abstractor 1.0.8

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Files changed (346) hide show
  1. checksums.yaml +15 -0
  2. data/MIT-LICENSE +20 -0
  3. data/README.md +14 -0
  4. data/Rakefile +33 -0
  5. data/app/assets/images/abstractor/add.png +0 -0
  6. data/app/assets/images/abstractor/ajax-loader.gif +0 -0
  7. data/app/assets/images/abstractor/bar.gif +0 -0
  8. data/app/assets/images/abstractor/bti_logo.jpg +0 -0
  9. data/app/assets/images/abstractor/bullet_arrow_down.png +0 -0
  10. data/app/assets/images/abstractor/bullet_arrow_up.png +0 -0
  11. data/app/assets/images/abstractor/cog.png +0 -0
  12. data/app/assets/images/abstractor/delete.png +0 -0
  13. data/app/assets/images/abstractor/edit.png +0 -0
  14. data/app/assets/images/abstractor/excel.png +0 -0
  15. data/app/assets/images/abstractor/favicon.ico +0 -0
  16. data/app/assets/images/abstractor/greencheck.gif +0 -0
  17. data/app/assets/images/abstractor/loading.gif +0 -0
  18. data/app/assets/images/abstractor/nu_logo.jpg +0 -0
  19. data/app/assets/images/abstractor/nubic_logo.png +0 -0
  20. data/app/assets/images/abstractor/page.png +0 -0
  21. data/app/assets/images/abstractor/rails.png +0 -0
  22. data/app/assets/images/abstractor/robert_h_lurie.jpg +0 -0
  23. data/app/assets/images/abstractor/show.png +0 -0
  24. data/app/assets/images/abstractor/switch_minus.gif +0 -0
  25. data/app/assets/images/abstractor/switch_plus.gif +0 -0
  26. data/app/assets/javascripts/abstractor/abstractor.js +89 -0
  27. data/app/assets/javascripts/abstractor/application.js +21 -0
  28. data/app/assets/javascripts/abstractor/combobox.js +301 -0
  29. data/app/assets/javascripts/abstractor/jquery/jquery.form.js +1074 -0
  30. data/app/assets/javascripts/abstractor/nested_attributes.js +69 -0
  31. data/app/assets/stylesheets/abstractor/abstractor_abstractions.css +312 -0
  32. data/app/assets/stylesheets/abstractor/application.css +21 -0
  33. data/app/assets/stylesheets/abstractor/jquery.ui.override.css.scss +73 -0
  34. data/app/controllers/abstractor/abstractor_abstraction_groups_controller.rb +5 -0
  35. data/app/controllers/abstractor/abstractor_abstractions_controller.rb +5 -0
  36. data/app/controllers/abstractor/abstractor_suggestions_controller.rb +5 -0
  37. data/app/controllers/abstractor/application_controller.rb +2 -0
  38. data/app/helpers/abstractor/application_helper.rb +4 -0
  39. data/app/models/abstractor/abstractor_abstraction.rb +6 -0
  40. data/app/models/abstractor/abstractor_abstraction_group.rb +6 -0
  41. data/app/models/abstractor/abstractor_abstraction_group_member.rb +6 -0
  42. data/app/models/abstractor/abstractor_abstraction_schema.rb +6 -0
  43. data/app/models/abstractor/abstractor_abstraction_schema_object_value.rb +6 -0
  44. data/app/models/abstractor/abstractor_abstraction_schema_predicate_variant.rb +6 -0
  45. data/app/models/abstractor/abstractor_abstraction_schema_relation.rb +6 -0
  46. data/app/models/abstractor/abstractor_abstraction_source.rb +6 -0
  47. data/app/models/abstractor/abstractor_object_type.rb +6 -0
  48. data/app/models/abstractor/abstractor_object_value.rb +6 -0
  49. data/app/models/abstractor/abstractor_object_value_variant.rb +6 -0
  50. data/app/models/abstractor/abstractor_relation_type.rb +6 -0
  51. data/app/models/abstractor/abstractor_rule_type.rb +6 -0
  52. data/app/models/abstractor/abstractor_subject.rb +6 -0
  53. data/app/models/abstractor/abstractor_subject_group.rb +6 -0
  54. data/app/models/abstractor/abstractor_subject_group_member.rb +6 -0
  55. data/app/models/abstractor/abstractor_subject_relation.rb +6 -0
  56. data/app/models/abstractor/abstractor_suggestion.rb +6 -0
  57. data/app/models/abstractor/abstractor_suggestion_object_value.rb +6 -0
  58. data/app/models/abstractor/abstractor_suggestion_source.rb +6 -0
  59. data/app/models/abstractor/abstractor_suggestion_status.rb +6 -0
  60. data/app/views/abstractor/abstractor_abstraction_groups/_form.html.haml +10 -0
  61. data/app/views/abstractor/abstractor_abstraction_groups/edit.html.haml +1 -0
  62. data/app/views/abstractor/abstractor_abstractions/_fields.html.haml +63 -0
  63. data/app/views/abstractor/abstractor_abstractions/_list.html.haml +45 -0
  64. data/app/views/abstractor/abstractor_abstractions/edit.html.haml +53 -0
  65. data/app/views/abstractor/abstractor_abstractions/show.html.haml +1 -0
  66. data/app/views/abstractor/shared/_error_messages.html.haml +5 -0
  67. data/config/cucumber.yml +8 -0
  68. data/config/routes.rb +7 -0
  69. data/db/migrate/20131227205140_create_abstractor_object_types.rb +10 -0
  70. data/db/migrate/20131227205219_create_abstractor_object_values.rb +10 -0
  71. data/db/migrate/20131227205256_create_abstractor_object_value_variants.rb +11 -0
  72. data/db/migrate/20131227205320_create_abstractor_relation_types.rb +10 -0
  73. data/db/migrate/20131227205354_create_abstractor_rule_types.rb +11 -0
  74. data/db/migrate/20131227205432_create_abstractor_abstraction_schemas.rb +13 -0
