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 +1,48 @@
1
+ require_relative '../../version1_0'
2
+ require_relative '../../relationship'
3
+
4
+ module BELParser
5
+ module Language
6
+ module Version1_0
7
+ module Relationships
8
+ # HasMember: +A hasMember A1+ - For term abundances A and B,
9
+ # +A hasMember B+ designates B as a member class of A. A member
10
+ # class is a distinguished sub-class. A is defined as a group
11
+ # by all of the members assigned to it. The member classes may
12
+ # or may not be overlapping and may or may not entirely cover
13
+ # all instances of A. A term may not appear in both the subject
14
+ # and object of the same hasMember statement.
15
+ class HasMember
16
+ extend Relationship
17
+
18
+ SHORT = :hasMember
19
+ LONG = :hasMember
20
+ DESCRIPTION = ' +A hasMember A1+ - For term abundances A and B,
21
+ A hasMember B+ designates B as a member class of
22
+ . A member class is a distinguished sub-class. A is
23
+ efined as a group by all of the members assigned to
24
+ t. The member classes may or may not be overlapping
25
+ nd may or may not entirely cover all instances
26
+ f A. A term may not appear in both the subject
27
+ nd object of the same hasMember statement.'.freeze
28
+
29
+ def self.short
30
+ SHORT
31
+ end
32
+
33
+ def self.long
34
+ LONG
35
+ end
36
+
37
+ def self.description
38
+ DESCRIPTION
39
+ end
40
+
41
+ def self.directed?
42
+ true
43
+ end
44
+ end
45
+ end
46
+ end
47
+ end
48
+ end
@@ -0,0 +1,57 @@
1
+ require_relative '../../version1_0'
2
+ require_relative '../../relationship'
3
+
4
+ module BELParser
5
+ module Language
6
+ module Version1_0
7
+ module Relationships
8
+ # HasMembers: +A hasMembers (B, C, D)+ - The hasMembers
9
+ # relationship is a special form which enables the assignment of
10
+ # multiple member classes in a single statement where the object
11
+ # of the statement is a set of abundance terms. A statement
12
+ # using hasMembers is exactly equivalent to multiple hasMember
13
+ # statements. A term may not appear in both the subject and
14
+ # object of a of the same hasMembers statement. For the abundance
15
+ # terms A, B, C and D, +A hasMembers B, C, D+ indicates that A
16
+ # is defined by its member abundance classes B, C and D.
17
+ class HasMembers
18
+ extend Relationship
19
+
20
+ SHORT = :hasMembers
21
+ LONG = :hasMembers
22
+ DESCRIPTION = ' +A hasMembers (B, C, D)+ - The hasMembers
23
+ elationship is a special form which enables the
24
+ ssignment of multiple member classes in a single
25
+ tatement where the object of the statement is a set
26
+ f abundance terms. A statement using hasMembers
27
+ s exactly equivalent to multiple hasMember
28
+ tatements. A term may not appear in both the
29
+ ubject and object of a of the same hasMembers
30
+ tatement. For the abundance terms A, B, C and D,
31
+ A hasMembers B, C, D+ indicates that A is defined
32
+ y its member abundance classes B, C and D.'.freeze
33
+
34
+ def self.short
35
+ SHORT
36
+ end
37
+
38
+ def self.long
39
+ LONG
40
+ end
41
+
42
+ def self.description
43
+ DESCRIPTION
44
+ end
45
+
46
+ def self.directed?
47
+ true
48
+ end
49
+
50
+ def self.listable?
51
+ true
52
+ end
53
+ end
54
+ end
55
+ end
56
+ end
57
+ end
@@ -0,0 +1,54 @@
1
+ require_relative '../../version1_0'
2
+ require_relative '../../relationship'
3
+
4
+ module BELParser
5
+ module Language
6
+ module Version1_0
7
+ module Relationships
8
+ # HasModification: +p(A) hasModification p(A, pmod(P, S, 473))+
9
+ # - This relationship links abundance terms modified by the
10
+ # +pmod()+ function to the unmodified abundance term. This is a
11
+ # direct relationship because it is a _self_ relationship. This
12
+ # relationship is introduced by the BEL Compiler and may not be
13
+ # used by statements in BEL documents.
14
+ class HasModification
15
+ extend Relationship
16
+
17
+ SHORT = :hasModification
18
+ LONG = :hasModification
19
+ DESCRIPTION = ' +p(A) hasModification p(A, pmod(P, S, 473))+ -
20
+ his relationship links abundance terms modified by
21
+ he +pmod()+ function to the unmodified abundance
22
+ erm. This is a direct relationship because it
23
+ s a _self_ relationship. This relationship is
24
+ ntroduced by the BEL Compiler and may not be used
25
+ y statements in BEL documents.'.freeze
26
+
27
+ def self.short
28
+ SHORT
29
+ end
30
+
31
+ def self.long
32
+ LONG
33
+ end
34
+
35
+ def self.description
36
+ DESCRIPTION
37
+ end
38
+
39
+ def self.direct?
