caruby-tissue 1.4.2 → 1.5.1

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Files changed (115) hide show
  1. data/History.md +53 -0
  2. data/bin/crtdump +1 -6
  3. data/bin/crtexample +1 -6
  4. data/bin/crtmigrate +1 -6
  5. data/bin/crtsmoke +1 -6
  6. data/conf/migration/filter_fields.yaml +1 -1
  7. data/conf/migration/general_fields.yaml +1 -1
  8. data/conf/migration/simple_fields.yaml +1 -1
  9. data/conf/migration/small_fields.yaml +1 -1
  10. data/examples/galena/README.md +34 -25
  11. data/examples/galena/bin/seed +2 -7
  12. data/examples/galena/conf/migration/annotation_fields.yaml +1 -1
  13. data/examples/galena/conf/migration/filter_fields.yaml +1 -1
  14. data/examples/galena/conf/migration/frozen_fields.yaml +2 -2
  15. data/examples/galena/conf/migration/general_fields.yaml +1 -1
  16. data/examples/galena/conf/migration/registration_fields.yaml +1 -0
  17. data/examples/galena/conf/migration/simple_fields.yaml +1 -1
  18. data/examples/galena/data/frozen.csv +1 -1
  19. data/examples/galena/data/general.csv +1 -1
  20. data/examples/galena/data/registration.csv +1 -1
  21. data/examples/galena/lib/galena/tissue/migration/frozen_shims.rb +8 -4
  22. data/examples/galena/lib/galena/tissue/seed/defaults.rb +16 -9
  23. data/examples/pcbin/README.md +8 -8
  24. data/examples/pcbin/conf/biopsy_fields.yaml +1 -1
  25. data/examples/pcbin/conf/patient_fields.yaml +1 -1
  26. data/examples/pcbin/conf/surgery_fields.yaml +1 -1
  27. data/examples/pcbin/conf/t_stage_fields.yaml +1 -1
  28. data/examples/pcbin/conf/therapy_fields.yaml +1 -1
  29. data/lib/catissue.rb +1 -1
  30. data/lib/catissue/annotation/annotatable.rb +12 -22
  31. data/lib/catissue/annotation/annotatable_class.rb +87 -114
  32. data/lib/catissue/annotation/annotation.rb +9 -44
  33. data/lib/catissue/annotation/annotation_class.rb +238 -145
  34. data/lib/catissue/annotation/annotation_module.rb +47 -59
  35. data/lib/catissue/annotation/de_integration.rb +12 -2
  36. data/lib/catissue/annotation/proxy.rb +11 -17
  37. data/lib/catissue/annotation/proxy_1_1.rb +47 -0
  38. data/lib/catissue/annotation/proxy_class.rb +55 -37
  39. data/lib/catissue/annotation/record_entry_proxy.rb +20 -0
  40. data/lib/catissue/database.rb +164 -112
  41. data/lib/catissue/database/annotation/annotation_service.rb +5 -5
  42. data/lib/catissue/database/annotation/annotator.rb +2 -2
  43. data/lib/catissue/database/annotation/entity_facade.rb +24 -21
  44. data/lib/catissue/database/annotation/id_generator.rb +26 -26
  45. data/lib/catissue/database/annotation/integration_service.rb +8 -8
  46. data/lib/catissue/database/annotation/record_entry_integrator.rb +24 -6
  47. data/lib/catissue/database/annotation/reference_writer.rb +33 -6
  48. data/lib/catissue/domain.rb +26 -0
  49. data/lib/catissue/domain/abstract_position.rb +1 -1
  50. data/lib/catissue/domain/abstract_specimen.rb +16 -16
  51. data/lib/catissue/domain/check_in_check_out_event_parameter.rb +1 -1
  52. data/lib/catissue/domain/collection_event_parameters.rb +1 -1
  53. data/lib/catissue/domain/collection_protocol.rb +9 -13
  54. data/lib/catissue/domain/collection_protocol_event.rb +4 -4
  55. data/lib/catissue/domain/collection_protocol_registration.rb +4 -4
  56. data/lib/catissue/domain/container.rb +12 -21
  57. data/lib/catissue/domain/container_type.rb +65 -64
  58. data/lib/catissue/domain/disposal_event_parameters.rb +1 -1
  59. data/lib/catissue/domain/hash_code.rb +3 -6
  60. data/lib/catissue/domain/new_specimen_array_order_item.rb +4 -4
  61. data/lib/catissue/domain/order_details.rb +3 -3
  62. data/lib/catissue/domain/participant.rb +28 -20
  63. data/lib/catissue/domain/participant/clinical/chemotherapy.rb +21 -0
  64. data/lib/catissue/domain/participant/clinical/duration.rb +11 -0
  65. data/lib/catissue/domain/participant/clinical/radiation_therapy.rb +21 -0
  66. data/lib/catissue/domain/participant_medical_identifier.rb +2 -2
  67. data/lib/catissue/domain/site.rb +6 -6
  68. data/lib/catissue/domain/specimen.rb +41 -34
  69. data/lib/catissue/domain/specimen/pathology/prostate_specimen_gleason_score.rb +18 -0
  70. data/lib/catissue/domain/specimen/pathology/prostate_specimen_pathology_annotation.rb +13 -8
  71. data/lib/catissue/domain/specimen/pathology/specimen_additional_finding.rb +21 -0
  72. data/lib/catissue/domain/specimen/pathology/specimen_base_solid_tissue_pathology_annotation.rb +30 -7
  73. data/lib/catissue/domain/specimen/pathology/specimen_details.rb +18 -0
  74. data/lib/catissue/domain/specimen/pathology/specimen_histologic_grade.rb +18 -0
  75. data/lib/catissue/domain/specimen/pathology/specimen_histologic_type.rb +22 -6
  76. data/lib/catissue/domain/specimen/pathology/specimen_histologic_variant_type.rb +18 -0
  77. data/lib/catissue/domain/specimen/pathology/specimen_invasion.rb +18 -0
  78. data/lib/catissue/domain/specimen_array.rb +8 -8
  79. data/lib/catissue/domain/specimen_array_content.rb +4 -4
  80. data/lib/catissue/domain/specimen_collection_group.rb +43 -41
  81. data/lib/catissue/domain/specimen_collection_group/pathology/base_pathology_annotation.rb +16 -0
  82. data/lib/catissue/domain/specimen_collection_group/pathology/base_solid_tissue_pathology_annotation.rb +16 -0
  83. data/lib/catissue/domain/specimen_position.rb +3 -3
  84. data/lib/catissue/domain/specimen_protocol.rb +7 -7
  85. data/lib/catissue/domain/specimen_requirement.rb +9 -9
  86. data/lib/catissue/domain/storage_container.rb +13 -13
  87. data/lib/catissue/domain/storage_type.rb +12 -7
  88. data/lib/catissue/domain/transfer_event_parameters.rb +2 -2
  89. data/lib/catissue/domain/user.rb +15 -15
  90. data/lib/catissue/extract/extractor.rb +1 -1
  91. data/lib/catissue/resource.rb +8 -36
  92. data/lib/catissue/util/location.rb +0 -13
  93. data/lib/catissue/util/person.rb +2 -1
  94. data/lib/catissue/util/position.rb +1 -11
  95. data/lib/catissue/util/uniquify.rb +1 -1
  96. data/lib/catissue/version.rb +1 -1
  97. data/lib/catissue/wustl/logger.rb +17 -16
  98. data/test/fixtures/lib/catissue/defaults_test_fixture.rb +6 -4
  99. data/test/lib/catissue/domain/collection_protocol_test.rb +0 -1
  100. data/test/lib/catissue/domain/participant_test.rb +74 -19
  101. data/test/lib/catissue/domain/specimen_collection_group_test.rb +14 -10