  75. data/db/migrate/20131227205456_create_abstractor_abstraction_schema_object_values.rb +10 -0
  76. data/db/migrate/20131227205529_create_abstractor_abstraction_schema_predicate_variants.rb +11 -0
  77. data/db/migrate/20131227205610_create_abstractor_abstraction_schema_relations.rb +11 -0
  78. data/db/migrate/20131227205652_create_abstractor_subjects.rb +12 -0
  79. data/db/migrate/20131227205732_create_abstractor_subject_relations.rb +11 -0
  80. data/db/migrate/20131227205831_create_abstractor_abstraction_sources.rb +11 -0
  81. data/db/migrate/20131227210211_create_abstractor_subject_groups.rb +10 -0
  82. data/db/migrate/20131227210244_create_abstractor_subject_group_members.rb +11 -0
  83. data/db/migrate/20131227210350_create_abstractor_abstraction_groups.rb +12 -0
  84. data/db/migrate/20131227210353_create_abstractor_abstraction_group_members.rb +11 -0
  85. data/db/migrate/20131227211050_create_abstractor_suggestion_statuses.rb +10 -0
  86. data/db/migrate/20131227211303_create_abstractor_abstractions.rb +15 -0
  87. data/db/migrate/20131227213427_create_abstractor_suggestions.rb +14 -0
  88. data/db/migrate/20131228041944_create_abstractor_suggestion_object_values.rb +11 -0
  89. data/db/migrate/20131228041945_create_abstractor_suggestion_sources.rb +16 -0
  90. data/db/seeds.rb +0 -0
  91. data/lib/abstractor.rb +8 -0
  92. data/lib/abstractor/abstractable.rb +190 -0
  93. data/lib/abstractor/core_ext/string.rb +99 -0
  94. data/lib/abstractor/engine.rb +14 -0
  95. data/lib/abstractor/methods/controllers/abstractor_abstraction_groups_controller.rb +37 -0
  96. data/lib/abstractor/methods/controllers/abstractor_abstractions_controller.rb +42 -0
  97. data/lib/abstractor/methods/controllers/abstractor_suggestions_controller.rb +28 -0
  98. data/lib/abstractor/methods/models/abstractor_abstraction.rb +65 -0
  99. data/lib/abstractor/methods/models/abstractor_abstraction_group.rb +37 -0
  100. data/lib/abstractor/methods/models/abstractor_abstraction_group_member.rb +17 -0
  101. data/lib/abstractor/methods/models/abstractor_abstraction_schema.rb +27 -0
  102. data/lib/abstractor/methods/models/abstractor_abstraction_schema_object_value.rb +17 -0
  103. data/lib/abstractor/methods/models/abstractor_abstraction_schema_predicate_variant.rb +16 -0
  104. data/lib/abstractor/methods/models/abstractor_abstraction_schema_relation.rb +18 -0
  105. data/lib/abstractor/methods/models/abstractor_abstraction_source.rb +29 -0
  106. data/lib/abstractor/methods/models/abstractor_object_type.rb +16 -0
  107. data/lib/abstractor/methods/models/abstractor_object_value.rb +24 -0
  108. data/lib/abstractor/methods/models/abstractor_object_value_variant.rb +16 -0
  109. data/lib/abstractor/methods/models/abstractor_relation_type.rb +16 -0
  110. data/lib/abstractor/methods/models/abstractor_rule_type.rb +17 -0
  111. data/lib/abstractor/methods/models/abstractor_subject.rb +258 -0
  112. data/lib/abstractor/methods/models/abstractor_subject_group.rb +19 -0
  113. data/lib/abstractor/methods/models/abstractor_subject_group_member.rb +17 -0
  114. data/lib/abstractor/methods/models/abstractor_subject_relation.rb +18 -0
  115. data/lib/abstractor/methods/models/abstractor_suggestion.rb +88 -0
  116. data/lib/abstractor/methods/models/abstractor_suggestion_object_value.rb +17 -0
  117. data/lib/abstractor/methods/models/abstractor_suggestion_source.rb +17 -0
  118. data/lib/abstractor/methods/models/abstractor_suggestion_status.rb +29 -0
  119. data/lib/abstractor/methods/models/soft_delete.rb +35 -0
  120. data/lib/abstractor/negation_detection.rb +43 -0
  121. data/lib/abstractor/parser.rb +76 -0
  122. data/lib/abstractor/setup.rb +24 -0
  123. data/lib/abstractor/user_interface.rb +40 -0
  124. data/lib/abstractor/utility.rb +8 -0
  125. data/lib/abstractor/version.rb +3 -0
  126. data/lib/generators/abstractor/install/install_generator.rb +118 -0
  127. data/lib/generators/abstractor/install/templates/controllers/abstractor_abstraction_groups_controller.rb +16 -0
  128. data/lib/generators/abstractor/install/templates/controllers/abstractor_abstractions_controller.rb +24 -0
  129. data/lib/generators/abstractor/install/templates/controllers/abstractor_suggestions_controller.rb +12 -0
  130. data/lib/generators/abstractor/install/templates/dictionaries.yml +235 -0
  131. data/lib/generators/abstractor/install/templates/helpers/abstractions_helper.rb +9 -0
  132. data/lib/generators/abstractor/install/templates/models/abstractor_abstraction.rb +9 -0
  133. data/lib/generators/abstractor/install/templates/models/abstractor_abstraction_group.rb +9 -0
  134. data/lib/generators/abstractor/install/templates/models/abstractor_abstraction_group_member.rb +9 -0
  135. data/lib/generators/abstractor/install/templates/models/abstractor_abstraction_schema.rb +9 -0
  136. data/lib/generators/abstractor/install/templates/models/abstractor_abstraction_schema_object_value.rb +9 -0
  137. data/lib/generators/abstractor/install/templates/models/abstractor_abstraction_schema_predicate_variant.rb +9 -0
