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/version2_0/functions/protein_modification.rb CHANGED
@@ -7,14 +7,16 @@ module BELParser
7
7
  module Language
8
8
  module Version2_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::Version2_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
+ # ProteinModificationWithTypeSignature
41
43
  class ProteinModificationWithTypeSignature
42
44
  extend BELParser::Language::Signature
43
45
 
@@ -46,16 +48,16 @@ module BELParser
46
48
  # TODO: More strict prefix validation for modification type?
47
49
  AST = BELParser::Language::Semantics::Builder.build do
48
50
  term(
49
- function(
50
- identifier(
51
- function_of(ProteinModification))),
52
- argument(
53
- parameter(
54
- prefix(any),
55
- value(
56
- value_type(
57
- has_encoding,
58
- encoding_of(:ModificationType))))))
51
+ function(
52
+ identifier(
53
+ function_of(ProteinModification))),
54
+ argument(
55
+ parameter(
56
+ prefix(any),
57
+ value(
58
+ value_type(
59
+ has_encoding,
60
+ encoding_of(:ModificationType))))))
59
61
  end
60
62
  private_constant :AST
61
63
 
@@ -70,7 +72,8 @@ module BELParser
70
72
  STRING_FORM
71
73
  end
72
74
  end
73
-
75
+
76
+ # ProteinModificationWithTypeAminoSignature
74
77
  class ProteinModificationWithTypeAminoSignature
75
78
  extend BELParser::Language::Signature
76
79
 
@@ -79,22 +82,22 @@ module BELParser
79
82
  # TODO: More strict prefix validation for modification type?
80
83
  AST = BELParser::Language::Semantics::Builder.build do
81
84
  term(
82
- function(
83
- identifier(
84
- function_of(ProteinModification))),
85
- argument(
86
- parameter(
87
- prefix(any),
88
- value(
89
- value_type(
90
- has_encoding,
91
- encoding_of(:ModificationType))))),
92
- argument(
93
- parameter(
94
- prefix(any),
95
- value(
96
- value_type(
97
- encoding_of(:*))))))
85
+ function(
86
+ identifier(
87
+ function_of(ProteinModification))),
88
+ argument(
89
+ parameter(
90
+ prefix(any),
91
+ value(
92
+ value_type(
93
+ has_encoding,
94
+ encoding_of(:ModificationType))))),
95
+ argument(
96
+ parameter(
97
+ prefix(any),
98
+ value(
99
+ value_type(
100
+ encoding_of(:*))))))
98
101
  end
99
102
  private_constant :AST
100
103
 
@@ -109,7 +112,8 @@ module BELParser
109
112
  STRING_FORM
110
113
  end
111
114
  end
112
-
115
+
116
+ # ProteinModificationWithTypeAminoPositionSignature
113
117
  class ProteinModificationWithTypeAminoPositionSignature
114
118
  extend BELParser::Language::Signature
115
119
 
@@ -118,28 +122,28 @@ module BELParser
118
122
  # TODO: More strict prefix validation for modification type?
119
123
  AST = BELParser::Language::Semantics::Builder.build do
120
124
  term(
121
- function(
122
- identifier(
123
- function_of(ProteinModification))),
124
- argument(
125
- parameter(
126
- prefix(any),
127
- value(
128
- value_type(
129
- has_encoding,
130
- encoding_of(:ModificationType))))),
131
- argument(
132
- parameter(
133
- prefix(any),
134
- value(
135
- value_type(
136
- encoding_of(:*))))),
137
- argument(
138
- parameter(
139
- prefix(any),
140
- value(
141
- value_type(
142
- encoding_of(:*))))))
125
+ function(
126
+ identifier(
127
+ function_of(ProteinModification))),
128
+ argument(
129
+ parameter(
130
+ prefix(any),
131
+ value(
132
+ value_type(
133
+ has_encoding,
134
+ encoding_of(:ModificationType))))),
135
+ argument(
136
+ parameter(
137
+ prefix(any),
138
+ value(
139
+ value_type(
140
+ encoding_of(:*))))),
141
+ argument(
142
+ parameter(
143
+ prefix(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/version2_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::Version2_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::Version2_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/version2_0/functions/reaction.rb CHANGED
@@ -7,14 +7,16 @@ module BELParser
7
7
  module Language
8
8
  module Version2_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::Version2_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::Version2_0::ReturnTypes::Reactants))))),
56
- argument(
57
- term(
58
- function(
59
- identifier(
60
- return_type_of(BELParser::Language::Version2_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::Version2_0::ReturnTypes::Reactants))))),
58
+ argument(
59
+ term(
60
+ function(
61
+ identifier(
62
+ return_type_of(BELParser::Language::Version2_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/version2_0/functions/rna_abundance.rb CHANGED
@@ -37,7 +37,7 @@ module BELParser
37
37
  end
38
38
 
