dimus-biodiversity 0.5.2 → 0.5.3

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Files changed (11) hide show
  1. data/lib/biodiversity.rb +0 -2
  2. data/lib/biodiversity/parser.rb +4 -7
  3. data/lib/biodiversity/parser/scientific_name_canonical.rb +22 -0
  4. data/lib/biodiversity/parser/scientific_name_canonical.treetop +18 -2
  5. data/lib/biodiversity/parser/scientific_name_clean.rb +139 -60
  6. data/lib/biodiversity/parser/scientific_name_clean.treetop +85 -9
  7. data/spec/parser/scientific_name.spec.rb +15 -5
  8. data/spec/parser/scientific_name_canonical.spec.rb +6 -5
  9. data/spec/parser/scientific_name_clean.spec.rb +79 -73
  10. data/spec/parser/scientific_name_dirty.spec.rb +13 -13
  11. metadata +1 -1
data/lib/biodiversity.rb CHANGED
@@ -7,5 +7,3 @@ BIODIVERSITY_ROOT = File.join(dir, 'biodiversity')
7
7
  require File.join(dir, "/../conf/environment")
8
8
  require File.join(BIODIVERSITY_ROOT, "parser")
9
9
  require File.join(BIODIVERSITY_ROOT, "guid")
10
-
11
-
data/lib/biodiversity/parser.rb CHANGED
@@ -23,17 +23,14 @@ class ScientificNameParser
23
23
  parsed = self.class != Hash
24
24
  res = {:parsed => parsed}
25
25
  if parsed
26
+ hybrid = self.hybrid rescue false
26
27
  res.merge!({
27
28
  :verbatim => self.text_value,
28
29
  :normalized => self.value,
29
- :canonical => self.canonical
30
+ :canonical => self.canonical,
31
+ :hybrid => hybrid,
32
+ :details => self.details
30
33
  })
31
- data = self.details
32
- if data[:species] && data[:species][:namedHybrid]
33
- data[:species].delete(:namedHybrid)
34
- data = {:namedHybrid => data}
35
- end
36
- res.merge!(data)
37
34
  else
38
35
  res.merge!(self)
39
36
  end
data/lib/biodiversity/parser/scientific_name_canonical.rb CHANGED
@@ -10,6 +10,26 @@ module ScientificNameCanonical
10
10
 
11
11
  include ScientificNameDirty
12
12
 
13
+ module Root0
14
+ def hybrid
15
+ false
16
+ end
17
+
18
+ def details
19
+ [super]
20
+ end
21
+ end
22
+
23
+ module Root1
24
+ def hybrid
25
+ false
26
+ end
27
+
28
+ def details
29
+ [super]
30
+ end
31
+ end
32
+
13
33
  def _nt_root
14
34
  start_index = index
15
35
  if node_cache[:root].has_key?(index)
@@ -20,10 +40,12 @@ module ScientificNameCanonical
20
40
 
21
41
  i0 = index
22
42
  r1 = _nt_multinomial_with_garbage
43
+ r1.extend(Root0)
23
44
  if r1
24
45
  r0 = r1
25
46
  else
26
47
  r2 = _nt_uninomial_with_garbage
48
+ r2.extend(Root1)
27
49
  if r2
28
50
  r0 = r2
29
51
  else
data/lib/biodiversity/parser/scientific_name_canonical.treetop CHANGED
@@ -4,9 +4,25 @@ grammar ScientificNameCanonical
4
4
  include ScientificNameDirty
5
5
 
6
6
  rule root
7
- multinomial_with_garbage
7
+ multinomial_with_garbage {
8
+ def hybrid
9
+ false
10
+ end
11
+
12
+ def details
13
+ [super]
14
+ end
15
+ }
8
16
  /
9
- uninomial_with_garbage
17
+ uninomial_with_garbage {
18
+ def hybrid
19
+ false
20
+ end
21
+
22
+ def details
23
+ [super]
24
+ end
25
+ }
10
26
  end
11
27
 
12
28
  rule multinomial_with_garbage
data/lib/biodiversity/parser/scientific_name_clean.rb CHANGED
@@ -33,8 +33,12 @@ module ScientificNameClean
33
33
  a.pos
34
34
  end
35
35
 
