caruby-tissue 1.4.2 → 1.5.1
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- data/History.md +53 -0
- data/bin/crtdump +1 -6
- data/bin/crtexample +1 -6
- data/bin/crtmigrate +1 -6
- data/bin/crtsmoke +1 -6
- data/conf/migration/filter_fields.yaml +1 -1
- data/conf/migration/general_fields.yaml +1 -1
- data/conf/migration/simple_fields.yaml +1 -1
- data/conf/migration/small_fields.yaml +1 -1
- data/examples/galena/README.md +34 -25
- data/examples/galena/bin/seed +2 -7
- data/examples/galena/conf/migration/annotation_fields.yaml +1 -1
- data/examples/galena/conf/migration/filter_fields.yaml +1 -1
- data/examples/galena/conf/migration/frozen_fields.yaml +2 -2
- data/examples/galena/conf/migration/general_fields.yaml +1 -1
- data/examples/galena/conf/migration/registration_fields.yaml +1 -0
- data/examples/galena/conf/migration/simple_fields.yaml +1 -1
- data/examples/galena/data/frozen.csv +1 -1
- data/examples/galena/data/general.csv +1 -1
- data/examples/galena/data/registration.csv +1 -1
- data/examples/galena/lib/galena/tissue/migration/frozen_shims.rb +8 -4
- data/examples/galena/lib/galena/tissue/seed/defaults.rb +16 -9
- data/examples/pcbin/README.md +8 -8
- data/examples/pcbin/conf/biopsy_fields.yaml +1 -1
- data/examples/pcbin/conf/patient_fields.yaml +1 -1
- data/examples/pcbin/conf/surgery_fields.yaml +1 -1
- data/examples/pcbin/conf/t_stage_fields.yaml +1 -1
- data/examples/pcbin/conf/therapy_fields.yaml +1 -1
- data/lib/catissue.rb +1 -1
- data/lib/catissue/annotation/annotatable.rb +12 -22
- data/lib/catissue/annotation/annotatable_class.rb +87 -114
- data/lib/catissue/annotation/annotation.rb +9 -44
- data/lib/catissue/annotation/annotation_class.rb +238 -145
- data/lib/catissue/annotation/annotation_module.rb +47 -59
- data/lib/catissue/annotation/de_integration.rb +12 -2
- data/lib/catissue/annotation/proxy.rb +11 -17
- data/lib/catissue/annotation/proxy_1_1.rb +47 -0
- data/lib/catissue/annotation/proxy_class.rb +55 -37
- data/lib/catissue/annotation/record_entry_proxy.rb +20 -0
- data/lib/catissue/database.rb +164 -112
- data/lib/catissue/database/annotation/annotation_service.rb +5 -5
- data/lib/catissue/database/annotation/annotator.rb +2 -2
- data/lib/catissue/database/annotation/entity_facade.rb +24 -21
- data/lib/catissue/database/annotation/id_generator.rb +26 -26
- data/lib/catissue/database/annotation/integration_service.rb +8 -8
- data/lib/catissue/database/annotation/record_entry_integrator.rb +24 -6
- data/lib/catissue/database/annotation/reference_writer.rb +33 -6
- data/lib/catissue/domain.rb +26 -0
- data/lib/catissue/domain/abstract_position.rb +1 -1
- data/lib/catissue/domain/abstract_specimen.rb +16 -16
- data/lib/catissue/domain/check_in_check_out_event_parameter.rb +1 -1
- data/lib/catissue/domain/collection_event_parameters.rb +1 -1
- data/lib/catissue/domain/collection_protocol.rb +9 -13
- data/lib/catissue/domain/collection_protocol_event.rb +4 -4
- data/lib/catissue/domain/collection_protocol_registration.rb +4 -4
- data/lib/catissue/domain/container.rb +12 -21
- data/lib/catissue/domain/container_type.rb +65 -64
- data/lib/catissue/domain/disposal_event_parameters.rb +1 -1
- data/lib/catissue/domain/hash_code.rb +3 -6
- data/lib/catissue/domain/new_specimen_array_order_item.rb +4 -4
- data/lib/catissue/domain/order_details.rb +3 -3
- data/lib/catissue/domain/participant.rb +28 -20
- data/lib/catissue/domain/participant/clinical/chemotherapy.rb +21 -0
- data/lib/catissue/domain/participant/clinical/duration.rb +11 -0
- data/lib/catissue/domain/participant/clinical/radiation_therapy.rb +21 -0
- data/lib/catissue/domain/participant_medical_identifier.rb +2 -2
- data/lib/catissue/domain/site.rb +6 -6
- data/lib/catissue/domain/specimen.rb +41 -34
- data/lib/catissue/domain/specimen/pathology/prostate_specimen_gleason_score.rb +18 -0
- data/lib/catissue/domain/specimen/pathology/prostate_specimen_pathology_annotation.rb +13 -8
- data/lib/catissue/domain/specimen/pathology/specimen_additional_finding.rb +21 -0
- data/lib/catissue/domain/specimen/pathology/specimen_base_solid_tissue_pathology_annotation.rb +30 -7
- data/lib/catissue/domain/specimen/pathology/specimen_details.rb +18 -0
- data/lib/catissue/domain/specimen/pathology/specimen_histologic_grade.rb +18 -0
- data/lib/catissue/domain/specimen/pathology/specimen_histologic_type.rb +22 -6
- data/lib/catissue/domain/specimen/pathology/specimen_histologic_variant_type.rb +18 -0
- data/lib/catissue/domain/specimen/pathology/specimen_invasion.rb +18 -0
- data/lib/catissue/domain/specimen_array.rb +8 -8
- data/lib/catissue/domain/specimen_array_content.rb +4 -4
- data/lib/catissue/domain/specimen_collection_group.rb +43 -41
- data/lib/catissue/domain/specimen_collection_group/pathology/base_pathology_annotation.rb +16 -0
- data/lib/catissue/domain/specimen_collection_group/pathology/base_solid_tissue_pathology_annotation.rb +16 -0
- data/lib/catissue/domain/specimen_position.rb +3 -3
- data/lib/catissue/domain/specimen_protocol.rb +7 -7
- data/lib/catissue/domain/specimen_requirement.rb +9 -9
- data/lib/catissue/domain/storage_container.rb +13 -13
- data/lib/catissue/domain/storage_type.rb +12 -7
- data/lib/catissue/domain/transfer_event_parameters.rb +2 -2
- data/lib/catissue/domain/user.rb +15 -15
- data/lib/catissue/extract/extractor.rb +1 -1
- data/lib/catissue/resource.rb +8 -36
