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
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  163. data/lib/lingscope/build/classes/lingscope/algorithms/NegexCueAnnotator.class +0 -0
  164. data/lib/lingscope/build/classes/lingscope/algorithms/NegexScopeAnnotator.class +0 -0
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  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
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  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
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  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
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  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
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  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
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  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
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  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
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  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 +1,24 @@
1
+ module Abstractor
2
+ module AbstractorAbstractionsControllerCustomMethods
3
+ def index
4
+ super
5
+ end
6
+
7
+ def show
8
+ super
9
+ end
10
+
11
+ def edit
12
+ super
13
+ end
14
+
15
+ def update
16
+ super
17
+ end
18
+ end
19
+
20
+ class AbstractorAbstractionsController < ApplicationController
21
+ include Abstractor::Methods::Controllers::AbstractorAbstractionsController
22
+ include Abstractor::AbstractorAbstractionsControllerCustomMethods
23
+ end
24
+ end
@@ -0,0 +1,12 @@
1
+ module Abstractor
2
+ module AbstractorSuggestionsControllerCustomMethods
3
+ def update
4
+ super
5
+ end
6
+ end
7
+
8
+ class AbstractorSuggestionsController < ApplicationController
9
+ include Abstractor::Methods::Controllers::AbstractorSuggestionsController
10
+ include Abstractor::AbstractorSuggestionsControllerCustomMethods
11
+ end
12
+ end
@@ -0,0 +1,235 @@
1
+ # ---- General structure:
2
+ # :dictionaries:
3
+ # - :name: string # has to be unique within not-deleted dictionaries
4
+ # :parameter_categories:
5
+ # - :name: string # has to be unique within the dictionary
6
+ # :parameters:
7
+ # - :name: string # used for display
8
+ # :unique_identifier: # has to be unique within the dictionary
9
+ # :export:
10
+ # :model # name of the model to be used for exporting
11
+ # :method # name of the model method to be used for exporting
12
+ # :search: # parameter search model and method combination has to be unique within the category
13
+ # :model: string # name of the model to be used for searching
14
+ # :method: string # name of the model method to be used for searching
15
+ # :parameter_type: numeric/date/list/combobox/text/string # used to define applicable operators/display options. does not have to be restricted to the given list, but additional parameters will require adding operators to match
16
+ # :parameter_value_categories_source: # used to define parameter value categories
17
+ # :model: string # source model to be used to load parameter value categiories
18
+ # :method: string # method in the source model that returns parameter_value_categories in a form of [{:name => 'string, :unique_identifier => 'adventure', :display_order => 1, :collapse => true}]
19
+ # :parameter_value_categories: # used to define parameter value categories
20
+ # - :name: string
21
+ # :unique_identifier: string # has to be unique within parameter
22
+ # :collapse: boolean # used to define if parameter category should be collapsed in the list and its values hidden from the view
