biodiversity19 3.1.5 → 3.1.6

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@@ -0,0 +1,10 @@
1
+ AllCops:
2
+ Exclude:
3
+ - features/**/*
4
+ - .bundle/**/*
5
+ - bundle_bin/**/*
6
+ Style/StringLiterals:
7
+ EnforcedStyle: double_quotes
8
+ Style/DotPosition:
9
+ EnforcedStyle: trailing
10
+
@@ -1 +1 @@
1
- 2.1.1
1
+ 2.1.5
data/CHANGELOG CHANGED
@@ -1,3 +1,5 @@
1
+ 3.1.5 -- added forma. to ranks, tests for species epithets with apostrophe
2
+
1
3
  3.1.5 -- updated depenencies
2
4
 
3
5
  3.1.4 -- added files generated by tt to repository
data/LICENSE CHANGED
@@ -1,6 +1,6 @@
1
1
  The MIT License (MIT)
2
2
 
3
- Copyright (c) 2008-2014 Marine Biological Laboratory
3
+ Copyright (c) 2008-2015 Marine Biological Laboratory
4
4
 
5
5
  Permission is hereby granted, free of charge, to any person obtaining
6
6
  a copy of this software and associated documentation files (the
data/README.md CHANGED
@@ -12,7 +12,7 @@ Parses taxonomic scientific name and breaks it into semantic elements.
12
12
  Support for Ruby 1.8.7 IS DROPPED. Both biodiversity and
13
13
  biodiversity19 will be for Ruby > 1.9.1 and will be identical gems.
14
14
 
15
- biodiversity19 is now deprecated and will be phased out in a couple of years.
15
+ biodiversity19 is now deprecated and will be phased out in 2015.
16
16
  You are strongly encouraged to change your dependencies from
17
17
  biodiversity19 to biodiversity
18
18
 
@@ -184,9 +184,9 @@ It should fix the problem.
184
184
  Copyright
185
185
  ---------
186
186
 
187
- Authors: [Dmitry Mozzherin][10],
187
+ Authors: [Dmitry Mozzherin][10]
188
188
 
189
- Copyright (c) 2008-2012 Marine Biological Laboratory. See LICENSE for
189
+ Copyright (c) 2008-2015 Marine Biological Laboratory. See LICENSE for
190
190
  further details.
191
191
 
192
192
  [1]: https://badge.fury.io/rb/biodiversity.png
data/Rakefile CHANGED
@@ -1,45 +1,45 @@
1
- require 'bundler'
1
+ require "bundler"
2
2
  Bundler::GemHelper.install_tasks
3
3
 
4
4
  begin
5
5
  Bundler.setup(:default, :development)
6
6
  rescue Bundler::BundlerError => e
7
7
  $stderr.puts e.message
8
- $stderr.puts 'Run `bundle install` to install missing gems'
8
+ $stderr.puts "Run `bundle install` to install missing gems"
9
9
  exit e.status_code
10
10
  end
11
11
 
12
- require 'rspec/core'
13
- require 'rspec/core/rake_task'
14
- require 'rake/dsl_definition'
15
- require 'rake'
16
- require 'rspec'
17
- require 'rspec/core/rake_task'
12
+ require "rspec/core"
13
+ require "rspec/core/rake_task"
14
+ require "rake/dsl_definition"
15
+ require "rake"
16
+ require "rspec"
17
+ require "rspec/core/rake_task"
18
18
 
19
19
 
20
20
  task :default => :spec
21
21
 
22
22
  RSpec::Core::RakeTask.new do |t|
23
- t.pattern = 'spec/**/*spec.rb'
23
+ t.pattern = "spec/**/*spec.rb"
24
24
  end
25
25
 
26
26
  task :tt do
27
27
  dir = File.dirname(__FILE__)
28
- ['scientific_name_clean',
29
- 'scientific_name_dirty',
30
- 'scientific_name_canonical'].each do |f|
28
+ ["scientific_name_clean",
29
+ "scientific_name_dirty",
30
+ "scientific_name_canonical"].each do |f|
31
31
  file = "#{dir}/lib/biodiversity/parser/#{f}"
32
32
  FileUtils.rm("#{file}.rb") if FileTest.exist?("#{file}.rb")
33
33
  system("tt #{file}.treetop")
34
34
  rf = "#{file}.rb"
35
- rfn = open(rf + '.tmp', 'w')
35
+ rfn = open(rf + ".tmp", "w")
36
36
  skip_head = false
37
37
  f = open(rf)
38
38
  # getting around a bug in treetop which prevents setting
39
39
  # UTF-8 encoding in ruby19
40
40
  f.each_with_index do |l, i|
41
41
  skip_head = l.match(/^# Autogenerated/) if i == 0
42
- if skip_head && (l.strip == '' || l.match(/^# Autogenerated/))
42
+ if skip_head && (l.strip == "" || l.match(/^# Autogenerated/))
43
43
  next
44
44
  else
45
45
  skip_head = false
@@ -1,29 +1,29 @@
1
1
  $:.push File.expand_path("../lib", __FILE__)
2
2
 
3
- require 'biodiversity/version'
3
+ require "biodiversity/version"
4
4
 
5
5
  Gem::Specification.new do |gem|
6
- gem.name = 'biodiversity19'
6
+ gem.name = "biodiversity19"
7
7
  gem.version = Biodiversity::VERSION
8
- gem.homepage = 'https://github.com/GlobalNamesArchitecture/biodiversity'
9
- gem.license = 'MIT'
10
- gem.summary = %Q{Parser of scientific names}
11
- gem.description = %Q{Tools for biodiversity informatics}
12
- gem.authors = ['Dmitry Mozzherin']
13
- gem.email = 'dmozzherin@gmail.com'
8
+ gem.homepage = "https://github.com/GlobalNamesArchitecture/biodiversity"
9
+ gem.license = "MIT"
10
+ gem.summary = "Parser of scientific names"
11
+ gem.description = "Tools for biodiversity informatics"
12
+ gem.authors = ["Dmitry Mozzherin"]
13
+ gem.email = "dmozzherin@gmail.com"
14
14
 
