caruby-core 1.4.1

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Files changed (86) hide show
  1. data/History.txt +4 -0
  2. data/LEGAL +5 -0
  3. data/LICENSE +22 -0
  4. data/README.md +51 -0
  5. data/doc/website/css/site.css +1 -5
  6. data/doc/website/images/avatar.png +0 -0
  7. data/doc/website/images/favicon.ico +0 -0
  8. data/doc/website/images/logo.png +0 -0
  9. data/doc/website/index.html +82 -0
  10. data/doc/website/install.html +87 -0
  11. data/doc/website/quick_start.html +87 -0
  12. data/doc/website/tissue.html +85 -0
  13. data/doc/website/uom.html +10 -0
  14. data/lib/caruby.rb +3 -0
  15. data/lib/caruby/active_support/README.txt +2 -0
  16. data/lib/caruby/active_support/core_ext/string.rb +7 -0
  17. data/lib/caruby/active_support/core_ext/string/inflections.rb +167 -0
  18. data/lib/caruby/active_support/inflections.rb +55 -0
  19. data/lib/caruby/active_support/inflector.rb +398 -0
  20. data/lib/caruby/cli/application.rb +36 -0
  21. data/lib/caruby/cli/command.rb +169 -0
  22. data/lib/caruby/csv/csv_mapper.rb +157 -0
  23. data/lib/caruby/csv/csvio.rb +185 -0
  24. data/lib/caruby/database.rb +252 -0
  25. data/lib/caruby/database/fetched_matcher.rb +66 -0
  26. data/lib/caruby/database/persistable.rb +432 -0
  27. data/lib/caruby/database/persistence_service.rb +162 -0
  28. data/lib/caruby/database/reader.rb +599 -0
  29. data/lib/caruby/database/saved_merger.rb +131 -0
  30. data/lib/caruby/database/search_template_builder.rb +59 -0
  31. data/lib/caruby/database/sql_executor.rb +75 -0
  32. data/lib/caruby/database/store_template_builder.rb +200 -0
  33. data/lib/caruby/database/writer.rb +469 -0
  34. data/lib/caruby/domain/annotatable.rb +25 -0
  35. data/lib/caruby/domain/annotation.rb +23 -0
  36. data/lib/caruby/domain/attribute_metadata.rb +447 -0
  37. data/lib/caruby/domain/java_attribute_metadata.rb +160 -0
  38. data/lib/caruby/domain/merge.rb +91 -0
  39. data/lib/caruby/domain/properties.rb +95 -0
  40. data/lib/caruby/domain/reference_visitor.rb +289 -0
  41. data/lib/caruby/domain/resource_attributes.rb +528 -0
  42. data/lib/caruby/domain/resource_dependency.rb +205 -0
  43. data/lib/caruby/domain/resource_introspection.rb +159 -0
  44. data/lib/caruby/domain/resource_metadata.rb +117 -0
  45. data/lib/caruby/domain/resource_module.rb +285 -0
  46. data/lib/caruby/domain/uniquify.rb +38 -0
  47. data/lib/caruby/import/annotatable_class.rb +28 -0
  48. data/lib/caruby/import/annotation_class.rb +27 -0
  49. data/lib/caruby/import/annotation_module.rb +67 -0
  50. data/lib/caruby/import/java.rb +338 -0
  51. data/lib/caruby/migration/migratable.rb +167 -0
  52. data/lib/caruby/migration/migrator.rb +533 -0
  53. data/lib/caruby/migration/resource.rb +8 -0
  54. data/lib/caruby/migration/resource_module.rb +11 -0
  55. data/lib/caruby/migration/uniquify.rb +20 -0
  56. data/lib/caruby/resource.rb +969 -0
  57. data/lib/caruby/util/attribute_path.rb +46 -0
  58. data/lib/caruby/util/cache.rb +53 -0
  59. data/lib/caruby/util/class.rb +99 -0
  60. data/lib/caruby/util/collection.rb +1053 -0
  61. data/lib/caruby/util/controlled_value.rb +35 -0
  62. data/lib/caruby/util/coordinate.rb +75 -0
  63. data/lib/caruby/util/domain_extent.rb +49 -0
  64. data/lib/caruby/util/file_separator.rb +65 -0
  65. data/lib/caruby/util/inflector.rb +20 -0
  66. data/lib/caruby/util/log.rb +95 -0
  67. data/lib/caruby/util/math.rb +12 -0
  68. data/lib/caruby/util/merge.rb +59 -0
  69. data/lib/caruby/util/module.rb +34 -0
  70. data/lib/caruby/util/options.rb +92 -0
  71. data/lib/caruby/util/partial_order.rb +36 -0
  72. data/lib/caruby/util/person.rb +119 -0
  73. data/lib/caruby/util/pretty_print.rb +184 -0
  74. data/lib/caruby/util/properties.rb +112 -0
  75. data/lib/caruby/util/stopwatch.rb +66 -0
  76. data/lib/caruby/util/topological_sync_enumerator.rb +53 -0
  77. data/lib/caruby/util/transitive_closure.rb +45 -0
  78. data/lib/caruby/util/tree.rb +48 -0
  79. data/lib/caruby/util/trie.rb +37 -0
  80. data/lib/caruby/util/uniquifier.rb +30 -0
  81. data/lib/caruby/util/validation.rb +48 -0
  82. data/lib/caruby/util/version.rb +56 -0
  83. data/lib/caruby/util/visitor.rb +351 -0
  84. data/lib/caruby/util/weak_hash.rb +36 -0
  85. data/lib/caruby/version.rb +3 -0
  86. metadata +186 -0
@@ -0,0 +1,36 @@
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+ require 'caruby/util/collection'
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+
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+ module CaRuby
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+ # A WeakHash associates a key with a value until the key and value are no longer referenced elsewhere.
