caruby-tissue 1.5.6 → 2.1.1

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Files changed (255) hide show
  1. data/Gemfile +17 -0
  2. data/History.md +5 -1
  3. data/README.md +2 -2
  4. data/bin/crtdump +2 -8
  5. data/bin/crtexample +2 -5
  6. data/bin/crtmigrate +3 -6
  7. data/bin/crtsmoke +3 -8
  8. data/conf/wustl/{log4j.properties → linux/log4j.properties} +3 -3
  9. data/conf/wustl/windows/log4j.properties +40 -0
  10. data/examples/galena/Gemfile +16 -0
  11. data/examples/galena/Gemfile.lock +88 -0
  12. data/examples/galena/README.md +16 -16
  13. data/examples/galena/Rakefile +30 -0
  14. data/examples/galena/bin/seed +5 -11
  15. data/examples/galena/conf/annotation/defaults.yaml +2 -0
  16. data/examples/galena/conf/{migration/annotation_fields.yaml → annotation/fields.yaml} +2 -4
  17. data/examples/galena/conf/defaults.yaml +9 -0
  18. data/examples/galena/conf/{migration/filter_fields.yaml → filter/fields.yaml} +0 -1
  19. data/examples/galena/conf/filter/values.yaml +8 -0
  20. data/examples/galena/conf/{migration/frozen_defaults.yaml → frozen/defaults.yaml} +0 -0
  21. data/examples/galena/conf/{migration/frozen_fields.yaml → frozen/fields.yaml} +0 -2
  22. data/examples/galena/conf/{migration/general_fields.yaml → general/fields.yaml} +0 -24
  23. data/examples/galena/conf/registration/fields.yaml +6 -0
  24. data/examples/galena/conf/{migration/simple_fields.yaml → simple/fields.yaml} +1 -6
  25. data/examples/galena/data/annotation.csv +1 -1
  26. data/examples/galena/data/filter.csv +1 -1
  27. data/examples/galena/data/frozen.csv +1 -1
  28. data/examples/galena/data/general.csv +1 -1
  29. data/examples/galena/data/registration.csv +1 -1
  30. data/examples/galena/data/simple.csv +1 -1
  31. data/examples/galena/galena.gemspec +24 -0
  32. data/examples/galena/lib/galena/filter.rb +25 -0
  33. data/examples/galena/lib/galena/{tissue/migration/frozen_shims.rb → frozen.rb} +6 -10
  34. data/examples/galena/lib/galena/seed.rb +126 -0
  35. data/examples/galena/lib/galena/version.rb +3 -0
  36. data/examples/galena/lib/galena.rb +18 -7
  37. data/examples/galena/log/galena.log +37351 -0
  38. data/examples/galena/log/galena.log.0 +147830 -0
  39. data/examples/galena/spec/annotation_spec.rb +46 -0
  40. data/examples/galena/spec/filter_spec.rb +94 -0
  41. data/examples/galena/spec/frozen_spec.rb +39 -0
  42. data/examples/galena/spec/general_spec.rb +62 -0
  43. data/examples/galena/spec/registration_spec.rb +37 -0
  44. data/examples/galena/spec/seed.rb +107 -0
  45. data/examples/galena/spec/simple_spec.rb +58 -0
  46. data/examples/galena/spec/spec_helper.rb +11 -0
  47. data/examples/galena/spec/support/migration.rb +70 -0
  48. data/lib/catissue/annotation/annotatable.rb +10 -8
  49. data/lib/catissue/annotation/annotation.rb +7 -7
  50. data/lib/catissue/annotation/de_integration.rb +9 -20
  51. data/lib/catissue/annotation/importer.rb +148 -0
  52. data/lib/catissue/annotation/introspector.rb +32 -0
  53. data/lib/catissue/annotation/metadata.rb +422 -0
  54. data/lib/catissue/annotation/proxy.rb +2 -2
  55. data/lib/catissue/annotation/proxy_class.rb +45 -30
  56. data/lib/catissue/annotation/record_entry_proxy.rb +2 -2
  57. data/lib/catissue/cli/command.rb +14 -24