15
15
  gem.files = `git ls-files`.split("\n")
16
- gem.executables = ['nnparse', 'parserver']
17
- gem.require_paths = ['lib']
16
+ gem.executables = ["nnparse", "parserver"]
17
+ gem.require_paths = ["lib"]
18
18
 
19
- gem.add_runtime_dependency 'treetop', '~> 1.5'
20
- gem.add_runtime_dependency 'parallel', '~> 1.2'
21
- gem.add_runtime_dependency 'unicode_utils', '~> 1.4'
19
+ gem.add_runtime_dependency "treetop", "~> 1.5"
20
+ gem.add_runtime_dependency "parallel", "~> 1.4"
21
+ gem.add_runtime_dependency "unicode_utils", "~> 1.4"
22
22
 
23
- gem.add_development_dependency 'bundler', '~> 1.6'
24
- gem.add_development_dependency 'rake', '~> 10.3'
25
- gem.add_development_dependency 'rspec', '~> 3.0'
26
- gem.add_development_dependency 'webmock', '~> 1.13'
27
- gem.add_development_dependency 'rr', '~> 1.1'
28
- gem.add_development_dependency 'debugger', '~> 1.6'
23
+ gem.add_development_dependency "bundler", "~> 1.8"
24
+ gem.add_development_dependency "rake", "~> 10.4"
25
+ gem.add_development_dependency "rspec", "~> 3.2"
26
+ gem.add_development_dependency "webmock", "~> 1.20"
27
+ gem.add_development_dependency "rr", "~> 1.1"
28
+ gem.add_development_dependency "rubocop", "~> 0.29"
29
29
  end
@@ -251,7 +251,7 @@ class ScientificNameParser
251
251
  surrogate1 = /BOLD:|[\d]{5,}/i
252
252
  surrogate2 = /\b(spp|sp|nr|cf)[\.]?[\s]*$/i
253
253
  is_surrogate = false
254
-
254
+
255
255
  ai_index = pos.index('annotation_identification')
256
256
  if ai_index
257
257
  ai = name[pos[ai_index - 1]..pos[ai_index + 1]]
@@ -29,7 +29,7 @@ module ScientificNameCanonical
29
29
  def hybrid
30
30
  false
31
31
  end
32
-
32
+
33
33
  def details
34
34
  [super]
35
35
  end
@@ -103,15 +103,15 @@ module ScientificNameCanonical
103
103
  def value
104
104
  a.value + " " + b.value + " " + c.value
105
105
  end
106
-
106
+
107
107
  def canonical
108
108
  a.canonical + " " + c.canonical
109
109
  end
110
-
110
+
111
111
  def pos
112
112
  a.pos.merge(b.pos).merge(c.pos)
113
113
  end
114
-
114
+
115
115
  def details
116
116
  a.details.merge(b.details).merge(c.details)
117
117
  end
@@ -139,15 +139,15 @@ module ScientificNameCanonical
139
139
  def value
140
140
  a.value + " " + b.value
141
141
  end
142
-
142
+
143
143
  def canonical
144
144
  a.canonical
145
145
  end
146
-
146
+
147
147
  def pos
148
148
  a.pos.merge(b.pos)
149
149
  end
150
-
150
+
151
151
  def details
152
152
  a.details.merge(b.details)
153
153
  end
@@ -175,15 +175,15 @@ module ScientificNameCanonical
175
175
  def value
176
176
  a.value + " " + b.value
177
177
  end
178
-
178
+
179
179
  def canonical
180
180
  a.canonical + " " + b.canonical
181
181
  end
182
-
182
+
183
183
  def pos
184
184
  a.pos.merge(b.pos)
185
185
  end
186
-
186
+
187
187
  def details
188
188
  a.details.merge(b.details)
189
189
  end
@@ -315,15 +315,15 @@ module ScientificNameCanonical
315
315
  def value
316
316
  a.value
317
317
  end
318
-
318
+
319
319
  def canonical
320
320
  a.canonical
321
321
  end
322
-
322
+
323
323
  def pos
324
324
  a.pos
325
325
  end
326
-
326
+
327
327
  def details
328
328
  {:uninomial => a.details[:uninomial]}
329
329
  end
@@ -21,7 +21,7 @@ grammar ScientificNameCanonical
21
21
  def hybrid
22
22
  false
23
23
  end
24
-
24
+
25
25
  def details
26
26
  [super]
27
27
  end
@@ -31,22 +31,22 @@ grammar ScientificNameCanonical
31
31
  end
32
32
  }
33
33
  end
34
-
34
+
35
35
  rule multinomial_with_garbage
36
-
36
+
37
37
  a:genus space b:infragenus space c:species garbage {
38
38
  def value
39
39
  a.value + " " + b.value + " " + c.value
40
40
  end
41
-
41
+
42
42
  def canonical
43
43
  a.canonical + " " + c.canonical
44
44
  end
45
-
45
+
46
46
  def pos
47
47
  a.pos.merge(b.pos).merge(c.pos)
48
48
  end
49
-
49
+
50
50
  def details
51
51
  a.details.merge(b.details).merge(c.details)
52
52
  end
@@ -56,15 +56,15 @@ grammar ScientificNameCanonical
56
56
  def value
57
57
  a.value + " " + b.value
58
58
  end
59
-
59
+
60
60
  def canonical
61
61
  a.canonical
62
62
  end
63
-
63
+
64
64
  def pos
65
65
  a.pos.merge(b.pos)
66
66
  end
67
-
67
+
68
68
  def details
69
69
  a.details.merge(b.details)
70
70
  end
@@ -74,41 +74,41 @@ grammar ScientificNameCanonical
74
74
  def value
75
75
  a.value + " " + b.value
76
76
  end
77
-
77
+
78
78
  def canonical
79
79
  a.canonical + " " + b.canonical
80
80
  end
81
-
81
+
82
82
  def pos
83
83
  a.pos.merge(b.pos)
84
84
  end
85
-
85
+
86
86
  def details
87
87
  a.details.merge(b.details)
88
88
  end
89
89
  }
90
90
  end
91
-
91
+
92
92
  rule uninomial_with_garbage
93
93
  a:uninomial_string b:garbage {
94
94
  def value
95
95
  a.value
96
96
  end
97
-
97
+
98
98
  def canonical
99
99
  a.canonical
100
100
  end
101
-
101
+
102
102
  def pos
103
103
  a.pos
104
104
  end
105
-
105
+
106
106
  def details
107
107
  {:uninomial => a.details[:uninomial]}
108
108
  end
109
109
  }
110
110
  end
111
-
111
+
112
112
  rule garbage
113
113
  space "$$g@rbg3$$"
114
114
  /
@@ -2,7 +2,7 @@
2
2
  # Autogenerated from a Treetop grammar. Edits may be lost.
3
3
 
