bel_parser 1.0.0.alpha.7 → 1.0.0.alpha.8

This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.
Files changed (153) hide show
  1. checksums.yaml +4 -4
  2. data/.gemspec +1 -1
  3. data/VERSION +1 -1
  4. data/bin/bel2_validator +7 -4
  5. data/lib/bel_parser/ast_filter.rb +2 -2
  6. data/lib/bel_parser/ast_generator.rb +11 -18
  7. data/lib/bel_parser/language/expression_validator.rb +8 -0
  8. data/lib/bel_parser/language/quoting.rb +19 -22
  9. data/lib/bel_parser/language/semantics/deeply_nested_statement.rb +65 -0
  10. data/lib/bel_parser/language/semantics/function_deprecation.rb +36 -0
  11. data/lib/bel_parser/language/semantics/list_function_subject.rb +45 -0
  12. data/lib/bel_parser/language/semantics/relationship_deprecation.rb +36 -0
  13. data/lib/bel_parser/language/semantics/signature_mapping.rb +30 -16
  14. data/lib/bel_parser/language/semantics.rb +7 -2
  15. data/lib/bel_parser/language/semantics_ast.rb +22 -12
  16. data/lib/bel_parser/language/semantics_function.rb +4 -1
  17. data/lib/bel_parser/language/semantics_result.rb +1 -0
  18. data/lib/bel_parser/language/semantics_warning.rb +2 -0
  19. data/lib/bel_parser/language/signature.rb +3 -3
  20. data/lib/bel_parser/language/syntax/invalid_function.rb +2 -2
  21. data/lib/bel_parser/language/syntax/invalid_relationship.rb +2 -2
  22. data/lib/bel_parser/language/syntax/undefined_namespace.rb +0 -1
  23. data/lib/bel_parser/language/syntax.rb +7 -2
  24. data/lib/bel_parser/language/syntax_error.rb +2 -0
  25. data/lib/bel_parser/language/syntax_function.rb +4 -1
  26. data/lib/bel_parser/language/syntax_result.rb +1 -0
  27. data/lib/bel_parser/language/syntax_warning.rb +2 -0
  28. data/lib/bel_parser/language/version1_0/functions/abundance.rb +14 -15
  29. data/lib/bel_parser/language/version1_0/functions/biological_process.rb +14 -15
  30. data/lib/bel_parser/language/version1_0/functions/catalytic_activity.rb +25 -21
  31. data/lib/bel_parser/language/version1_0/functions/cell_secretion.rb +15 -12
  32. data/lib/bel_parser/language/version1_0/functions/cell_surface_expression.rb +15 -12
  33. data/lib/bel_parser/language/version1_0/functions/chaperone_activity.rb +25 -21
  34. data/lib/bel_parser/language/version1_0/functions/complex_abundance.rb +26 -25
  35. data/lib/bel_parser/language/version1_0/functions/composite_abundance.rb +13 -12
  36. data/lib/bel_parser/language/version1_0/functions/degradation.rb +15 -12
  37. data/lib/bel_parser/language/version1_0/functions/fusion.rb +135 -129
  38. data/lib/bel_parser/language/version1_0/functions/gene_abundance.rb +34 -34
  39. data/lib/bel_parser/language/version1_0/functions/gtp_bound_activity.rb +24 -21
  40. data/lib/bel_parser/language/version1_0/functions/kinase_activity.rb +25 -21
  41. data/lib/bel_parser/language/version1_0/functions/list.rb +24 -24
  42. data/lib/bel_parser/language/version1_0/functions/micro_rna_abundance.rb +18 -17
  43. data/lib/bel_parser/language/version1_0/functions/molecular_activity.rb +14 -12
  44. data/lib/bel_parser/language/version1_0/functions/pathology.rb +14 -15
  45. data/lib/bel_parser/language/version1_0/functions/peptidase_activity.rb +23 -21
  46. data/lib/bel_parser/language/version1_0/functions/phosphatase_activity.rb +23 -21
  47. data/lib/bel_parser/language/version1_0/functions/products.rb +9 -10
  48. data/lib/bel_parser/language/version1_0/functions/protein_abundance.rb +94 -91
  49. data/lib/bel_parser/language/version1_0/functions/protein_modification.rb +60 -57
  50. data/lib/bel_parser/language/version1_0/functions/reactants.rb +9 -10
  51. data/lib/bel_parser/language/version1_0/functions/reaction.rb +18 -17
  52. data/lib/bel_parser/language/version1_0/functions/ribosylation_activity.rb +25 -21
  53. data/lib/bel_parser/language/version1_0/functions/rna_abundance.rb +34 -34
  54. data/lib/bel_parser/language/version1_0/functions/substitution.rb +29 -28
  55. data/lib/bel_parser/language/version1_0/functions/transcriptional_activity.rb +25 -21
