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