caruby-tissue 1.3.4 → 1.3.5

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Files changed (61) hide show
  1. data/History.txt +11 -7
  2. data/lib/catissue/annotation/annotatable_class.rb +18 -1
  3. data/lib/catissue/annotation/annotation.rb +5 -0
  4. data/lib/catissue/annotation/annotation_class.rb +15 -3
  5. data/lib/catissue/annotation/proxy_class.rb +2 -1
  6. data/lib/catissue/database/annotation/annotation_service.rb +13 -6
  7. data/lib/catissue/database/annotation/annotator.rb +3 -1
  8. data/lib/catissue/database/annotation/entity_facade.rb +21 -29
  9. data/lib/catissue/database/annotation/integration_service.rb +6 -4
  10. data/lib/catissue/database.rb +2 -2
  11. data/lib/catissue/domain/abstract_domain_object.rb +1 -1
  12. data/lib/catissue/domain/abstract_position.rb +1 -1
  13. data/lib/catissue/domain/abstract_specimen.rb +1 -1
  14. data/lib/catissue/domain/abstract_specimen_collection_group.rb +1 -1
  15. data/lib/catissue/domain/address.rb +1 -1
  16. data/lib/catissue/domain/cancer_research_group.rb +1 -1
  17. data/lib/catissue/domain/capacity.rb +1 -1
  18. data/lib/catissue/domain/check_in_check_out_event_parameter.rb +1 -1
  19. data/lib/catissue/domain/collection_event_parameters.rb +1 -1
  20. data/lib/catissue/domain/collection_protocol.rb +1 -1
  21. data/lib/catissue/domain/collection_protocol_event.rb +1 -1
  22. data/lib/catissue/domain/collection_protocol_registration.rb +1 -1
  23. data/lib/catissue/domain/consent_tier_response.rb +1 -1
  24. data/lib/catissue/domain/consent_tier_status.rb +1 -1
  25. data/lib/catissue/domain/container.rb +1 -1
  26. data/lib/catissue/domain/container_position.rb +4 -2
  27. data/lib/catissue/domain/container_type.rb +1 -1
  28. data/lib/catissue/domain/department.rb +1 -1
  29. data/lib/catissue/domain/disposal_event_parameters.rb +1 -1
  30. data/lib/catissue/domain/embedded_event_parameters.rb +1 -1
  31. data/lib/catissue/domain/external_identifier.rb +1 -1
  32. data/lib/catissue/domain/frozen_event_parameters.rb +1 -1
  33. data/lib/catissue/domain/institution.rb +1 -1
  34. data/lib/catissue/domain/new_specimen_array_order_item.rb +1 -1
  35. data/lib/catissue/domain/order_details.rb +1 -1
  36. data/lib/catissue/domain/participant.rb +2 -2
  37. data/lib/catissue/domain/participant_medical_identifier.rb +1 -1
  38. data/lib/catissue/domain/password.rb +1 -1
  39. data/lib/catissue/domain/race.rb +1 -1
  40. data/lib/catissue/domain/received_event_parameters.rb +1 -1
  41. data/lib/catissue/domain/site.rb +1 -1
  42. data/lib/catissue/domain/specimen.rb +49 -40
  43. data/lib/catissue/domain/specimen_array.rb +1 -1
  44. data/lib/catissue/domain/specimen_array_content.rb +1 -1
  45. data/lib/catissue/domain/specimen_array_type.rb +1 -1
  46. data/lib/catissue/domain/specimen_characteristics.rb +1 -1
  47. data/lib/catissue/domain/specimen_collection_group.rb +7 -7
  48. data/lib/catissue/domain/specimen_event_parameters.rb +6 -6
  49. data/lib/catissue/domain/specimen_position.rb +1 -1
  50. data/lib/catissue/domain/specimen_protocol.rb +1 -1
  51. data/lib/catissue/domain/specimen_requirement.rb +13 -13
  52. data/lib/catissue/domain/storage_container.rb +1 -1
  53. data/lib/catissue/domain/storage_type.rb +1 -1
  54. data/lib/catissue/domain/transfer_event_parameters.rb +1 -1
  55. data/lib/catissue/domain/user.rb +1 -1
  56. data/lib/catissue/migration/migrator.rb +2 -2
  57. data/lib/catissue/version.rb +1 -1
  58. data/test/lib/catissue/domain/specimen_test.rb +241 -242
  59. data/test/lib/catissue/test_case.rb +11 -7
  60. metadata +3 -4
  61. data/examples/galena/lib/galena/cli/seed.rb +0 -22
data/test/lib/catissue/test_case.rb CHANGED
@@ -124,13 +124,14 @@ module CaTissue
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  def verify_dependency(dependent)
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  return if dependent.class.owner_attribute.nil?
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- owner = dependent.owner
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- assert_not_nil(owner, "Owner missing for dependent: #{dependent}")
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- attribute = owner.class.dependent_attribute(dependent.class)
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- assert_not_nil(attribute, "Dependent attribute missing for #{dependent} owner #{owner}")
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+ # kludge for annotation proxy nonsense (cf. Annotation#owner)
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+ ownr = Annotation === dependent ? (dependent.hook or dependent.owner) : dependent.owner
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+ assert_not_nil(ownr, "Owner missing for dependent: #{dependent}")
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+ attribute = ownr.class.dependent_attribute(dependent.class)
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+ assert_not_nil(attribute, "Dependent attribute missing for #{dependent} owner #{ownr}")
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  # a dependent collection reference must be refetched
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- if owner.class.collection_attribute?(attribute) then
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- verify_saved_dependent_collection_member(dependent, owner, attribute)
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+ if ownr.class.collection_attribute?(attribute) then
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+ verify_saved_dependent_collection_member(dependent, ownr, attribute)
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  else
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  assert_not_nil(dependent.identifier, "Stored dependent #{dependent} identifier is not set")
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  end
@@ -138,9 +139,12 @@ module CaTissue
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  # Verifies that the given dependent has an identifier and that the given owner dependent attribute value
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  # contains the dependent.
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+ #
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+ # JRuby alert - Set include? incorrectly returns false in the OHSU PSR samples_test test_save_grade
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+ # call to this method. Work around by using Set detect rather than include?.
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  def verify_saved_dependent_collection_member(dependent, owner, attribute)
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  deps = owner.send(attribute)
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- assert(deps.include?(dependent), "Owner #{owner.qp} #{attribute} value #{deps.pp_s} does not contain #{dependent}")
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+ assert(deps.detect { |dep| dep == dependent }, "Owner #{owner.qp} #{attribute} value #{deps.pp_s} does not contain #{dependent}")
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  assert_not_nil(dependent.identifier, "Identifier not set for stored owner #{owner.qp} #{attribute} dependent collection member #{dependent}")
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  end
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metadata CHANGED
@@ -2,7 +2,7 @@
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  name: caruby-tissue
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  version: !ruby/object:Gem::Version
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  prerelease:
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- version: 1.3.4
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+ version: 1.3.5
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  platform: ruby
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  authors:
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  - OHSU
@@ -10,7 +10,7 @@ autorequire:
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  bindir: bin
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  cert_chain: []
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- date: 2011-02-26 00:00:00 -08:00
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+ date: 2011-03-04 00:00:00 -08:00
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  default_executable:
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  dependencies:
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  - !ruby/object:Gem::Dependency
@@ -67,7 +67,6 @@ files:
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  - examples/galena/data/simple.csv
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  - examples/galena/data/small.csv
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  - examples/galena/lib/galena.rb
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- - examples/galena/lib/galena/cli/seed.rb
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  - examples/galena/lib/galena/migration/filter_shims.rb
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  - examples/galena/lib/galena/migration/frozen_shims.rb
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  - examples/galena/lib/galena/seed/defaults.rb
@@ -232,7 +231,7 @@ required_rubygems_version: !ruby/object:Gem::Requirement
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  requirements: []
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  rubyforge_project: caruby
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- rubygems_version: 1.5.2
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+ rubygems_version: 1.5.3
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  signing_key:
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  specification_version: 3
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  summary: Ruby facade for caTissue.
data/examples/galena/lib/galena/cli/seed.rb DELETED
@@ -1,22 +0,0 @@
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- #!/usr/bin/env jruby
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- #
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-
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- # load the required gems
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- require 'rubygems'
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- begin
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- gem 'caruby-tissue'
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- rescue LoadError
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- # if the gem is not available, then try a local source
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- $:.unshift File.join(File.dirname(__FILE__), '..', 'lib')
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- $:.unshift File.join(File.dirname(__FILE__), '..', 'examples', 'galena', 'lib')
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- end
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-
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- # the default log file
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- DEF_LOG_FILE = 'log/migration.log'
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-
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- require 'catissue'
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- require 'catissue/cli/command'
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-
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- require 'galena/seed/defaults'
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-
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- CaTissue::Command.new.execute { Galena::Seed.defaults.ensure_exists }