bel_parser 1.0.8-java → 1.1.1-java

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Files changed (112) hide show
  1. checksums.yaml +4 -4
  2. data/{.gemspec-java → .gemspec} +11 -4
  3. data/VERSION +1 -1
  4. data/bin/bel2_compatibility +12 -9
  5. data/bin/bel2_upgrade +18 -6
  6. data/bin/bel2_validator +6 -3
  7. data/bin/bel_script_reader +1 -0
  8. data/lib/bel_parser/completion.rb +984 -0
  9. data/lib/bel_parser/language/apply_namespace_encoding.rb +14 -3
  10. data/lib/bel_parser/language/expression_validator.rb +1 -2
  11. data/lib/bel_parser/language/function.rb +4 -0
  12. data/lib/bel_parser/language/relationship.rb +4 -0
  13. data/lib/bel_parser/language/semantics/function_deprecation.rb +1 -0
  14. data/lib/bel_parser/language/semantics/list_function_subject.rb +2 -0
  15. data/lib/bel_parser/language/semantics/multiple_subject_object.rb +4 -1
  16. data/lib/bel_parser/language/semantics/nested_statement_without_object.rb +43 -0
  17. data/lib/bel_parser/language/semantics/non_object_list.rb +3 -0
  18. data/lib/bel_parser/language/semantics/relationship_not_listable.rb +2 -0
  19. data/lib/bel_parser/language/semantics/signature_mapping.rb +2 -0
  20. data/lib/bel_parser/language/semantics_ast.rb +0 -7
  21. data/lib/bel_parser/language/syntax/invalid_function.rb +6 -1
  22. data/lib/bel_parser/language/syntax/invalid_relationship.rb +1 -0
  23. data/lib/bel_parser/language/version1_0/relationships/acts_in.rb +9 -9
  24. data/lib/bel_parser/language/version1_0/relationships/analogous.rb +6 -4
  25. data/lib/bel_parser/language/version1_0/relationships/association.rb +8 -7
  26. data/lib/bel_parser/language/version1_0/relationships/biomarker_for.rb +6 -5
  27. data/lib/bel_parser/language/version1_0/relationships/causes_no_change.rb +8 -7
  28. data/lib/bel_parser/language/version1_0/relationships/decreases.rb +13 -12
  29. data/lib/bel_parser/language/version1_0/relationships/directly_decreases.rb +8 -6
  30. data/lib/bel_parser/language/version1_0/relationships/directly_increases.rb +8 -6
  31. data/lib/bel_parser/language/version1_0/relationships/has_component.rb +14 -14
  32. data/lib/bel_parser/language/version1_0/relationships/has_components.rb +12 -11
  33. data/lib/bel_parser/language/version1_0/relationships/has_member.rb +10 -8
  34. data/lib/bel_parser/language/version1_0/relationships/has_members.rb +12 -11
  35. data/lib/bel_parser/language/version1_0/relationships/has_modification.rb +9 -7
  36. data/lib/bel_parser/language/version1_0/relationships/has_product.rb +10 -8
  37. data/lib/bel_parser/language/version1_0/relationships/has_variant.rb +9 -7
  38. data/lib/bel_parser/language/version1_0/relationships/includes.rb +11 -10
  39. data/lib/bel_parser/language/version1_0/relationships/increases.rb +12 -13
  40. data/lib/bel_parser/language/version1_0/relationships/is_a.rb +10 -8
  41. data/lib/bel_parser/language/version1_0/relationships/negative_correlation.rb +9 -7
  42. data/lib/bel_parser/language/version1_0/relationships/orthologous.rb +9 -8
  43. data/lib/bel_parser/language/version1_0/relationships/positive_correlation.rb +8 -5
  44. data/lib/bel_parser/language/version1_0/relationships/prognostic_biomarker_for.rb +8 -6
  45. data/lib/bel_parser/language/version1_0/relationships/rate_limiting_step_of.rb +10 -9
  46. data/lib/bel_parser/language/version1_0/relationships/reactant_in.rb +10 -8
  47. data/lib/bel_parser/language/version1_0/relationships/sub_process_of.rb +13 -12
  48. data/lib/bel_parser/language/version1_0/relationships/transcribed_to.rb +8 -7
  49. data/lib/bel_parser/language/version1_0/relationships/translated_to.rb +9 -7
  50. data/lib/bel_parser/language/version1_0/relationships/translocates.rb +10 -9
  51. data/lib/bel_parser/language/version2_0/functions/protein_modification.rb +1 -2
  52. data/lib/bel_parser/language/version2_0/functions/translocation.rb +1 -2
  53. data/lib/bel_parser/language/version2_0/functions/variant.rb +1 -2
  54. data/lib/bel_parser/language/version2_0/relationships/acts_in.rb +10 -9
  55. data/lib/bel_parser/language/version2_0/relationships/biomarker_for.rb +7 -5
  56. data/lib/bel_parser/language/version2_0/relationships/causes_no_change.rb +9 -7
  57. data/lib/bel_parser/language/version2_0/relationships/decreases.rb +13 -12
