biodiversity19 3.1.1 → 3.1.2

Sign up to get free protection for your applications and to get access to all the features.
data/CHANGELOG CHANGED
@@ -1,6 +1,9 @@
1
- 3.1.1 -- fixed problem with names ending on sp
1
+ 3.1.2 -- fixed problems with infraspecies epithets starting with fo,
2
+ for example Peristernia nassatula forskali Tapparone-Canefri 1875
2
3
 
3
- 3.1.0 -- added surrogates: Genbank, Barcode of life names.
4
+ 3.1.1 -- fixed problem with names ending on sp
5
+
6
+ 3.1.0 -- added surrogates: Genbank, Barcode of life names.
4
7
  Also cf., sp. spp are flagged as surrogates
5
8
 
6
9
  3.0.1 -- updated gems
data/VERSION CHANGED
@@ -1 +1 @@
1
- 3.1.1
1
+ 3.1.2
@@ -560,7 +560,7 @@ grammar ScientificNameClean
560
560
  end
561
561
 
562
562
  rule rank
563
- ("morph."/"f.sp."/"B "/"ssp."/"ssp "/"mut."/"nat "/"nothosubsp."/"convar."/"pseudovar."/"sect."/"ser."/"var."/"subvar."/ "[var.]" /"var "/"subsp."/"subsp "/"subf."/"race "/"forma "/"fma."/"fma "/"form."/"form "/"fo."/"fo"/"f."/"α"/"ββ"/"β"/"γ"/"δ"/"ε"/"φ"/"θ"/"μ"/"a."/"b."/"c."/"d."/"e."/"g."/"k."/"****"/"**"/"*")
563
+ ("morph."/"f.sp."/"B "/"ssp."/"ssp "/"mut."/"nat "/"nothosubsp."/"convar."/"pseudovar."/"sect."/"ser."/"var."/"subvar."/ "[var.]" /"var "/"subsp."/"subsp "/"subf."/"race "/"forma "/"fma."/"fma "/"form."/"form "/"fo."/"fo "/"f."/"α"/"ββ"/"β"/"γ"/"δ"/"ε"/"φ"/"θ"/"μ"/"a."/"b."/"c."/"d."/"e."/"g."/"k."/"****"/"**"/"*")
564
564
  {
565
565
  def value
566
566
  text_value.strip
@@ -7,7 +7,7 @@ describe ScientificNameClean do
7
7
  before(:all) do
8
8
  set_parser(ScientificNameCleanParser.new)
9
9
  end
10
-
10
+
11
11
  it 'should parse uninomial' do
12
12
  sn = 'Pseudocercospora'
13
13
  parse(sn).should_not be_nil
@@ -16,12 +16,12 @@ describe ScientificNameClean do
16
16
  details(sn).should == [{:uninomial=>{:string=>"Pseudocercospora"}}]
17
17
  pos(sn).should == {0=>["uninomial", 16]}
18
18
  end
19
-
19
+
20
20
  it 'should parse uninomial with author and year' do
21
21
  sn = 'Pseudocercospora Speg.'
22
22
  parse(sn).should_not be_nil
23
23
  details(sn).should == [{:uninomial=>{:string=>"Pseudocercospora", :authorship=>"Speg.", :basionymAuthorTeam=>{:authorTeam=>"Speg.", :author=>["Speg."]}}}]
24
- pos(sn).should == {0=>["uninomial", 16], 17=>["author_word", 22]}
24
+ pos(sn).should == {0=>["uninomial", 16], 17=>["author_word", 22]}
25
25
  sn = 'Pseudocercospora Spegazzini, 1910'
26
26
  parse(sn).should_not be_nil
27
27
  value(sn).should == 'Pseudocercospora Spegazzini 1910'
@@ -34,7 +34,7 @@ describe ScientificNameClean do
34
34
  parse(sn).should_not be_nil
35
35
  details(sn).should == [{:uninomial=>{:string=>"Epacridaceae"}, :rank_uninomials=>"trib.", :uninomial2=>{:string=>"Archerieae", :authorship=>"Crayn & Quinn", :basionymAuthorTeam=>{:authorTeam=>"Crayn & Quinn", :author=>["Crayn", "Quinn"]}}}]
36
36
  end
37
-
37
+
38
38
  it 'should parse names with a valid 2 letter genus' do
39
39
  ["Ca Dyar 1914",
40
40
  "Ea Distant 1911",
@@ -59,7 +59,7 @@ describe ScientificNameClean do
59
59
  end
60
60
  canonical('Quoyula').should == 'Quoyula'
61
61
  end
62
-
62
+
63
63
  it 'should parse canonical' do
64
64
  sn = 'Pseudocercospora dendrobii'
65
65
  parse(sn).should_not be_nil
@@ -78,8 +78,8 @@ describe ScientificNameClean do
78
78
  value(sn).should == 'Ps. dendrobii'
79
79
  details(sn).should == [{:genus=>{:string=>"Ps."}, :species=>{:string=>"dendrobii"}}]
80
80
  end
81
-
82
-
81
+
82
+
83
83
  it 'should parse species name with author and year' do
84
84
