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 +1,114 @@
1
+ require_relative '../../version2_0'
2
+ require_relative '../../function'
3
+ require_relative '../../signature'
4
+ require_relative '../../semantics'
5
+
6
+ module BELParser
7
+ module Language
8
+ module Version2_0
9
+ module Functions
10
+ # List: Groups a list of terms together.
11
+ class List
12
+ extend Function
13
+
14
+ SHORT = :list
15
+ LONG = :list
16
+ RETURN_TYPE = BELParser::Language::Version2_0::ReturnTypes::List
17
+ A_ENC = Version2_0::ValueEncodings::Abundance
18
+ DESCRIPTION = 'Groups a list of terms together.'.freeze
19
+
20
+ def self.short
21
+ SHORT
22
+ end
23
+
24
+ def self.long
25
+ LONG
26
+ end
27
+
28
+ def self.return_type
29
+ RETURN_TYPE
30
+ end
31
+
32
+ def self.description
33
+ DESCRIPTION
34
+ end
35
+
36
+ def self.signatures
37
+ SIGNATURES
38
+ end
39
+
40
+ module Signatures
41
+ # ListOfAbundanceEncodingSignature
42
+ class ListOfAbundanceEncodingSignature
43
+ extend BELParser::Language::Signature
44
+
45
+ private_class_method :new
46
+
47
+ AST = BELParser::Language::Semantics::Builder.build do
48
+ term(
49
+ function(
50
+ identifier(
51
+ function_of(List))),
52
+ argument(
53
+ parameter(
54
+ prefix(
55
+ has_namespace,
56
+ namespace_of(:*)),
57
+ value(
58
+ has_encoding,
59
+ encoding_of(A_ENC)))))
60
+ end
61
+ private_constant :AST
62
+
63
+ STRING_FORM = 'list(E:abundance...)list'.freeze
64
+ private_constant :STRING_FORM
65
+
66
+ def self.semantic_ast
67
+ AST
68
+ end
69
+
70
+ def self.string_form
71
+ STRING_FORM
72
+ end
73
+ end
74
+
75
+ # ListOfAbundanceSignature
76
+ class ListOfAbundanceSignature
77
+ extend BELParser::Language::Signature
78
+
79
+ private_class_method :new
80
+
81
+ AST = BELParser::Language::Semantics::Builder.build do
82
+ term(
83
+ function(
84
+ identifier(
85
+ function_of(List))),
86
+ variadic_arguments(
87
+ term(
88
+ function(
89
+ identifier(
90
+ return_type_of(BELParser::Language::Version2_0::ReturnTypes::Abundance))))))
91
+ end
92
+ private_constant :AST
93
+
94
+ STRING_FORM = 'list(F:abundance...)list'.freeze
95
+ private_constant :STRING_FORM
96
+
97
+ def self.semantic_ast
98
+ AST
99
+ end
100
+
101
+ def self.string_form
102
+ STRING_FORM
103
+ end
104
+ end
105
+ end
106
+
107
+ SIGNATURES = Signatures.constants.map do |const|
108
+ Signatures.const_get(const)
109
+ end.freeze
110
+ end
111
+ end
112
+ end
113
+ end
114
+ end
@@ -0,0 +1,83 @@
1
+ require_relative '../../version2_0'
2
+ require_relative '../../function'
3
+ require_relative '../../signature'
4
+ require_relative '../../semantics'
5
+
6
+ module BELParser
7
+ module Language
8
+ module Version2_0
9
+ module Functions
10
+ # Location: Denotes the cellular location of the abundance.
11
+ class Location
12
+ extend Function
13
+
14
+ SHORT = :loc
15
+ LONG = :location
16
+ RETURN_TYPE = BELParser::Language::Version2_0::ReturnTypes::Location
17
+ L_ENC = Version2_0::ValueEncodings::Location
18
+ DESCRIPTION = 'Denotes the cellular location of the abundance.'.freeze
19
+
20
+ def self.short
21
+ SHORT
22
+ end
23
+
24
+ def self.long
25
+ LONG
26
+ end
27
+
28
+ def self.return_type
29
+ RETURN_TYPE
30
+ end
31
+
32
+ def self.description
33
+ DESCRIPTION
34
+ end
35
+
36
+ def self.signatures
37
+ SIGNATURES
38
+ end
39
+
40
+ module Signatures
41
+ # LocationSignature
42
+ class LocationSignature
43
+ extend BELParser::Language::Signature
44
+
45
+ private_class_method :new
46
+
47
+ AST = BELParser::Language::Semantics::Builder.build do
48
+ term(
49
+ function(
50
+ identifier(
51
+ function_of(Location))),
52
+ argument(
53
+ parameter(
54
+ prefix(
55
+ has_namespace,
56
+ namespace_of(:*)),
57
+ value(
58
+ has_encoding,
59
+ encoding_of(L_ENC)))))
60
+ end
61
+ private_constant :AST
62
+
63
+ STRING_FORM = 'location(E:location)location'.freeze
