bel_parser 1.0.0.alpha.1 → 1.0.0.alpha.2

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Files changed (184) hide show
  1. checksums.yaml +4 -4
  2. data/.gemspec +1 -1
  3. data/VERSION +1 -1
  4. data/bin/bel2_termcheck +2 -2
  5. data/lib/bel_parser/expression/term_semantics.rb +2 -2
  6. data/lib/bel_parser/language/expression_validator.rb +42 -0
  7. data/lib/bel_parser/language/function.rb +8 -0
  8. data/lib/bel_parser/language/relationship.rb +57 -0
  9. data/lib/bel_parser/language/{semantic_ast.rb → semantics/semantic_ast.rb} +5 -27
  10. data/lib/bel_parser/language/semantics/semantic_match.rb +28 -0
  11. data/lib/bel_parser/language/semantics.rb +2 -0
  12. data/lib/bel_parser/language/specification.rb +34 -10
  13. data/lib/bel_parser/language/syntax.rb +0 -0
  14. data/lib/bel_parser/language/{version1 → version1_0}/functions/abundance.rb +4 -4
  15. data/lib/bel_parser/language/{version1 → version1_0}/functions/biological_process.rb +4 -4
  16. data/lib/bel_parser/language/{version1 → version1_0}/functions/catalytic_activity.rb +6 -6
  17. data/lib/bel_parser/language/{version1 → version1_0}/functions/cell_secretion.rb +5 -5
  18. data/lib/bel_parser/language/{version1 → version1_0}/functions/cell_surface_expression.rb +5 -5
  19. data/lib/bel_parser/language/{version1 → version1_0}/functions/chaperone_activity.rb +6 -6
  20. data/lib/bel_parser/language/{version1 → version1_0}/functions/complex_abundance.rb +5 -5
  21. data/lib/bel_parser/language/{version1 → version1_0}/functions/composite_abundance.rb +5 -5
  22. data/lib/bel_parser/language/{version1 → version1_0}/functions/degradation.rb +5 -5
  23. data/lib/bel_parser/language/{version1 → version1_0}/functions/fusion.rb +4 -4
  24. data/lib/bel_parser/language/{version1 → version1_0}/functions/gene_abundance.rb +5 -5
  25. data/lib/bel_parser/language/{version1 → version1_0}/functions/gtp_bound_activity.rb +6 -6
  26. data/lib/bel_parser/language/{version1 → version1_0}/functions/kinase_activity.rb +6 -6
  27. data/lib/bel_parser/language/{version1 → version1_0}/functions/list.rb +5 -5
  28. data/lib/bel_parser/language/{version1 → version1_0}/functions/micro_rna_abundance.rb +4 -4
  29. data/lib/bel_parser/language/{version1 → version1_0}/functions/molecular_activity.rb +5 -5
  30. data/lib/bel_parser/language/{version2 → version1_0}/functions/pathology.rb +4 -4
  31. data/lib/bel_parser/language/{version1 → version1_0}/functions/peptidase_activity.rb +6 -6
  32. data/lib/bel_parser/language/{version1 → version1_0}/functions/phosphatase_activity.rb +6 -6
  33. data/lib/bel_parser/language/{version2 → version1_0}/functions/products.rb +5 -5
  34. data/lib/bel_parser/language/{version1 → version1_0}/functions/protein_abundance.rb +8 -8
  35. data/lib/bel_parser/language/{version1 → version1_0}/functions/protein_modification.rb +4 -4
  36. data/lib/bel_parser/language/{version2 → version1_0}/functions/reactants.rb +5 -5
  37. data/lib/bel_parser/language/{version1 → version1_0}/functions/reaction.rb +6 -6
  38. data/lib/bel_parser/language/{version1 → version1_0}/functions/ribosylation_activity.rb +6 -6
  39. data/lib/bel_parser/language/{version1 → version1_0}/functions/rna_abundance.rb +5 -5
  40. data/lib/bel_parser/language/{version1 → version1_0}/functions/substitution.rb +4 -4
  41. data/lib/bel_parser/language/{version1 → version1_0}/functions/transcriptional_activity.rb +6 -6
  42. data/lib/bel_parser/language/{version1 → version1_0}/functions/translocation.rb +5 -5
  43. data/lib/bel_parser/language/{version1 → version1_0}/functions/transport_activity.rb +6 -6
  44. data/lib/bel_parser/language/{version1 → version1_0}/functions/truncation.rb +4 -4
  45. data/lib/bel_parser/language/version1_0/relationships/acts_in.rb +31 -0
  46. data/lib/bel_parser/language/version1_0/relationships/analogous.rb +31 -0
  47. data/lib/bel_parser/language/version1_0/relationships/association.rb +31 -0
  48. data/lib/bel_parser/language/version1_0/relationships/biomarker_for.rb +31 -0
  49. data/lib/bel_parser/language/version1_0/relationships/causes_no_change.rb +31 -0
  50. data/lib/bel_parser/language/version1_0/relationships/decreases.rb +31 -0
  51. data/lib/bel_parser/language/version1_0/relationships/directly_decreases.rb +31 -0
  52. data/lib/bel_parser/language/version1_0/relationships/directly_increases.rb +31 -0
  53. data/lib/bel_parser/language/version1_0/relationships/has_component.rb +31 -0
  54. data/lib/bel_parser/language/version1_0/relationships/has_components.rb +31 -0
  55. data/lib/bel_parser/language/version1_0/relationships/has_member.rb +31 -0
  56. data/lib/bel_parser/language/version1_0/relationships/has_members.rb +31 -0
  57. data/lib/bel_parser/language/version1_0/relationships/has_modification.rb +31 -0
  58. data/lib/bel_parser/language/version1_0/relationships/has_product.rb +31 -0
  59. data/lib/bel_parser/language/version1_0/relationships/has_variant.rb +31 -0
  60. data/lib/bel_parser/language/version1_0/relationships/includes.rb +31 -0
  61. data/lib/bel_parser/language/version1_0/relationships/increases.rb +31 -0
  62. data/lib/bel_parser/language/version1_0/relationships/is_a.rb +31 -0
  63. data/lib/bel_parser/language/version1_0/relationships/negative_correlation.rb +31 -0
  64. data/lib/bel_parser/language/version1_0/relationships/orthologous.rb +31 -0
  65. data/lib/bel_parser/language/version1_0/relationships/positive_correlation.rb +31 -0
  66. data/lib/bel_parser/language/version1_0/relationships/prognostic_biomarker_for.rb +31 -0
  67. data/lib/bel_parser/language/version1_0/relationships/rate_limiting_step_of.rb +31 -0
  68. data/lib/bel_parser/language/version1_0/relationships/reactant_in.rb +31 -0
  69. data/lib/bel_parser/language/version1_0/relationships/sub_process_of.rb +31 -0
  70. data/lib/bel_parser/language/version1_0/relationships/transcribed_to.rb +31 -0
  71. data/lib/bel_parser/language/version1_0/relationships/translated_to.rb +31 -0
  72. data/lib/bel_parser/language/version1_0/relationships/translocates.rb +31 -0
  73. data/lib/bel_parser/language/{version2 → version1_0}/return_types/abundance.rb +1 -1
  74. data/lib/bel_parser/language/{version1 → version1_0}/return_types/any.rb +1 -1
  75. data/lib/bel_parser/language/{version1 → version1_0}/return_types/biological_process.rb +1 -1
