lims-core 3.2.3
This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.
- checksums.yaml +15 -0
- data/.gitignore +5 -0
- data/.rspec +1 -0
- data/.rvmrc +2 -0
- data/.travis.yml +2 -0
- data/.vimrc +27 -0
- data/.yard_templates/default/layout/html/footer.erb +0 -0
- data/.yardopts +1 -0
- data/Gemfile +54 -0
- data/Gemfile.lock +197 -0
- data/Guardfile +21 -0
- data/Guardfile.tmux +28 -0
- data/README.markdown +67 -0
- data/Rakefile +16 -0
- data/config/database.yml +16 -0
- data/doc/Array.html +116 -0
- data/doc/Array/ArrayLoggerPersistor.html +152 -0
- data/doc/Lims.html +114 -0
- data/doc/Lims/Core.html +178 -0
- data/doc/Lims/Core/Action.html +91 -0
- data/doc/Lims/Core/Actions.html +116 -0
- data/doc/Lims/Core/Actions/Action.html +216 -0
- data/doc/Lims/Core/Actions/Action/AfterEval.html +853 -0
- data/doc/Lims/Core/Actions/Action/InvalidParameters.html +268 -0
- data/doc/Lims/Core/Actions/ActionGroup.html +196 -0
- data/doc/Lims/Core/Actions/ActionGroup/AfterEval.html +315 -0
- data/doc/Lims/Core/Actions/BulkAction.html +224 -0
- data/doc/Lims/Core/Actions/BulkAction/AfterEval.html +253 -0
- data/doc/Lims/Core/Actions/TestActionGroup.html +101 -0
- data/doc/Lims/Core/Actions/TestActionGroup/Action.html +133 -0
- data/doc/Lims/Core/Actions/TestActionGroup/ActionGroup.html +127 -0
- data/doc/Lims/Core/Base.html +287 -0
- data/doc/Lims/Core/Base/AccessibleViaSuper.html +252 -0
- data/doc/Lims/Core/Base/ClassMethod.html +177 -0
- data/doc/Lims/Core/Base/HashString.html +177 -0
- data/doc/Lims/Core/Base/IsArrayOf.html +606 -0
- data/doc/Lims/Core/Base/State.html +130 -0
- data/doc/Lims/Core/Organization.html +113 -0
- data/doc/Lims/Core/Organization/Batch.html +106 -0
- data/doc/Lims/Core/Persistence.html +267 -0
- data/doc/Lims/Core/Persistence/ComparisonFilter.html +318 -0
- data/doc/Lims/Core/Persistence/Filter.html +252 -0
- data/doc/Lims/Core/Persistence/IdentityMap.html +409 -0
- data/doc/Lims/Core/Persistence/IdentityMap/Class.html +144 -0
- data/doc/Lims/Core/Persistence/IdentityMap/DuplicateError.html +126 -0
- data/doc/Lims/Core/Persistence/IdentityMap/DuplicateIdError.html +136 -0
- data/doc/Lims/Core/Persistence/IdentityMap/DuplicateObjectError.html +136 -0
- data/doc/Lims/Core/Persistence/IdentityMapClass.html +133 -0
- data/doc/Lims/Core/Persistence/Logger.html +105 -0
- data/doc/Lims/Core/Persistence/Logger/Persistor.html +334 -0
- data/doc/Lims/Core/Persistence/Logger/Session.html +452 -0
- data/doc/Lims/Core/Persistence/Logger/Store.html +470 -0
- data/doc/Lims/Core/Persistence/MessageBus.html +871 -0
- data/doc/Lims/Core/Persistence/MessageBus/ConnectionError.html +123 -0
- data/doc/Lims/Core/Persistence/MessageBus/InvalidSettingsError.html +122 -0
- data/doc/Lims/Core/Persistence/MultiCriteriaFilter.html +293 -0
- data/doc/Lims/Core/Persistence/PersistAssociationTrait.html +91 -0
- data/doc/Lims/Core/Persistence/PersistableTrait.html +91 -0
- data/doc/Lims/Core/Persistence/Persistor.html +3072 -0
- data/doc/Lims/Core/Persistence/Persistor/DuplicateError.html +205 -0
- data/doc/Lims/Core/Persistence/Persistor/DuplicateIdError.html +147 -0
- data/doc/Lims/Core/Persistence/Persistor/DuplicateObjectError.html +147 -0
- data/doc/Lims/Core/Persistence/PersistorTrait.html +91 -0
- data/doc/Lims/Core/Persistence/ResourceState.html +1738 -0
- data/doc/Lims/Core/Persistence/Search.html +269 -0
- data/doc/Lims/Core/Persistence/Search/CreateSearch.html +251 -0
- data/doc/Lims/Core/Persistence/Search/SearchPersistor.html +240 -0
- data/doc/Lims/Core/Persistence/Search/SearchSequelPersistor.html +396 -0
- data/doc/Lims/Core/Persistence/Sequel.html +117 -0
- data/doc/Lims/Core/Persistence/Sequel/Filters.html +462 -0
- data/doc/Lims/Core/Persistence/Sequel/ForTest.html +101 -0
- data/doc/Lims/Core/Persistence/Sequel/ForTest/Name.html +137 -0
- data/doc/Lims/Core/Persistence/Sequel/ForTest/Name/NamePersitor.html +143 -0
- data/doc/Lims/Core/Persistence/Sequel/Migrations.html +266 -0
- data/doc/Lims/Core/Persistence/Sequel/Persistor.html +665 -0
- data/doc/Lims/Core/Persistence/Sequel/Session.html +501 -0
- data/doc/Lims/Core/Persistence/Sequel/Store.html +417 -0
- data/doc/Lims/Core/Persistence/Session.html +2751 -0
- data/doc/Lims/Core/Persistence/Session/UnmanagedObjectError.html +111 -0
- data/doc/Lims/Core/Persistence/StateGroup.html +696 -0
- data/doc/Lims/Core/Persistence/StateList.html +498 -0
- data/doc/Lims/Core/Persistence/Store.html +695 -0
- data/doc/Lims/Core/Persistence/UuidResource.html +1044 -0
- data/doc/Lims/Core/Persistence/UuidResource/InvalidUuidError.html +111 -0
- data/doc/Lims/Core/Persistence/UuidResource/UuidResourcePersistor.html +337 -0
- data/doc/Lims/Core/Persistence/Uuidable.html +799 -0
- data/doc/Lims/Core/Persistor.html +320 -0
- data/doc/Lims/Core/Resource.html +165 -0
- data/doc/Object.html +228 -0
- data/doc/SessionSpec.html +101 -0
- data/doc/SessionSpec/Model.html +279 -0
- data/doc/SessionSpec/Model/ModelPersistor.html +327 -0
- data/doc/_index.html +732 -0
- data/doc/class_list.html +47 -0
- data/doc/css/common.css +1 -0
- data/doc/css/full_list.css +55 -0
- data/doc/css/style.css +322 -0
- data/doc/file.README.html +127 -0
- data/doc/file_list.html +49 -0
- data/doc/frames.html +13 -0
- data/doc/index.html +127 -0
- data/doc/js/app.js +205 -0
- data/doc/js/full_list.js +167 -0
- data/doc/js/jquery.js +16 -0
- data/doc/method_list.html +1894 -0
- data/doc/top-level-namespace.html +100 -0
- data/lib/common.rb +18 -0
- data/lib/lims-core.rb +29 -0
- data/lib/lims-core/actions.rb +10 -0
- data/lib/lims-core/actions/action.rb +185 -0
- data/lib/lims-core/actions/action_group.rb +54 -0
- data/lib/lims-core/actions/bulk_action.rb +65 -0
- data/lib/lims-core/base.rb +132 -0
- data/lib/lims-core/helpers.rb +41 -0
- data/lib/lims-core/persistence.rb +15 -0
- data/lib/lims-core/persistence/comparison_filter.rb +54 -0
- data/lib/lims-core/persistence/filter.rb +23 -0
- data/lib/lims-core/persistence/identity_map.rb +55 -0
- data/lib/lims-core/persistence/logger/all.rb +5 -0
- data/lib/lims-core/persistence/logger/persistor.rb +35 -0
- data/lib/lims-core/persistence/logger/session.rb +30 -0
- data/lib/lims-core/persistence/logger/store.rb +37 -0
- data/lib/lims-core/persistence/message_bus.rb +131 -0
- data/lib/lims-core/persistence/multi_criteria_filter.rb +50 -0
- data/lib/lims-core/persistence/persist_association_trait.rb +96 -0
- data/lib/lims-core/persistence/persistable_trait.rb +150 -0
- data/lib/lims-core/persistence/persistor.rb +495 -0
- data/lib/lims-core/persistence/resource_state.rb +157 -0
- data/lib/lims-core/persistence/search.rb +3 -0
- data/lib/lims-core/persistence/search/all.rb +3 -0
- data/lib/lims-core/persistence/search/create_search.rb +55 -0
- data/lib/lims-core/persistence/search/search_persistor.rb +45 -0
- data/lib/lims-core/persistence/search/search_sequel_persistor.rb +40 -0
- data/lib/lims-core/persistence/sequel.rb +14 -0
- data/lib/lims-core/persistence/sequel/filters.rb +106 -0
- data/lib/lims-core/persistence/sequel/migrations.rb +14 -0
- data/lib/lims-core/persistence/sequel/migrations/add_audit_tables.rb +147 -0
- data/lib/lims-core/persistence/sequel/migrations/initial.rb +156 -0
- data/lib/lims-core/persistence/sequel/persistor.rb +200 -0
- data/lib/lims-core/persistence/sequel/session.rb +136 -0
- data/lib/lims-core/persistence/sequel/store.rb +37 -0
- data/lib/lims-core/persistence/session.rb +409 -0
- data/lib/lims-core/persistence/state_group.rb +97 -0
- data/lib/lims-core/persistence/state_list.rb +56 -0
- data/lib/lims-core/persistence/store.rb +73 -0
- data/lib/lims-core/persistence/uuid_resource.rb +115 -0
- data/lib/lims-core/persistence/uuid_resource_persistor.rb +43 -0
- data/lib/lims-core/persistence/uuidable.rb +107 -0
- data/lib/lims-core/resource.rb +21 -0
- data/lib/lims-core/subclass_tracker.rb +30 -0
- data/lib/lims-core/version.rb +5 -0
- data/lims-core.gemspec +40 -0
- data/makefile +52 -0
- data/showoff/core-2012-06-11/core/01_slide.md +237 -0
- data/showoff/core-2012-06-11/core/02_slide.md +110 -0
- data/showoff/core-2012-06-11/custom.css +44 -0
- data/showoff/core-2012-06-11/main/01_slide.md +53 -0
- data/showoff/core-2012-06-11/showoff.json +10 -0
- data/showoff/core-2012-06-11/tp1.tpl +1 -0
- data/spec/actions/action_group_spec.rb +39 -0
- data/spec/actions/spec_helper.rb +1 -0
- data/spec/persistence/identity_map_spec.rb +55 -0
- data/spec/persistence/logger/spec_helper.rb +7 -0
- data/spec/persistence/logger/store_spec.rb +48 -0
- data/spec/persistence/message_bus_spec.rb +76 -0
- data/spec/persistence/sequel/session_spec.rb +125 -0
- data/spec/persistence/sequel/spec_helper.rb +39 -0
- data/spec/persistence/sequel/store_shared.rb +25 -0
