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/composite_abundance.rb CHANGED
@@ -7,14 +7,16 @@ module BELParser
7
7
  module Language
8
8
  module Version1_0
9
9
  module Functions
10
- # CompositeAbundance: Denotes the frequency or abundance of events in which members are present
10
+ # CompositeAbundance: Denotes the frequency or abundance of
11
+ # events in which members are present
11
12
  class CompositeAbundance
12
13
  extend Function
13
14
 
14
15
  SHORT = :composite
15
16
  LONG = :compositeAbundance
16
17
  RETURN_TYPE = BELParser::Language::Version1_0::ReturnTypes::Abundance
17
- DESCRIPTION = 'Denotes the frequency or abundance of events in which members are present'.freeze
18
+ DESCRIPTION = 'Denotes the frequency or abundance of events
19
+ n which members are present'.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
+ # CompositeAbundanceSignature
41
43
  class CompositeAbundanceSignature
42
44
  extend BELParser::Language::Signature
43
45
 
@@ -45,14 +47,14 @@ module BELParser
45
47
 
46
48
  AST = BELParser::Language::Semantics::Builder.build do
47
49
  term(
48
- function(
49
- identifier(
50
- function_of(CompositeAbundance))),
51
- variadic_arguments(
52
- term(
53
- function(
54
- identifier(
55
- return_type_of(BELParser::Language::Version1_0::ReturnTypes::Abundance))))))
50
+ function(
51
+ identifier(
52
+ function_of(CompositeAbundance))),
53
+ variadic_arguments(
54
+ term(
55
+ function(
56
+ identifier(
57
+ return_type_of(BELParser::Language::Version1_0::ReturnTypes::Abundance))))))
56
58
  end
57
59
  private_constant :AST
58
60
 
@@ -67,7 +69,6 @@ module BELParser
67
69
  STRING_FORM
68
70
  end
69
71
  end
70
-
71
72
  end
72
73
 
73
74
  SIGNATURES = Signatures.constants.map do |const|
data/lib/bel_parser/language/version1_0/functions/degradation.rb CHANGED
@@ -7,14 +7,18 @@ module BELParser
7
7
  module Language
8
8
  module Version1_0
9
9
  module Functions
10
- # Degradation: Denotes the frequency or abundance of events in which a member is degraded in some way such that it is no longer a member
10
+ # Degradation: Denotes the frequency or abundance of events
11
+ # in which a member is degraded in some way such that it is no
12
+ # longer a member
11
13
  class Degradation
12
14
  extend Function
13
15
 
14
16
  SHORT = :deg
15
17
  LONG = :degradation
16
18
  RETURN_TYPE = BELParser::Language::Version1_0::ReturnTypes::Abundance
17
- DESCRIPTION = 'Denotes the frequency or abundance of events in which a member is degraded in some way such that it is no longer a member'.freeze
19
+ DESCRIPTION = 'Denotes the frequency or abundance of events
20
+ n which a member is degraded in some way such
21
+ hat it is no longer a member'.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
+ # DegradationSignature
41
45
  class DegradationSignature
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(Degradation))),
51
- argument(
52
- term(
53
- function(
54
- identifier(
55
- return_type_of(BELParser::Language::Version1_0::ReturnTypes::Abundance))))))
52
+ function(
53
+ identifier(
54
+ function_of(Degradation))),
55
+ argument(
56
+ term(
57
+ function(
58
+ identifier(
59
+ return_type_of(BELParser::Language::Version1_0::ReturnTypes::Abundance))))))
56
60
  end
57
61
  private_constant :AST
58
62
 
@@ -67,7 +71,6 @@ module BELParser
67
71
  STRING_FORM
68
72
  end
69
73
  end
70
-
71
74
  end
72
75
 
73
76
  SIGNATURES = Signatures.constants.map do |const|
data/lib/bel_parser/language/version1_0/functions/fusion.rb CHANGED
@@ -7,14 +7,16 @@ module BELParser
7
7
  module Language
8
8
  module Version1_0
9
9
  module Functions
10
- # Fusion: Specifies the abundance of a protein translated from the fusion of a gene
10
+ # Fusion: Specifies the abundance of a protein translated from
11
+ # the fusion of a gene
11
12
  class Fusion
12
13
  extend Function
13
14
 
14
15
  SHORT = :fus
15
16
  LONG = :fusion
16
17
  RETURN_TYPE = BELParser::Language::Version1_0::ReturnTypes::Fusion
17
- DESCRIPTION = 'Specifies the abundance of a protein translated from the fusion of a gene'.freeze
18
+ DESCRIPTION = 'Specifies the abundance of a protein translated
19
+ rom the fusion of a gene'.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
+ # FusionGeneAbundanceWithBreakpointsSignature
41
43
  class FusionGeneAbundanceWithBreakpointsSignature
42
44
  extend BELParser::Language::Signature
43
45
 
@@ -45,33 +47,33 @@ module BELParser
45
47
 
46
48
  AST = BELParser::Language::Semantics::Builder.build do
47
49
  term(
48
- function(
49
- identifier(
50
- function_of(Fusion))),
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(:GeneAbundance))))),
61
- argument(
62
- parameter(
63
- prefix(
64
- any),
65
- value(
66
- value_type(
67
- encoding_of(:*))))),
68
- argument(
69
- parameter(
70
- prefix(
71
- any),
72
- value(
73
- value_type(
74
- encoding_of(:*))))))
50
+ function(
51
+ identifier(
52
+ function_of(Fusion))),
53
+ argument(
54
+ parameter(
55
+ prefix(
56
+ identifier(
57
+ has_namespace,
58
+ namespace_of(:*))),
59
+ value(
60
+ value_type(
61
+ has_encoding,
62
+ encoding_of(:GeneAbundance))))),
63
+ argument(
64
+ parameter(
65
+ prefix(
66
+ any),
67
+ value(
68
+ value_type(
69
+ encoding_of(:*))))),
70
+ argument(
71
+ parameter(
72
+ prefix(
73
+ any),
74
+ value(
75
+ value_type(
76
+ encoding_of(:*))))))
75
77
  end
76
78
  private_constant :AST
77
79
 
@@ -86,7 +88,8 @@ module BELParser
86
88
  STRING_FORM
87
89
  end
88
90
  end
89
-
91
+
92
+ # FusionGeneAbundanceSignature
90
93
  class FusionGeneAbundanceSignature
91
94
  extend BELParser::Language::Signature
92
95
 
@@ -94,19 +97,19 @@ module BELParser
94
97
 
95
98
  AST = BELParser::Language::Semantics::Builder.build do
96
99
  term(
97
- function(
98
- identifier(
99
- function_of(Fusion))),
100
- argument(
101
- parameter(
102
- prefix(
103
- identifier(
104
- has_namespace,
105
- namespace_of(:*))),
106
- value(
107
- value_type(
108
- has_encoding,
109
- encoding_of(:GeneAbundance))))))
100
+ function(
101
+ identifier(
102
+ function_of(Fusion))),
103
+ argument(
104
+ parameter(
105
+ prefix(
106
+ identifier(
107
+ has_namespace,
108
+ namespace_of(:*))),
109
+ value(
110
+ value_type(
111
+ has_encoding,
112
+ encoding_of(:GeneAbundance))))))
110
113
  end
111
114
  private_constant :AST
112
115
 
@@ -121,7 +124,8 @@ module BELParser
121
124
  STRING_FORM
122
125
  end
123
126
  end
124
-
127
+
128
+ # FusionProteinAbundanceWithBreakpointsSignature
125
129
  class FusionProteinAbundanceWithBreakpointsSignature
126
130
  extend BELParser::Language::Signature
127
131
 
@@ -129,33 +133,33 @@ module BELParser
129
133
 
130
134
  AST = BELParser::Language::Semantics::Builder.build do
131
135
  term(
132
- function(
133
- identifier(
134
- function_of(Fusion))),
135
- argument(
136
- parameter(
137
- prefix(
138
- identifier(
139
- has_namespace,
140
- namespace_of(:*))),
141
- value(
142
- value_type(
143
- has_encoding,
144
- encoding_of(:ProteinAbundance))))),
145
- argument(
146
- parameter(
147
- prefix(
148
- any),
149
- value(
150
- value_type(
151
- encoding_of(:*))))),
152
- argument(
153
- parameter(
154
- prefix(
155
- any),
156
- value(
157
- value_type(
158
- encoding_of(:*))))))
136
+ function(
137
+ identifier(
138
+ function_of(Fusion))),
139
+ argument(
140
+ parameter(
141
+ prefix(
142
+ identifier(
143
+ has_namespace,
144
+ namespace_of(:*))),
145
+ value(
146
+ value_type(
147
+ has_encoding,
148
+ encoding_of(:ProteinAbundance))))),
149
+ argument(
150
+ parameter(
151
+ prefix(
152
+ any),
153
+ value(
154
+ value_type(
155
+ encoding_of(:*))))),
156
+ argument(
157
+ parameter(
158
+ prefix(
159
+ any),
160
+ value(
161
+ value_type(
162
+ encoding_of(:*))))))
159
163
  end
160
164
  private_constant :AST
161
165
 
@@ -170,7 +174,8 @@ module BELParser
170
174
  STRING_FORM
171
175
  end
172
176
  end
173
-
177
+
178
+ # FusionProteinAbundanceSignature
174
179
  class FusionProteinAbundanceSignature
175
180
  extend BELParser::Language::Signature
176
181
 
@@ -178,19 +183,19 @@ module BELParser
178
183
 
179
184
  AST = BELParser::Language::Semantics::Builder.build do
180
185
  term(
181
- function(
182
- identifier(
183
- function_of(Fusion))),
184
- argument(
185
- parameter(
186
- prefix(
187
- identifier(
188
- has_namespace,
189
- namespace_of(:*))),
190
- value(
191
- value_type(
192
- has_encoding,
193
- encoding_of(:ProteinAbundance))))))
186
+ function(
187
+ identifier(
188
+ function_of(Fusion))),
189
+ argument(
190
+ parameter(
191
+ prefix(
192
+ identifier(
193
+ has_namespace,
194
+ namespace_of(:*))),
195
+ value(
196
+ value_type(
197
+ has_encoding,
198
+ encoding_of(:ProteinAbundance))))))
194
199
  end
195
200
  private_constant :AST
196
201
 
@@ -205,7 +210,8 @@ module BELParser
205
210
  STRING_FORM
206
211
  end
207
212
  end
208
-
213
+
214
+ # FusionRNAAbundanceWithBreakpointsSignature
209
215
  class FusionRNAAbundanceWithBreakpointsSignature
210
216
  extend BELParser::Language::Signature
211
217
 
@@ -213,33 +219,33 @@ module BELParser
213
219
 
214
220
  AST = BELParser::Language::Semantics::Builder.build do
215
221
  term(
216
- function(
217
- identifier(
218
- function_of(Fusion))),
219
- argument(
220
- parameter(
221
- prefix(
222
- identifier(
223
- has_namespace,
224
- namespace_of(:*))),
225
- value(
226
- value_type(
227
- has_encoding,
228
- encoding_of(:RnaAbundance))))),
229
- argument(
230
- parameter(
231
- prefix(
232
- any),
233
- value(
234
- value_type(
235
- encoding_of(:*))))),
236
- argument(
237
- parameter(
238
- prefix(
239
- any),
240
- value(
241
- value_type(
242
- encoding_of(:*))))))
222
+ function(
223
+ identifier(
224
+ function_of(Fusion))),
225
+ argument(
226
+ parameter(
227
+ prefix(
228
+ identifier(
229
+ has_namespace,
230
+ namespace_of(:*))),
231
+ value(
232
+ value_type(
233
+ has_encoding,
234
+ encoding_of(:RnaAbundance))))),
235
+ argument(
236
+ parameter(
237
+ prefix(
238
+ any),
239
+ value(
240
+ value_type(
241
+ encoding_of(:*))))),
242
+ argument(
243
+ parameter(
244
+ prefix(
245
+ any),
246
+ value(
247
+ value_type(
248
+ encoding_of(:*))))))
243
249
  end
244
250
  private_constant :AST
245
251
 
@@ -254,7 +260,8 @@ module BELParser
254
260
  STRING_FORM
255
261
  end
256
262
  end
257
-
263
+
264
+ # FusionRNAAbundanceSignature
258
265
  class FusionRNAAbundanceSignature
259
266
  extend BELParser::Language::Signature
260
267
 
@@ -262,19 +269,19 @@ module BELParser
262
269
 
263
270
  AST = BELParser::Language::Semantics::Builder.build do
264
271
  term(
265
- function(
266
- identifier(
267
- function_of(Fusion))),
268
- argument(
269
- parameter(
270
- prefix(
271
- identifier(
272
- has_namespace,
273
- namespace_of(:*))),
274
- value(
275
- value_type(
276
- has_encoding,
277
- encoding_of(:RnaAbundance))))))
272
+ function(
273
+ identifier(
274
+ function_of(Fusion))),
275
+ argument(
276
+ parameter(
277
+ prefix(
278
+ identifier(
279
+ has_namespace,
280
+ namespace_of(:*))),
281
+ value(
282
+ value_type(
283
+ has_encoding,
284
+ encoding_of(:RnaAbundance))))))
278
285
  end
279
286
  private_constant :AST
280
287
 
@@ -289,7 +296,6 @@ module BELParser
289
296
  STRING_FORM
290
297
  end
291
298
  end
292
-
293
299
  end
294
300
 
295
301
  SIGNATURES = Signatures.constants.map do |const|
data/lib/bel_parser/language/version1_0/functions/gene_abundance.rb CHANGED
@@ -37,7 +37,7 @@ module BELParser
37
37
  end
38
38
 
