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
metadata CHANGED
@@ -1,7 +1,7 @@
1
1
  --- !ruby/object:Gem::Specification
2
2
  name: bel_parser
3
3
  version: !ruby/object:Gem::Version
4
- version: 1.0.0.alpha.1
4
+ version: 1.0.0.alpha.2
5
5
  platform: ruby
6
6
  authors:
7
7
  - Anthony Bargnesi
@@ -9,7 +9,7 @@ authors:
9
9
  autorequire:
10
10
  bindir: bin
11
11
  cert_chain: []
12
- date: 2016-04-05 00:00:00.000000000 Z
12
+ date: 2016-04-08 00:00:00.000000000 Z
13
13
  dependencies: []
14
14
  description: Implements language versions 1.0 and 2.0.
15
15
  email: abargnesi@selventa.com
@@ -31,120 +31,181 @@ files:
31
31
  - lib/bel_parser/expression/parser.rb
32
32
  - lib/bel_parser/expression/term_semantics.rb
33
33
  - lib/bel_parser/language.rb
34
+ - lib/bel_parser/language/expression_validator.rb
34
35
  - lib/bel_parser/language/function.rb
35
36
  - lib/bel_parser/language/quoting.rb
36
- - lib/bel_parser/language/semantic_ast.rb
37
+ - lib/bel_parser/language/relationship.rb
38
+ - lib/bel_parser/language/semantics.rb
37
39
  - lib/bel_parser/language/semantics/analyzer.rb
40
+ - lib/bel_parser/language/semantics/semantic_ast.rb
41
+ - lib/bel_parser/language/semantics/semantic_match.rb
38
42
  - lib/bel_parser/language/signature.rb
39
43
  - lib/bel_parser/language/specification.rb
40
- - lib/bel_parser/language/syntax/expression/incomplete_node.rb
41
- - lib/bel_parser/language/syntax/expression/invalid_term_function.rb
42
- - lib/bel_parser/language/version1.rb
43
- - lib/bel_parser/language/version1/functions/abundance.rb
44
- - lib/bel_parser/language/version1/functions/biological_process.rb
45
- - lib/bel_parser/language/version1/functions/catalytic_activity.rb
46
- - lib/bel_parser/language/version1/functions/cell_secretion.rb
47
- - lib/bel_parser/language/version1/functions/cell_surface_expression.rb
48
- - lib/bel_parser/language/version1/functions/chaperone_activity.rb
49
- - lib/bel_parser/language/version1/functions/complex_abundance.rb
50
- - lib/bel_parser/language/version1/functions/composite_abundance.rb
51
- - lib/bel_parser/language/version1/functions/degradation.rb
52
- - lib/bel_parser/language/version1/functions/fusion.rb
53
- - lib/bel_parser/language/version1/functions/gene_abundance.rb
54
- - lib/bel_parser/language/version1/functions/gtp_bound_activity.rb
55
- - lib/bel_parser/language/version1/functions/kinase_activity.rb
56
- - lib/bel_parser/language/version1/functions/list.rb
57
- - lib/bel_parser/language/version1/functions/micro_rna_abundance.rb
58
- - lib/bel_parser/language/version1/functions/molecular_activity.rb
59
- - lib/bel_parser/language/version1/functions/pathology.rb
60
- - lib/bel_parser/language/version1/functions/peptidase_activity.rb
61
- - lib/bel_parser/language/version1/functions/phosphatase_activity.rb
62
- - lib/bel_parser/language/version1/functions/products.rb
63
- - lib/bel_parser/language/version1/functions/protein_abundance.rb
64
- - lib/bel_parser/language/version1/functions/protein_modification.rb
65
- - lib/bel_parser/language/version1/functions/reactants.rb
66
- - lib/bel_parser/language/version1/functions/reaction.rb
67
- - lib/bel_parser/language/version1/functions/ribosylation_activity.rb
68
- - lib/bel_parser/language/version1/functions/rna_abundance.rb
69
- - lib/bel_parser/language/version1/functions/substitution.rb
70
- - lib/bel_parser/language/version1/functions/transcriptional_activity.rb
71
- - lib/bel_parser/language/version1/functions/translocation.rb