  56. data/lib/bel_parser/language/version1_0/functions/translocation.rb +33 -32
  57. data/lib/bel_parser/language/version1_0/functions/transport_activity.rb +26 -21
  58. data/lib/bel_parser/language/version1_0/functions/truncation.rb +15 -14
  59. data/lib/bel_parser/language/version1_0/relationships/acts_in.rb +16 -2
  60. data/lib/bel_parser/language/version1_0/relationships/analogous.rb +8 -2
  61. data/lib/bel_parser/language/version1_0/relationships/association.rb +13 -2
  62. data/lib/bel_parser/language/version1_0/relationships/biomarker_for.rb +9 -2
  63. data/lib/bel_parser/language/version1_0/relationships/causes_no_change.rb +13 -2
  64. data/lib/bel_parser/language/version1_0/relationships/decreases.rb +22 -2
  65. data/lib/bel_parser/language/version1_0/relationships/directly_decreases.rb +11 -2
  66. data/lib/bel_parser/language/version1_0/relationships/directly_increases.rb +11 -2
  67. data/lib/bel_parser/language/version1_0/relationships/has_component.rb +25 -2
  68. data/lib/bel_parser/language/version1_0/relationships/has_components.rb +20 -2
  69. data/lib/bel_parser/language/version1_0/relationships/has_member.rb +15 -2
  70. data/lib/bel_parser/language/version1_0/relationships/has_members.rb +20 -2
  71. data/lib/bel_parser/language/version1_0/relationships/has_modification.rb +13 -2
  72. data/lib/bel_parser/language/version1_0/relationships/has_product.rb +15 -2
  73. data/lib/bel_parser/language/version1_0/relationships/has_variant.rb +13 -2
  74. data/lib/bel_parser/language/version1_0/relationships/includes.rb +18 -2
  75. data/lib/bel_parser/language/version1_0/relationships/increases.rb +22 -2
  76. data/lib/bel_parser/language/version1_0/relationships/is_a.rb +15 -2
  77. data/lib/bel_parser/language/version1_0/relationships/negative_correlation.rb +13 -2
  78. data/lib/bel_parser/language/version1_0/relationships/orthologous.rb +15 -2
  79. data/lib/bel_parser/language/version1_0/relationships/positive_correlation.rb +9 -2
  80. data/lib/bel_parser/language/version1_0/relationships/prognostic_biomarker_for.rb +11 -2
  81. data/lib/bel_parser/language/version1_0/relationships/rate_limiting_step_of.rb +16 -2
  82. data/lib/bel_parser/language/version1_0/relationships/reactant_in.rb +15 -2
  83. data/lib/bel_parser/language/version1_0/relationships/sub_process_of.rb +22 -2
  84. data/lib/bel_parser/language/version1_0/relationships/transcribed_to.rb +12 -2
  85. data/lib/bel_parser/language/version1_0/relationships/translated_to.rb +13 -2
  86. data/lib/bel_parser/language/version1_0/relationships/translocates.rb +16 -2
  87. data/lib/bel_parser/language/version1_0/syntax/function.rb +0 -1
  88. data/lib/bel_parser/language/version1_0.rb +13 -2
  89. data/lib/bel_parser/language/version2_0/functions/abundance.rb +54 -53
  90. data/lib/bel_parser/language/version2_0/functions/activity.rb +8 -5
  91. data/lib/bel_parser/language/version2_0/functions/biological_process.rb +16 -16
  92. data/lib/bel_parser/language/version2_0/functions/cell_secretion.rb +15 -12
  93. data/lib/bel_parser/language/version2_0/functions/cell_surface_expression.rb +15 -12
  94. data/lib/bel_parser/language/version2_0/functions/complex_abundance.rb +61 -58
  95. data/lib/bel_parser/language/version2_0/functions/composite_abundance.rb +13 -12
  96. data/lib/bel_parser/language/version2_0/functions/degradation.rb +15 -12
  97. data/lib/bel_parser/language/version2_0/functions/fragment.rb +8 -6
  98. data/lib/bel_parser/language/version2_0/functions/from_location.rb +18 -17
  99. data/lib/bel_parser/language/version2_0/functions/fusion.rb +120 -117
  100. data/lib/bel_parser/language/version2_0/functions/gene_abundance.rb +64 -62
  101. data/lib/bel_parser/language/version2_0/functions/list.rb +24 -24
  102. data/lib/bel_parser/language/version2_0/functions/location.rb +14 -15
  103. data/lib/bel_parser/language/version2_0/functions/micro_rna_abundance.rb +58 -55