- data/spec/persistence/sequel/store_spec.rb +22 -0
- data/spec/persistence/session_spec.rb +199 -0
- data/spec/persistence/spec_helper.rb +2 -0
- data/spec/persistence/uuid_resource_spec.rb +80 -0
- data/spec/spec_helper.rb +10 -0
- data/spec/subclass_tracker_sperc.rb +62 -0
- data/utils/constant_tree.rb +29 -0
- data/utils/stack.rb +48 -0
- metadata +402 -0
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Module: Lims::Core::Persistence::Sequel::Persistor
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<span class='title'><span class='object_link'><a href="../../../../Lims.html" title="Lims (module)">Lims</a></span></span> » <span class='title'><span class='object_link'><a href="../../../Core.html" title="Lims::Core (module)">Core</a></span></span> » <span class='title'><span class='object_link'><a href="../../Persistence.html" title="Lims::Core::Persistence (module)">Persistence</a></span></span> » <span class='title'><span class='object_link'><a href="../Sequel.html" title="Lims::Core::Persistence::Sequel (module)">Sequel</a></span></span>
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»
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<div id="content"><h1>Module: Lims::Core::Persistence::Sequel::Persistor
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<p class="inherited"><span class='object_link'><a href="Filters.html#add_comparison_filter-instance_method" title="Lims::Core::Persistence::Sequel::Filters#add_comparison_filter (method)">#add_comparison_filter</a></span>, <span class='object_link'><a href="Filters.html#comparison_filter-instance_method" title="Lims::Core::Persistence::Sequel::Filters#comparison_filter (method)">#comparison_filter</a></span>, <span class='object_link'><a href="Filters.html#multi_criteria_filter-instance_method" title="Lims::Core::Persistence::Sequel::Filters#multi_criteria_filter (method)">#multi_criteria_filter</a></span></p>
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<pre class="code"><span class="info file"># File 'lib/lims-core/persistence/sequel/persistor.rb', line 17</span>
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<span class='kw'>def</span> <span class='kw'>self</span><span class='period'>.</span><span class='id included'>included</span><span class='lparen'>(</span><span class='id klass'>klass</span><span class='rparen'>)</span>
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<span class='ivar'>@table_name</span> <span class='op'>||=</span> <span class='id parent_scope'>parent_scope</span><span class='period'>.</span><span class='id name'>name</span><span class='period'>.</span><span class='id split'>split</span><span class='lparen'>(</span><span class='tstring'><span class='tstring_beg'>'</span><span class='tstring_content'>::</span><span class='tstring_end'>'</span></span><span class='rparen'>)</span><span class='period'>.</span><span class='id last'>last</span><span class='period'>.</span><span class='id pluralize'>pluralize</span><span class='period'>.</span><span class='id snakecase'>snakecase</span><span class='period'>.</span><span class='id to_sym'>to_sym</span>
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<span class='kw'>end</span>
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</span> <span class='kw'>def</span> <span class='kw'>self</span><span class='period'>.</span><span class='id dataset'>dataset</span><span class='lparen'>(</span><span class='id session'>session</span><span class='rparen'>)</span>
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<span class='id session'>session</span><span class='period'>.</span><span class='id database'>database</span><span class='lbracket'>[</span><span class='kw'>self</span><span class='period'>.</span><span class='id table_name'>table_name</span><span class='rbracket'>]</span>
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<span class='kw'>end</span></pre>
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- (<tt><span class='object_link'><a href="../../../../Object.html" title="Object (class)">Object</a></span></tt>) <strong>bulk_insert</strong>(states, *params)
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<pre class="code"><span class="info file"># File 'lib/lims-core/persistence/sequel/persistor.rb', line 116</span>
|
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|
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<span class='kw'>def</span> <span class='id bulk_insert'>bulk_insert</span><span class='lparen'>(</span><span class='id states'>states</span><span class='comma'>,</span> <span class='op'>*</span><span class='id params'>params</span><span class='rparen'>)</span>
|
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<span class='comment'>#super(states, *params)
|
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</span> <span class='id bulk_insert_multi'>bulk_insert_multi</span><span class='lparen'>(</span><span class='id states'>states</span><span class='comma'>,</span> <span class='op'>*</span><span class='id params'>params</span><span class='rparen'>)</span>
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<span class='comment'>#bulk_insert_prepared(states, *params)
|
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</span><span class='kw'>end</span></pre>
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- (<tt><span class='object_link'><a href="../../../../Object.html" title="Object (class)">Object</a></span></tt>) <strong>bulk_load</strong>(ids, *params, &block)
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<pre class="code"><span class="info file"># File 'lib/lims-core/persistence/sequel/persistor.rb', line 92</span>
|
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|
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<span class='kw'>def</span> <span class='id bulk_load'>bulk_load</span><span class='lparen'>(</span><span class='id ids'>ids</span><span class='comma'>,</span> <span class='op'>*</span><span class='id params'>params</span><span class='comma'>,</span> <span class='op'>&</span><span class='id block'>block</span><span class='rparen'>)</span>
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<span class='id dataset'>dataset</span><span class='period'>.</span><span class='id filter'>filter</span><span class='lparen'>(</span><span class='id qualified_key'>qualified_key</span> <span class='op'>=></span> <span class='id ids'>ids</span><span class='period'>.</span><span class='id map'>map</span><span class='lparen'>(</span><span class='op'>&</span><span class='symbol'>:id</span><span class='rparen'>)</span><span class='rparen'>)</span><span class='period'>.</span><span class='id all'>all</span><span class='lparen'>(</span><span class='op'>&</span><span class='id block'>block</span><span class='rparen'>)</span>
|
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<span class='kw'>end</span></pre>
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- (<tt>Fixnum</tt>) <strong>count</strong>
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<div class="discussion">
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<p>Returns the number of object in the store</p>
|
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</div>
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<div class="tags">
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<h3>Returns:</h3>
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<ul class="return">
|
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<span class='type'>(<tt>Fixnum</tt>)</span>
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<pre class="lines">
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<td>
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<pre class="code"><span class="info file"># File 'lib/lims-core/persistence/sequel/persistor.rb', line 69</span>
|
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|
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<span class='kw'>def</span> <span class='id count'>count</span>
|
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<span class='id dataset'>dataset</span><span class='period'>.</span><span class='id count'>count</span>
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<span class='kw'>end</span></pre>
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|
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<div class="method_details ">
|
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<p class="signature " id="dataset-instance_method">
|
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- (<tt>::Sequel::Dataset</tt>) <strong>dataset</strong>
|
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</p><div class="docstring">
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<div class="discussion">
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<p>The Sequel::Dataset. Corresponds to a table.</p>
|
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|
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</div>
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<div class="tags">
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<h3>Returns:</h3>
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<ul class="return">
|
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<span class='type'>(<tt>::Sequel::Dataset</tt>)</span>
|
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|
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</div><table class="source_code">
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<pre class="lines">
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64</pre>
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<pre class="code"><span class="info file"># File 'lib/lims-core/persistence/sequel/persistor.rb', line 62</span>
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<span class='kw'>def</span> <span class='id dataset'>dataset</span>
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<span class='ivar'>@dataset</span>
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<span class='kw'>end</span></pre>
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<div class="method_details ">
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<p class="signature " id="initialize-instance_method">
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- (<tt><span class='object_link'><a href="" title="Lims::Core::Persistence::Sequel::Persistor (module)">Persistor</a></span></tt>) <strong>initialize</strong>(session_or_persistor, dataset = nil, *args, &block)
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</p><div class="docstring">
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<p>A new instance of Persistor</p>
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<div class="tags">
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</div><table class="source_code">
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<pre class="lines">
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<td>
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<pre class="code"><span class="info file"># File 'lib/lims-core/persistence/sequel/persistor.rb', line 33</span>
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<span class='kw'>def</span> <span class='id initialize'>initialize</span><span class='lparen'>(</span><span class='id session_or_persistor'>session_or_persistor</span><span class='comma'>,</span> <span class='id dataset'>dataset</span><span class='op'>=</span><span class='kw'>nil</span><span class='comma'>,</span> <span class='op'>*</span><span class='id args'>args</span><span class='comma'>,</span> <span class='op'>&</span><span class='id block'>block</span> <span class='rparen'>)</span>
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<span class='id id_to_state'>id_to_state</span><span class='comma'>,</span> <span class='id object_to_state'>object_to_state</span> <span class='op'>=</span> <span class='lbracket'>[</span><span class='kw'>nil</span><span class='comma'>,</span> <span class='kw'>nil</span><span class='rbracket'>]</span>
|
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|
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<span class='kw'>case</span> <span class='id session_or_persistor'>session_or_persistor</span>
|
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|
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<span class='kw'>when</span> <span class='const'>Sequel</span><span class='op'>::</span><span class='const'>Persistor</span>
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<span class='comment'># We link the session and the identity map variables,
|
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|
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</span> <span class='comment'># so that object loaded via this persistor can be found (and their id)
|
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</span> <span class='comment'># through the origial persistor.
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+
</span> <span class='comment'># Hack to get those private variables.
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|
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</span> <span class='id session'>session</span><span class='comma'>,</span> <span class='id identity_map_parameters'>identity_map_parameters</span> <span class='op'>=</span> <span class='id session_or_persistor'>session_or_persistor</span><span class='period'>.</span><span class='id instance_eval'>instance_eval</span> <span class='kw'>do</span>
|
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|
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<span class='lbracket'>[</span><span class='ivar'>@session</span><span class='comma'>,</span> <span class='lbracket'>[</span><span class='ivar'>@id_to_state</span><span class='comma'>,</span> <span class='ivar'>@object_to_state</span><span class='rbracket'>]</span><span class='rbracket'>]</span>
|
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|
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<span class='kw'>end</span>
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|
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<span class='kw'>super</span><span class='lparen'>(</span><span class='id session'>session</span><span class='comma'>,</span> <span class='op'>*</span><span class='id args'>args</span><span class='comma'>,</span> <span class='op'>&</span><span class='id block'>block</span><span class='rparen'>)</span>
|
|
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|
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<span class='ivar'>@id_to_state</span> <span class='comma'>,</span> <span class='ivar'>@object_to_state</span> <span class='op'>=</span> <span class='id identity_map_parameters'>identity_map_parameters</span>
|
|
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|
+
<span class='kw'>else</span> <span class='const'>Session</span>
|
|
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|
+
<span class='kw'>super</span><span class='lparen'>(</span><span class='id session_or_persistor'>session_or_persistor</span><span class='comma'>,</span> <span class='op'>*</span><span class='id args'>args</span><span class='comma'>,</span> <span class='op'>&</span><span class='id block'>block</span><span class='rparen'>)</span>
|
|
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|
+
<span class='kw'>end</span>
|
|
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|
+
|
|
595
|
+
<span class='ivar'>@dataset</span> <span class='op'>=</span> <span class='id dataset'>dataset</span> <span class='op'>||</span> <span class='kw'>self</span><span class='period'>.</span><span class='id class'>class</span><span class='period'>.</span><span class='id dataset'>dataset</span><span class='lparen'>(</span><span class='ivar'>@session</span><span class='rparen'>)</span>
|
|
596
|
+
<span class='kw'>end</span></pre>
|
|
597
|
+
</td>
|
|
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|
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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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|
|
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|
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<div class="method_details ">
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|
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|
+
<p class="signature " id="table_name-instance_method">
|
|
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|
+
|
|
605
|
+
- (<tt>String</tt>) <strong>table_name</strong>
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|
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|
+
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+
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|
+
|
|
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|
+
</p><div class="docstring">
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|
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|
+
<div class="discussion">
|
|
611
|
+
|
|
612
|
+
<p>The name of the table</p>
|
|
613
|
+
|
|
614
|
+
|
|
615
|
+
</div>
|
|
616
|
+
</div>
|
|
617
|
+
<div class="tags">
|
|
618
|
+
|
|
619
|
+
<h3>Returns:</h3>
|
|
620
|
+
<ul class="return">
|
|
621
|
+
|
|
622
|
+
<li>
|
|
623
|
+
|
|
624
|
+
|
|
625
|
+
<span class='type'>(<tt>String</tt>)</span>
|
|
626
|
+
|
|
627
|
+
|
|
628
|
+
|
|
629
|
+
—
|
|
630
|
+
<div class='inline'>
|
|
631
|
+
<p>the name of the table</p>
|
|
632
|
+
</div>
|
|
633
|
+
|
|
634
|
+
</li>
|
|
635
|
+
|
|
636
|
+
</ul>
|
|
637
|
+
|
|
638
|
+
</div><table class="source_code">
|
|
639
|
+
<tr>
|
|
640
|
+
<td>
|
|
641
|
+
<pre class="lines">
|
|
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|
+
|
|
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|
+
|
|
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|
+
54
|
|
645
|
+
55
|
|
646
|
+
56</pre>
|
|
647
|
+
</td>
|
|
648
|
+
<td>
|
|
649
|
+
<pre class="code"><span class="info file"># File 'lib/lims-core/persistence/sequel/persistor.rb', line 54</span>
|
|
650
|
+
|
|
651
|
+
<span class='kw'>def</span> <span class='id table_name'>table_name</span>
|
|
652
|
+
<span class='kw'>self</span><span class='period'>.</span><span class='id class'>class</span><span class='period'>.</span><span class='id table_name'>table_name</span>
|
|
653
|
+
<span class='kw'>end</span></pre>
|
|
654
|
+
</td>
|
|
655
|
+
</tr>
|
|
656
|
+
</table>
|
|
657
|
+
</div>
|
|
658
|
+
|
|
659
|
+
</div>
|
|
660
|
+
|
|
661
|
+
</div>
|
|
662
|
+
|
|
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|
+
|
|
664
|
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</body>
|
|
665
|
+
</html>
|