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

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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|