  138. data/lib/generators/abstractor/install/templates/models/abstractor_abstraction_schema_relation.rb +9 -0
  139. data/lib/generators/abstractor/install/templates/models/abstractor_abstraction_source.rb +9 -0
  140. data/lib/generators/abstractor/install/templates/models/abstractor_object_type.rb +9 -0
  141. data/lib/generators/abstractor/install/templates/models/abstractor_object_value.rb +9 -0
  142. data/lib/generators/abstractor/install/templates/models/abstractor_object_value_variant.rb +9 -0
  143. data/lib/generators/abstractor/install/templates/models/abstractor_relation_type.rb +9 -0
  144. data/lib/generators/abstractor/install/templates/models/abstractor_rule_type.rb +9 -0
  145. data/lib/generators/abstractor/install/templates/models/abstractor_subject.rb +9 -0
  146. data/lib/generators/abstractor/install/templates/models/abstractor_subject_group.rb +9 -0
  147. data/lib/generators/abstractor/install/templates/models/abstractor_subject_group_member.rb +9 -0
  148. data/lib/generators/abstractor/install/templates/models/abstractor_subject_relation.rb +9 -0
  149. data/lib/generators/abstractor/install/templates/models/abstractor_suggestion.rb +9 -0
  150. data/lib/generators/abstractor/install/templates/models/abstractor_suggestion_object_value.rb +9 -0
  151. data/lib/generators/abstractor/install/templates/models/abstractor_suggestion_source.rb +9 -0
  152. data/lib/generators/abstractor/install/templates/models/abstractor_suggestion_status.rb +9 -0
  153. data/lib/lingscope/build.xml +74 -0
  154. data/lib/lingscope/build/built-jar.properties +4 -0
  155. data/lib/lingscope/build/classes/lingscope/algorithms/AbnerTokenizer.class +0 -0
  156. data/lib/lingscope/build/classes/lingscope/algorithms/AnnotationComparer.class +0 -0
  157. data/lib/lingscope/build/classes/lingscope/algorithms/Annotator.class +0 -0
  158. data/lib/lingscope/build/classes/lingscope/algorithms/BaselineAnnotator.class +0 -0
  159. data/lib/lingscope/build/classes/lingscope/algorithms/BaselineCueAnnotator.class +0 -0
  160. data/lib/lingscope/build/classes/lingscope/algorithms/BaselineScopeAnnotator.class +0 -0
  161. data/lib/lingscope/build/classes/lingscope/algorithms/CrfAnnotator.class +0 -0
  162. data/lib/lingscope/build/classes/lingscope/algorithms/NegexAnnotator.class +0 -0
  163. data/lib/lingscope/build/classes/lingscope/algorithms/NegexCueAnnotator.class +0 -0
  164. data/lib/lingscope/build/classes/lingscope/algorithms/NegexScopeAnnotator.class +0 -0
  165. data/lib/lingscope/build/classes/lingscope/algorithms/PosTagger.class +0 -0
  166. data/lib/lingscope/build/classes/lingscope/algorithms/negex/GenNegEx.class +0 -0
  167. data/lib/lingscope/build/classes/lingscope/algorithms/negex/Sorter.class +0 -0
  168. data/lib/lingscope/build/classes/lingscope/drivers/AnnotatedFilesMerger.class +0 -0
  169. data/lib/lingscope/build/classes/lingscope/drivers/AnnotationComparerDriver.class +0 -0
  170. data/lib/lingscope/build/classes/lingscope/drivers/BaselineDriver.class +0 -0
  171. data/lib/lingscope/build/classes/lingscope/drivers/CrfDriver.class +0 -0
  172. data/lib/lingscope/build/classes/lingscope/drivers/CueAndPosFilesMerger.class +0 -0
  173. data/lib/lingscope/build/classes/lingscope/drivers/ModelTrainer.class +0 -0
  174. data/lib/lingscope/build/classes/lingscope/drivers/NegexDriver.class +0 -0
  175. data/lib/lingscope/build/classes/lingscope/drivers/PosTaggerDriver.class +0 -0
  176. data/lib/lingscope/build/classes/lingscope/drivers/SentencePosTagger.class +0 -0
  177. data/lib/lingscope/build/classes/lingscope/drivers/SentenceTagger.class +0 -0
  178. data/lib/lingscope/build/classes/lingscope/io/AnnotatedSentencesIO.class +0 -0
  179. data/lib/lingscope/build/classes/lingscope/structures/AnnotatedSentence.class +0 -0
  180. data/lib/lingscope/dist/README.TXT +32 -0
  181. data/lib/lingscope/dist/javadoc/allclasses-frame.html +80 -0
  182. data/lib/lingscope/dist/javadoc/allclasses-noframe.html +80 -0
  183. data/lib/lingscope/dist/javadoc/constant-values.html +199 -0
  184. data/lib/lingscope/dist/javadoc/deprecated-list.html +147 -0
  185. data/lib/lingscope/dist/javadoc/help-doc.html +224 -0
  186. data/lib/lingscope/dist/javadoc/index-files/index-1.html +188 -0
  187. data/lib/lingscope/dist/javadoc/index-files/index-10.html +149 -0
  188. data/lib/lingscope/dist/javadoc/index-files/index-11.html +158 -0
  189. data/lib/lingscope/dist/javadoc/index-files/index-12.html +157 -0
  190. data/lib/lingscope/dist/javadoc/index-files/index-13.html +177 -0
  191. data/lib/lingscope/dist/javadoc/index-files/index-14.html +155 -0
  192. data/lib/lingscope/dist/javadoc/index-files/index-15.html +152 -0
  193. data/lib/lingscope/dist/javadoc/index-files/index-16.html +146 -0
  194. data/lib/lingscope/dist/javadoc/index-files/index-2.html +158 -0
  195. data/lib/lingscope/dist/javadoc/index-files/index-3.html +165 -0
  196. data/lib/lingscope/dist/javadoc/index-files/index-4.html +146 -0
  197. data/lib/lingscope/dist/javadoc/index-files/index-5.html +219 -0
  198. data/lib/lingscope/dist/javadoc/index-files/index-6.html +149 -0