  104. data/lib/bel_parser/language/version2_0/functions/molecular_activity.rb +16 -14
  105. data/lib/bel_parser/language/version2_0/functions/pathology.rb +14 -15
  106. data/lib/bel_parser/language/version2_0/functions/products.rb +9 -10
  107. data/lib/bel_parser/language/version2_0/functions/protein_abundance.rb +96 -92
  108. data/lib/bel_parser/language/version2_0/functions/protein_modification.rb +57 -54
  109. data/lib/bel_parser/language/version2_0/functions/reactants.rb +9 -10
  110. data/lib/bel_parser/language/version2_0/functions/reaction.rb +18 -17
  111. data/lib/bel_parser/language/version2_0/functions/rna_abundance.rb +64 -62
  112. data/lib/bel_parser/language/version2_0/functions/to_location.rb +16 -16
  113. data/lib/bel_parser/language/version2_0/functions/translocation.rb +23 -22
  114. data/lib/bel_parser/language/version2_0/functions/variant.rb +13 -13
  115. data/lib/bel_parser/language/version2_0/relationships/acts_in.rb +16 -2
  116. data/lib/bel_parser/language/version2_0/relationships/analogous.rb +8 -2
  117. data/lib/bel_parser/language/version2_0/relationships/association.rb +13 -2
  118. data/lib/bel_parser/language/version2_0/relationships/biomarker_for.rb +9 -2
  119. data/lib/bel_parser/language/version2_0/relationships/causes_no_change.rb +13 -2
  120. data/lib/bel_parser/language/version2_0/relationships/decreases.rb +22 -2
  121. data/lib/bel_parser/language/version2_0/relationships/directly_decreases.rb +11 -2
  122. data/lib/bel_parser/language/version2_0/relationships/directly_increases.rb +11 -2
  123. data/lib/bel_parser/language/version2_0/relationships/has_component.rb +25 -2
  124. data/lib/bel_parser/language/version2_0/relationships/has_components.rb +20 -2
  125. data/lib/bel_parser/language/version2_0/relationships/has_member.rb +15 -2
  126. data/lib/bel_parser/language/version2_0/relationships/has_members.rb +20 -2
  127. data/lib/bel_parser/language/version2_0/relationships/has_modification.rb +13 -2
  128. data/lib/bel_parser/language/version2_0/relationships/has_product.rb +15 -2
  129. data/lib/bel_parser/language/version2_0/relationships/has_variant.rb +13 -2
  130. data/lib/bel_parser/language/version2_0/relationships/includes.rb +18 -2
  131. data/lib/bel_parser/language/version2_0/relationships/increases.rb +22 -2
  132. data/lib/bel_parser/language/version2_0/relationships/is_a.rb +15 -2
  133. data/lib/bel_parser/language/version2_0/relationships/negative_correlation.rb +13 -2
  134. data/lib/bel_parser/language/version2_0/relationships/orthologous.rb +15 -2
  135. data/lib/bel_parser/language/version2_0/relationships/positive_correlation.rb +9 -2
  136. data/lib/bel_parser/language/version2_0/relationships/prognostic_biomarker_for.rb +11 -2
  137. data/lib/bel_parser/language/version2_0/relationships/rate_limiting_step_of.rb +16 -2
  138. data/lib/bel_parser/language/version2_0/relationships/reactant_in.rb +15 -2
  139. data/lib/bel_parser/language/version2_0/relationships/regulates.rb +14 -2
  140. data/lib/bel_parser/language/version2_0/relationships/sub_process_of.rb +22 -2
  141. data/lib/bel_parser/language/version2_0/relationships/transcribed_to.rb +12 -2
  142. data/lib/bel_parser/language/version2_0/relationships/translated_to.rb +13 -2
  143. data/lib/bel_parser/language/version2_0/relationships/translocates.rb +16 -2
  144. data/lib/bel_parser/language.rb +18 -8
  145. data/lib/bel_parser/parser.rb +1 -0
  146. data/lib/bel_parser/parsers/ast/node.rb +112 -74
  147. data/lib/bel_parser/parsers/bel_script/set.rl +1 -1
  148. data/lib/bel_parser/parsers/bel_script/set_document.rb +7087 -0
  149. data/lib/bel_parser/parsers/bel_script/set_document.rl +97 -0
  150. data/lib/bel_parser/parsers/bel_script.rb +1 -0
  151. data/lib/bel_parser/parsers/common/common.rl +1 -1
  152. data/lib/bel_parser/script/parser.rb +1 -0
  153. metadata +8 -2
data/lib/bel_parser/language/version1_0/functions/protein_abundance.rb CHANGED
@@ -37,7 +37,7 @@ module BELParser
37
37
  end
38
38
 
