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 → version1_0}/functions/gene_abundance.rb RENAMED
@@ -1,11 +1,11 @@
1
- require_relative '../../version1'
1
+ require_relative '../../version1_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 Version1_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::Version1::ReturnTypes::GeneAbundance
16
+ RETURN_TYPE = BELParser::Language::Version1_0::ReturnTypes::GeneAbundance
17
17
  DESCRIPTION = 'Denotes the abundance of a gene'.freeze
18
18
 
19
19
  def self.short
@@ -62,7 +62,7 @@ module BELParser
62
62
  term(
63
63
  function(
64
64
  identifier(
65
- return_type_of(BELParser::Language::Version1::ReturnTypes::Fusion))))))
65
+ return_type_of(BELParser::Language::Version1_0::ReturnTypes::Fusion))))))
66
66
  end
67
67
  private_constant :AST
68
68
 
data/lib/bel_parser/language/{version1 → version1_0}/functions/gtp_bound_activity.rb RENAMED
@@ -1,11 +1,11 @@
1
- require_relative '../../version1'
1
+ require_relative '../../version1_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 Version1_0
9
9
  module Functions
10
10
  # GTPBoundActivity: Denotes the frequency or abundance of events in which a member of a G-protein abundance is GTP-bound
11
11
  class GTPBoundActivity
@@ -13,7 +13,7 @@ module BELParser
13
13
 
14
14
  SHORT = :gtp
15
15
  LONG = :gtpBoundActivity
16
- RETURN_TYPE = BELParser::Language::Version1::ReturnTypes::GTPBoundActivity
16
+ RETURN_TYPE = BELParser::Language::Version1_0::ReturnTypes::GTPBoundActivity
17
17
  DESCRIPTION = 'Denotes the frequency or abundance of events in which a member of a G-protein abundance is GTP-bound'.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::Version1::ReturnTypes::ComplexAbundance))))))
55
+ return_type_of(BELParser::Language::Version1_0::ReturnTypes::ComplexAbundance))))))
56
56
  end
57
57
  private_constant :AST
58
58
 
@@ -82,7 +82,7 @@ module BELParser
82
82
  term(
83
83
  function(
84
84
  identifier(
85
- return_type_of(BELParser::Language::Version1::ReturnTypes::ProteinAbundance))))))
85
+ return_type_of(BELParser::Language::Version1_0::ReturnTypes::ProteinAbundance))))))
86
86
  end
87
87
  private_constant :AST
88
88
 
data/lib/bel_parser/language/{version1 → version1_0}/functions/kinase_activity.rb RENAMED
@@ -1,11 +1,11 @@
1
- require_relative '../../version1'
1
+ require_relative '../../version1_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 Version1_0
9
9
  module Functions
10
10
  # KinaseActivity: Denotes the frequency or abundance of events in which a member acts as a kinase, performing enzymatic phosphorylation of a substrate
11
11
  class KinaseActivity
@@ -13,7 +13,7 @@ module BELParser
13
13
 
14
14
  SHORT = :kin
15
15
  LONG = :kinaseActivity
16
- RETURN_TYPE = BELParser::Language::Version1::ReturnTypes::KinaseActivity
16
+ RETURN_TYPE = BELParser::Language::Version1_0::ReturnTypes::KinaseActivity
17
17
  DESCRIPTION = 'Denotes the frequency or abundance of events in which a member acts as a kinase, performing enzymatic phosphorylation of a substrate'.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::Version1::ReturnTypes::ComplexAbundance))))))
55
+ return_type_of(BELParser::Language::Version1_0::ReturnTypes::ComplexAbundance))))))
56
56
  end
57
57
  private_constant :AST
58
58
 
