bel_parser 1.0.0.alpha.27-java

Sign up to get free protection for your applications and to get access to all the features.
Files changed (332) hide show
  1. checksums.yaml +7 -0
  2. data/.gemspec-java +32 -0
  3. data/CHANGELOG.md +10 -0
  4. data/LICENSE +191 -0
  5. data/README.md +20 -0
  6. data/VERSION +1 -0
  7. data/bin/bel2_validator +62 -0
  8. data/bin/bel_script_reader +132 -0
  9. data/lib/bel/translator/plugins/bel_script.rb +38 -0
  10. data/lib/bel/translator/plugins/bel_script/bel_citation_serialization.rb +125 -0
  11. data/lib/bel/translator/plugins/bel_script/bel_discrete_serialization.rb +109 -0
  12. data/lib/bel/translator/plugins/bel_script/bel_top_down_serialization.rb +100 -0
  13. data/lib/bel/translator/plugins/bel_script/nanopub_serialization.rb +79 -0
  14. data/lib/bel/translator/plugins/bel_script/reader.rb +39 -0
  15. data/lib/bel/translator/plugins/bel_script/translator.rb +37 -0
  16. data/lib/bel/translator/plugins/bel_script/writer.rb +180 -0
  17. data/lib/bel_parser.rb +23 -0
  18. data/lib/bel_parser/ast_filter.rb +44 -0
  19. data/lib/bel_parser/ast_generator.rb +83 -0
  20. data/lib/bel_parser/expression.rb +3 -0
  21. data/lib/bel_parser/expression/filter.rb +31 -0
  22. data/lib/bel_parser/expression/parser.rb +72 -0
  23. data/lib/bel_parser/expression/validator.rb +79 -0
  24. data/lib/bel_parser/language.rb +114 -0
  25. data/lib/bel_parser/language/amino_acid.rb +68 -0
  26. data/lib/bel_parser/language/apply_namespace_encoding.rb +98 -0
  27. data/lib/bel_parser/language/base_specification.rb +82 -0
  28. data/lib/bel_parser/language/covalent_protein_modification.rb +56 -0
  29. data/lib/bel_parser/language/expression_validator.rb +68 -0
  30. data/lib/bel_parser/language/function.rb +67 -0
  31. data/lib/bel_parser/language/relationship.rb +102 -0
  32. data/lib/bel_parser/language/semantics.rb +40 -0
  33. data/lib/bel_parser/language/semantics/deeply_nested_statement.rb +65 -0
  34. data/lib/bel_parser/language/semantics/function_deprecation.rb +43 -0
  35. data/lib/bel_parser/language/semantics/list_function_subject.rb +45 -0
  36. data/lib/bel_parser/language/semantics/multiple_subject_object.rb +55 -0
  37. data/lib/bel_parser/language/semantics/non_causal_nested_statement.rb +50 -0
  38. data/lib/bel_parser/language/semantics/non_object_list.rb +56 -0
  39. data/lib/bel_parser/language/semantics/relationship_deprecation.rb +44 -0
  40. data/lib/bel_parser/language/semantics/relationship_not_listable.rb +60 -0
  41. data/lib/bel_parser/language/semantics/signature_mapping.rb +83 -0
  42. data/lib/bel_parser/language/semantics_ast.rb +784 -0
  43. data/lib/bel_parser/language/semantics_ast_warnings.rb +180 -0
  44. data/lib/bel_parser/language/semantics_function.rb +16 -0
  45. data/lib/bel_parser/language/semantics_match.rb +28 -0
  46. data/lib/bel_parser/language/semantics_result.rb +33 -0
  47. data/lib/bel_parser/language/semantics_type_warning.rb +22 -0
  48. data/lib/bel_parser/language/semantics_warning.rb +27 -0
  49. data/lib/bel_parser/language/signature.rb +39 -0
  50. data/lib/bel_parser/language/specification.rb +118 -0
  51. data/lib/bel_parser/language/syntax.rb +38 -0
  52. data/lib/bel_parser/language/syntax/invalid_function.rb +39 -0
  53. data/lib/bel_parser/language/syntax/invalid_relationship.rb +42 -0
  54. data/lib/bel_parser/language/syntax/undefined_namespace.rb +49 -0
  55. data/lib/bel_parser/language/syntax/undefined_namespace_value.rb +44 -0
  56. data/lib/bel_parser/language/syntax_error.rb +32 -0
  57. data/lib/bel_parser/language/syntax_function.rb +16 -0
  58. data/lib/bel_parser/language/syntax_result.rb +32 -0
  59. data/lib/bel_parser/language/syntax_warning.rb +27 -0
  60. data/lib/bel_parser/language/version1_0.rb +20 -0
  61. data/lib/bel_parser/language/version1_0/functions/abundance.rb +83 -0
  62. data/lib/bel_parser/language/version1_0/functions/biological_process.rb +83 -0
  63. data/lib/bel_parser/language/version1_0/functions/catalytic_activity.rb +114 -0
  64. data/lib/bel_parser/language/version1_0/functions/cell_secretion.rb +83 -0
  65. data/lib/bel_parser/language/version1_0/functions/cell_surface_expression.rb +83 -0
  66. data/lib/bel_parser/language/version1_0/functions/chaperone_activity.rb +114 -0
  67. data/lib/bel_parser/language/version1_0/functions/complex_abundance.rb +115 -0
  68. data/lib/bel_parser/language/version1_0/functions/composite_abundance.rb +81 -0
  69. data/lib/bel_parser/language/version1_0/functions/degradation.rb +83 -0
  70. data/lib/bel_parser/language/version1_0/functions/fusion.rb +287 -0