39
39
  module Signatures
40
-
40
+ # RNAAbundanceSignature
41
41
  class RNAAbundanceSignature
42
42
  extend BELParser::Language::Signature
43
43
 
@@ -45,19 +45,19 @@ module BELParser
45
45
 
46
46
  AST = BELParser::Language::Semantics::Builder.build do
47
47
  term(
48
- function(
49
- identifier(
50
- function_of(RNAAbundance))),
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(:RnaAbundance))))))
48
+ function(
49
+ identifier(
50
+ function_of(RNAAbundance))),
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(:RnaAbundance))))))
61
61
  end
62
62
  private_constant :AST
63
63
 
@@ -72,7 +72,8 @@ module BELParser
72
72
  STRING_FORM
73
73
  end
74
74
  end
75
-
75
+
76
+ # RNAAbundanceWithFusionSignature
76
77
  class RNAAbundanceWithFusionSignature
77
78
  extend BELParser::Language::Signature
78
79
 
@@ -80,14 +81,14 @@ module BELParser
80
81
 
81
82
  AST = BELParser::Language::Semantics::Builder.build do
82
83
  term(
83
- function(
84
- identifier(
85
- function_of(RNAAbundance))),
86
- argument(
87
- term(
88
- function(
89
- identifier(
90
- return_type_of(BELParser::Language::Version2_0::ReturnTypes::Fusion))))))
84
+ function(
85
+ identifier(
86
+ function_of(RNAAbundance))),
87
+ argument(
88
+ term(
89
+ function(
90
+ identifier(
91
+ return_type_of(BELParser::Language::Version2_0::ReturnTypes::Fusion))))))
91
92
  end
92
93
  private_constant :AST
93
94
 
@@ -102,7 +103,8 @@ module BELParser
102
103
  STRING_FORM
103
104
  end
104
105
  end
105
-
106
+
107
+ # RNAAbundanceWithLocationSignature
106
108
  class RNAAbundanceWithLocationSignature
107
109
  extend BELParser::Language::Signature
108
110
 
@@ -110,24 +112,24 @@ module BELParser
110
112
 
111
113
  AST = BELParser::Language::Semantics::Builder.build do
112
114
  term(
113
- function(
114
- identifier(
115
- function_of(RNAAbundance))),
116
- argument(
117
- parameter(
118
- prefix(
119
- identifier(
120
- has_namespace,
121
- namespace_of(:*))),
122
- value(
123
- value_type(
124
- has_encoding,
125
- encoding_of(:RnaAbundance))))),
126
- argument(
127
- term(
128
- function(
129
- identifier(
130
- return_type_of(BELParser::Language::Version2_0::ReturnTypes::Location))))))
115
+ function(
116
+ identifier(
117
+ function_of(RNAAbundance))),
118
+ argument(
119
+ parameter(
120
+ prefix(
121
+ identifier(
122
+ has_namespace,
123
+ namespace_of(:*))),
124
+ value(
125
+ value_type(
126
+ has_encoding,
127
+ encoding_of(:RnaAbundance))))),
128
+ argument(
129
+ term(
130
+ function(
131
+ identifier(
132
+ return_type_of(BELParser::Language::Version2_0::ReturnTypes::Location))))))
131
133
  end
132
134
  private_constant :AST
133
135
 
