bel_parser 1.0.0.alpha.27-java

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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 +1,97 @@
1
+ # begin: ragel
2
+ =begin
3
+ %%{
4
+ machine bel;
5
+
6
+ include 'common.rl';
7
+
8
+ action start_comment_line {
9
+ @buffers[:comment_line] = []
10
+ }
11
+
12
+ action append_comment_line {
13
+ @buffers[:comment_line] << fc
14
+ }
15
+
16
+ action finish_comment_line {
17
+ @buffers[:comment_line] = comment_line(
18
+ utf8_string(@buffers[:comment_line]))
19
+ }
20
+
21
+ action yield_comment_line {
22
+ yield @buffers[:comment_line]
23
+ }
24
+
25
+ COMMENT_LINE =
26
+ SP*
27
+ NUMBER_SIGN
28
+ (any - NL)* >start_comment_line $append_comment_line %finish_comment_line;
29
+
30
+ comment_line := COMMENT_LINE %yield_comment_line NL;
31
+ }%%
32
+ =end
33
+ # end: ragel
34
+
35
+ require_relative '../ast/node'
36
+ require_relative '../mixin/buffer'
37
+ require_relative '../nonblocking_io_wrapper'
38
+
39
+ module BELParser
40
+ module Parsers
41
+ module Common
42
+ module CommentLine
43
+
44
+ class << self
45
+
46
+ MAX_LENGTH = 1024 * 128 # 128K
47
+
48
+ def parse(content)
49
+ return nil unless content
50
+
51
+ Parser.new(content).each do |obj|
52
+ yield obj
53
+ end
54
+ end
55
+ end
56
+
57
+ private
58
+
59
+ class Parser
60
+ include Enumerable
61
+ include BELParser::Parsers::Buffer
62
+ include BELParser::Parsers::AST::Sexp
63
+
64
+ def initialize(content)
65
+ @content = content
66
+ # begin: ragel
67
+ %% write data;
68
+ # end: ragel
69
+ end
70
+
71
+ def each
72
+ @buffers = {}
73
+ data = @content.unpack('C*')
74
+ p = 0
75
+ pe = data.length
76
+
77
+ # begin: ragel
78
+ %% write init;
79
+ %% write exec;
80
+ # end: ragel
81
+ end
82
+ end
83
+ end
84
+ end
85
+ end
86
+ end
87
+
88
+ if __FILE__ == $0
89
+ $stdin.each_line do |line|
90
+ BELParser::Parsers::Common::CommentLine.parse(line) { |obj|
91
+ puts obj.inspect
92
+ }
93
+ end
94
+ end
95
+
96
+ # vim: ft=ruby ts=2 sw=2:
97
+ # encoding: utf-8
@@ -0,0 +1,7 @@
1
+
2
+ =begin
3
+
4
+
5
+ =end
6
+ # vim: ts=2 sw=2 ft=ragel:
7
+ # encoding: utf-8
@@ -0,0 +1,13 @@
1
+ =begin
2
+ %%{
3
+ machine bel;
4
+
5
+ NL = '\n';
6
+ SP = ' ' | '\t';
7
+ EQL = '=';
8
+ NUMBER_SIGN = '#';
9
+
10
+ }%%
11
+ =end
12
+ # vim: ts=2 sw=2 ft=ragel:
13
+ # encoding: utf-8
@@ -0,0 +1,289 @@
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 Identifier
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, 48, 122, 10, 122,
48
+ 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, 75, 113, 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, 76, 190
65
+ ]
66
+
67
+ class << self
68
+ attr_accessor :_bel_indicies
69
+ private :_bel_indicies, :_bel_indicies=
70
+ end
71
+ self._bel_indicies = [
72
+ 1, 1, 1, 1, 1, 1, 1, 1,
73
+ 1, 1, 0, 0, 0, 0, 0, 0,
74
+ 0, 1, 1, 1, 1, 1, 1, 1,
75
+ 1, 1, 1, 1, 1, 1, 1, 1,
76
+ 1, 1, 1, 1, 1, 1, 1, 1,
77
+ 1, 1, 1, 0, 0, 0, 0, 1,
78
+ 0, 1, 1, 1, 1, 1, 1, 1,
79
+ 1, 1, 1, 1, 1, 1, 1, 1,
80
+ 1, 1, 1, 1, 1, 1, 1, 1,
81
+ 1, 1, 1, 0, 2, 0, 0, 0,
82
+ 0, 0, 0, 0, 0, 0, 0, 0,
83
+ 0, 0, 0, 0, 0, 0, 0, 0,
84
+ 0, 0, 0, 0, 0, 0, 0, 0,
85
+ 0, 0, 0, 0, 0, 0, 0, 0,