  58. data/lib/catissue/cli/example.rb +5 -3
  59. data/lib/catissue/cli/migrate.rb +45 -37
  60. data/lib/catissue/cli/smoke.rb +2 -3
  61. data/lib/catissue/database/annotation/annotation_service.rb +8 -17
  62. data/lib/catissue/database/annotation/entity_facade.rb +33 -30
  63. data/lib/catissue/database/annotation/id_generator.rb +1 -1
  64. data/lib/catissue/database/annotation/integration_service.rb +11 -4
  65. data/lib/catissue/database/annotation/reference_writer.rb +38 -38
  66. data/lib/catissue/database/controlled_value_finder.rb +13 -28
  67. data/lib/catissue/database/controlled_values.rb +73 -45
  68. data/lib/catissue/database.rb +637 -277
  69. data/lib/catissue/domain/abstract_domain_object.rb +5 -0
  70. data/lib/catissue/domain/abstract_position.rb +3 -5
  71. data/lib/catissue/domain/abstract_specimen.rb +79 -65
  72. data/lib/catissue/domain/abstract_specimen_collection_group.rb +3 -6
  73. data/lib/catissue/domain/address.rb +0 -2
  74. data/lib/catissue/domain/cancer_research_group.rb +0 -3
  75. data/lib/catissue/domain/capacity.rb +2 -4
  76. data/lib/catissue/domain/check_in_check_out_event_parameter.rb +0 -3
  77. data/lib/catissue/domain/collection_event_parameters.rb +2 -7
  78. data/lib/catissue/domain/collection_protocol.rb +11 -16
  79. data/lib/catissue/domain/collection_protocol_event.rb +19 -12
  80. data/lib/catissue/domain/collection_protocol_registration.rb +8 -12
  81. data/lib/catissue/domain/consent_tier_response.rb +0 -4
  82. data/lib/catissue/domain/consent_tier_status.rb +1 -4
  83. data/lib/catissue/domain/container.rb +10 -10
  84. data/lib/catissue/domain/container_position.rb +4 -7
  85. data/lib/catissue/domain/container_type.rb +4 -7
  86. data/lib/catissue/domain/department.rb +0 -3
  87. data/lib/catissue/domain/disposal_event_parameters.rb +5 -5
  88. data/lib/catissue/domain/embedded_event_parameters.rb +1 -4
  89. data/lib/catissue/domain/external_identifier.rb +0 -12
  90. data/lib/catissue/domain/frozen_event_parameters.rb +1 -4
  91. data/lib/catissue/domain/institution.rb +0 -3
  92. data/lib/catissue/domain/new_specimen_array_order_item.rb +0 -5
  93. data/lib/catissue/domain/order_details.rb +0 -2
  94. data/lib/catissue/domain/participant/clinical/chemotherapy.rb +1 -3
  95. data/lib/catissue/domain/participant/clinical/duration.rb +2 -4
  96. data/lib/catissue/domain/participant/clinical/radiation_therapy.rb +2 -4
  97. data/lib/catissue/domain/participant.rb +22 -24
  98. data/lib/catissue/domain/participant_medical_identifier.rb +0 -4
  99. data/lib/catissue/domain/password.rb +0 -4
  100. data/lib/catissue/domain/race.rb +0 -3
  101. data/lib/catissue/domain/received_event_parameters.rb +3 -6
  102. data/lib/catissue/domain/site.rb +1 -4
  103. data/lib/catissue/domain/specimen/pathology/additional_finding.rb +12 -0
  104. data/lib/catissue/domain/specimen/pathology/details.rb +12 -0
  105. data/lib/catissue/domain/specimen/pathology/gleason_score.rb +12 -0
  106. data/lib/catissue/domain/specimen/pathology/histologic_grade.rb +12 -0
  107. data/lib/catissue/domain/specimen/pathology/histologic_type.rb +19 -0
  108. data/lib/catissue/domain/specimen/pathology/histologic_variant_type.rb +12 -0
  109. data/lib/catissue/domain/specimen/pathology/invasion.rb +12 -0