39
39
  module Signatures
40
-
40
+ # ProteinAbundanceWithFusionSignature
41
41
  class ProteinAbundanceWithFusionSignature
42
42
  extend BELParser::Language::Signature
43
43
 
@@ -45,24 +45,24 @@ module BELParser
45
45
 
46
46
  AST = BELParser::Language::Semantics::Builder.build do
47
47
  term(
48
- function(
49
- identifier(
50
- function_of(ProteinAbundance))),
51
- argument(
52
- parameter(
53
- prefix(
54
- identifier(
55
- has_namespace,
56
- namespace_of(:*))),
57
- value(
58
- value_type(
59
- has_encoding,
60
- encoding_of(:ProteinAbundance))))),
61
- argument(
62
- term(
63
- function(
64
- identifier(
65
- return_type_of(BELParser::Language::Version1_0::ReturnTypes::Fusion))))))
48
+ function(
49
+ identifier(
50
+ function_of(ProteinAbundance))),
51
+ argument(
52
+ parameter(
53
+ prefix(
54
+ identifier(
55
+ has_namespace,
56
+ namespace_of(:*))),
57
+ value(
58
+ value_type(
59
+ has_encoding,
60
+ encoding_of(:ProteinAbundance))))),
61
+ argument(
62
+ term(
63
+ function(
64
+ identifier(
65
+ return_type_of(BELParser::Language::Version1_0::ReturnTypes::Fusion))))))
66
66
  end
67
67
  private_constant :AST
68
68
 
@@ -77,7 +77,8 @@ module BELParser
77
77
  STRING_FORM
78
78
  end
79
79
  end
80
-
80
+
81
+ # ProteinAbundanceWithProteinModificationSignature
81
82
  class ProteinAbundanceWithProteinModificationSignature
82
83
  extend BELParser::Language::Signature
83
84
 
@@ -85,24 +86,24 @@ module BELParser
85
86
 
86
87
  AST = BELParser::Language::Semantics::Builder.build do
87
88
  term(
88
- function(
89
- identifier(
90
- function_of(ProteinAbundance))),
91
- argument(
92
- parameter(
93
- prefix(
94
- identifier(
95
- has_namespace,
96
- namespace_of(:*))),
97
- value(
98
- value_type(
99
- has_encoding,
100
- encoding_of(:ProteinAbundance))))),
101
- argument(
102
- term(
103
- function(
104
- identifier(
105
- return_type_of(BELParser::Language::Version1_0::ReturnTypes::ProteinModification))))))
89
+ function(
90
+ identifier(
91
+ function_of(ProteinAbundance))),
92
+ argument(
93
+ parameter(
94
+ prefix(
95
+ identifier(
96
+ has_namespace,
97
+ namespace_of(:*))),
98
+ value(
99
+ value_type(
100
+ has_encoding,
101
+ encoding_of(:ProteinAbundance))))),
102
+ argument(
103
+ term(
104
+ function(
105
+ identifier(
106
+ return_type_of(BELParser::Language::Version1_0::ReturnTypes::ProteinModification))))))
106
107
  end
107
108
  private_constant :AST
108
109
 
