bel_parser 1.0.0.alpha.27-java

This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.
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 +1,95 @@
1
+ # begin: ragel
2
+ =begin
3
+ %%{
4
+ machine bel;
5
+
6
+ include 'common.rl';
7
+ include 'identifier.rl';
8
+
9
+ UNSET = [uU][nN][sS][eE][tT];
10
+
11
+ action unset_keyword {
12
+ @buffers[:unset] = unset()
13
+ }
14
+
15
+ action name {
16
+ @buffers[:unset] = @buffers[:unset] << name(@buffers[:ident])
17
+ }
18
+
19
+ action yield_set {
20
+ yield @buffers[:unset]
21
+ }
22
+
23
+ unset :=
24
+ UNSET %unset_keyword
25
+ SP+
26
+ IDENT %name
27
+ NL @yield_set;
28
+ }%%
29
+ =end
30
+ # end: ragel
31
+
32
+ require_relative '../ast/node'
33
+ require_relative '../mixin/buffer'
34
+ require_relative '../nonblocking_io_wrapper'
35
+
36
+ module BELParser
37
+ module Parsers
38
+ module BELScript
39
+ module Unset
40
+
41
+ class << self
42
+
43
+ MAX_LENGTH = 1024 * 128 # 128K
44
+
45
+ def parse(content)
46
+ return nil unless content
47
+
48
+ Parser.new(content).each do |obj|
49
+ yield obj
50
+ end
51
+ end
52
+ end
53
+
54
+ private
55
+
56
+ class Parser
57
+ include Enumerable
58
+ include BELParser::Parsers::Buffer
59
+ include BELParser::Parsers::AST::Sexp
60
+
61
+ def initialize(content)
62
+ @content = content
63
+ # begin: ragel
64
+ %% write data;
65
+ # end: ragel
66
+ end
67
+
68
+ def each
69
+ @buffers = {}
70
+ data = @content.unpack('C*')
71
+ p = 0
72
+ pe = data.length
73
+ eof = data.length
74
+
75
+ # begin: ragel
76
+ %% write init;
77
+ %% write exec;
78
+ # end: ragel
79
+ end
80
+ end
81
+ end
82
+ end
83
+ end
84
+ end
85
+
86
+ if __FILE__ == $0
87
+ $stdin.each_line do |line|
88
+ BELParser::Parsers::BELScript::Unset.parse(line) { |obj|
89
+ puts obj.inspect
90
+ }
91
+ end
92
+ end
93
+
94
+ # vim: ft=ruby ts=2 sw=2:
95
+ # encoding: utf-8
@@ -0,0 +1,5 @@
1
+ require_relative 'common/blank_line'
2
+ require_relative 'common/comment_line'
3
+ require_relative 'common/identifier'
4
+ require_relative 'common/string'
5
+ require_relative 'common/list'
@@ -0,0 +1,211 @@
1
+
2
+ # begin: ragel
3
+ =begin
4
+
5
+
6
+ =end
7
+ # end: ragel
8
+
9
+ require_relative '../ast/node'
10
+ require_relative '../mixin/buffer'
11
+ require_relative '../nonblocking_io_wrapper'
12
+
13
+ module BELParser
14
+ module Parsers
15
+ module Common
16
+ module BlankLine
17
+
18
+ class << self
19
+
20
+ MAX_LENGTH = 1024 * 128 # 128K
21
+
22
+ def parse(content)
23
+ return nil unless content
24
+
25
+ Parser.new(content).each do |obj|
26
+ yield obj
27
+ end
28
+ end
29
+ end
30
+
31
+ private
32
+
33
+ class Parser
34
+ include Enumerable
35
+ include BELParser::Parsers::Buffer
36
+ include BELParser::Parsers::AST::Sexp
37
+
38
+ def initialize(content)
39
+ @content = content
40
+ # begin: ragel
41
+
42
+ class << self
43
+ attr_accessor :_bel_trans_keys
44
+ private :_bel_trans_keys, :_bel_trans_keys=
45
+ end
46
+ self._bel_trans_keys = [
47
+ 0, 0, 9, 32, 0, 0,
48
+ 0
49
+ ]
50
+
51
+ class << self
52
+ attr_accessor :_bel_key_spans
53
+ private :_bel_key_spans, :_bel_key_spans=
54
+ end
55
+ self._bel_key_spans = [