  sn = "Platypus bicaudatulus Schedl 1935"
85
85
  parse(sn).should_not be_nil
@@ -95,7 +95,7 @@ describe ScientificNameClean do
95
95
  details(sn).should == [{:genus=>{:string=>"Platypus"}, :species=>{:string=>"bicaudatulus", :authorship=>"Schedl (1935h)", :basionymAuthorTeam=>{:authorTeam=>"Schedl", :author=>["Schedl"], :year=>"1935"}}}]
96
96
  parse("Platypus bicaudatulus Schedl 1935").should_not be_nil
97
97
  end
98
-
98
+
99
99
  it 'should parse species name with abbreviated genus, author and year' do
100
100
  sn = "P. bicaudatulus Schedl 1935"
101
101
  parse(sn).should_not be_nil
@@ -110,7 +110,7 @@ describe ScientificNameClean do
110
110
  end
111
111
 
112
112
  it "should parse species name with author's postfix f., filius (son of)" do
113
- names = [
113
+ names = [
114
114
  [ "Platypus bicaudatulus Schedl f. 1935", [{:genus=>{:string=>"Platypus"}, :species=>{:string=>"bicaudatulus", :authorship=>"Schedl f. 1935", :basionymAuthorTeam=>{:authorTeam=>"Schedl f.", :author=>["Schedl f."], :year=>"1935"}}}], 'Platypus bicaudatulus Schedl f. 1935'],
115
115
  [ "Platypus bicaudatulus Schedl filius 1935", [{:genus=>{:string=>"Platypus"}, :species=>{:string=>"bicaudatulus", :authorship=>"Schedl filius 1935", :basionymAuthorTeam=>{:authorTeam=>"Schedl filius", :author=>["Schedl filius"], :year=>"1935"}}}], 'Platypus bicaudatulus Schedl filius 1935'],
116
116
  [ "Fimbristylis ovata (Burm. f.) J. Kern", [{:genus=>{:string=>"Fimbristylis"}, :species=>{:string=>"ovata", :authorship=>"(Burm. f.) J. Kern", :combinationAuthorTeam=>{:authorTeam=>"J. Kern", :author=>["J. Kern"]}, :basionymAuthorTeam=>{:authorTeam=>"Burm. f.", :author=>["Burm. f."]}}}], 'Fimbristylis ovata (Burm. f.) J. Kern'],
@@ -123,14 +123,15 @@ describe ScientificNameClean do
123
123
  ["Betula pendula fo. dalecarlica (L. f.) C.K. Schneid.", [{:infraspecies=>[{:basionymAuthorTeam=>{:author=>["L. f."], :authorTeam=>"L. f."}, :string=>"dalecarlica", :rank=>"fo.", :combinationAuthorTeam=>{:author=>["C.K. Schneid."], :authorTeam=>"C.K. Schneid."}, :authorship=>"(L. f.) C.K. Schneid."}], :genus=>{:string=>"Betula"}, :species=>{:string=>"pendula"}}], "Betula pendula fo. dalecarlica (L. f.) C.K. Schneid."],
124
124
  ["Racomitrium canescens f. ericoides (F. Weber ex Brid.) Mönk.", [{:genus=>{:string=>"Racomitrium"}, :species=>{:string=>"canescens"}, :infraspecies=>[{:string=>"ericoides", :rank=>"f.", :authorship=>"(F. Weber ex Brid.) Mönk.", :combinationAuthorTeam=>{:authorTeam=>"Mönk.", :author=>["Mönk."]}, :basionymAuthorTeam=>{:authorTeam=>"F. Weber", :author=>["F. Weber"], :exAuthorTeam=>{:authorTeam=>"Brid.", :author=>["Brid."]}}}]}], "Racomitrium canescens f. ericoides (F. Weber ex Brid.) Mönk."],
125
125
  ["Racomitrium canescens forma ericoides (F. Weber ex Brid.) Mönk.", [{:genus=>{:string=>"Racomitrium"}, :species=>{:string=>"canescens"}, :infraspecies=>[{:string=>"ericoides", :rank=>"forma", :authorship=>"(F. Weber ex Brid.) Mönk.", :combinationAuthorTeam=>{:authorTeam=>"Mönk.", :author=>["Mönk."]}, :basionymAuthorTeam=>{:authorTeam=>"F. Weber", :author=>["F. Weber"], :exAuthorTeam=>{:authorTeam=>"Brid.", :author=>["Brid."]}}}]}], "Racomitrium canescens forma ericoides (F. Weber ex Brid.) Mönk."],
126
+ ["Peristernia nassatula forskali Tapparone-Canefri 1875", [{:genus=>{:string=>"Peristernia"}, :species=>{:string=>"nassatula"}, :infraspecies=>[{:string=>"forskali", :rank=>"n/a", :authorship=>"Tapparone-Canefri 1875", :basionymAuthorTeam=>{:authorTeam=>"Tapparone-Canefri", :author=>["Tapparone-Canefri"], :year=>"1875"}}]}], "Peristernia nassatula forskali Tapparone-Canefri 1875"],