23
+ # :display_order: integer
24
+ # :parameter_values: # needs to be defined for list/combobox parameters unless parameter values come from the model, see ':source'
25
+ # - :name: string # used for display, if not provided, 'search_value' will be used instead
26
+ # :search_value: string # has to be unique within parameter, intendend to be used as a database value while searching
27
+ # :parameter_value_category: string # used to define category for parameter value, should match one of parameter_value_categories unique_identifiers listed above
28
+ # :source:
29
+ # :model: string # source model to be used to load parameter values
30
+ # :method: string # method/method in the source model to be used to load parameter values
31
+
32
+ ---
33
+ :dictionaries:
34
+ - :name: Sample dictionary
35
+ :parameter_categories:
36
+ - :name: Demographic criteria
37
+ :parameters:
38
+ - :name: Age at case collection date
39
+ :unique_identifier: age_at_case_collect
40
+ :search:
41
+ :model: Patient
42
+ :method: age_at_case_collect
43
+ :parameter_type: numeric
44
+
45
+ - :name: Age based on current date
46
+ :unique_identifier: age_based_on_current_date
47
+ :export:
48
+ :model: Patient
49
+ :method: age_based_on_current_date
50
+
51
+ - :name: Date of birth
52
+ :unique_identifier: birth_dt_tm
53
+ :search:
54
+ :model: Patient
55
+ :method: birth_dt_tm
56
+ :parameter_type: date
57
+ :export:
58
+ :model: Patient
59
+ :method: age_based_on_current_date
60
+
61
+ - :name: Ethnic group
62
+ :unique_identifier: ethnic_grp
63
+ :search:
64
+ :model: Patient
65
+ :method: ethnic_grp
66
+ :parameter_type: combobox
67
+ :parameter_values:
68
+ - :name: Hispanic or Latino
69
+ :search_value: hisp_or_latino
70
+ - :name: NOT Hispanic or Latino
71
+ :search_value: not_hisp_or_latino
72
+ - :name: Unable to answer
73
+ :search_value: unknown
74
+ - :name: Declined to answer
75
+ :search_value: declined
76
+
77
+ - :name: Consented
78
+ :unique_identifier: surg_inpatient_mortality
79
+ :search:
80
+ :model: Surgery
81
+ :method: consented
82
+ :parameter_type: list
83
+ :parameter_values:
84
+ - :search_value: yes
85
+ - :search_value: no
86
+
87
+ - :name: Gender
88
+ :unique_identifier: sex
89
+ :search:
90
+ :model: Patient
91
+ :method: sex
92
+ :parameter_type: list
93
+ :parameter_values:
94
+ - :name: Male
95
+ :search_value: male
96
+ - :name: Female
97
+ :search_value: female
98
+ - :name: Indeterminent
99
+ :search_value: indeterminent
100
+ - :name: Unknown
101
+ :search_value: unknown
102
+ - :name: Unspecified
103
+ :search_value: uncpecified
104
+ :export:
105
+ :model: Patient
106
+ :method: gender
107
+
108
+ - :name: Race
109
+ :exclusive: false
110
+ :unique_identifier: race
111
+ :search:
112
+ :model: Patient
113
+ :method: race
114
+ :parameter_type: combobox
115
+ :parameter_values:
116
+ - :search_value: American Indian or Alaska Native
117
+ - :search_value: Asian
118
+ - :search_value: Black or African American
119
+ - :search_value: Hispanic or Latino
120
+ - :search_value: Native Hawaiian or Other Pacific Islander
121
+ - :search_value: White or Caucasian
122
+ - :search_value: Other
123
+ - :search_value: Declined to answer
124
+ - :search_value: Unable to answer
125
+ :export:
126
+ :model: Patient
127
+ :method: race
128
+
129
+ - :name: Case criteria
130
+ :parameters:
131
+ - :name: Accession date
132
+ :unique_identifier: accessioned_dt_tm
133
+ :search:
134
+ :model: Case
135
+ :method: accessioned_dt_tm
136
+ :parameter_type: date
137
+
138
+ - :name: Text search diagnosis
139
+ :exclusive: false
140
+ :unique_identifier: case_specimen_diagnosis
141