56
+ 0, 24, 0
57
+ ]
58
+
59
+ class << self
60
+ attr_accessor :_bel_index_offsets
61
+ private :_bel_index_offsets, :_bel_index_offsets=
62
+ end
63
+ self._bel_index_offsets = [
64
+ 0, 0, 25
65
+ ]
66
+
67
+ class << self
68
+ attr_accessor :_bel_indicies
69
+ private :_bel_indicies, :_bel_indicies=
70
+ end
71
+ self._bel_indicies = [
72
+ 0, 2, 1, 1, 1, 1, 1, 1,
73
+ 1, 1, 1, 1, 1, 1, 1, 1,
74
+ 1, 1, 1, 1, 1, 1, 1, 0,
75
+ 1, 1, 0
76
+ ]
77
+
78
+ class << self
79
+ attr_accessor :_bel_trans_targs
80
+ private :_bel_trans_targs, :_bel_trans_targs=
81
+ end
82
+ self._bel_trans_targs = [
83
+ 1, 0, 2
84
+ ]
85
+
86
+ class << self
87
+ attr_accessor :_bel_trans_actions
88
+ private :_bel_trans_actions, :_bel_trans_actions=
89
+ end
90
+ self._bel_trans_actions = [
91
+ 0, 0, 1
92
+ ]
93
+
94
+ class << self
95
+ attr_accessor :bel_start
96
+ end
97
+ self.bel_start = 1;
98
+ class << self
99
+ attr_accessor :bel_first_final
100
+ end
101
+ self.bel_first_final = 2;
102
+ class << self
103
+ attr_accessor :bel_error
104
+ end
105
+ self.bel_error = 0;
106
+
107
+ class << self
108
+ attr_accessor :bel_en_blank
109
+ end
110
+ self.bel_en_blank = 1;
111
+
112
+
113
+ # end: ragel
114
+ end
115
+
116
+ def each
117
+ @buffers = {}
118
+ data = @content.unpack('C*')
119
+ p = 0
120
+ pe = data.length
121
+
122
+ # begin: ragel
123
+
124
+ begin
125
+ p ||= 0
126
+ pe ||= data.length
127
+ cs = bel_start
128
+ end
129
+
130
+
131
+ begin
132
+ testEof = false
133
+ _slen, _trans, _keys, _inds, _acts, _nacts = nil
134
+ _goto_level = 0
135
+ _resume = 10
136
+ _eof_trans = 15
137
+ _again = 20
138
+ _test_eof = 30
139
+ _out = 40
140
+ while true
141
+ if _goto_level <= 0
142
+ if p == pe
143
+ _goto_level = _test_eof
144
+ next
145
+ end
146
+ if cs == 0
147
+ _goto_level = _out
148
+ next
149
+ end
150
+ end
151
+ if _goto_level <= _resume
152
+ _keys = cs << 1
153
+ _inds = _bel_index_offsets[cs]
154
+ _slen = _bel_key_spans[cs]
155
+ _wide = data[p].ord
156
+ _trans = if ( _slen > 0 &&
157
+ _bel_trans_keys[_keys] <= _wide &&
158
+ _wide <= _bel_trans_keys[_keys + 1]
159
+ ) then
160
+ _bel_indicies[ _inds + _wide - _bel_trans_keys[_keys] ]
161
+ else
162
+ _bel_indicies[ _inds + _slen ]
163
+ end
164
+ cs = _bel_trans_targs[_trans]
165
+ if _bel_trans_actions[_trans] != 0
166
+ case _bel_trans_actions[_trans]
167
+ when 1 then
168
+ begin
169
+
170
+ yield blank_line
171
+ end
172
+ end
173
+ end
174
+ end
175
+ if _goto_level <= _again
176
+ if cs == 0
177
+ _goto_level = _out
178
+ next
179
+ end
180
+ p += 1
181
+ if p != pe
182
+ _goto_level = _resume
183
+ next
184
+ end
185
+ end
186
+ if _goto_level <= _test_eof
187
+ end
188
+ if _goto_level <= _out
189
+ break
190
+ end
191
+ end
192
+ end
193
+
194
+ # end: ragel
195
+ end
196
+ end
197
+ end
198
+ end
199
+ end
200
+ end
201
+
202
+ if __FILE__ == $0
203
+ $stdin.each_line do |line|
204
+ BELParser::Parsers::Common::BlankLine.parse(line) { |obj|
205
+ puts obj.inspect
206
+ }
207
+ end
208
+ end
209
+
210
+ # vim: ft=ruby ts=2 sw=2:
211
+ # encoding: utf-8
@@ -0,0 +1,81 @@
1
+ # begin: ragel
2
+ =begin
3
+ %%{