@@ -142,7 +144,8 @@ module BELParser
142
144
  STRING_FORM
143
145
  end
144
146
  end
145
-
147
+
148
+ # RNAAbundanceWithVariantSignature
146
149
  class RNAAbundanceWithVariantSignature
147
150
  extend BELParser::Language::Signature
148
151
 
@@ -150,24 +153,24 @@ module BELParser
150
153
 
151
154
  AST = BELParser::Language::Semantics::Builder.build do
152
155
  term(
153
- function(
154
- identifier(
155
- function_of(RNAAbundance))),
156
- argument(
157
- parameter(
158
- prefix(
159
- identifier(
160
- has_namespace,
161
- namespace_of(:*))),
162
- value(
163
- value_type(
164
- has_encoding,
165
- encoding_of(:RnaAbundance))))),
166
- argument(
167
- term(
168
- function(
169
- identifier(
170
- return_type_of(BELParser::Language::Version2_0::ReturnTypes::Variant))))))
156
+ function(
157
+ identifier(
158
+ function_of(RNAAbundance))),
159
+ argument(
160
+ parameter(
161
+ prefix(
162
+ identifier(
163
+ has_namespace,
164
+ namespace_of(:*))),
165
+ value(
166
+ value_type(
167
+ has_encoding,
168
+ encoding_of(:RnaAbundance))))),
169
+ argument(
170
+ term(
171
+ function(
172
+ identifier(
173
+ return_type_of(BELParser::Language::Version2_0::ReturnTypes::Variant))))))
171
174
  end
172
175
  private_constant :AST
173
176
 
@@ -182,7 +185,6 @@ module BELParser
182
185
  STRING_FORM
183
186
  end
184
187
  end
185
-
186
188
  end
187
189
 
188
190
  SIGNATURES = Signatures.constants.map do |const|
data/lib/bel_parser/language/version2_0/functions/to_location.rb CHANGED
@@ -14,7 +14,8 @@ module BELParser
14
14
  SHORT = :toLoc
15
15
  LONG = :toLocation
16
16
  RETURN_TYPE = BELParser::Language::Version2_0::ReturnTypes::ToLocation
17
- DESCRIPTION = 'Denotes the to cellular location of the abundance.'.freeze
17
+ DESCRIPTION = 'Denotes the to cellular location of the
18
+ bundance.'.freeze
18
19
 
19
20
  def self.short
20
21
  SHORT
@@ -37,7 +38,7 @@ module BELParser
37
38
  end
38
39
 
39
40
  module Signatures
40
-
41
+ # ToLocationSignature
41
42
  class ToLocationSignature
42
43
  extend BELParser::Language::Signature
43
44
 
@@ -45,19 +46,19 @@ module BELParser
45
46
 
46
47
  AST = BELParser::Language::Semantics::Builder.build do
47
48
  term(
48
- function(
49
- identifier(
50
- function_of(ToLocation))),
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(:Location))))))
49
+ function(
50
+ identifier(
51
+ function_of(ToLocation))),
52
+ argument(
53
+ parameter(
54
+ prefix(
55
+ identifier(
56
+ has_namespace,
57
+ namespace_of(:*))),
58
+ value(
59
+ value_type(
60
+ has_encoding,
61
+ encoding_of(:Location))))))
61
62
  end
62
63
  private_constant :AST
63
64
 
@@ -72,7 +73,6 @@ module BELParser
72
73
  STRING_FORM
73
74
  end
74
75
  end
75
-
76
76
  end
77
77
 
78
78
  SIGNATURES = Signatures.constants.map do |const|
data/lib/bel_parser/language/version2_0/functions/translocation.rb CHANGED
@@ -7,14 +7,16 @@ module BELParser
7
7
  module Language
8
8
  module Version2_0
9
9
  module Functions
10
- # Translocation: Denotes the frequency or abundance of events in which members move between locations
10
+ # Translocation: Denotes the frequency or abundance of events
11
+ # in which members move between locations
11
12
  class Translocation
12
13
  extend Function
13
14
 
14
15
  SHORT = :tloc
15
16
  LONG = :translocation
16
17
  RETURN_TYPE = BELParser::Language::Version2_0::ReturnTypes::Abundance
17
- DESCRIPTION = 'Denotes the frequency or abundance of events in which members move between locations'.freeze
18
+ DESCRIPTION = 'Denotes the frequency or abundance of events
19
+ n which members move between locations'.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
+ # TranslocationSignature
41
43
  class TranslocationSignature
42
44
  extend BELParser::Language::Signature
43
45
 
@@ -45,24 +47,24 @@ module BELParser
45
47
 
46
48
  AST = BELParser::Language::Semantics::Builder.build do
47
49
  term(
48
- function(
49
- identifier(
50
- function_of(Translocation))),
51
- argument(
52
- term(
53
- function(
54
- identifier(
55
- return_type_of(BELParser::Language::Version2_0::ReturnTypes::Abundance))))),
56
- argument(
57
- term(
58
- function(
59
- identifier(
60
- return_type_of(BELParser::Language::Version2_0::ReturnTypes::FromLocation))))),
61
- argument(
62
- term(
63
- function(
64
- identifier(
65
- return_type_of(BELParser::Language::Version2_0::ReturnTypes::ToLocation))))))
50
+ function(
51
+ identifier(
52
+ function_of(Translocation))),
53
+ argument(
54
+ term(
55
+ function(
56
+ identifier(
57
+ return_type_of(BELParser::Language::Version2_0::ReturnTypes::Abundance))))),
58
+ argument(
59
+ term(
60
+ function(
61
+ identifier(
62
+ return_type_of(BELParser::Language::Version2_0::ReturnTypes::FromLocation))))),
63
+ argument(
64
+ term(
65
+ function(
66
+ identifier(
67
+ return_type_of(BELParser::Language::Version2_0::ReturnTypes::ToLocation))))))
66
68
  end
67
69
  private_constant :AST
68
70
 
@@ -77,7 +79,6 @@ module BELParser
77
79
  STRING_FORM
78
80
  end
79
81
  end
80
-
81
82
  end
82
83
 
83
84
  SIGNATURES = Signatures.constants.map do |const|
data/lib/bel_parser/language/version2_0/functions/variant.rb CHANGED
@@ -14,7 +14,8 @@ module BELParser
14
14
  SHORT = :var
15
15
  LONG = :variant
16
16
  RETURN_TYPE = BELParser::Language::Version2_0::ReturnTypes::Variant
17
- DESCRIPTION = 'Denotes a sequence variant of the specified abundance.'.freeze
17
+ DESCRIPTION = 'Denotes a sequence variant of the specified
18
+ bundance.'.freeze
18
19
 
19
20
  def self.short
20
21
  SHORT
@@ -37,7 +38,7 @@ module BELParser
37
38
  end
38
39
 
39
40
  module Signatures
40
-
41
+ # VariantSignature
41
42
  class VariantSignature
42
43
  extend BELParser::Language::Signature
43
44
 
@@ -46,16 +47,16 @@ module BELParser
46
47
  # TODO: More strict prefix validation for variant namespace?
47
48
  AST = BELParser::Language::Semantics::Builder.build do
48
49
  term(
49
- function(
50
- identifier(
51
- function_of(Variant))),
52
- argument(
53
- parameter(
54
- prefix(any),
55
- value(
56
- value_type(
57
- has_encoding,
58
- encoding_of(:HgvsVariantDescription))))))
50
+ function(
51
+ identifier(
52
+ function_of(Variant))),
53
+ argument(
54
+ parameter(
55
+ prefix(any),
56
+ value(
57
+ value_type(
58
+ has_encoding,
59
+ encoding_of(:HgvsVariantDescription))))))
59
60
  end
60
61
  private_constant :AST
61
62
 
@@ -70,7 +71,6 @@ module BELParser
70
71
  STRING_FORM
71
72
  end
72
73
  end
73
-
74
74
  end
75
75
 
76
76
  SIGNATURES = Signatures.constants.map do |const|