64
+ private_constant :STRING_FORM
65
+
66
+ def self.semantic_ast
67
+ AST
68
+ end
69
+
70
+ def self.string_form
71
+ STRING_FORM
72
+ end
73
+ end
74
+ end
75
+
76
+ SIGNATURES = Signatures.constants.map do |const|
77
+ Signatures.const_get(const)
78
+ end.freeze
79
+ end
80
+ end
81
+ end
82
+ end
83
+ end
@@ -0,0 +1,163 @@
1
+ require_relative '../../version2_0'
2
+ require_relative '../../function'
3
+ require_relative '../../signature'
4
+ require_relative '../../semantics'
5
+
6
+ module BELParser
7
+ module Language
8
+ module Version2_0
9
+ module Functions
10
+ # MicroRNAAbundance: Denotes the abundance of a processed,
11
+ # functional microRNA
12
+ class MicroRNAAbundance
13
+ extend Function
14
+
15
+ SHORT = :m
16
+ LONG = :microRNAAbundance
17
+ RETURN_TYPE = BELParser::Language::Version2_0::ReturnTypes::MicroRNAAbundance
18
+ M_ENC = Version2_0::ValueEncodings::MicroRNAAbundance
19
+ DESCRIPTION = 'Denotes the abundance of a processed, functional
20
+ icroRNA'.freeze
21
+
22
+ def self.short
23
+ SHORT
24
+ end
25
+
26
+ def self.long
27
+ LONG
28
+ end
29
+
30
+ def self.return_type
31
+ RETURN_TYPE
32
+ end
33
+
34
+ def self.description
35
+ DESCRIPTION
36
+ end
37
+
38
+ def self.signatures
39
+ SIGNATURES
40
+ end
41
+
42
+ module Signatures
43
+ # MicroRNAAbundanceSignature
44
+ class MicroRNAAbundanceSignature
45
+ extend BELParser::Language::Signature
46
+
47
+ private_class_method :new
48
+
49
+ AST = BELParser::Language::Semantics::Builder.build do
50
+ term(
51
+ function(
52
+ identifier(
53
+ function_of(MicroRNAAbundance))),
54
+ argument(
55
+ parameter(
56
+ prefix(
57
+ has_namespace,
58
+ namespace_of(:*)),
59
+ value(
60
+ has_encoding,
61
+ encoding_of(M_ENC)))))
62
+ end
63
+ private_constant :AST
64
+
65
+ STRING_FORM = 'microRNAAbundance(E:microRNAAbundance)microRNAAbundance'.freeze
66
+ private_constant :STRING_FORM
67
+
68
+ def self.semantic_ast
69
+ AST
70
+ end
71
+
72
+ def self.string_form
73
+ STRING_FORM
74
+ end
75
+ end
76
+
77
+ # MicroRNAAbundanceWithLocationSignature
78
+ class MicroRNAAbundanceWithLocationSignature
79
+ extend BELParser::Language::Signature
80
+
81
+ private_class_method :new
82
+
83
+ AST = BELParser::Language::Semantics::Builder.build do
84
+ term(
85
+ function(
86
+ identifier(
87
+ function_of(MicroRNAAbundance))),
88
+ argument(
89
+ parameter(
90
+ prefix(
91
+ has_namespace,
92
+ namespace_of(:*)),
93
+ value(
94
+ has_encoding,
95
+ encoding_of(M_ENC)))),
96
+ argument(
97
+ term(
98
+ function(
99
+ identifier(
100
+ return_type_of(BELParser::Language::Version2_0::ReturnTypes::Location))))))
101
+ end
102
+ private_constant :AST
103
+
104
+ STRING_FORM = 'microRNAAbundance(E:microRNAAbundance,F:location)microRNAAbundance'.freeze
105
+ private_constant :STRING_FORM
106
+
107
+ def self.semantic_ast
108
+ AST
109
+ end
110
+
111
+ def self.string_form
112
+ STRING_FORM
113
+ end
114
+ end
115
+
116
+ # MicroRNAAbundanceWithVariantSignature
117
+ class MicroRNAAbundanceWithVariantSignature
118
+ extend BELParser::Language::Signature
119
+
120
+ private_class_method :new
121
+
122
+ AST = BELParser::Language::Semantics::Builder.build do
123
+ term(
124
+ function(
125
+ identifier(
126
+ function_of(MicroRNAAbundance))),
127
+ argument(
128
+ parameter(
129
+ prefix(
130
+ has_namespace,
131
+ namespace_of(:*)),
132
+ value(
133
+ has_encoding,
134
+ encoding_of(M_ENC)))),
135
+ argument(
136
+ term(
137
+ function(
138
+ identifier(
139
+ return_type_of(BELParser::Language::Version2_0::ReturnTypes::Variant))))))
140
+ end
141
+ private_constant :AST
142
+
143
+ STRING_FORM = 'microRNAAbundance(E:microRNAAbundance,F:variant)microRNAAbundance'.freeze
144
+ private_constant :STRING_FORM
145
+
146
+ def self.semantic_ast
147
+ AST
148
+ end
149
+
150
+ def self.string_form
151
+ STRING_FORM
152