4
+ machine bel;
5
+
6
+ include 'common.rl';
7
+
8
+ action yield_blank_line {
9
+ yield blank_line
10
+ }
11
+
12
+ BLANK = SP*;
13
+
14
+ blank := BLANK %yield_blank_line NL;
15
+ }%%
16
+ =end
17
+ # end: ragel
18
+
19
+ require_relative '../ast/node'
20
+ require_relative '../mixin/buffer'
21
+ require_relative '../nonblocking_io_wrapper'
22
+
23
+ module BELParser
24
+ module Parsers
25
+ module Common
26
+ module BlankLine
27
+
28
+ class << self
29
+
30
+ MAX_LENGTH = 1024 * 128 # 128K
31
+
32
+ def parse(content)
33
+ return nil unless content
34
+
35
+ Parser.new(content).each do |obj|
36
+ yield obj
37
+ end
38
+ end
39
+ end
40
+
41
+ private
42
+
43
+ class Parser
44
+ include Enumerable
45
+ include BELParser::Parsers::Buffer
46
+ include BELParser::Parsers::AST::Sexp
47
+
48
+ def initialize(content)
49
+ @content = content
50
+ # begin: ragel
51
+ %% write data;
52
+ # end: ragel
53
+ end
54
+
55
+ def each
56
+ @buffers = {}
57
+ data = @content.unpack('C*')
58
+ p = 0
59
+ pe = data.length
60
+
61
+ # begin: ragel
62
+ %% write init;
63
+ %% write exec;
64
+ # end: ragel
65
+ end
66
+ end
67
+ end
68
+ end
69
+ end
70
+ end
71
+
72
+ if __FILE__ == $0
73
+ $stdin.each_line do |line|
74
+ BELParser::Parsers::Common::BlankLine.parse(line) { |obj|
75
+ puts obj.inspect
76
+ }
77
+ end
78
+ end
79
+
80
+ # vim: ft=ruby ts=2 sw=2:
81
+ # encoding: utf-8
@@ -0,0 +1,245 @@
1
+
2
+ # begin: ragel
3
+ =begin
4
+
5
+
6
+ =end
7
+ # end: ragel
8
+
9
+ require_relative '../ast/node'
10
+ require_relative '../mixin/buffer'
11
+ require_relative '../nonblocking_io_wrapper'
12
+
13
+ module BELParser
14
+ module Parsers
15
+ module Common
16
+ module CommentLine
17
+
18
+ class << self
19
+
20
+ MAX_LENGTH = 1024 * 128 # 128K
21
+
22
+ def parse(content)
23
+ return nil unless content
24
+
25
+ Parser.new(content).each do |obj|
26
+ yield obj
27
+ end
28
+ end
29
+ end
30
+
31
+ private
32
+
33
+ class Parser
34
+ include Enumerable
35
+ include BELParser::Parsers::Buffer
36
+ include BELParser::Parsers::AST::Sexp
37
+
38
+ def initialize(content)
39
+ @content = content
40
+ # begin: ragel
41
+
42
+ class << self
43
+ attr_accessor :_bel_trans_keys
44
+ private :_bel_trans_keys, :_bel_trans_keys=
45
+ end
46
+ self._bel_trans_keys = [
47
+ 0, 0, 9, 35, 10, 10,
48
+ 10, 10, 0, 0, 0
49
+ ]
50
+
51
+ class << self
52
+ attr_accessor :_bel_key_spans
53
+ private :_bel_key_spans, :_bel_key_spans=
54
+ end
55
+ self._bel_key_spans = [
56
+ 0, 27, 1, 1, 0
57
+ ]
58
+
59
+ class << self
60
+ attr_accessor :_bel_index_offsets
61
+ private :_bel_index_offsets, :_bel_index_offsets=
62
+ end
63
+ self._bel_index_offsets = [
64
+ 0, 0, 28, 30, 32
65
+ ]
66
+
67
+ class << self
68
+ attr_accessor :_bel_indicies
69
+ private :_bel_indicies, :_bel_indicies=
70
+ end
71
+ self._bel_indicies = [
72
+ 0, 1, 1, 1, 1, 1, 1, 1,
73
+ 1, 1, 1, 1, 1, 1, 1, 1,
74
+ 1, 1, 1, 1, 1, 1, 1, 0,
75
+ 1, 1, 2, 1, 4, 3, 6, 5,
76
+ 1, 0
77
+ ]
78
+
79
+ class << self
80
+ attr_accessor :_bel_trans_targs
81
+ private :_bel_trans_targs, :_bel_trans_targs=
82
+ end
83
+ self._bel_trans_targs = [
84
+ 1, 0, 2, 3, 4, 3, 4