  71. data/lib/bel_parser/language/version1_0/functions/gene_abundance.rb +122 -0
  72. data/lib/bel_parser/language/version1_0/functions/gtp_bound_activity.rb +113 -0
  73. data/lib/bel_parser/language/version1_0/functions/kinase_activity.rb +114 -0
  74. data/lib/bel_parser/language/version1_0/functions/list.rb +114 -0
  75. data/lib/bel_parser/language/version1_0/functions/micro_rna_abundance.rb +85 -0
  76. data/lib/bel_parser/language/version1_0/functions/molecular_activity.rb +82 -0
  77. data/lib/bel_parser/language/version1_0/functions/pathology.rb +83 -0
  78. data/lib/bel_parser/language/version1_0/functions/peptidase_activity.rb +112 -0
  79. data/lib/bel_parser/language/version1_0/functions/phosphatase_activity.rb +112 -0
  80. data/lib/bel_parser/language/version1_0/functions/products.rb +79 -0
  81. data/lib/bel_parser/language/version1_0/functions/protein_abundance.rb +234 -0
  82. data/lib/bel_parser/language/version1_0/functions/protein_modification.rb +179 -0
  83. data/lib/bel_parser/language/version1_0/functions/reactants.rb +79 -0
  84. data/lib/bel_parser/language/version1_0/functions/reaction.rb +86 -0
  85. data/lib/bel_parser/language/version1_0/functions/ribosylation_activity.rb +114 -0
  86. data/lib/bel_parser/language/version1_0/functions/rna_abundance.rb +122 -0
  87. data/lib/bel_parser/language/version1_0/functions/substitution.rb +93 -0
  88. data/lib/bel_parser/language/version1_0/functions/transcriptional_activity.rb +114 -0
  89. data/lib/bel_parser/language/version1_0/functions/translocation.rb +98 -0
  90. data/lib/bel_parser/language/version1_0/functions/transport_activity.rb +115 -0
  91. data/lib/bel_parser/language/version1_0/functions/truncation.rb +81 -0
  92. data/lib/bel_parser/language/version1_0/relationships/acts_in.rb +61 -0
  93. data/lib/bel_parser/language/version1_0/relationships/analogous.rb +41 -0
  94. data/lib/bel_parser/language/version1_0/relationships/association.rb +42 -0
  95. data/lib/bel_parser/language/version1_0/relationships/biomarker_for.rb +42 -0
  96. data/lib/bel_parser/language/version1_0/relationships/causes_no_change.rb +50 -0
  97. data/lib/bel_parser/language/version1_0/relationships/decreases.rb +63 -0
  98. data/lib/bel_parser/language/version1_0/relationships/directly_decreases.rb +56 -0
  99. data/lib/bel_parser/language/version1_0/relationships/directly_increases.rb +56 -0
  100. data/lib/bel_parser/language/version1_0/relationships/has_component.rb +62 -0
  101. data/lib/bel_parser/language/version1_0/relationships/has_components.rb +61 -0
  102. data/lib/bel_parser/language/version1_0/relationships/has_member.rb +48 -0
  103. data/lib/bel_parser/language/version1_0/relationships/has_members.rb +57 -0
  104. data/lib/bel_parser/language/version1_0/relationships/has_modification.rb +54 -0
  105. data/lib/bel_parser/language/version1_0/relationships/has_product.rb +60 -0
  106. data/lib/bel_parser/language/version1_0/relationships/has_variant.rb +54 -0
  107. data/lib/bel_parser/language/version1_0/relationships/includes.rb +59 -0
  108. data/lib/bel_parser/language/version1_0/relationships/increases.rb +63 -0
  109. data/lib/bel_parser/language/version1_0/relationships/is_a.rb +48 -0
  110. data/lib/bel_parser/language/version1_0/relationships/negative_correlation.rb +50 -0
  111. data/lib/bel_parser/language/version1_0/relationships/orthologous.rb +48 -0
  112. data/lib/bel_parser/language/version1_0/relationships/positive_correlation.rb +46 -0
  113. data/lib/bel_parser/language/version1_0/relationships/prognostic_biomarker_for.rb +44 -0
  114. data/lib/bel_parser/language/version1_0/relationships/rate_limiting_step_of.rb +53 -0
  115. data/lib/bel_parser/language/version1_0/relationships/reactant_in.rb +60 -0
  116. data/lib/bel_parser/language/version1_0/relationships/sub_process_of.rb +55 -0
  117. data/lib/bel_parser/language/version1_0/relationships/transcribed_to.rb +53 -0
  118. data/lib/bel_parser/language/version1_0/relationships/translated_to.rb +54 -0
  119. data/lib/bel_parser/language/version1_0/relationships/translocates.rb +57 -0
  120. data/lib/bel_parser/language/version1_0/return_types/abundance.rb +20 -0
  121. data/lib/bel_parser/language/version1_0/return_types/any.rb +74 -0
  122. data/lib/bel_parser/language/version1_0/return_types/biological_process.rb +17 -0
  123. data/lib/bel_parser/language/version1_0/return_types/catalytic_activity.rb +20 -0
  124. data/lib/bel_parser/language/version1_0/return_types/chaperone_activity.rb +20 -0
  125. data/lib/bel_parser/language/version1_0/return_types/complex_abundance.rb +17 -0