36
+ def hybrid
37
+ a.hybrid
38
+ end
39
+
36
40
  def details
37
- a.details
41
+ a.details.class == Array ? a.details : [a.details]
38
42
  end
39
43
  end
40
44
 
@@ -105,7 +109,11 @@ module ScientificNameClean
105
109
  def pos
106
110
  a.pos.merge(c.pos)
107
111
  end
108
-
112
+
113
+ def hybrid
114
+ a.hybrid
115
+ end
116
+
109
117
  def details
110
118
  a.details.merge(b.details(c))
111
119
  end
@@ -199,8 +207,12 @@ module ScientificNameClean
199
207
  a.pos.merge(b.pos)
200
208
  end
201
209
 
210
+ def hybrid
211
+ true
212
+ end
213
+
202
214
  def details
203
- {:hybridFormula => [a.details, b.details]}
215
+ [a.details, b.details]
204
216
  end
205
217
  end
206
218
 
@@ -236,8 +248,12 @@ module ScientificNameClean
236
248
  a.pos
237
249
  end
238
250
 
251
+ def hybrid
252
+ true
253
+ end
254
+
239
255
  def details
240
- {:hybridFormula => [a.details, "?"]}
256
+ [a.details, "?"]
241
257
  end
242
258
  end
243
259
 
@@ -362,8 +378,12 @@ module ScientificNameClean
362
378
  b.pos
363
379
  end
364
380
 
381
+ def hybrid
382
+ true
383
+ end
384
+
365
385
  def details
366
- {:namedHybrid => b.details}
386
+ b.details
367
387
  end
368
388
  end
369
389
 
@@ -439,6 +459,10 @@ module ScientificNameClean
439
459
  a.pos
440
460
  end
441
461
 
462
+ def hybrid
463
+ a.hybrid rescue false
464
+ end
465
+
442
466
  def details
443
467
  a.details.merge(b.details)
444
468
  end
@@ -680,6 +704,10 @@ module ScientificNameClean
680
704
  def pos
681
705
  a.pos.merge(b.pos).merge(c.pos).merge(d.pos)
682
706
  end
707
+
708
+ def hybrid
709
+ c.hybrid rescue false
710
+ end
683
711
 
684
712
  def details
685
713
  a.details.merge(b.details).merge(c.details).merge(d.details)
@@ -725,6 +753,10 @@ module ScientificNameClean
725
753
  a.pos.merge(b.pos).merge(c.pos)
726
754
  end
727
755
 
756
+ def hybrid
757
+ c.hybrid rescue false
758
+ end
759
+
728
760
  def details
729
761
  a.details.merge(b.details).merge(c.details)
730
762
  end
@@ -768,6 +800,10 @@ module ScientificNameClean
768
800
  def pos
769
801
  a.pos.merge(b.pos).merge(c.pos)
770
802
  end
803
+
804
+ def hybrid
805
+ b.hybrid rescue false
806
+ end
771
807
 
772
808
  def details
773
809
  a.details.merge(b.details).merge(c.details)
@@ -805,6 +841,10 @@ module ScientificNameClean
805
841
  a.pos.merge(b.pos)
806
842
  end
807
843
 
844
+ def hybrid
845
+ b.hybrid rescue false
846
+ end
847
+
808
848
  def details
809
849
  a.details.merge(b.details)
810
850
  end
@@ -1037,6 +1077,12 @@ module ScientificNameClean
1037
1077
  end
1038
1078
  end
1039
1079
 
1080
+ module InfraspeciesMult2
1081
+ def details
1082
+ {:infraspecies => [super[:infraspecies]]}
1083
+ end
1084
+ end
1085
+
1040
1086
  def _nt_infraspecies_mult
1041
1087
  start_index = index
1042
1088
  if node_cache[:infraspecies_mult].has_key?(index)
@@ -1069,6 +1115,7 @@ module ScientificNameClean
1069
1115
  r0 = r1
1070
1116
  else
1071
1117
  r5 = _nt_infraspecies
1118
+ r5.extend(InfraspeciesMult2)
1072
1119
  if r5
1073
1120
  r0 = r5
1074
1121
  else
@@ -1544,8 +1591,8 @@ module ScientificNameClean
1544
1591
  r1.extend(Rank0)
1545
1592
  else
1546
1593
  if input.index("α", index) == index
1547
- r18 = instantiate_node(SyntaxNode,input, index...(index + 1))
1548
- @index += 1
1594
+ r18 = instantiate_node(SyntaxNode,input, index...(index + 2))
1595
+ @index += 2
1549
1596
  else
1550
1597
  terminal_parse_failure("α")
1551
1598
  r18 = nil
@@ -1555,8 +1602,8 @@ module ScientificNameClean
1555
1602
  r1.extend(Rank0)
1556
1603
  else
1557
1604
  if input.index("ββ", index) == index
1558
- r19 = instantiate_node(SyntaxNode,input, index...(index + 2))
1559
- @index += 2
1605
+ r19 = instantiate_node(SyntaxNode,input, index...(index + 4))
1606
+ @index += 4
1560
1607
  else
1561
1608
  terminal_parse_failure("ββ")
1562
1609
  r19 = nil
@@ -1566,8 +1613,8 @@ module ScientificNameClean
1566
1613
  r1.extend(Rank0)
1567
1614
  else
1568
1615
  if input.index("β", index) == index
1569
- r20 = instantiate_node(SyntaxNode,input, index...(index + 1))
1570
- @index += 1
1616
+ r20 = instantiate_node(SyntaxNode,input, index...(index + 2))
1617
+ @index += 2
1571
1618
  else
1572
1619
  terminal_parse_failure("β")
1573
1620
  r20 = nil
@@ -1577,8 +1624,8 @@ module ScientificNameClean
1577
1624
  r1.extend(Rank0)
1578
1625
  else
1579
1626
  if input.index("γ", index) == index
1580
- r21 = instantiate_node(SyntaxNode,input, index...(index + 1))
1581
- @index += 1
1627
+ r21 = instantiate_node(SyntaxNode,input, index...(index + 2))
1628
+ @index += 2
1582
1629
  else
1583
1630
  terminal_parse_failure("γ")
1584
1631
  r21 = nil
@@ -1588,8 +1635,8 @@ module ScientificNameClean
1588
1635
  r1.extend(Rank0)
1589
1636
  else
1590
1637
  if input.index("δ", index) == index
1591
- r22 = instantiate_node(SyntaxNode,input, index...(index + 1))
1592
- @index += 1
1638
+ r22 = instantiate_node(SyntaxNode,input, index...(index + 2))
1639
+ @index += 2
1593
1640
  else
1594
1641
  terminal_parse_failure("δ")
1595
1642
  r22 = nil
@@ -1599,8 +1646,8 @@ module ScientificNameClean
1599
1646
  r1.extend(Rank0)
1600
1647
  else
1601
1648
  if input.index("ε", index) == index
1602
- r23 = instantiate_node(SyntaxNode,input, index...(index + 1))
1603
- @index += 1
1649
+ r23 = instantiate_node(SyntaxNode,input, index...(index + 2))
1650
+ @index += 2
1604
1651
  else
1605
1652
  terminal_parse_failure("ε")
1606
1653
  r23 = nil
@@ -1610,8 +1657,8 @@ module ScientificNameClean
1610
1657
  r1.extend(Rank0)
1611
1658
  else
1612
1659
  if input.index("φ", index) == index
1613
- r24 = instantiate_node(SyntaxNode,input, index...(index + 1))
1614
- @index += 1
1660
+ r24 = instantiate_node(SyntaxNode,input, index...(index + 2))
1661
+ @index += 2
1615
1662
  else
1616
1663
  terminal_parse_failure("φ")
1617
1664
  r24 = nil
@@ -1621,8 +1668,8 @@ module ScientificNameClean
1621
1668
  r1.extend(Rank0)
1622
1669
  else
1623
1670
  if input.index("θ", index) == index
1624
- r25 = instantiate_node(SyntaxNode,input, index...(index + 1))
1625
- @index += 1
1671
+ r25 = instantiate_node(SyntaxNode,input, index...(index + 2))
1672
+ @index += 2
1626
1673
  else
1627
1674
  terminal_parse_failure("θ")
1628
1675
  r25 = nil
@@ -1632,8 +1679,8 @@ module ScientificNameClean
1632
1679
  r1.extend(Rank0)
1633
1680
  else
1634
1681
  if input.index("μ", index) == index
1635
- r26 = instantiate_node(SyntaxNode,input, index...(index + 1))
1636
- @index += 1
1682
+ r26 = instantiate_node(SyntaxNode,input, index...(index + 2))
1683
+ @index += 2
1637
1684
  else
1638
1685
  terminal_parse_failure("μ")
1639
1686
  r26 = nil
@@ -1909,6 +1956,10 @@ module ScientificNameClean
1909
1956
  a.canonical
1910
1957
  end
1911
1958
 