126
127
  ]
127
- names.each do |sn, sn_details, sn_value|
128
+ names.each do |sn, sn_details, sn_value|
128
129
  parse(sn).should_not be_nil
129
130
  details(sn).should == sn_details
130
131
  value(sn).should == sn_value
131
132
  end
132
133
  end
133
-
134
+
134
135
  it 'should parse genus with "?"' do
135
136
  sn = "Ferganoconcha? oblonga"
136
137
  parse(sn).should_not be_nil
@@ -138,7 +139,7 @@ describe ScientificNameClean do
138
139
  details(sn).should == [{:genus=>{:string=>"Ferganoconcha"}, :species=>{:string=>"oblonga"}}]
139
140
  pos(sn).should == {0=>["genus", 14], 15=>["species", 22]}
140
141
  end
141
-
142
+
142
143
  it 'should parse æ in the name' do
143
144
  names = [
144
145
  ["Læptura laetifica Dow, 1913", "Laeptura laetifica Dow 1913"],
@@ -157,7 +158,7 @@ describe ScientificNameClean do
157
158
  value(name_pair[0]).should == name_pair[1]
158
159
  end
159
160
  end
160
-
161
+
161
162
  it 'should parse names with e-umlaut' do
162
163
  sn = 'Kalanchoë tuberosa'
163
164
  canonical(sn).should == 'Kalanchoe tuberosa'
@@ -174,7 +175,7 @@ describe ScientificNameClean do
174
175
  pos(sn).should == {0=>["genus", 7], 9=>["infragenus", 16], 18=>["species", 29], 30=>["author_word", 38], 39=>["author_word", 40], 41=>["year", 45]}
175
176
  sn = "Ixodes (Ixodes) hexagonus hexagonus Neumann, 1911"
176
177
  canonical(sn).should == "Ixodes hexagonus hexagonus"
177
- sn = "Brachytrypus (B.) grandidieri"
178
+ sn = "Brachytrypus (B.) grandidieri"
178
179
  canonical(sn).should == "Brachytrypus grandidieri"
179
180
  details(sn).should == [{:genus=>{:string=>"Brachytrypus"}, :infragenus=>{:string=>"B."}, :species=>{:string=>"grandidieri"}}]
180
181
  sn = "Empis (Argyrandrus) Bezzi 1909"
@@ -185,7 +186,7 @@ describe ScientificNameClean do
185
186
  sn = "Platydoris (B.)"
186
187
  details(sn).should == [{:uninomial=>{:string=>"Platydoris", :infragenus=>{:string=>"B."}}}]
187
188
  end
188
-
189
+
189
190
  it 'should parse several authors without a year' do
190
191
  sn = "Pseudocercospora dendrobii U. Braun & Crous"
191
192
  parse(sn).should_not be_nil
@@ -199,14 +200,14 @@ describe ScientificNameClean do
199
200
  pos(sn).should == {0=>["genus", 16], 17=>["species", 26], 27=>["author_word", 29], 30=>["author_word", 35], 40=>["author_word", 45]}
200
201
  sn = "Pseudocercospora dendrobii U. Braun et Crous"
201
202
  parse(sn).should_not be_nil
202
- value(sn).should == "Pseudocercospora dendrobii U. Braun & Crous"
203
+ value(sn).should == "Pseudocercospora dendrobii U. Braun & Crous"
203
204
  sn = "Arthopyrenia hyalospora(Nyl.)R.C. Harris"
204
205
  parse(sn).should_not be_nil
205
206
  value(sn).should == "Arthopyrenia hyalospora (Nyl.) R.C. Harris"
206
207
  canonical(sn).should == "Arthopyrenia hyalospora"
207
208
  details(sn).should == [{:genus=>{:string=>"Arthopyrenia"}, :species=>{:string=>"hyalospora", :authorship=>"(Nyl.)R.C. Harris", :combinationAuthorTeam=>{:authorTeam=>"R.C. Harris", :author=>["R.C. Harris"]}, :basionymAuthorTeam=>{:authorTeam=>"Nyl.", :author=>["Nyl."]}}}]
208
209
  end
209
-
210
+
210
211
  it 'should parse several authors with a year' do
211
212
  sn = "Pseudocercospora dendrobii U. Braun & Crous 2003"
212
213
  parse(sn).should_not be_nil
@@ -217,7 +218,7 @@ describe ScientificNameClean do
217
218
  sn = "Pseudocercospora dendrobii Crous, 2003"
218
219
  parse(sn).should_not be_nil
219
220
  end