  126. data/lib/bel_parser/language/version1_0/return_types/fusion.rb +17 -0
  127. data/lib/bel_parser/language/version1_0/return_types/gene_abundance.rb +17 -0
  128. data/lib/bel_parser/language/version1_0/return_types/gtp_bound_activity.rb +20 -0
  129. data/lib/bel_parser/language/version1_0/return_types/kinase_activity.rb +20 -0
  130. data/lib/bel_parser/language/version1_0/return_types/list.rb +17 -0
  131. data/lib/bel_parser/language/version1_0/return_types/micro_rna_abundance.rb +17 -0
  132. data/lib/bel_parser/language/version1_0/return_types/molecular_activity.rb +20 -0
  133. data/lib/bel_parser/language/version1_0/return_types/pathology.rb +17 -0
  134. data/lib/bel_parser/language/version1_0/return_types/peptidase_activity.rb +20 -0
  135. data/lib/bel_parser/language/version1_0/return_types/phosphatase_activity.rb +20 -0
  136. data/lib/bel_parser/language/version1_0/return_types/products.rb +17 -0
  137. data/lib/bel_parser/language/version1_0/return_types/protein_abundance.rb +17 -0
  138. data/lib/bel_parser/language/version1_0/return_types/protein_modification.rb +17 -0
  139. data/lib/bel_parser/language/version1_0/return_types/reactants.rb +17 -0
  140. data/lib/bel_parser/language/version1_0/return_types/ribosylation_activity.rb +20 -0
  141. data/lib/bel_parser/language/version1_0/return_types/rna_abundance.rb +17 -0
  142. data/lib/bel_parser/language/version1_0/return_types/substitution.rb +17 -0
  143. data/lib/bel_parser/language/version1_0/return_types/transcriptional_activity.rb +20 -0
  144. data/lib/bel_parser/language/version1_0/return_types/transport_activity.rb +20 -0
  145. data/lib/bel_parser/language/version1_0/return_types/truncation.rb +17 -0
  146. data/lib/bel_parser/language/version1_0/value_encodings/abundance.rb +21 -0
  147. data/lib/bel_parser/language/version1_0/value_encodings/any.rb +74 -0
  148. data/lib/bel_parser/language/version1_0/value_encodings/biological_process.rb +21 -0
  149. data/lib/bel_parser/language/version1_0/value_encodings/complex_abundance.rb +21 -0
  150. data/lib/bel_parser/language/version1_0/value_encodings/gene_abundance.rb +21 -0
  151. data/lib/bel_parser/language/version1_0/value_encodings/micro_rna_abundance.rb +21 -0
  152. data/lib/bel_parser/language/version1_0/value_encodings/pathology.rb +21 -0
  153. data/lib/bel_parser/language/version1_0/value_encodings/protein_abundance.rb +21 -0
  154. data/lib/bel_parser/language/version1_0/value_encodings/rna_abundance.rb +21 -0
  155. data/lib/bel_parser/language/version2_0.rb +20 -0
  156. data/lib/bel_parser/language/version2_0/functions/abundance.rb +161 -0
  157. data/lib/bel_parser/language/version2_0/functions/activity.rb +118 -0
  158. data/lib/bel_parser/language/version2_0/functions/biological_process.rb +84 -0
  159. data/lib/bel_parser/language/version2_0/functions/cell_secretion.rb +83 -0
  160. data/lib/bel_parser/language/version2_0/functions/cell_surface_expression.rb +83 -0
  161. data/lib/bel_parser/language/version2_0/functions/complex_abundance.rb +190 -0
  162. data/lib/bel_parser/language/version2_0/functions/composite_abundance.rb +81 -0
  163. data/lib/bel_parser/language/version2_0/functions/degradation.rb +83 -0
  164. data/lib/bel_parser/language/version2_0/functions/fragment.rb +116 -0
  165. data/lib/bel_parser/language/version2_0/functions/from_location.rb +85 -0
  166. data/lib/bel_parser/language/version2_0/functions/fusion.rb +203 -0
  167. data/lib/bel_parser/language/version2_0/functions/gene_abundance.rb +192 -0
  168. data/lib/bel_parser/language/version2_0/functions/list.rb +114 -0
  169. data/lib/bel_parser/language/version2_0/functions/location.rb +83 -0
  170. data/lib/bel_parser/language/version2_0/functions/micro_rna_abundance.rb +163 -0
  171. data/lib/bel_parser/language/version2_0/functions/molecular_activity.rb +86 -0
  172. data/lib/bel_parser/language/version2_0/functions/pathology.rb +83 -0
  173. data/lib/bel_parser/language/version2_0/functions/products.rb +79 -0
  174. data/lib/bel_parser/language/version2_0/functions/protein_abundance.rb +270 -0
  175. data/lib/bel_parser/language/version2_0/functions/protein_modification.rb +172 -0
  176. data/lib/bel_parser/language/version2_0/functions/reactants.rb +79 -0
  177. data/lib/bel_parser/language/version2_0/functions/reaction.rb +86 -0
  178. data/lib/bel_parser/language/version2_0/functions/rna_abundance.rb +192 -0
  179. data/lib/bel_parser/language/version2_0/functions/to_location.rb +84 -0
  180. data/lib/bel_parser/language/version2_0/functions/translocation.rb +91 -0
  181. data/lib/bel_parser/language/version2_0/functions/variant.rb +80 -0
