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/class_list.html ADDED
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+ <div id="search">Search: <input type="text" /></div>
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+ <ul id="full_list" class="class">
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+ <li><span class='object_link'><a href="top-level-namespace.html" title=" (root)">Top Level Namespace</a></span></li>
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+ <li><a class='toggle'></a> <span class='object_link'><a href="Array.html" title="Array (class)">Array</a></span> &lt; Object<small class='search_info'>Top Level Namespace</small></li><ul><li><span class='object_link'><a href="Array/ArrayLoggerPersistor.html" title="Array::ArrayLoggerPersistor (class)">ArrayLoggerPersistor</a></span> &lt; Persistor<small class='search_info'>Array</small></li></ul><li><a class='toggle'></a> <span class='object_link'><a href="Lims.html" title="Lims (module)">Lims</a></span><small class='search_info'>Top Level Namespace</small></li><ul><li><a class='toggle'></a> <span class='object_link'><a href="Lims/Core.html" title="Lims::Core (module)">Core</a></span><small class='search_info'>Lims</small></li><ul><li><a class='toggle'></a> <span class='object_link'><a href="Lims/Core/Actions.html" title="Lims::Core::Actions (module)">Actions</a></span><small class='search_info'>Lims::Core</small></li><ul><li><a class='toggle'></a> <span class='object_link'><a href="Lims/Core/Actions/Action.html" title="Lims::Core::Actions::Action (module)">Action</a></span><small class='search_info'>Lims::Core::Actions</small></li><ul><li><span class='object_link'><a href="Lims/Core/Actions/Action/AfterEval.html" title="Lims::Core::Actions::Action::AfterEval (module)">AfterEval</a></span><small class='search_info'>Lims::Core::Actions::Action</small></li><li><span class='object_link'><a href="Lims/Core/Actions/Action/InvalidParameters.html" title="Lims::Core::Actions::Action::InvalidParameters (class)">InvalidParameters</a></span> &lt; RuntimeError<small class='search_info'>Lims::Core::Actions::Action</small></li></ul><li><a class='toggle'></a> <span class='object_link'><a href="Lims/Core/Actions/ActionGroup.html" title="Lims::Core::Actions::ActionGroup (module)">ActionGroup</a></span><small class='search_info'>Lims::Core::Actions</small></li><ul><li><span class='object_link'><a href="Lims/Core/Actions/ActionGroup/AfterEval.html" title="Lims::Core::Actions::ActionGroup::AfterEval (module)">AfterEval</a></span><small class='search_info'>Lims::Core::Actions::ActionGroup</small></li></ul><li><a class='toggle'></a> <span class='object_link'><a href="Lims/Core/Actions/BulkAction.html" title="Lims::Core::Actions::BulkAction (module)">BulkAction</a></span><small class='search_info'>Lims::Core::Actions</small></li><ul><li><span class='object_link'><a href="Lims/Core/Actions/BulkAction/AfterEval.html" title="Lims::Core::Actions::BulkAction::AfterEval (module)">AfterEval</a></span><small class='search_info'>Lims::Core::Actions::BulkAction</small></li></ul><li><a class='toggle'></a> <span class='object_link'><a href="Lims/Core/Actions/TestActionGroup.html" title="Lims::Core::Actions::TestActionGroup (module)">TestActionGroup</a></span><small class='search_info'>Lims::Core::Actions</small></li><ul><li><span class='object_link'><a href="Lims/Core/Actions/TestActionGroup/Action.html" title="Lims::Core::Actions::TestActionGroup::Action (class)">Action</a></span> &lt; Object<small class='search_info'>Lims::Core::Actions::TestActionGroup</small></li><li><span class='object_link'><a href="Lims/Core/Actions/TestActionGroup/ActionGroup.html" title="Lims::Core::Actions::TestActionGroup::ActionGroup (class)">ActionGroup</a></span> &lt; Object<small class='search_info'>Lims::Core::Actions::TestActionGroup</small></li></ul></ul><li><a class='toggle'></a> <span class='object_link'><a href="Lims/Core/Base.html" title="Lims::Core::Base (module)">Base</a></span><small class='search_info'>Lims::Core</small></li><ul><li><span class='object_link'><a href="Lims/Core/Base/AccessibleViaSuper.html" title="Lims::Core::Base::AccessibleViaSuper (module)">AccessibleViaSuper</a></span><small class='search_info'>Lims::Core::Base</small></li><li><span class='object_link'><a href="Lims/Core/Base/ClassMethod.html" title="Lims::Core::Base::ClassMethod (module)">ClassMethod</a></span><small class='search_info'>Lims::Core::Base</small></li><li><span class='object_link'><a href="Lims/Core/Base/HashString.html" title="Lims::Core::Base::HashString (class)">HashString</a></span> &lt; Object<small class='search_info'>Lims::Core::Base</small></li><li><span class='object_link'><a