220
-
221
+
221
222
  it 'should parse basionym authors in parenthesis' do
222
223
  sn = "Zophosis persis (Chatanay, 1914)"
223
224
  parse(sn).should_not be_nil
@@ -232,9 +233,9 @@ describe ScientificNameClean do
232
233
  pos(sn).should == {0=>["genus", 8], 9=>["species", 15], 17=>["author_word", 25], 28=>["year", 32]}
233
234
  parse("Zophosis persis (Chatanay) 1914").should_not be_nil
234
235
  #parse("Zophosis persis Chatanay (1914)").should_not be_nil
235
- end
236
+ end
236
237
 
237
- it "should be able to parse name with identificaation annotation -- aff cf sp spp" do
238
+ it "should be able to parse name with identificaation annotation -- aff cf sp spp" do
238
239
  sn = 'Diplocephalus aff. procerus Thaler, 1972'
239
240
  details(sn).should == [{:genus=>{:string=>"Diplocephalus"}, :annotation_identification=>"aff.", :ignored=>{:species=>{:string=>"procerus", :authorship=>"Thaler, 1972", :basionymAuthorTeam=>{:authorTeam=>"Thaler", :author=>["Thaler"], :year=>"1972"}}}}]
240
241
  sn = 'Diplocephalus aff procerus Thaler, 1972'
@@ -250,7 +251,7 @@ describe ScientificNameClean do
250
251
  sn = "Thryothorus leucotis spp. bogotensis"
251
252
  details(sn).should == [{:genus=>{:string=>"Thryothorus"}, :species=>{:string=>"leucotis"}, :infraspecies=>[{:annotation_identification=>"spp.", :ignored=>{:infraspecies=>{:string=>"bogotensis", :rank=>"n/a"}}}]}]
252
253
  end
253
-
254
+
254
255
  it 'should parse scientific name' do
255
256
  sn = "Pseudocercospora dendrobii(H.C. Burnett)U. Braun & Crous 2003"
256
257
  parse(sn).should_not be_nil
@@ -262,7 +263,7 @@ describe ScientificNameClean do
262
263
  value(sn).should == "Pseudocercospora dendrobii (H.C. Burnett 1873) U. Braun & Crous 2003"
263
264
  details(sn).should == [{:genus=>{:string=>"Pseudocercospora"}, :species=>{:string=>"dendrobii", :authorship=>"(H.C. Burnett,1873)U. Braun & Crous 2003", :combinationAuthorTeam=>{:authorTeam=>"U. Braun & Crous", :author=>["U. Braun", "Crous"], :year=>"2003"}, :basionymAuthorTeam=>{:authorTeam=>"H.C. Burnett", :author=>["H.C. Burnett"], :year=>"1873"}}}]
264
265
  end
265
-
266
+
266
267
  it 'should parse several authors with several years' do
267
268
  sn = "Pseudocercospora dendrobii (H.C. Burnett 1883) U. Braun & Crous 2003"
268
269
  parse(sn).should_not be_nil
@@ -301,7 +302,7 @@ describe ScientificNameClean do
301
302
  sn = "Cassytha peninsularis J. Z. Weber var. flindersii"
302
303
  canonical(sn).should == "Cassytha peninsularis flindersii"
303
304
  sn = "Prunus armeniaca convar. budae (Pénzes) Soó"
304
-
305
+
305
306
  canonical(sn).should == "Prunus armeniaca budae"
306
307
  sn = "Polypodium pectinatum L. f. typica Rosenst."
307
308
  canonical(sn).should == "Polypodium pectinatum typica"
@@ -330,8 +331,8 @@ describe ScientificNameClean do
330
331
  value(sn).should == "Lachenalia tricolor var. nelsonii (auct.) Baker"
331
332
  details(sn).should == [{:genus=>{:string=>"Lachenalia"}, :species=>{:string=>"tricolor"}, :infraspecies=>[{:string=>"nelsonii", :rank=>"var.", :authorship=>"(auct.) Baker", :combinationAuthorTeam=>{:authorTeam=>"Baker", :author=>["Baker"]}, :basionymAuthorTeam=>{:authorTeam=>"auct.", :author=>["unknown"]}}]}]
332
333
  pos(sn).should == {0=>["genus", 10], 11=>["species", 19], 20=>["infraspecific_type", 24], 25=>["infraspecies", 33], 35=>["unknown_author", 40], 42=>["author_word", 47]}
333
- end
334
-
334
+ end
335
+
335
336
  it 'should parse unknown authors auct./anon./hort./ht.' do
336
337
  sn = "Puya acris ht."
337
338
  parse(sn).should_not be_nil
@@ -343,7 +344,7 @@ describe ScientificNameClean do
343
344
  pr = parse(sn).should_not be_nil
344
345
  pos(sn).should == {0=>["genus", 3], 4=>["species", 12], 13=>["infraspecies", 23]}
345
346
  end
346
-
347
+
347
348
  it 'should parse real world examples' do
348
349
  sn = "Stagonospora polyspora M.T. Lucas & Sousa da Câmara 1934"
349
350
  parse(sn).should_not be_nil
@@ -358,7 +359,7 @@ describe ScientificNameClean do
358
359
  parse("Physalospora rubiginosa (Fr.) anon.").should_not be_nil
359
360
  parse("Pleurotus ëous (Berk.) Sacc. 1887").should_not be_nil
360
361
  parse("Lecanora wetmorei Śliwa 2004").should_not be_nil
361
- # valid
362
+ # valid
362
363
  # infraspecific
363
364
  parse("Calicium furfuraceum * furfuraceum (L.) Pers. 1797").should_not be_nil
364
365
  parse("Exobasidium vaccinii ** andromedae (P. Karst.) P. Karst. 1882").should_not be_nil
@@ -411,7 +412,7 @@ describe ScientificNameClean do
411
412
  pos(sn).should == {0=>["genus", 13], 14=>["species", 25], 26=>["infraspecific_type", 32], 33=>["infraspecies", 41], 42=>["author_word", 47], 48=>["year", 52]}
412
413
  end
413
414
 
414
-
415
+
415
416
  it "should parse name with forma/fo./form./f." do
416
417
  sn = "Caulerpa cupressoides forma nuda"
417
418
  parse(sn).should_not be_nil
@@ -440,18 +441,18 @@ describe ScientificNameClean do
440
441
  pos(sn).should == {0=>["genus", 12], 16=>["species", 25], 29=>["infraspecific_type", 31], 36=>["infraspecies", 43], 47=>["author_word", 53], 58=>["year", 62]}
441
442
  parse('Polypodium vulgare nothosubsp. mantoniae (Rothm.) Schidlay').should_not be_nil
442
443
  end
443
-
444
+
444
445
  it "should parse name with several subspecies names NOT BOTANICAL CODE BUT NOT INFREQUENT" do
445
446
  sn = "Hydnellum scrobiculatum var. zonatum f. parvum (Banker) D. Hall & D.E. Stuntz 1972"
446
447
  parse(sn).should_not be_nil
447
448
  value(sn).should == "Hydnellum scrobiculatum var. zonatum f. parvum (Banker) D. Hall & D.E. Stuntz 1972"
448
449
  details(sn).should == [{:genus=>{:string=>"Hydnellum"}, :species=>{:string=>"scrobiculatum"}, :infraspecies=>[{:string=>"zonatum", :rank=>"var."}, {:string=>"parvum", :rank=>"f.", :authorship=>"(Banker) D. Hall & D.E. Stuntz 1972", :combinationAuthorTeam=>{:authorTeam=>"D. Hall & D.E. Stuntz", :author=>["D. Hall", "D.E. Stuntz"], :year=>"1972"}, :basionymAuthorTeam=>{:authorTeam=>"Banker", :author=>["Banker"]}}]}]
449
- pos(sn).should == {0=>["genus", 9], 10=>["species", 23], 24=>["infraspecific_type", 28], 29=>["infraspecies", 36], 37=>["infraspecific_type", 39], 40=>["infraspecies", 46], 48=>["author_word", 54], 56=>["author_word", 58], 59=>["author_word", 63], 66=>["author_word", 70], 71=>["author_word", 77], 78=>["year", 82]}
450
+ pos(sn).should == {0=>["genus", 9], 10=>["species", 23], 24=>["infraspecific_type", 28], 29=>["infraspecies", 36], 37=>["infraspecific_type", 39], 40=>["infraspecies", 46], 48=>["author_word", 54], 56=>["author_word", 58], 59=>["author_word", 63], 66=>["author_word", 70], 71=>["author_word", 77], 78=>["year", 82]}
450
451
  parse('Senecio fuchsii C.C.Gmel. subsp. fuchsii var. expansus (Boiss. & Heldr.) Hayek').should_not be_nil
451
452
  parse('Senecio fuchsii C.C.Gmel. subsp. fuchsii var. fuchsii').should_not be_nil
452
453
  end
453
-
454
-
454
+
455
+
455
456
  it "should parse status BOTANICAL RARE" do
456
457
  #it is always latin abbrev often 2 words
457
458
  sn = "Arthopyrenia hyalospora (Nyl.) R.C. Harris comb. nov."