@@ -117,7 +118,8 @@ module BELParser
117
118
  STRING_FORM
118
119
  end
119
120
  end
120
-
121
+
122
+ # ProteinAbundanceWithSubstitutionSignature
121
123
  class ProteinAbundanceWithSubstitutionSignature
122
124
  extend BELParser::Language::Signature
123
125
 
@@ -125,24 +127,24 @@ module BELParser
125
127
 
126
128
  AST = BELParser::Language::Semantics::Builder.build do
127
129
  term(
128
- function(
129
- identifier(
130
- function_of(ProteinAbundance))),
131
- argument(
132
- parameter(
133
- prefix(
134
- identifier(
135
- has_namespace,
136
- namespace_of(:*))),
137
- value(
138
- value_type(
139
- has_encoding,
140
- encoding_of(:ProteinAbundance))))),
141
- argument(
142
- term(
143
- function(
144
- identifier(
145
- return_type_of(BELParser::Language::Version1_0::ReturnTypes::Substitution))))))
130
+ function(
131
+ identifier(
132
+ function_of(ProteinAbundance))),
133
+ argument(
134
+ parameter(
135
+ prefix(
136
+ identifier(
137
+ has_namespace,
138
+ namespace_of(:*))),
139
+ value(
140
+ value_type(
141
+ has_encoding,
142
+ encoding_of(:ProteinAbundance))))),
143
+ argument(
144
+ term(
145
+ function(
146
+ identifier(
147
+ return_type_of(BELParser::Language::Version1_0::ReturnTypes::Substitution))))))
146
148
  end
147
149
  private_constant :AST
148
150
 
@@ -157,7 +159,8 @@ module BELParser
157
159
  STRING_FORM
158
160
  end
159
161
  end
160
-
162
+
163
+ # ProteinAbundanceWithTruncationSignature
161
164
  class ProteinAbundanceWithTruncationSignature
162
165
  extend BELParser::Language::Signature
163
166
 
@@ -165,24 +168,24 @@ module BELParser
165
168
 
166
169
  AST = BELParser::Language::Semantics::Builder.build do
167
170
  term(
168
- function(
169
- identifier(
170
- function_of(ProteinAbundance))),
171
- argument(
172
- parameter(
173
- prefix(
174
- identifier(
175
- has_namespace,
176
- namespace_of(:*))),
177
- value(
178
- value_type(
179
- has_encoding,
180
- encoding_of(:ProteinAbundance))))),
181
- argument(
182
- term(
183
- function(
184
- identifier(
185
- return_type_of(BELParser::Language::Version1_0::ReturnTypes::Truncation))))))
171
+ function(
172
+ identifier(
173
+ function_of(ProteinAbundance))),
174
+ argument(
175
+ parameter(
176
+ prefix(
177
+ identifier(
178
+ has_namespace,
179
+ namespace_of(:*))),
180
+ value(
181
+ value_type(
182
+ has_encoding,
183
+ encoding_of(:ProteinAbundance))))),
184
+ argument(
185
+ term(
186
+ function(
187
+ identifier(
188
+ return_type_of(BELParser::Language::Version1_0::ReturnTypes::Truncation))))))
186
189
  end
187
190
  private_constant :AST
188
191
 
@@ -197,7 +200,8 @@ module BELParser
197
200
  STRING_FORM
198
201
  end
199
202
  end
200
-
203
+
204
+ # ProteinAbundanceSignature
201
205
  class ProteinAbundanceSignature
202
206
  extend BELParser::Language::Signature
203
207
 
@@ -205,19 +209,19 @@ module BELParser
205
209
 
206
210
  AST = BELParser::Language::Semantics::Builder.build do
207
211
  term(
208
- function(
209
- identifier(
210
- function_of(ProteinAbundance))),
211
- argument(
212
- parameter(
213
- prefix(
214
- identifier(
215
- has_namespace,
216
- namespace_of(:*))),
217
- value(
218
- value_type(
219
- has_encoding,
220
- encoding_of(:ProteinAbundance))))))
212
+ function(
213
+ identifier(
214
+ function_of(ProteinAbundance))),
215
+ argument(
216
+ parameter(
217
+ prefix(
218
+ identifier(
219
+ has_namespace,
220
+ namespace_of(:*))),
221
+ value(
222
+ value_type(
223
+ has_encoding,
224
+ encoding_of(:ProteinAbundance))))))
221
225
  end
222
226
  private_constant :AST
223
227
 