39
39
  module Signatures
40
-
40
+ # GeneAbundanceWithFusionSignature
41
41
  class GeneAbundanceWithFusionSignature
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(GeneAbundance))),
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(:GeneAbundance))))),
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(GeneAbundance))),
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(:GeneAbundance))))),
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
+ # GeneAbundanceSignature
81
82
  class GeneAbundanceSignature
82
83
  extend BELParser::Language::Signature
83
84
 
@@ -85,19 +86,19 @@ module BELParser
85
86
 
86
87
  AST = BELParser::Language::Semantics::Builder.build do
87
88
  term(
88
- function(
89
- identifier(
90
- function_of(GeneAbundance))),
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(:GeneAbundance))))))
89
+ function(
90
+ identifier(
91
+ function_of(GeneAbundance))),
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(:GeneAbundance))))))
101
102
  end
102
103
  private_constant :AST
103
104
 
@@ -112,7 +113,6 @@ module BELParser
112
113
  STRING_FORM
113
114
  end
114
115
  end
115
-
116
116
  end
117
117
 
118
118
  SIGNATURES = Signatures.constants.map do |const|
data/lib/bel_parser/language/version1_0/functions/gtp_bound_activity.rb CHANGED
@@ -7,14 +7,17 @@ module BELParser
7
7
  module Language
8
8
  module Version1_0
9
9
  module Functions
10
- # GTPBoundActivity: Denotes the frequency or abundance of events in which a member of a G-protein abundance is GTP-bound
10
+ # GTPBoundActivity: Denotes the frequency or abundance of events
11
+ # in which a member of a G-protein abundance is GTP-bound
11
12
  class GTPBoundActivity
12
13
  extend Function
13
14
 
14
15
  SHORT = :gtp
15
16
  LONG = :gtpBoundActivity
16
17
  RETURN_TYPE = BELParser::Language::Version1_0::ReturnTypes::GTPBoundActivity
17
- DESCRIPTION = 'Denotes the frequency or abundance of events in which a member of a G-protein abundance is GTP-bound'.freeze
18
+ DESCRIPTION = 'Denotes the frequency or abundance of events
19
+ n which a member of a G-protein abundance is
20
+ TP-bound'.freeze
18
21
 
19
22
  def self.short
20
23
  SHORT
@@ -37,7 +40,7 @@ module BELParser
37
40
  end
38
41
 
39
42
  module Signatures
40
-
43
+ # GTPBoundActivityOfComplexAbundanceSignature
41
44
  class GTPBoundActivityOfComplexAbundanceSignature
42
45
  extend BELParser::Language::Signature
43
46
 
@@ -45,14 +48,14 @@ module BELParser
45
48
 
46
49
  AST = BELParser::Language::Semantics::Builder.build do
47
50
  term(
48
- function(
49
- identifier(
50
- function_of(GTPBoundActivity))),
51
- argument(
52
- term(
53
- function(
54
- identifier(
55
- return_type_of(BELParser::Language::Version1_0::ReturnTypes::ComplexAbundance))))))
51
+ function(
52
+ identifier(
53
+ function_of(GTPBoundActivity))),
54
+ argument(
55
+ term(
56
+ function(
57
+ identifier(
58
+ return_type_of(BELParser::Language::Version1_0::ReturnTypes::ComplexAbundance))))))
56
59
  end
57
60
  private_constant :AST
58
61
 
@@ -67,7 +70,8 @@ module BELParser
67
70
  STRING_FORM
68
71
  end
69
72
  end
70
-
73
+
74
+ # GTPBoundActivityOfProteinAbundanceSignature
71
75
  class GTPBoundActivityOfProteinAbundanceSignature
72
76
  extend BELParser::Language::Signature
73
77
 
@@ -75,14 +79,14 @@ module BELParser
75
79
 
76
80
  AST = BELParser::Language::Semantics::Builder.build do
77
81
  term(
78
- function(
79
- identifier(
80
- function_of(GTPBoundActivity))),
81
- argument(
82
- term(
83
- function(
84
- identifier(
85
- return_type_of(BELParser::Language::Version1_0::ReturnTypes::ProteinAbundance))))))
82
+ function(
83
+ identifier(
84
+ function_of(GTPBoundActivity))),
85
+ argument(
86
+ term(
87
+ function(
88
+ identifier(
89
+ return_type_of(BELParser::Language::Version1_0::ReturnTypes::ProteinAbundance))))))
86
90
  end
87
91
  private_constant :AST
88
92
 
@@ -97,7 +101,6 @@ module BELParser
97
101
  STRING_FORM
98
102
  end
99
103
  end
100
-
101
104
  end
102
105
 
103
106
  SIGNATURES = Signatures.constants.map do |const|