  110. data/lib/catissue/domain/specimen/pathology/prostate_specimen_gleason_score.rb +5 -11
  111. data/lib/catissue/domain/specimen/pathology/prostate_specimen_pathology_annotation.rb +12 -12
  112. data/lib/catissue/domain/specimen/pathology/specimen_additional_finding.rb +5 -14
  113. data/lib/catissue/domain/specimen/pathology/specimen_base_solid_tissue_pathology_annotation.rb +6 -21
  114. data/lib/catissue/domain/specimen/pathology/specimen_details.rb +4 -10
  115. data/lib/catissue/domain/specimen/pathology/specimen_histologic_grade.rb +4 -10
  116. data/lib/catissue/domain/specimen/pathology/specimen_histologic_type.rb +6 -14
  117. data/lib/catissue/domain/specimen/pathology/specimen_histologic_variant_type.rb +5 -11
  118. data/lib/catissue/domain/specimen/pathology/specimen_invasion.rb +5 -11
  119. data/lib/catissue/domain/specimen.rb +113 -76
  120. data/lib/catissue/domain/specimen_array.rb +0 -3
  121. data/lib/catissue/domain/specimen_array_content.rb +1 -4
  122. data/lib/catissue/domain/specimen_array_type.rb +1 -4
  123. data/lib/catissue/domain/specimen_characteristics.rb +0 -3
  124. data/lib/catissue/domain/specimen_collection_group/pathology/base_pathology_annotation.rb +2 -4
  125. data/lib/catissue/domain/specimen_collection_group/pathology/base_solid_tissue_pathology_annotation.rb +2 -4
  126. data/lib/catissue/domain/specimen_collection_group.rb +43 -53
  127. data/lib/catissue/domain/specimen_event_parameters.rb +24 -32
  128. data/lib/catissue/domain/specimen_position.rb +8 -5
  129. data/lib/catissue/domain/specimen_protocol.rb +3 -6
  130. data/lib/catissue/domain/specimen_requirement.rb +22 -20
  131. data/lib/catissue/domain/storage_container.rb +9 -12
  132. data/lib/catissue/domain/storage_type.rb +6 -10
  133. data/lib/catissue/domain/transfer_event_parameters.rb +3 -6
  134. data/lib/catissue/domain/user.rb +22 -29
  135. data/lib/catissue/{util → helpers}/collectible.rb +23 -18
  136. data/lib/catissue/helpers/collectible_event_parameters.rb +68 -0
  137. data/lib/catissue/helpers/controlled_value.rb +35 -0
  138. data/lib/catissue/{domain → helpers}/hash_code.rb +0 -0
  139. data/lib/catissue/{util → helpers}/location.rb +6 -5
  140. data/lib/catissue/helpers/log.rb +4 -0
  141. data/lib/catissue/{util → helpers}/person.rb +1 -1
  142. data/lib/catissue/{util → helpers}/position.rb +10 -8
  143. data/lib/catissue/helpers/properties_loader.rb +143 -0
  144. data/lib/catissue/{util → helpers}/storable.rb +2 -1
  145. data/lib/catissue/{util → helpers}/storage_type_holder.rb +9 -3
  146. data/lib/catissue/{annotation/annotatable_class.rb → metadata.rb} +73 -95
  147. data/lib/catissue/migration/migratable.rb +93 -44
  148. data/lib/catissue/migration/migrator.rb +26 -42
  149. data/lib/catissue/migration/shims.rb +1 -1
  150. data/lib/catissue/migration/unique.rb +76 -0
  151. data/lib/catissue/resource.rb +16 -20
  152. data/lib/catissue/version.rb +1 -1
  153. data/lib/catissue/wustl/logger.rb +52 -32
  154. data/lib/catissue.rb +38 -20
  155. data/test/lib/catissue/database/controlled_values_test.rb +22 -27
  156. data/test/lib/catissue/database/database_test.rb +18 -0
  157. data/test/lib/catissue/domain/address_test.rb +9 -11