1959
+ def hybrid
1960
+ a.hybrid rescue false
1961
+ end
1962
+
1912
1963
  def pos
1913
1964
  a.pos.merge(b.pos)
1914
1965
  end
@@ -1992,6 +2043,10 @@ module ScientificNameClean
1992
2043
  def canonical
1993
2044
  a.value
1994
2045
  end
2046
+
2047
+ def hybrid
2048
+ a.hybrid rescue false
2049
+ end
1995
2050
 
1996
2051
  def pos
1997
2052
  {a.interval.begin => ['species', a.interval.end]}
@@ -2011,6 +2066,10 @@ module ScientificNameClean
2011
2066
  {interval.begin => ['species', interval.end]}
2012
2067
  end
2013
2068
 
2069
+ def hybrid
2070
+ false
2071
+ end
2072
+
2014
2073
  def details
2015
2074
  {:species => {:epitheton => value}}
2016
2075
  end
@@ -2295,6 +2354,10 @@ module ScientificNameClean
2295
2354
  a.pos.merge(b.pos)
2296
2355
  end
2297
2356
 
2357
+ def hybrid
2358
+ false
2359
+ end
2360
+
2298
2361
  def details
2299
2362
  {:uninomial => a.details[:uninomial].merge(b.details)}
2300
2363
  end
@@ -2354,6 +2417,10 @@ module ScientificNameClean
2354
2417
  {interval.begin => ['uninomial', interval.end]}
2355
2418
  end
2356
2419
 
