caruby-tissue 1.2.1

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Files changed (133) hide show
  1. data/History.txt +4 -0
  2. data/LEGAL +5 -0
  3. data/LICENSE +22 -0
  4. data/README.md +44 -0
  5. data/bin/crtdump +31 -0
  6. data/bin/crtexample +18 -0
  7. data/bin/crtextract +47 -0
  8. data/bin/crtmigrate +17 -0
  9. data/bin/crtsmoke +27 -0
  10. data/examples/galena/README.md +53 -0
  11. data/examples/galena/bin/migrate.rb +42 -0
  12. data/examples/galena/bin/seed.rb +43 -0
  13. data/examples/galena/conf/extract/simple_fields.yaml +4 -0
  14. data/examples/galena/conf/migration/filter_fields.yaml +7 -0
  15. data/examples/galena/conf/migration/filter_migration.yaml +9 -0
  16. data/examples/galena/conf/migration/frozen_fields.yaml +11 -0
  17. data/examples/galena/conf/migration/frozen_migration.yaml +9 -0
  18. data/examples/galena/conf/migration/general_fields.yaml +42 -0
  19. data/examples/galena/conf/migration/general_migration.yaml +9 -0
  20. data/examples/galena/conf/migration/simple_fields.yaml +30 -0
  21. data/examples/galena/conf/migration/simple_migration.yaml +7 -0
  22. data/examples/galena/conf/migration/small_fields.yaml +24 -0
  23. data/examples/galena/conf/migration/small_migration.yaml +9 -0
  24. data/examples/galena/data/filter.csv +1 -0
  25. data/examples/galena/data/frozen.csv +1 -0
  26. data/examples/galena/data/general.csv +1 -0
  27. data/examples/galena/data/minimal.csv +1 -0
  28. data/examples/galena/data/simple.csv +1 -0
  29. data/examples/galena/data/small.csv +1 -0
  30. data/examples/galena/doc/CaTissue.html +93 -0
  31. data/examples/galena/doc/CaTissue/CollectionProtocolRegistration.html +181 -0
  32. data/examples/galena/doc/CaTissue/Participant.html +241 -0
  33. data/examples/galena/doc/CaTissue/SpecimenCollectionGroup.html +190 -0
  34. data/examples/galena/doc/CaTissue/StorageContainer.html +179 -0
  35. data/examples/galena/doc/CaTissue/TissueSpecimen.html +320 -0
  36. data/examples/galena/doc/Galena.html +290 -0
  37. data/examples/galena/doc/Galena/Seed.html +203 -0
  38. data/examples/galena/doc/Galena/Seed/Defaults.html +646 -0
  39. data/examples/galena/doc/_index.html +188 -0
  40. data/examples/galena/doc/class_list.html +36 -0
  41. data/examples/galena/doc/css/common.css +1 -0
  42. data/examples/galena/doc/css/full_list.css +53 -0
  43. data/examples/galena/doc/css/style.css +307 -0
  44. data/examples/galena/doc/file.README.html +108 -0
  45. data/examples/galena/doc/file_list.html +38 -0
  46. data/examples/galena/doc/frames.html +13 -0
  47. data/examples/galena/doc/index.html +108 -0
  48. data/examples/galena/doc/js/app.js +202 -0
  49. data/examples/galena/doc/js/full_list.js +149 -0
  50. data/examples/galena/doc/js/jquery.js +154 -0
  51. data/examples/galena/doc/method_list.html +179 -0
  52. data/examples/galena/doc/top-level-namespace.html +112 -0
  53. data/examples/galena/lib/README.html +33 -0
  54. data/examples/galena/lib/galena.rb +8 -0
  55. data/examples/galena/lib/galena/cli/seed.rb +43 -0
  56. data/examples/galena/lib/galena/migration/filter_shims.rb +43 -0
  57. data/examples/galena/lib/galena/migration/frozen_shims.rb +54 -0
  58. data/examples/galena/lib/galena/seed/defaults.rb +97 -0
  59. data/lib/catissue.rb +26 -0
  60. data/lib/catissue/cli/command.rb +51 -0
  61. data/lib/catissue/cli/example.rb +31 -0
  62. data/lib/catissue/cli/migrate.rb +60 -0
  63. data/lib/catissue/cli/smoke.rb +45 -0
  64. data/lib/catissue/database.rb +451 -0
  65. data/lib/catissue/database/annotation/annotatable_service.rb +25 -0
  66. data/lib/catissue/database/annotation/annotation_service.rb +79 -0
  67. data/lib/catissue/database/annotation/annotator.rb +84 -0
  68. data/lib/catissue/database/annotation/entity_manager.rb +10 -0
  69. data/lib/catissue/database/annotation/integration_service.rb +87 -0
  70. data/lib/catissue/database/controlled_value_finder.rb +43 -0
  71. data/lib/catissue/database/controlled_values.rb +162 -0
  72. data/lib/catissue/domain/abstract_domain_object.rb +8 -0
  73. data/lib/catissue/domain/abstract_position.rb +22 -0
  74. data/lib/catissue/domain/abstract_specimen.rb +288 -0
  75. data/lib/catissue/domain/abstract_specimen_collection_group.rb +25 -0
  76. data/lib/catissue/domain/address.rb +13 -0
  77. data/lib/catissue/domain/cancer_research_group.rb +11 -0
  78. data/lib/catissue/domain/capacity.rb +34 -0
  79. data/lib/catissue/domain/check_in_check_out_event_parameter.rb +19 -0
  80. data/lib/catissue/domain/collection_event_parameters.rb +13 -0
  81. data/lib/catissue/domain/collection_protocol.rb +177 -0
  82. data/lib/catissue/domain/collection_protocol_event.rb +108 -0
  83. data/lib/catissue/domain/collection_protocol_registration.rb +108 -0
  84. data/lib/catissue/domain/consent_tier_response.rb +13 -0
  85. data/lib/catissue/domain/consent_tier_status.rb +29 -0
  86. data/lib/catissue/domain/container.rb +234 -0
  87. data/lib/catissue/domain/container_position.rb +21 -0
  88. data/lib/catissue/domain/container_type.rb +131 -0
  89. data/lib/catissue/domain/department.rb +13 -0
  90. data/lib/catissue/domain/disposal_event_parameters.rb +13 -0
  91. data/lib/catissue/domain/embedded_event_parameters.rb +10 -0
  92. data/lib/catissue/domain/external_identifier.rb +22 -0
  93. data/lib/catissue/domain/frozen_event_parameters.rb +10 -0
  94. data/lib/catissue/domain/institution.rb +13 -0
  95. data/lib/catissue/domain/new_specimen_array_order_item.rb +35 -0
  96. data/lib/catissue/domain/order_details.rb +25 -0
  97. data/lib/catissue/domain/participant.rb +138 -0
  98. data/lib/catissue/domain/participant_medical_identifier.rb +38 -0
  99. data/lib/catissue/domain/password.rb +11 -0
  100. data/lib/catissue/domain/race.rb +11 -0
  101. data/lib/catissue/domain/received_event_parameters.rb +25 -0
  102. data/lib/catissue/domain/scg_event_parameters.rb +11 -0
  103. data/lib/catissue/domain/site.rb +30 -0
  104. data/lib/catissue/domain/specimen.rb +456 -0
  105. data/lib/catissue/domain/specimen_array.rb +47 -0
  106. data/lib/catissue/domain/specimen_array_content.rb +19 -0
  107. data/lib/catissue/domain/specimen_array_type.rb +20 -0
  108. data/lib/catissue/domain/specimen_characteristics.rb +20 -0
  109. data/lib/catissue/domain/specimen_collection_group.rb +412 -0
  110. data/lib/catissue/domain/specimen_event_parameters.rb +111 -0
  111. data/lib/catissue/domain/specimen_position.rb +38 -0
  112. data/lib/catissue/domain/specimen_protocol.rb +34 -0
  113. data/lib/catissue/domain/specimen_requirement.rb +143 -0
  114. data/lib/catissue/domain/storage_container.rb +204 -0
  115. data/lib/catissue/domain/storage_type.rb +82 -0
  116. data/lib/catissue/domain/transfer_event_parameters.rb +53 -0
  117. data/lib/catissue/domain/user.rb +100 -0
  118. data/lib/catissue/extract/command.rb +31 -0
  119. data/lib/catissue/extract/delta.rb +62 -0
  120. data/lib/catissue/extract/extractor.rb +99 -0
  121. data/lib/catissue/migration/migrator.rb +101 -0
  122. data/lib/catissue/migration/shims.rb +108 -0
  123. data/lib/catissue/migration/uniquify.rb +111 -0
  124. data/lib/catissue/resource.rb +84 -0
  125. data/lib/catissue/util/controlled_value.rb +29 -0
  126. data/lib/catissue/util/location.rb +116 -0
  127. data/lib/catissue/util/log.rb +30 -0
  128. data/lib/catissue/util/person.rb +31 -0
  129. data/lib/catissue/util/position.rb +54 -0
  130. data/lib/catissue/util/storable.rb +34 -0
  131. data/lib/catissue/util/storage_type_holder.rb +30 -0
  132. data/lib/catissue/version.rb +7 -0
  133. metadata +212 -0
data/examples/galena/doc/Galena.html ADDED
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+ <!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN"
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+ "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
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+ <html xmlns="http://www.w3.org/1999/xhtml" xml:lang="en" lang="en">
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+ <head>
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+ <meta name="Content-Type" content="text/html; charset=utf-8" />
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+ <title>Module: Galena</title>
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+ <link rel="stylesheet" href="css/style.css" type="text/css" media="screen" charset="utf-8" />
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+ <link rel="stylesheet" href="css/common.css" type="text/css" media="screen" charset="utf-8" />
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+ relpath = '';
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+ if (relpath != '') relpath += '/';
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+ </script>
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+ </head>
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+ <body>
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+ <script type="text/javascript" charset="utf-8">
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+ if (window.top.frames.main) document.body.className = 'frames';
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+ </script>
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+ <div id="header">
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+ <div id="menu">
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+ <a href="_index.html">Index (G)</a> &raquo;
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+ <span class="title">Galena</span>
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+ <div class="noframes"><span class="title">(</span><a href="." target="_top">no frames</a><span class="title">)</span></div>
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+ </div>
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+
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+ <div id="search">
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+ <a id="class_list_link" href="#">Class List</a>
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+ <a id="method_list_link" href="#">Method List</a>
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+ <a id ="file_list_link" href="#">File List</a>
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+ </div>
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+
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+ <div class="clear"></div>
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+ </div>
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+
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+ <iframe id="search_frame"></iframe>
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+
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+ <div id="content"><h1>Module: Galena
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+
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+
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+
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+ </h1>
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+
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+ <dl class="box">
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+
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+
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+
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+
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+
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+
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+
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+
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+ <dt class="r1 last">Defined in:</dt>
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+ <dd class="r1 last">examples/galena/lib/galena.rb<span class="defines">,<br />
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+ examples/galena/lib/galena/seed/defaults.rb</span>
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+ </dd>
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+
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+ </dl>
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+ <div class="clear"></div>
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+
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+ <h2>Overview</h2><div class="docstring">
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+ <div class="discussion">
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+ <p>
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+ The caRuby Tissue Galena example module.
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+ </p>
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+
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+
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+ </div>
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+ </div>
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+ <div class="tags">
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+
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+ </div><h2>Defined Under Namespace</h2>
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+ <p class="children">
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+
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+
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+ <strong class="modules">Modules:</strong> <span class='object_link'><a href="Galena/Seed.html" title="Galena::Seed (module)">Seed</a></span>
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+
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+
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+
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+
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+ </p>
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+
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+
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+
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+
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+ <h2>
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+ Class Method Summary
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+ <small>(<a href="#" class="summary_toggle">collapse</a>)</small>
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+ </h2>
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+
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+ <ul class="summary">
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+
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+ <li class="public ">
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+ <span class="summary_signature">
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+
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+ <a href="#resource-class_method" title="resource (class method)">+ (String<sup>?</sup>) <strong>resource</strong>(path) </a>
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+
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+
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+
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+ </span>
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+
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+
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+
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+ <span class="summary_desc"><div class='inline'><p>
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+ The file in this gem which matches the given path.
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+ </p>
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+ </div></span>
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+
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+ </li>
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+
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+
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+ <li class="public ">
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+ <span class="summary_signature">
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+
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+ <a href="#seed-class_method" title="seed (class method)">+ (Object) <strong>seed</strong> </a>
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+
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+
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+
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+ </span>
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+
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+
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+
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+
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+ <span class="summary_desc"><div class='inline'><p>
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+ Creates the <span class='object_link'><a href="Galena/Seed/Defaults.html" title="Galena::Seed::Defaults (class)">Seed::Defaults</a></span> administrative objects as necessary.
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+ </p>
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+ </div></span>
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+
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+ </li>
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+
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+ </ul>
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+
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+
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+ <div id="class_method_details" class="method_details_list">
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+ <h2>Class Method Details</h2>
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+
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+
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+ <div class="method_details first">
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+ <p class="signature first" id="resource-class_method">
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+
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+ + (<tt>String</tt><sup>?</sup>) <strong>resource</strong>(path)
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+
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+
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+
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+ </p><div class="docstring">
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+ <div class="discussion">
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+ <p>
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+ The file in this gem which matches the given path
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+ </p>
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+
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+
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+ </div>
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+ </div>
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+ <div class="tags">
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+ <h3>Parameters:</h3>
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+ <ul class="param">
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+
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+ <li>
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+
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+ <span class='type'>(<tt>String</tt>)</span>
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+
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+
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+ <span class='name'>the</span>
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+
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+
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+
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+ &mdash;
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+ <div class='inline'><p>
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+ path (without wildcards) of the desired file relative to the gem root
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+ directory
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+ </p>
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+ </div>
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+
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+ </li>
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+
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+ </ul>
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+ <h3>Returns:</h3>
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+ <ul class="return">
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+
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+ <li>
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+
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+ <span class='type'>(<tt>String</tt>, <tt>nil</tt>)</span>
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+
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+
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+
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+
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+ &mdash;
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+ <div class='inline'><p>
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+ the file in this gem which matches the given path
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+ </p>
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+ </div>
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+
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+ </li>
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+
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+ </ul>
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+
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+ </div><table class="source_code">
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+ <tr>
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+ <td>
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+ <pre class="lines">
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+
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+ 5
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+ 6
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+ 7</pre>
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+ </td>
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+ <td>
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+ <pre class="code"><span class="info file"># File 'examples/galena/lib/galena.rb', line 5</span>
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+
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+ <span class='def def kw'>def</span> <span class='self self kw'>self</span><span class='dot token'>.</span><span class='resource identifier id'>resource</span><span class='lparen token'>(</span><span class='path identifier id'>path</span><span class='rparen token'>)</span>
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+ <span class='File constant id'>File</span><span class='dot token'>.</span><span class='expand_path identifier id'>expand_path</span><span class='lparen token'>(</span><span class='File constant id'>File</span><span class='dot token'>.</span><span class='join identifier id'>join</span><span class='lparen token'>(</span><span class='File constant id'>File</span><span class='dot token'>.</span><span class='dirname identifier id'>dirname</span><span class='lparen token'>(</span><span class='__FILE__ __file__ kw'>__FILE__</span><span class='rparen token'>)</span><span class='comma token'>,</span> <span class='string val'>'..'</span><span class='comma token'>,</span> <span class='path identifier id'>path</span><span class='rparen token'>)</span><span class='rparen token'>)</span>
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+ <span class='end end kw'>end</span>
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+ </pre>
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+ </td>
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+ </tr>
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+ </table>
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+ </div>
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+
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+ <div class="method_details ">
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+ <p class="signature " id="seed-class_method">
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+
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+ + (<tt>Object</tt>) <strong>seed</strong>
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+
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+
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+
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+ </p><div class="docstring">
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+ <div class="discussion">
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+ <p>
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+ Creates the <span class='object_link'><a href="Galena/Seed/Defaults.html" title="Galena::Seed::Defaults (class)">Seed::Defaults</a></span> administrative objects as necessary.
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+ </p>
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+
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+
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+ </div>
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+ </div>
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+ <div class="tags">
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+
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+ </div><table class="source_code">
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+ <tr>
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+ <td>
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+ <pre class="lines">
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+ 6
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+ 7
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+ 8</pre>
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+ </td>
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+ <td>
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+ <pre class="code"><span class="info file"># File 'examples/galena/lib/galena/seed/defaults.rb', line 6</span>
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+
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+ <span class='def def kw'>def</span> <span class='self self kw'>self</span><span class='dot token'>.</span><span class='seed identifier id'>seed</span>
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+ <span class='Seed constant id'>Seed</span><span class='dot token'>.</span><span class='defaults identifier id'>defaults</span><span class='dot token'>.</span><span class='ensure_exists identifier id'>ensure_exists</span>
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+ <span class='end end kw'>end</span>
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+ </pre>
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+ </td>
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+ </tr>
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+ </table>
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+ </div>
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+
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+ </div>
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+
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+ </div>
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+
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+ <div id="footer">
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+ Generated on Tue Nov 23 11:38:43 2010 by
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+ <a href="http://yardoc.org" title="Yay! A Ruby Documentation Tool" target="_parent">yard</a>
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+ 0.6.1 (ruby-1.8.6).
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+ </div>
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+
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+ </body>
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+ </html>
data/examples/galena/doc/Galena/Seed.html ADDED
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+ <!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN"
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+ "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
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+ <html xmlns="http://www.w3.org/1999/xhtml" xml:lang="en" lang="en">
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+ <head>
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+ <meta name="Content-Type" content="text/html; charset=utf-8" />
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+ <title>Module: Galena::Seed</title>
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+ <link rel="stylesheet" href="../css/style.css" type="text/css" media="screen" charset="utf-8" />
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+ <link rel="stylesheet" href="../css/common.css" type="text/css" media="screen" charset="utf-8" />
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+
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+ <script type="text/javascript" charset="utf-8">
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+ relpath = '..';
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+ if (relpath != '') relpath += '/';
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+ </script>
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+ <script type="text/javascript" charset="utf-8" src="../js/jquery.js"></script>
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+ <script type="text/javascript" charset="utf-8" src="../js/app.js"></script>
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+
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+ </head>
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+ <body>
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+ <script type="text/javascript" charset="utf-8">
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+ if (window.top.frames.main) document.body.className = 'frames';
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+ </script>
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+
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+ <div id="header">
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+ <div id="menu">
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+
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+ <a href="../_index.html">Index (S)</a> &raquo;
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+ <span class='title'><span class='object_link'><a href="../Galena.html" title="Galena (module)">Galena</a></span></span>
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+ &raquo;
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+ <span class="title">Seed</span>
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+
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+
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+ <div class="noframes"><span class="title">(</span><a href="." target="_top">no frames</a><span class="title">)</span></div>
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+ </div>
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+
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+ <div id="search">
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+ <a id="class_list_link" href="#">Class List</a>
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+ <a id="method_list_link" href="#">Method List</a>
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+
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+ <div class="clear"></div>
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+ </div>
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+
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+ <iframe id="search_frame"></iframe>
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+
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+ <div id="content"><h1>Module: Galena::Seed
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+
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+
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+
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+ </h1>
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+
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+ <dl class="box">
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+
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+
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+
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+
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+
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+
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+
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+
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+ <dt class="r1 last">Defined in:</dt>
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+ <dd class="r1 last">examples/galena/lib/galena/seed/defaults.rb</dd>
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+
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+ </dl>
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+ <div class="clear"></div>
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+
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+ <h2>Overview</h2><div class="docstring">
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+ <div class="discussion">
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+ <p>
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+ Galena example utility module to populate the database with pre-defined
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+ administrative objects.
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+ </p>
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+
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+
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+ </div>
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+ </div>
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+ <div class="tags">
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+
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+ </div><h2>Defined Under Namespace</h2>
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+ <p class="children">
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+
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+
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+
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+
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+ <strong class="classes">Classes:</strong> <span class='object_link'><a href="Seed/Defaults.html" title="Galena::Seed::Defaults (class)">Defaults</a></span>
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+
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+
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+ </p>
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+
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+
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+
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+
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+ <h2>
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+ Class Method Summary
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+ <small>(<a href="#" class="summary_toggle">collapse</a>)</small>
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+ </h2>
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+
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+ <ul class="summary">
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+
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+ <li class="public ">
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+ <span class="summary_signature">
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+
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+ <a href="#defaults-class_method" title="defaults (class method)">+ (Defaults) <strong>defaults</strong> </a>
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+
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+
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+
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+ </span>
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+
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+
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+
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+
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+
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+
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+
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+
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+ <span class="summary_desc"><div class='inline'><p>
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+ The defaults instance.
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+ </p>
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+ </div></span>
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+
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+ </li>
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+
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+
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+ </ul>
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+
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+
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+
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+
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+ <div id="class_method_details" class="method_details_list">
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+ <h2>Class Method Details</h2>
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+
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+
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+ <div class="method_details first">
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+ <p class="signature first" id="defaults-class_method">
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+
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+ + (<tt><span class='object_link'><a href="Seed/Defaults.html" title="Galena::Seed::Defaults (class)">Defaults</a></span></tt>) <strong>defaults</strong>
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+
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+
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+
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+ </p><div class="docstring">
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+ <div class="discussion">
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+ <p>
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+ The defaults instance
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+ </p>
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+
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+
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+ </div>
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+ </div>
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+ <div class="tags">
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+ <h3>Returns:</h3>
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+ <ul class="return">
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+
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+ <li>
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+
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+ <span class='type'>(<tt><span class='object_link'><a href="Seed/Defaults.html" title="Galena::Seed::Defaults (class)">Defaults</a></span></tt>)</span>
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+
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+
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+
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+
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+ &mdash;
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+ <div class='inline'><p>
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+ the defaults instance
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+ </p>
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+ </div>
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+
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+ </li>
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+
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+ </ul>
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+
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+ </div><table class="source_code">
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+ <tr>
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+ <td>
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+ <pre class="lines">
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+
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+
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+ 13
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+ 14
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+ 15</pre>
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+ </td>
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+ <td>
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+ <pre class="code"><span class="info file"># File 'examples/galena/lib/galena/seed/defaults.rb', line 13</span>
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+
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+ <span class='def def kw'>def</span> <span class='self self kw'>self</span><span class='dot token'>.</span><span class='defaults identifier id'>defaults</span>
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+ <span class='Defaults constant id'>Defaults</span><span class='dot token'>.</span><span class='instance identifier id'>instance</span>
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+ <span class='end end kw'>end</span>
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+ </pre>
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+ </td>
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+ </tr>
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+ </table>
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+ </div>
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+
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+ </div>
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+
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+ </div>
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+
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+ <div id="footer">
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+ Generated on Tue Nov 23 11:38:42 2010 by
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+ <a href="http://yardoc.org" title="Yay! A Ruby Documentation Tool" target="_parent">yard</a>
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+ 0.6.1 (ruby-1.8.6).
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+ </div>
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+
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+ </body>
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+ </html>