myexperiment-rest 0.2.7 → 0.2.8

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  1. data/CHANGES +3 -0
  2. data/README +1 -1
  3. data/Rakefile +7 -7
  4. data/bin/get_workflow_data.rb +7 -0
  5. data/doc/rdoc/CHANGES.html +123 -0
  6. data/doc/rdoc/LICENSE.html +121 -0
  7. data/doc/rdoc/MyExperimentREST.html +160 -0
  8. data/doc/rdoc/MyExperimentREST/TavernaIOData.html +255 -0
  9. data/doc/rdoc/MyExperimentREST/TavernaUser.html +303 -0
  10. data/doc/rdoc/MyExperimentREST/TavernaWorkflow.html +346 -0
  11. data/doc/rdoc/MyExperimentREST/Workflows.html +258 -0
  12. data/doc/rdoc/README.html +138 -0
  13. data/doc/rdoc/created.rid +6 -1
  14. data/doc/rdoc/images/brick.png +0 -0
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  33. data/doc/rdoc/images/zoom.png +0 -0
  34. data/doc/rdoc/index.html +115 -20
  35. data/doc/rdoc/js/darkfish.js +116 -0
  36. data/doc/rdoc/js/jquery.js +32 -0
  37. data/doc/rdoc/js/quicksearch.js +114 -0
  38. data/doc/rdoc/js/thickbox-compressed.js +10 -0
  39. data/doc/rdoc/lib/myexperiment-rest/myexperiment_rest_rb.html +60 -0
  40. data/doc/rdoc/lib/myexperiment-rest_rb.html +54 -0
  41. data/doc/rdoc/rdoc.css +763 -0
  42. data/lib/myexperiment-rest/myexperiment_rest.rb +53 -9
  43. metadata +41 -52
  44. data/doc/classes/MyExperimentREST.html +0 -113
  45. data/doc/classes/MyExperimentREST/IOData.html +0 -169
  46. data/doc/classes/MyExperimentREST/IOData.src/M000003.html +0 -20
  47. data/doc/classes/MyExperimentREST/ReadWorkflow.html +0 -184
  48. data/doc/classes/MyExperimentREST/ReadWorkflow.src/M000002.html +0 -39
  49. data/doc/classes/MyExperimentREST/ReadWorkflow.src/M000005.html +0 -41
  50. data/doc/classes/MyExperimentREST/TavernaIOData.html +0 -167
  51. data/doc/classes/MyExperimentREST/TavernaIOData.src/M000006.html +0 -20
  52. data/doc/classes/MyExperimentREST/TavernaIOData.src/M000007.html +0 -20
  53. data/doc/classes/MyExperimentREST/TavernaWorkflow.html +0 -209
  54. data/doc/classes/MyExperimentREST/TavernaWorkflow.src/M000005.html +0 -23
  55. data/doc/classes/MyExperimentREST/TavernaWorkflow.src/M000006.html +0 -22
  56. data/doc/classes/MyExperimentREST/Workflow.html +0 -172
  57. data/doc/classes/MyExperimentREST/Workflow.src/M000001.html +0 -21
  58. data/doc/classes/MyExperimentREST/Workflows.html +0 -167
  59. data/doc/classes/MyExperimentREST/Workflows.src/M000004.html +0 -41
  60. data/doc/classes/TestReadWorkflow.html +0 -167
  61. data/doc/classes/TestReadWorkflow.src/M000001.html +0 -18
  62. data/doc/classes/TestReadWorkflow.src/M000002.html +0 -24
  63. data/doc/classes/TestReadWorkflow.src/M000003.html +0 -20
  64. data/doc/classes/TestReadWorkflow.src/M000004.html +0 -20
  65. data/doc/created.rid +0 -1
  66. data/doc/files/README.html +0 -148
  67. data/doc/files/bin/get_workflow_data_rb.html +0 -116
  68. data/doc/files/lib/myexperiment-rest/my_experiment_rest_rb.html +0 -110
  69. data/doc/files/lib/myexperiment-rest/myexperiment_rest_rb.html +0 -110
  70. data/doc/files/lib/myexperiment-rest_rb.html +0 -108
  71. data/doc/files/test/test_read_workflow_rb.html +0 -122
  72. data/doc/fr_class_index.html +0 -26
  73. data/doc/fr_file_index.html +0 -27
  74. data/doc/fr_method_index.html +0 -26
  75. data/doc/index.html +0 -24
  76. data/doc/rdoc-style.css +0 -208
  77. data/doc/rdoc/classes/MyExperimentREST.html +0 -117
  78. data/doc/rdoc/classes/MyExperimentREST/TavernaIOData.html +0 -178
  79. data/doc/rdoc/classes/MyExperimentREST/TavernaWorkflow.html +0 -223
  80. data/doc/rdoc/classes/MyExperimentREST/Workflows.html +0 -199
  81. data/doc/rdoc/files/CHANGES.html +0 -130
  82. data/doc/rdoc/files/LICENSE.html +0 -133
  83. data/doc/rdoc/files/README.html +0 -146
  84. data/doc/rdoc/files/lib/myexperiment-rest/myexperiment_rest_rb.html +0 -110
  85. data/doc/rdoc/files/lib/myexperiment-rest_rb.html +0 -108
  86. data/doc/rdoc/fr_class_index.html +0 -30
  87. data/doc/rdoc/fr_file_index.html +0 -31
  88. data/doc/rdoc/fr_method_index.html +0 -29
  89. data/doc/rdoc/rdoc-style.css +0 -208
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+ <?xml version="1.0" encoding="UTF-8"?>
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+ <!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Strict//EN"
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+ "http://www.w3.org/TR/xhtml1/DTD/xhtml1-strict.dtd">
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+ <html xmlns="http://www.w3.org/1999/xhtml" xml:lang="en" lang="en">
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+ <head>
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+ <meta content="text/html; charset=UTF-8" http-equiv="Content-Type" />
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+
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+ <title>Class: MyExperimentREST::TavernaWorkflow</title>
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+ <link rel="stylesheet" href="../rdoc.css" type="text/css" media="screen" />
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+ <script src="../js/jquery.js" type="text/javascript" charset="utf-8"></script>
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+ <script src="../js/thickbox-compressed.js" type="text/javascript" charset="utf-8"></script>
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+ <script src="../js/quicksearch.js" type="text/javascript" charset="utf-8"></script>
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+ <script src="../js/darkfish.js" type="text/javascript" charset="utf-8"></script>
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+ </head>
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+ <body id="top" class="class">
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+ <div id="metadata">
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+ <div id="home-metadata">
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+ <div id="home-section" class="section">
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+ <h3 class="section-header">
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+ <a href="../index.html">Home</a>
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+ <a href="../index.html#classes">Classes</a>
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+ <a href="../index.html#methods">Methods</a>
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+ </h3>
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+ </div>
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+ </div>
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+
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+ <div id="file-metadata">
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+ <div id="file-list-section" class="section">
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+ <h3 class="section-header">In Files</h3>
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+ <div class="section-body">
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+ <ul>
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+
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+ <li><a href="../lib/myexperiment-rest/myexperiment_rest_rb.html?TB_iframe=true&amp;height=550&amp;width=785"