2420
+ def hybrid
2421
+ false
2422
+ end
2423
+
2357
2424
  def details
2358
2425
  {:uninomial => {:epitheton => value}}
2359
2426
  end
@@ -3932,8 +3999,8 @@ module ScientificNameClean
3932
3999
  i6, s6 = index, []
3933
4000
  i7 = index
3934
4001
  if input.index("Å", index) == index
3935
- r8 = instantiate_node(SyntaxNode,input, index...(index + 1))
3936
- @index += 1
4002
+ r8 = instantiate_node(SyntaxNode,input, index...(index + 2))
4003
+ @index += 2
3937
4004
  else
3938
4005
  terminal_parse_failure("Å")
3939
4006
  r8 = nil
@@ -3942,8 +4009,8 @@ module ScientificNameClean
3942
4009
  r7 = r8
3943
4010
  else
3944
4011
  if input.index("Ö", index) == index
3945
- r9 = instantiate_node(SyntaxNode,input, index...(index + 1))
3946
- @index += 1
4012
+ r9 = instantiate_node(SyntaxNode,input, index...(index + 2))
4013
+ @index += 2
3947
4014
  else
3948
4015
  terminal_parse_failure("Ö")
3949
4016
  r9 = nil
@@ -3952,8 +4019,8 @@ module ScientificNameClean
3952
4019
  r7 = r9
3953
4020
  else
3954
4021
  if input.index("Á", index) == index
3955
- r10 = instantiate_node(SyntaxNode,input, index...(index + 1))
3956
- @index += 1
4022
+ r10 = instantiate_node(SyntaxNode,input, index...(index + 2))
4023
+ @index += 2
3957
4024
  else
3958
4025
  terminal_parse_failure("Á")
3959
4026
  r10 = nil
@@ -3962,8 +4029,8 @@ module ScientificNameClean
3962
4029
  r7 = r10
3963
4030
  else
3964
4031
  if input.index("Ø", index) == index
3965
- r11 = instantiate_node(SyntaxNode,input, index...(index + 1))
3966
- @index += 1
4032
+ r11 = instantiate_node(SyntaxNode,input, index...(index + 2))
4033
+ @index += 2
3967
4034
  else
3968
4035
  terminal_parse_failure("Ø")
3969
4036
  r11 = nil
@@ -3972,8 +4039,8 @@ module ScientificNameClean
3972
4039
  r7 = r11
3973
4040
  else
3974
4041
  if input.index("Ô", index) == index
3975
- r12 = instantiate_node(SyntaxNode,input, index...(index + 1))
3976
- @index += 1
4042
+ r12 = instantiate_node(SyntaxNode,input, index...(index + 2))
4043
+ @index += 2
3977
4044
  else
3978
4045
  terminal_parse_failure("Ô")
3979
4046
  r12 = nil
@@ -3982,8 +4049,8 @@ module ScientificNameClean
3982
4049
  r7 = r12
3983
4050
  else
3984
4051
  if input.index("Š", index) == index
3985
- r13 = instantiate_node(SyntaxNode,input, index...(index + 1))
3986
- @index += 1
4052
+ r13 = instantiate_node(SyntaxNode,input, index...(index + 2))
4053
+ @index += 2
3987
4054
  else
3988
4055
  terminal_parse_failure("Š")
3989
4056
  r13 = nil
@@ -3992,8 +4059,8 @@ module ScientificNameClean
3992
4059
  r7 = r13
3993
4060
  else
3994
4061
  if input.index("Ś", index) == index
3995
- r14 = instantiate_node(SyntaxNode,input, index...(index + 1))
3996
- @index += 1
4062
+ r14 = instantiate_node(SyntaxNode,input, index...(index + 2))
4063
+ @index += 2
3997
4064
  else
3998
4065
  terminal_parse_failure("Ś")
3999
4066
  r14 = nil
@@ -4002,8 +4069,8 @@ module ScientificNameClean
4002
4069
  r7 = r14
4003
4070
  else
4004
4071
  if input.index("Č", index) == index
4005
- r15 = instantiate_node(SyntaxNode,input, index...(index + 1))
4006
- @index += 1
4072
+ r15 = instantiate_node(SyntaxNode,input, index...(index + 2))
4073
+ @index += 2
4007
4074
  else
4008
4075
  terminal_parse_failure("Č")
4009
4076
  r15 = nil
@@ -4012,8 +4079,8 @@ module ScientificNameClean
4012
4079
  r7 = r15
4013
4080
  else
4014
4081
  if input.index("Ķ", index) == index
4015
- r16 = instantiate_node(SyntaxNode,input, index...(index + 1))
4016
- @index += 1
4082
+ r16 = instantiate_node(SyntaxNode,input, index...(index + 2))
4083
+ @index += 2
4017
4084
  else
4018
4085
  terminal_parse_failure("Ķ")
4019
4086
  r16 = nil
@@ -4022,8 +4089,8 @@ module ScientificNameClean
4022
4089
  r7 = r16
4023
4090
  else
4024
4091
  if input.index("Ł", index) == index
4025
- r17 = instantiate_node(SyntaxNode,input, index...(index + 1))
4026
- @index += 1
4092
+ r17 = instantiate_node(SyntaxNode,input, index...(index + 2))
4093
+ @index += 2
4027
4094
  else
4028
4095
  terminal_parse_failure("Ł")
4029
4096
  r17 = nil
@@ -4032,8 +4099,8 @@ module ScientificNameClean
4032
4099
  r7 = r17
4033
4100
  else
4034
4101
  if input.index("É", index) == index
4035
- r18 = instantiate_node(SyntaxNode,input, index...(index + 1))
4036
- @index += 1
4102
+ r18 = instantiate_node(SyntaxNode,input, index...(index + 2))
4103
+ @index += 2
4037
4104
  else
4038
4105
  terminal_parse_failure("É")
4039
4106
  r18 = nil
@@ -4042,8 +4109,8 @@ module ScientificNameClean
4042
4109
  r7 = r18
4043
4110
  else
4044
4111
  if input.index("Ž", index) == index
4045
- r19 = instantiate_node(SyntaxNode,input, index...(index + 1))
4046
- @index += 1
4112
+ r19 = instantiate_node(SyntaxNode,input, index...(index + 2))
4113
+ @index += 2
4047
4114
  else
4048
4115
  terminal_parse_failure("Ž")
4049
4116
  r19 = nil
@@ -4785,12 +4852,16 @@ module ScientificNameClean
4785
4852
  b.value
4786
4853
  end
4787
4854
 
4855
+ def hybrid
4856
+ true
4857
+ end
4858
+
4788
4859
  def pos
4789
4860
  {b.interval.begin => ['species', b.interval.end]}
4790
4861
  end
4791
4862
 