  182. data/lib/bel_parser/language/version2_0/relationships/acts_in.rb +61 -0
  183. data/lib/bel_parser/language/version2_0/relationships/analogous.rb +45 -0
  184. data/lib/bel_parser/language/version2_0/relationships/association.rb +42 -0
  185. data/lib/bel_parser/language/version2_0/relationships/biomarker_for.rb +46 -0
  186. data/lib/bel_parser/language/version2_0/relationships/causes_no_change.rb +50 -0
  187. data/lib/bel_parser/language/version2_0/relationships/decreases.rb +63 -0
  188. data/lib/bel_parser/language/version2_0/relationships/directly_decreases.rb +56 -0
  189. data/lib/bel_parser/language/version2_0/relationships/directly_increases.rb +56 -0
  190. data/lib/bel_parser/language/version2_0/relationships/has_component.rb +62 -0
  191. data/lib/bel_parser/language/version2_0/relationships/has_components.rb +61 -0
  192. data/lib/bel_parser/language/version2_0/relationships/has_member.rb +48 -0
  193. data/lib/bel_parser/language/version2_0/relationships/has_members.rb +57 -0
  194. data/lib/bel_parser/language/version2_0/relationships/has_modification.rb +54 -0
  195. data/lib/bel_parser/language/version2_0/relationships/has_product.rb +60 -0
  196. data/lib/bel_parser/language/version2_0/relationships/has_variant.rb +54 -0
  197. data/lib/bel_parser/language/version2_0/relationships/includes.rb +59 -0
  198. data/lib/bel_parser/language/version2_0/relationships/increases.rb +63 -0
  199. data/lib/bel_parser/language/version2_0/relationships/is_a.rb +48 -0
  200. data/lib/bel_parser/language/version2_0/relationships/negative_correlation.rb +50 -0
  201. data/lib/bel_parser/language/version2_0/relationships/orthologous.rb +48 -0
  202. data/lib/bel_parser/language/version2_0/relationships/positive_correlation.rb +46 -0
  203. data/lib/bel_parser/language/version2_0/relationships/prognostic_biomarker_for.rb +48 -0
  204. data/lib/bel_parser/language/version2_0/relationships/rate_limiting_step_of.rb +53 -0
  205. data/lib/bel_parser/language/version2_0/relationships/reactant_in.rb +60 -0
  206. data/lib/bel_parser/language/version2_0/relationships/regulates.rb +51 -0
  207. data/lib/bel_parser/language/version2_0/relationships/sub_process_of.rb +55 -0
  208. data/lib/bel_parser/language/version2_0/relationships/transcribed_to.rb +53 -0
  209. data/lib/bel_parser/language/version2_0/relationships/translated_to.rb +54 -0
  210. data/lib/bel_parser/language/version2_0/relationships/translocates.rb +57 -0
  211. data/lib/bel_parser/language/version2_0/return_types/abundance.rb +20 -0
  212. data/lib/bel_parser/language/version2_0/return_types/activity.rb +20 -0
  213. data/lib/bel_parser/language/version2_0/return_types/any.rb +74 -0
  214. data/lib/bel_parser/language/version2_0/return_types/biological_process.rb +17 -0
  215. data/lib/bel_parser/language/version2_0/return_types/complex_abundance.rb +17 -0
  216. data/lib/bel_parser/language/version2_0/return_types/fragment.rb +20 -0
  217. data/lib/bel_parser/language/version2_0/return_types/from_location.rb +20 -0
  218. data/lib/bel_parser/language/version2_0/return_types/fusion.rb +17 -0
  219. data/lib/bel_parser/language/version2_0/return_types/gene_abundance.rb +17 -0
  220. data/lib/bel_parser/language/version2_0/return_types/list.rb +17 -0
  221. data/lib/bel_parser/language/version2_0/return_types/location.rb +20 -0
  222. data/lib/bel_parser/language/version2_0/return_types/micro_rna_abundance.rb +17 -0
  223. data/lib/bel_parser/language/version2_0/return_types/molecular_activity.rb +20 -0
  224. data/lib/bel_parser/language/version2_0/return_types/pathology.rb +17 -0
  225. data/lib/bel_parser/language/version2_0/return_types/products.rb +17 -0
  226. data/lib/bel_parser/language/version2_0/return_types/protein_abundance.rb +17 -0
  227. data/lib/bel_parser/language/version2_0/return_types/protein_modification.rb +17 -0
  228. data/lib/bel_parser/language/version2_0/return_types/reactants.rb +17 -0
  229. data/lib/bel_parser/language/version2_0/return_types/rna_abundance.rb +17 -0
  230. data/lib/bel_parser/language/version2_0/return_types/to_location.rb +20 -0
  231. data/lib/bel_parser/language/version2_0/return_types/variant.rb +20 -0
  232. data/lib/bel_parser/language/version2_0/value_encodings/abundance.rb +21 -0
  233. data/lib/bel_parser/language/version2_0/value_encodings/activity.rb +21 -0
  234. data/lib/bel_parser/language/version2_0/value_encodings/any.rb +74 -0
  235. data/lib/bel_parser/language/version2_0/value_encodings/biological_process.rb +21 -0
  236. data/lib/bel_parser/language/version2_0/value_encodings/complex_abundance.rb +21 -0
  237. data/lib/bel_parser/language/version2_0/value_encodings/gene_abundance.rb +21 -0
  238. data/lib/bel_parser/language/version2_0/value_encodings/location.rb +21 -0
  239. data/lib/bel_parser/language/version2_0/value_encodings/micro_rna_abundance.rb +21 -0
  240. data/lib/bel_parser/language/version2_0/value_encodings/pathology.rb +21 -0
  241. data/lib/bel_parser/language/version2_0/value_encodings/protein_abundance.rb +21 -0
  242. data/lib/bel_parser/language/version2_0/value_encodings/protein_modification.rb +21 -0
  243. data/lib/bel_parser/language/version2_0/value_encodings/rna_abundance.rb +21 -0
  244. data/lib/bel_parser/mixin/line_continuator.rb +15 -0
  245. data/lib/bel_parser/mixin/line_mapping.rb +14 -0
  246. data/lib/bel_parser/parsers/ast/node.rb +987 -0
  247. data/lib/bel_parser/parsers/ast/sexp.rb +8 -0
  248. data/lib/bel_parser/parsers/bel_script.rb +5 -0
  249. data/lib/bel_parser/parsers/bel_script/define_annotation.rb +5920 -0
  250. data/lib/bel_parser/parsers/bel_script/define_annotation.rl +141 -0
  251. data/lib/bel_parser/parsers/bel_script/define_namespace.rb +1780 -0
  252. data/lib/bel_parser/parsers/bel_script/define_namespace.rl +121 -0
  253. data/lib/bel_parser/parsers/bel_script/set.rb +5008 -0
  254. data/lib/bel_parser/parsers/bel_script/set.rl +116 -0
  255. data/lib/bel_parser/parsers/bel_script/set_document.rb +7722 -0
  256. data/lib/bel_parser/parsers/bel_script/set_document.rl +97 -0
  257. data/lib/bel_parser/parsers/bel_script/unset.rb +706 -0
  258. data/lib/bel_parser/parsers/bel_script/unset.rl +95 -0
  259. data/lib/bel_parser/parsers/common.rb +5 -0
  260. data/lib/bel_parser/parsers/common/blank_line.rb +211 -0
  261. data/lib/bel_parser/parsers/common/blank_line.rl +81 -0
  262. data/lib/bel_parser/parsers/common/comment_line.rb +245 -0
  263. data/lib/bel_parser/parsers/common/comment_line.rl +97 -0
  264. data/lib/bel_parser/parsers/common/common.rb +7 -0
  265. data/lib/bel_parser/parsers/common/common.rl +13 -0
  266. data/lib/bel_parser/parsers/common/identifier.rb +289 -0
  267. data/lib/bel_parser/parsers/common/identifier.rl +106 -0
  268. data/lib/bel_parser/parsers/common/list.rb +2388 -0
  269. data/lib/bel_parser/parsers/common/list.rl +146 -0
  270. data/lib/bel_parser/parsers/common/string.rb +271 -0
  271. data/lib/bel_parser/parsers/common/string.rl +107 -0
  272. data/lib/bel_parser/parsers/expression.rb +7 -0
  273. data/lib/bel_parser/parsers/expression/comment.rb +239 -0
  274. data/lib/bel_parser/parsers/expression/comment.rl +97 -0
  275. data/lib/bel_parser/parsers/expression/nested_statement.rb +17802 -0
  276. data/lib/bel_parser/parsers/expression/nested_statement.rl +141 -0
  277. data/lib/bel_parser/parsers/expression/observed_term.rb +7291 -0
  278. data/lib/bel_parser/parsers/expression/observed_term.rl +92 -0
  279. data/lib/bel_parser/parsers/expression/parameter.rb +1506 -0
  280. data/lib/bel_parser/parsers/expression/parameter.rl +97 -0
  281. data/lib/bel_parser/parsers/expression/relationship.rb +254 -0
  282. data/lib/bel_parser/parsers/expression/relationship.rl +98 -0
  283. data/lib/bel_parser/parsers/expression/simple_statement.rb +10475 -0
  284. data/lib/bel_parser/parsers/expression/simple_statement.rl +112 -0
  285. data/lib/bel_parser/parsers/expression/term.rb +3989 -0
  286. data/lib/bel_parser/parsers/expression/term.rl +157 -0
  287. data/lib/bel_parser/parsers/line_parser.rb +92 -0
  288. data/lib/bel_parser/parsers/mixin/buffer.rb +10 -0
  289. data/lib/bel_parser/parsers/nonblocking_io_wrapper.rb +50 -0
  290. data/lib/bel_parser/parsers/serializer.rb +205 -0
  291. data/lib/bel_parser/quoting.rb +177 -0
  292. data/lib/bel_parser/resource/concept.rb +56 -0
  293. data/lib/bel_parser/resource/concept_scheme.rb +35 -0
  294. data/lib/bel_parser/resource/dataset.rb +34 -0
  295. data/lib/bel_parser/resource/eager_reader.rb +89 -0
  296. data/lib/bel_parser/resource/eager_sparql_reader.rb +51 -0
  297. data/lib/bel_parser/resource/file_resource.rb +21 -0
  298. data/lib/bel_parser/resource/file_resource_value.rb +24 -0
  299. data/lib/bel_parser/resource/jena_tdb_reader.rb +246 -0
  300. data/lib/bel_parser/resource/lru_cache.rb +111 -0
  301. data/lib/bel_parser/resource/lru_reader.rb +34 -0
  302. data/lib/bel_parser/resource/reader.rb +18 -0
  303. data/lib/bel_parser/resource/resource_url_reader.rb +181 -0
  304. data/lib/bel_parser/resource/sparql_reader.rb +179 -0
  305. data/lib/bel_parser/resource/value.rb +31 -0
  306. data/lib/bel_parser/script.rb +8 -0
  307. data/lib/bel_parser/script/filter.rb +35 -0
  308. data/lib/bel_parser/script/first_node.rb +21 -0
  309. data/lib/bel_parser/script/keywords.rb +32 -0
  310. data/lib/bel_parser/script/nanopub_mapper.rb +182 -0
  311. data/lib/bel_parser/script/parser.rb +51 -0
  312. data/lib/bel_parser/script/state/annotation_definition.rb +62 -0
  313. data/lib/bel_parser/script/state/bel_version.rb +36 -0
  314. data/lib/bel_parser/script/state/document_property.rb +29 -0
  315. data/lib/bel_parser/script/state/namespace_definition.rb +32 -0
  316. data/lib/bel_parser/script/state/set.rb +82 -0
  317. data/lib/bel_parser/script/state/unset.rb +46 -0
  318. data/lib/bel_parser/script/state_aggregator.rb +49 -0
  319. data/lib/bel_parser/script/state_function.rb +10 -0
  320. data/lib/bel_parser/script/syntax/expression_validation.rb +46 -0
  321. data/lib/bel_parser/script/syntax/invalid_regex_pattern.rb +49 -0
  322. data/lib/bel_parser/script/syntax/undefined_annotation.rb +61 -0
  323. data/lib/bel_parser/script/syntax/undefined_annotation_value.rb +84 -0
  324. data/lib/bel_parser/script/syntax/unresolvable_namespace.rb +54 -0
  325. data/lib/bel_parser/script/syntax/unsupported_bel_version.rb +59 -0
  326. data/lib/bel_parser/script/validator.rb +65 -0
  327. data/lib/bel_parser/vendor/ast.rb +17 -0
  328. data/lib/bel_parser/vendor/ast/node.rb +254 -0
  329. data/lib/bel_parser/vendor/ast/processor.rb +12 -0
  330. data/lib/bel_parser/vendor/ast/processor/mixin.rb +282 -0
  331. data/lib/bel_parser/vendor/ast/sexp.rb +30 -0
  332. metadata +390 -0
@@ -0,0 +1,41 @@
1
+ require_relative '../../version1_0'
2
+ require_relative '../../relationship'
3
+
4
+ module BELParser
5
+ module Language
6
+ module Version1_0
7
+ module Relationships
8
+ # Analogous: +A analogous B+ - For terms A and B, +A analogousTo
9
+ # B+ indicates that A and B represent abundances or molecular
10
+ # activities in different species which function in a similar
11
+ # manner.
12
+ class Analogous
13
+ extend Relationship
14
+
15
+ SHORT = :analogous
16
+ LONG = :analogous
17
+ DESCRIPTION = ' +A analogous B+ - For terms A and B, +A
18
+ nalogousTo B+ indicates that A and B represent
19
+ bundances or molecular activities in different
20
+ pecies which function in a similar manner.'.freeze
21
+
22
+ def self.short
23
+ SHORT
24
+ end
25
+
26
+ def self.long
27
+ LONG
28
+ end
29
+
30
+ def self.description
31
+ DESCRIPTION
32
+ end
33
+
34
+ def self.genomic?
35
+ true
36
+ end
37
+ end
38
+ end
39
+ end
40
+ end
41
+ end
@@ -0,0 +1,42 @@
1
+ require_relative '../../version1_0'
2
+ require_relative '../../relationship'
3
+
4
+ module BELParser
5
+ module Language
6
+ module Version1_0
7
+ module Relationships
8
+ # Association: +A -- B+ - For terms A and B, +A association
9
+ # B+ or +A -- B+ indicates that A and B are associated in an
10
+ # unspecified manner. This relationship is used when not enough
11
+ # information about the association is available to describe
12
+ # it using more specific relationships, like increases or
13
+ # positiveCorrelation.
14
+ class Association
15
+ extend Relationship
16
+
17
+ SHORT = :'--'
18
+ LONG = :association
19
+ DESCRIPTION = ' +A -- B+ - For terms A and B, +A association B+
20
+ r +A -- B+ indicates that A and B are associated
21
+ n an unspecified manner. This relationship
22
+ s used when not enough information about the
23
+ ssociation is available to describe it using
24
+ ore specific relationships, like increases or
25
+ ositiveCorrelation.'.freeze
26
+
27
+ def self.short
28
+ SHORT
29
+ end
30
+
31
+ def self.long
32
+ LONG
33
+ end
34
+
35
+ def self.description
36
+ DESCRIPTION
37
+ end
38
+ end
39
+ end
40
+ end
41
+ end
42
+ end
@@ -0,0 +1,42 @@
1
+ require_relative '../../version1_0'
2
+ require_relative '../../relationship'
3
+
4
+ module BELParser
5
+ module Language
6
+ module Version1_0
7
+ module Relationships
8
+ # BiomarkerFor: +A biomarkerFor P+ - For term A and process term
9
+ # P, +A biomarkerFor P+ indicates that changes in or detection
10
+ # of A is used in some way to be a biomarker for pathology or
11
+ # biological process P.
12
+ class BiomarkerFor
13
+ extend Relationship
14
+
15
+ SHORT = :biomarkerFor
16
+ LONG = :biomarkerFor
17
+ DESCRIPTION = ' +A biomarkerFor P+ - For term A and process
18
+ erm P, +A biomarkerFor P+ indicates that changes
19
+ n or detection of A is used in some way to be
20
+ biomarker for pathology or biological process
21
+ .'.freeze
22
+
23
+ def self.short
24
+ SHORT
25
+ end
26
+
27
+ def self.long
28
+ LONG
29
+ end
30
+
31
+ def self.description
32
+ DESCRIPTION
33
+ end
34
+
35
+ def self.directed?
36
+ true
37
+ end
38
+ end
39
+ end
40
+ end
41
+ end
42
+ end
@@ -0,0 +1,50 @@
1
+ require_relative '../../version1_0'
2
+ require_relative '../../relationship'
3
+
4
+ module BELParser
5
+ module Language
6
+ module Version1_0
7
+ module Relationships
8
+ # CausesNoChange: +A causesNoChange B+ - For terms A and B,
9
+ # +A causesNoChange B+ indicates that B was observed not to
10
+ # change in response to changes in A. Statements using this
11
+ # relationship correspond to cases where explicit measurement
12
+ # of B demonstrates lack of significant change, not for cases
13
+ # where the state of B is unknown.
14
+ class CausesNoChange
15
+ extend Relationship
16
+
17
+ SHORT = :causesNoChange
18
+ LONG = :causesNoChange
19
+ DESCRIPTION = ' +A causesNoChange B+ - For terms A and B, +A
20
+ ausesNoChange B+ indicates that B was observed not
21
+ o change in response to changes in A. Statements
22
+ sing this relationship correspond to cases where
23
+ xplicit measurement of B demonstrates lack of
24
+ ignificant change, not for cases where the state
25
+ f B is unknown.'.freeze
26
+
27
+ def self.short
28
+ SHORT
29
+ end
30
+
31
+ def self.long
32
+ LONG
33
+ end
34
+
35
+ def self.description
36
+ DESCRIPTION
37
+ end
38
+
39
+ def self.causal?
40
+ true
41
+ end
42
+
43
+ def self.directed?
44
+ true
45
+ end
46
+ end
47
+ end
48
+ end
49
+ end
50
+ end
@@ -0,0 +1,63 @@
1
+ require_relative '../../version1_0'
2
+ require_relative '../../relationship'
3
+
4
+ module BELParser
5
+ module Language
6
+ module Version1_0
7
+ module Relationships
8
+ # Decreases: +A -| B+ - For terms A and B, +A decreases B or
9
+ # A -| B+ indicates that increases in A have been observed to
10
+ # cause decreases in B. +A decreases B+ also represents cases
11
+ # where decreases in A have been observed to cause increases in B,
12
+ # for example, in recording the results of gene deletion or other
13
+ # inhibition experiments. A is a BEL Term and B is either a BEL
14
+ # Term or a BEL Statement. The relationship does not indicate
15
+ # that the changes in A are either necessary for changes in B,
16
+ # nor does it indicate that changes in A are sufficient to cause
17
+ # changes in B.
18
+ class Decreases
19
+ extend Relationship
20
+
21
+ SHORT = :'-|'
22
+ LONG = :decreases
23
+ DESCRIPTION = ' +A -| B+ - For terms A and B, +A decreases B
24
+ r A -| B+ indicates that increases in A have been
25
+ bserved to cause decreases in B. +A decreases
26
+ + also represents cases where decreases in A
27
+ ave been observed to cause increases in B, for
28
+ xample, in recording the results of gene deletion
29
+ r other inhibition experiments. A is a BEL Term
30
+ nd B is either a BEL Term or a BEL Statement. The
31
+ elationship does not indicate that the changes
32
+ n A are either necessary for changes in B, nor
33
+ oes it indicate that changes in A are sufficient
34
+ o cause changes in B.'.freeze
35
+
36
+ def self.short
37
+ SHORT
38
+ end
39
+
40
+ def self.long
41
+ LONG
42
+ end
43
+
44
+ def self.description
45
+ DESCRIPTION
46
+ end
47
+
48
+ def self.causal?
49
+ true
50
+ end
51
+
52
+ def self.decreasing?
53
+ true
54
+ end
55
+
56
+ def self.directed?
57
+ true
58
+ end
59
+ end
60
+ end
61
+ end
62
+ end
63
+ end
@@ -0,0 +1,56 @@
1
+ require_relative '../../version1_0'
2
+ require_relative '../../relationship'
3
+
4
+ module BELParser
5
+ module Language
6
+ module Version1_0
7
+ module Relationships
8
+ # DirectlyDecreases: +A =| B+ - For terms A and B, +A
9
+ # directlyDecreases B or A =| B+ indicates A decreases B and that
10
+ # the mechanism of the causal relationship is based on physical
11
+ # interaction of entities related to A and B. This is a direct
12
+ # version of the decreases relationship.
13
+ class DirectlyDecreases
14
+ extend Relationship
15
+
16
+ SHORT = :'=|'
17
+ LONG = :directlyDecreases
18
+ DESCRIPTION = ' +A =| B+ - For terms A and B,
19
+ A directlyDecreases B or A =| B+ indicates A
20
+ ecreases B and that the mechanism of the causal
21
+ elationship is based on physical interaction
22
+ f entities related to A and B. This is a direct
23
+ ersion of the decreases relationship.'.freeze
24
+
25
+ def self.short
26
+ SHORT
27
+ end
28
+
29
+ def self.long
30
+ LONG
31
+ end
32
+
33
+ def self.description
34
+ DESCRIPTION
35
+ end
36
+
37
+ def self.causal?
38
+ true
39
+ end
40
+
41
+ def self.decreasing?
42
+ true
43
+ end
44
+
45
+ def self.direct?
46
+ true
47
+ end
48
+
49
+ def self.directed?
50
+ true
51
+ end
52
+ end
53
+ end
54
+ end
55
+ end
56
+ end
@@ -0,0 +1,56 @@
1
+ require_relative '../../version1_0'
2
+ require_relative '../../relationship'
3
+
4
+ module BELParser
5
+ module Language
6
+ module Version1_0
7
+ module Relationships
8
+ # DirectlyIncreases: +A => B+ - For terms A and B, +A
9
+ # directlyIncreases B or A => B+ indicate A increases B and that
10
+ # the mechanism of the causal relationship is based on physical
11
+ # interaction of entities related to A and B. This is a direct
12
+ # version of the increases relationship.
13
+ class DirectlyIncreases
14
+ extend Relationship
15
+
16
+ SHORT = :'=>'
17
+ LONG = :directlyIncreases
18
+ DESCRIPTION = ' +A => B+ - For terms A and B,
19
+ A directlyIncreases B or A => B+ indicate A
20
+ ncreases B and that the mechanism of the causal
21
+ elationship is based on physical interaction
22
+ f entities related to A and B. This is a direct
23
+ ersion of the increases relationship.'.freeze
24
+
25
+ def self.short
26
+ SHORT
27
+ end
28
+
29
+ def self.long
30
+ LONG
31
+ end
32
+
33
+ def self.description
34
+ DESCRIPTION
35
+ end
36
+
37
+ def self.causal?
38
+ true
39
+ end
40
+
41
+ def self.increasing?
42
+ true
43
+ end
44
+
45
+ def self.direct?
46
+ true
47
+ end
48
+
49
+ def self.directed?
50
+ true
51
+ end
52
+ end
53
+ end
54
+ end
55
+ end
56
+ end
@@ -0,0 +1,62 @@
1
+ require_relative '../../version1_0'
2
+ require_relative '../../relationship'
3
+
4
+ module BELParser
5
+ module Language
6
+ module Version1_0
7
+ module Relationships
8
+ # HasComponent: +A hasComponent A1+ - For complexAbundance
9
+ # term A and abundance term B, +A hasComponent B+ designates
10
+ # B as a component of A, that complexes that are instances of
11
+ # A have instances of B as possible components. Note that, the
12
+ # stoichiometry of A is not described, nor is it stated that B is
13
+ # a required component. The use of hasComponent relationships is
14
+ # complementary to the use of functionally composed complexes and
15
+ # is intended to enable the assignment of components to complexes
16
+ # designated by names in external vocabularies. The assignment
17
+ # of components can potentially enable the reconciliation of
18
+ # equivalent complexes at knowledge assembly time.
19
+ class HasComponent
20
+ extend Relationship
21
+
22
+ SHORT = :hasComponent
23
+ LONG = :hasComponent
24
+ DESCRIPTION = ' +A hasComponent A1+ - For complexAbundance
25
+ erm A and abundance term B, +A hasComponent B+
26
+ esignates B as a component of A, that complexes
27
+ hat are instances of A have instances of B as
28
+ ossible components. Note that, the stoichiometry
29
+ f A is not described, nor is it stated that B
30
+ s a required component. The use of hasComponent
31
+ elationships is complementary to the use of
32
+ unctionally composed complexes and is intended to
33
+ nable the assignment of components to complexes
34
+ esignated by names in external vocabularies. The
35
+ ssignment of components can potentially enable
36
+ he reconciliation of equivalent complexes at
37
+ nowledge assembly time.'.freeze
38
+
39
+ def self.short
40
+ SHORT
41
+ end
42
+
43
+ def self.long
44
+ LONG
45
+ end
46
+
47
+ def self.description
48
+ DESCRIPTION
49
+ end
50
+
51
+ def self.direct?
52
+ true
53
+ end
54
+
55
+ def self.directed?
56
+ true
57
+ end
58
+ end
59
+ end
60
+ end
61
+ end
62
+ end
@@ -0,0 +1,61 @@
1
+ require_relative '../../version1_0'
2
+ require_relative '../../relationship'
3
+
4
+ module BELParser
5
+ module Language
6
+ module Version1_0
7
+ module Relationships
8
+ # HasComponents: +A hasComponents (B, C, D)+ - The hasComponents
9
+ # relationship is a special form which enables the assignment
10
+ # of multiple complex components in a single statement where
11
+ # the object of the statement is a set of abundance terms. A
12
+ # statement using hasComponents is exactly equivalent to multiple
13
+ # hasComponent statements. A term may not appear in both the
14
+ # subject and object of the same hasComponents statement. For
15
+ # the abundance terms A, B, C and D, +A hasComponents B, C, D+
16
+ # indicates that A has components B, C and D.
17
+ class HasComponents
18
+ extend Relationship
19
+
20
+ SHORT = :hasComponents
21
+ LONG = :hasComponents
22
+ DESCRIPTION = ' +A hasComponents (B, C, D)+ - The hasComponents
23
+ elationship is a special form which enables
24
+ he assignment of multiple complex components
25
+ n a single statement where the object of the
26
+ tatement is a set of abundance terms. A statement
27
+ sing hasComponents is exactly equivalent to
28
+ ultiple hasComponent statements. A term may not
29
+ ppear in both the subject and object of the same
30
+ asComponents statement. For the abundance terms A,
31
+ , C and D, +A hasComponents B, C, D+ indicates
32
+ hat A has components B, C and D.'.freeze
33
+
34
+ def self.short
35
+ SHORT
36
+ end
37
+
38
+ def self.long
39
+ LONG
40
+ end
41
+
42
+ def self.description
43
+ DESCRIPTION
44
+ end
45
+
46
+ def self.direct?
47
+ true
48
+ end
49
+
50
+ def self.directed?
51
+ true
52
+ end
53
+
54
+ def self.listable?
55
+ true
56
+ end
57
+ end
58
+ end
59
+ end
60
+ end
61
+ end