biodiversity 3.1.5 → 3.1.6

data/spec/parser/scientific_name_dirty_spec.rb

@@ -5,69 +5,70 @@ describe ScientificNameDirty do
   before(:all) do
    set_parser(ScientificNameDirtyParser.new)
   end
-  
+
   it 'parses clean names' do
     expect(parse('Betula verucosa (L.) Bar. 1899')).to_not be_nil
   end
-  
+
   it 'parses double parenthesis' do
     sn = 'Eichornia crassipes ( (Martius) ) Solms-Laub.'
     expect(parse(sn)).to_not be_nil
     expect(value(sn)).to eq 'Eichornia crassipes (Martius) Solms-Laub.'
-    expect(details(sn)).to eq [{:genus=>{:string=>'Eichornia'}, 
-      :species=>{:string=>'crassipes', 
-      :authorship=>'( (Martius) ) Solms-Laub.', 
-      :combinationAuthorTeam=>{:authorTeam=>'Solms-Laub.', 
-        :author=>['Solms-Laub.']}, 
-        :basionymAuthorTeam=>{:authorTeam=>'Martius', 
-          :author=>['Martius']}}}]
-    expect(pos(sn)).to eq({0=>['genus', 9], 10=>['species', 19],
-                           23=>['author_word', 30], 34=>['author_word', 45]})
+    expect(details(sn)).to eq [{ genus: { string: 'Eichornia' },
+      species: { string: 'crassipes',
+      authorship: '( (Martius) ) Solms-Laub.',
+      combinationAuthorTeam: { authorTeam: 'Solms-Laub.',
+        author: ['Solms-Laub.'] },
+        basionymAuthorTeam: { authorTeam: 'Martius',
+          author: ['Martius'] } } }]
+    expect(pos(sn)).to eq({ 0 => ['genus', 9], 10 => ['species', 19],
+                           23 => ['author_word', 30],
+                           34 => ['author_word', 45] })
   end
-  
+
   it 'parses year without author' do
     sn = 'Acarospora cratericola 1929'
     expect(parse(sn)).to_not be_nil
-    expect(pos(sn)).to eq({0=>['genus', 10],
-                           11=>['species', 22], 23=>['year', 27]})
-    expect(details(sn)).to eq [{:genus=>{:string=>'Acarospora'}, 
-                                :species=>{:string=>'cratericola', 
-                                           :year=>'1929'}}]
+    expect(pos(sn)).to eq({ 0 => ['genus', 10],
+                           11 => ['species', 22], 23 => ['year', 27] })
+    expect(details(sn)).to eq [{ genus: { string: 'Acarospora' },
+                                species: { string: 'cratericola',
+                                           year: '1929' } }]
   end
-  
+
   it 'parses double years' do
     sn = 'Tridentella tangeroae Bruce, 1987-92'
     expect(parse(sn)).to_not be_nil
-    expect(pos(sn)).to eq({0=>['genus', 11], 12=>['species', 21], 
-                           22=>['author_word', 27], 29=>['year', 36]})
-    expect(details(sn)).to eq [{:genus=>{:string=>'Tridentella'}, 
-      :species=>{:string=>'tangeroae', :authorship=>'Bruce, 1987-92', 
-      :basionymAuthorTeam=>{:authorTeam=>'Bruce', :author=>['Bruce'], 
-      :year=>'1987-92'}}}]
+    expect(pos(sn)).to eq({ 0 => ['genus', 11], 12 => ['species', 21],
+                           22 => ['author_word', 27], 29 => ['year', 36] })
+    expect(details(sn)).to eq [{ genus: { string: 'Tridentella' },
+      species: { string: 'tangeroae', authorship: 'Bruce, 1987-92',
+      basionymAuthorTeam: { authorTeam: 'Bruce', author: ['Bruce'],
+      year: '1987-92' } } }]
   end
-  
+
   it 'parses dirty years' do
     expect(parse('Tridentella tangeroae Bruce, 1988B')).to_not be_nil
     expect(parse('Tridentella tangeroae Bruce, 1988b')).to_not be_nil
     expect(parse('Tridentella tangeroae Bruce, 1988d')).to_not be_nil
     sn = 'Tridentella tangeroae Bruce, 198?'
     expect(parse(sn)).to_not be_nil
-    expect(pos(sn)).to eq({0=>['genus', 11], 12=>['species', 21], 
-                           22=>['author_word', 27], 29=>['year', 33]})
+    expect(pos(sn)).to eq({ 0 => ['genus', 11], 12 => ['species', 21],
+                           22 => ['author_word', 27], 29 => ['year', 33] })
   end
-  
+
   it 'parses year with page number' do
     sn = 'Gymnodactylus irregularis WERMUTH 1965: 54'
     expect(parse(sn)).to_not be_nil
     expect(value(sn)).to eq 'Gymnodactylus irregularis Wermuth 1965'
-    expect(details(sn)).to eq [{:genus=>{:string=>'Gymnodactylus'}, 
-      :species=>{:string=>'irregularis', :authorship=>'WERMUTH 1965: 54', 
-      :basionymAuthorTeam=>{:authorTeam=>'WERMUTH', :author=>['Wermuth'], 
-      :year=>'1965'}}}]
-    expect(pos(sn)).to eq({0=>['genus', 13], 14=>['species', 25], 
-                           26=>['author_word', 33], 34=>['year', 38]})
+    expect(details(sn)).to eq [{ genus: { string: 'Gymnodactylus' },
+      species: { string: 'irregularis', authorship: 'WERMUTH 1965: 54',
+      basionymAuthorTeam: { authorTeam: 'WERMUTH', author: ['Wermuth'],
+      year: '1965' } } }]
+    expect(pos(sn)).to eq({ 0 => ['genus', 13], 14 => ['species', 25],
+                           26 => ['author_word', 33], 34 => ['year', 38] })
   end
-  
+
   it 'parses year with []' do
     expect(parse('Anthoscopus Cabanis [1851]')).to_not be_nil
     expect(value('Anthoscopus Cabanis [185?]')).
@@ -77,86 +78,86 @@ describe ScientificNameDirty do
       to eq 'Anthoscopus Cabanis (1851)'
     sn = 'Anthoscopus Cabanis [1851?]'
     expect(value(sn)).to eq 'Anthoscopus Cabanis (1851?)'
-    expect(details(sn)).to eq [{:uninomial=>{:string=>'Anthoscopus', 
-      :authorship=>'Cabanis [1851?]', :basionymAuthorTeam=>
-      {:authorTeam=>'Cabanis', :author=>['Cabanis'], 
-      :approximate_year=>'(1851?)'}}}]
-    expect(pos(sn)).to eq({0=>['uninomial', 11], 
-                           12=>['author_word', 19], 21=>['year', 26]})
+    expect(details(sn)).to eq [{ uninomial: { string: 'Anthoscopus',
+      authorship: 'Cabanis [1851?]', basionymAuthorTeam:
+      { authorTeam: 'Cabanis', author: ['Cabanis'],
+      approximate_year: '(1851?)' } } }]
+    expect(pos(sn)).to eq({ 0 => ['uninomial', 11],
+                           12 => ['author_word', 19], 21 => ['year', 26] })
     sn = 'Trismegistia monodii Ando, 1973 [1974]'
     expect(parse(sn)).to_not be_nil
 