4
4
 
5
- require 'unicode_utils'
5
+ require "unicode_utils"
6
6
 
7
7
  module ScientificNameClean
8
8
  include Treetop::Runtime
@@ -27,11 +27,11 @@ module ScientificNameClean
27
27
 
28
28
  module Root1
29
29
  def value
30
- a.value.gsub(/\s{2,}/, ' ').strip
30
+ a.value.gsub(/\s{2,}/, " ").strip
31
31
  end
32
32
 
33
33
  def canonical
34
- a.canonical.gsub(/\s{2,}/, ' ').strip
34
+ a.canonical.gsub(/\s{2,}/, " ").strip
35
35
  end
36
36
 
37
37
  def pos
@@ -797,7 +797,7 @@ module ScientificNameClean
797
797
  module Unparsed1
798
798
 
799
799
  def value
800
- ''
800
+ ""
801
801
  end
802
802
 
803
803
  def hybrid
@@ -805,11 +805,11 @@ module ScientificNameClean
805
805
  end
806
806
 
807
807
  def canonical
808
- ''
808
+ ""
809
809
  end
810
810
 
811
811
  def pos
812
- {interval.begin => ['unparsed', interval.end]}
812
+ {interval.begin => ["unparsed", interval.end]}
813
813
  end
814
814
 
815
815
  def details
@@ -1837,14 +1837,14 @@ module ScientificNameClean
1837
1837
 
1838
1838
  def pos
1839
1839
  def a.pos
1840
- {interval.begin => ['infraspecies', a.interval.end]}
1840
+ {interval.begin => ["infraspecies", a.interval.end]}
1841
1841
  end
1842
1842
  aid.pos(a)
1843
1843
  end
1844
1844
 
1845
1845
  def details
1846
1846
  def a.details
1847
- {:infraspecies => {:string => value, :rank => 'n/a'}}
1847
+ {:infraspecies => {:string => value, :rank => "n/a"}}
1848
1848
  end
1849
1849
  aid.details(a)
1850
1850
  end
@@ -1867,11 +1867,11 @@ module ScientificNameClean
1867
1867
  end
1868
1868
 
1869
1869
  def pos
1870
- {interval.begin => ['infraspecies', interval.end]}
1870
+ {interval.begin => ["infraspecies", interval.end]}
1871
1871
  end
1872
1872
 
1873
1873
  def details
1874
- {:infraspecies => {:string => value, :rank => 'n/a'}}
1874
+ {:infraspecies => {:string => value, :rank => "n/a"}}
1875
1875
  end
1876
1876
  end
1877
1877
 
@@ -2065,8 +2065,8 @@ module ScientificNameClean
2065
2065
  end
2066
2066
 
2067
2067
  def pos(a)
2068
- interval_end = text_value[-1] == ' ' ? interval.end - 1 : interval.end
2069
- {interval.begin => ['infraspecific_type', interval_end], a.interval.begin => ['infraspecies', a.interval.end]}
2068
+ interval_end = text_value[-1] == " " ? interval.end - 1 : interval.end
2069
+ {interval.begin => ["infraspecific_type", interval_end], a.interval.begin => ["infraspecies", a.interval.end]}
2070
2070
  end
2071
2071
 