  58. data/lib/bel_parser/language/version2_0/relationships/directly_decreases.rb +8 -6
  59. data/lib/bel_parser/language/version2_0/relationships/directly_increases.rb +8 -6
  60. data/lib/bel_parser/language/version2_0/relationships/has_component.rb +15 -14
  61. data/lib/bel_parser/language/version2_0/relationships/has_components.rb +12 -11
  62. data/lib/bel_parser/language/version2_0/relationships/has_member.rb +9 -8
  63. data/lib/bel_parser/language/version2_0/relationships/has_members.rb +12 -11
  64. data/lib/bel_parser/language/version2_0/relationships/has_modification.rb +9 -7
  65. data/lib/bel_parser/language/version2_0/relationships/has_product.rb +10 -8
  66. data/lib/bel_parser/language/version2_0/relationships/has_variant.rb +9 -7
  67. data/lib/bel_parser/language/version2_0/relationships/includes.rb +11 -10
  68. data/lib/bel_parser/language/version2_0/relationships/increases.rb +13 -12
  69. data/lib/bel_parser/language/version2_0/relationships/is_a.rb +10 -8
  70. data/lib/bel_parser/language/version2_0/relationships/negative_correlation.rb +9 -7
  71. data/lib/bel_parser/language/version2_0/relationships/orthologous.rb +10 -8
  72. data/lib/bel_parser/language/version2_0/relationships/positive_correlation.rb +7 -5
  73. data/lib/bel_parser/language/version2_0/relationships/prognostic_biomarker_for.rb +8 -6
  74. data/lib/bel_parser/language/version2_0/relationships/rate_limiting_step_of.rb +10 -9
  75. data/lib/bel_parser/language/version2_0/relationships/reactant_in.rb +10 -8
  76. data/lib/bel_parser/language/version2_0/relationships/regulates.rb +9 -8
  77. data/lib/bel_parser/language/version2_0/relationships/sub_process_of.rb +13 -12
  78. data/lib/bel_parser/language/version2_0/relationships/transcribed_to.rb +8 -7
  79. data/lib/bel_parser/language/version2_0/relationships/translated_to.rb +9 -7
  80. data/lib/bel_parser/language/version2_0/relationships/translocates.rb +10 -9
  81. data/lib/bel_parser/mixin/levenshtein.rb +20 -0
  82. data/lib/bel_parser/parsers/ast/node.rb +49 -2
  83. data/lib/bel_parser/parsers/bel_script/define_annotation.rb +156 -156
  84. data/lib/bel_parser/parsers/bel_script/define_namespace.rb +60 -60
  85. data/lib/bel_parser/parsers/bel_script/set.rb +200 -200
  86. data/lib/bel_parser/parsers/bel_script/set_document.rb +188 -188
  87. data/lib/bel_parser/parsers/bel_script/unset.rb +14 -14
  88. data/lib/bel_parser/parsers/common/common.rl +1 -0
  89. data/lib/bel_parser/parsers/common/function.rb +8 -8
  90. data/lib/bel_parser/parsers/common/function.rl +6 -6
  91. data/lib/bel_parser/parsers/common/identifier.rb +3 -3
  92. data/lib/bel_parser/parsers/common/identifier.rl +4 -4
  93. data/lib/bel_parser/parsers/common/list.rb +78 -78
  94. data/lib/bel_parser/parsers/common/multi_identifier.rb +275 -0
  95. data/lib/bel_parser/parsers/common/multi_identifier.rl +141 -0
  96. data/lib/bel_parser/parsers/common/string.rb +6 -6
  97. data/lib/bel_parser/parsers/common/string.rl +4 -4
  98. data/lib/bel_parser/parsers/common.rb +1 -0
  99. data/lib/bel_parser/parsers/expression/nested_statement.rb +30180 -29055
  100. data/lib/bel_parser/parsers/expression/observed_term.rb +1456 -1099
  101. data/lib/bel_parser/parsers/expression/parameter.rb +192 -111
  102. data/lib/bel_parser/parsers/expression/parameter.rl +6 -3
  103. data/lib/bel_parser/parsers/expression/relationship.rb +43 -19
  104. data/lib/bel_parser/parsers/expression/relationship.rl +1 -0
  105. data/lib/bel_parser/parsers/expression/simple_statement.rb +17805 -17093
  106. data/lib/bel_parser/parsers/expression/statement_autocomplete.rb +1035 -0
  107. data/lib/bel_parser/parsers/expression/statement_autocomplete.rl +736 -0
  108. data/lib/bel_parser/parsers/expression/term.rb +960 -705
  109. data/lib/bel_parser/parsers/serializer.rb +8 -4
  110. data/lib/bel_parser/version.rb +33 -0
  111. data/lib/bel_parser.rb +3 -0
  112. metadata +26 -4
data/lib/bel_parser/parsers/expression/parameter.rl CHANGED
@@ -10,14 +10,14 @@
10
10
  action add_ident_param_value {
11
11
  trace('PARAMETER add_ident_param_value')
12
12
  ident = @buffers.delete(:ident)
13
- value_node = value(ident, complete: ident.complete)
13
+ value_node = value(ident, complete: ident.complete, character_range: ident.character_range)
14
14
  @buffers[:param_value] = value_node
15
15
  }
16
16
 