href="Lims/Core/Base/IsArrayOf.html" title="Lims::Core::Base::IsArrayOf (module)">IsArrayOf</a></span><small class='search_info'>Lims::Core::Base</small></li><li><span class='object_link'><a href="Lims/Core/Base/State.html" title="Lims::Core::Base::State (class)">State</a></span> &lt; Object<small class='search_info'>Lims::Core::Base</small></li></ul><li><a class='toggle'></a> <span class='object_link'><a href="Lims/Core/Persistence.html" title="Lims::Core::Persistence (module)">Persistence</a></span><small class='search_info'>Lims::Core</small></li><ul><li><span class='object_link'><a href="Lims/Core/Persistence/ComparisonFilter.html" title="Lims::Core::Persistence::ComparisonFilter (class)">ComparisonFilter</a></span> &lt; Filter<small class='search_info'>Lims::Core::Persistence</small></li><li><span class='object_link'><a href="Lims/Core/Persistence/Filter.html" title="Lims::Core::Persistence::Filter (class)">Filter</a></span> &lt; Object<small class='search_info'>Lims::Core::Persistence</small></li><li><a class='toggle'></a> <span class='object_link'><a href="Lims/Core/Persistence/IdentityMap.html" title="Lims::Core::Persistence::IdentityMap (module)">IdentityMap</a></span><small class='search_info'>Lims::Core::Persistence</small></li><ul><li><span class='object_link'><a href="Lims/Core/Persistence/IdentityMap/Class.html" title="Lims::Core::Persistence::IdentityMap::Class (class)">Class</a></span> &lt; Object<small class='search_info'>Lims::Core::Persistence::IdentityMap</small></li><li><span class='object_link'><a href="Lims/Core/Persistence/IdentityMap/DuplicateError.html" title="Lims::Core::Persistence::IdentityMap::DuplicateError (class)">DuplicateError</a></span> &lt; RuntimeError<small class='search_info'>Lims::Core::Persistence::IdentityMap</small></li><li><span class='object_link'><a href="Lims/Core/Persistence/IdentityMap/DuplicateIdError.html" title="Lims::Core::Persistence::IdentityMap::DuplicateIdError (class)">DuplicateIdError</a></span> &lt; DuplicateError<small class='search_info'>Lims::Core::Persistence::IdentityMap</small></li><li><span class='object_link'><a href="Lims/Core/Persistence/IdentityMap/DuplicateObjectError.html" title="Lims::Core::Persistence::IdentityMap::DuplicateObjectError (class)">DuplicateObjectError</a></span> &lt; DuplicateError<small class='search_info'>Lims::Core::Persistence::IdentityMap</small></li></ul><li><span class='object_link'><a href="Lims/Core/Persistence/IdentityMapClass.html" title="Lims::Core::Persistence::IdentityMapClass (class)">IdentityMapClass</a></span> &lt; Object<small class='search_info'>Lims::Core::Persistence</small></li><li><a class='toggle'></a> <span class='object_link'><a href="Lims/Core/Persistence/Logger.html" title="Lims::Core::Persistence::Logger (module)">Logger</a></span><small class='search_info'>Lims::Core::Persistence</small></li><ul><li><span class='object_link'><a href="Lims/Core/Persistence/Logger/Persistor.html" title="Lims::Core::Persistence::Logger::Persistor (module)">Persistor</a></span><small class='search_info'>Lims::Core::Persistence::Logger</small></li><li><span class='object_link'><a href="Lims/Core/Persistence/Logger/Session.html" title="Lims::Core::Persistence::Logger::Session (class)">Session</a></span> &lt; Session<small class='search_info'>Lims::Core::Persistence::Logger</small></li><li><span class='object_link'><a href="Lims/Core/Persistence/Logger/Store.html" title="Lims::Core::Persistence::Logger::Store (class)">Store</a></span> &lt; Store<small class='search_info'>Lims::Core::Persistence::Logger</small></li></ul><li><a class='toggle'></a> <span class='object_link'><a href="Lims/Core/Persistence/MessageBus.html" title="Lims::Core::Persistence::MessageBus (class)">MessageBus</a></span> &lt; Object<small class='search_info'>Lims::Core::Persistence</small></li><ul><li><span class='object_link'><a href="Lims/Core/Persistence/MessageBus/ConnectionError.html" title="Lims::Core::Persistence::MessageBus::ConnectionError (class)">ConnectionError</a></span> &lt; StandardError<small class='search_info'>Lims::Core::Persistence::MessageBus</small></li><li><span class='object_link'><a href="Lims/Core/Persistence/MessageBus/InvalidSettingsError.html" title="Lims::Core::Persistence::MessageBus::InvalidSettingsError (class)">InvalidSettingsError</a></span> &lt; StandardError<small class='search_info'>Lims::Core::Persistence::MessageBus</small></li></ul><li><span class='object_link'><a href="Lims/Core/Persistence/MultiCriteriaFilter.html" title="Lims::Core::Persistence::MultiCriteriaFilter (class)">MultiCriteriaFilter</a></span> &lt; Filter<small class='search_info'>Lims::Core::Persistence</small></li><li><span