2072
2072
  def details(a = nil)
@@ -2326,11 +2326,11 @@ module ScientificNameClean
2326
2326
  r0 = r20
2327
2327
  r0.extend(Rank0)
2328
2328
  else
2329
- if (match_len = has_terminal?("forma ", false, index))
2329
+ if (match_len = has_terminal?("forma.", false, index))
2330
2330
  r21 = instantiate_node(SyntaxNode,input, index...(index + match_len))
2331
2331
  @index += match_len
2332
2332
  else
2333
- terminal_parse_failure("forma ")
2333
+ terminal_parse_failure("forma.")
2334
2334
  r21 = nil
2335
2335
  end
2336
2336
  if r21
@@ -2338,11 +2338,11 @@ module ScientificNameClean
2338
2338
  r0 = r21
2339
2339
  r0.extend(Rank0)
2340
2340
  else
2341
- if (match_len = has_terminal?("fma.", false, index))
2341
+ if (match_len = has_terminal?("forma ", false, index))
2342
2342
  r22 = instantiate_node(SyntaxNode,input, index...(index + match_len))
2343
2343
  @index += match_len
2344
2344
  else
2345
- terminal_parse_failure("fma.")
2345
+ terminal_parse_failure("forma ")
2346
2346
  r22 = nil
2347
2347
  end
2348
2348
  if r22
@@ -2350,11 +2350,11 @@ module ScientificNameClean
2350
2350
  r0 = r22
2351
2351
  r0.extend(Rank0)
2352
2352
  else
2353
- if (match_len = has_terminal?("fma ", false, index))
2353
+ if (match_len = has_terminal?("fma.", false, index))
2354
2354
  r23 = instantiate_node(SyntaxNode,input, index...(index + match_len))
2355
2355
  @index += match_len
2356
2356
  else
2357
- terminal_parse_failure("fma ")
2357
+ terminal_parse_failure("fma.")
2358
2358
  r23 = nil
2359
2359
  end
2360
2360
  if r23
@@ -2362,11 +2362,11 @@ module ScientificNameClean
2362
2362
  r0 = r23
2363
2363
  r0.extend(Rank0)
2364
2364
  else
2365
- if (match_len = has_terminal?("form.", false, index))
2365
+ if (match_len = has_terminal?("fma ", false, index))
2366
2366
  r24 = instantiate_node(SyntaxNode,input, index...(index + match_len))
2367
2367
  @index += match_len
2368
2368
  else
2369
- terminal_parse_failure("form.")
2369
+ terminal_parse_failure("fma ")
2370
2370
  r24 = nil
2371
2371
  end
2372
2372
  if r24
@@ -2374,11 +2374,11 @@ module ScientificNameClean
2374
2374
  r0 = r24
2375
2375
  r0.extend(Rank0)
2376
2376
  else
2377
- if (match_len = has_terminal?("form ", false, index))
2377
+ if (match_len = has_terminal?("form.", false, index))
2378
2378
  r25 = instantiate_node(SyntaxNode,input, index...(index + match_len))
2379
2379
  @index += match_len
2380
2380
  else
2381
- terminal_parse_failure("form ")
2381
+ terminal_parse_failure("form.")
2382
2382
  r25 = nil
2383
2383
  end
2384
2384
  if r25
@@ -2386,11 +2386,11 @@ module ScientificNameClean
2386
2386
  r0 = r25
2387
2387
  r0.extend(Rank0)
2388
2388
  else
2389
- if (match_len = has_terminal?("fo.", false, index))
2389
+ if (match_len = has_terminal?("form ", false, index))
2390
2390
  r26 = instantiate_node(SyntaxNode,input, index...(index + match_len))
2391
2391
  @index += match_len
2392
2392
  else
2393
- terminal_parse_failure("fo.")
2393
+ terminal_parse_failure("form ")
2394
2394
  r26 = nil
2395
2395
  end
2396
2396
  if r26
@@ -2398,11 +2398,11 @@ module ScientificNameClean
2398
2398
  r0 = r26
2399
2399
  r0.extend(Rank0)
2400
2400
  else
2401
- if (match_len = has_terminal?("fo ", false, index))
2401
+ if (match_len = has_terminal?("fo.", false, index))
2402
2402
  r27 = instantiate_node(SyntaxNode,input, index...(index + match_len))
2403
2403
  @index += match_len
2404
2404
  else
2405
- terminal_parse_failure("fo ")
2405
+ terminal_parse_failure("fo.")
2406
2406
  r27 = nil
2407
2407
  end
2408
2408
  if r27
@@ -2410,11 +2410,11 @@ module ScientificNameClean
2410
2410
  r0 = r27
2411
2411
  r0.extend(Rank0)
2412
2412
  else
2413
- if (match_len = has_terminal?("f.", false, index))
2413
+ if (match_len = has_terminal?("fo ", false, index))
2414
2414
  r28 = instantiate_node(SyntaxNode,input, index...(index + match_len))
2415
2415
  @index += match_len
2416
2416
  else
2417
- terminal_parse_failure("f.")
2417
+ terminal_parse_failure("fo ")
2418
2418
  r28 = nil
2419
2419
  end
2420
2420
  if r28
@@ -2422,11 +2422,11 @@ module ScientificNameClean
2422
2422
  r0 = r28
2423
2423
  r0.extend(Rank0)
2424
2424
  else
2425
- if (match_len = has_terminal?("α", false, index))
2426
- r29 = true
2425
+ if (match_len = has_terminal?("f.", false, index))
2426
+ r29 = instantiate_node(SyntaxNode,input, index...(index + match_len))
2427
2427
  @index += match_len
2428
2428
  else
2429
- terminal_parse_failure("α")
2429
+ terminal_parse_failure("f.")
2430
2430
  r29 = nil
2431
2431
  end
2432
2432
  if r29
@@ -2434,11 +2434,11 @@ module ScientificNameClean
2434
2434
  r0 = r29
2435
2435
  r0.extend(Rank0)
2436
2436
  else
2437
- if (match_len = has_terminal?("ββ", false, index))
2438
- r30 = instantiate_node(SyntaxNode,input, index...(index + match_len))
2437
+ if (match_len = has_terminal?("α", false, index))
2438
+ r30 = true
2439
2439
  @index += match_len
2440
2440
  else
2441
- terminal_parse_failure("ββ")
2441
+ terminal_parse_failure("α")
2442
2442
  r30 = nil
2443
2443
  end
2444
2444
  if r30
@@ -2446,11 +2446,11 @@ module ScientificNameClean
2446
2446
  r0 = r30
2447
2447
  r0.extend(Rank0)
2448
2448
  else
2449
- if (match_len = has_terminal?("β", false, index))
2450
- r31 = true
2449
+ if (match_len = has_terminal?("ββ", false, index))
2450
+ r31 = instantiate_node(SyntaxNode,input, index...(index + match_len))
2451
2451
  @index += match_len
2452
2452
  else
2453
- terminal_parse_failure("β")
2453
+ terminal_parse_failure("ββ")
2454
2454
  r31 = nil
2455
2455
  end
2456
2456
  if r31
@@ -2458,11 +2458,11 @@ module ScientificNameClean
2458
2458
  r0 = r31
2459
2459
  r0.extend(Rank0)
2460
2460
  else
2461
- if (match_len = has_terminal?("γ", false, index))
2461
+ if (match_len = has_terminal?("β", false, index))
2462
2462
  r32 = true
2463
2463
  @index += match_len
2464
2464
  else
2465
- terminal_parse_failure("γ")
2465
+ terminal_parse_failure("β")
2466
2466
  r32 = nil
2467
2467
  end
2468
2468
  if r32
@@ -2470,11 +2470,11 @@ module ScientificNameClean
2470
2470
  r0 = r32
2471
2471
  r0.extend(Rank0)
2472
2472
  else
2473
- if (match_len = has_terminal?("δ", false, index))
2473
+ if (match_len = has_terminal?("γ", false, index))
2474
2474
  r33 = true
2475
2475
  @index += match_len
2476
2476
  else
2477
- terminal_parse_failure("δ")
2477
+ terminal_parse_failure("γ")
2478
2478
  r33 = nil
2479
2479
  end
2480
2480
  if r33
@@ -2482,11 +2482,11 @@ module ScientificNameClean
2482
2482
  r0 = r33
2483
2483
  r0.extend(Rank0)
2484
2484
  else
2485
- if (match_len = has_terminal?("ε", false, index))
2485
+ if (match_len = has_terminal?("δ", false, index))
2486
2486
  r34 = true
2487
2487
  @index += match_len
2488
2488
  else
2489
- terminal_parse_failure("ε")
2489
+ terminal_parse_failure("δ")
2490
2490
  r34 = nil
2491
2491
  end
2492
2492
  if r34