17
17
  action add_string_param_value {
18
18
  trace('PARAMETER add_string_param_value')
19
19
  string_node = @buffers.delete(:string)
20
- value_node = value(string_node, complete: string_node.complete)
20
+ value_node = value(string_node, complete: string_node.complete, character_range: string_node.character_range)
21
21
  @buffers[:param_value] = value_node
22
22
  }
23
23
 
@@ -32,6 +32,7 @@
32
32
  trace('PN incomplete')
33
33
  completed = false
34
34
  end
35
+ param_start = prefix_node.range_start
35
36
  else
36
37
  prefix_node = prefix(nil)
37
38
  prefix_node.complete = true
@@ -48,6 +49,8 @@
48
49
  trace('VN incomplete')
49
50
  completed = false
50
51
  end
52
+ param_start ||= value_node.range_start
53
+ param_node.character_range = [param_start, value_node.range_end]
51
54
  else
52
55
  completed = false
53
56
  end
@@ -59,7 +62,7 @@
59
62
  action add_prefix {
60
63
  trace('PARAMETER add_prefix')
61
64
  ident = @buffers.delete(:ident)
62
- prefix_node = prefix(ident, complete: ident.complete)
65
+ prefix_node = prefix(ident, complete: ident.complete, character_range: ident.character_range)
63
66
  @buffers[:param_prefix] = prefix_node
64
67
  }
65
68
 
data/lib/bel_parser/parsers/expression/relationship.rb CHANGED
@@ -46,8 +46,8 @@ class << self
46
46
  private :_bel_trans_keys, :_bel_trans_keys=
47
47
  end
48
48
  self._bel_trans_keys = [
49
- 0, 0, 33, 126, 33, 126,
50
- 0
49
+ 0, 0, 33, 126, 10, 126,
50
+ 0, 0, 0
51
51
  ]
52
52
 
53
53
  class << self
@@ -55,7 +55,7 @@ class << self
55
55
  private :_bel_key_spans, :_bel_key_spans=
56
56
  end
57
57
  self._bel_key_spans = [
58
- 0, 94, 94
58
+ 0, 94, 117, 0
59
59
  ]
60
60
 
61
61
  class << self
@@ -63,7 +63,7 @@ class << self
63
63
  private :_bel_index_offsets, :_bel_index_offsets=
64
64
  end
65
65
  self._bel_index_offsets = [
66
- 0, 0, 95
66
+ 0, 0, 95, 213
67
67
  ]
68
68
 