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+ class="thickbox" title="lib/myexperiment-rest/myexperiment_rest.rb">lib/myexperiment-rest/myexperiment_rest.rb</a></li>
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+ </ul>
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+ </div>
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+ </div>
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+ </div>
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+ <div id="class-metadata">
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+
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+ <!-- Parent Class -->
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+ <div id="parent-class-section" class="section">
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+ <h3 class="section-header">Parent</h3>
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+
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+ <p class="link">Object</p>
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+ </div>
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+ <!-- Method Quickref -->
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+ <div id="method-list-section" class="section">
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+ <h3 class="section-header">Methods</h3>
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+ <ul class="link-list">
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+
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+ <li><a href="#method-c-new">::new</a></li>
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+ </ul>
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+ </div>
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+ </div>
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+
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+ <div id="project-metadata">
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+ <div id="fileindex-section" class="section project-section">
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+ <h3 class="section-header">Files</h3>
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+ <ul>
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+
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+ <li class="file"><a href="../CHANGES.html">CHANGES</a></li>
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+
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+ <li class="file"><a href="../LICENSE.html">LICENSE</a></li>
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+
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+ <li class="file"><a href="../README.html">README</a></li>
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+ </ul>
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+ </div>
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+ <div id="classindex-section" class="section project-section">
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+ <h3 class="section-header">Class/Module Index
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+ <span class="search-toggle"><img src="../images/find.png"
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+ height="16" width="16" alt="[+]"
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+ title="show/hide quicksearch" /></span></h3>
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+ <form action="#" method="get" accept-charset="utf-8" class="initially-hidden">
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+ <fieldset>
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+ <legend>Quicksearch</legend>
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+ <input type="text" name="quicksearch" value=""
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+ class="quicksearch-field" />
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+ </fieldset>
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+ </form>
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+
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+ <ul class="link-list">
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+
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+ <li><a href="../MyExperimentREST.html">MyExperimentREST</a></li>
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+
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+ <li><a href="../MyExperimentREST/TavernaIOData.html">MyExperimentREST::TavernaIOData</a></li>
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+
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+ <li><a href="../MyExperimentREST/TavernaUser.html">MyExperimentREST::TavernaUser</a></li>
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+ <li><a href="../MyExperimentREST/TavernaWorkflow.html">MyExperimentREST::TavernaWorkflow</a></li>
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+ <li><a href="../MyExperimentREST/Workflows.html">MyExperimentREST::Workflows</a></li>
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+ </ul>
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+ <div id="no-class-search-results" style="display: none;">No matching classes.</div>
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+ </div>
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+ </div>
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+ </div>
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+
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+ <div id="documentation">
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+ <h1 class="class">MyExperimentREST::TavernaWorkflow</h1>
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+
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+ <div id="description" class="description">
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+
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+ <p>Contains all available information about a workflow: <em><a
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+ href="TavernaWorkflow.html#attribute-i-input_type">input_type</a></em>,
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+ <em><a href="TavernaWorkflow.html#attribute-i-xml_uri">xml_uri</a></em>,
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+ <em>title</em>, <em>description</em>,<em>inputs</em>, <em>outputs</em> and
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+ <em>user</em>. The <em><a
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+ href="TavernaWorkflow.html#attribute-i-xml_uri">xml_uri</a></em> specifies
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+ the XML description on myExperiment and not the XML of the workflow itself.
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+ <em><a
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+ href="TavernaWorkflow.html#attribute-i-input_type">input_type</a></em>
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+ specifies the kind of input. Currently, either “myexperiment”
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+ (myExperiment’s xml uri) or “t2flow” (filename)</p>
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+
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+ </div><!-- description -->
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+
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+ <div id="5Buntitled-5D" class="documentation-section">