class='object_link'><a href="Lims/Core/Persistence/PersistAssociationTrait.html" title="Lims::Core::Persistence::PersistAssociationTrait (module)">PersistAssociationTrait</a></span><small class='search_info'>Lims::Core::Persistence</small></li><li><span class='object_link'><a href="Lims/Core/Persistence/PersistableTrait.html" title="Lims::Core::Persistence::PersistableTrait (module)">PersistableTrait</a></span><small class='search_info'>Lims::Core::Persistence</small></li><li><a class='toggle'></a> <span class='object_link'><a href="Lims/Core/Persistence/Persistor.html" title="Lims::Core::Persistence::Persistor (class)">Persistor</a></span> &lt; Object<small class='search_info'>Lims::Core::Persistence</small></li><ul><li><span class='object_link'><a href="Lims/Core/Persistence/Persistor/DuplicateError.html" title="Lims::Core::Persistence::Persistor::DuplicateError (class)">DuplicateError</a></span> &lt; RuntimeError<small class='search_info'>Lims::Core::Persistence::Persistor</small></li><li><span class='object_link'><a href="Lims/Core/Persistence/Persistor/DuplicateIdError.html" title="Lims::Core::Persistence::Persistor::DuplicateIdError (class)">DuplicateIdError</a></span> &lt; DuplicateError<small class='search_info'>Lims::Core::Persistence::Persistor</small></li><li><span class='object_link'><a href="Lims/Core/Persistence/Persistor/DuplicateObjectError.html" title="Lims::Core::Persistence::Persistor::DuplicateObjectError (class)">DuplicateObjectError</a></span> &lt; DuplicateError<small class='search_info'>Lims::Core::Persistence::Persistor</small></li></ul><li><span class='object_link'><a href="Lims/Core/Persistence/PersistorTrait.html" title="Lims::Core::Persistence::PersistorTrait (module)">PersistorTrait</a></span><small class='search_info'>Lims::Core::Persistence</small></li><li><span class='object_link'><a href="Lims/Core/Persistence/ResourceState.html" title="Lims::Core::Persistence::ResourceState (class)">ResourceState</a></span> &lt; Object<small class='search_info'>Lims::Core::Persistence</small></li><li><a class='toggle'></a> <span class='object_link'><a href="Lims/Core/Persistence/Search.html" title="Lims::Core::Persistence::Search (class)">Search</a></span> &lt; Object<small class='search_info'>Lims::Core::Persistence</small></li><ul><li><span class='object_link'><a href="Lims/Core/Persistence/Search/CreateSearch.html" title="Lims::Core::Persistence::Search::CreateSearch (class)">CreateSearch</a></span> &lt; Object<small class='search_info'>Lims::Core::Persistence::Search</small></li><li><span class='object_link'><a href="Lims/Core/Persistence/Search/SearchPersistor.html" title="Lims::Core::Persistence::Search::SearchPersistor (class)">SearchPersistor</a></span> &lt; Persistor<small class='search_info'>Lims::Core::Persistence::Search</small></li><li><span class='object_link'><a href="Lims/Core/Persistence/Search/SearchSequelPersistor.html" title="Lims::Core::Persistence::Search::SearchSequelPersistor (class)">SearchSequelPersistor</a></span> &lt; SearchPersistor<small class='search_info'>Lims::Core::Persistence::Search</small></li></ul><li><a class='toggle'></a> <span class='object_link'><a href="Lims/Core/Persistence/Sequel.html" title="Lims::Core::Persistence::Sequel (module)">Sequel</a></span><small class='search_info'>Lims::Core::Persistence</small></li><ul><li><span class='object_link'><a href="Lims/Core/Persistence/Sequel/Filters.html" title="Lims::Core::Persistence::Sequel::Filters (module)">Filters</a></span><small class='search_info'>Lims::Core::Persistence::Sequel</small></li><li><a class='toggle'></a> <span class='object_link'><a href="Lims/Core/Persistence/Sequel/ForTest.html" title="Lims::Core::Persistence::Sequel::ForTest (module)">ForTest</a></span><small class='search_info'>Lims::Core::Persistence::Sequel</small></li><ul><li><a class='toggle'></a> <span class='object_link'><a href="Lims/Core/Persistence/Sequel/ForTest/Name.html" title="Lims::Core::Persistence::Sequel::ForTest::Name (class)">Name</a></span> &lt; Object<small class='search_info'>Lims::Core::Persistence::Sequel::ForTest</small></li><ul><li><span class='object_link'><a href="Lims/Core/Persistence/Sequel/ForTest/Name/NamePersitor.html" title="Lims::Core::Persistence::Sequel::ForTest::Name::NamePersitor (class)">NamePersitor</a></span> &lt; Persistor<small class='search_info'>Lims::Core::Persistence::Sequel::ForTest::Name</small></li></ul></ul><li><span class='object_link'><a href="Lims/Core/Persistence/Sequel/Migrations.html" title="Lims::Core::Persistence::Sequel::Migrations (module)">Migrations</a></span><small class='search_info'>Lims::Core::Persistence::Sequel</small></li><li><span class='object_link'><a href="Lims/Core/Persistence/Sequel/Persistor.html" title="Lims::Core::Persistence::Sequel::Persistor (module)">Persistor</a></span><small class='search_info'>Lims::Core::Persistence::Sequel</small></li><li><span class='object_link'><a href="Lims/Core/Persistence/Sequel/Session.html" title="Lims::Core::Persistence::Sequel::Session (class)">Session</a></span> &lt; Session<small class='search_info'>Lims::Core::Persistence::Sequel</small></li><li><span class='object_link'><a href="Lims/Core/Persistence/Sequel/Store.html" title="Lims::Core::Persistence::Sequel::Store (class)">Store</a></span> &lt; Store<small class='search_info'>Lims::Core::Persistence::Sequel</small></li></ul><li><a class='toggle'></a> <span class='object_link'><a href="Lims/Core/Persistence/Session.html" title="Lims::Core::Persistence::Session (class)">Session</a></span> &lt; Object<small class='search_info'>Lims::Core::Persistence</small></li><ul><li><span class='object_link'><a href="Lims/Core/Persistence/Session/UnmanagedObjectError.html" title="Lims::Core::Persistence::Session::UnmanagedObjectError (class)">UnmanagedObjectError</a></span> &lt; RuntimeError<small class='search_info'>Lims::Core::Persistence::Session</small></li></ul><li><span class='object_link'><a href="Lims/Core/Persistence/StateGroup.html" title="Lims::Core::Persistence::StateGroup (class)">StateGroup</a></span> &lt; StateList<small class='search_info'>Lims::Core::Persistence</small></li><li><span class='object_link'><a href="Lims/Core/Persistence/StateList.html" title="Lims::Core::Persistence::StateList (class)">StateList</a></span> &lt; Set<small class='search_info'>Lims::Core::Persistence</small></li><li><span class='object_link'><a href="Lims/Core/Persistence/Store.html" title="Lims::Core::Persistence::Store (class)">Store</a></span> &lt; Object<small class='search_info'>Lims::Core::Persistence</small></li><li><a class='toggle'></a> <span class='object_link'><a href="Lims/Core/Persistence/UuidResource.html" title="Lims::Core::Persistence::UuidResource (class)">UuidResource</a></span> &lt; Object<small class='search_info'>Lims::Core::Persistence</small></li><ul><li><span class='object_link'><a href="Lims/Core/Persistence/UuidResource/InvalidUuidError.html" title="Lims::Core::Persistence::UuidResource::InvalidUuidError (class)">InvalidUuidError</a></span> &lt; RuntimeError<small class='search_info'>Lims::Core::Persistence::UuidResource</small></li><li><span class='object_link'><a href="Lims/Core/Persistence/UuidResource/UuidResourcePersistor.html" title="Lims::Core::Persistence::UuidResource::UuidResourcePersistor (class)">UuidResourcePersistor</a></span> &lt; Persistor<small class='search_info'>Lims::Core::Persistence::UuidResource</small></li></ul><li><span class='object_link'><a href="Lims/Core/Persistence/Uuidable.html" title="Lims::Core::Persistence::Uuidable (module)">Uuidable</a></span><small class='search_info'>Lims::Core::Persistence</small></li></ul><li><span class='object_link'><a href="Lims/Core/Persistor.html" title="Lims::Core::Persistor (class)">Persistor</a></span> &lt; Object<small class='search_info'>Lims::Core</small></li><li><span class='object_link'><a href="Lims/Core/Resource.html" title="Lims::Core::Resource (module)">Resource</a></span><small class='search_info'>Lims::Core</small></li></ul></ul><li><span class='object_link'><a href="Object.html" title="Object (class)">Object</a></span> &lt; BasicObject<small class='search_info'>Top Level Namespace</small></li><li><a class='toggle'></a> <span class='object_link'><a href="SessionSpec.html" title="SessionSpec (module)">SessionSpec</a></span><small class='search_info'>Top Level Namespace</small></li><ul><li><a class='toggle'></a> <span class='object_link'><a href="SessionSpec/Model.html" title="SessionSpec::Model (class)">Model</a></span> &lt; Object<small class='search_info'>SessionSpec</small></li><ul><li><span class='object_link'><a href="SessionSpec/Model/ModelPersistor.html" title="SessionSpec::Model::ModelPersistor (class)">ModelPersistor</a></span> &lt; Persistor<small class='search_info'>SessionSpec::Model</small></li></ul></ul>
43
+
44
+ </ul>
45
+ </div>
46
+ </body>
47
+ </html>
data/doc/css/common.css ADDED
@@ -0,0 +1 @@
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+ font-size: 13px;
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+ height: 101%;
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+ overflow-x: hidden;
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+ }
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+ h1 { padding: 12px 10px; padding-bottom: 0; margin: 0; font-size: 1.4em; }
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+ .clear { clear: both; }
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+ #full_list { padding: 0; list-style: none; margin-left: 0; }
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+ #full_list ul { padding: 0; }
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+ #full_list li { padding: 5px; padding-left: 12px; margin: 0; font-size: 1.1em; list-style: none; }
16
+ #noresults { padding: 7px 12px; }
17
+ #content.insearch #noresults { margin-left: 7px; }
18
+ ul.collapsed ul, ul.collapsed li { display: none; }
19
+ ul.collapsed.search_uncollapsed { display: block; }
20
+ ul.collapsed.search_uncollapsed li { display: list-item; }
21
+ li a.toggle { cursor: default; position: relative; left: -5px; top: 4px; text-indent: -999px; width: 10px; height: 9px; margin-left: -10px; display: block; float: left; background: url(data:image/png;base64,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) no-repeat bottom left; }
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+ li.collapsed a.toggle { opacity: 0.5; cursor: default; background-position: top left; }
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+ li { color: #888; cursor: pointer; }
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+ li.deprecated { text-decoration: line-through; font-style: italic; }
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+ li.r1 { background: #f0f0f0; }
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+ li.r2 { background: #fafafa; }
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+ li:hover { background: #ddd; }
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+ li small:before { content: "("; }
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+ li small:after { content: ")"; }
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+ li small.search_info { display: none; }
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+ a:link, a:visited { text-decoration: none; color: #05a; }
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+ li.clicked { background: #05a; color: #ccc; }
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+ li.clicked a:link, li.clicked a:visited { color: #eee; }
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+ li.clicked a.toggle { opacity: 0.5; background-position: bottom right; }
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+ li.collapsed.clicked a.toggle { background-position: top right; }
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+ #search input { border: 1px solid #bbb; -moz-border-radius: 3px; -webkit-border-radius: 3px; }
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+ #nav { margin-left: 10px; font-size: 0.9em; display: none; color: #aaa; }
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+ #nav a:link, #nav a:visited { color: #358; }
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+ #nav a:hover { background: transparent; color: #5af; }
40
+
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+ .frames #content h1 { margin-top: 0; }
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+ .frames li { white-space: nowrap; cursor: normal; }
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+ .frames li small { display: block; font-size: 0.8em; }
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+ .frames li small:before { content: ""; }
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+ .frames li small:after { content: ""; }
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+ .frames li small.search_info { display: none; }
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+ .frames #search { width: 170px; position: static; margin: 3px; margin-left: 10px; font-size: 0.9em; color: #888; padding-left: 0; padding-right: 24px; }
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+ .frames #content.insearch #search { background-position: center right; }
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+ .frames #search input { width: 110px; }
50
+ .frames #nav { display: block; }
51
+
52
+ #full_list.insearch li { display: none; }
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+ #full_list.insearch li.found { display: list-item; padding-left: 10px; }
54
+ #full_list.insearch li a.toggle { display: none; }
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+ #full_list.insearch li small.search_info { display: block; }
data/doc/css/style.css ADDED
@@ -0,0 +1,322 @@
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+ body {
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+ padding: 0 20px;
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+ font-family: "Lucida Sans", "Lucida Grande", Verdana, Arial, sans-serif;
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+ font-size: 13px;
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+ }
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+ body.frames { padding: 0 5px; }
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+ h1 { font-size: 25px; margin: 1em 0 0.5em; padding-top: 4px; border-top: 1px dotted #d5d5d5; }
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+ h1.noborder { border-top: 0px; margin-top: 0; padding-top: 4px; }
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+ h1.title { margin-bottom: 10px; }
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+ h1.alphaindex { margin-top: 0; font-size: 22px; }
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+ h2 {
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+ padding: 0;
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+ padding-bottom: 3px;
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+ border-bottom: 1px #aaa solid;
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+ font-size: 1.4em;
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+ margin: 1.8em 0 0.5em;
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+ }
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+ h2 small { font-weight: normal; font-size: 0.7em; display: block; float: right; }
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+ .clear { clear: both; }
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+ .inline { display: inline; }
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+ .inline p:first-child { display: inline; }
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+ .docstring h1, .docstring h2, .docstring h3, .docstring h4 { padding: 0; border: 0; border-bottom: 1px dotted #bbb; }
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+ .docstring h1 { font-size: 1.2em; }
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+ .docstring h2 { font-size: 1.1em; }
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+ .docstring h3, .docstring h4 { font-size: 1em; border-bottom: 0; padding-top: 10px; }
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+ .summary_desc .object_link, .docstring .object_link { font-family: monospace; }
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+ .rdoc-term { padding-right: 25px; font-weight: bold; }
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+ .rdoc-list p { margin: 0; padding: 0; margin-bottom: 4px; }
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+
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+ /* style for <ul> */
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+ #filecontents li > p, .docstring li > p { margin: 0px; }
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+ #filecontents ul, .docstring ul { padding-left: 20px; }
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+ /* style for <dl> */
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+ #filecontents dl, .docstring dl { border: 1px solid #ccc; }
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+ #filecontents dt, .docstring dt { background: #ddd; font-weight: bold; padding: 3px 5px; }
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+ #filecontents dd, .docstring dd { padding: 5px 0px; margin-left: 18px; }
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+ #filecontents dd > p, .docstring dd > p { margin: 0px; }
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+
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+ .note {
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+ color: #222;
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+ -moz-border-radius: 3px; -webkit-border-radius: 3px;
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+ background: #e3e4e3; border: 1px solid #d5d5d5; padding: 7px 10px;
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+ display: block;
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+ }
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+ .note.todo { background: #ffffc5; border-color: #ececaa; }
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+ .note.returns_void { background: #efefef; }
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+ .note.deprecated { background: #ffe5e5; border-color: #e9dada; }
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+ .note.private { background: #ffffc5; border-color: #ececaa; }
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+ .note.title { text-transform: lowercase; padding: 1px 5px; font-size: 0.9em; font-family: "Lucida Sans", "Lucida Grande", Verdana, Arial, sans-serif; display: inline; }
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+ .summary_signature + .note.title { margin-left: 7px; }
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+ h1 .note.title { font-size: 0.5em; font-weight: normal; padding: 3px 5px; position: relative; top: -3px; text-transform: capitalize; }
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+ .note.title.constructor { color: #fff; background: #6a98d6; border-color: #6689d6; }
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+ .note.title.writeonly { color: #fff; background: #45a638; border-color: #2da31d; }
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+ .note.title.readonly { color: #fff; background: #6a98d6; border-color: #6689d6; }
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+ .note.title.private { background: #d5d5d5; border-color: #c5c5c5; }
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+ .discussion .note { margin-top: 6px; }
57
+ .discussion .note:first-child { margin-top: 0; }
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+
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+ h3.inherited {
60
+ font-style: italic;
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+ font-family: "Lucida Sans", "Lucida Grande", Verdana, Arial, sans-serif;
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+ font-weight: normal;
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+ padding: 0;
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+ margin: 0;
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+ margin-top: 12px;
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+ margin-bottom: 3px;
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+ font-size: 13px;
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+ }
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+ p.inherited {
70
+ padding: 0;
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+ margin: 0;
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+ margin-left: 25px;
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+ }
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+
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+ #filecontents dl.box, dl.box {
76
+ border: 0;
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+ width: 520px;
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+ font-size: 1em;
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+ }
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+ #filecontents dl.box dt, dl.box dt {
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+ float: left;
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+ display: block;
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+ width: 100px;
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+ margin: 0;
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+ text-align: right;
86
+ font-weight: bold;
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+ background: transparent;
88
+ border: 1px solid #aaa;
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+ border-width: 1px 0px 0px 1px;
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+ padding: 6px 0;
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+ padding-right: 10px;
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+ <div id="menu">
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+
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+ <a href="_index.html" title="Index">Index</a> &raquo;
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+ <span class="title">File: README</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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+
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+ <a id="class_list_link" href="#">Class List</a>
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+
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+ <a id="method_list_link" href="#">Method List</a>
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+
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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>
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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"><div id='filecontents'><!-- vim: spell:spelllang=en tw=80
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+ Yard markup
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+ # @markup markdown
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+ # @title README
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+ -->
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+
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+
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+ <h1>Overview </h1>
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+
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+ <p>This gem implements the core functionalities of the LIMS (Laboratory Information Management System).
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+ It's not meant to be a stand alone application but the core library of the LIMS
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+ server.</p>
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+
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+ <p>For more information consult the documentation.</p>
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+
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+ <h1>Installation</h1>
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+
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+ <pre class="code"><span class='id gem'>gem</span> <span class='id install'>install</span> <span class='id lims'>lims</span><span class='op'>-</span><span class='id core'>core</span>
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+ </pre>
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+
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+ <p>Or, if you are using <a href="http://gembundler.com/">bundler</a> , add the following line</p>
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+
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+ <pre class="code"> <span class='id gem'>gem</span> <span class='symbol'>:lims</span><span class='op'>-</span><span class='id core'>core</span><span class='comma'>,</span> <span class='symbol'>:git</span> <span class='op'>=&gt;</span> <span class='tstring'><span class='tstring_beg'>&quot;</span><span class='tstring_end'>git+ssh://git@github.com/sanger/lims-core.git'
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+ </span></span></pre>
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+
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+ <p>in your <code>Gemfile</code>.</p>
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+
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+ <h1>Documentation</h1>
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+
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+ <p>The documentation is generated using <a href="http://yardoc.org/index.html">yard</a> and can
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+ be found under the <code>doc/</code> directory or using a <code>yard server</code></p>
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+
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+ <h1>Developers Guide</h1>
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+
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+ <h2>Gem requirements</h2>
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+
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+ <p>Ideally each should be loadable on its own. This mean that every file should
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+ require everything it needs. The exception is for gems re-opening ruby basic
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+ classes as facet do. The common requirements are grouped in the <code>lib/common.rb</code>
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+ file.</p>
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+
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+ <p>For the user convenience, requiring a directory should requires everything
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+ underneath. However, requiring <code>lims-core</code> will require <code>Persistence</code>, but not
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+ the subdirectories of it (specific to each different stores like <code>Sequel</code>, or
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+ <code>Logger</code>). This to not force to install all the dependencies specific to each
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+ store.</p>
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+
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+ <h2>Documentation Guide</h2>
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+
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+ <p>The documentation is written using <a href="http://yardoc.org/index.html">yard</a>.
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+ It allows to write documentation within the doc and add <em>typing</em> hints/
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+ expectations.
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+ The recommended format for stand alone documentation files is
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+ <a href="http://daringfireball.net/projects/markdown/">markdown</a>, however
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+ it's easier to keep the native markup language used by <strong>yard</strong>, i.e. the
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+ <a href="http://rdoc.sourceforge.net/">rdoc</a> one.
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+ This allows the code to be parsed via <strong>rdoc</strong> and doesn't need the extra spaces at
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+ the end of a line needed by <strong>markdown</strong>.</p>
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+
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+ <p>However, when the usage of pure <strong>markdown</strong> seems appropriate, it's still
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+ possible to the use <code>@markup</code> switch.</p>
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+
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+ <p>Some documentation can also be added in the specs.</p>
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+
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+ <h2>Tests</h2>
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+
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+ <p>We are using <a href="http://rspec.info/">rspec</a>.</p></div></div>
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+
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+
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+ </body>
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+ </html>