+ :search:
142
+ :model: Case
143
+ :method: case_specimen_diagnosis
144
+ :parameter_type: text
145
+
146
+ - :name: Librarian dictionary
147
+ :parameter_categories:
148
+ - :name: By author
149
+ :parameters:
150
+ - :name: "Last name"
151
+ :unique_identifier: autor_last_name
152
+ :search:
153
+ :model: Author
154
+ :method: autor_last_name
155
+ :parameter_type: string
156
+
157
+ - :name: "First name"
158
+ :unique_identifier: autor_first_name
159
+ :search:
160
+ :model: Author
161
+ :method: autor_first_name
162
+ :parameter_type: text
163
+
164
+ - :name: "Country"
165
+ :unique_identifier: country
166
+ :search:
167
+ :model: Author
168
+ :method: country
169
+ :parameter_type: text
170
+
171
+ - :name: "Type"
172
+ :unique_identifier: author_type
173
+ :search:
174
+ :model: Book
175
+ :method: type
176
+ :parameter_type: list
177
+ :parameter_values:
178
+ - :search_value: author
179
+ - :search_value: co-author
180
+ - :search_value: reviewer
181
+ - :name: Book criteria
182
+ :parameters:
183
+ - :name: "Type"
184
+ :unique_identifier: book_type
185
+ :search:
186
+ :model: Book
187
+ :method: type
188
+ :parameter_type: combobox
189
+ :parameter_values:
190
+ - :search_value: book
191
+ - :search_value: journal
192
+ - :search_value: article
193
+ - :search_value: electronic journal
194
+
195
+ - :name: "Genre"
196
+ :unique_identifier: book_genre
197
+ :search:
198
+ :model: Book
199
+ :method: Genre
200
+ :parameter_type: combobox
201
+ :parameter_value_categories:
202
+ - :name: Adventure
203
+ :unique_identifier: adventure
204
+ :collapse: true
205
+ :display_order: 1
206
+ - :name: Comic novel
207
+ :unique_identifier: comic
208
+ - :name: Historical
209
+ :unique_identifier: historical
210
+ :parameter_values:
211
+ - :search_value: "Robinsonade"
212
+ :parameter_value_category: adventure
213
+ - :search_value: "Black comedy"
214
+ :parameter_value_category: comic
215
+ - :search_value: "Parody"
216
+ :parameter_value_category: comic
217
+ - :search_value: "Lost World"
218
+ :parameter_value_category: adventure
219
+ - :search_value: "Brit lit"
220
+ - :search_value: "Pulp fiction"
221
+
222
+ - :name: "Title"
223
+ :unique_identifier: title
224
+ :search:
225
+ :model: Book
226
+ :method: title
227
+ :parameter_type: text
228
+
229
+ - :name: "Keyword"
230
+ :unique_identifier: text
231
+ :search:
232
+ :model: Book
233
+ :method: text
234
+ :parameter_type: text
235
+
@@ -0,0 +1,9 @@
1
+ module Abstractor
2
+ module AbstractionsHelperCustomMethods
3
+ end
4
+
5
+ module AbstractionsHelper
6
+ include Abstractor::Methods::Helpers::AbstractionsHelper
7
+ include Abstractor::AbstractionsHelperCustomMethods
8
+ end
9
+ end
@@ -0,0 +1,9 @@
1
+ module Abstractor
2
+ module AbstractorAbstractionCustomMethods
3
+ end
4
+
5
+ class AbstractorAbstraction < ActiveRecord::Base
6
+ include Abstractor::Methods::Models::AbstractorAbstraction
7
+ include Abstractor::AbstractorAbstractionCustomMethods
8
+ end
9
+ end
@@ -0,0 +1,9 @@
1
+ module Abstractor
2
+ module AbstractorAbstractionGroupCustomMethods
3
+ end
4
+
5
+ class AbstractorAbstractionGroup < ActiveRecord::Base
6
+ include Abstractor::Methods::Models::AbstractorAbstractionGroup
7
+ include Abstractor::AbstractorAbstractionGroupCustomMethods
8
+ end
9
+ end
@@ -0,0 +1,9 @@
1
+ module Abstractor
2
+ module AbstractorAbstractionGroupMemberCustomMethods
3
+ end
4
+
5
+ class AbstractorAbstractionGroupMember < ActiveRecord::Base
6
+ include Abstractor::Methods::Models::AbstractorAbstractionGroupMember
7
+ include Abstractor::AbstractorAbstractionGroupMemberCustomMethods
8
+ end
9
+ end
@@ -0,0 +1,9 @@
1
+ module Abstractor
2