4792
4863
  def details
4793
- {:species => {:epitheton => b.value, :namedHybrid => true}}
4864
+ {:species => {:epitheton => b.value}}
4794
4865
  end
4795
4866
  end
4796
4867
 
@@ -4817,12 +4888,16 @@ module ScientificNameClean
4817
4888
  b.value
4818
4889
  end
4819
4890
 
4891
+ def hybrid
4892
+ true
4893
+ end
4894
+
4820
4895
  def pos
4821
4896
  {b.interval.begin => ['species', b.interval.end]}
4822
4897
  end
4823
4898
 
4824
4899
  def details
4825
- {:species => {:epitheton => b.value, :namedHybrid => true}}
4900
+ {:species => {:epitheton => b.value}}
4826
4901
  end
4827
4902
  end
4828
4903
 
@@ -4849,12 +4924,16 @@ module ScientificNameClean
4849
4924
  b.value
4850
4925
  end
4851
4926
 
4927
+ def hybrid
4928
+ true
4929
+ end
4930
+
4852
4931
  def pos
4853
4932
  {b.interval.begin => ['species', b.interval.end]}
4854
4933
  end
4855
4934
 
4856
4935
  def details
4857
- {:species => {:epitheton => b.value, :namedHybrid => true}}
4936
+ {:species => {:epitheton => b.value}}
4858
4937
  end
4859
4938
  end
4860
4939
 
@@ -5375,9 +5454,9 @@ module ScientificNameClean
5375
5454
 
5376
5455
  i0 = index
5377
5456
  if input.index("Æ", index) == index
5378
- r1 = instantiate_node(SyntaxNode,input, index...(index + 1))
5457
+ r1 = instantiate_node(SyntaxNode,input, index...(index + 2))
5379
5458
  r1.extend(CapDigraph0)
5380
- @index += 1
5459
+ @index += 2
5381
5460
  else
5382
5461
  terminal_parse_failure("Æ")
5383
5462
  r1 = nil
@@ -5386,9 +5465,9 @@ module ScientificNameClean
5386
5465
  r0 = r1
5387
5466
  else
5388
5467
  if input.index("Œ", index) == index
5389
- r2 = instantiate_node(SyntaxNode,input, index...(index + 1))
5468
+ r2 = instantiate_node(SyntaxNode,input, index...(index + 2))
5390
5469
  r2.extend(CapDigraph1)
5391
- @index += 1
5470
+ @index += 2
5392
5471
  else
5393
5472
  terminal_parse_failure("Œ")
5394
5473
  r2 = nil
@@ -5428,9 +5507,9 @@ module ScientificNameClean
5428
5507
 
5429
5508
  i0 = index
5430
5509
  if input.index("æ", index) == index
5431
- r1 = instantiate_node(SyntaxNode,input, index...(index + 1))
5510
+ r1 = instantiate_node(SyntaxNode,input, index...(index + 2))
5432
5511
  r1.extend(Digraph0)
5433
- @index += 1
5512
+ @index += 2
5434
5513
  else
5435
5514
  terminal_parse_failure("æ")
5436
5515
  r1 = nil
@@ -5439,9 +5518,9 @@ module ScientificNameClean
5439
5518
  r0 = r1
5440
5519
  else
5441
5520
  if input.index("œ", index) == index
5442
- r2 = instantiate_node(SyntaxNode,input, index...(index + 1))
5521
+ r2 = instantiate_node(SyntaxNode,input, index...(index + 2))
5443
5522
  r2.extend(Digraph1)
5444
- @index += 1
5523
+ @index += 2
5445
5524
  else
5446
5525
  terminal_parse_failure("œ")
5447
5526
  r2 = nil
@@ -5829,9 +5908,9 @@ module ScientificNameClean
5829
5908
  end
5830
5909
 
5831
5910
  if input.index("×", index) == index
5832
- r0 = instantiate_node(SyntaxNode,input, index...(index + 1))
5911
+ r0 = instantiate_node(SyntaxNode,input, index...(index + 2))
5833
5912
  r0.extend(MultiplicationSign0)
5834
- @index += 1
5913
+ @index += 2
5835
5914
  else
5836
5915
  terminal_parse_failure("×")
5837
5916
  r0 = nil