     #should it be 'Trismegistia monodii Ando 1973 (1974)' instead?
-    expect(value(sn)).to eq 'Trismegistia monodii Ando 1973 (1974)' 
-    
-    expect(details(sn)).to eq [{:genus=>{:string=>'Trismegistia'}, 
-      :species=>{:string=>'monodii', :authorship=>'Ando, 1973 [1974]', 
-      :basionymAuthorTeam=>{:authorTeam=>'Ando', :author=>['Ando'], 
-      :year=>'1973', :approximate_year=>'(1974)'}}}]
-    expect(pos(sn)).to eq({0=>['genus', 12], 13=>['species', 20], 
-      21=>['author_word', 25], 27=>['year', 31], 33=>['year', 37]})
+    expect(value(sn)).to eq 'Trismegistia monodii Ando 1973 (1974)'
+
+    expect(details(sn)).to eq [{ genus: { string: 'Trismegistia' },
+      species: { string: 'monodii', authorship: 'Ando, 1973 [1974]',
+      basionymAuthorTeam: { authorTeam: 'Ando', author: ['Ando'],
+      year: '1973', approximate_year: '(1974)' } } }]
+    expect(pos(sn)).to eq({ 0 => ['genus', 12], 13 => ['species', 20],
+      21 => ['author_word', 25], 27 => ['year', 31], 33 => ['year', 37] })
     expect(parse('Zygaena witti Wiegel [1973]')).to_not be_nil
     sn = 'Deyeuxia coarctata Kunth, 1815 [1816]'
     expect(parse(sn)).to_not be_nil
-    expect(pos(sn)).to eq({0=>['genus', 8], 9=>['species', 18], 
-                          19=>['author_word', 24], 26=>['year', 30], 
-                          32=>['year', 36]})
+    expect(pos(sn)).to eq({ 0 => ['genus', 8], 9 => ['species', 18],
+                          19 => ['author_word', 24], 26 => ['year', 30],
+                          32 => ['year', 36] })
   end
-  
+
   it 'parses new stuff' do
     sn = 'Zoropsis (TaKeoa) nishimurai Yaginuma, 1971' #skipping for now
     sn = 'Campylobacter pyloridis Marshall et al.1985.'
-    expect(details(sn)).to eq [{:genus=>{:string=>'Campylobacter'}, 
-      :species=>{:string=>'pyloridis', :authorship=>'Marshall et al.1985.', 
-      :basionymAuthorTeam=>{:authorTeam=>'Marshall et al.', 
-      :author=>['Marshall et al.'], :year=>'1985'}}}]
+    expect(details(sn)).to eq [{ genus: { string: 'Campylobacter' },
+      species: { string: 'pyloridis', authorship: 'Marshall et al.1985.',
+      basionymAuthorTeam: { authorTeam: 'Marshall et al.',
+      author: ['Marshall et al.'], year: '1985' } } }]
     sn = 'Beijerinckia derxii venezuelae corrig. Thompson and Skerman, 1981'
-    expect(details(sn)).to eq [{:genus=>{:string=>'Beijerinckia'}, 
-      :species=>{:string=>'derxii'}, :infraspecies=>[{:string=>'venezuelae', 
-      :rank=>'n/a', :authorship=>'Thompson and Skerman, 1981', 
-      :basionymAuthorTeam=>{:authorTeam=>'Thompson and Skerman', 
-      :author=>['Thompson', 'Skerman'], :year=>'1981'}}]}]
+    expect(details(sn)).to eq [{ genus: { string: 'Beijerinckia' },
+      species: { string: 'derxii' }, infraspecies: [{ string: 'venezuelae',
+      rank: 'n/a', authorship: 'Thompson and Skerman, 1981',
+      basionymAuthorTeam: { authorTeam: 'Thompson and Skerman',
+      author: ['Thompson', 'Skerman'], year: '1981' } }] }]
     expect(details('Streptomyces parvisporogenes ignotus 1960')).
-      to eq [{:genus=>{:string=>'Streptomyces'}, 
-        :species=>{:string=>'parvisporogenes'}, 
-        :infraspecies=>[{:string=>'ignotus', :rank=>'n/a', :year=>'1960'}]}]
+      to eq [{ genus: { string: 'Streptomyces' },
+        species: { string: 'parvisporogenes' },
+        infraspecies: [{ string: 'ignotus', rank: 'n/a', year: '1960' }] }]
     expect(details('Oscillaria caviae Simons 1920, according to Simons 1922')).
-      to eq [{:genus=>{:string=>'Oscillaria'}, :species=>{:string=>'caviae', 
-        :authorship=>'Simons 1920', :basionymAuthorTeam=>
-        {:authorTeam=>'Simons', :author=>['Simons'], :year=>'1920'}}}]
+      to eq [{ genus: { string: 'Oscillaria' }, species: { string: 'caviae',
+        authorship: 'Simons 1920', basionymAuthorTeam:
+        { authorTeam: 'Simons', author: ['Simons'], year: '1920' } } }]
     sn = 'Bacterium monocytogenes hominis\'\' Nyfeldt 1932'
-    expect(details(sn)).to eq [{:genus=>{:string=>'Bacterium'}, 
-      :species=>{:string=>'monocytogenes'}, 
-      :infraspecies=>[{:string=>'hominis', :rank=>'n/a'}]}]
+    expect(details(sn)).to eq [{ genus: { string: 'Bacterium' },
+      species: { string: 'monocytogenes' },
+      infraspecies: [{ string: 'hominis', rank: 'n/a' }] }]
     sn = 'Choriozopella trägårdhi Lawrence, 1947'
-    expect(details(sn)).to eq [{:genus=>{:string=>'Choriozopella'}, 
-      :species=>{:string=>'tragardhi', :authorship=>'Lawrence, 1947', 
-      :basionymAuthorTeam=>{:authorTeam=>'Lawrence', :author=>['Lawrence'], 
-      :year=>'1947'}}}]
+    expect(details(sn)).to eq [{ genus: { string: 'Choriozopella' },
+      species: { string: 'tragardhi', authorship: 'Lawrence, 1947',
+      basionymAuthorTeam: { authorTeam: 'Lawrence', author: ['Lawrence'],
+      year: '1947' } } }]
     sn = 'Sparassus françoisi Simon, 1898'
-    expect(details(sn)).to eq [{:genus=>{:string=>'Sparassus'}, 
-      :species=>{:string=>'francoisi', :authorship=>'Simon, 1898', 
-      :basionymAuthorTeam=>{:authorTeam=>'Simon', :author=>['Simon'], 
-      :year=>'1898'}}}]
+    expect(details(sn)).to eq [{ genus: { string: 'Sparassus' },
+      species: { string: 'francoisi', authorship: 'Simon, 1898',
+      basionymAuthorTeam: { authorTeam: 'Simon', author: ['Simon'],
+      year: '1898' } } }]
     sn = 'Dyarcyops birói Kulczynski, 1908'
-    expect(details(sn)).to eq [{:genus=>{:string=>'Dyarcyops'}, 
-      :species=>{:string=>'biroi', :authorship=>'Kulczynski, 1908', 
-      :basionymAuthorTeam=>{:authorTeam=>'Kulczynski', 
-      :author=>['Kulczynski'], :year=>'1908'}}}]
+    expect(details(sn)).to eq [{ genus: { string: 'Dyarcyops' },
+      species: { string: 'biroi', authorship: 'Kulczynski, 1908',
+      basionymAuthorTeam: { authorTeam: 'Kulczynski',
+      author: ['Kulczynski'], year: '1908' } } }]
   end
-  
+
   it 'parses names with common utf-8 charactes' do
-    names = ['Rühlella','Sténométope laevissimus Bibron 1855', 
+    names = ['Rühlella','Sténométope laevissimus Bibron 1855',
              'Döringina Ihering 1929'].each do |name|
       expect(parse(name)).to_not be_nil
     end
-    expect(details('Hirsutëlla mâle')).to eq [{:genus=>{:string=>'Hirsutella'}, 
-                                              :species=>{:string=>'male'}}] 
+    expect(details('Hirsutëlla mâle')).to eq [{ genus: { string: 'Hirsutella' },
+                                              species: { string: 'male' } }]
     expect(details('Triticum repens vulgäre')).
-      to eq [{:genus=>{:string=>'Triticum'}, :species=>{:string=>'repens'}, 
-              :infraspecies=>[{:string=>'vulgare', :rank=>'n/a'}]}]
+      to eq [{ genus: { string: 'Triticum' }, species: { string: 'repens' },
+              infraspecies: [{ string: 'vulgare', rank: 'n/a' }] }]
   end
-  
+
 # AsterophUa japonica
 # AsyTuktus ridiculw Parent 1931
 # AtremOEa Staud 1870

data/spec/parser/scientific_name_spec.rb

@@ -91,7 +91,9 @@ describe 'ScientificNameParser with ranked canonicals' do
       ['Abies homolepis forma umbilicata (Mayr) Schelle',
        'Abies homolepis forma umbilicata'],
       ['Quercus ilex ssp. ballota (Desf.) Samp',
-       'Quercus ilex ssp. ballota']
+       'Quercus ilex ssp. ballota'],
+      ["Physarum globuliferum forma. flavum Leontyev & Dudka",
+       "Physarum globuliferum forma. flavum"]
     ]
     data.each do |d|
       parsed = @parser.parse(d[0])[:scientificName][:canonical]

data/spec/spec_helper.rb

@@ -1,8 +1,8 @@
-require 'yaml'
-require 'treetop'
-require 'json'
-require 'biodiversity'
-require 'webmock/rspec'
+require "yaml"
+require "treetop"
+require "json"
+require "biodiversity"
+require "webmock/rspec"
 
 
 RSpec.configure do |c|
@@ -10,14 +10,14 @@ RSpec.configure do |c|
 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')))
+             "../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'
+PARSER_TEST_VERSION = "test_version"
 
 def set_parser(parser)
   @parser = parser
@@ -45,36 +45,36 @@ end
 
 def json(input)
   parse(input).
-    to_json.gsub(/"parser_version":"[^"]*"/, 
+    to_json.gsub(/"parser_version":"[^"]*"/,
                  %Q["parser_version":"#{PARSER_TEST_VERSION}"])
 end
 
 def debug(input)
   res = parse(input)
-  puts '<pre>'
+  puts "<pre>"
     if res
-      puts 'success!'
+      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"
+        to_s.gsub(/column /, "").to_i
+      print ("-" * (val - 1))
+      print "^   Computer says 'ni'!\n"
       puts @parser.failure_reason
       puts @parser.to_yaml
     end
-  puts '</pre>'
+  puts "</pre>"
 end
 
 def read_test_file
-  f = open(File.expand_path('../files/test_data.txt', __FILE__))
+  f = open(File.expand_path("../files/test_data.txt", __FILE__))
   f.each do |line|
     name, jsn = line.split("|")
     if line.match(/^\s*#/) == nil && name && jsn
-      yield({:name => name, :jsn => jsn})
+      yield({ name: name, jsn: jsn })
     else
-      yield({:comment => line})
+      yield({ comment: line })
     end
   end
 end

metadata

@@ -1,14 +1,14 @@
 --- !ruby/object:Gem::Specification
 name: biodiversity
 version: !ruby/object:Gem::Version
-  version: 3.1.5
+  version: 3.1.6
 platform: ruby
 authors:
 - Dmitry Mozzherin
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2014-08-07 00:00:00.000000000 Z
+date: 2015-03-13 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: treetop
@@ -30,14 +30,14 @@ dependencies:
     requirements:
     - - "~>"
       - !ruby/object:Gem::Version
-        version: '1.2'
+        version: '1.4'
   type: :runtime
   prerelease: false
   version_requirements: !ruby/object:Gem::Requirement
     requirements:
     - - "~>"
       - !ruby/object:Gem::Version
-        version: '1.2'
+        version: '1.4'
 - !ruby/object:Gem::Dependency
   name: unicode_utils
   requirement: !ruby/object:Gem::Requirement
@@ -58,56 +58,56 @@ dependencies:
     requirements:
     - - "~>"
       - !ruby/object:Gem::Version
-        version: '1.6'
+        version: '1.8'
   type: :development
   prerelease: false
   version_requirements: !ruby/object:Gem::Requirement
     requirements:
     - - "~>"
       - !ruby/object:Gem::Version
-        version: '1.6'
+        version: '1.8'
 - !ruby/object:Gem::Dependency
   name: rake
   requirement: !ruby/object:Gem::Requirement
     requirements:
     - - "~>"
       - !ruby/object:Gem::Version
-        version: '10.3'
+        version: '10.4'
   type: :development
   prerelease: false
   version_requirements: !ruby/object:Gem::Requirement
     requirements:
     - - "~>"
       - !ruby/object:Gem::Version
-        version: '10.3'
+        version: '10.4'
 - !ruby/object:Gem::Dependency
   name: rspec
   requirement: !ruby/object:Gem::Requirement
     requirements:
     - - "~>"
       - !ruby/object:Gem::Version
-        version: '3.0'
+        version: '3.2'
   type: :development
   prerelease: false
   version_requirements: !ruby/object:Gem::Requirement
     requirements:
     - - "~>"
       - !ruby/object:Gem::Version
-        version: '3.0'
+        version: '3.2'
 - !ruby/object:Gem::Dependency
   name: webmock
   requirement: !ruby/object:Gem::Requirement
     requirements:
     - - "~>"
       - !ruby/object:Gem::Version
-        version: '1.13'
+        version: '1.20'
   type: :development
   prerelease: false
   version_requirements: !ruby/object:Gem::Requirement
     requirements:
     - - "~>"
       - !ruby/object:Gem::Version
-        version: '1.13'
+        version: '1.20'
 - !ruby/object:Gem::Dependency
   name: rr
   requirement: !ruby/object:Gem::Requirement
@@ -123,19 +123,19 @@ dependencies:
       - !ruby/object:Gem::Version
         version: '1.1'
 - !ruby/object:Gem::Dependency
-  name: debugger
+  name: rubocop
   requirement: !ruby/object:Gem::Requirement
     requirements:
     - - "~>"
       - !ruby/object:Gem::Version
-        version: '1.6'
+        version: '0.29'
   type: :development
   prerelease: false
   version_requirements: !ruby/object:Gem::Requirement
     requirements:
     - - "~>"
       - !ruby/object:Gem::Version
-        version: '1.6'
+        version: '0.29'
 description: Tools for biodiversity informatics
 email: dmozzherin@gmail.com
 executables:
@@ -146,6 +146,7 @@ extra_rdoc_files: []
 files:
 - ".document"
 - ".gitignore"
+- ".rubocop.yml"
 - ".ruby-version"
 - ".travis.yml"
 - CHANGELOG
@@ -199,7 +200,7 @@ required_rubygems_version: !ruby/object:Gem::Requirement
       version: '0'
 requirements: []
 rubyforge_project: 
-rubygems_version: 2.2.2
+rubygems_version: 2.4.3
 signing_key: 
 specification_version: 4
 summary: Parser of scientific names