  76. data/lib/bel_parser/language/{version1 → version1_0}/return_types/catalytic_activity.rb +1 -1
  77. data/lib/bel_parser/language/{version1 → version1_0}/return_types/chaperone_activity.rb +1 -1
  78. data/lib/bel_parser/language/{version2 → version1_0}/return_types/complex_abundance.rb +1 -1
  79. data/lib/bel_parser/language/{version1 → version1_0}/return_types/fusion.rb +1 -1
  80. data/lib/bel_parser/language/{version2 → version1_0}/return_types/gene_abundance.rb +1 -1
  81. data/lib/bel_parser/language/{version1 → version1_0}/return_types/gtp_bound_activity.rb +1 -1
  82. data/lib/bel_parser/language/{version1 → version1_0}/return_types/kinase_activity.rb +1 -1
  83. data/lib/bel_parser/language/{version1 → version1_0}/return_types/list.rb +1 -1
  84. data/lib/bel_parser/language/{version1 → version1_0}/return_types/micro_rna_abundance.rb +1 -1
  85. data/lib/bel_parser/language/{version1 → version1_0}/return_types/molecular_activity.rb +1 -1
  86. data/lib/bel_parser/language/{version1 → version1_0}/return_types/pathology.rb +1 -1
  87. data/lib/bel_parser/language/{version1 → version1_0}/return_types/peptidase_activity.rb +1 -1
  88. data/lib/bel_parser/language/{version1 → version1_0}/return_types/phosphatase_activity.rb +1 -1
  89. data/lib/bel_parser/language/{version2 → version1_0}/return_types/products.rb +1 -1
  90. data/lib/bel_parser/language/{version2 → version1_0}/return_types/protein_abundance.rb +1 -1
  91. data/lib/bel_parser/language/{version1 → version1_0}/return_types/protein_modification.rb +1 -1
  92. data/lib/bel_parser/language/{version2 → version1_0}/return_types/reactants.rb +1 -1
  93. data/lib/bel_parser/language/{version1 → version1_0}/return_types/ribosylation_activity.rb +1 -1
  94. data/lib/bel_parser/language/{version1 → version1_0}/return_types/rna_abundance.rb +1 -1
  95. data/lib/bel_parser/language/{version1 → version1_0}/return_types/substitution.rb +1 -1
  96. data/lib/bel_parser/language/{version1 → version1_0}/return_types/transcriptional_activity.rb +1 -1
  97. data/lib/bel_parser/language/{version1 → version1_0}/return_types/transport_activity.rb +1 -1
  98. data/lib/bel_parser/language/{version1 → version1_0}/return_types/truncation.rb +1 -1
  99. data/lib/bel_parser/language/version1_0/syntax/function.rb +29 -0
  100. data/lib/bel_parser/language/version1_0.rb +89 -0
  101. data/lib/bel_parser/language/{version2 → version2_0}/functions/abundance.rb +6 -6
  102. data/lib/bel_parser/language/{version2 → version2_0}/functions/activity.rb +7 -7
  103. data/lib/bel_parser/language/{version2 → version2_0}/functions/biological_process.rb +4 -4
  104. data/lib/bel_parser/language/{version2 → version2_0}/functions/cell_secretion.rb +5 -5
  105. data/lib/bel_parser/language/{version2 → version2_0}/functions/cell_surface_expression.rb +5 -5
  106. data/lib/bel_parser/language/{version2 → version2_0}/functions/complex_abundance.rb +8 -8
  107. data/lib/bel_parser/language/{version2 → version2_0}/functions/composite_abundance.rb +5 -5
  108. data/lib/bel_parser/language/{version2 → version2_0}/functions/degradation.rb +5 -5
  109. data/lib/bel_parser/language/{version2 → version2_0}/functions/fragment.rb +4 -4
  110. data/lib/bel_parser/language/{version2 → version2_0}/functions/from_location.rb +4 -4
  111. data/lib/bel_parser/language/{version2 → version2_0}/functions/fusion.rb +4 -4
  112. data/lib/bel_parser/language/{version2 → version2_0}/functions/gene_abundance.rb +7 -7
  113. data/lib/bel_parser/language/{version2 → version2_0}/functions/list.rb +5 -5
  114. data/lib/bel_parser/language/{version2 → version2_0}/functions/location.rb +4 -4
  115. data/lib/bel_parser/language/{version2 → version2_0}/functions/micro_rna_abundance.rb +6 -6
  116. data/lib/bel_parser/language/{version2 → version2_0}/functions/molecular_activity.rb +4 -4
  117. data/lib/bel_parser/language/{version1 → version2_0}/functions/pathology.rb +4 -4
  118. data/lib/bel_parser/language/{version1 → version2_0}/functions/products.rb +5 -5
  119. data/lib/bel_parser/language/{version2 → version2_0}/functions/protein_abundance.rb +9 -9
  120. data/lib/bel_parser/language/{version2 → version2_0}/functions/protein_modification.rb +7 -7
  121. data/lib/bel_parser/language/{version1 → version2_0}/functions/reactants.rb +5 -5
  122. data/lib/bel_parser/language/{version2 → version2_0}/functions/reaction.rb +6 -6
  123. data/lib/bel_parser/language/{version2 → version2_0}/functions/rna_abundance.rb +11 -11
  124. data/lib/bel_parser/language/{version2 → version2_0}/functions/to_location.rb +4 -4
  125. data/lib/bel_parser/language/{version2 → version2_0}/functions/translocation.rb +8 -8
  126. data/lib/bel_parser/language/{version2 → version2_0}/functions/variant.rb +4 -4
  127. data/lib/bel_parser/language/version2_0/relationships/acts_in.rb +31 -0
  128. data/lib/bel_parser/language/version2_0/relationships/analogous.rb +35 -0
  129. data/lib/bel_parser/language/version2_0/relationships/association.rb +31 -0
  130. data/lib/bel_parser/language/version2_0/relationships/biomarker_for.rb +35 -0
  131. data/lib/bel_parser/language/version2_0/relationships/causes_no_change.rb +31 -0
  132. data/lib/bel_parser/language/version2_0/relationships/decreases.rb +31 -0
  133. data/lib/bel_parser/language/version2_0/relationships/directly_decreases.rb +31 -0
  134. data/lib/bel_parser/language/version2_0/relationships/directly_increases.rb +31 -0
  135. data/lib/bel_parser/language/version2_0/relationships/has_component.rb +31 -0
  136. data/lib/bel_parser/language/version2_0/relationships/has_components.rb +31 -0
  137. data/lib/bel_parser/language/version2_0/relationships/has_member.rb +31 -0
  138. data/lib/bel_parser/language/version2_0/relationships/has_members.rb +31 -0
  139. data/lib/bel_parser/language/version2_0/relationships/has_modification.rb +31 -0
  140. data/lib/bel_parser/language/version2_0/relationships/has_product.rb +31 -0
  141. data/lib/bel_parser/language/version2_0/relationships/has_variant.rb +31 -0
  142. data/lib/bel_parser/language/version2_0/relationships/includes.rb +31 -0
  143. data/lib/bel_parser/language/version2_0/relationships/increases.rb +31 -0
  144. data/lib/bel_parser/language/version2_0/relationships/is_a.rb +31 -0
  145. data/lib/bel_parser/language/version2_0/relationships/negative_correlation.rb +31 -0
  146. data/lib/bel_parser/language/version2_0/relationships/orthologous.rb +31 -0
  147. data/lib/bel_parser/language/version2_0/relationships/positive_correlation.rb +31 -0
  148. data/lib/bel_parser/language/version2_0/relationships/prognostic_biomarker_for.rb +35 -0
  149. data/lib/bel_parser/language/version2_0/relationships/rate_limiting_step_of.rb +31 -0
  150. data/lib/bel_parser/language/version2_0/relationships/reactant_in.rb +31 -0
  151. data/lib/bel_parser/language/version2_0/relationships/regulates.rb +31 -0
  152. data/lib/bel_parser/language/version2_0/relationships/sub_process_of.rb +31 -0
  153. data/lib/bel_parser/language/version2_0/relationships/transcribed_to.rb +31 -0
  154. data/lib/bel_parser/language/version2_0/relationships/translated_to.rb +31 -0
  155. data/lib/bel_parser/language/version2_0/relationships/translocates.rb +31 -0
  156. data/lib/bel_parser/language/{version1 → version2_0}/return_types/abundance.rb +1 -1
  157. data/lib/bel_parser/language/{version2 → version2_0}/return_types/activity.rb +1 -1
  158. data/lib/bel_parser/language/{version2 → version2_0}/return_types/any.rb +1 -1
  159. data/lib/bel_parser/language/{version2 → version2_0}/return_types/biological_process.rb +1 -1
  160. data/lib/bel_parser/language/{version1 → version2_0}/return_types/complex_abundance.rb +1 -1
  161. data/lib/bel_parser/language/{version2 → version2_0}/return_types/fragment.rb +1 -1
  162. data/lib/bel_parser/language/{version2 → version2_0}/return_types/from_location.rb +1 -1
  163. data/lib/bel_parser/language/{version2 → version2_0}/return_types/fusion.rb +1 -1
  164. data/lib/bel_parser/language/{version1 → version2_0}/return_types/gene_abundance.rb +1 -1
  165. data/lib/bel_parser/language/{version2 → version2_0}/return_types/list.rb +1 -1
  166. data/lib/bel_parser/language/{version2 → version2_0}/return_types/location.rb +1 -1
  167. data/lib/bel_parser/language/{version2 → version2_0}/return_types/micro_rna_abundance.rb +1 -1
  168. data/lib/bel_parser/language/{version2 → version2_0}/return_types/molecular_activity.rb +1 -1
  169. data/lib/bel_parser/language/{version2 → version2_0}/return_types/pathology.rb +1 -1
  170. data/lib/bel_parser/language/{version1 → version2_0}/return_types/products.rb +1 -1
  171. data/lib/bel_parser/language/{version1 → version2_0}/return_types/protein_abundance.rb +1 -1
  172. data/lib/bel_parser/language/{version2 → version2_0}/return_types/protein_modification.rb +1 -1
  173. data/lib/bel_parser/language/{version1 → version2_0}/return_types/reactants.rb +1 -1
  174. data/lib/bel_parser/language/{version2 → version2_0}/return_types/rna_abundance.rb +1 -1
  175. data/lib/bel_parser/language/{version2 → version2_0}/return_types/to_location.rb +1 -1
  176. data/lib/bel_parser/language/{version2 → version2_0}/return_types/variant.rb +1 -1
  177. data/lib/bel_parser/language/version2_0.rb +73 -0
  178. data/lib/bel_parser/language.rb +90 -2
  179. data/lib/bel_parser/parsers/ast/node.rb +11 -1
  180. metadata +172 -111
  181. data/lib/bel_parser/language/syntax/expression/incomplete_node.rb +0 -14
  182. data/lib/bel_parser/language/syntax/expression/invalid_term_function.rb +0 -22
  183. data/lib/bel_parser/language/version1.rb +0 -50
  184. data/lib/bel_parser/language/version2.rb +0 -50
data/lib/bel_parser/language/version1_0.rb ADDED
@@ -0,0 +1,89 @@
1
+ require_relative 'function'
2
+ require_relative 'specification'
3
+
4
+ module BELParser
5
+ module Language
6
+ module Version1_0
7
+ # Specification defines the BEL, version 1.0 specification.
8
+ class Specification
9
+ include BELParser::Language::Specification
10
+ def initialize
11
+ @version = '1.0'.freeze
12
+
13
+ # Collect return types
14
+ ret_classes = Version1_0::ReturnTypes.constants.collect do |symbol|
15
+ const = Version1_0::ReturnTypes.const_get(symbol)
16
+ const if const.respond_to?(:subtypes)
17
+ end
18
+ @return_types = ret_classes.compact
19
+ @indexed_return_types = index_sym(@return_types)
20
+
21
+ # Collect functions
22
+ function_classes = Version1_0::Functions.constants.collect do |symbol|
23
+ const = Version1_0::Functions.const_get(symbol)
24
+ const if
25
+ const.respond_to?(:short) &&
26
+ const.respond_to?(:long)
27
+ end
28
+ @functions = function_classes.compact
29
+ @indexed_functions = index_long_short(@functions)
30
+
31
+ # Collect relationships
32
+ rel_classes = Version1_0::Relationships.constants.collect do |symbol|
33
+ const = Version1_0::Relationships.const_get(symbol)
34
+ const if
35
+ const.respond_to?(:short) &&
36
+ const.respond_to?(:long)
37
+ end
38
+ @relationships = rel_classes.compact
39
+ @indexed_relationships = index_long_short(@relationships)
40
+
41
+ # Collect syntax checkers.
42
+ syntax_classes = Version1_0::Syntax.constants.collect do |symbol|
43
+ const = Version1_0::Syntax.const_get(symbol)
44
+ const if const.respond_to?(:match)
45
+ end
46
+ @syntax = syntax_classes.compact
47
+
48
+ freeze
49
+ end
50
+ end
51
+ end
52
+ end
53
+ end
54
+
55
+ # Require all version 1.0 return types
56
+ Dir[
57
+ File.join(
58
+ File.dirname(File.expand_path(__FILE__)),
59
+ 'version1_0', 'return_types', '*.rb')
60
+ ].each do |path|
61
+ require_relative "version1_0/return_types/#{File.basename(path)}"
62
+ end
63
+
64
+ # Require all version 1.0 functions.
65
+ Dir[
66
+ File.join(
67
+ File.dirname(File.expand_path(__FILE__)),
68
+ 'version1_0', 'functions', '*.rb')
69
+ ].each do |path|
70
+ require_relative "version1_0/functions/#{File.basename(path)}"
71
+ end
72
+
73
+ # Require all version 1.0 relationships.
74
+ Dir[
75
+ File.join(
76
+ File.dirname(File.expand_path(__FILE__)),
77
+ 'version1_0', 'relationships', '*.rb')
78
+ ].each do |path|
79
+ require_relative "version1_0/relationships/#{File.basename(path)}"
80
+ end
81
+
82
+ # Require all version 1.0 syntax checkers.
83
+ Dir[
84
+ File.join(
85
+ File.dirname(File.expand_path(__FILE__)),
86
+ 'version1_0', 'syntax', '*.rb')
87
+ ].each do |path|
88
+ require_relative "version1_0/syntax/#{File.basename(path)}"
89
+ end
data/lib/bel_parser/language/{version2 → version2_0}/functions/abundance.rb RENAMED
@@ -1,11 +1,11 @@
1
- require_relative '../../version1'
1
+ require_relative '../../version2_0'
2
2
  require_relative '../../function'
3
3
  require_relative '../../signature'
4
- require_relative '../../semantic_ast'
4
+ require_relative '../../semantics'
5
5
 
6
6
  module BELParser
7
7
  module Language
8
- module Version2
8
+ module Version2_0
9
9
  module Functions
10
10
  # Abundance: Denotes the abundance of an entity.
11
11
  class Abundance
@@ -13,7 +13,7 @@ module BELParser
13
13
 
14
14
  SHORT = :a
15
15
  LONG = :abundance
16
- RETURN_TYPE = BELParser::Language::Version2::ReturnTypes::Abundance
16
+ RETURN_TYPE = BELParser::Language::Version2_0::ReturnTypes::Abundance
17
17
  DESCRIPTION = 'Denotes the abundance of an entity.'.freeze
18
18
 
19
19
  def self.short
@@ -97,7 +97,7 @@ module BELParser
97
97
  term(
98
98
  function(
99
99
  identifier(
100
- return_type_of(BELParser::Language::Version2::ReturnTypes::Location))))))
100
+ return_type_of(BELParser::Language::Version2_0::ReturnTypes::Location))))))
101
101
  end
102
102
  private_constant :AST
103
103
 
@@ -137,7 +137,7 @@ module BELParser
137
137
  term(
138
138
  function(
139
139
  identifier(
140
- return_type_of(BELParser::Language::Version2::ReturnTypes::MolecularActivity))))))
140
+ return_type_of(BELParser::Language::Version2_0::ReturnTypes::MolecularActivity))))))
141
141
  end
142
142
  private_constant :AST
143
143
 
data/lib/bel_parser/language/{version2 → version2_0}/functions/activity.rb RENAMED
@@ -1,11 +1,11 @@
1
- require_relative '../../version2'
1
+ require_relative '../../version2_0'
2
2
  require_relative '../../function'
3
3
  require_relative '../../signature'
4
- require_relative '../../semantic_ast'
4
+ require_relative '../../semantics'
5
5
 
6
6
  module BELParser
7
7
  module Language
8
- module Version2
8
+ module Version2_0
9
9
  module Functions
10
10
  # Activity: Denotes the frequency or abundance of events in which a member acts as a causal agent at the molecular scale.
11
11
  class Activity
@@ -13,7 +13,7 @@ module BELParser
13
13
 
14
14
  SHORT = :act
15
15
  LONG = :activity
16
- RETURN_TYPE = BELParser::Language::Version2::ReturnTypes::Activity
16
+ RETURN_TYPE = BELParser::Language::Version2_0::ReturnTypes::Activity
17
17
  DESCRIPTION = 'Denotes the frequency or abundance of events in which a member acts as a causal agent at the molecular scale.'.freeze
18
18
 
19
19
  def self.short
@@ -52,7 +52,7 @@ module BELParser
52
52
  term(
53
53
  function(
54
54
  identifier(
55
- return_type_of(BELParser::Language::Version2::ReturnTypes::Abundance))))))
55
+ return_type_of(BELParser::Language::Version2_0::ReturnTypes::Abundance))))))
56
56
  end
57
57
  private_constant :AST
58
58
 
@@ -82,12 +82,12 @@ module BELParser
82
82
  term(
83
83
  function(
84
84
  identifier(
85
- return_type_of(BELParser::Language::Version2::ReturnTypes::Abundance))))),
85
+ return_type_of(BELParser::Language::Version2_0::ReturnTypes::Abundance))))),
86
86
  argument(
87
87
  term(
88
88
  function(
89
89
  identifier(
90
- return_type_of(BELParser::Language::Version2::ReturnTypes::MolecularActivity))))))
90
+ return_type_of(BELParser::Language::Version2_0::ReturnTypes::MolecularActivity))))))
91
91
  end
92
92
  private_constant :AST
93
93
 
data/lib/bel_parser/language/{version2 → version2_0}/functions/biological_process.rb RENAMED
@@ -1,11 +1,11 @@
1
- require_relative '../../version1'
1
+ require_relative '../../version2_0'
2
2
  require_relative '../../function'
3
3
  require_relative '../../signature'
4
- require_relative '../../semantic_ast'
4
+ require_relative '../../semantics'
5
5
 
6
6
  module BELParser
7
7
  module Language
8
- module Version2
8
+ module Version2_0
9
9
  module Functions
10
10
  # BiologicalProcess: Denotes a process or population of events.
11
11
  class BiologicalProcess
@@ -13,7 +13,7 @@ module BELParser
13
13
 
14
14
  SHORT = :bp
15
15
  LONG = :biologicalProcess
16
- RETURN_TYPE = BELParser::Language::Version2::ReturnTypes::BiologicalProcess
16
+ RETURN_TYPE = BELParser::Language::Version2_0::ReturnTypes::BiologicalProcess
17
17
  DESCRIPTION = 'Denotes a process or population of events.'.freeze
18
18
 
19
19
  def self.short
data/lib/bel_parser/language/{version2 → version2_0}/functions/cell_secretion.rb RENAMED
@@ -1,11 +1,11 @@
1
- require_relative '../../version1'
1
+ require_relative '../../version2_0'
2
2
  require_relative '../../function'
3
3
  require_relative '../../signature'
4
- require_relative '../../semantic_ast'
4
+ require_relative '../../semantics'
5
5
 
6
6
  module BELParser
7
7
  module Language
8
- module Version2
8
+ module Version2_0
9
9
  module Functions
10
10
  # CellSecretion: Denotes the frequency or abundance of events in which members of an abundance move from cells to regions outside of the cells.
11
11
  class CellSecretion
@@ -13,7 +13,7 @@ module BELParser
13
13
 
14
14
  SHORT = :sec
15
15
  LONG = :cellSecretion
16
- RETURN_TYPE = BELParser::Language::Version2::ReturnTypes::Abundance
16
+ RETURN_TYPE = BELParser::Language::Version2_0::ReturnTypes::Abundance
17
17
  DESCRIPTION = 'Denotes the frequency or abundance of events in which members of an abundance move from cells to regions outside of the cells.'.freeze
18
18
 
19
19
  def self.short
@@ -52,7 +52,7 @@ module BELParser
52
52
  term(
53
53
  function(
54
54
  identifier(
55
- return_type_of(BELParser::Language::Version2::ReturnTypes::Abundance))))))
55
+ return_type_of(BELParser::Language::Version2_0::ReturnTypes::Abundance))))))
56
56
  end
57
57
  private_constant :AST
58
58
 
data/lib/bel_parser/language/{version2 → version2_0}/functions/cell_surface_expression.rb RENAMED
@@ -1,11 +1,11 @@
1
- require_relative '../../version1'
1
+ require_relative '../../version2_0'
2
2
  require_relative '../../function'
3
3
  require_relative '../../signature'
4
- require_relative '../../semantic_ast'
4
+ require_relative '../../semantics'
5
5
 
6
6
  module BELParser
7
7
  module Language
8
- module Version2
8
+ module Version2_0
9
9
  module Functions
10
10
  # CellSurfaceExpression: Denotes the frequency or abundance of events in which members of an abundance move to the surface of cells.
11
11
  class CellSurfaceExpression
@@ -13,7 +13,7 @@ module BELParser
13
13
 
14
14
  SHORT = :surf
15
15
  LONG = :cellSurfaceExpression
16
- RETURN_TYPE = BELParser::Language::Version2::ReturnTypes::Abundance
16
+ RETURN_TYPE = BELParser::Language::Version2_0::ReturnTypes::Abundance
17
17
  DESCRIPTION = 'Denotes the frequency or abundance of events in which members of an abundance move to the surface of cells.'.freeze
18
18
 
19
19
  def self.short
@@ -52,7 +52,7 @@ module BELParser
52
52
  term(
53
53
  function(
54
54
  identifier(
55
- return_type_of(BELParser::Language::Version2::ReturnTypes::Abundance))))))
55
+ return_type_of(BELParser::Language::Version2_0::ReturnTypes::Abundance))))))
56
56
  end
57
57
  private_constant :AST
58
58
 
data/lib/bel_parser/language/{version2 → version2_0}/functions/complex_abundance.rb RENAMED
@@ -1,11 +1,11 @@
1
- require_relative '../../version1'
1
+ require_relative '../../version2_0'
2
2
  require_relative '../../function'
3
3
  require_relative '../../signature'
4
- require_relative '../../semantic_ast'
4
+ require_relative '../../semantics'
5
5
 
6
6
  module BELParser
7
7
  module Language
8
- module Version2
8
+ module Version2_0
9
9
  module Functions
10
10
  # ComplexAbundance: Denotes the abundance of a molecular complex.
11
11
  class ComplexAbundance
@@ -13,7 +13,7 @@ module BELParser
13
13
 
14
14
  SHORT = :complex
15
15
  LONG = :complexAbundance
16
- RETURN_TYPE = BELParser::Language::Version2::ReturnTypes::ComplexAbundance
16
+ RETURN_TYPE = BELParser::Language::Version2_0::ReturnTypes::ComplexAbundance
17
17
  DESCRIPTION = 'Denotes the abundance of a molecular complex.'.freeze
18
18
 
19
19
  def self.short
@@ -97,7 +97,7 @@ module BELParser
97
97
  term(
98
98
  function(
99
99
  identifier(
100
- return_type_of(BELParser::Language::Version2::ReturnTypes::Location))))))
100
+ return_type_of(BELParser::Language::Version2_0::ReturnTypes::Location))))))
101
101
  end
102
102
  private_constant :AST
103
103
 
@@ -127,7 +127,7 @@ module BELParser
127
127
  term(
128
128
  function(
129
129
  identifier(
130
- return_type_of(BELParser::Language::Version2::ReturnTypes::Abundance))))))
130
+ return_type_of(BELParser::Language::Version2_0::ReturnTypes::Abundance))))))
131
131
  end
132
132
  private_constant :AST
133
133
 
@@ -157,12 +157,12 @@ module BELParser
157
157
  term(
158
158
  function(
159
159
  identifier(
160
- return_type_of(BELParser::Language::Version2::ReturnTypes::Abundance))))),
160
+ return_type_of(BELParser::Language::Version2_0::ReturnTypes::Abundance))))),
161
161
  argument(
162
162
  term(
163
163
  function(
164
164
  identifier(
165
- return_type_of(BELParser::Language::Version2::ReturnTypes::Location))))))
165
+ return_type_of(BELParser::Language::Version2_0::ReturnTypes::Location))))))
166
166
  end
167
167
  private_constant :AST
168
168
 
data/lib/bel_parser/language/{version2 → version2_0}/functions/composite_abundance.rb RENAMED
@@ -1,11 +1,11 @@
1
- require_relative '../../version1'
1
+ require_relative '../../version2_0'
2
2
  require_relative '../../function'
3
3
  require_relative '../../signature'
4
- require_relative '../../semantic_ast'
4
+ require_relative '../../semantics'
5
5
 
6
6
  module BELParser
7
7
  module Language
8
- module Version2
8
+ module Version2_0
9
9
  module Functions
10
10
  # CompositeAbundance: Denotes the frequency or abundance of events in which members are present.
11
11
  class CompositeAbundance
@@ -13,7 +13,7 @@ module BELParser
13
13
 
14
14
  SHORT = :composite
15
15
  LONG = :compositeAbundance
16
- RETURN_TYPE = BELParser::Language::Version2::ReturnTypes::Abundance
16
+ RETURN_TYPE = BELParser::Language::Version2_0::ReturnTypes::Abundance
17
17
  DESCRIPTION = 'Denotes the frequency or abundance of events in which members are present.'.freeze
18
18
 
19
19
  def self.short
@@ -52,7 +52,7 @@ module BELParser
52
52
  term(
53
53
  function(
54
54
  identifier(
55
- return_type_of(BELParser::Language::Version2::ReturnTypes::Abundance))))))
55
+ return_type_of(BELParser::Language::Version2_0::ReturnTypes::Abundance))))))
56
56
  end
57
57
  private_constant :AST
58
58
 
data/lib/bel_parser/language/{version2 → version2_0}/functions/degradation.rb RENAMED
@@ -1,11 +1,11 @@
1
- require_relative '../../version1'
1
+ require_relative '../../version2_0'
2
2
  require_relative '../../function'
3
3
  require_relative '../../signature'
4
- require_relative '../../semantic_ast'
4
+ require_relative '../../semantics'
5
5
 
6
6
  module BELParser
7
7
  module Language
8
- module Version2
8
+ module Version2_0
9
9
  module Functions
10
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.
11
11
  class Degradation
@@ -13,7 +13,7 @@ module BELParser
13
13
 
14
14
  SHORT = :deg
15
15
  LONG = :degradation
16
- RETURN_TYPE = BELParser::Language::Version2::ReturnTypes::Abundance
16
+ RETURN_TYPE = BELParser::Language::Version2_0::ReturnTypes::Abundance
17
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
18
18
 
19
19
  def self.short
@@ -52,7 +52,7 @@ module BELParser
52
52
  term(
53
53
  function(
54
54
  identifier(
55
- return_type_of(BELParser::Language::Version2::ReturnTypes::Abundance))))))
55
+ return_type_of(BELParser::Language::Version2_0::ReturnTypes::Abundance))))))
56
56
  end
57
57
  private_constant :AST
58
58
 
data/lib/bel_parser/language/{version2 → version2_0}/functions/fragment.rb RENAMED
@@ -1,11 +1,11 @@
1
- require_relative '../../version1'
1
+ require_relative '../../version2_0'
2
2
  require_relative '../../function'
3
3
  require_relative '../../signature'
4
- require_relative '../../semantic_ast'
4
+ require_relative '../../semantics'
5
5
 