@@ -2494,11 +2494,11 @@ module ScientificNameClean
2494
2494
  r0 = r34
2495
2495
  r0.extend(Rank0)
2496
2496
  else
2497
- if (match_len = has_terminal?("φ", false, index))
2497
+ if (match_len = has_terminal?("ε", false, index))
2498
2498
  r35 = true
2499
2499
  @index += match_len
2500
2500
  else
2501
- terminal_parse_failure("φ")
2501
+ terminal_parse_failure("ε")
2502
2502
  r35 = nil
2503
2503
  end
2504
2504
  if r35
@@ -2506,11 +2506,11 @@ module ScientificNameClean
2506
2506
  r0 = r35
2507
2507
  r0.extend(Rank0)
2508
2508
  else
2509
- if (match_len = has_terminal?("θ", false, index))
2509
+ if (match_len = has_terminal?("φ", false, index))
2510
2510
  r36 = true
2511
2511
  @index += match_len
2512
2512
  else
2513
- terminal_parse_failure("θ")
2513
+ terminal_parse_failure("φ")
2514
2514
  r36 = nil
2515
2515
  end
2516
2516
  if r36
@@ -2518,11 +2518,11 @@ module ScientificNameClean
2518
2518
  r0 = r36
2519
2519
  r0.extend(Rank0)
2520
2520
  else
2521
- if (match_len = has_terminal?("μ", false, index))
2521
+ if (match_len = has_terminal?("θ", false, index))
2522
2522
  r37 = true
2523
2523
  @index += match_len
2524
2524
  else
2525
- terminal_parse_failure("μ")
2525
+ terminal_parse_failure("θ")
2526
2526
  r37 = nil
2527
2527
  end
2528
2528
  if r37
@@ -2530,11 +2530,11 @@ module ScientificNameClean
2530
2530
  r0 = r37
2531
2531
  r0.extend(Rank0)
2532
2532
  else
2533
- if (match_len = has_terminal?("a.", false, index))
2534
- r38 = instantiate_node(SyntaxNode,input, index...(index + match_len))
2533
+ if (match_len = has_terminal?("μ", false, index))
2534
+ r38 = true
2535
2535
  @index += match_len
2536
2536
  else
2537
- terminal_parse_failure("a.")
2537
+ terminal_parse_failure("μ")
2538
2538
  r38 = nil
2539
2539
  end
2540
2540
  if r38
@@ -2542,11 +2542,11 @@ module ScientificNameClean
2542
2542
  r0 = r38
2543
2543
  r0.extend(Rank0)
2544
2544
  else
2545
- if (match_len = has_terminal?("b.", false, index))
2545
+ if (match_len = has_terminal?("a.", false, index))
2546
2546
  r39 = instantiate_node(SyntaxNode,input, index...(index + match_len))
2547
2547
  @index += match_len
2548
2548
  else
2549
- terminal_parse_failure("b.")
2549
+ terminal_parse_failure("a.")
2550
2550
  r39 = nil
2551
2551
  end
2552
2552
  if r39
@@ -2554,11 +2554,11 @@ module ScientificNameClean
2554
2554
  r0 = r39
2555
2555
  r0.extend(Rank0)
2556
2556
  else
2557
- if (match_len = has_terminal?("c.", false, index))
2557
+ if (match_len = has_terminal?("b.", false, index))
2558
2558
  r40 = instantiate_node(SyntaxNode,input, index...(index + match_len))
2559
2559
  @index += match_len
2560
2560
  else
2561
- terminal_parse_failure("c.")
2561
+ terminal_parse_failure("b.")
2562
2562
  r40 = nil
2563
2563
  end
2564
2564
  if r40
@@ -2566,11 +2566,11 @@ module ScientificNameClean
2566
2566
  r0 = r40
2567
2567
  r0.extend(Rank0)
2568
2568
  else
2569
- if (match_len = has_terminal?("d.", false, index))
2569
+ if (match_len = has_terminal?("c.", false, index))
2570
2570
  r41 = instantiate_node(SyntaxNode,input, index...(index + match_len))
2571
2571
  @index += match_len
2572
2572
  else
2573
- terminal_parse_failure("d.")
2573
+ terminal_parse_failure("c.")
2574
2574
  r41 = nil
2575
2575
  end
2576
2576
  if r41
@@ -2578,11 +2578,11 @@ module ScientificNameClean
2578
2578
  r0 = r41
2579
2579
  r0.extend(Rank0)
2580
2580
  else
2581
- if (match_len = has_terminal?("e.", false, index))
2581
+ if (match_len = has_terminal?("d.", false, index))
2582
2582
  r42 = instantiate_node(SyntaxNode,input, index...(index + match_len))
2583
2583
  @index += match_len
2584
2584
  else
2585
- terminal_parse_failure("e.")
2585
+ terminal_parse_failure("d.")
2586
2586
  r42 = nil
2587
2587
  end
2588
2588
  if r42
@@ -2590,11 +2590,11 @@ module ScientificNameClean
2590
2590
  r0 = r42
2591
2591
  r0.extend(Rank0)
2592
2592
  else
2593
- if (match_len = has_terminal?("g.", false, index))
2593
+ if (match_len = has_terminal?("e.", false, index))
2594
2594
  r43 = instantiate_node(SyntaxNode,input, index...(index + match_len))
2595
2595
  @index += match_len
2596
2596
  else
2597
- terminal_parse_failure("g.")
2597
+ terminal_parse_failure("e.")
2598
2598
  r43 = nil
2599
2599
  end
2600
2600
  if r43
@@ -2602,11 +2602,11 @@ module ScientificNameClean
2602
2602
  r0 = r43
2603
2603
  r0.extend(Rank0)
2604
2604
  else
2605
- if (match_len = has_terminal?("k.", false, index))
2605
+ if (match_len = has_terminal?("g.", false, index))
2606
2606
  r44 = instantiate_node(SyntaxNode,input, index...(index + match_len))
2607
2607
  @index += match_len
2608
2608
  else
2609
- terminal_parse_failure("k.")
2609
+ terminal_parse_failure("g.")
2610
2610
  r44 = nil
2611
2611
  end
2612
2612
  if r44
@@ -2614,11 +2614,11 @@ module ScientificNameClean
2614
2614
  r0 = r44
2615
2615
  r0.extend(Rank0)
2616
2616
  else
2617
- if (match_len = has_terminal?("****", false, index))
2617
+ if (match_len = has_terminal?("k.", false, index))
2618
2618
  r45 = instantiate_node(SyntaxNode,input, index...(index + match_len))
2619
2619
  @index += match_len
2620
2620
  else
2621
- terminal_parse_failure("****")
2621
+ terminal_parse_failure("k.")
2622
2622
  r45 = nil
2623
2623
  end
2624
2624
  if r45
@@ -2626,11 +2626,11 @@ module ScientificNameClean
2626
2626
  r0 = r45
2627
2627
  r0.extend(Rank0)
2628
2628
  else
2629
- if (match_len = has_terminal?("**", false, index))
2629
+ if (match_len = has_terminal?("****", false, index))
2630
2630
  r46 = instantiate_node(SyntaxNode,input, index...(index + match_len))
2631
2631
  @index += match_len
2632
2632
  else
2633
- terminal_parse_failure("**")
2633
+ terminal_parse_failure("****")
2634
2634
  r46 = nil
2635
2635
  end
2636
2636
  if r46
@@ -2638,11 +2638,11 @@ module ScientificNameClean
2638
2638
  r0 = r46
2639
2639
  r0.extend(Rank0)
2640
2640
  else
2641
- if (match_len = has_terminal?("*", false, index))
2642
- r47 = true
2641
+ if (match_len = has_terminal?("**", false, index))
2642
+ r47 = instantiate_node(SyntaxNode,input, index...(index + match_len))
2643
2643
  @index += match_len
2644
2644
  else
2645
- terminal_parse_failure("*")
2645
+ terminal_parse_failure("**")
2646
2646
  r47 = nil
2647
2647
  end
2648
2648
  if r47
@@ -2650,8 +2650,21 @@ module ScientificNameClean
2650
2650
  r0 = r47
2651
2651
  r0.extend(Rank0)
2652
2652
  else
2653
- @index = i0
2654
- r0 = nil
2653
+ if (match_len = has_terminal?("*", false, index))
2654
+ r48 = true
2655
+ @index += match_len
2656
+ else
2657
+ terminal_parse_failure("*")
2658
+ r48 = nil
2659
+ end
2660
+ if r48
2661
+ r48 = SyntaxNode.new(input, (index-1)...index) if r48 == true
2662
+ r0 = r48
2663
+ r0.extend(Rank0)
2664
+ else
2665
+ @index = i0
2666
+ r0 = nil
2667
+ end
2655
2668
  end
2656
2669
  end
2657
2670
  end
@@ -2711,7 +2724,7 @@ module ScientificNameClean
2711
2724
  end
2712
2725
 