86
+ 0, 0, 3, 3, 3, 3, 3, 3,
87
+ 3, 3, 3, 3, 0, 0, 0, 0,
88
+ 0, 0, 0, 3, 3, 3, 3, 3,
89
+ 3, 3, 3, 3, 3, 3, 3, 3,
90
+ 3, 3, 3, 3, 3, 3, 3, 3,
91
+ 3, 3, 3, 3, 3, 0, 0, 0,
92
+ 0, 3, 0, 3, 3, 3, 3, 3,
93
+ 3, 3, 3, 3, 3, 3, 3, 3,
94
+ 3, 3, 3, 3, 3, 3, 3, 3,
95
+ 3, 3, 3, 3, 3, 0, 4, 0
96
+ ]
97
+
98
+ class << self
99
+ attr_accessor :_bel_trans_targs
100
+ private :_bel_trans_targs, :_bel_trans_targs=
101
+ end
102
+ self._bel_trans_targs = [
103
+ 0, 2, 3, 2, 0
104
+ ]
105
+
106
+ class << self
107
+ attr_accessor :_bel_trans_actions
108
+ private :_bel_trans_actions, :_bel_trans_actions=
109
+ end
110
+ self._bel_trans_actions = [
111
+ 1, 2, 3, 4, 0
112
+ ]
113
+
114
+ class << self
115
+ attr_accessor :_bel_eof_actions
116
+ private :_bel_eof_actions, :_bel_eof_actions=
117
+ end
118
+ self._bel_eof_actions = [
119
+ 0, 1, 1, 0
120
+ ]
121
+
122
+ class << self
123
+ attr_accessor :bel_start
124
+ end
125
+ self.bel_start = 1;
126
+ class << self
127
+ attr_accessor :bel_first_final
128
+ end
129
+ self.bel_first_final = 3;
130
+ class << self
131
+ attr_accessor :bel_error
132
+ end
133
+ self.bel_error = 0;
134
+
135
+ class << self
136
+ attr_accessor :bel_en_ident
137
+ end
138
+ self.bel_en_ident = 1;
139
+
140
+
141
+ # end: ragel
142
+ end
143
+
144
+ def each
145
+ @buffers = {}
146
+ data = @content.unpack('C*')
147
+ p = 0
148
+ pe = data.length
149
+ eof = data.length
150
+
151
+ # begin: ragel
152
+
153
+ begin
154
+ p ||= 0
155
+ pe ||= data.length
156
+ cs = bel_start
157
+ end
158
+
159
+
160
+ begin
161
+ testEof = false
162
+ _slen, _trans, _keys, _inds, _acts, _nacts = nil
163
+ _goto_level = 0
164
+ _resume = 10
165
+ _eof_trans = 15
166
+ _again = 20
167
+ _test_eof = 30
168
+ _out = 40
169
+ while true
170
+ if _goto_level <= 0
171
+ if p == pe
172
+ _goto_level = _test_eof
173
+ next
174
+ end
175
+ if cs == 0
176
+ _goto_level = _out
177
+ next
178
+ end
179
+ end
180
+ if _goto_level <= _resume
181
+ _keys = cs << 1
182
+ _inds = _bel_index_offsets[cs]
183
+ _slen = _bel_key_spans[cs]
184
+ _wide = data[p].ord
185
+ _trans = if ( _slen > 0 &&
186
+ _bel_trans_keys[_keys] <= _wide &&
187
+ _wide <= _bel_trans_keys[_keys + 1]
188
+ ) then
189
+ _bel_indicies[ _inds + _wide - _bel_trans_keys[_keys] ]
190
+ else
191
+ _bel_indicies[ _inds + _slen ]
192
+ end
193
+ cs = _bel_trans_targs[_trans]
194
+ if _bel_trans_actions[_trans] != 0
195
+ case _bel_trans_actions[_trans]
196
+ when 4 then
197
+ begin
198
+
199
+ (@buffers[:ident] ||= []) << data[p].ord
200
+ end
201
+ when 2 then
202
+ begin
203
+
204
+ @buffers[:ident] = []
205
+ end
206
+ begin
207
+
208
+ (@buffers[:ident] ||= []) << data[p].ord
209
+ end
210
+ when 3 then
211
+ begin
212
+
213
+ @buffers[:ident] = identifier(utf8_string(@buffers[:ident]))
214
+ end
215
+ begin
216
+
217
+ yield @buffers[:ident]
218
+ end
219
+ when 1 then
220
+ begin
221
+
222
+ unless @buffers[:ident].is_a?(::AST::Node)
223
+ @buffers[:ident] ||= []
224
+ @buffers[:ident] = identifier(utf8_string(@buffers[:ident]).sub(/\n$/, ''))
225
+ end
226
+ end
227
+ begin
228
+
229
+ @buffers[:ident] ||= []
230
+ yield @buffers[:ident]
231
+ end
232
