caruby-tissue 1.5.4 → 1.5.5

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Files changed (78) hide show
  1. data/History.md +4 -0
  2. data/examples/galena/README.md +2 -11
  3. data/examples/galena/conf/migration/filter_defaults.yaml +1 -0
  4. data/examples/galena/conf/migration/filter_values.yaml +13 -0
  5. data/examples/galena/lib/galena/tissue/migration/filter_shims.rb +3 -15
  6. data/examples/galena/lib/galena/tissue/migration/frozen_shims.rb +3 -6
  7. data/examples/galena/lib/galena/tissue/seed/defaults.rb +2 -2
  8. data/lib/catissue/annotation/annotatable_class.rb +10 -8
  9. data/lib/catissue/annotation/annotation_class.rb +6 -3
  10. data/lib/catissue/annotation/annotation_module.rb +7 -2
  11. data/lib/catissue/cli/command.rb +11 -4
  12. data/lib/catissue/cli/migrate.rb +5 -16
  13. data/lib/catissue/database/annotation/annotation_service.rb +2 -2
  14. data/lib/catissue/database/annotation/entity_facade.rb +6 -11
  15. data/lib/catissue/database/annotation/record_entry_integrator.rb +4 -4
  16. data/lib/catissue/database/controlled_values.rb +2 -3
  17. data/lib/catissue/database.rb +64 -35
  18. data/lib/catissue/domain/abstract_specimen.rb +24 -26
  19. data/lib/catissue/domain/abstract_specimen_collection_group.rb +1 -1
  20. data/lib/catissue/domain/capacity.rb +1 -1
  21. data/lib/catissue/domain/collection_protocol.rb +12 -9
  22. data/lib/catissue/domain/collection_protocol_event.rb +9 -11
  23. data/lib/catissue/domain/collection_protocol_registration.rb +5 -5
  24. data/lib/catissue/domain/container.rb +3 -4
  25. data/lib/catissue/domain/container_type.rb +11 -12
  26. data/lib/catissue/domain/disposal_event_parameters.rb +1 -1
  27. data/lib/catissue/domain/new_specimen_array_order_item.rb +6 -5
  28. data/lib/catissue/domain/order_details.rb +4 -0
  29. data/lib/catissue/domain/participant.rb +17 -17
  30. data/lib/catissue/domain/participant_medical_identifier.rb +2 -3
  31. data/lib/catissue/domain/site.rb +7 -9
  32. data/lib/catissue/domain/specimen/pathology/prostate_specimen_gleason_score.rb +2 -3
  33. data/lib/catissue/domain/specimen/pathology/prostate_specimen_pathology_annotation.rb +4 -3
  34. data/lib/catissue/domain/specimen/pathology/specimen_additional_finding.rb +5 -7
  35. data/lib/catissue/domain/specimen/pathology/specimen_base_solid_tissue_pathology_annotation.rb +11 -11
  36. data/lib/catissue/domain/specimen/pathology/specimen_details.rb +2 -4
  37. data/lib/catissue/domain/specimen/pathology/specimen_histologic_grade.rb +2 -4
  38. data/lib/catissue/domain/specimen/pathology/specimen_histologic_type.rb +6 -6
  39. data/lib/catissue/domain/specimen/pathology/specimen_histologic_variant_type.rb +2 -4
  40. data/lib/catissue/domain/specimen/pathology/specimen_invasion.rb +2 -4
  41. data/lib/catissue/domain/specimen.rb +35 -45
  42. data/lib/catissue/domain/specimen_array.rb +1 -1
  43. data/lib/catissue/domain/specimen_collection_group/pathology/base_pathology_annotation.rb +4 -4
  44. data/lib/catissue/domain/specimen_collection_group/pathology/base_solid_tissue_pathology_annotation.rb +4 -4
  45. data/lib/catissue/domain/specimen_collection_group.rb +40 -46
  46. data/lib/catissue/domain/specimen_protocol.rb +4 -6
  47. data/lib/catissue/domain/specimen_requirement.rb +13 -16
  48. data/lib/catissue/domain/storage_container.rb +5 -2
  49. data/lib/catissue/domain/storage_type.rb +1 -1
  50. data/lib/catissue/domain/user.rb +16 -7
  51. data/lib/catissue/extract/command.rb +1 -1
  52. data/lib/catissue/extract/delta.rb +7 -15
  53. data/lib/catissue/migration/migratable.rb +106 -8
  54. data/lib/catissue/migration/migrator.rb +20 -12
  55. data/lib/catissue/migration/shims.rb +3 -3
  56. data/lib/catissue/util/collectible.rb +2 -2
  57. data/lib/catissue/util/collectible_event_parameters.rb +2 -2
  58. data/lib/catissue/util/position.rb +3 -3
  59. data/lib/catissue/version.rb +1 -1
  60. data/test/lib/catissue/domain/address_test.rb +3 -2
  61. data/test/lib/catissue/domain/participant_test.rb +11 -0
  62. data/test/lib/catissue/domain/specimen_collection_group_test.rb +62 -12
  63. data/test/lib/catissue/domain/specimen_test.rb +0 -1
  64. data/test/lib/catissue/test_case.rb +2 -2
  65. data/test/lib/examples/galena/tissue/migration/seedify.rb +5 -5
  66. data/test/lib/examples/galena/tissue/migration/test_case.rb +9 -5
  67. metadata +8 -17
  68. data/conf/extract/simple_fields.yaml +0 -4
  69. data/conf/migration/filter_fields.yaml +0 -7
  70. data/conf/migration/filter_migration.yaml +0 -9
  71. data/conf/migration/frozen_fields.yaml +0 -11
  72. data/conf/migration/frozen_migration.yaml +0 -9
  73. data/conf/migration/general_fields.yaml +0 -44
  74. data/conf/migration/general_migration.yaml +0 -9
  75. data/conf/migration/simple_fields.yaml +0 -30
  76. data/conf/migration/simple_migration.yaml +0 -7
  77. data/conf/migration/small_fields.yaml +0 -24
  78. data/conf/migration/small_migration.yaml +0 -9
data/conf/migration/small_migration.yaml DELETED
@@ -1,9 +0,0 @@
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- #
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- # This is the Galena tiny example migration configuration file.
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- #
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-
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- # The field heading => CaTissue mapping file.
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- mapping: examples/galena/conf/migration/tiny_fields.yaml
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-
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- # The migration target class for each record.
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- target: TissueSpecimen