  158. data/test/lib/catissue/domain/ca_tissue_test_defaults_test.rb +5 -16
  159. data/test/lib/catissue/domain/capacity_test.rb +2 -2
  160. data/test/lib/catissue/domain/collection_event_parameters_test.rb +16 -8
  161. data/test/lib/catissue/domain/collection_protocol_event_test.rb +1 -1
  162. data/test/lib/catissue/domain/collection_protocol_registration_test.rb +26 -16
  163. data/test/lib/catissue/domain/collection_protocol_test.rb +2 -2
  164. data/test/lib/catissue/domain/container_position_test.rb +7 -4
  165. data/test/lib/catissue/domain/department_test.rb +3 -3
  166. data/test/lib/catissue/domain/disposal_event_parameters_test.rb +1 -1
  167. data/test/lib/catissue/domain/external_identifier_test.rb +5 -1
  168. data/test/lib/catissue/domain/location_test.rb +4 -4
  169. data/test/lib/catissue/domain/participant_medical_identifier_test.rb +3 -3
  170. data/test/lib/catissue/domain/participant_test.rb +33 -20
  171. data/test/lib/catissue/domain/received_event_parameters_test.rb +19 -0
  172. data/test/lib/catissue/domain/site_test.rb +2 -2
  173. data/test/lib/catissue/domain/specimen_array_test.rb +3 -3
  174. data/test/lib/catissue/domain/specimen_array_type_test.rb +6 -6
  175. data/test/lib/catissue/domain/specimen_characteristics_test.rb +1 -1
  176. data/test/lib/catissue/domain/specimen_collection_group_test.rb +49 -13
  177. data/test/lib/catissue/domain/specimen_event_parameters_test.rb +4 -4
  178. data/test/lib/catissue/domain/specimen_position_test.rb +1 -1
  179. data/test/lib/catissue/domain/specimen_requirement_test.rb +2 -2
  180. data/test/lib/catissue/domain/specimen_test.rb +58 -24
  181. data/test/lib/catissue/domain/storage_container_test.rb +3 -16
  182. data/test/lib/catissue/domain/storage_type_test.rb +3 -3
  183. data/test/lib/catissue/domain/transfer_event_parameters_test.rb +17 -17
  184. data/test/lib/catissue/domain/user_test.rb +32 -34
  185. data/test/lib/catissue/helpers/properties_loader_test.rb +19 -0
  186. data/test/lib/catissue/migration/{test_case.rb → helpers/test_case.rb} +30 -20
  187. data/test/lib/examples/galena/tissue/domain/examples_test.rb +28 -38
  188. data/test/lib/examples/galena/tissue/helpers/test_case.rb +24 -0
  189. metadata +175 -99
  190. data/bin/crtextract +0 -47
  191. data/examples/galena/conf/extract/simple_fields.yaml +0 -4
  192. data/examples/galena/conf/migration/annotation_defaults.yaml +0 -2
  193. data/examples/galena/conf/migration/filter_defaults.yaml +0 -1
  194. data/examples/galena/conf/migration/filter_values.yaml +0 -13
  195. data/examples/galena/conf/migration/participant_fields.yaml +0 -4
  196. data/examples/galena/conf/migration/registration_fields.yaml +0 -5
  197. data/examples/galena/data/participant.csv +0 -1
  198. data/examples/galena/lib/galena/tissue/migration/filter_shims.rb +0 -41
  199. data/examples/galena/lib/galena/tissue/seed/defaults.rb +0 -127
  200. data/examples/psbin/README.md +0 -45
  201. data/examples/psbin/conf/adjuvant_hormone_defaults.yaml +0 -2
  202. data/examples/psbin/conf/adjuvant_radiation_defaults.yaml +0 -3
  203. data/examples/psbin/conf/biopsy_defaults.yaml +0 -3
  204. data/examples/psbin/conf/biopsy_fields.yaml +0 -9
  205. data/examples/psbin/conf/neoadjuvant_hormone_defaults.yaml +0 -2
  206. data/examples/psbin/conf/neoadjuvant_radiation_defaults.yaml +0 -3
  207. data/examples/psbin/conf/patient_defaults.yaml +0 -3
  208. data/examples/psbin/conf/patient_fields.yaml +0 -5
  209. data/examples/psbin/conf/surgery_defaults.yaml +0 -4
  210. data/examples/psbin/conf/surgery_fields.yaml +0 -15
  211. data/examples/psbin/conf/t_stage_defaults.yaml +0 -1
  212. data/examples/psbin/conf/t_stage_fields.yaml +0 -4
  213. data/examples/psbin/conf/therapy_fields.yaml +0 -5
  214. data/examples/psbin/data/adjuvant_hormone.csv +0 -1
  215. data/examples/psbin/data/adjuvant_radiation.csv +0 -1
  216. data/examples/psbin/data/biopsy.csv +0 -1
  217. data/examples/psbin/data/neoadjuvant_hormone.csv +0 -1
  218. data/examples/psbin/data/neoadjuvant_radiation.csv +0 -1
  219. data/examples/psbin/data/patient.csv +0 -1
  220. data/examples/psbin/data/surgery.csv +0 -1
  221. data/examples/psbin/data/t_stage.csv +0 -1
  222. data/examples/psbin/lib/psbin/biopsy_shims.rb +0 -15
  223. data/examples/psbin/lib/psbin/surgery_shims.rb +0 -15
  224. data/lib/catissue/annotation/annotation_class.rb +0 -406
  225. data/lib/catissue/annotation/annotation_module.rb +0 -106
  226. data/lib/catissue/domain.rb +0 -26
  227. data/lib/catissue/extract/command.rb +0 -31
  228. data/lib/catissue/extract/delta.rb +0 -58
  229. data/lib/catissue/extract/extractor.rb +0 -99
  230. data/lib/catissue/migration/uniquify.rb +0 -2
  231. data/lib/catissue/util/collectible_event_parameters.rb +0 -71
  232. data/lib/catissue/util/controlled_value.rb +0 -29
  233. data/lib/catissue/util/uniquify.rb +0 -86
  234. data/test/fixtures/catissue/domain/conf/catissue_override.yaml +0 -9
  235. data/test/fixtures/catissue/extract/conf/scg_extract.yaml +0 -3
  236. data/test/fixtures/catissue/extract/conf/scg_fields.yaml +0 -3
  237. data/test/fixtures/catissue/extract/conf/spc_extract.yaml +0 -3
  238. data/test/fixtures/catissue/extract/conf/spc_fields.yaml +0 -4
  239. data/test/fixtures/lib/catissue/defaults_test_fixture.rb +0 -206
  240. data/test/fixtures/lib/examples/galena/migration/alt_key_shims.rb +0 -7
  241. data/test/lib/catissue/domain/base_haemotology_pathology_test.rb +0 -24
  242. data/test/lib/catissue/extract/delta_test.rb +0 -25
  243. data/test/lib/catissue/extract/extractor_test.rb +0 -43
  244. data/test/lib/catissue/import/importable_module_test.rb +0 -14
  245. data/test/lib/catissue/test_case.rb +0 -247
  246. data/test/lib/examples/galena/tissue/migration/annotation_test.rb +0 -29
  247. data/test/lib/examples/galena/tissue/migration/filter_test.rb +0 -29
  248. data/test/lib/examples/galena/tissue/migration/frozen_test.rb +0 -36
  249. data/test/lib/examples/galena/tissue/migration/general_test.rb +0 -56
  250. data/test/lib/examples/galena/tissue/migration/participant_test.rb +0 -61
  251. data/test/lib/examples/galena/tissue/migration/registration_test.rb +0 -17
  252. data/test/lib/examples/galena/tissue/migration/seedify.rb +0 -119
  253. data/test/lib/examples/galena/tissue/migration/simple_test.rb +0 -30
  254. data/test/lib/examples/galena/tissue/migration/test_case.rb +0 -72
  255. data/test/lib/examples/psbin/migration_test.rb +0 -153

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