85
+ ]
86
+
87
+ class << self
88
+ attr_accessor :_bel_trans_actions
89
+ private :_bel_trans_actions, :_bel_trans_actions=
90
+ end
91
+ self._bel_trans_actions = [
92
+ 0, 0, 0, 1, 2, 3, 4
93
+ ]
94
+
95
+ class << self
96
+ attr_accessor :bel_start
97
+ end
98
+ self.bel_start = 1;
99
+ class << self
100
+ attr_accessor :bel_first_final
101
+ end
102
+ self.bel_first_final = 4;
103
+ class << self
104
+ attr_accessor :bel_error
105
+ end
106
+ self.bel_error = 0;
107
+
108
+ class << self
109
+ attr_accessor :bel_en_comment_line
110
+ end
111
+ self.bel_en_comment_line = 1;
112
+
113
+
114
+ # end: ragel
115
+ end
116
+
117
+ def each
118
+ @buffers = {}
119
+ data = @content.unpack('C*')
120
+ p = 0
121
+ pe = data.length
122
+
123
+ # begin: ragel
124
+
125
+ begin
126
+ p ||= 0
127
+ pe ||= data.length
128
+ cs = bel_start
129
+ end
130
+
131
+
132
+ begin
133
+ testEof = false
134
+ _slen, _trans, _keys, _inds, _acts, _nacts = nil
135
+ _goto_level = 0
136
+ _resume = 10
137
+ _eof_trans = 15
138
+ _again = 20
139
+ _test_eof = 30
140
+ _out = 40
141
+ while true
142
+ if _goto_level <= 0
143
+ if p == pe
144
+ _goto_level = _test_eof
145
+ next
146
+ end
147
+ if cs == 0
148
+ _goto_level = _out
149
+ next
150
+ end
151
+ end
152
+ if _goto_level <= _resume
153
+ _keys = cs << 1
154
+ _inds = _bel_index_offsets[cs]
155
+ _slen = _bel_key_spans[cs]
156
+ _wide = data[p].ord
157
+ _trans = if ( _slen > 0 &&
158
+ _bel_trans_keys[_keys] <= _wide &&
159
+ _wide <= _bel_trans_keys[_keys + 1]
160
+ ) then
161
+ _bel_indicies[ _inds + _wide - _bel_trans_keys[_keys] ]
162
+ else
163
+ _bel_indicies[ _inds + _slen ]
164
+ end
165
+ cs = _bel_trans_targs[_trans]
166
+ if _bel_trans_actions[_trans] != 0
167
+ case _bel_trans_actions[_trans]
168
+ when 3 then
169
+ begin
170
+
171
+ @buffers[:comment_line] << data[p].ord
172
+ end
173
+ when 1 then
174
+ begin
175
+
176
+ @buffers[:comment_line] = []
177
+ end
178
+ begin
179
+
180
+ @buffers[:comment_line] << data[p].ord
181
+ end
182
+ when 4 then
183
+ begin
184
+
185
+ @buffers[:comment_line] = comment_line(
186
+ utf8_string(@buffers[:comment_line]))
187
+ end
188
+ begin
189
+
190
+ yield @buffers[:comment_line]
191
+ end
192
+ when 2 then
193
+ begin
194
+
195
+ @buffers[:comment_line] = []
196
+ end
197
+ begin
198
+
199
+ @buffers[:comment_line] = comment_line(
200
+ utf8_string(@buffers[:comment_line]))
201
+ end
202
+ begin
203
+
204
+ yield @buffers[:comment_line]
205
+ end
206
+ end
207
+ end
208
+ end
209
+ if _goto_level <= _again
210
+ if cs == 0
211
+ _goto_level = _out
212
+ next
213
+ end
214
+ p += 1
215
+ if p != pe
216
+ _goto_level = _resume
217
+ next
218
+ end
219
+ end
220
+ if _goto_level <= _test_eof
221
+ end
222
+ if _goto_level <= _out
223
+ break
224
+ end
225
+ end
226
+ end
227
+
228
+ # end: ragel
229
+ end
230
+ end
231
+ end
232
+ end
233
+ end
234
+ end
235
+
236
+ if __FILE__ == $0
237
+ $stdin.each_line do |line|
238
+ BELParser::Parsers::Common::CommentLine.parse(line) { |obj|
239
+ puts obj.inspect
240
+ }
241
+ end
242
+ end
243
+
244
+ # vim: ft=ruby ts=2 sw=2:
245
+ # encoding: utf-8