@@ -82,7 +82,7 @@ module BELParser
82
82
  term(
83
83
  function(
84
84
  identifier(
85
- return_type_of(BELParser::Language::Version1::ReturnTypes::ProteinAbundance))))))
85
+ return_type_of(BELParser::Language::Version1_0::ReturnTypes::ProteinAbundance))))))
86
86
  end
87
87
  private_constant :AST
88
88
 
data/lib/bel_parser/language/{version1 → version1_0}/functions/list.rb RENAMED
@@ -1,11 +1,11 @@
1
- require_relative '../../version1'
1
+ require_relative '../../version1_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 Version1_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::Version1::ReturnTypes::List
16
+ RETURN_TYPE = BELParser::Language::Version1_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::Version1::ReturnTypes::Abundance))))))
90
+ return_type_of(BELParser::Language::Version1_0::ReturnTypes::Abundance))))))
91
91
  end
92
92
  private_constant :AST
93
93
 
data/lib/bel_parser/language/{version1 → version1_0}/functions/micro_rna_abundance.rb RENAMED
@@ -1,11 +1,11 @@
1
- require_relative '../../version1'
1
+ require_relative '../../version1_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 Version1_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::Version1::ReturnTypes::MicroRNAAbundance
16
+ RETURN_TYPE = BELParser::Language::Version1_0::ReturnTypes::MicroRNAAbundance
17
17
  DESCRIPTION = 'Denotes the abundance of a processed, functional microRNA'.freeze
18
18
 
19
19
  def self.short
data/lib/bel_parser/language/{version1 → version1_0}/functions/molecular_activity.rb RENAMED
@@ -1,11 +1,11 @@
1
- require_relative '../../version1'
1
+ require_relative '../../version1_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 Version1_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 = :act
15
15
  LONG = :molecularActivity
16
- RETURN_TYPE = BELParser::Language::Version1::ReturnTypes::MolecularActivity
16
+ RETURN_TYPE = BELParser::Language::Version1_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
@@ -52,7 +52,7 @@ module BELParser
52
52
  term(
53
53
  function(
54
54
  identifier(
55
- return_type_of(BELParser::Language::Version1::ReturnTypes::Abundance))))))
55
+ return_type_of(BELParser::Language::Version1_0::ReturnTypes::Abundance))))))
56
56
  end
57
57
  private_constant :AST
58
58
 
data/lib/bel_parser/language/{version2 → version1_0}/functions/pathology.rb RENAMED
@@ -1,11 +1,11 @@
1
- require_relative '../../version1'
1
+ require_relative '../../version1_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 Version1_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::Version2::ReturnTypes::Pathology
16
+ RETURN_TYPE = BELParser::Language::Version1_0::ReturnTypes::Pathology
17
17
  DESCRIPTION = 'Denotes a disease or pathology process'.freeze
18
18
 
19
19
  def self.short
data/lib/bel_parser/language/{version1 → version1_0}/functions/peptidase_activity.rb RENAMED
@@ -1,11 +1,11 @@
1
- require_relative '../../version1'
1
+ require_relative '../../version1_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 Version1_0
9
9
  module Functions
10
10
  # PeptidaseActivity: Denotes the frequency or abundance of events in which a member acts to cleave a protein
11
11
  class PeptidaseActivity
@@ -13,7 +13,7 @@ module BELParser
13
13
 
14
14
  SHORT = :pep
15
15
  LONG = :peptidaseActivity
16
- RETURN_TYPE = BELParser::Language::Version1::ReturnTypes::PeptidaseActivity
16
+ RETURN_TYPE = BELParser::Language::Version1_0::ReturnTypes::PeptidaseActivity
17
17
  DESCRIPTION = 'Denotes the frequency or abundance of events in which a member acts to cleave a protein'.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::Version1::ReturnTypes::ComplexAbundance))))))
55
+ return_type_of(BELParser::Language::Version1_0::ReturnTypes::ComplexAbundance))))))
56
56
  end
57
57
  private_constant :AST
58
58
 
@@ -82,7 +82,7 @@ module BELParser
82
82
  term(
83
83
  function(
84
84
  identifier(
85
- return_type_of(BELParser::Language::Version1::ReturnTypes::ProteinAbundance))))))
85
+ return_type_of(BELParser::Language::Version1_0::ReturnTypes::ProteinAbundance))))))
86
86
  end
87
87
  private_constant :AST
88
88
 
data/lib/bel_parser/language/{version1 → version1_0}/functions/phosphatase_activity.rb RENAMED
@@ -1,11 +1,11 @@
1
- require_relative '../../version1'
1
+ require_relative '../../version1_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 Version1_0
9
9
  module Functions
10
10
  # PhosphataseActivity: Denotes the frequency or abundance of events in which a member acts as a phosphatase
11
11
  class PhosphataseActivity
@@ -13,7 +13,7 @@ module BELParser
13
13
 
14
14
  SHORT = :phos
15
15
  LONG = :phosphataseActivity
16
- RETURN_TYPE = BELParser::Language::Version1::ReturnTypes::PhosphataseActivity
16
+ RETURN_TYPE = BELParser::Language::Version1_0::ReturnTypes::PhosphataseActivity
17
17
  DESCRIPTION = 'Denotes the frequency or abundance of events in which a member acts as a phosphatase'.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::Version1::ReturnTypes::ComplexAbundance))))))
55
+ return_type_of(BELParser::Language::Version1_0::ReturnTypes::ComplexAbundance))))))
56
56
  end
57
57
  private_constant :AST
58
58
 
@@ -82,7 +82,7 @@ module BELParser
82
82
  term(
83
83
  function(
84
84
  identifier(
85
- return_type_of(BELParser::Language::Version1::ReturnTypes::ProteinAbundance))))))
85
+ return_type_of(BELParser::Language::Version1_0::ReturnTypes::ProteinAbundance))))))
86
86
  end
87
87
  private_constant :AST
88
88
 
data/lib/bel_parser/language/{version2 → version1_0}/functions/products.rb RENAMED
@@ -1,11 +1,11 @@
1
- require_relative '../../version1'
1
+ require_relative '../../version1_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 Version1_0
9
9
  module Functions
10
10
  # Products: Denotes the products of a reaction
11
11
  class Products
@@ -13,7 +13,7 @@ module BELParser
13
13
 
14
14
  SHORT = :products
15
15
  LONG = :products
16
- RETURN_TYPE = BELParser::Language::Version2::ReturnTypes::Products
16
+ RETURN_TYPE = BELParser::Language::Version1_0::ReturnTypes::Products
17
17
  DESCRIPTION = 'Denotes the products of a reaction'.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::Version1_0::ReturnTypes::Abundance))))))
56
56
  end
57
57
  private_constant :AST
58
58
 
data/lib/bel_parser/language/{version1 → version1_0}/functions/protein_abundance.rb RENAMED
@@ -1,11 +1,11 @@
1
- require_relative '../../version1'
1
+ require_relative '../../version1_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 Version1_0
9
9
  module Functions
10
10
  # ProteinAbundance: Denotes the abundance of a protein
11
11
  class ProteinAbundance
@@ -13,7 +13,7 @@ module BELParser
13
13
 
14
14
  SHORT = :p
15
15
  LONG = :proteinAbundance
16
- RETURN_TYPE = BELParser::Language::Version1::ReturnTypes::ProteinAbundance
16
+ RETURN_TYPE = BELParser::Language::Version1_0::ReturnTypes::ProteinAbundance
17
17
  DESCRIPTION = 'Denotes the abundance of a protein'.freeze
18
18
 
19
19
  def self.short
@@ -62,7 +62,7 @@ module BELParser
62
62
  term(
63
63
  function(
64
64
  identifier(
65
- return_type_of(BELParser::Language::Version1::ReturnTypes::Fusion))))))
65
+ return_type_of(BELParser::Language::Version1_0::ReturnTypes::Fusion))))))
66
66
  end
67
67
  private_constant :AST
68
68
 
@@ -102,7 +102,7 @@ module BELParser
102
102
  term(
103
103
  function(
104
104
  identifier(
105
- return_type_of(BELParser::Language::Version1::ReturnTypes::ProteinModification))))))
105
+ return_type_of(BELParser::Language::Version1_0::ReturnTypes::ProteinModification))))))
106
106
  end
107
107
  private_constant :AST
108
108
 
@@ -142,7 +142,7 @@ module BELParser
142
142
  term(
143
143
  function(
144
144
  identifier(
145
- return_type_of(BELParser::Language::Version1::ReturnTypes::Substitution))))))
145
+ return_type_of(BELParser::Language::Version1_0::ReturnTypes::Substitution))))))
146
146
  end
147
147
  private_constant :AST
148
148
 
@@ -182,7 +182,7 @@ module BELParser
182
182
  term(
183
183
  function(
184
184
  identifier(
185
- return_type_of(BELParser::Language::Version1::ReturnTypes::Truncation))))))
185
+ return_type_of(BELParser::Language::Version1_0::ReturnTypes::Truncation))))))
186
186
  end
187
187
  private_constant :AST
188
188
 
data/lib/bel_parser/language/{version1 → version1_0}/functions/protein_modification.rb RENAMED
@@ -1,11 +1,11 @@
1
- require_relative '../../version1'
1
+ require_relative '../../version1_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 Version1_0
9
9
  module Functions
10
10
  # ProteinModification: Denotes a covalently modified protein abundance
11
11
  class ProteinModification
@@ -13,7 +13,7 @@ module BELParser
13
13
 
14
14
  SHORT = :pmod
15
15
  LONG = :proteinModification
16
- RETURN_TYPE = BELParser::Language::Version1::ReturnTypes::ProteinModification
16
+ RETURN_TYPE = BELParser::Language::Version1_0::ReturnTypes::ProteinModification
17
17
  DESCRIPTION = 'Denotes a covalently modified protein abundance'.freeze
18
18
 
19
19
  def self.short
data/lib/bel_parser/language/{version2 → version1_0}/functions/reactants.rb RENAMED
@@ -1,11 +1,11 @@
1
- require_relative '../../version1'
1
+ require_relative '../../version1_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 Version1_0
9
9
  module Functions
10
10
  # Reactants: Denotes the reactants of a reaction
11
11
  class Reactants
@@ -13,7 +13,7 @@ module BELParser
13
13
 
14
14
  SHORT = :reactants
15
15
  LONG = :reactants
16
- RETURN_TYPE = BELParser::Language::Version2::ReturnTypes::Reactants
16
+ RETURN_TYPE = BELParser::Language::Version1_0::ReturnTypes::Reactants
17
17
  DESCRIPTION = 'Denotes the reactants of a reaction'.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::Version1_0::ReturnTypes::Abundance))))))
56
56
  end
57
57
  private_constant :AST
58
58
 
data/lib/bel_parser/language/{version1 → version1_0}/functions/reaction.rb RENAMED
@@ -1,11 +1,11 @@
1
- require_relative '../../version1'
1
+ require_relative '../../version1_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 Version1_0
9
9
  module Functions
10
10
  # Reaction: Denotes the frequency or abundance of events in a reaction
11
11
  class Reaction
@@ -13,7 +13,7 @@ module BELParser
13
13
 
14
14
  SHORT = :rxn
15
15
  LONG = :reaction
16
- RETURN_TYPE = BELParser::Language::Version1::ReturnTypes::Abundance
16
+ RETURN_TYPE = BELParser::Language::Version1_0::ReturnTypes::Abundance
17
17
  DESCRIPTION = 'Denotes the frequency or abundance of events in a reaction'.freeze
18
18
 
19
19
  def self.short
@@ -52,12 +52,12 @@ module BELParser
52
52
  term(
53
53
  function(
54
54
  identifier(
55
- return_type_of(BELParser::Language::Version1::ReturnTypes::Reactants))))),
55
+ return_type_of(BELParser::Language::Version1_0::ReturnTypes::Reactants))))),
56
56
  argument(
57
57
  term(
58
58
  function(
59
59
  identifier(
60
- return_type_of(BELParser::Language::Version1::ReturnTypes::Products))))))
60
+ return_type_of(BELParser::Language::Version1_0::ReturnTypes::Products))))))
61
61
  end
62
62
  private_constant :AST
63
63
 
data/lib/bel_parser/language/{version1 → version1_0}/functions/ribosylation_activity.rb RENAMED
@@ -1,11 +1,11 @@
1
- require_relative '../../version1'
1
+ require_relative '../../version1_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 Version1_0
9
9
  module Functions
10
10
  # RibosylationActivity: Denotes the frequency or abundance of events in which a member acts to perform post-translational modification of proteins
11
11
  class RibosylationActivity
@@ -13,7 +13,7 @@ module BELParser
13
13
 
14
14
  SHORT = :ribo
15
15
  LONG = :ribosylationActivity
16
- RETURN_TYPE = BELParser::Language::Version1::ReturnTypes::RibosylationActivity
16
+ RETURN_TYPE = BELParser::Language::Version1_0::ReturnTypes::RibosylationActivity
17
17
  DESCRIPTION = 'Denotes the frequency or abundance of events in which a member acts to perform post-translational modification of proteins'.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::Version1::ReturnTypes::ComplexAbundance))))))
55
+ return_type_of(BELParser::Language::Version1_0::ReturnTypes::ComplexAbundance))))))
56
56
  end
57
57
  private_constant :AST
58
58
 
@@ -82,7 +82,7 @@ module BELParser
82
82
  term(
83
83
  function(
84
84
  identifier(
85
- return_type_of(BELParser::Language::Version1::ReturnTypes::ProteinAbundance))))))
85
+ return_type_of(BELParser::Language::Version1_0::ReturnTypes::ProteinAbundance))))))
86
86
  end
87
87
  private_constant :AST
88
88
 
data/lib/bel_parser/language/{version1 → version1_0}/functions/rna_abundance.rb RENAMED
@@ -1,11 +1,11 @@
1
- require_relative '../../version1'
1
+ require_relative '../../version1_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 Version1_0
9
9
  module Functions
10
10
  # RNAAbundance: Denotes the abundance of a gene
11
11
  class RNAAbundance
@@ -13,7 +13,7 @@ module BELParser
13
13
 
14
14
  SHORT = :r
15
15
  LONG = :rnaAbundance
16
- RETURN_TYPE = BELParser::Language::Version1::ReturnTypes::GeneAbundance
16
+ RETURN_TYPE = BELParser::Language::Version1_0::ReturnTypes::GeneAbundance
17
17
  DESCRIPTION = 'Denotes the abundance of a gene'.freeze
18
18
 
19
19
  def self.short
@@ -62,7 +62,7 @@ module BELParser
62
62
  term(
63
63
  function(
64
64
  identifier(
65
- return_type_of(BELParser::Language::Version1::ReturnTypes::Fusion))))))
65
+ return_type_of(BELParser::Language::Version1_0::ReturnTypes::Fusion))))))
66
66
  end
67
67
  private_constant :AST
68
68
 
data/lib/bel_parser/language/{version1 → version1_0}/functions/substitution.rb RENAMED
@@ -1,11 +1,11 @@
1
- require_relative '../../version1'
1
+ require_relative '../../version1_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 Version1_0
9
9
  module Functions
10
10
  # Substitution: Indicates the abundance of proteins with amino acid substitution sequence
11
11
  class Substitution
@@ -13,7 +13,7 @@ module BELParser
13
13
 
14
14
  SHORT = :sub
15
15
  LONG = :substitution
16
- RETURN_TYPE = BELParser::Language::Version1::ReturnTypes::Substitution
16
+ RETURN_TYPE = BELParser::Language::Version1_0::ReturnTypes::Substitution
17
17
  DESCRIPTION = 'Indicates the abundance of proteins with amino acid substitution sequence'.freeze
18
18
 
19
19
  def self.short
data/lib/bel_parser/language/{version1 → version1_0}/functions/transcriptional_activity.rb RENAMED
@@ -1,11 +1,11 @@
1
- require_relative '../../version1'
1
+ require_relative '../../version1_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 Version1_0
9
9
  module Functions
10
10
  # TranscriptionalActivity: Denotes the frequency or abundance of events in which a member directly acts to control transcription of genes
11
11
  class TranscriptionalActivity
@@ -13,7 +13,7 @@ module BELParser
13
13
 
14
14
  SHORT = :tscript
15
15
  LONG = :transcriptionalActivity
16
- RETURN_TYPE = BELParser::Language::Version1::ReturnTypes::TranscriptionalActivity
16
+ RETURN_TYPE = BELParser::Language::Version1_0::ReturnTypes::TranscriptionalActivity
17
17
  DESCRIPTION = 'Denotes the frequency or abundance of events in which a member directly acts to control transcription of genes'.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::Version1::ReturnTypes::ComplexAbundance))))))
55
+ return_type_of(BELParser::Language::Version1_0::ReturnTypes::ComplexAbundance))))))
56
56
  end
57
57
  private_constant :AST
58
58
 
@@ -82,7 +82,7 @@ module BELParser
82
82
  term(
83
83
  function(
84
84
  identifier(
85
- return_type_of(BELParser::Language::Version1::ReturnTypes::ProteinAbundance))))))
85
+ return_type_of(BELParser::Language::Version1_0::ReturnTypes::ProteinAbundance))))))
86
86
  end
87
87
  private_constant :AST
88
88