  199. data/lib/lingscope/dist/javadoc/index-files/index-7.html +155 -0
  200. data/lib/lingscope/dist/javadoc/index-files/index-8.html +185 -0
  201. data/lib/lingscope/dist/javadoc/index-files/index-9.html +164 -0
  202. data/lib/lingscope/dist/javadoc/index.html +74 -0
  203. data/lib/lingscope/dist/javadoc/lingscope/algorithms/AbnerTokenizer.html +280 -0
  204. data/lib/lingscope/dist/javadoc/lingscope/algorithms/AnnotationComparer.html +526 -0
  205. data/lib/lingscope/dist/javadoc/lingscope/algorithms/Annotator.html +401 -0
  206. data/lib/lingscope/dist/javadoc/lingscope/algorithms/BaselineAnnotator.html +375 -0
  207. data/lib/lingscope/dist/javadoc/lingscope/algorithms/BaselineCueAnnotator.html +309 -0
  208. data/lib/lingscope/dist/javadoc/lingscope/algorithms/BaselineScopeAnnotator.html +340 -0
  209. data/lib/lingscope/dist/javadoc/lingscope/algorithms/CrfAnnotator.html +340 -0
  210. data/lib/lingscope/dist/javadoc/lingscope/algorithms/NegexAnnotator.html +364 -0
  211. data/lib/lingscope/dist/javadoc/lingscope/algorithms/NegexCueAnnotator.html +309 -0
  212. data/lib/lingscope/dist/javadoc/lingscope/algorithms/NegexScopeAnnotator.html +309 -0
  213. data/lib/lingscope/dist/javadoc/lingscope/algorithms/PosTagger.html +268 -0
  214. data/lib/lingscope/dist/javadoc/lingscope/algorithms/class-use/AbnerTokenizer.html +145 -0
  215. data/lib/lingscope/dist/javadoc/lingscope/algorithms/class-use/AnnotationComparer.html +145 -0
  216. data/lib/lingscope/dist/javadoc/lingscope/algorithms/class-use/Annotator.html +299 -0
  217. data/lib/lingscope/dist/javadoc/lingscope/algorithms/class-use/BaselineAnnotator.html +189 -0
  218. data/lib/lingscope/dist/javadoc/lingscope/algorithms/class-use/BaselineCueAnnotator.html +145 -0
  219. data/lib/lingscope/dist/javadoc/lingscope/algorithms/class-use/BaselineScopeAnnotator.html +145 -0
  220. data/lib/lingscope/dist/javadoc/lingscope/algorithms/class-use/CrfAnnotator.html +145 -0
  221. data/lib/lingscope/dist/javadoc/lingscope/algorithms/class-use/NegexAnnotator.html +189 -0
  222. data/lib/lingscope/dist/javadoc/lingscope/algorithms/class-use/NegexCueAnnotator.html +145 -0
  223. data/lib/lingscope/dist/javadoc/lingscope/algorithms/class-use/NegexScopeAnnotator.html +145 -0
  224. data/lib/lingscope/dist/javadoc/lingscope/algorithms/class-use/PosTagger.html +145 -0
  225. data/lib/lingscope/dist/javadoc/lingscope/algorithms/negex/GenNegEx.html +369 -0
  226. data/lib/lingscope/dist/javadoc/lingscope/algorithms/negex/Sorter.html +253 -0
  227. data/lib/lingscope/dist/javadoc/lingscope/algorithms/negex/class-use/GenNegEx.html +181 -0
  228. data/lib/lingscope/dist/javadoc/lingscope/algorithms/negex/class-use/Sorter.html +145 -0
  229. data/lib/lingscope/dist/javadoc/lingscope/algorithms/negex/package-frame.html +35 -0
  230. data/lib/lingscope/dist/javadoc/lingscope/algorithms/negex/package-summary.html +165 -0
  231. data/lib/lingscope/dist/javadoc/lingscope/algorithms/negex/package-tree.html +154 -0
  232. data/lib/lingscope/dist/javadoc/lingscope/algorithms/negex/package-use.html +174 -0
  233. data/lib/lingscope/dist/javadoc/lingscope/algorithms/package-frame.html +53 -0
  234. data/lib/lingscope/dist/javadoc/lingscope/algorithms/package-summary.html +198 -0
  235. data/lib/lingscope/dist/javadoc/lingscope/algorithms/package-tree.html +160 -0
  236. data/lib/lingscope/dist/javadoc/lingscope/algorithms/package-use.html +202 -0
  237. data/lib/lingscope/dist/javadoc/lingscope/drivers/AnnotatedFilesMerger.html +284 -0
  238. data/lib/lingscope/dist/javadoc/lingscope/drivers/AnnotationComparerDriver.html +258 -0
  239. data/lib/lingscope/dist/javadoc/lingscope/drivers/BaselineDriver.html +260 -0
  240. data/lib/lingscope/dist/javadoc/lingscope/drivers/CrfDriver.html +262 -0
  241. data/lib/lingscope/dist/javadoc/lingscope/drivers/CueAndPosFilesMerger.html +310 -0
  242. data/lib/lingscope/dist/javadoc/lingscope/drivers/ModelTrainer.html +281 -0
  243. data/lib/lingscope/dist/javadoc/lingscope/drivers/NegexDriver.html +262 -0
  244. data/lib/lingscope/dist/javadoc/lingscope/drivers/PosTaggerDriver.html +289 -0
  245. data/lib/lingscope/dist/javadoc/lingscope/drivers/SentencePosTagger.html +313 -0
  246. data/lib/lingscope/dist/javadoc/lingscope/drivers/SentenceTagger.html +512 -0
  247. data/lib/lingscope/dist/javadoc/lingscope/drivers/class-use/AnnotatedFilesMerger.html +145 -0
  248. data/lib/lingscope/dist/javadoc/lingscope/drivers/class-use/AnnotationComparerDriver.html +145 -0
  249. data/lib/lingscope/dist/javadoc/lingscope/drivers/class-use/BaselineDriver.html +145 -0
  250. data/lib/lingscope/dist/javadoc/lingscope/drivers/class-use/CrfDriver.html +145 -0
  251. data/lib/lingscope/dist/javadoc/lingscope/drivers/class-use/CueAndPosFilesMerger.html +145 -0
  252. data/lib/lingscope/dist/javadoc/lingscope/drivers/class-use/ModelTrainer.html +145 -0
  253. data/lib/lingscope/dist/javadoc/lingscope/drivers/class-use/NegexDriver.html +145 -0
  254. data/lib/lingscope/dist/javadoc/lingscope/drivers/class-use/PosTaggerDriver.html +145 -0