40
+ true
41
+ end
42
+
43
+ def self.directed?
44
+ true
45
+ end
46
+
47
+ def self.injected?
48
+ true
49
+ end
50
+ end
51
+ end
52
+ end
53
+ end
54
+ end
@@ -0,0 +1,60 @@
1
+ require_relative '../../version1_0'
2
+ require_relative '../../relationship'
3
+
4
+ module BELParser
5
+ module Language
6
+ module Version1_0
7
+ module Relationships
8
+ # HasProduct: +reaction(reactants(A), products(B))
9
+ # hasProduct B+ - This relationship links abundance
10
+ # terms from the +products(<list>)+ in a reaction to the
11
+ # reaction. This is a direct relationship because it is a _self_
12
+ # relationship. Products are produced directly by a reaction. This
13
+ # relationship is introduced by the BEL Compiler and may not be
14
+ # used by statements in BEL documents.
15
+ class HasProduct
16
+ extend Relationship
17
+
18
+ SHORT = :hasProduct
19
+ LONG = :hasProduct
20
+ DESCRIPTION = ' +reaction(reactants(A), products(B)) hasProduct
21
+ + - This relationship links abundance terms
22
+ rom the +products(<list>)+ in a reaction to the
23
+ eaction. This is a direct relationship because it
24
+ s a _self_ relationship. Products are produced
25
+ irectly by a reaction. This relationship is
26
+ ntroduced by the BEL Compiler and may not be used
27
+ y statements in BEL documents.'.freeze
28
+
29
+ def self.short
30
+ SHORT
31
+ end
32
+
33
+ def self.long
34
+ LONG
35
+ end
36
+
37
+ def self.description
38
+ DESCRIPTION
39
+ end
40
+
41
+ def self.direct?
42
+ true
43
+ end
44
+
45
+ def self.directed?
46
+ true
47
+ end
48
+
49
+ def self.injected?
50
+ true
51
+ end
52
+
53
+ def self.self?
54
+ true
55
+ end
56
+ end
57
+ end
58
+ end
59
+ end
60
+ end
@@ -0,0 +1,54 @@
1
+ require_relative '../../version1_0'
2
+ require_relative '../../relationship'
3
+
4
+ module BELParser
5
+ module Language
6
+ module Version1_0
7
+ module Relationships
8
+ # HasVariant: +p(A) hasVariant p(A, sub(G, 12, V))+ -
9
+ # This relationship links abundance terms modified by the
10
+ # +substitution()+, +fusion()+, or +truncation()+ functions to
11
+ # the unmodified abundance term. This relationship is introduced
12
+ # by the BEL Compiler and does not need to be used by statements
13
+ # in BEL documents.
14
+ class HasVariant
15
+ extend Relationship
16
+
17
+ SHORT = :hasVariant
18
+ LONG = :hasVariant
19
+ DESCRIPTION = ' +p(A) hasVariant p(A, sub(G, 12, V))+ - This
20
+ elationship links abundance terms modified by the
21
+ substitution()+, +fusion()+, or +truncation()+
22
+ unctions to the unmodified abundance term. This
23
+ elationship is introduced by the BEL Compiler
24
+ nd does not need to be used by statements in
25
+ EL documents.'.freeze
26
+
27
+ def self.short
28
+ SHORT
29
+ end
30
+
31
+ def self.long
32
+ LONG
33
+ end
34
+
35
+ def self.description
36
+ DESCRIPTION
37
+ end
38
+
39
+ def self.direct?
40
+ true
41
+ end
42
+
43
+ def self.directed?
44
+ true
45
+ end
46
+
47
+ def self.injected?
48
+ true
49
+ end
50
+ end
51
+ end
52
+ end
53
+ end
54
+ end
@@ -0,0 +1,59 @@
1
+ require_relative '../../version1_0'
2
+ require_relative '../../relationship'
3
+
4
+ module BELParser
5
+ module Language
6
+ module Version1_0
7
+ module Relationships
8
+ # Includes: +compositeAbundance(A,B) includes A+ - This
9
+ # relationship links each individual abundance term in a
10
+ # +compositeAbundance(<list>)+ to the compositeAbundance. For
11
+ # example, +compositeAbundance(A, B) includes A+ and
12
+ # +compositeAbundance(A, B) includes B+. This relationship is
13
+ # direct because it is a _self_ relationship. This relationship
14
+ # is introduced by the BEL Compiler and may not be used by
15
+ # statements in BEL documents.
16
+ class Includes
17
+ extend Relationship
18
+
19
+ SHORT = :includes
20
+ LONG = :includes
21
+ DESCRIPTION = ' +compositeAbundance(A,B) includes A+ - This
22
+ elationship links each individual abundance
23
+ erm in a +compositeAbundance(<list>)+
24
+ o the compositeAbundance. For example,
25
+ compositeAbundance(A, B) includes A+ and
26
+ compositeAbundance(A, B) includes B+. This
27
+ elationship is direct because it is a _self_
28
+ elationship. This relationship is introduced by
29
+ he BEL Compiler and may not be used by statements
30
+ n BEL documents.'.freeze
31
+
32
+ def self.short
33
+ SHORT
34
+ end
35
+
36
+ def self.long
37
+ LONG
38
+ end
39
+
40
+ def self.description
41
+ DESCRIPTION
42
+ end
43
+
44
+ def self.directed?
45
+ true
46
+ end
47
+
48
+ def self.injected?
49
+ true
50
+ end
51
+
52
+ def self.self?
53
+ true
54
+ end
55
+ end
56
+ end
57
+ end
58
+ end
59
+ end
@@ -0,0 +1,63 @@
1
+ require_relative '../../version1_0'
2
+ require_relative '../../relationship'
3
+
4
+ module BELParser
5
+ module Language
6
+ module Version1_0
7
+ module Relationships
8
+ # Increases: +A -> B+ - For terms A and B, +A increases B or
9
+ # A -> B+ indicates that increases in A have been observed to
10
+ # cause increases in B. +A increases B+ also represents cases
11
+ # where decreases in A have been observed to cause decreases in B,
12
+ # for example, in recording the results of gene deletion or other
13
+ # inhibition experiments. A is a BEL Term and B is either a BEL
14
+ # Term or a BEL Statement. The relationship does not indicate
15
+ # that the changes in A are either necessary for changes in B,
16
+ # nor does it indicate that changes in A are sufficient to cause
17
+ # changes in B.
18
+ class Increases
19
+ extend Relationship
20
+
21
+ SHORT = :'->'
22
+ LONG = :increases
23
+ DESCRIPTION = ' +A -> B+ - For terms A and B, +A increases B
24
+ r A -> B+ indicates that increases in A have been
25
+ bserved to cause increases in B. +A increases
26
+ + also represents cases where decreases in A
27
+ ave been observed to cause decreases in B, for
28
+ xample, in recording the results of gene deletion
29
+ r other inhibition experiments. A is a BEL Term
30
+ nd B is either a BEL Term or a BEL Statement. The
31
+ elationship does not indicate that the changes
32
+ n A are either necessary for changes in B, nor
33
+ oes it indicate that changes in A are sufficient
34
+ o cause changes in B.'.freeze
35
+
36
+ def self.short
37
+ SHORT
38
+ end
39
+
40
+ def self.long
41
+ LONG
42
+ end
43
+
44
+ def self.description
45
+ DESCRIPTION
46
+ end
47
+
48
+ def self.causal?
49
+ true
50
+ end
51
+
52
+ def self.directed?
53
+ true
54
+ end
55
+
56
+ def self.increasing?
57
+ true
58
+ end
59
+ end
60
+ end
61
+ end
62
+ end
63
+ end
@@ -0,0 +1,48 @@
1
+ require_relative '../../version1_0'
2
+ require_relative '../../relationship'
3
+
4
+ module BELParser
5
+ module Language
6
+ module Version1_0
7
+ module Relationships
8
+ # IsA: +A isA B+ - For terms A and B, +A isA B+ indicates
9
+ # that A is a subset of B. All terms in BEL represent classes,
10
+ # but given that classes implicitly have instances, one can
11
+ # also interpret +A isA B+ to mean that any instance of A must
12
+ # also be an instance of B. This relationship can be used to
13
+ # represent GO and MeSH hierarchies: +pathology(MESH:Psoriasis)
14
+ # isA pathology(MESH:"Skin Diseases")+
15
+ class IsA
16
+ extend Relationship
17
+
18
+ SHORT = :isA
19
+ LONG = :isA
20
+ DESCRIPTION = ' +A isA B+ - For terms A and B, +A isA B+
21
+ ndicates that A is a subset of B. All terms in BEL
22
+ epresent classes, but given that classes implicitly
23
+ ave instances, one can also interpret +A isA B+ to
24
+ ean that any instance of A must also be an instance
25
+ f B. This relationship can be used to represent
26
+ O and MeSH hierarchies: +pathology(MESH:Psoriasis)
27
+ sA pathology(MESH:"Skin Diseases")+'.freeze
28
+
29
+ def self.short
30
+ SHORT
31
+ end
32
+
33
+ def self.long
34
+ LONG
35
+ end
36
+
37
+ def self.description
38
+ DESCRIPTION
39
+ end
40
+
41
+ def self.directed?
42
+ true
43
+ end
44
+ end
45
+ end
46
+ end
47
+ end
48
+ end