6
6
  module BELParser
7
7
  module Language
8
- module Version2
8
+ module Version2_0
9
9
  module Functions
10
10
  # Fragment: Denotes a protein fragment, e.g., a product of proteolytic cleavage.
11
11
  class Fragment
@@ -13,7 +13,7 @@ module BELParser
13
13
 
14
14
  SHORT = :frag
15
15
  LONG = :fragment
16
- RETURN_TYPE = BELParser::Language::Version2::ReturnTypes::Fragment
16
+ RETURN_TYPE = BELParser::Language::Version2_0::ReturnTypes::Fragment
17
17
  DESCRIPTION = 'Denotes a protein fragment, e.g., a product of proteolytic cleavage.'.freeze
18
18
 
19
19
  def self.short
data/lib/bel_parser/language/{version2 → version2_0}/functions/from_location.rb RENAMED
@@ -1,11 +1,11 @@
1
- require_relative '../../version1'
1
+ require_relative '../../version2_0'
2
2
  require_relative '../../function'
3
3
  require_relative '../../signature'
4
- require_relative '../../semantic_ast'
4
+ require_relative '../../semantics'
5
5
 
6
6
  module BELParser
7
7
  module Language
8
- module Version2
8
+ module Version2_0
9
9
  module Functions
10
10
  # FromLocation: Denotes the from cellular location of the abundance.
11
11
  class FromLocation
@@ -13,7 +13,7 @@ module BELParser
13
13
 
14
14
  SHORT = :fromLoc
15
15
  LONG = :fromLocation
16
- RETURN_TYPE = BELParser::Language::Version2::ReturnTypes::FromLocation
16
+ RETURN_TYPE = BELParser::Language::Version2_0::ReturnTypes::FromLocation
17
17
  DESCRIPTION = 'Denotes the from cellular location of the abundance.'.freeze
18
18
 
19
19
  def self.short
data/lib/bel_parser/language/{version2 → version2_0}/functions/fusion.rb RENAMED
@@ -1,11 +1,11 @@
1
- require_relative '../../version1'
1
+ require_relative '../../version2_0'
2
2
  require_relative '../../function'
3
3
  require_relative '../../signature'
4
- require_relative '../../semantic_ast'
4
+ require_relative '../../semantics'
5
5
 
6
6
  module BELParser
7
7
  module Language
8
- module Version2
8
+ module Version2_0
9
9
  module Functions
10
10
  # Fusion: Specifies the abundance of a protein translated from the fusion of a gene.
11
11
  class Fusion
@@ -13,7 +13,7 @@ module BELParser
13
13
 
14
14
  SHORT = :fus
15
15
  LONG = :fusion
16
- RETURN_TYPE = BELParser::Language::Version2::ReturnTypes::Fusion
16
+ RETURN_TYPE = BELParser::Language::Version2_0::ReturnTypes::Fusion
17
17
  DESCRIPTION = 'Specifies the abundance of a protein translated from the fusion of a gene.'.freeze
18
18
 
19
19
  def self.short
data/lib/bel_parser/language/{version2 → version2_0}/functions/gene_abundance.rb RENAMED
@@ -1,11 +1,11 @@
1
- require_relative '../../version1'
1
+ require_relative '../../version2_0'
2
2
  require_relative '../../function'
3
3
  require_relative '../../signature'
4
- require_relative '../../semantic_ast'
4
+ require_relative '../../semantics'
5
5
 
6
6
  module BELParser
7
7
  module Language
8
- module Version2
8
+ module Version2_0
9
9
  module Functions
10
10
  # GeneAbundance: Denotes the abundance of a gene.
11
11
  class GeneAbundance
@@ -13,7 +13,7 @@ module BELParser
13
13
 
14
14
  SHORT = :g
15
15
  LONG = :geneAbundance
16
- RETURN_TYPE = BELParser::Language::Version2::ReturnTypes::GeneAbundance
16
+ RETURN_TYPE = BELParser::Language::Version2_0::ReturnTypes::GeneAbundance
17
17
  DESCRIPTION = 'Denotes the abundance of a gene.'.freeze
18
18
 
19
19
  def self.short
@@ -87,7 +87,7 @@ module BELParser
87
87
  term(
88
88
  function(
89
89
  identifier(
90
- return_type_of(BELParser::Language::Version2::ReturnTypes::Fusion))))))
90
+ return_type_of(BELParser::Language::Version2_0::ReturnTypes::Fusion))))))
91
91
  end
92
92
  private_constant :AST
93
93
 
@@ -127,7 +127,7 @@ module BELParser
127
127
  term(
128
128
  function(
129
129
  identifier(
130
- return_type_of(BELParser::Language::Version2::ReturnTypes::Location))))))
130
+ return_type_of(BELParser::Language::Version2_0::ReturnTypes::Location))))))
131
131
  end
132
132
  private_constant :AST
133
133
 
@@ -167,7 +167,7 @@ module BELParser
167
167
  term(
168
168
  function(
169
169
  identifier(
170
- return_type_of(BELParser::Language::Version2::ReturnTypes::Variant))))))
170
+ return_type_of(BELParser::Language::Version2_0::ReturnTypes::Variant))))))
171
171
  end
172
172
  private_constant :AST
173
173
 
data/lib/bel_parser/language/{version2 → version2_0}/functions/list.rb RENAMED
@@ -1,11 +1,11 @@
1
- require_relative '../../version1'
1
+ require_relative '../../version2_0'
2
2
  require_relative '../../function'
3
3
  require_relative '../../signature'
4
- require_relative '../../semantic_ast'
4
+ require_relative '../../semantics'
5
5
 
6
6
  module BELParser
7
7
  module Language
8
- module Version2
8
+ module Version2_0
9
9
  module Functions
10
10
  # List: Groups a list of terms together.
11
11
  class List
@@ -13,7 +13,7 @@ module BELParser
13
13
 
14
14
  SHORT = :list
15
15
  LONG = :list
16
- RETURN_TYPE = BELParser::Language::Version2::ReturnTypes::List
16
+ RETURN_TYPE = BELParser::Language::Version2_0::ReturnTypes::List
17
17
  DESCRIPTION = 'Groups a list of terms together.'.freeze
18
18
 
19
19
  def self.short
@@ -87,7 +87,7 @@ module BELParser
87
87
  term(
88
88
  function(
89
89
  identifier(
90
- return_type_of(BELParser::Language::Version2::ReturnTypes::Abundance))))))
90
+ return_type_of(BELParser::Language::Version2_0::ReturnTypes::Abundance))))))
91
91
  end
92
92
  private_constant :AST
93
93
 
data/lib/bel_parser/language/{version2 → version2_0}/functions/location.rb RENAMED
@@ -1,11 +1,11 @@
1
- require_relative '../../version1'
1
+ require_relative '../../version2_0'
2
2
  require_relative '../../function'
3
3
  require_relative '../../signature'
4
- require_relative '../../semantic_ast'
4
+ require_relative '../../semantics'
5
5
 
6
6
  module BELParser
7
7
  module Language
8
- module Version2
8
+ module Version2_0
9
9
  module Functions
10
10
  # Location: Denotes the cellular location of the abundance.
11
11
  class Location
@@ -13,7 +13,7 @@ module BELParser
13
13
 
14
14
  SHORT = :loc
15
15
  LONG = :location
16
- RETURN_TYPE = BELParser::Language::Version2::ReturnTypes::Location
16
+ RETURN_TYPE = BELParser::Language::Version2_0::ReturnTypes::Location
17
17
  DESCRIPTION = 'Denotes the cellular location of the abundance.'.freeze
18
18
 
19
19
  def self.short
data/lib/bel_parser/language/{version2 → version2_0}/functions/micro_rna_abundance.rb RENAMED
@@ -1,11 +1,11 @@
1
- require_relative '../../version1'
1
+ require_relative '../../version2_0'
2
2
  require_relative '../../function'
3
3
  require_relative '../../signature'
4
- require_relative '../../semantic_ast'
4
+ require_relative '../../semantics'
5
5
 
6
6
  module BELParser
7
7
  module Language
8
- module Version2
8
+ module Version2_0
9
9
  module Functions
10
10
  # MicroRNAAbundance: Denotes the abundance of a processed, functional microRNA
11
11
  class MicroRNAAbundance
@@ -13,7 +13,7 @@ module BELParser
13
13
 
14
14
  SHORT = :m
15
15
  LONG = :microRNAAbundance
16
- RETURN_TYPE = BELParser::Language::Version2::ReturnTypes::MicroRNAAbundance
16
+ RETURN_TYPE = BELParser::Language::Version2_0::ReturnTypes::MicroRNAAbundance
17
17
  DESCRIPTION = 'Denotes the abundance of a processed, functional microRNA'.freeze
18
18
 
19
19
  def self.short
@@ -97,7 +97,7 @@ module BELParser
97
97
  term(
98
98
  function(
99
99
  identifier(
100
- return_type_of(BELParser::Language::Version2::ReturnTypes::Location))))))
100
+ return_type_of(BELParser::Language::Version2_0::ReturnTypes::Location))))))
101
101
  end
102
102
  private_constant :AST
103
103
 
@@ -137,7 +137,7 @@ module BELParser
137
137
  term(
138
138
  function(
139
139
  identifier(
140
- return_type_of(BELParser::Language::Version2::ReturnTypes::Variant))))))
140
+ return_type_of(BELParser::Language::Version2_0::ReturnTypes::Variant))))))
141
141
  end
142
142
  private_constant :AST
143
143
 
data/lib/bel_parser/language/{version2 → version2_0}/functions/molecular_activity.rb RENAMED
@@ -1,11 +1,11 @@
1
- require_relative '../../version1'
1
+ require_relative '../../version2_0'
2
2
  require_relative '../../function'
3
3
  require_relative '../../signature'
4
- require_relative '../../semantic_ast'
4
+ require_relative '../../semantics'
5
5
 
6
6
  module BELParser
7
7
  module Language
8
- module Version2
8
+ module Version2_0
9
9
  module Functions
10
10
  # MolecularActivity: Denotes the frequency or abundance of events in which a member acts as a causal agent at the molecular scale
11
11
  class MolecularActivity
@@ -13,7 +13,7 @@ module BELParser
13
13
 
14
14
  SHORT = :ma
15
15
  LONG = :molecularActivity
16
- RETURN_TYPE = BELParser::Language::Version2::ReturnTypes::MolecularActivity
16
+ RETURN_TYPE = BELParser::Language::Version2_0::ReturnTypes::MolecularActivity
17
17
  DESCRIPTION = 'Denotes the frequency or abundance of events in which a member acts as a causal agent at the molecular scale'.freeze
18
18
 
19
19
  def self.short
data/lib/bel_parser/language/{version1 → version2_0}/functions/pathology.rb RENAMED
@@ -1,11 +1,11 @@
1
- require_relative '../../version1'
1
+ require_relative '../../version2_0'
2
2
  require_relative '../../function'
3
3
  require_relative '../../signature'
4
- require_relative '../../semantic_ast'
4
+ require_relative '../../semantics'
5
5
 
6
6
  module BELParser
7
7
  module Language
8
- module Version1
8
+ module Version2_0
9
9
  module Functions
10
10
  # Pathology: Denotes a disease or pathology process
11
11
  class Pathology
@@ -13,7 +13,7 @@ module BELParser
13
13
 
14
14
  SHORT = :path
15
15
  LONG = :pathology
16
- RETURN_TYPE = BELParser::Language::Version1::ReturnTypes::Pathology
16
+ RETURN_TYPE = BELParser::Language::Version2_0::ReturnTypes::Pathology
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17
  DESCRIPTION = 'Denotes a disease or pathology process'.freeze
18
18
 
19
19
  def self.short