lims-core 3.2.3

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  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
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  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
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  45. data/doc/Lims/Core/Persistence/IdentityMap/DuplicateError.html +126 -0
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  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
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  63. data/doc/Lims/Core/Persistence/PersistorTrait.html +91 -0
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  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
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  81. data/doc/Lims/Core/Persistence/StateList.html +498 -0
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  83. data/doc/Lims/Core/Persistence/UuidResource.html +1044 -0
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  90. data/doc/SessionSpec.html +101 -0
  91. data/doc/SessionSpec/Model.html +279 -0
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  107. data/lib/common.rb +18 -0
  108. data/lib/lims-core.rb +29 -0
  109. data/lib/lims-core/actions.rb +10 -0
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  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
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  160. data/spec/actions/action_group_spec.rb +39 -0
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  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
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  170. data/spec/persistence/session_spec.rb +199 -0
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  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/Logger/Store.html ADDED
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+ <!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN"
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+ <head>
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+ <meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
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+ <title>
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+ Class: Lims::Core::Persistence::Logger::Store
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+
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+ &mdash; Documentation by YARD 0.7.3
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+ </title>
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+ <link rel="stylesheet" href="../../../../css/style.css" type="text/css" media="screen" charset="utf-8" />
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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="../../../../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="../Logger.html" title="Lims::Core::Persistence::Logger (module)">Logger</a></span></span>
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+ &raquo;
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+ <span class="title">Store</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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+ <div id="search">
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+ <a id="class_list_link" href="#">Class List</a>
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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"><h1>Class: Lims::Core::Persistence::Logger::Store
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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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+ <dt class="r1">Inherits:</dt>
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+ <dd class="r1">
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+ <span class="inheritName"><span class='object_link'><a href="../Store.html" title="Lims::Core::Persistence::Store (class)">Store</a></span></span>
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+
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+ <ul class="fullTree">
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+ <li><span class='object_link'><a href="../../../../Object.html" title="Object (class)">Object</a></span></li>
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+
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+ <li class="next"><span class='object_link'><a href="../Store.html" title="Lims::Core::Persistence::Store (class)">Store</a></span></li>
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+
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+ <li class="next">Lims::Core::Persistence::Logger::Store</li>
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+
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+ </ul>
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+ <a href="#" class="inheritanceTree">show all</a>
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+
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+ </dd>
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+ <dt class="r2 last">Defined in:</dt>
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+ <dd class="r2 last">lib/lims-core/persistence/logger/store.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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+
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+ <p>An Logger::Store, a store 'logging' object instead of saving them.</p>
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+ </div>
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+ </div>
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+ <div class="tags">
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+ <h2>Constant Summary</h2>
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+ <h3 class="inherited">Constants inherited from <span class='object_link'><a href="../Store.html" title="Lims::Core::Persistence::Store (class)">Store</a></span></h3>
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+ <p class="inherited"><span class='object_link'><a href="../Store.html#DIRTY_ATTRIBUTE_STRATEGY_DEEP_COPY-constant" title="Lims::Core::Persistence::Store::DIRTY_ATTRIBUTE_STRATEGY_DEEP_COPY (constant)">DIRTY_ATTRIBUTE_STRATEGY_DEEP_COPY</a></span>, <span class='object_link'><a href="../Store.html#DIRTY_ATTRIBUTE_STRATEGY_MD5-constant" title="Lims::Core::Persistence::Store::DIRTY_ATTRIBUTE_STRATEGY_MD5 (constant)">DIRTY_ATTRIBUTE_STRATEGY_MD5</a></span>, <span class='object_link'><a href="../Store.html#DIRTY_ATTRIBUTE_STRATEGY_QUICK_HASH-constant" title="Lims::Core::Persistence::Store::DIRTY_ATTRIBUTE_STRATEGY_QUICK_HASH (constant)">DIRTY_ATTRIBUTE_STRATEGY_QUICK_HASH</a></span>, <span class='object_link'><a href="../Store.html#DIRTY_ATTRIBUTE_STRATEGY_SHA1-constant" title="Lims::Core::Persistence::Store::DIRTY_ATTRIBUTE_STRATEGY_SHA1 (constant)">DIRTY_ATTRIBUTE_STRATEGY_SHA1</a></span></p>
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+
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+ <h2>Instance Attribute Summary <small>(<a href="#" class="summary_toggle">collapse</a>)</small></h2>
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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="#logger-instance_method" title="#logger (instance method)">- (Object) <strong>logger</strong> </a>
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+ </span>
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+ <span class="note title readonly">readonly</span>
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+ <p>Returns the value of attribute logger.</p>
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+ <a href="#method-instance_method" title="#method (instance method)">- (Object) <strong>method</strong> </a>
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+ <p>Returns the value of attribute method.</p>
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+ <h3 class="inherited">Attributes inherited from <span class='object_link'><a href="../Store.html" title="Lims::Core::Persistence::Store (class)">Store</a></span></h3>
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+ <p class="inherited"><span class='object_link'><a href="../Store.html#dirty_attribute_strategy-instance_method" title="Lims::Core::Persistence::Store#dirty_attribute_strategy (method)">dirty_attribute_strategy</a></span></p>
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+ <h2>
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+ Instance Method Summary
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+ <small>(<a href="#" class="summary_toggle">collapse</a>)</small>
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+ </h2>
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+ <ul class="summary">
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+ <span class="summary_signature">
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+ <a href="#initialize-instance_method" title="#initialize (instance method)">- (Store) <strong>initialize</strong>(logger, method = :info, *args) </a>
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+ </span>
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+ <p>Create a store with an underlying logger.</p>
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+ </div></span>
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+ </li>
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+ <a href="#log-instance_method" title="#log (instance method)">- (Object) <strong>log</strong>(msg) </a>
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+ <h3 class="inherited">Methods inherited from <span class='object_link'><a href="../Store.html" title="Lims::Core::Persistence::Store (class)">Store</a></span></h3>
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+ <p class="inherited"><span class='object_link'><a href="../Store.html#base_module-instance_method" title="Lims::Core::Persistence::Store#base_module (method)">#base_module</a></span>, <span class='object_link'><a href="../Store.html#base_module-class_method" title="Lims::Core::Persistence::Store.base_module (method)">base_module</a></span>, <span class='object_link'><a href="../Store.html#const_missing-class_method" title="Lims::Core::Persistence::Store.const_missing (method)">const_missing</a></span>, <span class='object_link'><a href="../Store.html#create_session-instance_method" title="Lims::Core::Persistence::Store#create_session (method)">#create_session</a></span>, <span class='object_link'><a href="../Store.html#transaction-instance_method" title="Lims::Core::Persistence::Store#transaction (method)">#transaction</a></span>, <span class='object_link'><a href="../Store.html#with_session-instance_method" title="Lims::Core::Persistence::Store#with_session (method)">#with_session</a></span></p>
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+ <div id="constructor_details" class="method_details_list">
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+ <h2>Constructor Details</h2>
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+ <p class="signature first" id="initialize-instance_method">
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+
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+ - (<tt><span class='object_link'><a href="" title="Lims::Core::Persistence::Logger::Store (class)">Store</a></span></tt>) <strong>initialize</strong>(logger, method = :info, *args)
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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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+
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+ <p>Create a store with an underlying logger. send information to the logger.</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='name'>logger</span>
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+
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+
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+ <span class='type'>(<tt><span class='object_link'><a href="../Logger.html" title="Lims::Core::Persistence::Logger (module)">Logger</a></span></tt>, <tt>file</tt>)</span>
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+
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+
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+
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+ </li>
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+
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+ <li>
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+
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+ <span class='name'>method</span>
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+
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+
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+ <span class='type'>(<tt>Symbol</tt>, <tt>String</tt>)</span>
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+
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+
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+ <em class="default">(defaults to: <tt>:info</tt>)</em>
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+
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+
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+ &mdash;
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+ <div class='inline'>
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+ <p>the method call to</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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+
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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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+ 22
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+ 23
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+ 24
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+ 25
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+ 26
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+ 27
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+ 28
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+ 29</pre>
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+ </td>
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+ <td>
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+ <pre class="code"><span class="info file"># File 'lib/lims-core/persistence/logger/store.rb', line 22</span>
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+
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+ <span class='kw'>def</span> <span class='id initialize'>initialize</span><span class='lparen'>(</span><span class='id logger'>logger</span><span class='comma'>,</span> <span class='id method'>method</span><span class='op'>=</span><span class='symbol'>:info</span><span class='comma'>,</span> <span class='op'>*</span><span class='id args'>args</span><span class='rparen'>)</span>
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+ <span class='ivar'>@logger</span> <span class='op'>=</span> <span class='kw'>case</span> <span class='id logger'>logger</span>
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+ <span class='kw'>when</span> <span class='op'>::</span><span class='const'>Logger</span> <span class='kw'>then</span> <span class='id logger'>logger</span>
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+ <span class='kw'>else</span> <span class='op'>::</span><span class='const'>Logger</span><span class='period'>.</span><span class='id new'>new</span><span class='lparen'>(</span><span class='id logger'>logger</span><span class='rparen'>)</span>
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+ <span class='kw'>end</span>
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+ <span class='ivar'>@method</span> <span class='op'>=</span> <span class='id method'>method</span>
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+ <span class='kw'>super</span><span class='lparen'>(</span><span class='op'>*</span><span class='id args'>args</span><span class='rparen'>)</span>
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+ <span class='kw'>end</span></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 id="instance_attr_details" class="attr_details">
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+ <h2>Instance Attribute Details</h2>
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+
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+
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+ <span id=""></span>
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+ <span id="logger-instance_method"></span>
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+ <div class="method_details first">
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+ <p class="signature first" id="logger-instance_method">
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+
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+ - (<tt><span class='object_link'><a href="../../../../Object.html" title="Object (class)">Object</a></span></tt>) <strong>logger</strong> <span class="extras">(readonly)</span>
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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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+
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+ <p>Returns the value of attribute logger</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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+
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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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+ 15
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+ 16
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+ 17</pre>
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+ </td>
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+ <td>
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+ <pre class="code"><span class="info file"># File 'lib/lims-core/persistence/logger/store.rb', line 15</span>
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+
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+ <span class='kw'>def</span> <span class='id logger'>logger</span>
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+ <span class='ivar'>@logger</span>
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+ <span class='kw'>end</span></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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+
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+ <span id=""></span>
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+ <span id="method-instance_method"></span>
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+ <div class="method_details ">
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+ <p class="signature " id="method-instance_method">
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+
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+ - (<tt><span class='object_link'><a href="../../../../Object.html" title="Object (class)">Object</a></span></tt>) <strong>method</strong> <span class="extras">(readonly)</span>
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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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+
400
+ <p>Returns the value of attribute method</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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+
407
+
408
+ </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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+ 16
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+ 17
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+ 18</pre>
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+ </td>
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+ <td>
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+ <pre class="code"><span class="info file"># File 'lib/lims-core/persistence/logger/store.rb', line 16</span>
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+
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+ <span class='kw'>def</span> <span class='id method'>method</span>
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+ <span class='ivar'>@method</span>
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+ <span class='kw'>end</span></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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+
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+ <div id="instance_method_details" class="method_details_list">
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+ <h2>Instance 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="log-instance_method">
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+
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+ - (<tt><span class='object_link'><a href="../../../../Object.html" title="Object (class)">Object</a></span></tt>) <strong>log</strong>(msg)
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+
441
+
442
+
443
+ </p><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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+ 31
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+ 32
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+ 33</pre>
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+ </td>
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+ <td>
454
+ <pre class="code"><span class="info file"># File 'lib/lims-core/persistence/logger/store.rb', line 31</span>
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+
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+ <span class='kw'>def</span> <span class='id log'>log</span><span class='lparen'>(</span><span class='id msg'>msg</span><span class='rparen'>)</span>
457
+ <span class='ivar'>@logger</span><span class='period'>.</span><span class='id send'>send</span><span class='lparen'>(</span><span class='ivar'>@method</span><span class='comma'>,</span> <span class='id msg'>msg</span><span class='rparen'>)</span>
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+ <span class='kw'>end</span></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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+
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+ </body>
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+ </html>