+ end
233
+ end
234
+ end
235
+ if _goto_level <= _again
236
+ if cs == 0
237
+ _goto_level = _out
238
+ next
239
+ end
240
+ p += 1
241
+ if p != pe
242
+ _goto_level = _resume
243
+ next
244
+ end
245
+ end
246
+ if _goto_level <= _test_eof
247
+ if p == eof
248
+ case _bel_eof_actions[cs]
249
+ when 1 then
250
+ begin
251
+
252
+ unless @buffers[:ident].is_a?(::AST::Node)
253
+ @buffers[:ident] ||= []
254
+ @buffers[:ident] = identifier(utf8_string(@buffers[:ident]).sub(/\n$/, ''))
255
+ end
256
+ end
257
+ begin
258
+
259
+ @buffers[:ident] ||= []
260
+ yield @buffers[:ident]
261
+ end
262
+ end
263
+ end
264
+
265
+ end
266
+ if _goto_level <= _out
267
+ break
268
+ end
269
+ end
270
+ end
271
+
272
+ # end: ragel
273
+ end
274
+ end
275
+ end
276
+ end
277
+ end
278
+ end
279
+
280
+ if __FILE__ == $0
281
+ $stdin.each_line do |line|
282
+ BELParser::Parsers::Common::Identifier.parse(line) { |obj|
283
+ puts obj.inspect
284
+ }
285
+ end
286
+ end
287
+
288
+ # vim: ft=ruby ts=2 sw=2:
289
+ # encoding: utf-8
@@ -0,0 +1,106 @@
1
+ # begin: ragel
2
+ =begin
3
+ %%{
4
+ machine bel;
5
+
6
+ include 'common.rl';
7
+
8
+ action start_ident {
9
+ @buffers[:ident] = []
10
+ }
11
+
12
+ action append_ident {
13
+ (@buffers[:ident] ||= []) << fc
14
+ }
15
+
16
+ action finish_ident {
17
+ @buffers[:ident] = identifier(utf8_string(@buffers[:ident]))
18
+ }
19
+
20
+ action yield_complete_ident {
21
+ yield @buffers[:ident]
22
+ }
23
+
24
+ action error_ident {
25
+ unless @buffers[:ident].is_a?(::AST::Node)
26
+ @buffers[:ident] ||= []
27
+ @buffers[:ident] = identifier(utf8_string(@buffers[:ident]).sub(/\n$/, ''))
28
+ end
29
+ }
30
+
31
+ action yield_error_ident {
32
+ @buffers[:ident] ||= []
33
+ yield @buffers[:ident]
34
+ }
35
+
36
+ IDENT = [a-zA-Z0-9_]+ >start_ident $append_ident %finish_ident $err(error_ident);
37
+
38
+ ident := IDENT $err(yield_error_ident) %yield_complete_ident NL;
39
+ }%%
40
+ =end
41
+ # end: ragel
42
+
43
+ require_relative '../ast/node'
44
+ require_relative '../mixin/buffer'
45
+ require_relative '../nonblocking_io_wrapper'
46
+
47
+ module BELParser
48
+ module Parsers
49
+ module Common
50
+ module Identifier
51
+
52
+ class << self
53
+
54
+ MAX_LENGTH = 1024 * 128 # 128K
55
+
56
+ def parse(content)
57
+ return nil unless content
58
+
59
+ Parser.new(content).each do |obj|
60
+ yield obj
61
+ end
62
+ end
63
+ end
64
+
65
+ private
66
+
67
+ class Parser
68
+ include Enumerable
69
+ include BELParser::Parsers::Buffer
70
+ include BELParser::Parsers::AST::Sexp
71
+
72
+ def initialize(content)
73
+ @content = content
74
+ # begin: ragel
75
+ %% write data;
76
+ # end: ragel
77
+ end
78
+
79
+ def each
80
+ @buffers = {}
81
+ data = @content.unpack('C*')
82
+ p = 0
83
+ pe = data.length
84
+ eof = data.length
85
+
86
+ # begin: ragel
87
+ %% write init;
88
+ %% write exec;
89
+ # end: ragel
90
+ end
91
+ end
92
+ end
93
+ end
94
+ end
95
+ end
96
+
97
+ if __FILE__ == $0
98
+ $stdin.each_line do |line|
99
+ BELParser::Parsers::Common::Identifier.parse(line) { |obj|
100
+ puts obj.inspect
101
+ }
102
+ end
103
+ end
104
+
105
+ # vim: ft=ruby ts=2 sw=2:
106
+ # encoding: utf-8