  255. data/lib/lingscope/dist/javadoc/lingscope/drivers/class-use/SentencePosTagger.html +145 -0
  256. data/lib/lingscope/dist/javadoc/lingscope/drivers/class-use/SentenceTagger.html +145 -0
  257. data/lib/lingscope/dist/javadoc/lingscope/drivers/package-frame.html +51 -0
  258. data/lib/lingscope/dist/javadoc/lingscope/drivers/package-summary.html +195 -0
  259. data/lib/lingscope/dist/javadoc/lingscope/drivers/package-tree.html +154 -0
  260. data/lib/lingscope/dist/javadoc/lingscope/drivers/package-use.html +145 -0
  261. data/lib/lingscope/dist/javadoc/lingscope/io/AnnotatedSentencesIO.html +285 -0
  262. data/lib/lingscope/dist/javadoc/lingscope/io/class-use/AnnotatedSentencesIO.html +145 -0
  263. data/lib/lingscope/dist/javadoc/lingscope/io/package-frame.html +33 -0
  264. data/lib/lingscope/dist/javadoc/lingscope/io/package-summary.html +158 -0
  265. data/lib/lingscope/dist/javadoc/lingscope/io/package-tree.html +154 -0
  266. data/lib/lingscope/dist/javadoc/lingscope/io/package-use.html +145 -0
  267. data/lib/lingscope/dist/javadoc/lingscope/structures/AnnotatedSentence.html +425 -0
  268. data/lib/lingscope/dist/javadoc/lingscope/structures/class-use/AnnotatedSentence.html +423 -0
  269. data/lib/lingscope/dist/javadoc/lingscope/structures/package-frame.html +33 -0
  270. data/lib/lingscope/dist/javadoc/lingscope/structures/package-summary.html +158 -0
  271. data/lib/lingscope/dist/javadoc/lingscope/structures/package-tree.html +154 -0
  272. data/lib/lingscope/dist/javadoc/lingscope/structures/package-use.html +209 -0
  273. data/lib/lingscope/dist/javadoc/overview-frame.html +51 -0
  274. data/lib/lingscope/dist/javadoc/overview-summary.html +168 -0
  275. data/lib/lingscope/dist/javadoc/overview-tree.html +159 -0
  276. data/lib/lingscope/dist/javadoc/package-list +5 -0
  277. data/lib/lingscope/dist/javadoc/resources/inherit.gif +0 -0
  278. data/lib/lingscope/dist/javadoc/stylesheet.css +29 -0
  279. data/lib/lingscope/dist/lib/abner.jar +0 -0
  280. data/lib/lingscope/dist/lib/commons-lang-2.4.jar +0 -0
  281. data/lib/lingscope/dist/lib/java_utils.jar +0 -0
  282. data/lib/lingscope/dist/lib/sptoolkit.jar +0 -0
  283. data/lib/lingscope/dist/lib/stanford-postagger.jar +0 -0
  284. data/lib/lingscope/dist/lingscope.jar +0 -0
  285. data/lib/lingscope/lingscope.zip +0 -0
  286. data/lib/lingscope/manifest.mf +3 -0
  287. data/lib/lingscope/nbproject/build-impl.xml +1338 -0
  288. data/lib/lingscope/nbproject/genfiles.properties +8 -0
  289. data/lib/lingscope/nbproject/private/config.properties +0 -0
  290. data/lib/lingscope/nbproject/private/private.properties +10 -0
  291. data/lib/lingscope/nbproject/private/private.xml +5 -0
  292. data/lib/lingscope/nbproject/project.properties +85 -0
  293. data/lib/lingscope/nbproject/project.xml +15 -0
  294. data/lib/lingscope/negation_models.zip +0 -0
  295. data/lib/lingscope/negation_models/baseline_cue_all_both.model +49 -0
  296. data/lib/lingscope/negation_models/baseline_cue_all_clinical.model +19 -0
  297. data/lib/lingscope/negation_models/crf_cue_all_both.model +0 -0
  298. data/lib/lingscope/negation_models/crf_cue_all_clinical.model +0 -0
  299. data/lib/lingscope/negation_models/crf_scope_cue_crf_all_both.model +0 -0
  300. data/lib/lingscope/negation_models/crf_scope_cue_crf_all_clinical.model +0 -0
  301. data/lib/lingscope/negation_models/crf_scope_cue_regex_all_both.model +0 -0
  302. data/lib/lingscope/negation_models/crf_scope_cue_regex_all_clinical.model +0 -0
  303. data/lib/lingscope/negation_models/crf_scope_words_all_both.model +0 -0
  304. data/lib/lingscope/negation_models/crf_scope_words_all_clinical.model +0 -0
  305. data/lib/lingscope/negation_models/crf_scope_words_crf_all_both.model +0 -0
  306. data/lib/lingscope/negation_models/crf_scope_words_crf_all_clinical.model +0 -0
  307. data/lib/lingscope/negation_models/crf_scope_words_regex_all_both.model +0 -0
  308. data/lib/lingscope/negation_models/crf_scope_words_regex_all_clinical.model +0 -0
  309. data/lib/lingscope/src/lingscope/algorithms/AbnerTokenizer.java +58 -0
  310. data/lib/lingscope/src/lingscope/algorithms/AnnotationComparer.java +207 -0
  311. data/lib/lingscope/src/lingscope/algorithms/Annotator.java +51 -0
  312. data/lib/lingscope/src/lingscope/algorithms/BaselineAnnotator.java +80 -0
  313. data/lib/lingscope/src/lingscope/algorithms/BaselineCueAnnotator.java +84 -0
  314. data/lib/lingscope/src/lingscope/algorithms/BaselineScopeAnnotator.java +101 -0
  315. data/lib/lingscope/src/lingscope/algorithms/CrfAnnotator.java +45 -0
  316. data/lib/lingscope/src/lingscope/algorithms/NegexAnnotator.java +52 -0
  317. data/lib/lingscope/src/lingscope/algorithms/NegexCueAnnotator.java +26 -0
  318. data/lib/lingscope/src/lingscope/algorithms/NegexScopeAnnotator.java +26 -0
  319. data/lib/lingscope/src/lingscope/algorithms/PosTagger.java +54 -0
  320. data/lib/lingscope/src/lingscope/algorithms/negex/GenNegEx.java +530 -0
  321. data/lib/lingscope/src/lingscope/algorithms/negex/Sorter.java +36 -0