+ end
153
+ end
154
+ end
155
+
156
+ SIGNATURES = Signatures.constants.map do |const|
157
+ Signatures.const_get(const)
158
+ end.freeze
159
+ end
160
+ end
161
+ end
162
+ end
163
+ end
@@ -0,0 +1,86 @@
1
+ require_relative '../../version2_0'
2
+ require_relative '../../function'
3
+ require_relative '../../signature'
4
+ require_relative '../../semantics'
5
+
6
+ module BELParser
7
+ module Language
8
+ module Version2_0
9
+ module Functions
10
+ # MolecularActivity: Denotes the frequency or abundance of events
11
+ # in which a member acts as a causal agent at the molecular scale
12
+ class MolecularActivity
13
+ extend Function
14
+
15
+ SHORT = :ma
16
+ LONG = :molecularActivity
17
+ RETURN_TYPE = BELParser::Language::Version2_0::ReturnTypes::MolecularActivity
18
+ T_ENC = Version2_0::ValueEncodings::Activity
19
+ DESCRIPTION = 'Denotes the frequency or abundance of events
20
+ n which a member acts as a causal agent at the
21
+ olecular scale'.freeze
22
+
23
+ def self.short
24
+ SHORT
25
+ end
26
+
27
+ def self.long
28
+ LONG
29
+ end
30
+
31
+ def self.return_type
32
+ RETURN_TYPE
33
+ end
34
+
35
+ def self.description
36
+ DESCRIPTION
37
+ end
38
+
39
+ def self.signatures
40
+ SIGNATURES
41
+ end
42
+
43
+ module Signatures
44
+ # MolecularActivitySignature
45
+ class MolecularActivitySignature
46
+ extend BELParser::Language::Signature
47
+
48
+ private_class_method :new
49
+
50
+ AST = BELParser::Language::Semantics::Builder.build do
51
+ term(
52
+ function(
53
+ identifier(
54
+ function_of(MolecularActivity))),
55
+ argument(
56
+ parameter(
57
+ prefix(
58
+ has_namespace,
59
+ namespace_of(:*)),
60
+ value(
61
+ has_encoding,
62
+ encoding_of(T_ENC)))))
63
+ end
64
+ private_constant :AST
65
+
66
+ STRING_FORM = 'molecularActivity(E:activity)molecularActivity'.freeze
67
+ private_constant :STRING_FORM
68
+
69
+ def self.semantic_ast
70
+ AST
71
+ end
72
+
73
+ def self.string_form
74
+ STRING_FORM
75
+ end
76
+ end
77
+ end
78
+
79
+ SIGNATURES = Signatures.constants.map do |const|
80
+ Signatures.const_get(const)
81
+ end.freeze
82
+ end
83
+ end
84
+ end
85
+ end
86
+ end
@@ -0,0 +1,83 @@
1
+ require_relative '../../version2_0'
2
+ require_relative '../../function'
3
+ require_relative '../../signature'
4
+ require_relative '../../semantics'
5
+
6
+ module BELParser
7
+ module Language
8
+ module Version2_0
9
+ module Functions
10
+ # Pathology: Denotes a disease or pathology process
11
+ class Pathology
12
+ extend Function
13
+
14
+ SHORT = :path
15
+ LONG = :pathology
16
+ RETURN_TYPE = BELParser::Language::Version2_0::ReturnTypes::Pathology
17
+ O_ENC = Version2_0::ValueEncodings::Pathology
18
+ DESCRIPTION = 'Denotes a disease or pathology process'.freeze
19
+
20
+ def self.short
21
+ SHORT
22
+ end
23
+
24
+ def self.long
25
+ LONG
26
+ end
27
+
28
+ def self.return_type
29
+ RETURN_TYPE
30
+ end
31
+
32
+ def self.description
33
+ DESCRIPTION
34
+ end
35
+
36
+ def self.signatures
37
+ SIGNATURES
38
+ end
39
+
40
+ module Signatures
41
+ # PathologySignature
42
+ class PathologySignature
43
+ extend BELParser::Language::Signature
44
+
45
+ private_class_method :new
46
+
47
+ AST = BELParser::Language::Semantics::Builder.build do
48
+ term(
49
+ function(
50
+ identifier(
51
+ function_of(Pathology))),
52
+ argument(
53
+ parameter(
54
+ prefix(
55
+ has_namespace,
56
+ namespace_of(:*)),
57
+ value(
58
+ has_encoding,
59
+ encoding_of(O_ENC)))))
60
+ end
61
+ private_constant :AST
62
+
63
+ STRING_FORM = 'pathology(E:pathology)pathology'.freeze
64
+ private_constant :STRING_FORM
65
+
66
+ def self.semantic_ast
67
+ AST
68
+ end
69
+
70
+ def self.string_form
71
+ STRING_FORM
72
+ end
73
+ end
74
+ end
75
+
76
+ SIGNATURES = Signatures.constants.map do |const|
77
+ Signatures.const_get(const)
78
+ end.freeze
79
+ end
80
+ end
81
+ end
82
+ end
83
+ end