viruses' do
     parse('Nile virus')[:scientificName][:parser_version].should_not be_nil
   end
 end
 
-describe "ScientificNameParser with ranked canonicals" do
+describe 'ScientificNameParser with ranked canonicals' do
   before(:all) do
     @parser = ScientificNameParser.new(canonical_with_rank: true)
   end
@@ -101,12 +100,12 @@ describe "ScientificNameParser with ranked canonicals" do
 end
 
 describe ParallelParser do
-  it "should find number of cpus" do
+  it 'should find number of cpus' do
     pparser = ParallelParser.new
     pparser.cpu_num.should > 0
   end
 
-  it "should parse several names in parallel" do
+  it 'should parse several names in parallel' do
     names = []
     read_test_file { |n| names << (n[:name]) if n[:name] }
     names.uniq!
@@ -116,7 +115,7 @@ describe ParallelParser do
     res.keys.size.should == names.size
   end
 
-  it "should parse several names in parallel with given num of processes" do
+  it 'should parse several names in parallel with given num of processes' do
     names = []
     read_test_file { |n| names << (n[:name]) if n[:name] }
     names.uniq!
@@ -126,8 +125,8 @@ describe ParallelParser do
     res.keys.size.should == names.size
   end
 
-  it "should have parsed name in native ruby format and in returned as \
-      a hash with name as a key and parsed data as value" do
+  it 'should have parsed name in native ruby format and in returned as \
+      a hash with name as a key and parsed data as value' do
     names = []
     read_test_file { |n| names << (n[:name]) if n[:name] }
     names.uniq!

data/spec/spec_helper.rb

@@ -0,0 +1,82 @@
+require 'yaml'
+require 'treetop'
+require 'json'
+require 'biodiversity'
+
+
+RSpec.configure do |c|
+  c.mock_with :rr
+end
+
+dir = File.dirname(__FILE__)
+Treetop.load(File.expand_path(File.join(dir, 
+             '../lib/biodiversity/parser/scientific_name_clean')))
+Treetop.load(File.expand_path(File.join(dir,
+             '../lib/biodiversity/parser/scientific_name_dirty')))
+Treetop.load(File.expand_path(File.join(dir, 
+             '../lib/biodiversity/parser/scientific_name_canonical')))
+
+PARSER_TEST_VERSION = 'test_version'
+
+def set_parser(parser)
+  @parser = parser
+end
+
+def parse(input)
+  @parser.parse(input)
+end
+
+def value(input)
+  parse(input).value
+end
+
+def canonical(input)
+  parse(input).canonical
+end
+
+def details(input)
+  parse(input).details
+end
+
+def pos(input)
+  parse(input).pos
+end
+
+def json(input)
+  parse(input).
+    to_json.gsub(/"parser_version":"[^"]*"/, 
+                 %Q["parser_version":"#{PARSER_TEST_VERSION}"])
+end
+
+def debug(input)
+  res = parse(input)
+  puts '<pre>'
+    if res
+      puts 'success!'
+      puts res.inspect
+    else
+      puts input
+      val = @parser.failure_reason.to_s.match(/column [0-9]*/).
+        to_s.gsub(/column /,'').to_i
+      print ('-' * (val - 1))
+      print "^   Computer says 'no'!\n"
+      puts @parser.failure_reason
+      puts @parser.to_yaml
+    end
+  puts '</pre>'
+end
+
+def read_test_file
+  f = open(File.expand_path(File.join(File.dirname(__FILE__), 
+                            'parser/test_data.txt')))
+  f.each do |line|
+    name, jsn = line.split("|")
+    if line.match(/^\s*#/) == nil && name && jsn
+      yield({:name => name, :jsn => jsn})
+    else
+      yield({:comment => line})
+    end
+  end
+end
+
+

metadata

@@ -1,36 +1,18 @@
 --- !ruby/object:Gem::Specification
 name: biodiversity
 version: !ruby/object:Gem::Version
-  version: 3.1.2
-  prerelease: 
+  version: 3.1.3
 platform: ruby
 authors:
 - Dmitry Mozzherin
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2013-06-21 00:00:00.000000000 Z
+date: 2013-12-18 00:00:00.000000000 Z
 dependencies:
-- !ruby/object:Gem::Dependency
-  name: rake
-  requirement: !ruby/object:Gem::Requirement
-    none: false
-    requirements:
-    - - ~>
-      - !ruby/object:Gem::Version
-        version: '10.0'
-  type: :runtime
-  prerelease: false
-  version_requirements: !ruby/object:Gem::Requirement
-    none: false
-    requirements:
-    - - ~>
-      - !ruby/object:Gem::Version
-        version: '10.0'
 - !ruby/object:Gem::Dependency
   name: treetop
   requirement: !ruby/object:Gem::Requirement
-    none: false
     requirements:
     - - ~>
       - !ruby/object:Gem::Version
@@ -38,7 +20,6 @@ dependencies:
   type: :runtime
   prerelease: false
   version_requirements: !ruby/object:Gem::Requirement
-    none: false
     requirements:
     - - ~>
       - !ruby/object:Gem::Version
@@ -46,23 +27,20 @@ dependencies:
 - !ruby/object:Gem::Dependency
   name: parallel
   requirement: !ruby/object:Gem::Requirement
-    none: false
     requirements:
     - - ~>
       - !ruby/object:Gem::Version
-        version: '0.6'
+        version: '0.7'
   type: :runtime
   prerelease: false
   version_requirements: !ruby/object:Gem::Requirement
-    none: false
     requirements:
     - - ~>
       - !ruby/object:Gem::Version
-        version: '0.6'
+        version: '0.7'
 - !ruby/object:Gem::Dependency
   name: unicode_utils
   requirement: !ruby/object:Gem::Requirement
-    none: false
     requirements:
     - - ~>
       - !ruby/object:Gem::Version
@@ -70,114 +48,100 @@ dependencies:
   type: :runtime
   prerelease: false
   version_requirements: !ruby/object:Gem::Requirement
-    none: false
     requirements:
     - - ~>
       - !ruby/object:Gem::Version
         version: '1.4'
 - !ruby/object:Gem::Dependency
-  name: debugger
+  name: bundler
   requirement: !ruby/object:Gem::Requirement
-    none: false
     requirements:
     - - ~>
       - !ruby/object:Gem::Version
-        version: '1.5'
+        version: '1.3'
   type: :development
   prerelease: false
   version_requirements: !ruby/object:Gem::Requirement
-    none: false
     requirements:
     - - ~>
       - !ruby/object:Gem::Version
-        version: '1.5'
+        version: '1.3'
 - !ruby/object:Gem::Dependency
-  name: jeweler
+  name: rake
   requirement: !ruby/object:Gem::Requirement
-    none: false
     requirements:
     - - ~>
       - !ruby/object:Gem::Version
-        version: '1.8'
+        version: '10.1'
   type: :development
   prerelease: false
   version_requirements: !ruby/object:Gem::Requirement
-    none: false
     requirements:
     - - ~>
       - !ruby/object:Gem::Version
-        version: '1.8'
+        version: '10.1'
 - !ruby/object:Gem::Dependency
-  name: treetop
+  name: rspec
   requirement: !ruby/object:Gem::Requirement
-    none: false
     requirements:
-    - - ! '>='
+    - - ~>
       - !ruby/object:Gem::Version
-        version: '0'
-  type: :runtime
+        version: '2.14'
+  type: :development
   prerelease: false
   version_requirements: !ruby/object:Gem::Requirement
-    none: false
     requirements:
-    - - ! '>='
+    - - ~>
       - !ruby/object:Gem::Version
-        version: '0'
+        version: '2.14'
 - !ruby/object:Gem::Dependency
-  name: parallel
+  name: rr
   requirement: !ruby/object:Gem::Requirement
-    none: false
     requirements:
-    - - ! '>='
+    - - ~>
       - !ruby/object:Gem::Version
-        version: '0'
-  type: :runtime
+        version: '1.1'
+  type: :development
   prerelease: false
   version_requirements: !ruby/object:Gem::Requirement
-    none: false
     requirements:
-    - - ! '>='
+    - - ~>
       - !ruby/object:Gem::Version
-        version: '0'
+        version: '1.1'
 - !ruby/object:Gem::Dependency
-  name: rspec
+  name: debugger
   requirement: !ruby/object:Gem::Requirement
-    none: false
     requirements:
-    - - ! '>='
+    - - ~>
       - !ruby/object:Gem::Version
-        version: '0'
+        version: '1.6'
   type: :development
   prerelease: false
   version_requirements: !ruby/object:Gem::Requirement
-    none: false
     requirements:
-    - - ! '>='
+    - - ~>
       - !ruby/object:Gem::Version
-        version: '0'
+        version: '1.6'
 description: Tools for biodiversity informatics
 email: dmozzherin@gmail.com
 executables:
 - nnparse
 - parserver
 extensions: []
-extra_rdoc_files:
-- LICENSE
-- README.md
+extra_rdoc_files: []
 files:
 - .document
-- .rvmrc
+- .gitignore
+- .ruby-version
 - .travis.yml
 - CHANGELOG
 - Gemfile
-- Gemfile.lock
 - LICENSE
 - README.md
 - Rakefile
-- VERSION
 - bin/nnparse
 - bin/parserver
-- conf/environment.rb
+- biodiversity.gemspec
 - examples/socket_client.rb
 - lib/biodiversity.rb
 - lib/biodiversity/guid.rb
@@ -186,42 +150,39 @@ files:
 - lib/biodiversity/parser/scientific_name_canonical.treetop
 - lib/biodiversity/parser/scientific_name_clean.treetop
 - lib/biodiversity/parser/scientific_name_dirty.treetop
-- pkg/.gitignore
+- lib/biodiversity/version.rb
+- pkg/.gitkeep
 - spec/biodiversity_spec.rb
 - spec/guid/lsid.spec.rb
-- spec/parser/scientific_name.spec.rb
-- spec/parser/scientific_name_canonical.spec.rb
-- spec/parser/scientific_name_clean.spec.rb
-- spec/parser/scientific_name_dirty.spec.rb
-- spec/parser/spec_helper.rb
+- spec/parser/scientific_name_canonical_spec.rb
+- spec/parser/scientific_name_clean_spec.rb
+- spec/parser/scientific_name_dirty_spec.rb
+- spec/parser/scientific_name_spec.rb
 - spec/parser/test_data.txt
 - spec/parser/todo.txt
 - spec/spec_helper.rb
-homepage: http://github.com/GlobalNamesArchitecture/biodiversity
-licenses: []
+homepage: https://github.com/GlobalNamesArchitecture/biodiversity
+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: 3336294247914629914
 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: 2.0.14
 signing_key: 
-specification_version: 3
+specification_version: 4
 summary: Parser of scientific names
 test_files: []

data/.rvmrc

@@ -1 +0,0 @@
-rvm use ruby-1.9.3-p392@biodiversity --create

data/Gemfile.lock

@@ -1,47 +0,0 @@
-GEM
-  remote: https://rubygems.org/
-  specs:
-    columnize (0.3.6)
-    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)
-    git (1.2.5)
-    jeweler (1.8.4)
-      bundler (~> 1.0)
-      git (>= 1.2.5)
-      rake
-      rdoc
-    json (1.7.7)
-    parallel (0.6.4)
-    polyglot (0.3.3)
-    rake (10.0.4)
-    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)
-    treetop (1.4.12)
-      polyglot
-      polyglot (>= 0.3.1)
-    unicode_utils (1.4.0)
-
-PLATFORMS
-  ruby
-
-DEPENDENCIES
-  debugger (~> 1.5)
-  jeweler (~> 1.8)
-  parallel (~> 0.6)
-  rake (~> 10.0)
-  rspec (~> 2.13)
-  treetop (~> 1.4)
-  unicode_utils (~> 1.4)

data/VERSION

@@ -1 +0,0 @@
-3.1.2

data/conf/environment.rb

@@ -1,3 +0,0 @@
-
-#Constants
-LSID_RESOLVER_URL = "http://lsid.tdwg.org/" 

data/spec/parser/scientific_name_canonical.spec.rb

@@ -1,26 +0,0 @@
-# encoding: UTF-8
-dir = File.dirname("__FILE__")
-require File.expand_path(dir + '../../spec/parser/spec_helper')
-
-describe ScientificNameCanonical do
-  before(:all) do
-    set_parser(ScientificNameCanonicalParser.new)
-  end
-
-  it 'should parse names with valid name part and unparseable rest' do
-    [
-      ['Morea ssjjlajajaj324$33 234243242','Morea', [{:uninomial=>{:string=>"Morea"}}], {0=>["uninomial", 5]}],
-      ['Morea (Morea) Burt 2342343242 23424322342 23424234', 'Morea (Morea)', [{:genus=>{:string=>"Morea"}, :infragenus=>{:string=>"Morea"}}], {0=>["genus", 5], 7=>["infragenus", 12]}],      
-      ['Morea (Morea) burtius 2342343242 23424322342 23424234', 'Morea (Morea) burtius', [{:genus=>{:string=>"Morea"}, :infragenus=>{:string=>"Morea"}, :species=>{:string=>"burtius"}}], {0=>["genus", 5], 7=>["infragenus", 12], 14=>["species", 21]}],
-      ['Moraea spathulata ( (L. f. Klatt','Moraea spathulata',[{:genus=>{:string=>"Moraea"}, :species=>{:string=>"spathulata"}}], {0=>["genus", 6], 7=>["species", 17]} ],
-      ['Verpericola megasoma ""Dall" Pils.','Verpericola megasoma',[{:genus=>{:string=>"Verpericola"}, :species=>{:string=>"megasoma"}}], {0=>["genus", 11], 12=>["species", 20]}] 
-    ].each do |n|
-      parse(n[0]).should_not be_nil
-      value(n[0]).should == n[1]
-      details(n[0]).should == n[2]
-      pos(n[0]).should == n[3]
-      parse(n[0]).hybrid.should be_false
-    end
-  end  
-  
-end

data/spec/parser/spec_helper.rb

@@ -1,70 +0,0 @@
-dir = File.dirname("__FILE__")
-require 'rubygems'
-require 'yaml'
-require 'treetop'
-require 'json'
-require File.expand_path(dir + '../../lib/biodiversity/parser')
-
-Treetop.load(File.expand_path(dir + '../../lib/biodiversity/parser/scientific_name_clean'))
-Treetop.load(File.expand_path(dir + '../../lib/biodiversity/parser/scientific_name_dirty'))
-Treetop.load(File.expand_path(dir + '../../lib/biodiversity/parser/scientific_name_canonical'))
-
-PARSER_TEST_VERSION = "test_version"
-
-def set_parser(parser)
-  @parser = parser
-end
-
-def parse(input)
-  @parser.parse(input)
-end
-
-def value(input)
-  parse(input).value
-end
-
-def canonical(input)
-  parse(input).canonical
-end
-
-def details(input)
-  parse(input).details
-end
-
-def pos(input)
-  parse(input).pos
-end
-
-def json(input)
-  parse(input).to_json.gsub(/"parser_version":"[^"]*"/, %Q["parser_version":"#{PARSER_TEST_VERSION}"])
-end
-
-def debug(input)
-  res = parse(input)
-  puts "<pre>"
-    if res
-      puts 'success!'
-      puts res.inspect
-    else
-      puts input
-      val = @parser.failure_reason.to_s.match(/column [0-9]*/).to_s.gsub(/column /,'').to_i
-      print ("-" * (val - 1))
-      print "^   Computer says 'no'!\n"
-      puts @parser.failure_reason
-      puts @parser.to_yaml
-    end
-  puts "</pre>"
-end
-
-def read_test_file
-  f = open(File.expand_path(File.dirname("__FILE__") + "../../spec/parser/test_data.txt"))
-  f.each do |line|
-    name, jsn = line.split("|")
-    if line.match(/^\s*#/) == nil && name && jsn
-      yield({:name => name, :jsn => jsn})
-    else
-      yield({:comment => line})
-    end
-  end
-end
-