  322. data/lib/lingscope/src/lingscope/drivers/AnnotatedFilesMerger.java +61 -0
  323. data/lib/lingscope/src/lingscope/drivers/AnnotationComparerDriver.java +22 -0
  324. data/lib/lingscope/src/lingscope/drivers/BaselineDriver.java +45 -0
  325. data/lib/lingscope/src/lingscope/drivers/CrfDriver.java +31 -0
  326. data/lib/lingscope/src/lingscope/drivers/CueAndPosFilesMerger.java +86 -0
  327. data/lib/lingscope/src/lingscope/drivers/ModelTrainer.java +39 -0
  328. data/lib/lingscope/src/lingscope/drivers/NegexDriver.java +32 -0
  329. data/lib/lingscope/src/lingscope/drivers/PosTaggerDriver.java +62 -0
  330. data/lib/lingscope/src/lingscope/drivers/SentencePosTagger.java +89 -0
  331. data/lib/lingscope/src/lingscope/drivers/SentenceTagger.java +158 -0
  332. data/lib/lingscope/src/lingscope/io/AnnotatedSentencesIO.java +53 -0
  333. data/lib/lingscope/src/lingscope/structures/AnnotatedSentence.java +105 -0
  334. data/lib/setup/data/ICD-O-3_CSV-metadata/Morphenglish.csv +1 -0
  335. data/lib/setup/data/ICD-O-3_CSV-metadata/Morphenglish.txt +2273 -0
  336. data/lib/setup/data/ICD-O-3_CSV-metadata/Topoenglish.csv +1 -0
  337. data/lib/setup/data/ICD-O-3_CSV-metadata/Topoenglish.txt +1342 -0
  338. data/lib/setup/data/ICD-O-3_CSV-metadata/icd-o3 readme.txt +21 -0
  339. data/lib/setup/data/custom_site_synonyms.csv +1 -0
  340. data/lib/setup/data/diagnosis_categorizations.csv +1 -0
  341. data/lib/setup/data/high_level_primary_cns_diagnosis_categorizations.yml +597 -0
  342. data/lib/setup/data/icdo3_sites_with_laterality.txt +11 -0
  343. data/lib/setup/data/site_site_categories.txt +28 -0
  344. data/lib/tasks/abstractor_tasks.rake +22 -0
  345. data/lib/tasks/cucumber.rake +65 -0
  346. metadata +754 -0
@@ -0,0 +1,99 @@
1
+ class Regexp
2
+ NUMERIC = Regexp.union(%r{^-?\d{1,3}(,\d{3}|\d+)*(\.\d+)*$},
3
+ %r{^\(?\d{1,3}(,\d{3}|\d+)*(\.\d+)*\)?$})
4
+ end
5
+
6
+ class String
7
+ def to_boolean
8
+ return true if self == true || self =~ (/(true|t|yes|y|1)$/i)
9
+ return false if self == false || self.blank? || self =~ (/(false|f|no|n|0)$/i)
10
+ raise ArgumentError.new("invalid value for Boolean: \"#{self}\"")
11
+ end
12
+
13
+ # Like #index but returns a Range.
14
+ #
15
+ # "This is a test!".range('test') #=> (10..13)
16
+ #
17
+ # CREDIT: Trans
18
+
19
+ def range(pattern, offset=0)
20
+ unless Regexp === pattern
21
+ pattern = Regexp.new(Regexp.escape(pattern.to_s))
22
+ end
23
+ string = self[offset..-1]
24
+ if md = pattern.match(string)
25
+ return (md.begin(0)+offset)..(md.end(0)+offset-1)
26
+ end
27
+ nil
28
+ end
29
+
30
+ # Like #index_all but returns an array of Ranges.
31
+ #
32
+ # "abc123abc123".range_all('abc') #=> [0..2, 6..8]
33
+ #
34
+ # TODO: Add offset ?
35
+ #
36
+ # CREDIT: Trans
37
+
38
+ def range_all(pattern, reuse=false)
39
+ r = []; i = 0
40
+ while i < self.length
41
+ rng = range(pattern, i)
42
+ if rng
43
+ r << rng
44
+ i += reuse ? 1 : rng.end + 1
45
+ else
46
+ break
47
+ end
48
+ end
49
+ r.uniq
50
+ end
51
+
52
+ # Returns an array of ranges mapping
53
+ # the characters per line.
54
+ #
55
+ # "this\nis\na\ntest".range_of_line
56
+ # #=> [0..4, 5..7, 8..9, 10..13]
57
+ #
58
+ # CREDIT: Trans
59
+
60
+ def range_of_line
61
+ offset=0; charmap = []
62
+ each_line do |line|
63
+ charmap << (offset..(offset + line.length - 1))
64
+ offset += line.length
65
+ end
66
+ charmap
67
+ end
68
+
69
+ def numeric?
70
+ match(Regexp::NUMERIC) != nil
71
+ end
72
+
73
+ def integer?
74
+ begin
75
+ Integer(self)
76
+ self
77
+ rescue ArgumentError => e
78
+ nil
79
+ end
80
+ end
81
+
82
+ def date?
83
+ begin
84
+ d = Date.parse(self)
85
+ rescue ArgumentError => e
86
+ nil
87
+ end
88
+ end
89
+
90
+ def ssn?
91
+ if (integer? && length == 9)
92
+ self
93
+ elsif ((self =~ /[0-9]{3}-[0-9]{2}-[0-9]{4}/ ) == 0)
94
+ self.gsub('-','')
95
+ else
96
+ nil
97
+ end
98
+ end
99
+ end
@@ -0,0 +1,14 @@
1
+ require 'haml'
2
+
3
+ module Abstractor
4
+ class Engine < ::Rails::Engine
5
+ isolate_namespace Abstractor
6
+ root = File.expand_path('../../', __FILE__)
7
+ config.autoload_paths << root
8
+ config.generators do |g|
9
+ g.test_framework :rspec
10
+ g.integration_tool :rspec
11
+ g.template_engine :haml
12
+ end
13
+ end
14
+ end
@@ -0,0 +1,37 @@
1
+ module Abstractor
2
+ module Methods
3
+ module Controllers
4
+ module AbstractorAbstractionGroupsController
5
+ def self.included(base)
6
+ base.send :helper, :all
7
+ end
8
+
9
+ def create
10
+ @abstractor_abstraction_group = Abstractor::AbstractorAbstractionGroup.create(abstractor_subject_group_id: params[:abstractor_subject_group_id], about_type: params[:about_type], about_id: params[:about_id])
11
+ @abstractor_abstraction_group.abstractor_subject_group.abstractor_subjects.each do |abstractor_subject|
12
+ abstraction = abstractor_subject.abstractor_abstractions.build(about_id: params[:about_id], about_type: params[:about_type])
13
+ abstraction.build_abstractor_abstraction_group_member(abstractor_abstraction_group: @abstractor_abstraction_group)
14
+ abstraction.save!
15
+ end
16
+
17
+ respond_to do |format|
18
+ format.html { render action: "edit", layout: false }
19
+ end
20
+ end
21
+
22
+ def destroy
23
+ abstractor_abstraction_group = Abstractor::AbstractorAbstractionGroup.find(params[:id])
24
+ if abstractor_abstraction_group.soft_delete!
25
+ flash[:notice] = "Group was successfully deleted."
26
+ else
27
+ flash[:error] = "Group could not be deactivated: #{abstractor_abstraction_group.errors.full_messages.join(',')}"
28
+ end
29
+ respond_to do |format|
30
+ format.js { head :no_content }
31
+ format.json { head :no_content }
32
+ end
33
+ end
34
+ end
35
+ end
36
+ end
37
+ end
@@ -0,0 +1,42 @@
1
+ module Abstractor
2
+ module Methods
3
+ module Controllers
4
+ module AbstractorAbstractionsController
5
+ def self.included(base)
6
+ base.send :before_filter, :set_abstractor_abstraction, :only => [:show, :edit, :update]
7
+ end
8
+
9
+ def index
10
+ end
11
+
12
+ def show
13
+ respond_to do |format|
14
+ format.html { render :layout => false }
15
+ end
16
+ end
17
+
18
+ def edit
19
+ respond_to do |format|
20
+ format.html { render :layout => false }
21
+ end
22
+ end
23
+
24
+ def update
25
+ respond_to do |format|
26
+ if @abstractor_abstraction.update_attributes(params[:abstractor_abstraction])
27
+ format.html { redirect_to(abstractor_abstraction_path(@abstractor_abstraction)) }
28
+ else
29
+ format.html { render :action => "edit" }
30
+ end
31
+ end
32
+ end
33
+
34
+ private
35
+ def set_abstractor_abstraction
36
+ @abstractor_abstraction = Abstractor::AbstractorAbstraction.find(params[:id])
37
+ @about = @abstractor_abstraction.about
38
+ end
39
+ end
40
+ end
41
+ end
42
+ end
@@ -0,0 +1,28 @@
1
+ module Abstractor
2
+ module Methods
3
+ module Controllers
4
+ module AbstractorSuggestionsController
5
+ def self.included(base)
6
+ base.send :before_filter, :set_abstractor_suggestion, :only => [:update]
7
+ end
8
+
9
+ def update
10
+ respond_to do |format|
11
+ if @abstractor_suggestion.update_attributes(params[:abstractor_suggestion])
12
+ format.html { redirect_to(abstractor_abstraction_path(@abstractor_abstraction)) }
13
+ else
14
+ format.html { render "abstractor_abstractions/show" }
15
+ end
16
+ end
17
+ end
18
+
19
+ private
20
+ def set_abstractor_suggestion
21
+ @abstractor_abstraction = Abstractor::AbstractorAbstraction.find(params[:abstractor_abstraction_id])
22
+ @abstractor_suggestion = Abstractor::AbstractorSuggestion.find(params[:id])
23
+ @about = @abstractor_abstraction.about
24
+ end
25
+ end
26
+ end
27
+ end
28
+ end
@@ -0,0 +1,65 @@
1
+ module Abstractor
2
+ module Methods
3
+ module Models
4
+ module AbstractorAbstraction
5
+ def self.included(base)
6
+ base.send :include, SoftDelete
7
+ base.send :has_paper_trail
8
+
9
+ # Associations
10
+ base.send :belongs_to, :abstractor_subject
11
+
12
+ base.send :has_many, :abstractor_suggestions
13
+ base.send :has_many, :abstractor_abstraction_sources, :through => :abstractor_abstractor_suggestions
14
+
15
+ base.send :has_one, :abstractor_abstraction_group_member
16
+ base.send :has_one, :abstractor_abstraction_group, :through => :abstractor_abstraction_group_member
17
+ base.send :has_one, :abstractor_abstraction_schema, :through => :abstractor_subject
18
+
19
+ base.send :accepts_nested_attributes_for, :abstractor_suggestions
20
+
21
+ base.send :belongs_to, :about, polymorphic: true
22
+
23
+ base.send :attr_accessible, :about, :abstractor_subject, :abstractor_subject_id, :value, :about_type, :about_id, :unknown, :not_applicable, :deleted_at
24
+
25
+ # Hooks
26
+ base.send :after_save, :review_matching_suggestions#, :if => lambda {|abstractor_abstraction| abstractor_abstraction.value_changed?}
27
+ end
28
+
29
+ def review_matching_suggestions
30
+ accepted_status = Abstractor::AbstractorSuggestionStatus.where(:name => 'Accepted').first
31
+ matching_abstractor_suggestions.each do |abstractor_suggestion|
32
+ abstractor_suggestion.abstractor_suggestion_status = accepted_status
33
+ abstractor_suggestion.save!
34
+ end
35
+ end
36
+
37
+ def matching_abstractor_suggestions
38
+ unknown_values = unknown ? unknown : [unknown, nil]
39
+ not_applicable_values = not_applicable ? not_applicable : [not_applicable, nil]
40
+ suggested_values = value.blank? ? ['', nil] : value
41
+ abstractor_suggestions.where(unknown: unknown_values, not_applicable: not_applicable_values, suggested_value: suggested_values)
42
+ end
43
+
44
+ def display_value
45
+ if unknown
46
+ 'unknown'
47
+ elsif not_applicable
48
+ 'not applicable'
49
+ elsif value.blank?
50
+ '[Not set]'
51
+ else
52
+ value
53
+ end
54
+ end
55
+
56
+ def detect_abstractor_suggestion(suggested_value)
57
+ abstractor_suggestion = nil
58
+ abstractor_suggestion = abstractor_suggestions(true).detect do |abstractor_suggestion|
59
+ abstractor_suggestion.suggested_value == suggested_value
60
+ end
61
+ end
62
+ end
63
+ end
64
+ end
65
+ end
@@ -0,0 +1,37 @@
1
+ module Abstractor
2
+ module Methods
3
+ module Models
4
+ module AbstractorAbstractionGroup
5
+ def self.included(base)
6
+ base.send :include, SoftDelete
7
+
8
+ # Associations
9
+ base.send :belongs_to, :abstractor_subject_group
10
+ base.send :belongs_to, :about, polymorphic: true
11
+
12
+ base.send :has_many, :abstractor_abstraction_group_members
13
+ base.send :has_many, :abstractor_abstractions, :through => :abstractor_abstraction_group_members
14
+
15
+ base.send :attr_accessible, :abstractor_subject_group, :abstractor_subject_group_id, :deleted_at, :about, :about_type, :about_id
16
+
17
+ # Hooks
18
+ base.send :after_commit, :update_abstractor_abstraction_group_members, :on => :update, :if => Proc.new { |record| record.previous_changes.include?('deleted_at') }
19
+ end
20
+
21
+ # Instance Methods
22
+ def removable?
23
+ abstractor_abstractions.map(&:abstractor_suggestions).flatten.empty?
24
+ end
25
+
26
+ private
27
+ def update_abstractor_abstraction_group_members
28
+ return unless deleted?
29
+ abstractor_abstraction_group_members.each do |gm|
30
+ gm.soft_delete!
31
+ gm.abstractor_abstraction.soft_delete!
32
+ end
33
+ end
34
+ end
35
+ end
36
+ end
37
+ end
@@ -0,0 +1,17 @@
1
+ module Abstractor
2
+ module Methods
3
+ module Models
4
+ module AbstractorAbstractionGroupMember
5
+ def self.included(base)
6
+ base.send :include, SoftDelete
7
+
8
+ # Associations
9
+ base.send :belongs_to, :abstractor_abstraction_group
10
+ base.send :belongs_to, :abstractor_abstraction
11
+
12
+ base.send :attr_accessible, :abstractor_abstraction_group, :abstractor_abstraction_group_id, :abstractor_abstraction, :abstractor_abstraction_id, :deleted_at
13
+ end
14
+ end
15
+ end
16
+ end
17
+ end
@@ -0,0 +1,27 @@
1
+ module Abstractor
2
+ module Methods
3
+ module Models
4
+ module AbstractorAbstractionSchema
5
+ def self.included(base)
6
+ base.send :include, SoftDelete
7
+
8
+ # Associations
9
+ base.send :belongs_to, :abstractor_object_type
10
+ base.send :has_many, :abstractor_subjects
11
+ base.send :has_many, :abstractor_abstraction_schema_predicate_variants
12
+ base.send :has_many, :abstractor_abstraction_schema_object_values
13
+ base.send :has_many, :abstractor_object_values, :through => :abstractor_abstraction_schema_object_values
14
+ base.send :has_many, :object_relations, :class_name => "Abstractor::AbstractorAbstractionSchemaRelation", :foreign_key => "object_id"
15
+ base.send :has_many, :subject_relations, :class_name => "Abstractor::AbstractorAbstractionSchemaRelation", :foreign_key => "subject_id"
16
+
17
+ base.send :attr_accessible, :abstractor_object_type, :abstractor_object_type_id, :display_name, :predicate, :preferred_name, :deleted_at
18
+ end
19
+
20
+ # Instance Methods
21
+ def predicate_variants
22
+ [preferred_name].concat(abstractor_abstraction_schema_predicate_variants.map(&:value))
23
+ end
24
+ end
25
+ end
26
+ end
27
+ end
@@ -0,0 +1,17 @@
1
+ module Abstractor
2
+ module Methods
3
+ module Models
4
+ module AbstractorAbstractionSchemaObjectValue
5
+ def self.included(base)
6
+ base.send :include, SoftDelete
7
+
8
+ # Associations
9
+ base.send :belongs_to, :abstractor_abstraction_schema
10
+ base.send :belongs_to, :abstractor_object_value
11
+
12
+ base.send :attr_accessible, :abstractor_abstraction_schema, :abstractor_abstraction_schema_id, :abstractor_object_value, :abstractor_object_value_id
13
+ end
14
+ end
15
+ end
16
+ end
17
+ end
@@ -0,0 +1,16 @@
1
+ module Abstractor
2
+ module Methods
3
+ module Models
4
+ module AbstractorAbstractionSchemaPredicateVariant
5
+ def self.included(base)
6
+ base.send :include, SoftDelete
7
+
8
+ # Associations
9
+ base.send :belongs_to, :abstractor_abstraction_schema
10
+
11
+ base.send :attr_accessible, :abstractor_abstraction_schema, :abstractor_abstraction_schema_id, :deleted_at, :value
12
+ end
13
+ end
14
+ end
15
+ end
16
+ end
@@ -0,0 +1,18 @@
1
+ module Abstractor
2
+ module Methods
3
+ module Models
4
+ module AbstractorAbstractionSchemaRelation
5
+ def self.included(base)
6
+ base.send :include, SoftDelete
7
+
8
+ # Associations
9
+ base.send :belongs_to, :abstractor_relation_type
10
+ base.send :belongs_to, :object, :class_name => "Abstractor::AbstractorAbstractionSchema", :foreign_key => "object_id"
11
+ base.send :belongs_to, :subject, :class_name => "Abstractor::AbstractorAbstractionSchema", :foreign_key => "subject_id"
12
+
13
+ base.send :attr_accessible, :abstractor_relation_type, :abstractor_relation_type_id, :object, :object_id, :subject, :subject_id, :deleted_at
14
+ end
15
+ end
16
+ end
17
+ end
18
+ end
@@ -0,0 +1,29 @@
1
+ module Abstractor
2
+ module Methods
3
+ module Models
4
+ module AbstractorAbstractionSource
5
+ def self.included(base)
6
+ base.send :include, SoftDelete
7
+
8
+ # Associations
9
+ base.send :belongs_to, :abstractor_subject
10
+ base.send :has_many, :abstractor_suggestion_sources
11
+ base.send :has_many, :abstractor_abstractions, :through => :abstractor_suggestion_sources
12
+
13
+ base.send :attr_accessible, :abstractor_subject, :abstractor_subject_id, :deleted_at, :from_method
14
+ end
15
+
16
+ def normalize_from_method_to_sources(about)
17
+ sources = []
18
+ fm = about.send(from_method)
19
+ if fm.is_a?(String) || fm.nil?
20
+ sources = [{ source_type: about.class , source_id: about.id , source_method: from_method }]
21
+ else
22
+ sources = fm
23
+ end
24
+ sources
25
+ end
26
+ end
27
+ end
28
+ end
29
+ end