@@ -232,7 +236,6 @@ module BELParser
232
236
  STRING_FORM
233
237
  end
234
238
  end
235
-
236
239
  end
237
240
 
238
241
  SIGNATURES = Signatures.constants.map do |const|
data/lib/bel_parser/language/version1_0/functions/protein_modification.rb CHANGED
@@ -7,14 +7,16 @@ module BELParser
7
7
  module Language
8
8
  module Version1_0
9
9
  module Functions
10
- # ProteinModification: Denotes a covalently modified protein abundance
10
+ # ProteinModification: Denotes a covalently modified protein
11
+ # abundance
11
12
  class ProteinModification
12
13
  extend Function
13
14
 
14
15
  SHORT = :pmod
15
16
  LONG = :proteinModification
16
17
  RETURN_TYPE = BELParser::Language::Version1_0::ReturnTypes::ProteinModification
17
- DESCRIPTION = 'Denotes a covalently modified protein abundance'.freeze
18
+ DESCRIPTION = 'Denotes a covalently modified protein
19
+ bundance'.freeze
18
20
 
19
21
  def self.short
20
22
  SHORT
@@ -37,7 +39,7 @@ module BELParser
37
39
  end
38
40
 
39
41
  module Signatures
40
-
42
+ # ProteinModificationWithCovalentAminoPositionSignature
41
43
  class ProteinModificationWithCovalentAminoPositionSignature
42
44
  extend BELParser::Language::Signature
43
45
 
@@ -45,30 +47,30 @@ module BELParser
45
47
 
46
48
  AST = BELParser::Language::Semantics::Builder.build do
47
49
  term(
48
- function(
49
- identifier(
50
- function_of(ProteinModification))),
51
- argument(
52
- parameter(
53
- prefix(
54
- any),
55
- value(
56
- value_type(
57
- encoding_of(:*))))),
58
- argument(
59
- parameter(
60
- prefix(
61
- any),
62
- value(
63
- value_type(
64
- encoding_of(:*))))),
65
- argument(
66
- parameter(
67
- prefix(
68
- any),
69
- value(
70
- value_type(
71
- encoding_of(:*))))))
50
+ function(
51
+ identifier(
52
+ function_of(ProteinModification))),
53
+ argument(
54
+ parameter(
55
+ prefix(
56
+ any),
57
+ value(
58
+ value_type(
59
+ encoding_of(:*))))),
60
+ argument(
61
+ parameter(
62
+ prefix(
63
+ any),
64
+ value(
65
+ value_type(
66
+ encoding_of(:*))))),
67
+ argument(
68
+ parameter(
69
+ prefix(
70
+ any),
71
+ value(
72
+ value_type(
73
+ encoding_of(:*))))))
72
74
  end
73
75
  private_constant :AST
74
76
 
@@ -83,7 +85,8 @@ module BELParser
83
85
  STRING_FORM
84
86
  end
85
87
  end
86
-
88
+
89
+ # ProteinModificationWithCovalentAminoSignature
87
90
  class ProteinModificationWithCovalentAminoSignature
88
91
  extend BELParser::Language::Signature
89
92
 
@@ -91,23 +94,23 @@ module BELParser
91
94
 
92
95
  AST = BELParser::Language::Semantics::Builder.build do
93
96
  term(
94
- function(
95
- identifier(
96
- function_of(ProteinModification))),
97
- argument(
98
- parameter(
99
- prefix(
100
- any),
101
- value(
102
- value_type(
103
- encoding_of(:*))))),
104
- argument(
105
- parameter(
106
- prefix(
107
- any),
108
- value(
109
- value_type(
110
- encoding_of(:*))))))
97
+ function(
98
+ identifier(
99
+ function_of(ProteinModification))),
100
+ argument(
101
+ parameter(
102
+ prefix(
103
+ any),
104
+ value(
105
+ value_type(
106
+ encoding_of(:*))))),
107
+ argument(
108
+ parameter(
109
+ prefix(
110
+ any),
111
+ value(
112
+ value_type(
113
+ encoding_of(:*))))))
111
114
  end
112
115
  private_constant :AST
113
116
 