  102. data/test/lib/catissue/domain/specimen_test.rb +36 -60
  103. data/test/lib/catissue/domain/storage_type_test.rb +5 -5
  104. data/test/lib/catissue/domain/transfer_event_parameters_test.rb +14 -12
  105. data/test/lib/catissue/migration/test_case.rb +0 -1
  106. data/test/lib/catissue/test_case.rb +12 -12
  107. data/test/lib/examples/galena/tissue/domain/examples_test.rb +1 -1
  108. data/test/lib/examples/galena/tissue/migration/annotation_test.rb +9 -7
  109. data/test/lib/examples/galena/tissue/migration/frozen_test.rb +1 -1
  110. data/test/lib/examples/galena/tissue/migration/general_test.rb +1 -1
  111. data/test/lib/examples/galena/tissue/migration/registration_test.rb +3 -9
  112. data/test/lib/examples/galena/tissue/migration/seedify.rb +3 -3
  113. data/test/lib/examples/pcbin/migration_test.rb +37 -16
  114. metadata +24 -10
  115. data/History.txt +0 -50
metadata CHANGED
@@ -1,13 +1,13 @@
1
1
  --- !ruby/object:Gem::Specification
2
2
  name: caruby-tissue
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3
  version: !ruby/object:Gem::Version
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- hash: 3
4
+ hash: 1
5
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  prerelease: false
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  segments:
7
7
  - 1
8
- - 4
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- - 2
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- version: 1.4.2
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+ - 5
9
+ - 1
10
+ version: 1.5.1
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  platform: ruby
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  authors:
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  - OHSU
@@ -15,7 +15,7 @@ autorequire:
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  bindir: bin
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  cert_chain: []
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- date: 2011-05-09 00:00:00 -07:00
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+ date: 2011-07-05 00:00:00 -07:00
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  default_executable:
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  dependencies:
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  - !ruby/object:Gem::Dependency
@@ -26,12 +26,12 @@ dependencies:
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  requirements:
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  - - ">="
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  - !ruby/object:Gem::Version
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- hash: 21
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+ hash: 1
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  segments:
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  - 1
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- - 4
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- - 9
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- version: 1.4.9
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+ - 5
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+ - 1
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+ version: 1.5.1
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  type: :runtime
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  version_requirements: *id001
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  description: " The caruby-tissue gem applies the caRuby facade to the caTissue application.\n"
@@ -119,7 +119,9 @@ files:
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  - lib/catissue/annotation/annotation_module.rb
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  - lib/catissue/annotation/de_integration.rb
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  - lib/catissue/annotation/proxy.rb
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+ - lib/catissue/annotation/proxy_1_1.rb
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  - lib/catissue/annotation/proxy_class.rb
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+ - lib/catissue/annotation/record_entry_proxy.rb
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  - lib/catissue/cli/command.rb
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  - lib/catissue/cli/example.rb
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  - lib/catissue/cli/migrate.rb
@@ -160,20 +162,31 @@ files:
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  - lib/catissue/domain/institution.rb
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  - lib/catissue/domain/new_specimen_array_order_item.rb
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  - lib/catissue/domain/order_details.rb
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+ - lib/catissue/domain/participant/clinical/chemotherapy.rb
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+ - lib/catissue/domain/participant/clinical/duration.rb
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+ - lib/catissue/domain/participant/clinical/radiation_therapy.rb
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  - lib/catissue/domain/participant.rb
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  - lib/catissue/domain/participant_medical_identifier.rb
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  - lib/catissue/domain/password.rb
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  - lib/catissue/domain/race.rb
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  - lib/catissue/domain/received_event_parameters.rb
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  - lib/catissue/domain/site.rb
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+ - lib/catissue/domain/specimen/pathology/prostate_specimen_gleason_score.rb
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  - lib/catissue/domain/specimen/pathology/prostate_specimen_pathology_annotation.rb
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+ - lib/catissue/domain/specimen/pathology/specimen_additional_finding.rb
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  - lib/catissue/domain/specimen/pathology/specimen_base_solid_tissue_pathology_annotation.rb
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+ - lib/catissue/domain/specimen/pathology/specimen_details.rb
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+ - lib/catissue/domain/specimen/pathology/specimen_histologic_grade.rb
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  - lib/catissue/domain/specimen/pathology/specimen_histologic_type.rb
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+ - lib/catissue/domain/specimen/pathology/specimen_histologic_variant_type.rb
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+ - lib/catissue/domain/specimen/pathology/specimen_invasion.rb
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  - lib/catissue/domain/specimen.rb
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  - lib/catissue/domain/specimen_array.rb
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  - lib/catissue/domain/specimen_array_content.rb
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  - lib/catissue/domain/specimen_array_type.rb
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  - lib/catissue/domain/specimen_characteristics.rb
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+ - lib/catissue/domain/specimen_collection_group/pathology/base_pathology_annotation.rb
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+ - lib/catissue/domain/specimen_collection_group/pathology/base_solid_tissue_pathology_annotation.rb
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  - lib/catissue/domain/specimen_collection_group.rb
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  - lib/catissue/domain/specimen_event_parameters.rb
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  - lib/catissue/domain/specimen_position.rb
@@ -183,6 +196,7 @@ files:
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  - lib/catissue/domain/storage_type.rb
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  - lib/catissue/domain/transfer_event_parameters.rb
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  - lib/catissue/domain/user.rb
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+ - lib/catissue/domain.rb
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  - lib/catissue/extract/command.rb
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  - lib/catissue/extract/delta.rb
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  - lib/catissue/extract/extractor.rb
@@ -255,7 +269,7 @@ files:
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  - test/lib/examples/galena/tissue/migration/simple_test.rb
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  - test/lib/examples/galena/tissue/migration/test_case.rb
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  - test/lib/examples/pcbin/migration_test.rb
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- - History.txt
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+ - History.md
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  - LEGAL
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  - LICENSE
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  - README.md
data/History.txt DELETED
@@ -1,50 +0,0 @@
1
- This history lists major release themes. See the GitHub source (https://github.com/caruby/tissue)
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- for change details.
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-
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- === 1.2.1 / 2010-11-23
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-
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- * Initial public release.
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-
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- === 1.2.2 / 2010-11-30
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-
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- * Galena example.
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-
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- === 1.2.3 / 2011-02-18
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-
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- * Dynamic Extensions Support.
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-
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- === 1.3.1 / 2011-02-18
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-
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- * Prostate Spore PCBIN DE support.
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-
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- === 1.3.2 / 2011-02-25
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-
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- * Migration bug fixes.
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-
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- === 1.3.3 / 2011-02-26
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-
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- * JRuby 1.5 upgrade.
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-
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- === 1.3.4 / 2011-02-26
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-
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- * Use caruby-core JRuby 1.5 bug work-around.
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-
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- === 1.3.5 / 2011-03-04
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-
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- * Annotation migration.
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-
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- === 1.3.6 / 2011-03-04
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-
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- * Specify caruby-core gem version dependency.
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-
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- === 1.4.1 / 2011-05-03
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-
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- * caTissue 1.2 support.
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-
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- * embed Java-caRuby bridge subproject.
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-
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- === 1.4.2 / 2011-05-04
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-
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- * Add registration and PCBIN examples.
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-
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-