- data/lib/catissue/util/location.rb +0 -13
- data/lib/catissue/util/person.rb +2 -1
- data/lib/catissue/util/position.rb +1 -11
- data/lib/catissue/util/uniquify.rb +1 -1
- data/lib/catissue/version.rb +1 -1
- data/lib/catissue/wustl/logger.rb +17 -16
- data/test/fixtures/lib/catissue/defaults_test_fixture.rb +6 -4
- data/test/lib/catissue/domain/collection_protocol_test.rb +0 -1
- data/test/lib/catissue/domain/participant_test.rb +74 -19
- data/test/lib/catissue/domain/specimen_collection_group_test.rb +14 -10
- data/test/lib/catissue/domain/specimen_test.rb +36 -60
- data/test/lib/catissue/domain/storage_type_test.rb +5 -5
- data/test/lib/catissue/domain/transfer_event_parameters_test.rb +14 -12
- data/test/lib/catissue/migration/test_case.rb +0 -1
- data/test/lib/catissue/test_case.rb +12 -12
- data/test/lib/examples/galena/tissue/domain/examples_test.rb +1 -1
- data/test/lib/examples/galena/tissue/migration/annotation_test.rb +9 -7
- data/test/lib/examples/galena/tissue/migration/frozen_test.rb +1 -1
- data/test/lib/examples/galena/tissue/migration/general_test.rb +1 -1
- data/test/lib/examples/galena/tissue/migration/registration_test.rb +3 -9
- data/test/lib/examples/galena/tissue/migration/seedify.rb +3 -3
- data/test/lib/examples/pcbin/migration_test.rb +37 -16
- metadata +24 -10
- data/History.txt +0 -50
metadata
CHANGED
@@ -1,13 +1,13 @@
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--- !ruby/object:Gem::Specification
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name: caruby-tissue
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version: !ruby/object:Gem::Version
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hash:
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hash: 1
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prerelease: false
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version: 1.
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version: 1.5.1
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platform: ruby
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authors:
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- OHSU
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bindir: bin
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cert_chain: []
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date: 2011-05
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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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requirements:
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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"
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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
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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
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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
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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.
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- History.md
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- LEGAL
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- LICENSE
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- README.md
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data/History.txt
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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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=== 1.2.1 / 2010-11-23
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* Initial public release.
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=== 1.2.2 / 2010-11-30
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* Galena example.
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=== 1.2.3 / 2011-02-18
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* Dynamic Extensions Support.
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=== 1.3.1 / 2011-02-18
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* Prostate Spore PCBIN DE support.
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=== 1.3.2 / 2011-02-25
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* Migration bug fixes.
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=== 1.3.3 / 2011-02-26
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* JRuby 1.5 upgrade.
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=== 1.3.4 / 2011-02-26
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* Use caruby-core JRuby 1.5 bug work-around.
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=== 1.3.5 / 2011-03-04
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* Annotation migration.
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=== 1.3.6 / 2011-03-04
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* Specify caruby-core gem version dependency.
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=== 1.4.1 / 2011-05-03
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* caTissue 1.2 support.
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* embed Java-caRuby bridge subproject.
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=== 1.4.2 / 2011-05-04
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* Add registration and PCBIN examples.
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