@@ -122,7 +125,8 @@ module BELParser
122
125
  STRING_FORM
123
126
  end
124
127
  end
125
-
128
+
129
+ # ProteinModificationWithCovalentSignature
126
130
  class ProteinModificationWithCovalentSignature
127
131
  extend BELParser::Language::Signature
128
132
 
@@ -130,16 +134,16 @@ module BELParser
130
134
 
131
135
  AST = BELParser::Language::Semantics::Builder.build do
132
136
  term(
133
- function(
134
- identifier(
135
- function_of(ProteinModification))),
136
- argument(
137
- parameter(
138
- prefix(
139
- any),
140
- value(
141
- value_type(
142
- encoding_of(:*))))))
137
+ function(
138
+ identifier(
139
+ function_of(ProteinModification))),
140
+ argument(
141
+ parameter(
142
+ prefix(
143
+ any),
144
+ value(
145
+ value_type(
146
+ encoding_of(:*))))))
143
147
  end
144
148
  private_constant :AST
145
149
 
@@ -154,7 +158,6 @@ module BELParser
154
158
  STRING_FORM
155
159
  end
156
160
  end
157
-
158
161
  end
159
162
 
160
163
  SIGNATURES = Signatures.constants.map do |const|
data/lib/bel_parser/language/version1_0/functions/reactants.rb CHANGED
@@ -37,7 +37,7 @@ module BELParser
37
37
  end
38
38
 
39
39
  module Signatures
40
-
40
+ # ReactantsSignature
41
41
  class ReactantsSignature
42
42
  extend BELParser::Language::Signature
43
43
 
@@ -45,14 +45,14 @@ module BELParser
45
45
 
46
46
  AST = BELParser::Language::Semantics::Builder.build do
47
47
  term(
48
- function(
49
- identifier(
50
- function_of(Reactants))),
51
- variadic_arguments(
52
- term(
53
- function(
54
- identifier(
55
- return_type_of(BELParser::Language::Version1_0::ReturnTypes::Abundance))))))
48
+ function(
49
+ identifier(
50
+ function_of(Reactants))),
51
+ variadic_arguments(
52
+ term(
53
+ function(
54
+ identifier(
55
+ return_type_of(BELParser::Language::Version1_0::ReturnTypes::Abundance))))))
56
56
  end
57
57
  private_constant :AST
58
58
 
@@ -67,7 +67,6 @@ module BELParser
67
67
  STRING_FORM
68
68
  end
69
69
  end
70
-
71
70
  end
72
71
 
73
72
  SIGNATURES = Signatures.constants.map do |const|
data/lib/bel_parser/language/version1_0/functions/reaction.rb CHANGED
@@ -7,14 +7,16 @@ module BELParser
7
7
  module Language
8
8
  module Version1_0
9
9
  module Functions
10
- # Reaction: Denotes the frequency or abundance of events in a reaction
10
+ # Reaction: Denotes the frequency or abundance of events in
11
+ # a reaction
11
12
  class Reaction
12
13
  extend Function
13
14
 
14
15
  SHORT = :rxn
15
16
  LONG = :reaction
16
17
  RETURN_TYPE = BELParser::Language::Version1_0::ReturnTypes::Abundance
17
- DESCRIPTION = 'Denotes the frequency or abundance of events in a reaction'.freeze
18
+ DESCRIPTION = 'Denotes the frequency or abundance of events
19
+ n a reaction'.freeze
18
20
 
19
21
  def self.short
20
22
  SHORT
@@ -37,7 +39,7 @@ module BELParser
37
39
  end
38
40
 
39
41
  module Signatures
40
-
42
+ # ReactionSignature
41
43
  class ReactionSignature
42
44
  extend BELParser::Language::Signature
43
45
 
@@ -45,19 +47,19 @@ module BELParser
45
47
 
46
48
  AST = BELParser::Language::Semantics::Builder.build do
47
49
  term(
48
- function(
49
- identifier(
50
- function_of(Reaction))),
51
- argument(
52
- term(
53
- function(
54
- identifier(
55
- return_type_of(BELParser::Language::Version1_0::ReturnTypes::Reactants))))),
56
- argument(
57
- term(
58
- function(
59
- identifier(
60
- return_type_of(BELParser::Language::Version1_0::ReturnTypes::Products))))))
50
+ function(
51
+ identifier(
52
+ function_of(Reaction))),
53
+ argument(
54
+ term(
55
+ function(
56
+ identifier(
57
+ return_type_of(BELParser::Language::Version1_0::ReturnTypes::Reactants))))),
58
+ argument(
59
+ term(
60
+ function(
61
+ identifier(
62
+ return_type_of(BELParser::Language::Version1_0::ReturnTypes::Products))))))
61
63
  end
62
64
  private_constant :AST
63
65
 