69
69
  class << self
@@ -83,18 +83,21 @@ self._bel_indicies = [
83
83
  0, 0, 0, 0, 0, 0, 0, 0,
84
84
  0, 0, 0, 0, 0, 0, 0, 0,
85
85
  0, 0, 0, 0, 0, 0, 1, 2,
86
- 2, 2, 2, 2, 2, 2, 2, 2,
87
- 2, 2, 2, 2, 2, 2, 2, 2,
88
- 2, 2, 2, 2, 2, 2, 2, 2,
89
- 2, 2, 2, 2, 2, 2, 2, 2,
90
- 2, 2, 2, 2, 2, 2, 2, 2,
91
- 2, 2, 2, 2, 2, 2, 2, 2,
92
- 2, 2, 2, 2, 2, 2, 2, 2,
93
- 2, 2, 2, 2, 2, 2, 2, 2,
94
- 2, 2, 2, 2, 2, 2, 2, 2,
95
- 2, 2, 2, 2, 2, 2, 2, 2,
96
- 2, 2, 2, 2, 2, 2, 2, 2,
97
- 2, 2, 2, 2, 2, 1, 0
86
+ 1, 1, 1, 1, 1, 1, 1, 1,
87
+ 1, 1, 1, 1, 1, 1, 1, 1,
88
+ 1, 1, 1, 1, 1, 1, 3, 3,
89
+ 3, 3, 3, 3, 3, 3, 3, 3,
90
+ 3, 3, 3, 3, 3, 3, 3, 3,
91
+ 3, 3, 3, 3, 3, 3, 3, 3,
92
+ 3, 3, 3, 3, 3, 3, 3, 3,
93
+ 3, 3, 3, 3, 3, 3, 3, 3,
94
+ 3, 3, 3, 3, 3, 3, 3, 3,
95
+ 3, 3, 3, 3, 3, 3, 3, 3,
96
+ 3, 3, 3, 3, 3, 3, 3, 3,
97
+ 3, 3, 3, 3, 3, 3, 3, 3,
98
+ 3, 3, 3, 3, 3, 3, 3, 3,
99
+ 3, 3, 3, 3, 3, 3, 3, 3,
100
+ 3, 3, 3, 3, 1, 1, 0
98
101
  ]
99
102
 
100
103
  class << self
@@ -102,7 +105,7 @@ class << self
102
105
  private :_bel_trans_targs, :_bel_trans_targs=
103
106
  end
104
107
  self._bel_trans_targs = [
105
- 2, 0, 2
108
+ 2, 0, 3, 2
106
109
  ]
107
110
 
108
111
  class << self
@@ -110,7 +113,7 @@ class << self
110
113
  private :_bel_trans_actions, :_bel_trans_actions=
111
114
  end
112
115
  self._bel_trans_actions = [
113
- 1, 0, 0
116
+ 1, 0, 3, 0
114
117
  ]
115
118
 
116
119
  class << self
@@ -118,7 +121,7 @@ class << self
118
121
  private :_bel_eof_actions, :_bel_eof_actions=
119
122
  end
120
123
  self._bel_eof_actions = [
121
- 0, 0, 2
124
+ 0, 0, 2, 4
122
125
  ]
123
126
 
124
127
  class << self
@@ -205,6 +208,14 @@ begin
205
208
  trace('RELATIONSHIP start_relationship')
206
209
  p_start = p;
207
210
  end
211
+ when 3 then
212
+ begin
213
+
214
+ trace('RELATIONSHIP stop_relationship')
215
+ # It's not you, it's me. You're a p and I'm a non-protein coding r. It
216
+ # would never work, I just can't reach you.
217
+ p_end = p;
218
+ end
208
219
  end
209
220
  end
210
221
  end
@@ -222,6 +233,19 @@ begin
222
233
  if _goto_level <= _test_eof
223
234
  if p == eof
224
235
  case _bel_eof_actions[cs]
236
+ when 4 then
237
+ begin
238
+
239
+ trace('RELATIONSHIP relationship_end')
240
+ chars = data[p_start...p_end]
241
+ completed = !chars.empty?
242
+ ast_node = relationship(utf8_string(chars), complete: completed)
243
+ @buffers[:relationship] = ast_node
244
+ end
245
+ begin
246
+
247
+ yield @buffers[:relationship]
248
+ end
225
249
  when 2 then
226
250
  begin
227
251
 
data/lib/bel_parser/parsers/expression/relationship.rl CHANGED
@@ -33,6 +33,7 @@
33
33
  RELATIONSHIP
34
34
  >start_relationship
35
35
  %stop_relationship
36
+ NL?
36
37
  ;
37
38
 
38
39
  relationship_node :=