2713
2726
  def pos(uni)
2714
- {interval.begin => ['rank_uninomial', interval.end], uni.interval.begin => ['uninomial', uni.interval.end]}
2727
+ {interval.begin => ["rank_uninomial", interval.end], uni.interval.begin => ["uninomial", uni.interval.end]}
2715
2728
  end
2716
2729
 
2717
2730
  def details(uni)
@@ -3065,7 +3078,7 @@ module ScientificNameClean
3065
3078
  end
3066
3079
 
3067
3080
  def pos
3068
- {interval.begin => ['species', interval.end]}
3081
+ {interval.begin => ["species", interval.end]}
3069
3082
  end
3070
3083
 
3071
3084
  def hybrid
@@ -3142,7 +3155,7 @@ module ScientificNameClean
3142
3155
  end
3143
3156
 
3144
3157
  def pos
3145
- {a.interval.begin => ['infragenus', a.interval.end]}
3158
+ {a.interval.begin => ["infragenus", a.interval.end]}
3146
3159
  end
3147
3160
 
3148
3161
  def details
@@ -3239,7 +3252,7 @@ module ScientificNameClean
3239
3252
  end
3240
3253
 
3241
3254
  def pos
3242
- {a.interval.begin => ['genus', a.interval.end]}
3255
+ {a.interval.begin => ["genus", a.interval.end]}
3243
3256
  end
3244
3257
 
3245
3258
  def canonical
@@ -3655,7 +3668,7 @@ module ScientificNameClean
3655
3668
  end
3656
3669
 
3657
3670
  def pos
3658
- {interval.begin => ['uninomial', interval.end]}
3671
+ {interval.begin => ["uninomial", interval.end]}
3659
3672
  end
3660
3673
 
3661
3674
  def hybrid
@@ -4103,11 +4116,11 @@ module ScientificNameClean
4103
4116
  end
4104
4117
 
4105
4118
  def pos
4106
- {a.interval.begin => ['unknown_author', a.interval.end]}
4119
+ {a.interval.begin => ["unknown_author", a.interval.end]}
4107
4120
  end
4108
4121
 
4109
4122
  def details
4110
- {:authorship => text_value, :basionymAuthorTeam => {:authorTeam => text_value, :author => ['?']}}
4123
+ {:authorship => text_value, :basionymAuthorTeam => {:authorTeam => text_value, :author => ["?"]}}
4111
4124
  end
4112
4125
  end
4113
4126
 
@@ -4435,7 +4448,7 @@ module ScientificNameClean
4435
4448
  details_with_arg(:basionymAuthorTeam)
4436
4449
  end
4437
4450
 
4438
- def details_with_arg(authorTeamType = 'basionymAuthorTeam')
4451
+ def details_with_arg(authorTeamType = "basionymAuthorTeam")
4439
4452
  { :authorship => text_value,
4440
4453
  authorTeamType.to_sym => {
4441
4454
  :authorTeam => a.text_value.strip
@@ -4475,7 +4488,7 @@ module ScientificNameClean
4475
4488
  details_with_arg(:basionymAuthorTeam)
4476
4489
  end
4477
4490
 
4478
- def details_with_arg(authorTeamType = 'basionymAuthorTeam')
4491
+ def details_with_arg(authorTeamType = "basionymAuthorTeam")
4479
4492
  { :authorship => text_value,
4480
4493
  authorTeamType.to_sym => {
4481
4494
  :authorTeam => a.text_value.strip
@@ -4491,7 +4504,7 @@ module ScientificNameClean
4491
4504
  details
4492
4505
  end
4493
4506
 
4494
- def details_with_arg(authorTeamType = 'basionymAuthorTeam')
4507
+ def details_with_arg(authorTeamType = "basionymAuthorTeam")
4495
4508
  { :authorship => text_value,
4496
4509
  authorTeamType.to_sym => {
4497
4510
  :authorTeam => text_value,
@@ -4791,7 +4804,7 @@ module ScientificNameClean
4791
4804
  end
4792
4805
 
4793
4806
  def pos
4794
- {interval.begin => ['unknown_author', interval.end]}
4807
+ {interval.begin => ["unknown_author", interval.end]}
4795
4808
  end
4796
4809
 
4797
4810
  def details
@@ -5135,7 +5148,7 @@ module ScientificNameClean
5135
5148
 
5136
5149
  module AuthorName1
5137
5150
  def value
5138
- a.value + ' ' + b.value
5151
+ a.value + " " + b.value
5139
5152
  end
5140
5153
 
5141
5154
  def pos
@@ -5360,7 +5373,7 @@ module ScientificNameClean
5360
5373
  end
5361
5374
 
5362
5375
  def pos
5363
- {interval.begin => ['author_word', 1], (interval.begin + 2) => ['author_word', 2], (interval.begin + 5) => ['author_word', 2]}
5376
+ {interval.begin => ["author_word", 1], (interval.begin + 2) => ["author_word", 2], (interval.begin + 5) => ["author_word", 2]}
5364
5377
  end
5365
5378
 
5366
5379
  def details
@@ -5375,7 +5388,7 @@ module ScientificNameClean
5375
5388
 
5376
5389
  def pos
5377
5390
  #cheating because there are several words in some of them
5378
- {interval.begin => ['author_word', interval.end]}
5391
+ {interval.begin => ["author_word", interval.end]}
5379
5392
  end
5380
5393
 
5381
5394
  def details
@@ -5394,7 +5407,7 @@ module ScientificNameClean
5394
5407
  end
5395
5408
 
5396
5409
  def pos
5397
- {interval.begin => ['author_word', interval.end]}
5410
+ {interval.begin => ["author_word", interval.end]}
5398
5411
  end
5399
5412
 
5400
5413
  def details
@@ -5411,7 +5424,7 @@ module ScientificNameClean
5411
5424
  end
5412
5425
 
5413
5426
  def pos
5414
- {interval.begin => ['author_word', interval.end]}
5427
+ {interval.begin => ["author_word", interval.end]}
5415
5428
  end
5416
5429
 
5417
5430
  def details
@@ -5783,7 +5796,7 @@ module ScientificNameClean
5783
5796
 
5784
5797
  def pos
5785
5798
  #cheating because there are several words in some of them
5786
- {interval.begin => ['author_word', interval.end]}
5799
+ {interval.begin => ["author_word", interval.end]}
5787
5800
  end
5788
5801
  end
5789
5802
 
@@ -6030,7 +6043,7 @@ module ScientificNameClean
6030
6043
  end
6031
6044
 
6032
6045
  def pos
6033
- {interval.begin => ['author_word', interval.end]}
6046
+ {interval.begin => ["author_word", interval.end]}
6034
6047
  end
6035
6048
  end
6036
6049
 
@@ -6183,7 +6196,7 @@ module ScientificNameClean
6183
6196
 
6184
6197
  module CapLatinWord5
6185
6198
  def value
6186
- a.text_value[0..0] + 'e' + b.value
6199
+ a.text_value[0..0] + "e" + b.value
6187
6200
  end
6188
6201
  end
6189
6202
 
@@ -6685,7 +6698,7 @@ module ScientificNameClean
6685
6698
  end
6686
6699
 
6687
6700
  def pos
6688
- {b.interval.begin => ['species', b.interval.end]}
6701
+ {b.interval.begin => ["species", b.interval.end]}
6689
6702
  end
6690
6703
 
6691
6704
  def details
@@ -6721,7 +6734,7 @@ module ScientificNameClean
6721
6734
  end
6722
6735
 
6723
6736
  def pos
6724
- {b.interval.begin => ['species', b.interval.end]}
6737
+ {b.interval.begin => ["species", b.interval.end]}
6725
6738
  end
6726
6739
 
6727
6740
  def details
@@ -6757,7 +6770,7 @@ module ScientificNameClean
6757
6770
  end
6758
6771
 
6759
6772
  def pos
6760
- {b.interval.begin => ['species', b.interval.end]}
6773
+ {b.interval.begin => ["species", b.interval.end]}
6761
6774
  end
6762
6775
 
6763
6776
  def details
@@ -6876,16 +6889,16 @@ module ScientificNameClean
6876
6889
  end
6877
6890
 
6878
6891
  def apply(sp)
6879
- ''
6892
+ ""
6880
6893
  end
6881
6894
 
6882
6895
  def canonical(sp)
6883
- ''
6896
+ ""
6884
6897
  end
6885
6898
 
6886
6899
  def pos(sp)
6887
- interval_end = text_value[-1] == ' ' ? interval.end - 1 : interval.end
6888
- {interval.begin => ['annotation_identification', interval.end]}
6900
+ interval_end = text_value[-1] == " " ? interval.end - 1 : interval.end
6901
+ {interval.begin => ["annotation_identification", interval.end]}
6889
6902
  end
6890
6903
 
6891
6904
  def details(sp)
@@ -6899,16 +6912,16 @@ module ScientificNameClean
6899
6912
  end
6900
6913
 
6901
6914
  def apply(sp)
6902
- ' ' + value + ' ' + sp.value
6915
+ " " + value + " " + sp.value
6903
6916
  end
6904
6917
 
6905
6918
  def canonical(sp)
6906
- ' ' + sp.canonical
6919
+ " " + sp.canonical
6907
6920
  end
6908
6921
 
6909
6922
  def pos(sp)
6910
- interval_end = text_value[-1] == ' ' ? interval.end - 1 : interval.end
6911
- {interval.begin => ['annotation_identification', interval.end]}.merge(sp.pos)
6923
+ interval_end = text_value[-1] == " " ? interval.end - 1 : interval.end
6924
+ {interval.begin => ["annotation_identification", interval.end]}.merge(sp.pos)
6912
6925
  end
6913
6926
 
6914
6927
  def details(sp)
@@ -7295,6 +7308,12 @@ module ScientificNameClean
7295
7308
  end
7296
7309
 
7297
7310
  module LatinWord3
7311
+ def value
7312
+ "oneili"
7313
+ end
7314
+ end
7315
+
7316
+ module LatinWord4
7298
7317
  def a
7299
7318
  elements[0]
7300
7319
  end
@@ -7304,7 +7323,7 @@ module ScientificNameClean
7304
7323
  end
7305
7324
  end
7306
7325
 
7307
- module LatinWord4
7326
+ module LatinWord5
7308
7327
  def value
7309
7328
  a.value + b.value
7310
7329
  end
@@ -7351,39 +7370,52 @@ module ScientificNameClean
7351
7370
  r1 = SyntaxNode.new(input, (index-1)...index) if r1 == true
7352
7371
  r0 = r1
7353
7372
  else
7354
- if (match_len = has_terminal?("o\'donelli", false, index))
7373
+ if (match_len = has_terminal?("o'donelli", false, index))
7355
7374
  r5 = instantiate_node(SyntaxNode,input, index...(index + match_len))
7356
7375
  r5.extend(LatinWord2)
7357
7376
  @index += match_len
7358
7377
  else
7359
- terminal_parse_failure("o\'donelli")
7378
+ terminal_parse_failure("o'donelli")
7360
7379
  r5 = nil
7361
7380
  end
7362
7381
  if r5
7363
7382
  r5 = SyntaxNode.new(input, (index-1)...index) if r5 == true
7364
7383
  r0 = r5
7365
7384
  else
7366
- i6, s6 = index, []
7367
- r7 = _nt_valid_name_letter
7368
- s6 << r7
7369
- if r7
7370
- r8 = _nt_valid_name_letters
7371
- s6 << r8
7372
- end
7373
- if s6.last
7374
- r6 = instantiate_node(SyntaxNode,input, i6...index, s6)
7385
+ if (match_len = has_terminal?("o'neili", false, index))
7386
+ r6 = instantiate_node(SyntaxNode,input, index...(index + match_len))
7375
7387
  r6.extend(LatinWord3)
7376
- r6.extend(LatinWord4)
7388
+ @index += match_len
7377
7389
  else
7378
- @index = i6
7390
+ terminal_parse_failure("o'neili")
7379
7391
  r6 = nil
7380
7392
  end
7381
7393
  if r6
7382
7394
  r6 = SyntaxNode.new(input, (index-1)...index) if r6 == true
7383
7395
  r0 = r6
7384
7396
  else
7385
- @index = i0
7386
- r0 = nil
7397
+ i7, s7 = index, []
7398
+ r8 = _nt_valid_name_letter
7399
+ s7 << r8
7400
+ if r8
7401
+ r9 = _nt_valid_name_letters
7402
+ s7 << r9
7403
+ end
7404
+ if s7.last
7405
+ r7 = instantiate_node(SyntaxNode,input, i7...index, s7)
7406
+ r7.extend(LatinWord4)
7407
+ r7.extend(LatinWord5)
7408
+ else
7409
+ @index = i7
7410
+ r7 = nil
7411
+ end
7412
+ if r7
7413
+ r7 = SyntaxNode.new(input, (index-1)...index) if r7 == true
7414
+ r0 = r7
7415
+ else
7416
+ @index = i0
7417
+ r0 = nil
7418
+ end
7387
7419
  end
7388
7420
  end
7389
7421
  end
@@ -7395,13 +7427,13 @@ module ScientificNameClean
7395
7427
 
7396
7428
  module ValidNameLetters0
7397
7429
  def value
7398
- res = ''
7399
- text_value.split('').each do |l|
7400
- l = 'ae' if l == 'æ'
7401
- l = 'oe' if l == 'œ'
7430
+ res = ""
7431
+ text_value.split("").each do |l|
7432
+ l = "ae" if l == "æ"
7433
+ l = "oe" if l == "œ"
7402
7434
  # We normalize ë as well. It is legal in botanical code, but it
7403
7435
  # is beneficial to normalize it for the reconsiliation purposes
7404
- l = 'e' if l == 'ë'
7436
+ l = "e" if l == "ë"
7405
7437
  res << l
7406
7438
  end
7407
7439
  res
@@ -7450,9 +7482,9 @@ module ScientificNameClean
7450
7482
  module ValidNameLetter0
7451
7483
  def value
7452
7484
  res = text_value
7453
- res = 'ae' if res == 'æ'
7454
- res = 'oe' if res == 'œ'
7455
- res = 'e' if res == 'ë'
7485
+ res = "ae" if res == "æ"
7486
+ res = "oe" if res == "œ"
7487
+ res = "e" if res == "ë"
7456
7488
  res
7457
7489
  end
7458
7490
  end
@@ -7484,13 +7516,13 @@ module ScientificNameClean
7484
7516
 
7485
7517
  module CapDigraph0
7486
7518
  def value
7487
- 'Ae'
7519
+ "Ae"
7488
7520
  end
7489
7521
  end
7490
7522
 
7491
7523
  module CapDigraph1
7492
7524
  def value
7493
- 'Oe'
7525
+ "Oe"
7494
7526
  end
7495
7527
  end
7496
7528
 
@@ -7667,7 +7699,7 @@ module ScientificNameClean
7667
7699
  end
7668
7700
 
7669
7701
  def pos
7670
- {interval.begin => ['year', interval.end]}
7702
+ {interval.begin => ["year", interval.end]}
7671
7703
  end
7672
7704
 
7673
7705
  def details
@@ -7725,7 +7757,7 @@ module ScientificNameClean
7725
7757
  end
7726
7758
 
7727
7759
  def pos
7728
- {interval.begin => ['year', interval.end]}
7760
+ {interval.begin => ["year", interval.end]}
7729
7761
  end
7730
7762
 
7731
7763
  def details