@@ -461,7 +462,7 @@ describe ScientificNameClean do
461
462
  details(sn).should == [{:genus=>{:string=>"Arthopyrenia"}, :species=>{:string=>"hyalospora", :authorship=>"(Nyl.) R.C. Harris", :combinationAuthorTeam=>{:authorTeam=>"R.C. Harris", :author=>["R.C. Harris"]}, :basionymAuthorTeam=>{:authorTeam=>"Nyl.", :author=>["Nyl."]}}, :status=>"comb. nov."}]
462
463
  pos(sn).should == {0=>["genus", 12], 13=>["species", 23], 25=>["author_word", 29], 31=>["author_word", 35], 36=>["author_word", 42]}
463
464
  end
464
-
465
+
465
466
  it "should parse revised (ex) names" do
466
467
  #invalidly published
467
468
  sn = "Arthopyrenia hyalospora (Nyl. ex Banker) R.C. Harris"
@@ -490,7 +491,7 @@ describe ScientificNameClean do
490
491
  details(sn).should == [{:genus=>{:string=>"Salmonella"}, :species=>{:string=>"werahensis", :authorship=>"(Castellani) Hauduroy and Ehringer in Hauduroy 1937", :combinationAuthorTeam=>{:authorTeam=>"Hauduroy and Ehringer", :author=>["Hauduroy", "Ehringer"], :exAuthorTeam=>{:authorTeam=>"Hauduroy", :author=>["Hauduroy"], :year=>"1937"}}, :basionymAuthorTeam=>{:authorTeam=>"Castellani", :author=>["Castellani"]}}}]
491
492
  pos(sn).should == {0=>["genus", 10], 11=>["species", 21], 23=>["author_word", 33], 35=>["author_word", 43], 48=>["author_word", 56], 60=>["author_word", 68], 69=>["year", 73]}
492
493
  end
493
-
494
+
494
495
  it 'should parse named hybrids' do
495
496
  [
496
497
  ["×Agropogon P. Fourn. 1934", [{:uninomial=>{:string=>"Agropogon", :authorship=>"P. Fourn. 1934", :basionymAuthorTeam=>{:authorTeam=>"P. Fourn.", :author=>["P. Fourn."], :year=>"1934"}}}]],
@@ -504,12 +505,12 @@ describe ScientificNameClean do
504
505
  ["xHeucherella tiarelloides", [{:genus=>{:string=>"Heucherella"}, :species=>{:string=>"tiarelloides"}}]],
505
506
  ["x Heucherella tiarelloides", [{:genus=>{:string=>"Heucherella"}, :species=>{:string=>"tiarelloides"}}]],
506
507
  ["×Agropogon littoralis (Sm.) C. E. Hubb. 1946", [{:genus=>{:string=>"Agropogon"}, :species=>{:string=>"littoralis", :authorship=>"(Sm.) C. E. Hubb. 1946", :combinationAuthorTeam=>{:authorTeam=>"C. E. Hubb.", :author=>["C. E. Hubb."], :year=>"1946"}, :basionymAuthorTeam=>{:authorTeam=>"Sm.", :author=>["Sm."]}}}]]
507
- ].each do |res|
508
+ ].each do |res|
508
509
  parse(res[0]).should_not be_nil
509
510
  parse(res[0]).hybrid.should be_true
510
511
  details(res[0]).should == res[1]
511
512
  end
512
- [
513
+ [
513
514
  ['Asplenium X inexpectatum (E.L. Braun 1940) Morton (1956)',[{:genus=>{:string=>"Asplenium"}, :species=>{:string=>"inexpectatum", :authorship=>"(E.L. Braun 1940) Morton (1956)", :combinationAuthorTeam=>{:authorTeam=>"Morton", :author=>["Morton"], :year=>"1956"}, :basionymAuthorTeam=>{:authorTeam=>"E.L. Braun", :author=>["E.L. Braun"], :year=>"1940"}}}]],
514
515
  ['Mentha ×smithiana R. A. Graham 1949',[{:genus=>{:string=>"Mentha"}, :species=>{:string=>"smithiana", :authorship=>"R. A. Graham 1949", :basionymAuthorTeam=>{:authorTeam=>"R. A. Graham", :author=>["R. A. Graham"], :year=>"1949"}}}]],
515
516
  ['Salix ×capreola Andersson (1867)',[{:genus=>{:string=>"Salix"}, :species=>{:string=>"capreola", :authorship=>"Andersson (1867)", :basionymAuthorTeam=>{:authorTeam=>"Andersson", :author=>["Andersson"], :year=>"1867"}}}]],
@@ -523,7 +524,7 @@ describe ScientificNameClean do
523
524
  canonical(sn).should == "Rosa alpina × pomifera"
524
525
  parse(sn).details.should == [{:genus=>{:string=>"Rosa"}, :species=>{:string=>"alpina"}}, {:species=>{:string=>"pomifera"}, :genus=>{:string=>"Rosa"}}]
525
526
  end
526
-
527
+
527
528
  it "should parse hybrid combination" do
528
529
  sn = "Arthopyrenia hyalospora X Hydnellum scrobiculatum"
529
530
  parse(sn).should_not be_nil
@@ -538,7 +539,7 @@ describe ScientificNameClean do
538
539
  value(sn).should == "Arthopyrenia hyalospora (Banker) D. Hall \303\227 Hydnellum scrobiculatum D.E. Stuntz"
539
540
  canonical(sn).should == "Arthopyrenia hyalospora × Hydnellum scrobiculatum"
540
541
  pos(sn).should == {0=>["genus", 12], 13=>["species", 23], 25=>["author_word", 31], 33=>["author_word", 35], 36=>["author_word", 40], 43=>["genus", 52], 53=>["species", 66], 67=>["author_word", 71], 72=>["author_word", 78]}
541
- value("Arthopyrenia hyalospora X").should == "Arthopyrenia hyalospora \303\227 ?"
542
+ value("Arthopyrenia hyalospora X").should == "Arthopyrenia hyalospora \303\227 ?"
542
543
  sn = "Arthopyrenia hyalospora x"
543
544
  parse(sn).should_not be_nil
544
545
  parse(sn).hybrid.should be_true
@@ -551,7 +552,7 @@ describe ScientificNameClean do
551
552
  details(sn).should == [{:genus=>{:string=>"Arthopyrenia"}, :species=>{:string=>"hyalospora"}}, "?"]
552
553
  pos(sn).should == {0=>["genus", 12], 13=>["species", 23]}
553
554
  end
554
-
555
+
555
556
  it 'should parse names with taxon concept' do
556
557
  sn = "Stenometope laevissimus sec. Eschmeyer 2004"
557
558
  details(sn).should == [{:genus=>{:string=>"Stenometope"}, :species=>{:string=>"laevissimus"}, :taxon_concept=>{:authorship=>"Eschmeyer 2004", :basionymAuthorTeam=>{:authorTeam=>"Eschmeyer", :author=>["Eschmeyer"], :year=>"2004"}}}]
@@ -561,12 +562,12 @@ describe ScientificNameClean do
561
562
  details(sn).should == [{:genus=>{:string=>"Stenometope"}, :species=>{:string=>"laevissimus", :authorship=>"Bibron 1855", :basionymAuthorTeam=>{:authorTeam=>"Bibron", :author=>["Bibron"], :year=>"1855"}}, :taxon_concept=>{:authorship=>"Eschmeyer 2004", :basionymAuthorTeam=>{:authorTeam=>"Eschmeyer", :author=>["Eschmeyer"], :year=>"2004"}}}]
562
563
  pos(sn).should == {0=>["genus", 11], 12=>["species", 23], 24=>["author_word", 30], 31=>["year", 35], 41=>["author_word", 50], 51=>["year", 55]}
563
564
  end
564
-
565
+
565
566
  it 'should parse names with spaces inconsistencies at the start and the end and in the middle' do
566
567
  parse(" Asplenium X inexpectatum (E.L. Braun 1940) Morton (1956) ").should_not be_nil
567
568
  end
568
-
569
- it 'should parse names with any number of spaces' do
569
+
570
+ it 'should parse names with any number of spaces' do
570
571
  sn = "Trematosphaeria phaeospora (E. Müll.) L. Holm 1957"
571
572
  parse(sn).should_not be_nil
572
573
  value(sn).should == "Trematosphaeria phaeospora (E. Müll.) L. Holm 1957"
@@ -574,7 +575,7 @@ describe ScientificNameClean do
574
575
  details(sn).should == [{:genus=>{:string=>"Trematosphaeria"}, :species=>{:string=>"phaeospora", :authorship=>"(E. Müll.) L. Holm 1957", :combinationAuthorTeam=>{:authorTeam=>"L. Holm", :author=>["L. Holm"], :year=>"1957"}, :basionymAuthorTeam=>{:authorTeam=>"E. Müll.", :author=>["E. Müll."]}}}]
575
576
  pos(sn).should == {0=>["genus", 15], 16=>["species", 26], 28=>["author_word", 30], 31=>["author_word", 36], 46=>["author_word", 48], 61=>["author_word", 65], 66=>["year", 70]}
576
577
  end
577
-
578
+
578
579
  it 'should not parse serveral authors groups with several years NOT CORRECT' do
579
580
  parse("Pseudocercospora dendrobii (H.C. Burnett 1883) (Leight.) (Movss. 1967) U. Braun & Crous 2003").should be_nil
580
581
  end
@@ -609,7 +610,7 @@ describe ScientificNameClean do
609
610
  sn = 'Deschampsia cespitosa ssp pumila'
610
611
  details(sn).should == [{:genus=>{:string=>"Deschampsia"}, :species=>{:string=>"cespitosa"}, :infraspecies=>[{:string=>"pumila", :rank=>"ssp"}]}]
611
612
  end
612
-
613
+
613
614
  # Combination genus names should be merged without dash or capital letter
614
615
  it 'should parse hybrid names with capitalized second name in genus (botanical code error)' do
615
616
  sn = 'Anacampti-Platanthera P. Fourn.'
@@ -627,13 +628,13 @@ describe ScientificNameClean do
627
628
  canonical(sn).should == 'Oemona simplex'
628
629
  end
629
630
  #"Arthrosamanea eriorhachis (Harms & sine ref. ) Aubrév." -- ignore & sine ref. (means without reference)
630
-
631
+
631
632
  =begin
632
633
  new stuff
633
634
 
634
635
  sn = "Orchidaceae × Asconopsis hort."
635
636
  canonical(sn).should == "Orchidaceae x Asconopsis"
636
- sn
637
+ sn
637
638
  Tamiops swinhoei near hainanus|Tamiops swinhoei near hainanus
638
639
  Conus textile form archiepiscopus|Conus textile form archiepiscopus|
639
640
  Crypticus pseudosericeus ssp. olivieri Desbrochers des Loges,1881|Crypticus pseudosericeus olivieri des
@@ -414,6 +414,7 @@ Buteo borealis ? ventralis|{"scientificName":{"parsed":true, "parser_version":"t
414
414
  Cetraria islandica ? islandica|{"scientificName":{"parsed":true, "parser_version":"test_version", "verbatim":"Cetraria islandica ? islandica", "normalized":"Cetraria islandica", "canonical":"Cetraria islandica", "hybrid":false, "details":[{"genus":{"string":"Cetraria"}, "species":{"string":"islandica"}, "infraspecies":[{"annotation_identification":"?", "ignored":{"infraspecies":{"string":"islandica", "rank":"n/a"}}}]}], "parser_run":1, "positions":{"0":["genus", 8], "9":["species", 18], "19":["annotation_identification", 21]}}}
415
415
  Euxoa nr. idahoensis sp. 1clay|{"scientificName":{"parsed":true, "parser_version":"test_version", "verbatim":"Euxoa nr. idahoensis sp. 1clay", "normalized":"Euxoa idahoensis", "canonical":"Euxoa idahoensis", "hybrid":false, "details":[{"genus":{"string":"Euxoa"}, "species":{"string":"idahoensis"}, "infraspecies":[{"annotation_identification":"sp.", "ignored":{"infraspecies":{"string":"uniclay", "rank":"n/a"}}}]}], "parser_run":1, "positions":{"0":["genus", 5], "10":["species", 20], "21":["annotation_identification", 24]}, "surrogate": true}}
416
416
  Parus caeruleus species complex|{"scientificName":{"parsed":true, "parser_version":"test_version", "verbatim":"Parus caeruleus species complex", "normalized":"Parus caeruleus", "canonical":"Parus caeruleus", "hybrid":false, "details":[{"genus":{"string":"Parus"}, "species":{"string":"caeruleus"}}], "parser_run":1, "positions":{"0":["genus", 5], "6":["species", 15]}}}
417
+ Peristernia nassatula forskali Tapparone-Canefri 1875|{"scientificName":{"parsed":true, "parser_version":"test_version", "verbatim":"Peristernia nassatula forskali Tapparone-Canefri 1875", "normalized":"Peristernia nassatula forskali Tapparone-Canefri 1875", "canonical":"Peristernia nassatula forskali", "hybrid":false, "details":[{"genus":{"string":"Peristernia"}, "species":{"string":"nassatula"}, "infraspecies":[{"string":"forskali", "rank":"n/a", "authorship":"Tapparone-Canefri 1875", "basionymAuthorTeam":{"authorTeam":"Tapparone-Canefri", "author":["Tapparone-Canefri"], "year":"1875"}}]}], "parser_run":1, "positions":{"0":["genus", 11], "12":["species", 21], "22":["infraspecies", 30], "31":["author_word", 48], "49":["year", 53]}}}
417
418
 
418
419
  #should flag surrogate names
419
420
  Coleoptera sp. BOLD:AAV0432|{"scientificName":{"parsed":true, "parser_version":"test_version", "verbatim":"Coleoptera sp. BOLD:AAV0432", "normalized":"Coleoptera", "canonical":"Coleoptera", "hybrid":false, "details":[{"genus":{"string":"Coleoptera"}, "annotation_identification":"sp.", "ignored":{"unparsed":"BOLD:AAV0432"}}], "parser_run":1, "positions":{"0":["genus", 10], "11":["annotation_identification", 14]}, "surrogate":true}}
metadata CHANGED
@@ -1,7 +1,7 @@
1
1
  --- !ruby/object:Gem::Specification
2
2
  name: biodiversity19
3
3
  version: !ruby/object:Gem::Version
4
- version: 3.1.1
4
+ version: 3.1.2
5
5
  prerelease:
6
6
  platform: ruby
7
7
  authors:
@@ -9,7 +9,7 @@ authors:
9
9
  autorequire:
10
10
  bindir: bin
11
11
  cert_chain: []
12
- date: 2013-06-18 00:00:00.000000000 Z
12
+ date: 2013-06-21 00:00:00.000000000 Z
13
13
  dependencies:
14
14
  - !ruby/object:Gem::Dependency
15
15
  name: rake
@@ -209,6 +209,9 @@ required_ruby_version: !ruby/object:Gem::Requirement
209
209
  - - ! '>='
210
210
  - !ruby/object:Gem::Version
211
211
  version: '0'
212
+ segments:
213
+ - 0
214
+ hash: 4103623909009962506
212
215
  required_rubygems_version: !ruby/object:Gem::Requirement
213
216
  none: false
214
217
  requirements: