lims-core 3.2.3

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Files changed (177) hide show
  1. checksums.yaml +15 -0
  2. data/.gitignore +5 -0
  3. data/.rspec +1 -0
  4. data/.rvmrc +2 -0
  5. data/.travis.yml +2 -0
  6. data/.vimrc +27 -0
  7. data/.yard_templates/default/layout/html/footer.erb +0 -0
  8. data/.yardopts +1 -0
  9. data/Gemfile +54 -0
  10. data/Gemfile.lock +197 -0
  11. data/Guardfile +21 -0
  12. data/Guardfile.tmux +28 -0
  13. data/README.markdown +67 -0
  14. data/Rakefile +16 -0
  15. data/config/database.yml +16 -0
  16. data/doc/Array.html +116 -0
  17. data/doc/Array/ArrayLoggerPersistor.html +152 -0
  18. data/doc/Lims.html +114 -0
  19. data/doc/Lims/Core.html +178 -0
  20. data/doc/Lims/Core/Action.html +91 -0
  21. data/doc/Lims/Core/Actions.html +116 -0
  22. data/doc/Lims/Core/Actions/Action.html +216 -0
  23. data/doc/Lims/Core/Actions/Action/AfterEval.html +853 -0
  24. data/doc/Lims/Core/Actions/Action/InvalidParameters.html +268 -0
  25. data/doc/Lims/Core/Actions/ActionGroup.html +196 -0
  26. data/doc/Lims/Core/Actions/ActionGroup/AfterEval.html +315 -0
  27. data/doc/Lims/Core/Actions/BulkAction.html +224 -0
  28. data/doc/Lims/Core/Actions/BulkAction/AfterEval.html +253 -0
  29. data/doc/Lims/Core/Actions/TestActionGroup.html +101 -0
  30. data/doc/Lims/Core/Actions/TestActionGroup/Action.html +133 -0
  31. data/doc/Lims/Core/Actions/TestActionGroup/ActionGroup.html +127 -0
  32. data/doc/Lims/Core/Base.html +287 -0
  33. data/doc/Lims/Core/Base/AccessibleViaSuper.html +252 -0
  34. data/doc/Lims/Core/Base/ClassMethod.html +177 -0
  35. data/doc/Lims/Core/Base/HashString.html +177 -0
  36. data/doc/Lims/Core/Base/IsArrayOf.html +606 -0
  37. data/doc/Lims/Core/Base/State.html +130 -0
  38. data/doc/Lims/Core/Organization.html +113 -0
  39. data/doc/Lims/Core/Organization/Batch.html +106 -0
  40. data/doc/Lims/Core/Persistence.html +267 -0
  41. data/doc/Lims/Core/Persistence/ComparisonFilter.html +318 -0
  42. data/doc/Lims/Core/Persistence/Filter.html +252 -0
  43. data/doc/Lims/Core/Persistence/IdentityMap.html +409 -0
  44. data/doc/Lims/Core/Persistence/IdentityMap/Class.html +144 -0
  45. data/doc/Lims/Core/Persistence/IdentityMap/DuplicateError.html +126 -0
  46. data/doc/Lims/Core/Persistence/IdentityMap/DuplicateIdError.html +136 -0
  47. data/doc/Lims/Core/Persistence/IdentityMap/DuplicateObjectError.html +136 -0
  48. data/doc/Lims/Core/Persistence/IdentityMapClass.html +133 -0
  49. data/doc/Lims/Core/Persistence/Logger.html +105 -0
  50. data/doc/Lims/Core/Persistence/Logger/Persistor.html +334 -0
  51. data/doc/Lims/Core/Persistence/Logger/Session.html +452 -0
  52. data/doc/Lims/Core/Persistence/Logger/Store.html +470 -0
  53. data/doc/Lims/Core/Persistence/MessageBus.html +871 -0
  54. data/doc/Lims/Core/Persistence/MessageBus/ConnectionError.html +123 -0
  55. data/doc/Lims/Core/Persistence/MessageBus/InvalidSettingsError.html +122 -0
  56. data/doc/Lims/Core/Persistence/MultiCriteriaFilter.html +293 -0
  57. data/doc/Lims/Core/Persistence/PersistAssociationTrait.html +91 -0
  58. data/doc/Lims/Core/Persistence/PersistableTrait.html +91 -0
  59. data/doc/Lims/Core/Persistence/Persistor.html +3072 -0
  60. data/doc/Lims/Core/Persistence/Persistor/DuplicateError.html +205 -0
  61. data/doc/Lims/Core/Persistence/Persistor/DuplicateIdError.html +147 -0
  62. data/doc/Lims/Core/Persistence/Persistor/DuplicateObjectError.html +147 -0
  63. data/doc/Lims/Core/Persistence/PersistorTrait.html +91 -0
  64. data/doc/Lims/Core/Persistence/ResourceState.html +1738 -0
  65. data/doc/Lims/Core/Persistence/Search.html +269 -0
  66. data/doc/Lims/Core/Persistence/Search/CreateSearch.html +251 -0
  67. data/doc/Lims/Core/Persistence/Search/SearchPersistor.html +240 -0
  68. data/doc/Lims/Core/Persistence/Search/SearchSequelPersistor.html +396 -0
  69. data/doc/Lims/Core/Persistence/Sequel.html +117 -0
  70. data/doc/Lims/Core/Persistence/Sequel/Filters.html +462 -0
  71. data/doc/Lims/Core/Persistence/Sequel/ForTest.html +101 -0
  72. data/doc/Lims/Core/Persistence/Sequel/ForTest/Name.html +137 -0
  73. data/doc/Lims/Core/Persistence/Sequel/ForTest/Name/NamePersitor.html +143 -0
  74. data/doc/Lims/Core/Persistence/Sequel/Migrations.html +266 -0
  75. data/doc/Lims/Core/Persistence/Sequel/Persistor.html +665 -0
  76. data/doc/Lims/Core/Persistence/Sequel/Session.html +501 -0
  77. data/doc/Lims/Core/Persistence/Sequel/Store.html +417 -0
  78. data/doc/Lims/Core/Persistence/Session.html +2751 -0
  79. data/doc/Lims/Core/Persistence/Session/UnmanagedObjectError.html +111 -0
  80. data/doc/Lims/Core/Persistence/StateGroup.html +696 -0
  81. data/doc/Lims/Core/Persistence/StateList.html +498 -0
  82. data/doc/Lims/Core/Persistence/Store.html +695 -0
  83. data/doc/Lims/Core/Persistence/UuidResource.html +1044 -0
  84. data/doc/Lims/Core/Persistence/UuidResource/InvalidUuidError.html +111 -0
  85. data/doc/Lims/Core/Persistence/UuidResource/UuidResourcePersistor.html +337 -0
  86. data/doc/Lims/Core/Persistence/Uuidable.html +799 -0
  87. data/doc/Lims/Core/Persistor.html +320 -0
  88. data/doc/Lims/Core/Resource.html +165 -0
  89. data/doc/Object.html +228 -0
  90. data/doc/SessionSpec.html +101 -0
  91. data/doc/SessionSpec/Model.html +279 -0
  92. data/doc/SessionSpec/Model/ModelPersistor.html +327 -0
  93. data/doc/_index.html +732 -0
  94. data/doc/class_list.html +47 -0
  95. data/doc/css/common.css +1 -0
  96. data/doc/css/full_list.css +55 -0
  97. data/doc/css/style.css +322 -0
  98. data/doc/file.README.html +127 -0
  99. data/doc/file_list.html +49 -0
  100. data/doc/frames.html +13 -0
  101. data/doc/index.html +127 -0
  102. data/doc/js/app.js +205 -0
  103. data/doc/js/full_list.js +167 -0
  104. data/doc/js/jquery.js +16 -0
  105. data/doc/method_list.html +1894 -0
  106. data/doc/top-level-namespace.html +100 -0
  107. data/lib/common.rb +18 -0
  108. data/lib/lims-core.rb +29 -0
  109. data/lib/lims-core/actions.rb +10 -0
  110. data/lib/lims-core/actions/action.rb +185 -0
  111. data/lib/lims-core/actions/action_group.rb +54 -0
  112. data/lib/lims-core/actions/bulk_action.rb +65 -0
  113. data/lib/lims-core/base.rb +132 -0
  114. data/lib/lims-core/helpers.rb +41 -0
  115. data/lib/lims-core/persistence.rb +15 -0
  116. data/lib/lims-core/persistence/comparison_filter.rb +54 -0
  117. data/lib/lims-core/persistence/filter.rb +23 -0
  118. data/lib/lims-core/persistence/identity_map.rb +55 -0
  119. data/lib/lims-core/persistence/logger/all.rb +5 -0
  120. data/lib/lims-core/persistence/logger/persistor.rb +35 -0
  121. data/lib/lims-core/persistence/logger/session.rb +30 -0
  122. data/lib/lims-core/persistence/logger/store.rb +37 -0
  123. data/lib/lims-core/persistence/message_bus.rb +131 -0
  124. data/lib/lims-core/persistence/multi_criteria_filter.rb +50 -0
  125. data/lib/lims-core/persistence/persist_association_trait.rb +96 -0
  126. data/lib/lims-core/persistence/persistable_trait.rb +150 -0
  127. data/lib/lims-core/persistence/persistor.rb +495 -0
  128. data/lib/lims-core/persistence/resource_state.rb +157 -0
  129. data/lib/lims-core/persistence/search.rb +3 -0
  130. data/lib/lims-core/persistence/search/all.rb +3 -0
  131. data/lib/lims-core/persistence/search/create_search.rb +55 -0
  132. data/lib/lims-core/persistence/search/search_persistor.rb +45 -0
  133. data/lib/lims-core/persistence/search/search_sequel_persistor.rb +40 -0
  134. data/lib/lims-core/persistence/sequel.rb +14 -0
  135. data/lib/lims-core/persistence/sequel/filters.rb +106 -0
  136. data/lib/lims-core/persistence/sequel/migrations.rb +14 -0
  137. data/lib/lims-core/persistence/sequel/migrations/add_audit_tables.rb +147 -0
  138. data/lib/lims-core/persistence/sequel/migrations/initial.rb +156 -0
  139. data/lib/lims-core/persistence/sequel/persistor.rb +200 -0
  140. data/lib/lims-core/persistence/sequel/session.rb +136 -0
  141. data/lib/lims-core/persistence/sequel/store.rb +37 -0
  142. data/lib/lims-core/persistence/session.rb +409 -0
  143. data/lib/lims-core/persistence/state_group.rb +97 -0
  144. data/lib/lims-core/persistence/state_list.rb +56 -0
  145. data/lib/lims-core/persistence/store.rb +73 -0
  146. data/lib/lims-core/persistence/uuid_resource.rb +115 -0
  147. data/lib/lims-core/persistence/uuid_resource_persistor.rb +43 -0
  148. data/lib/lims-core/persistence/uuidable.rb +107 -0
  149. data/lib/lims-core/resource.rb +21 -0
  150. data/lib/lims-core/subclass_tracker.rb +30 -0
  151. data/lib/lims-core/version.rb +5 -0
  152. data/lims-core.gemspec +40 -0
  153. data/makefile +52 -0
  154. data/showoff/core-2012-06-11/core/01_slide.md +237 -0
  155. data/showoff/core-2012-06-11/core/02_slide.md +110 -0
  156. data/showoff/core-2012-06-11/custom.css +44 -0
  157. data/showoff/core-2012-06-11/main/01_slide.md +53 -0
  158. data/showoff/core-2012-06-11/showoff.json +10 -0
  159. data/showoff/core-2012-06-11/tp1.tpl +1 -0
  160. data/spec/actions/action_group_spec.rb +39 -0
  161. data/spec/actions/spec_helper.rb +1 -0
  162. data/spec/persistence/identity_map_spec.rb +55 -0
  163. data/spec/persistence/logger/spec_helper.rb +7 -0
  164. data/spec/persistence/logger/store_spec.rb +48 -0
  165. data/spec/persistence/message_bus_spec.rb +76 -0
  166. data/spec/persistence/sequel/session_spec.rb +125 -0
  167. data/spec/persistence/sequel/spec_helper.rb +39 -0
  168. data/spec/persistence/sequel/store_shared.rb +25 -0
  169. data/spec/persistence/sequel/store_spec.rb +22 -0
  170. data/spec/persistence/session_spec.rb +199 -0
  171. data/spec/persistence/spec_helper.rb +2 -0
  172. data/spec/persistence/uuid_resource_spec.rb +80 -0
  173. data/spec/spec_helper.rb +10 -0
  174. data/spec/subclass_tracker_sperc.rb +62 -0
  175. data/utils/constant_tree.rb +29 -0
  176. data/utils/stack.rb +48 -0
  177. metadata +402 -0
data/doc/Lims/Core/Persistence/Sequel/ForTest.html ADDED
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data/doc/Lims/Core/Persistence/Sequel/ForTest/Name.html ADDED
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+ Class: Lims::Core::Persistence::Sequel::ForTest::Name
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+ <dt class="r1 last">Defined in:</dt>
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+ <dd class="r1 last">spec/persistence/sequel/session_spec.rb</dd>
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data/doc/Lims/Core/Persistence/Sequel/ForTest/Name/NamePersitor.html ADDED
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+ <meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
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+ Class: Lims::Core::Persistence::Sequel::ForTest::Name::NamePersitor
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+ <a href="../../../../../../_index.html">Index (N)</a> &raquo;
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+ <span class='title'><span class='object_link'><a href="../../../../../../Lims.html" title="Lims (module)">Lims</a></span></span> &raquo; <span class='title'><span class='object_link'><a href="../../../../../Core.html" title="Lims::Core (module)">Core</a></span></span> &raquo; <span class='title'><span class='object_link'><a href="../../../../Persistence.html" title="Lims::Core::Persistence (module)">Persistence</a></span></span> &raquo; <span class='title'><span class='object_link'><a href="../../../Sequel.html" title="Lims::Core::Persistence::Sequel (module)">Sequel</a></span></span> &raquo; <span class='title'><span class='object_link'><a href="../../ForTest.html" title="Lims::Core::Persistence::Sequel::ForTest (module)">ForTest</a></span></span> &raquo; <span class='title'><span class='object_link'><a href="../Name.html" title="Lims::Core::Persistence::Sequel::ForTest::Name (class)">Name</a></span></span>
38
+ &raquo;
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+ <span class="title">NamePersitor</span>
40
+
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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 class="clear"></div>
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+ </div>
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+ <iframe id="search_frame"></iframe>
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+
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+ <div id="content"><h1>Class: Lims::Core::Persistence::Sequel::ForTest::Name::NamePersitor
60
+
61
+
62
+
63
+ </h1>
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+
65
+ <dl class="box">
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+
67
+ <dt class="r1">Inherits:</dt>
68
+ <dd class="r1">
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+ <span class="inheritName"><span class='object_link'><a href="../../../Persistor.html" title="Lims::Core::Persistence::Persistor (class)">Persistor</a></span></span>
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+
71
+ <ul class="fullTree">
72
+ <li><span class='object_link'><a href="../../../../../../Object.html" title="Object (class)">Object</a></span></li>
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+
74
+ <li class="next"><span class='object_link'><a href="../../../Persistor.html" title="Lims::Core::Persistence::Persistor (class)">Persistor</a></span></li>
75
+
76
+ <li class="next">Lims::Core::Persistence::Sequel::ForTest::Name::NamePersitor</li>
77
+
78
+ </ul>
79
+ <a href="#" class="inheritanceTree">show all</a>
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+
81
+ </dd>
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+
83
+
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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="r2 last">Defined in:</dt>
92
+ <dd class="r2 last">spec/persistence/sequel/session_spec.rb</dd>
93
+
94
+ </dl>
95
+ <div class="clear"></div>
96
+
97
+
98
+ <h2>Constant Summary</h2>
99
+
100
+ <dl class="constants">
101
+
102
+ <dt id="Model-constant" class="">Model =
103
+
104
+ </dt>
105
+ <dd><pre class="code"><span class='const'>Name</span></pre></dd>
106
+
107
+ </dl>
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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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+
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+
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+
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+
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+
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+
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+ <h2>Method Summary</h2>
128
+
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+ <h3 class="inherited">Methods inherited from <span class='object_link'><a href="../../../Persistor.html" title="Lims::Core::Persistence::Persistor (class)">Persistor</a></span></h3>
130
+ <p class="inherited"><span class='object_link'><a href="../../../Persistor.html#%5B%5D-instance_method" title="Lims::Core::Persistence::Persistor#[] (method)">#[]</a></span>, <span class='object_link'><a href="../../../Persistor.html#bind_state_to_id-instance_method" title="Lims::Core::Persistence::Persistor#bind_state_to_id (method)">#bind_state_to_id</a></span>, <span class='object_link'><a href="../../../Persistor.html#bind_state_to_resource-instance_method" title="Lims::Core::Persistence::Persistor#bind_state_to_resource (method)">#bind_state_to_resource</a></span>, <span class='object_link'><a href="../../../Persistor.html#bulk_delete-instance_method" title="Lims::Core::Persistence::Persistor#bulk_delete (method)">#bulk_delete</a></span>, <span class='object_link'><a href="../../../Persistor.html#bulk_delete_raw-instance_method" title="Lims::Core::Persistence::Persistor#bulk_delete_raw (method)">#bulk_delete_raw</a></span>, <span class='object_link'><a href="../../../Persistor.html#bulk_insert-instance_method" title="Lims::Core::Persistence::Persistor#bulk_insert (method)">#bulk_insert</a></span>, <span class='object_link'><a href="../../../Persistor.html#bulk_retrieve-instance_method" title="Lims::Core::Persistence::Persistor#bulk_retrieve (method)">#bulk_retrieve</a></span>, <span class='object_link'><a href="../../../Persistor.html#bulk_update-instance_method" title="Lims::Core::Persistence::Persistor#bulk_update (method)">#bulk_update</a></span>, <span class='object_link'><a href="../../../Persistor.html#children-instance_method" title="Lims::Core::Persistence::Persistor#children (method)">#children</a></span>, <span class='object_link'><a href="../../../Persistor.html#count-instance_method" title="Lims::Core::Persistence::Persistor#count (method)">#count</a></span>, <span class='object_link'><a href="../../../Persistor.html#deletable_children-instance_method" title="Lims::Core::Persistence::Persistor#deletable_children (method)">#deletable_children</a></span>, <span class='object_link'><a href="../../../Persistor.html#deletable_parents-instance_method" title="Lims::Core::Persistence::Persistor#deletable_parents (method)">#deletable_parents</a></span>, <span class='object_link'><a href="../../../Persistor.html#dirty_key_for-instance_method" title="Lims::Core::Persistence::Persistor#dirty_key_for (method)">#dirty_key_for</a></span>, <span class='object_link'><a href="../../../Persistor.html#for_each_in_slice-instance_method" title="Lims::Core::Persistence::Persistor#for_each_in_slice (method)">#for_each_in_slice</a></span>, <span class='object_link'><a href="../../../Persistor.html#id_for-instance_method" title="Lims::Core::Persistence::Persistor#id_for (method)">#id_for</a></span>, <span class='object_link'><a href="../../../Persistor.html#ids_for-instance_method" title="Lims::Core::Persistence::Persistor#ids_for (method)">#ids_for</a></span>, <span class='object_link'><a href="../../../Persistor.html#inherited-class_method" title="Lims::Core::Persistence::Persistor.inherited (method)">inherited</a></span>, <span class='object_link'><a href="../../../Persistor.html#initialize-instance_method" title="Lims::Core::Persistence::Persistor#initialize (method)">#initialize</a></span>, <span class='object_link'><a href="../../../Persistor.html#invalid_resource%3F-instance_method" title="Lims::Core::Persistence::Persistor#invalid_resource? (method)">#invalid_resource?</a></span>, <span class='object_link'><a href="../../../Persistor.html#load_children-instance_method" title="Lims::Core::Persistence::Persistor#load_children (method)">#load_children</a></span>, <span class='object_link'><a href="../../../Persistor.html#model-instance_method" title="Lims::Core::Persistence::Persistor#model (method)">#model</a></span>, <span class='object_link'><a href="../../../Persistor.html#new_from_attributes-instance_method" title="Lims::Core::Persistence::Persistor#new_from_attributes (method)">#new_from_attributes</a></span>, <span class='object_link'><a href="../../../Persistor.html#new_object-instance_method" title="Lims::Core::Persistence::Persistor#new_object (method)">#new_object</a></span>, <span class='object_link'><a href="../../../Persistor.html#object_for-instance_method" title="Lims::Core::Persistence::Persistor#object_for (method)">#object_for</a></span>, <span class='object_link'><a href="../../../Persistor.html#on_object_load-instance_method" title="Lims::Core::Persistence::Persistor#on_object_load (method)">#on_object_load</a></span>, <span class='object_link'><a href="../../../Persistor.html#parents-instance_method" title="Lims::Core::Persistence::Persistor#parents (method)">#parents</a></span>, <span class='object_link'><a href="../../../Persistor.html#parents_for_attributes-instance_method" title="Lims::Core::Persistence::Persistor#parents_for_attributes (method)">#parents_for_attributes</a></span>, <span class='object_link'><a href="../../../Persistor.html#purge_invalid_object-instance_method" title="Lims::Core::Persistence::Persistor#purge_invalid_object (method)">#purge_invalid_object</a></span>, <span class='object_link'><a href="../../../Persistor.html#register_model-class_method" title="Lims::Core::Persistence::Persistor.register_model (method)">register_model</a></span>, <span class='object_link'><a href="../../../Persistor.html#retrieve-instance_method" title="Lims::Core::Persistence::Persistor#retrieve (method)">#retrieve</a></span>, <span class='object_link'><a href="../../../Persistor.html#slice-instance_method" title="Lims::Core::Persistence::Persistor#slice (method)">#slice</a></span>, <span class='object_link'><a href="../../../Persistor.html#state_for-instance_method" title="Lims::Core::Persistence::Persistor#state_for (method)">#state_for</a></span>, <span class='object_link'><a href="../../../Persistor.html#state_for_id-instance_method" title="Lims::Core::Persistence::Persistor#state_for_id (method)">#state_for_id</a></span></p>
131
+ <div id="constructor_details" class="method_details_list">
132
+ <h2>Constructor Details</h2>
133
+
134
+ <p class="notice">This class inherits a constructor from <span class='object_link'><a href="../../../Persistor.html#initialize-instance_method" title="Lims::Core::Persistence::Persistor#initialize (method)">Lims::Core::Persistence::Persistor</a></span></p>
135
+
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+ </div>
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+
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+
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+ </div>
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+
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+
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+ </body>
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+ </html>
data/doc/Lims/Core/Persistence/Sequel/Migrations.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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+ <head>
5
+ <meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
6
+ <title>
7
+ Module: Lims::Core::Persistence::Sequel::Migrations
8
+
9
+ &mdash; Documentation by YARD 0.7.3
10
+
11
+ </title>
12
+
13
+ <link rel="stylesheet" href="../../../../css/style.css" type="text/css" media="screen" charset="utf-8" />
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+
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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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+ </head>
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+ <body>
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+ <script type="text/javascript" charset="utf-8">
30
+ 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 (M)</a> &raquo;
37
+ <span class='title'><span class='object_link'><a href="../../../../Lims.html" title="Lims (module)">Lims</a></span></span> &raquo; <span class='title'><span class='object_link'><a href="../../../Core.html" title="Lims::Core (module)">Core</a></span></span> &raquo; <span class='title'><span class='object_link'><a href="../../Persistence.html" title="Lims::Core::Persistence (module)">Persistence</a></span></span> &raquo; <span class='title'><span class='object_link'><a href="../Sequel.html" title="Lims::Core::Persistence::Sequel (module)">Sequel</a></span></span>
38
+ &raquo;
39
+ <span class="title">Migrations</span>
40
+
41
+
42
+ <div class="noframes"><span class="title">(</span><a href="." target="_top">no frames</a><span class="title">)</span></div>
43
+ </div>
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+
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+ <div id="search">
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+
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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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+
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+ </div>
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+ <div class="clear"></div>
55
+ </div>
56
+
57
+ <iframe id="search_frame"></iframe>
58
+
59
+ <div id="content"><h1>Module: Lims::Core::Persistence::Sequel::Migrations
60
+
61
+
62
+
63
+ </h1>
64
+
65
+ <dl class="box">
66
+
67
+
68
+
69
+
70
+
71
+
72
+
73
+
74
+ <dt class="r1 last">Defined in:</dt>
75
+ <dd class="r1 last">lib/lims-core/persistence/sequel/migrations/initial.rb<span class="defines">,<br />
76
+ lib/lims-core/persistence/sequel/migrations.rb</span>
77
+ </dd>
78
+
79
+ </dl>
80
+ <div class="clear"></div>
81
+
82
+ <h2>Overview</h2><div class="docstring">
83
+ <div class="discussion">
84
+
85
+ <p>This module should not be require on it's own. Require migrations instead.</p>
86
+
87
+
88
+ </div>
89
+ </div>
90
+ <div class="tags">
91
+
92
+
93
+ </div>
94
+ <h2>Constant Summary</h2>
95
+
96
+ <dl class="constants">
97
+
98
+ <dt id="Initial-constant" class="">Initial =
99
+
100
+ </dt>
101
+ <dd><pre class="code"><span class='const'>Proc</span><span class='period'>.</span><span class='id new'>new</span> <span class='kw'>do</span>
102
+ <span class='id change'>change</span> <span class='kw'>do</span>
103
+ <span class='id create_table'>create_table</span> <span class='symbol'>:samples</span> <span class='kw'>do</span>
104
+ <span class='id primary_key'>primary_key</span> <span class='symbol'>:id</span>
105
+ <span class='const'>String</span> <span class='symbol'>:name</span>
106
+ <span class='kw'>end</span>
107
+
108
+ <span class='id create_table'>create_table</span> <span class='symbol'>:oligos</span> <span class='kw'>do</span>
109
+ <span class='id primary_key'>primary_key</span> <span class='symbol'>:id</span>
110
+ <span class='const'>String</span> <span class='symbol'>:sequence</span>
111
+ <span class='kw'>end</span>
112
+
113
+ <span class='id create_table'>create_table</span> <span class='symbol'>:aliquots</span> <span class='kw'>do</span>
114
+ <span class='id primary_key'>primary_key</span> <span class='symbol'>:id</span>
115
+ <span class='id foreign_key'>foreign_key</span> <span class='symbol'>:sample_id</span><span class='comma'>,</span> <span class='symbol'>:samples</span><span class='comma'>,</span> <span class='symbol'>:key</span> <span class='op'>=&gt;</span> <span class='symbol'>:id</span>
116
+ <span class='id foreign_key'>foreign_key</span> <span class='symbol'>:tag_id</span><span class='comma'>,</span> <span class='symbol'>:oligos</span><span class='comma'>,</span> <span class='symbol'>:key</span> <span class='op'>=&gt;</span> <span class='symbol'>:id</span>
117
+ <span class='const'>Integer</span> <span class='symbol'>:quantity</span>
118
+ <span class='const'>String</span> <span class='symbol'>:type</span>
119
+ <span class='kw'>end</span>
120
+
121
+ <span class='id create_table'>create_table</span> <span class='symbol'>:flowcells</span> <span class='kw'>do</span>
122
+ <span class='id primary_key'>primary_key</span> <span class='symbol'>:id</span>
123
+ <span class='const'>Integer</span> <span class='symbol'>:number_of_lanes</span>
124
+ <span class='kw'>end</span>
125
+
126
+ <span class='id create_table'>create_table</span> <span class='symbol'>:lanes</span> <span class='kw'>do</span>
127
+ <span class='comment'>#primary_key :flowcell_id, :position
128
+ </span> <span class='id primary_key'>primary_key</span> <span class='symbol'>:id</span>
129
+ <span class='id foreign_key'>foreign_key</span> <span class='symbol'>:flowcell_id</span><span class='comma'>,</span> <span class='symbol'>:flowcells</span><span class='comma'>,</span> <span class='symbol'>:key</span> <span class='op'>=&gt;</span> <span class='symbol'>:id</span>
130
+ <span class='const'>Integer</span> <span class='symbol'>:position</span>
131
+ <span class='id foreign_key'>foreign_key</span> <span class='symbol'>:aliquot_id</span><span class='comma'>,</span> <span class='symbol'>:aliquots</span><span class='comma'>,</span> <span class='symbol'>:key</span> <span class='op'>=&gt;</span> <span class='symbol'>:id</span>
132
+ <span class='kw'>end</span>
133
+
134
+ <span class='id create_table'>create_table</span> <span class='symbol'>:tubes</span> <span class='kw'>do</span>
135
+ <span class='id primary_key'>primary_key</span> <span class='symbol'>:id</span>
136
+ <span class='kw'>end</span>
137
+
138
+ <span class='id create_table'>create_table</span> <span class='symbol'>:tube_aliquots</span> <span class='kw'>do</span>
139
+ <span class='id primary_key'>primary_key</span> <span class='symbol'>:id</span>
140
+ <span class='const'>Integer</span> <span class='symbol'>:tube_id</span>
141
+ <span class='id foreign_key'>foreign_key</span> <span class='symbol'>:aliquot_id</span><span class='comma'>,</span> <span class='symbol'>:aliquots</span><span class='comma'>,</span> <span class='symbol'>:key</span> <span class='op'>=&gt;</span> <span class='symbol'>:id</span>
142
+ <span class='kw'>end</span>
143
+
144
+ <span class='id create_table'>create_table</span> <span class='symbol'>:spin_columns</span> <span class='kw'>do</span>
145
+ <span class='id primary_key'>primary_key</span> <span class='symbol'>:id</span>
146
+ <span class='kw'>end</span>
147
+
148
+ <span class='id create_table'>create_table</span> <span class='symbol'>:spin_column_aliquots</span> <span class='kw'>do</span>
149
+ <span class='id primary_key'>primary_key</span> <span class='symbol'>:id</span>
150
+ <span class='const'>Integer</span> <span class='symbol'>:spin_column_id</span>
151
+ <span class='id foreign_key'>foreign_key</span> <span class='symbol'>:aliquot_id</span><span class='comma'>,</span> <span class='symbol'>:aliquots</span><span class='comma'>,</span> <span class='symbol'>:key</span> <span class='op'>=&gt;</span> <span class='symbol'>:id</span>
152
+ <span class='kw'>end</span>
153
+
154
+ <span class='id create_table'>create_table</span> <span class='symbol'>:plates</span> <span class='kw'>do</span>
155
+ <span class='id primary_key'>primary_key</span> <span class='symbol'>:id</span>
156
+ <span class='const'>Integer</span> <span class='symbol'>:number_of_rows</span>
157
+ <span class='const'>Integer</span> <span class='symbol'>:number_of_columns</span>
158
+ <span class='kw'>end</span>
159
+
160
+ <span class='id create_table'>create_table</span> <span class='symbol'>:wells</span> <span class='kw'>do</span>
161
+ <span class='id primary_key'>primary_key</span> <span class='symbol'>:id</span>
162
+ <span class='id foreign_key'>foreign_key</span> <span class='symbol'>:plate_id</span><span class='comma'>,</span> <span class='symbol'>:plates</span><span class='comma'>,</span> <span class='symbol'>:key</span> <span class='op'>=&gt;</span> <span class='symbol'>:id</span>
163
+ <span class='const'>Integer</span> <span class='symbol'>:position</span>
164
+ <span class='id foreign_key'>foreign_key</span> <span class='symbol'>:aliquot_id</span><span class='comma'>,</span> <span class='symbol'>:aliquots</span><span class='comma'>,</span> <span class='symbol'>:key</span> <span class='op'>=&gt;</span> <span class='symbol'>:id</span>
165
+ <span class='kw'>end</span>
166
+
167
+ <span class='id create_table'>create_table</span> <span class='symbol'>:tube_racks</span> <span class='kw'>do</span>
168
+ <span class='id primary_key'>primary_key</span> <span class='symbol'>:id</span>
169
+ <span class='const'>Integer</span> <span class='symbol'>:number_of_rows</span>
170
+ <span class='const'>Integer</span> <span class='symbol'>:number_of_columns</span>
171
+ <span class='kw'>end</span>
172
+
173
+ <span class='id create_table'>create_table</span> <span class='symbol'>:tube_rack_slots</span> <span class='kw'>do</span>
174
+ <span class='id primary_key'>primary_key</span> <span class='symbol'>:id</span>
175
+ <span class='id foreign_key'>foreign_key</span> <span class='symbol'>:tube_rack_id</span><span class='comma'>,</span> <span class='symbol'>:tube_racks</span><span class='comma'>,</span> <span class='symbol'>:key</span> <span class='op'>=&gt;</span> <span class='symbol'>:id</span>
176
+ <span class='const'>Integer</span> <span class='symbol'>:position</span>
177
+ <span class='id foreign_key'>foreign_key</span> <span class='symbol'>:tube_id</span><span class='comma'>,</span> <span class='symbol'>:tubes</span><span class='comma'>,</span> <span class='symbol'>:key</span><span class='op'>=&gt;</span> <span class='symbol'>:id</span>
178
+ <span class='kw'>end</span>
179
+
180
+ <span class='id create_table'>create_table</span> <span class='symbol'>:tag_groups</span> <span class='kw'>do</span>
181
+ <span class='id primary_key'>primary_key</span> <span class='symbol'>:id</span>
182
+ <span class='const'>String</span> <span class='symbol'>:name</span>
183
+ <span class='kw'>end</span>
184
+
185
+ <span class='id create_table'>create_table</span> <span class='symbol'>:tag_group_associations</span> <span class='kw'>do</span>
186
+ <span class='id primary_key'>primary_key</span> <span class='symbol'>:id</span>
187
+ <span class='id foreign_key'>foreign_key</span> <span class='symbol'>:tag_group_id</span><span class='comma'>,</span> <span class='symbol'>:tag_groups</span><span class='comma'>,</span> <span class='symbol'>:key</span> <span class='op'>=&gt;</span> <span class='symbol'>:id</span>
188
+ <span class='const'>Integer</span> <span class='symbol'>:position</span>
189
+ <span class='id foreign_key'>foreign_key</span> <span class='symbol'>:oligo_id</span><span class='comma'>,</span> <span class='symbol'>:oligos</span><span class='comma'>,</span> <span class='symbol'>:key</span> <span class='op'>=&gt;</span> <span class='symbol'>:id</span>
190
+ <span class='kw'>end</span>
191
+
192
+ <span class='id create_table'>create_table</span> <span class='symbol'>:uuid_resources</span> <span class='kw'>do</span>
193
+ <span class='id primary_key'>primary_key</span> <span class='symbol'>:id</span>
194
+ <span class='const'>String</span> <span class='symbol'>:uuid</span><span class='comma'>,</span> <span class='symbol'>:fixed</span> <span class='op'>=&gt;</span> <span class='kw'>true</span><span class='comma'>,</span> <span class='symbol'>:size</span> <span class='op'>=&gt;</span> <span class='int'>64</span>
195
+ <span class='const'>String</span> <span class='symbol'>:model_class</span>
196
+ <span class='const'>Integer</span> <span class='symbol'>:key</span>
197
+ <span class='kw'>end</span>
198
+
199
+ <span class='id create_table'>create_table</span> <span class='symbol'>:users</span> <span class='kw'>do</span>
200
+ <span class='id primary_key'>primary_key</span> <span class='symbol'>:id</span>
201
+ <span class='kw'>end</span>
202
+
203
+ <span class='id create_table'>create_table</span> <span class='symbol'>:studies</span> <span class='kw'>do</span>
204
+ <span class='id primary_key'>primary_key</span> <span class='symbol'>:id</span>
205
+ <span class='kw'>end</span>
206
+
207
+ <span class='id create_table'>create_table</span> <span class='symbol'>:orders</span> <span class='kw'>do</span>
208
+ <span class='id primary_key'>primary_key</span> <span class='symbol'>:id</span>
209
+ <span class='id foreign_key'>foreign_key</span> <span class='symbol'>:creator_id</span><span class='comma'>,</span> <span class='symbol'>:users</span><span class='comma'>,</span> <span class='symbol'>:key</span> <span class='op'>=&gt;</span> <span class='symbol'>:id</span>
210
+
211
+ <span class='const'>String</span> <span class='symbol'>:pipeline</span>
212
+ <span class='const'>String</span> <span class='symbol'>:parameters</span>
213
+ <span class='const'>String</span> <span class='symbol'>:status</span>
214
+ <span class='id blob'>blob</span> <span class='symbol'>:state</span>
215
+ <span class='id foreign_key'>foreign_key</span> <span class='symbol'>:study_id</span><span class='comma'>,</span> <span class='symbol'>:studies</span><span class='comma'>,</span> <span class='symbol'>:key</span> <span class='op'>=&gt;</span> <span class='symbol'>:id</span>
216
+ <span class='const'>String</span> <span class='symbol'>:cost_code</span>
217
+ <span class='kw'>end</span>
218
+
219
+ <span class='id create_table'>create_table</span> <span class='symbol'>:items</span> <span class='kw'>do</span>
220
+ <span class='id primary_key'>primary_key</span> <span class='symbol'>:id</span>
221
+ <span class='id foreign_key'>foreign_key</span> <span class='symbol'>:order_id</span><span class='comma'>,</span> <span class='symbol'>:orders</span><span class='comma'>,</span> <span class='symbol'>:key</span> <span class='op'>=&gt;</span> <span class='symbol'>:id</span>
222
+ <span class='const'>String</span> <span class='symbol'>:role</span>
223
+ <span class='id foreign_key'>foreign_key</span> <span class='symbol'>:resource_id</span><span class='comma'>,</span> <span class='symbol'>:uuid_resources</span><span class='comma'>,</span> <span class='symbol'>:key</span> <span class='op'>=&gt;</span> <span class='symbol'>:id</span>
224
+ <span class='const'>String</span> <span class='symbol'>:uuid</span><span class='comma'>,</span> <span class='symbol'>:fixed</span> <span class='op'>=&gt;</span> <span class='kw'>true</span><span class='comma'>,</span> <span class='symbol'>:size</span> <span class='op'>=&gt;</span> <span class='int'>64</span>
225
+ <span class='const'>String</span> <span class='symbol'>:status</span>
226
+ <span class='const'>Integer</span> <span class='symbol'>:iteration</span><span class='comma'>,</span> <span class='symbol'>:default</span> <span class='op'>=&gt;</span> <span class='int'>0</span>
227
+ <span class='kw'>end</span>
228
+
229
+ <span class='id create_table'>create_table</span> <span class='symbol'>:searches</span> <span class='kw'>do</span>
230
+ <span class='id primary_key'>primary_key</span> <span class='symbol'>:id</span>
231
+ <span class='const'>String</span> <span class='symbol'>:description</span>
232
+ <span class='const'>String</span> <span class='symbol'>:filter_type</span>
233
+ <span class='const'>String</span> <span class='symbol'>:model</span>
234
+ <span class='id blob'>blob</span> <span class='symbol'>:filter_parameters</span>
235
+ <span class='kw'>end</span>
236
+
237
+ <span class='id create_table'>create_table</span> <span class='symbol'>:labellables</span> <span class='kw'>do</span>
238
+ <span class='id primary_key'>primary_key</span> <span class='symbol'>:id</span>
239
+ <span class='const'>String</span> <span class='symbol'>:name</span>
240
+ <span class='const'>String</span> <span class='symbol'>:type</span>
241
+ <span class='kw'>end</span>
242
+
243
+ <span class='id create_table'>create_table</span> <span class='symbol'>:labels</span> <span class='kw'>do</span>
244
+ <span class='id primary_key'>primary_key</span> <span class='symbol'>:id</span>
245
+ <span class='id foreign_key'>foreign_key</span> <span class='symbol'>:labellable_id</span><span class='comma'>,</span> <span class='symbol'>:labellables</span><span class='comma'>,</span> <span class='symbol'>:key</span> <span class='op'>=&gt;</span> <span class='symbol'>:id</span>
246
+ <span class='const'>String</span> <span class='symbol'>:type</span>
247
+ <span class='const'>String</span> <span class='symbol'>:position</span>
248
+ <span class='const'>String</span> <span class='symbol'>:value</span>
249
+ <span class='kw'>end</span>
250
+ <span class='kw'>end</span>
251
+ <span class='kw'>end</span></pre></dd>
252
+
253
+ </dl>
254
+
255
+
256
+
257
+
258
+
259
+
260
+
261
+
262
+ </div>
263
+
264
+
265
+ </body>
266
+ </html>