+ module AbstractorAbstractionSchemaCustomMethods
3
+ end
4
+
5
+ class AbstractorAbstractionSchema < ActiveRecord::Base
6
+ include Abstractor::Methods::Models::AbstractorAbstractionSchema
7
+ include Abstractor::AbstractorAbstractionSchemaCustomMethods
8
+ end
9
+ end
@@ -0,0 +1,9 @@
1
+ module Abstractor
2
+ module AbstractorAbstractionSchemaObjectValueCustomMethods
3
+ end
4
+
5
+ class AbstractorAbstractionSchemaObjectValue < ActiveRecord::Base
6
+ include Abstractor::Methods::Models::AbstractorAbstractionSchemaObjectValue
7
+ include Abstractor::AbstractorAbstractionSchemaObjectValueCustomMethods
8
+ end
9
+ end
@@ -0,0 +1,9 @@
1
+ module Abstractor
2
+ module AbstractorAbstractionSchemaPredicateVariantCustomMethods
3
+ end
4
+
5
+ class AbstractorAbstractionSchemaPredicateVariant < ActiveRecord::Base
6
+ include Abstractor::Methods::Models::AbstractorAbstractionSchemaPredicateVariant
7
+ include Abstractor::AbstractorAbstractionSchemaPredicateVariantCustomMethods
8
+ end
9
+ end
@@ -0,0 +1,9 @@
1
+ module Abstractor
2
+ module AbstractorAbstractionSchemaRelationCustomMethods
3
+ end
4
+
5
+ class AbstractorAbstractionSchemaRelation < ActiveRecord::Base
6
+ include Abstractor::Methods::Models::AbstractorAbstractionSchemaRelation
7
+ include Abstractor::AbstractorAbstractionSchemaRelationCustomMethods
8
+ end
9
+ end
@@ -0,0 +1,9 @@
1
+ module Abstractor
2
+ module AbstractorAbstractionSourceCustomMethods
3
+ end
4
+
5
+ class AbstractorAbstractionSource < ActiveRecord::Base
6
+ include Abstractor::Methods::Models::AbstractorAbstractionSource
7
+ include Abstractor::AbstractorAbstractionSourceCustomMethods
8
+ end
9
+ end
@@ -0,0 +1,9 @@
1
+ module Abstractor
2
+ module AbstractorObjectTypeCustomMethods
3
+ end
4
+
5
+ class AbstractorObjectType < ActiveRecord::Base
6
+ include Abstractor::Methods::Models::AbstractorObjectType
7
+ include Abstractor::AbstractorObjectTypeCustomMethods
8
+ end
9
+ end
@@ -0,0 +1,9 @@
1
+ module Abstractor
2
+ module AbstractorObjectValueCustomMethods
3
+ end
4
+
5
+ class AbstractorObjectValue < ActiveRecord::Base
6
+ include Abstractor::Methods::Models::AbstractorObjectValue
7
+ include Abstractor::AbstractorObjectValueCustomMethods
8
+ end
9
+ end
@@ -0,0 +1,9 @@
1
+ module Abstractor
2
+ module AbstractorObjectValueVariantCustomMethods
3
+ end
4
+
5
+ class AbstractorObjectValueVariant < ActiveRecord::Base
6
+ include Abstractor::Methods::Models::AbstractorObjectValueVariant
7
+ include Abstractor::AbstractorObjectValueVariantCustomMethods
8
+ end
9
+ end
@@ -0,0 +1,9 @@
1
+ module Abstractor
2
+ module AbstractorRelationTypeCustomMethods
3
+ end
4
+
5
+ class AbstractorRelationType < ActiveRecord::Base
6
+ include Abstractor::Methods::Models::AbstractorRelationType
7
+ include Abstractor::AbstractorRelationTypeCustomMethods
8
+ end
9
+ end
@@ -0,0 +1,9 @@
1
+ module Abstractor
2
+ module AbstractorRuleTypeCustomMethods
3
+ end
4
+
5
+ class RuleType < ActiveRecord::Base
6
+ include Abstractor::Methods::Models::AbstractorRuleType
7
+ include Abstractor::AbstractorRuleTypeCustomMethods
8
+ end
9
+ end
@@ -0,0 +1,9 @@
1
+ module Abstractor
2
+ module AbstractorSubjectCustomMethods
3
+ end
4
+
5
+ class AbstractorSubject < ActiveRecord::Base
6
+ include Abstractor::Methods::Models::AbstractorSubject
7
+ include Abstractor::AbstractorSubjectCustomMethods
8
+ end
9
+ end
@@ -0,0 +1,9 @@
1
+ module Abstractor
2
+ module AbstractorSubjectGroupCustomMethods
3
+ end
4
+
5
+ class AbstractorSubjectGroup < ActiveRecord::Base
6
+ include Abstractor::Methods::Models::AbstractorSubjectGroup
7
+ include Abstractor::AbstractorSubjectGroupCustomMethods
8
+ end
9
+ end