72
- - lib/bel_parser/language/version1/functions/transport_activity.rb
73
- - lib/bel_parser/language/version1/functions/truncation.rb
74
- - lib/bel_parser/language/version1/return_types/abundance.rb
75
- - lib/bel_parser/language/version1/return_types/any.rb
76
- - lib/bel_parser/language/version1/return_types/biological_process.rb
77
- - lib/bel_parser/language/version1/return_types/catalytic_activity.rb
78
- - lib/bel_parser/language/version1/return_types/chaperone_activity.rb
79
- - lib/bel_parser/language/version1/return_types/complex_abundance.rb
80
- - lib/bel_parser/language/version1/return_types/fusion.rb
81
- - lib/bel_parser/language/version1/return_types/gene_abundance.rb
82
- - lib/bel_parser/language/version1/return_types/gtp_bound_activity.rb
83
- - lib/bel_parser/language/version1/return_types/kinase_activity.rb
84
- - lib/bel_parser/language/version1/return_types/list.rb
85
- - lib/bel_parser/language/version1/return_types/micro_rna_abundance.rb
86
- - lib/bel_parser/language/version1/return_types/molecular_activity.rb
87
- - lib/bel_parser/language/version1/return_types/pathology.rb
88
- - lib/bel_parser/language/version1/return_types/peptidase_activity.rb
89
- - lib/bel_parser/language/version1/return_types/phosphatase_activity.rb
90
- - lib/bel_parser/language/version1/return_types/products.rb
91
- - lib/bel_parser/language/version1/return_types/protein_abundance.rb
92
- - lib/bel_parser/language/version1/return_types/protein_modification.rb
93
- - lib/bel_parser/language/version1/return_types/reactants.rb
94
- - lib/bel_parser/language/version1/return_types/ribosylation_activity.rb
95
- - lib/bel_parser/language/version1/return_types/rna_abundance.rb
96
- - lib/bel_parser/language/version1/return_types/substitution.rb
97
- - lib/bel_parser/language/version1/return_types/transcriptional_activity.rb
98
- - lib/bel_parser/language/version1/return_types/transport_activity.rb
99
- - lib/bel_parser/language/version1/return_types/truncation.rb
100
- - lib/bel_parser/language/version2.rb
101
- - lib/bel_parser/language/version2/functions/abundance.rb
102
- - lib/bel_parser/language/version2/functions/activity.rb
103
- - lib/bel_parser/language/version2/functions/biological_process.rb
104
- - lib/bel_parser/language/version2/functions/cell_secretion.rb
105
- - lib/bel_parser/language/version2/functions/cell_surface_expression.rb
106
- - lib/bel_parser/language/version2/functions/complex_abundance.rb
107
- - lib/bel_parser/language/version2/functions/composite_abundance.rb
108
- - lib/bel_parser/language/version2/functions/degradation.rb
109
- - lib/bel_parser/language/version2/functions/fragment.rb
110
- - lib/bel_parser/language/version2/functions/from_location.rb
111
- - lib/bel_parser/language/version2/functions/fusion.rb
112
- - lib/bel_parser/language/version2/functions/gene_abundance.rb
113
- - lib/bel_parser/language/version2/functions/list.rb
114
- - lib/bel_parser/language/version2/functions/location.rb
115
- - lib/bel_parser/language/version2/functions/micro_rna_abundance.rb
116
- - lib/bel_parser/language/version2/functions/molecular_activity.rb
117
- - lib/bel_parser/language/version2/functions/pathology.rb
118
- - lib/bel_parser/language/version2/functions/products.rb
119
- - lib/bel_parser/language/version2/functions/protein_abundance.rb
120
- - lib/bel_parser/language/version2/functions/protein_modification.rb
121
- - lib/bel_parser/language/version2/functions/reactants.rb
122
- - lib/bel_parser/language/version2/functions/reaction.rb
123
- - lib/bel_parser/language/version2/functions/rna_abundance.rb
124
- - lib/bel_parser/language/version2/functions/to_location.rb
125
- - lib/bel_parser/language/version2/functions/translocation.rb
126
- - lib/bel_parser/language/version2/functions/variant.rb
127
- - lib/bel_parser/language/version2/return_types/abundance.rb
128
- - lib/bel_parser/language/version2/return_types/activity.rb
129
- - lib/bel_parser/language/version2/return_types/any.rb
130
- - lib/bel_parser/language/version2/return_types/biological_process.rb
131
- - lib/bel_parser/language/version2/return_types/complex_abundance.rb
132
- - lib/bel_parser/language/version2/return_types/fragment.rb
133
- - lib/bel_parser/language/version2/return_types/from_location.rb
134
- - lib/bel_parser/language/version2/return_types/fusion.rb
135
- - lib/bel_parser/language/version2/return_types/gene_abundance.rb
136
- - lib/bel_parser/language/version2/return_types/list.rb
137
- - lib/bel_parser/language/version2/return_types/location.rb
138
- - lib/bel_parser/language/version2/return_types/micro_rna_abundance.rb
139
- - lib/bel_parser/language/version2/return_types/molecular_activity.rb
140
- - lib/bel_parser/language/version2/return_types/pathology.rb
141
- - lib/bel_parser/language/version2/return_types/products.rb
142
- - lib/bel_parser/language/version2/return_types/protein_abundance.rb
143
- - lib/bel_parser/language/version2/return_types/protein_modification.rb
144
- - lib/bel_parser/language/version2/return_types/reactants.rb
145
- - lib/bel_parser/language/version2/return_types/rna_abundance.rb
146
- - lib/bel_parser/language/version2/return_types/to_location.rb
147
- - lib/bel_parser/language/version2/return_types/variant.rb
44
+ - lib/bel_parser/language/syntax.rb
45
+ - lib/bel_parser/language/version1_0.rb
46
+ - lib/bel_parser/language/version1_0/functions/abundance.rb
47
+ - lib/bel_parser/language/version1_0/functions/biological_process.rb
48
+ - lib/bel_parser/language/version1_0/functions/catalytic_activity.rb
49
+ - lib/bel_parser/language/version1_0/functions/cell_secretion.rb
50
+ - lib/bel_parser/language/version1_0/functions/cell_surface_expression.rb
51
+ - lib/bel_parser/language/version1_0/functions/chaperone_activity.rb
52
+ - lib/bel_parser/language/version1_0/functions/complex_abundance.rb
53
+ - lib/bel_parser/language/version1_0/functions/composite_abundance.rb
54
+ - lib/bel_parser/language/version1_0/functions/degradation.rb
55
+ - lib/bel_parser/language/version1_0/functions/fusion.rb
56
+ - lib/bel_parser/language/version1_0/functions/gene_abundance.rb
57
+ - lib/bel_parser/language/version1_0/functions/gtp_bound_activity.rb
58
+ - lib/bel_parser/language/version1_0/functions/kinase_activity.rb
59
+ - lib/bel_parser/language/version1_0/functions/list.rb
60
+ - lib/bel_parser/language/version1_0/functions/micro_rna_abundance.rb
61
+ - lib/bel_parser/language/version1_0/functions/molecular_activity.rb
62
+ - lib/bel_parser/language/version1_0/functions/pathology.rb
63
+ - lib/bel_parser/language/version1_0/functions/peptidase_activity.rb
64
+ - lib/bel_parser/language/version1_0/functions/phosphatase_activity.rb
65
+ - lib/bel_parser/language/version1_0/functions/products.rb
66
+ - lib/bel_parser/language/version1_0/functions/protein_abundance.rb
67
+ - lib/bel_parser/language/version1_0/functions/protein_modification.rb
68
+ - lib/bel_parser/language/version1_0/functions/reactants.rb
69
+ - lib/bel_parser/language/version1_0/functions/reaction.rb
70
+ - lib/bel_parser/language/version1_0/functions/ribosylation_activity.rb
71
+ - lib/bel_parser/language/version1_0/functions/rna_abundance.rb
72
+ - lib/bel_parser/language/version1_0/functions/substitution.rb
73
+ - lib/bel_parser/language/version1_0/functions/transcriptional_activity.rb
74
+ - lib/bel_parser/language/version1_0/functions/translocation.rb
75
+ - lib/bel_parser/language/version1_0/functions/transport_activity.rb
76
+ - lib/bel_parser/language/version1_0/functions/truncation.rb
77
+ - lib/bel_parser/language/version1_0/relationships/acts_in.rb
78
+ - lib/bel_parser/language/version1_0/relationships/analogous.rb
79
+ - lib/bel_parser/language/version1_0/relationships/association.rb
80
+ - lib/bel_parser/language/version1_0/relationships/biomarker_for.rb
81
+ - lib/bel_parser/language/version1_0/relationships/causes_no_change.rb
82
+ - lib/bel_parser/language/version1_0/relationships/decreases.rb
83
+ - lib/bel_parser/language/version1_0/relationships/directly_decreases.rb
84
+ - lib/bel_parser/language/version1_0/relationships/directly_increases.rb
85
+ - lib/bel_parser/language/version1_0/relationships/has_component.rb
86
+ - lib/bel_parser/language/version1_0/relationships/has_components.rb
87
+ - lib/bel_parser/language/version1_0/relationships/has_member.rb
88
+ - lib/bel_parser/language/version1_0/relationships/has_members.rb
89
+ - lib/bel_parser/language/version1_0/relationships/has_modification.rb
90
+ - lib/bel_parser/language/version1_0/relationships/has_product.rb
91
+ - lib/bel_parser/language/version1_0/relationships/has_variant.rb
92
+ - lib/bel_parser/language/version1_0/relationships/includes.rb
93
+ - lib/bel_parser/language/version1_0/relationships/increases.rb
94
+ - lib/bel_parser/language/version1_0/relationships/is_a.rb
95
+ - lib/bel_parser/language/version1_0/relationships/negative_correlation.rb
96
+ - lib/bel_parser/language/version1_0/relationships/orthologous.rb
97
+ - lib/bel_parser/language/version1_0/relationships/positive_correlation.rb
98
+ - lib/bel_parser/language/version1_0/relationships/prognostic_biomarker_for.rb
99
+ - lib/bel_parser/language/version1_0/relationships/rate_limiting_step_of.rb
100
+ - lib/bel_parser/language/version1_0/relationships/reactant_in.rb
101
+ - lib/bel_parser/language/version1_0/relationships/sub_process_of.rb
102
+ - lib/bel_parser/language/version1_0/relationships/transcribed_to.rb
103
+ - lib/bel_parser/language/version1_0/relationships/translated_to.rb
104
+ - lib/bel_parser/language/version1_0/relationships/translocates.rb
105
+ - lib/bel_parser/language/version1_0/return_types/abundance.rb
106
+ - lib/bel_parser/language/version1_0/return_types/any.rb
107
+ - lib/bel_parser/language/version1_0/return_types/biological_process.rb
108
+ - lib/bel_parser/language/version1_0/return_types/catalytic_activity.rb
109
+ - lib/bel_parser/language/version1_0/return_types/chaperone_activity.rb
110
+ - lib/bel_parser/language/version1_0/return_types/complex_abundance.rb
111
+ - lib/bel_parser/language/version1_0/return_types/fusion.rb
112
+ - lib/bel_parser/language/version1_0/return_types/gene_abundance.rb
113
+ - lib/bel_parser/language/version1_0/return_types/gtp_bound_activity.rb
114
+ - lib/bel_parser/language/version1_0/return_types/kinase_activity.rb
115
+ - lib/bel_parser/language/version1_0/return_types/list.rb
116
+ - lib/bel_parser/language/version1_0/return_types/micro_rna_abundance.rb
117
+ - lib/bel_parser/language/version1_0/return_types/molecular_activity.rb
118
+ - lib/bel_parser/language/version1_0/return_types/pathology.rb
119
+ - lib/bel_parser/language/version1_0/return_types/peptidase_activity.rb
120
+ - lib/bel_parser/language/version1_0/return_types/phosphatase_activity.rb
121
+ - lib/bel_parser/language/version1_0/return_types/products.rb
122
+ - lib/bel_parser/language/version1_0/return_types/protein_abundance.rb
123
+ - lib/bel_parser/language/version1_0/return_types/protein_modification.rb
124
+ - lib/bel_parser/language/version1_0/return_types/reactants.rb
125
+ - lib/bel_parser/language/version1_0/return_types/ribosylation_activity.rb
126
+ - lib/bel_parser/language/version1_0/return_types/rna_abundance.rb
127
+ - lib/bel_parser/language/version1_0/return_types/substitution.rb
128
+ - lib/bel_parser/language/version1_0/return_types/transcriptional_activity.rb
129
+ - lib/bel_parser/language/version1_0/return_types/transport_activity.rb
130
+ - lib/bel_parser/language/version1_0/return_types/truncation.rb
131
+ - lib/bel_parser/language/version1_0/syntax/function.rb
132
+ - lib/bel_parser/language/version2_0.rb
133
+ - lib/bel_parser/language/version2_0/functions/abundance.rb
134
+ - lib/bel_parser/language/version2_0/functions/activity.rb
135
+ - lib/bel_parser/language/version2_0/functions/biological_process.rb
136
+ - lib/bel_parser/language/version2_0/functions/cell_secretion.rb
137
+ - lib/bel_parser/language/version2_0/functions/cell_surface_expression.rb
138
+ - lib/bel_parser/language/version2_0/functions/complex_abundance.rb
139
+ - lib/bel_parser/language/version2_0/functions/composite_abundance.rb
140
+ - lib/bel_parser/language/version2_0/functions/degradation.rb
141
+ - lib/bel_parser/language/version2_0/functions/fragment.rb
142
+ - lib/bel_parser/language/version2_0/functions/from_location.rb
143
+ - lib/bel_parser/language/version2_0/functions/fusion.rb
144
+ - lib/bel_parser/language/version2_0/functions/gene_abundance.rb
145
+ - lib/bel_parser/language/version2_0/functions/list.rb
146
+ - lib/bel_parser/language/version2_0/functions/location.rb
147
+ - lib/bel_parser/language/version2_0/functions/micro_rna_abundance.rb
148
+ - lib/bel_parser/language/version2_0/functions/molecular_activity.rb
149
+ - lib/bel_parser/language/version2_0/functions/pathology.rb
150
+ - lib/bel_parser/language/version2_0/functions/products.rb
151
+ - lib/bel_parser/language/version2_0/functions/protein_abundance.rb
152
+ - lib/bel_parser/language/version2_0/functions/protein_modification.rb
153
+ - lib/bel_parser/language/version2_0/functions/reactants.rb
154
+ - lib/bel_parser/language/version2_0/functions/reaction.rb
155
+ - lib/bel_parser/language/version2_0/functions/rna_abundance.rb
156
+ - lib/bel_parser/language/version2_0/functions/to_location.rb
157
+ - lib/bel_parser/language/version2_0/functions/translocation.rb
158
+ - lib/bel_parser/language/version2_0/functions/variant.rb
159
+ - lib/bel_parser/language/version2_0/relationships/acts_in.rb
160
+ - lib/bel_parser/language/version2_0/relationships/analogous.rb
161
+ - lib/bel_parser/language/version2_0/relationships/association.rb
162
+ - lib/bel_parser/language/version2_0/relationships/biomarker_for.rb
163
+ - lib/bel_parser/language/version2_0/relationships/causes_no_change.rb
164
+ - lib/bel_parser/language/version2_0/relationships/decreases.rb
165
+ - lib/bel_parser/language/version2_0/relationships/directly_decreases.rb
166
+ - lib/bel_parser/language/version2_0/relationships/directly_increases.rb
167
+ - lib/bel_parser/language/version2_0/relationships/has_component.rb
168
+ - lib/bel_parser/language/version2_0/relationships/has_components.rb
169
+ - lib/bel_parser/language/version2_0/relationships/has_member.rb
170
+ - lib/bel_parser/language/version2_0/relationships/has_members.rb
171
+ - lib/bel_parser/language/version2_0/relationships/has_modification.rb
172
+ - lib/bel_parser/language/version2_0/relationships/has_product.rb
173
+ - lib/bel_parser/language/version2_0/relationships/has_variant.rb
174
+ - lib/bel_parser/language/version2_0/relationships/includes.rb
175
+ - lib/bel_parser/language/version2_0/relationships/increases.rb
176
+ - lib/bel_parser/language/version2_0/relationships/is_a.rb
177
+ - lib/bel_parser/language/version2_0/relationships/negative_correlation.rb
178
+ - lib/bel_parser/language/version2_0/relationships/orthologous.rb
179
+ - lib/bel_parser/language/version2_0/relationships/positive_correlation.rb
180
+ - lib/bel_parser/language/version2_0/relationships/prognostic_biomarker_for.rb
181
+ - lib/bel_parser/language/version2_0/relationships/rate_limiting_step_of.rb
182
+ - lib/bel_parser/language/version2_0/relationships/reactant_in.rb
183
+ - lib/bel_parser/language/version2_0/relationships/regulates.rb
184
+ - lib/bel_parser/language/version2_0/relationships/sub_process_of.rb
185
+ - lib/bel_parser/language/version2_0/relationships/transcribed_to.rb
186
+ - lib/bel_parser/language/version2_0/relationships/translated_to.rb
187
+ - lib/bel_parser/language/version2_0/relationships/translocates.rb
188
+ - lib/bel_parser/language/version2_0/return_types/abundance.rb
189
+ - lib/bel_parser/language/version2_0/return_types/activity.rb
190
+ - lib/bel_parser/language/version2_0/return_types/any.rb
191
+ - lib/bel_parser/language/version2_0/return_types/biological_process.rb
192
+ - lib/bel_parser/language/version2_0/return_types/complex_abundance.rb
193
+ - lib/bel_parser/language/version2_0/return_types/fragment.rb
194
+ - lib/bel_parser/language/version2_0/return_types/from_location.rb
195
+ - lib/bel_parser/language/version2_0/return_types/fusion.rb
196
+ - lib/bel_parser/language/version2_0/return_types/gene_abundance.rb
197
+ - lib/bel_parser/language/version2_0/return_types/list.rb
198
+ - lib/bel_parser/language/version2_0/return_types/location.rb
199
+ - lib/bel_parser/language/version2_0/return_types/micro_rna_abundance.rb
200
+ - lib/bel_parser/language/version2_0/return_types/molecular_activity.rb
201
+ - lib/bel_parser/language/version2_0/return_types/pathology.rb
202
+ - lib/bel_parser/language/version2_0/return_types/products.rb
203
+ - lib/bel_parser/language/version2_0/return_types/protein_abundance.rb
204
+ - lib/bel_parser/language/version2_0/return_types/protein_modification.rb
205
+ - lib/bel_parser/language/version2_0/return_types/reactants.rb
206
+ - lib/bel_parser/language/version2_0/return_types/rna_abundance.rb
207
+ - lib/bel_parser/language/version2_0/return_types/to_location.rb
208
+ - lib/bel_parser/language/version2_0/return_types/variant.rb
148
209
  - lib/bel_parser/mixin/line_continuator.rb
149
210
  - lib/bel_parser/mixin/line_mapping.rb
150
211
  - lib/bel_parser/parser.rb
@@ -1,14 +0,0 @@
1
- module BELParser
2
- module Language
3
- module Syntax
4
- module Expression
5
- # AST traversal observer that reports if any node is incomplete.
6
- class IncompleteNode
7
- def update(node)
8
- "[#{node.type}] Incomplete #{node.type}." if node.incomplete?
9
- end
10
- end
11
- end
12
- end
13
- end
14
- end
@@ -1,22 +0,0 @@
1
- module BELParser
2
- module Language
3
- module Syntax
4
- module Expression
5
- # AST traversal observer that reports if term functions are invalid
6
- # according to a {BELParser::Language::Specification}.
7
- class InvalidTermFunction
8
- def initialize(specification)
9
- @specification = specification
10
- end
11
-
12
- def update(node)
13
- return unless node.type == :term
14
- function_string = node.children[0].children[0].children[0]
15
- msg = "[#{node.type}] Invalid function: #{function_string}"
16
- msg unless @specification.function(function_string.to_sym)
17
- end
18
- end
19
- end
20
- end
21
- end
22
- end
@@ -1,50 +0,0 @@
1
- require_relative 'function'
2
- require_relative 'specification'
3
-
4
- # Require all version 1.0 return types
5
- Dir[
6
- File.join(
7
- File.dirname(File.expand_path(__FILE__)),
8
- 'version1', 'return_types', '*.rb')
9
- ].each do |path|
10
- require_relative "version1/return_types/#{File.basename(path)}"
11
- end
12
-
13
- # Require all version 1.0 functions.
14
- Dir[
15
- File.join(
16
- File.dirname(File.expand_path(__FILE__)),
17
- 'version1', 'functions', '*.rb')
18
- ].each do |path|
19
- require_relative "version1/functions/#{File.basename(path)}"
20
- end
21
-
22
- module BELParser
23
- module Language
24
- module Version1
25
- # Version1Specification defines the BEL, version 1.0 specification.
26
- class Specification
27
- include BELParser::Language::Specification
28
- def initialize
29
- # Establish functions
30
- function_classes = Version1::Functions.constants.collect do |symbol|
31
- const = Version1::Functions.const_get(symbol)
32
- const if
33
- const.respond_to?(:short) &&
34
- const.respond_to?(:long)
35
- end
36
- @functions = function_classes.compact
37
- @indexed_functions = index_functions(@functions)
38
-
39
- # Establish return types
40
- ret_classes = Version1::ReturnTypes.constants.collect do |symbol|
41
- const = Version1::ReturnTypes.const_get(symbol)
42
- const if const.respond_to?(:subtypes)
43
- end
44
- @return_types = ret_classes.compact
45
- @indexed_return_types = index_return_types(@return_types)
46
- end
47
- end
48
- end
49
- end
50
- end
@@ -1,50 +0,0 @@
1
- require_relative 'function'
2
- require_relative 'specification'
3
-
4
- # Require all version 2.0 return types
5
- Dir[
6
- File.join(
7
- File.dirname(File.expand_path(__FILE__)),
8
- 'version2', 'return_types', '*.rb')
9
- ].each do |path|
10
- require_relative "version2/return_types/#{File.basename(path)}"
11
- end
12
-
13
- # Require all version 2.0 functions.
14
- Dir[
15
- File.join(
16
- File.dirname(File.expand_path(__FILE__)),
17
- 'version2', 'functions', '*.rb')
18
- ].each do |path|
19
- require_relative "version2/functions/#{File.basename(path)}"
20
- end
21
-
22
- module BELParser
23
- module Language
24
- module Version2
25
- # Version2Specification defines the BEL, version 2.0 specification.
26
- class Specification
27
- include BELParser::Language::Specification
28
- def initialize
29
- # Establish functions
30
- function_classes = Version2::Functions.constants.collect do |symbol|
31
- const = Version2::Functions.const_get(symbol)
32
- const if
33
- const.respond_to?(:short) &&
34
- const.respond_to?(:long)
35
- end
36
- @functions = function_classes.compact
37
- @indexed_functions = index_functions(@functions)
38
-
39
- # Establish return types
40
- ret_classes = Version2::ReturnTypes.constants.collect do |symbol|
41
- const = Version2::ReturnTypes.const_get(symbol)
42
- const if const.respond_to?(:subtypes)
43
- end
44
- @return_types = ret_classes.compact
45
- @indexed_return_types = index_return_types(@return_types)
46
- end
47
- end
48
- end
49
- end
50
- end