@@ -72,7 +74,6 @@ module BELParser
72
74
  STRING_FORM
73
75
  end
74
76
  end
75
-
76
77
  end
77
78
 
78
79
  SIGNATURES = Signatures.constants.map do |const|
data/lib/bel_parser/language/version1_0/functions/ribosylation_activity.rb CHANGED
@@ -7,14 +7,18 @@ module BELParser
7
7
  module Language
8
8
  module Version1_0
9
9
  module Functions
10
- # RibosylationActivity: Denotes the frequency or abundance of events in which a member acts to perform post-translational modification of proteins
10
+ # RibosylationActivity: Denotes the frequency or abundance of
11
+ # events in which a member acts to perform post-translational
12
+ # modification of proteins
11
13
  class RibosylationActivity
12
14
  extend Function
13
15
 
14
16
  SHORT = :ribo
15
17
  LONG = :ribosylationActivity
16
18
  RETURN_TYPE = BELParser::Language::Version1_0::ReturnTypes::RibosylationActivity
17
- DESCRIPTION = 'Denotes the frequency or abundance of events in which a member acts to perform post-translational modification of proteins'.freeze
19
+ DESCRIPTION = 'Denotes the frequency or abundance of events in
20
+ hich a member acts to perform post-translational
21
+ odification of proteins'.freeze
18
22
 
19
23
  def self.short
20
24
  SHORT
@@ -37,7 +41,7 @@ module BELParser
37
41
  end
38
42
 
39
43
  module Signatures
40
-
44
+ # RibosylationActivityWithComplexAbundanceSignature
41
45
  class RibosylationActivityWithComplexAbundanceSignature
42
46
  extend BELParser::Language::Signature
43
47
 
@@ -45,14 +49,14 @@ module BELParser
45
49
 
46
50
  AST = BELParser::Language::Semantics::Builder.build do
47
51
  term(
48
- function(
49
- identifier(
50
- function_of(RibosylationActivity))),
51
- argument(
52
- term(
53
- function(
54
- identifier(
55
- return_type_of(BELParser::Language::Version1_0::ReturnTypes::ComplexAbundance))))))
52
+ function(
53
+ identifier(
54
+ function_of(RibosylationActivity))),
55
+ argument(
56
+ term(
57
+ function(
58
+ identifier(
59
+ return_type_of(BELParser::Language::Version1_0::ReturnTypes::ComplexAbundance))))))
56
60
  end
57
61
  private_constant :AST
58
62
 
@@ -67,7 +71,8 @@ module BELParser
67
71
  STRING_FORM
68
72
  end
69
73
  end
70
-
74
+
75
+ # RibosylationActivityWithProteinAbundanceSignature
71
76
  class RibosylationActivityWithProteinAbundanceSignature
72
77
  extend BELParser::Language::Signature
73
78
 
@@ -75,14 +80,14 @@ module BELParser
75
80
 
76
81
  AST = BELParser::Language::Semantics::Builder.build do
77
82
  term(
78
- function(
79
- identifier(
80
- function_of(RibosylationActivity))),
81
- argument(
82
- term(
83
- function(
84
- identifier(
85
- return_type_of(BELParser::Language::Version1_0::ReturnTypes::ProteinAbundance))))))
83
+ function(
84
+ identifier(
85
+ function_of(RibosylationActivity))),
86
+ argument(
87
+ term(
88
+ function(
89
+ identifier(
90
+ return_type_of(BELParser::Language::Version1_0::ReturnTypes::ProteinAbundance))))))
86
91
  end
87
92
  private_constant :AST
88
93
 
@@ -97,7 +102,6 @@ module BELParser
97
102
  STRING_FORM
98
103
  end
99
104
  end
100
-
101
105
  end
102
106
 
103
107
  SIGNATURES = Signatures.constants.map do |const|