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+
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+
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+
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+ <!-- Constants -->
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+ <div id="constants-list" class="section">
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+ <h3 class="section-header">Constants</h3>
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+ <dl>
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+
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+ <dt><a name="MY_EXPERIMENT">MY_EXPERIMENT</a></dt>
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+
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+ <dd class="description"><p>possible input types</p></dd>
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+ <dt><a name="T2_FLOW">T2_FLOW</a></dt>
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+ <dd class="description"></dd>
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+ </dl>
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+ </div>
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+ <!-- Attributes -->
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+ <div id="attribute-method-details" class="method-section section">
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+ <h3 class="section-header">Attributes</h3>
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+ <div id="description-attribute-method" class="method-detail">
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+ <a name="description"></a>
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+ <div class="method-heading attribute-method-heading">
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+ <span class="method-name">description</span><span
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+ </div>
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+ </div>
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+ <div id="input_type-attribute-method" class="method-detail">
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+ <a name="input_type"></a>
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+ <div class="method-heading attribute-method-heading">
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+ <span class="method-name">input_type</span><span
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+ class="attribute-access-type">[R]</span>
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+ </div>
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+ </div>
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+ <div id="inputs-attribute-method" class="method-detail">
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+ <a name="inputs"></a>
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+ <div class="method-heading attribute-method-heading">
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+ <span class="method-name">inputs</span><span
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+ class="attribute-access-type">[R]</span>
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+ </div>
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+ <div id="outputs-attribute-method" class="method-detail">
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+ <a name="outputs"></a>
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+ <div class="method-heading attribute-method-heading">
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+ <span class="method-name">outputs</span><span
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+ </div>
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+ <div id="title-attribute-method" class="method-detail">
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+ <a name="title"></a>
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+ <div class="method-heading attribute-method-heading">
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+ <span class="method-name">title</span><span
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+ class="attribute-access-type">[R]</span>
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+ </div>
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+ <div class="method-description">
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+ </div>
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+ <div id="user-attribute-method" class="method-detail">
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+ <a name="user"></a>
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+ <div class="method-heading attribute-method-heading">
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+ <span class="method-name">user</span><span
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+ </div>
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+ <div class="method-description">
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+ </div>
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+ </div>
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+ <div id="xml_uri-attribute-method" class="method-detail">
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+ <a name="xml_uri"></a>
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+ <div class="method-heading attribute-method-heading">
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+ <span class="method-name">xml_uri</span><span
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+ </div>
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+ </div><!-- attribute-method-details -->
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+ <!-- Methods -->
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+ <div id="public-class-method-details" class="method-section section">
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+ <h3 class="section-header">Public Class Methods</h3>
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+ <div id="new-method" class="method-detail ">
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+ <a name="method-c-new"></a>
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+ <div class="method-heading">
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+ <span class="method-name">new</span><span
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+ class="method-args">(input_type, xml_uri, title, description, inputs, outputs, user)</span>
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+ <span class="method-click-advice">click to toggle source</span>
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+ </div>
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+ <pre>
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+ <span class="ruby-comment"># File lib/myexperiment-rest/myexperiment_rest.rb, line 137</span>
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+ <span class="ruby-keyword">def</span> <span class="ruby-identifier">initialize</span>(<span class="ruby-identifier">input_type</span>, <span class="ruby-identifier">xml_uri</span>, <span class="ruby-identifier">title</span>, <span class="ruby-identifier">description</span>, <span class="ruby-identifier">inputs</span>, <span class="ruby-identifier">outputs</span>, <span class="ruby-identifier">user</span>)
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+ <span class="ruby-ivar">@input_type</span> = <span class="ruby-identifier">input_type</span>
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+ <span class="ruby-ivar">@xml_uri</span> = <span class="ruby-identifier">xml_uri</span>
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+ <span class="ruby-ivar">@title</span> = <span class="ruby-identifier">title</span>
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+ <span class="ruby-ivar">@description</span> = <span class="ruby-identifier">description</span>
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+ <span class="ruby-ivar">@inputs</span> = <span class="ruby-identifier">inputs</span>
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+ <span class="ruby-ivar">@outputs</span> = <span class="ruby-identifier">outputs</span>
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+ <span class="ruby-ivar">@user</span> = <span class="ruby-identifier">user</span>
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+ <span class="ruby-keyword">end</span></pre>
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+ </div><!-- new-source -->
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+ </div>
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+ </div><!-- new-method -->
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+ </div><!-- public-class-method-details -->
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+ </div><!-- 5Buntitled-5D -->
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+
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+ </div><!-- documentation -->
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+
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+ <div id="validator-badges">
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+ <p><small><a href="http://validator.w3.org/check/referer">[Validate]</a></small></p>
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+ <p><small>Generated with the <a href="http://deveiate.org/projects/Darkfish-Rdoc/">Darkfish
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+ Rdoc Generator</a> 2</small>.</p>
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+ </div>
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+ <?xml version="1.0" encoding="UTF-8"?>
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+ <!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Strict//EN"
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+ "http://www.w3.org/TR/xhtml1/DTD/xhtml1-strict.dtd">
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+ <html xmlns="http://www.w3.org/1999/xhtml" xml:lang="en" lang="en">
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+ <head>
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+ <meta content="text/html; charset=UTF-8" http-equiv="Content-Type" />
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+
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+ <title>Class: MyExperimentREST::Workflows</title>
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+ <link rel="stylesheet" href="../rdoc.css" type="text/css" media="screen" />
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+ <script src="../js/jquery.js" type="text/javascript" charset="utf-8"></script>
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+ <script src="../js/thickbox-compressed.js" type="text/javascript" charset="utf-8"></script>
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+ <script src="../js/quicksearch.js" type="text/javascript" charset="utf-8"></script>
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+ <script src="../js/darkfish.js" type="text/javascript" charset="utf-8"></script>
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+
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+ </head>
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+ <body id="top" class="class">
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+
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+ <div id="metadata">
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+ <div id="home-metadata">
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+ <div id="home-section" class="section">
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+ <h3 class="section-header">
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+ <a href="../index.html">Home</a>
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+ <a href="../index.html#classes">Classes</a>
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+ <a href="../index.html#methods">Methods</a>
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+ </h3>
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+ </div>
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+ </div>
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+
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+ <div id="file-metadata">
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+ <div id="file-list-section" class="section">
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+ <h3 class="section-header">In Files</h3>
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+ <div class="section-body">
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+ <ul>
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+
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+ <li><a href="../lib/myexperiment-rest/myexperiment_rest_rb.html?TB_iframe=true&amp;height=550&amp;width=785"
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+ class="thickbox" title="lib/myexperiment-rest/myexperiment_rest.rb">lib/myexperiment-rest/myexperiment_rest.rb</a></li>
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+
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+ </ul>
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+ </div>
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+ </div>
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+
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+ </div>
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+
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+ <div id="class-metadata">
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+
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+ <!-- Parent Class -->
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+ <div id="parent-class-section" class="section">
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+ <h3 class="section-header">Parent</h3>
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+
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+ <p class="link">Object</p>
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+
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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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+
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+ <!-- Method Quickref -->
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+ <div id="method-list-section" class="section">
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+ <h3 class="section-header">Methods</h3>
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+ <ul class="link-list">
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+
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+ <li><a href="#method-i-read">#read</a></li>
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+
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+ </ul>
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+ </div>
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+
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+
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+ <!-- Included Modules -->
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+ <div id="includes-section" class="section">
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+ <h3 class="section-header">Included Modules</h3>
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+ <ul class="link-list">
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+ <div id="project-metadata">
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+ <div id="fileindex-section" class="section project-section">
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+ <h3 class="section-header">Files</h3>
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+ <li class="file"><a href="../CHANGES.html">CHANGES</a></li>
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+ <li class="file"><a href="../LICENSE.html">LICENSE</a></li>
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+ <div id="classindex-section" class="section project-section">
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+ <h3 class="section-header">Class/Module Index
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+ <span class="search-toggle"><img src="../images/find.png"
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+ height="16" width="16" alt="[+]"
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+ title="show/hide quicksearch" /></span></h3>
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+ <form action="#" method="get" accept-charset="utf-8" class="initially-hidden">
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+ <fieldset>
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+ <legend>Quicksearch</legend>
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+ <input type="text" name="quicksearch" value=""
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+ class="quicksearch-field" />
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+ </fieldset>
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+ </form>
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+
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+ <ul class="link-list">
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+
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+ <li><a href="../MyExperimentREST.html">MyExperimentREST</a></li>
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+ <li><a href="../MyExperimentREST/TavernaIOData.html">MyExperimentREST::TavernaIOData</a></li>
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+
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+ <li><a href="../MyExperimentREST/TavernaUser.html">MyExperimentREST::TavernaUser</a></li>
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+ <li><a href="../MyExperimentREST/TavernaWorkflow.html">MyExperimentREST::TavernaWorkflow</a></li>
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+ <li><a href="../MyExperimentREST/Workflows.html">MyExperimentREST::Workflows</a></li>
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+ <div id="no-class-search-results" style="display: none;">No matching classes.</div>
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+ </div>
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+ </div>
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+ </div>
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+
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+ <div id="documentation">
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+ <h1 class="class">MyExperimentREST::Workflows</h1>
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+
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+ <div id="description" class="description">
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+
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+ <p>Connects to myExperiment REST API and creates a <em><a
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+ href="TavernaWorkflow.html">TavernaWorkflow</a></em> object.</p>
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+
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+ </div><!-- description -->
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+
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+
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+ <div id="5Buntitled-5D" class="documentation-section">
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+
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+
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+
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+
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+
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+
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+
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+ <!-- Attributes -->
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+ <div id="attribute-method-details" class="method-section section">
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+ <h3 class="section-header">Attributes</h3>
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+
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+
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+ <div id="uri-attribute-method" class="method-detail">
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+ <a name="uri"></a>
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+
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+ <div class="method-heading attribute-method-heading">
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+ <span class="method-name">uri</span><span
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+ class="attribute-access-type">[R]</span>
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+ </div>
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+
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+ <div class="method-description">
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+
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+
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+
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+ </div>
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+ </div>
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+
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+ </div><!-- attribute-method-details -->
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+
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+
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+ <!-- Methods -->
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+
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+ <div id="public-instance-method-details" class="method-section section">
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+ <h3 class="section-header">Public Instance Methods</h3>
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+
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+
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+ <div id="read-method" class="method-detail ">
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+ <a name="method-i-read"></a>
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+
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+
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+ <div class="method-heading">
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+ <span class="method-name">read</span><span
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+ class="method-args">(uri)</span>
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+ <span class="method-click-advice">click to toggle source</span>
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+ </div>
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+
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+
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+ <div class="method-description">
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+
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+ <p>Requires the URI of the workflow in the repository as a String.</p>
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+
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+
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+
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+ <div class="method-source-code" id="read-source">
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+ <pre>
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+ <span class="ruby-comment"># File lib/myexperiment-rest/myexperiment_rest.rb, line 20</span>
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+ <span class="ruby-keyword">def</span> <span class="ruby-identifier">read</span>(<span class="ruby-identifier">uri</span>)
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+
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+ <span class="ruby-identifier">workflow_id</span> = <span class="ruby-string">''</span>
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+ <span class="ruby-identifier">workflow_version</span> = <span class="ruby-string">''</span>
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+
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+ <span class="ruby-comment"># Get workflow id</span>
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+ <span class="ruby-identifier">uri_id</span> = <span class="ruby-identifier">uri</span>.<span class="ruby-identifier">match</span>(<span class="ruby-regexp">/workflows\/(\d+)/</span>)
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+ <span class="ruby-keyword">if</span> <span class="ruby-identifier">uri_id</span> <span class="ruby-operator">!=</span> <span class="ruby-keyword">nil</span>
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+ <span class="ruby-identifier">workflow_id</span> = <span class="ruby-identifier">uri_id</span>[<span class="ruby-value">1</span>]
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+ <span class="ruby-keyword">else</span>
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+ <span class="ruby-identifier">raise</span> <span class="ruby-string">&quot;Could not match workflow id.&quot;</span>
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+ <span class="ruby-keyword">end</span>
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+
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+ <span class="ruby-comment"># Get workflow version if it exists</span>
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+ <span class="ruby-identifier">uri_version</span> = <span class="ruby-identifier">uri</span>.<span class="ruby-identifier">match</span>(<span class="ruby-regexp">/version=(\d+)/</span>)
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+ <span class="ruby-keyword">if</span> <span class="ruby-identifier">uri_version</span> <span class="ruby-operator">!=</span> <span class="ruby-keyword">nil</span>
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+ <span class="ruby-identifier">workflow_version</span> = <span class="ruby-identifier">uri_version</span>[<span class="ruby-value">1</span>]
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+ <span class="ruby-keyword">end</span>
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+
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+ <span class="ruby-comment"># Get workflow resource information -- if version is empty it returns the current version</span>
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+ <span class="ruby-identifier">response</span> = <span class="ruby-constant">RestClient</span>.<span class="ruby-identifier">get</span>(<span class="ruby-string">'http://www.myexperiment.org/workflow.xml'</span>, {<span class="ruby-value">:params</span> =<span class="ruby-operator">&gt;</span> {<span class="ruby-string">'id'</span> =<span class="ruby-operator">&gt;</span> <span class="ruby-node">&quot;#{workflow_id}&quot;</span>,
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+ <span class="ruby-string">'version'</span> =<span class="ruby-operator">&gt;</span> <span class="ruby-node">&quot;#{workflow_version}&quot;</span>,
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+ <span class="ruby-string">'elements'</span> =<span class="ruby-operator">&gt;</span> <span class="ruby-string">'title,description,content-uri,components,uploader'</span>} } )
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+
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+ <span class="ruby-identifier">populate_workflow</span>(<span class="ruby-identifier">response</span>)
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+ <span class="ruby-keyword">end</span></pre>
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+ </div><!-- read-source -->
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+
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+ </div>
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+
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+
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+ </div><!-- read-method -->
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+
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+
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+ </div><!-- public-instance-method-details -->
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+
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+ </div><!-- 5Buntitled-5D -->
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+
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+
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+ </div><!-- documentation -->
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+
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+ <div id="validator-badges">
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+ <p><small><a href="http://validator.w3.org/check/referer">[Validate]</a></small></p>
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+ <p><small>Generated with the <a href="http://deveiate.org/projects/Darkfish-Rdoc/">Darkfish
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+ Rdoc Generator</a> 2</small>.</p>
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+ </body>
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+