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+ #
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+ # The key and value must each be a jRuby wrapper for a Java object, i.e. a Ruby primitive such as String
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+ # or Integer, or an instance of a Java class imported into jRuby.
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+ class WeakHash
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+ include Hashable
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+
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+ # Creates a new WeakHash.
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+ def initialize
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+ super
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+ @map = Java::JavaUtil::WeakHashMap.new
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+ end
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+
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+ def each
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+ @map.each { |key, wref| yield(key, wref.get) }
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+ end
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+
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+ # Returns the
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+ def [](key)
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+ # the weak reference mapped by the key
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+ wref = @map.get(key)
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+ # the referenced object
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+ wref.get if wref
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+ end
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+
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+ def []=(key, value)
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+ # make a weak reference to the value
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+ wref = Java::JavaLangRef::WeakReference.new(value)
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+ # associate the object identifier with the weak reference
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+ @map.put(key, wref)
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+ end
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+ end
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+ end
@@ -0,0 +1,3 @@
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+ module CaRuby
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+ VERSION = "1.4.1"
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+ end
metadata ADDED
@@ -0,0 +1,186 @@
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+ --- !ruby/object:Gem::Specification
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+ extensions: []
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+
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+ homepage: http://rubyforge.org/projects/caruby
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+ executables: []
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+
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+ version: !ruby/object:Gem::Version
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+ prerelease: false
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+ version: 1.4.1
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+ segments:
11
+ - 1
12
+ - 4
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+ - 1
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+ post_install_message:
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+ date: 2010-10-17 07:00:00 +00:00
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+ files:
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+ - doc/website/index.html
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+ - doc/website/install.html
19
+ - doc/website/quick_start.html
20
+ - doc/website/tissue.html
21
+ - doc/website/uom.html
22
+ - doc/website/css/site.css
23
+ - doc/website/images/avatar.png
24
+ - doc/website/images/favicon.ico
25
+ - doc/website/images/logo.png
26
+ - lib/caruby.rb
27
+ - lib/caruby/database.rb
28
+ - lib/caruby/resource.rb
29
+ - lib/caruby/version.rb
30
+ - lib/caruby/active_support/inflections.rb
31
+ - lib/caruby/active_support/inflector.rb
32
+ - lib/caruby/active_support/README.txt
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+ - lib/caruby/active_support/core_ext/string.rb
34
+ - lib/caruby/active_support/core_ext/string/inflections.rb
35
+ - lib/caruby/cli/application.rb
36
+ - lib/caruby/cli/command.rb
37
+ - lib/caruby/csv/csv_mapper.rb
38
+ - lib/caruby/csv/csvio.rb
39
+ - lib/caruby/database/fetched_matcher.rb
40
+ - lib/caruby/database/persistable.rb
41
+ - lib/caruby/database/persistence_service.rb
42
+ - lib/caruby/database/reader.rb
43
+ - lib/caruby/database/saved_merger.rb
44
+ - lib/caruby/database/search_template_builder.rb
45
+ - lib/caruby/database/sql_executor.rb
46
+ - lib/caruby/database/store_template_builder.rb
47
+ - lib/caruby/database/writer.rb
48
+ - lib/caruby/domain/annotatable.rb
49
+ - lib/caruby/domain/annotation.rb
50
+ - lib/caruby/domain/attribute_metadata.rb
51
+ - lib/caruby/domain/java_attribute_metadata.rb
52
+ - lib/caruby/domain/merge.rb
53
+ - lib/caruby/domain/properties.rb
54
+ - lib/caruby/domain/reference_visitor.rb
55
+ - lib/caruby/domain/resource_attributes.rb
56
+ - lib/caruby/domain/resource_dependency.rb
57
+ - lib/caruby/domain/resource_introspection.rb
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+ - lib/caruby/domain/resource_metadata.rb
59
+ - lib/caruby/domain/resource_module.rb
60
+ - lib/caruby/domain/uniquify.rb
61
+ - lib/caruby/import/annotatable_class.rb
62
+ - lib/caruby/import/annotation_class.rb
63
+ - lib/caruby/import/annotation_module.rb
64
+ - lib/caruby/import/java.rb
65
+ - lib/caruby/migration/migratable.rb
66
+ - lib/caruby/migration/migrator.rb
67
+ - lib/caruby/migration/resource.rb
68
+ - lib/caruby/migration/resource_module.rb
69
+ - lib/caruby/migration/uniquify.rb
70
+ - lib/caruby/util/attribute_path.rb
71
+ - lib/caruby/util/cache.rb
72
+ - lib/caruby/util/class.rb
73
+ - lib/caruby/util/collection.rb
74
+ - lib/caruby/util/controlled_value.rb
75
+ - lib/caruby/util/coordinate.rb
76
+ - lib/caruby/util/domain_extent.rb
77
+ - lib/caruby/util/file_separator.rb
78
+ - lib/caruby/util/inflector.rb
79
+ - lib/caruby/util/log.rb
80
+ - lib/caruby/util/math.rb
81
+ - lib/caruby/util/merge.rb
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+ - lib/caruby/util/module.rb
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+ - lib/caruby/util/options.rb
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+ - lib/caruby/util/partial_order.rb
85
+ - lib/caruby/util/person.rb
86
+ - lib/caruby/util/pretty_print.rb
87
+ - lib/caruby/util/properties.rb
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+ - lib/caruby/util/stopwatch.rb
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+ - lib/caruby/util/topological_sync_enumerator.rb
90
+ - lib/caruby/util/transitive_closure.rb
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+ - lib/caruby/util/tree.rb
92
+ - lib/caruby/util/trie.rb
93
+ - lib/caruby/util/uniquifier.rb
94
+ - lib/caruby/util/validation.rb
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+ - lib/caruby/util/version.rb
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+ - lib/caruby/util/visitor.rb
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+ - lib/caruby/util/weak_hash.rb
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+ - History.txt
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+ - LEGAL
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+ - LICENSE
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+ - README.md
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+ rubygems_version: 1.3.7
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+ rdoc_options: []
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+
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+ signing_key:
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+ cert_chain: []
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+
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+ name: caruby-core
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+ has_rdoc: true
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+ platform: ruby
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+ summary: Ruby facade for caBIG applications.
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+ default_executable:
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+ bindir: bin
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+ licenses: []
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+
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+ required_rubygems_version: !ruby/object:Gem::Requirement
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+ none: false
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+ requirements:
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+ - - '>='
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+ - !ruby/object:Gem::Version
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+ version: "0"
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+ segments:
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+ - 0
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+ required_ruby_version: !ruby/object:Gem::Requirement
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+ none: false
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+ requirements:
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+ - - '>='
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+ - !ruby/object:Gem::Version
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+ version: "0"
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+ segments:
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+ - 0
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+ require_paths:
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+ - lib
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+ specification_version: 3
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+ test_files: []
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+
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+ dependencies:
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+ - !ruby/object:Gem::Dependency
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+ prerelease: false
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+ type: :runtime
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+ name: dbi
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+ version_requirements: &id001 !ruby/object:Gem::Requirement
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+ none: false
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+ requirements:
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+ - - '>='
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+ - !ruby/object:Gem::Version
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+ version: "0"
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+ segments:
149
+ - 0
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+ requirement: *id001
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+ - !ruby/object:Gem::Dependency
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+ prerelease: false
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+ type: :runtime
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+ name: fastercsv
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+ version_requirements: &id002 !ruby/object:Gem::Requirement
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+ none: false
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+ requirements:
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+ - - '>='
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+ - !ruby/object:Gem::Version
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+ version: "0"
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+ segments:
162
+ - 0
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+ requirement: *id002
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+ - !ruby/object:Gem::Dependency
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+ prerelease: false
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+ type: :runtime
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+ name: uom
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+ version_requirements: &id003 !ruby/object:Gem::Requirement
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+ none: false
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+ requirements:
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+ - - '>='
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+ - !ruby/object:Gem::Version
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+ version: "0"
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+ segments:
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+ - 0
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+ requirement: *id003
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+ description: " caRuby is a JRuby facade for interaction with caBIG applications.\n"
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+ email: caruby.org@gmail.com
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+ authors:
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+ - OHSU
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+ extra_rdoc_files: []
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+
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+ requirements: []
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+
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+ rubyforge_project: caruby
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+ autorequire: