myexperiment-rest 0.2.6

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  1. data/CHANGES +9 -0
  2. data/LICENSE +23 -0
  3. data/README +33 -0
  4. data/Rakefile +45 -0
  5. data/bin/get_workflow_data.rb +31 -0
  6. data/doc/classes/MyExperimentREST.html +113 -0
  7. data/doc/classes/MyExperimentREST/IOData.html +169 -0
  8. data/doc/classes/MyExperimentREST/IOData.src/M000003.html +20 -0
  9. data/doc/classes/MyExperimentREST/ReadWorkflow.html +184 -0
  10. data/doc/classes/MyExperimentREST/ReadWorkflow.src/M000002.html +39 -0
  11. data/doc/classes/MyExperimentREST/ReadWorkflow.src/M000005.html +41 -0
  12. data/doc/classes/MyExperimentREST/TavernaIOData.html +167 -0
  13. data/doc/classes/MyExperimentREST/TavernaIOData.src/M000006.html +20 -0
  14. data/doc/classes/MyExperimentREST/TavernaIOData.src/M000007.html +20 -0
  15. data/doc/classes/MyExperimentREST/TavernaWorkflow.html +209 -0
  16. data/doc/classes/MyExperimentREST/TavernaWorkflow.src/M000005.html +23 -0
  17. data/doc/classes/MyExperimentREST/TavernaWorkflow.src/M000006.html +22 -0
  18. data/doc/classes/MyExperimentREST/Workflow.html +172 -0
  19. data/doc/classes/MyExperimentREST/Workflow.src/M000001.html +21 -0
  20. data/doc/classes/MyExperimentREST/Workflows.html +167 -0
  21. data/doc/classes/MyExperimentREST/Workflows.src/M000004.html +41 -0
  22. data/doc/classes/TestReadWorkflow.html +167 -0
  23. data/doc/classes/TestReadWorkflow.src/M000001.html +18 -0
  24. data/doc/classes/TestReadWorkflow.src/M000002.html +24 -0
  25. data/doc/classes/TestReadWorkflow.src/M000003.html +20 -0
  26. data/doc/classes/TestReadWorkflow.src/M000004.html +20 -0
  27. data/doc/created.rid +1 -0
  28. data/doc/files/bin/get_workflow_data_rb.html +116 -0
  29. data/doc/files/lib/myexperiment-rest/my_experiment_rest_rb.html +110 -0
  30. data/doc/files/lib/myexperiment-rest/myexperiment_rest_rb.html +110 -0
  31. data/doc/files/lib/myexperiment-rest_rb.html +108 -0
  32. data/doc/files/test/test_read_workflow_rb.html +122 -0
  33. data/doc/fr_class_index.html +31 -0
  34. data/doc/fr_file_index.html +29 -0
  35. data/doc/fr_method_index.html +32 -0
  36. data/doc/index.html +24 -0
  37. data/doc/rdoc-style.css +208 -0
  38. data/doc/rdoc/classes/MyExperimentREST.html +117 -0
  39. data/doc/rdoc/classes/MyExperimentREST/TavernaIOData.html +178 -0
  40. data/doc/rdoc/classes/MyExperimentREST/TavernaWorkflow.html +223 -0
  41. data/doc/rdoc/classes/MyExperimentREST/Workflows.html +199 -0
  42. data/doc/rdoc/created.rid +1 -0
  43. data/doc/rdoc/files/CHANGES.html +121 -0
  44. data/doc/rdoc/files/LICENSE.html +133 -0
  45. data/doc/rdoc/files/README.html +148 -0
  46. data/doc/rdoc/files/lib/myexperiment-rest/myexperiment_rest_rb.html +110 -0
  47. data/doc/rdoc/files/lib/myexperiment-rest_rb.html +108 -0
  48. data/doc/rdoc/fr_class_index.html +30 -0
  49. data/doc/rdoc/fr_file_index.html +31 -0
  50. data/doc/rdoc/fr_method_index.html +29 -0
  51. data/doc/rdoc/index.html +24 -0
  52. data/doc/rdoc/rdoc-style.css +208 -0
  53. data/lib/myexperiment-rest.rb +5 -0
  54. data/lib/myexperiment-rest/myexperiment_rest.rb +146 -0
  55. metadata +133 -0
data/doc/classes/MyExperimentREST/ReadWorkflow.html ADDED
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+ <?xml version="1.0" encoding="iso-8859-1"?>
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+ <!DOCTYPE html
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+ PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN"
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+ "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
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+
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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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+ <title>Class: MyExperimentREST::ReadWorkflow</title>
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+ <meta http-equiv="Content-Type" content="text/html; charset=iso-8859-1" />
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+ <meta http-equiv="Content-Script-Type" content="text/javascript" />
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+ <link rel="stylesheet" href="../.././rdoc-style.css" type="text/css" media="screen" />
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+ <script type="text/javascript">
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+ // <![CDATA[
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+
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+ function popupCode( url ) {
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+ window.open(url, "Code", "resizable=yes,scrollbars=yes,toolbar=no,status=no,height=150,width=400")
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+ }
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+
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+ function toggleCode( id ) {
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+ if ( document.getElementById )
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+ elem = document.getElementById( id );
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+ else if ( document.all )
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+ elem = eval( "document.all." + id );
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+ else
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+ return false;
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+
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+ elemStyle = elem.style;
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+
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+ if ( elemStyle.display != "block" ) {
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+ elemStyle.display = "block"
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+ } else {
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+ elemStyle.display = "none"
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+ }
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+
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+ return true;
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+ }
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+
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+ // Make codeblocks hidden by default
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+ document.writeln( "<style type=\"text/css\">div.method-source-code { display: none }</style>" )
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+
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+ // ]]>
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+ </script>
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+
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+ </head>
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+ <body>
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+
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+
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+
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+ <div id="classHeader">
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+ <table class="header-table">
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+ <tr class="top-aligned-row">
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+ <td><strong>Class</strong></td>
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+ <td class="class-name-in-header">MyExperimentREST::ReadWorkflow</td>
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+ </tr>
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+ <tr class="top-aligned-row">
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+ <td><strong>In:</strong></td>
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+ <td>
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+ <a href="../../files/lib/myexperiment-rest/myexperiment_rest_rb.html">
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+ lib/myexperiment-rest/myexperiment_rest.rb
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+ </a>
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+ <br />
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+ </td>
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+ </tr>
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+
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+ <tr class="top-aligned-row">
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+ <td><strong>Parent:</strong></td>
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+ <td>
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+ Object
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+ </td>
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+ </tr>
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+ </table>
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+ </div>
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+ <!-- banner header -->
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+
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+ <div id="bodyContent">
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+
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+
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+
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+ <div id="contextContent">
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+
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+ <div id="description">
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+ <p>
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+ Connects to myExperiment REST API and creates a <em><a
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+ href="TavernaWorkflow.html">TavernaWorkflow</a></em> object. It initialises
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+ the following attributes that you can access: <em>uri</em>,
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+ <em>workflow_id</em>, <em>workflow_version</em> and <em>workflow</em>.
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+ </p>
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+
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+ </div>
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+
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+
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+ </div>
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+
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+ <div id="method-list">
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+ <h3 class="section-bar">Methods</h3>
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+
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+ <div class="name-list">
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+ <a href="#M000005">new</a>&nbsp;&nbsp;
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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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+
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+ <!-- if includes -->
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+ <div id="includes">
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+ <h3 class="section-bar">Included Modules</h3>
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+
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+ <div id="includes-list">
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+ <span class="include-name">LibXML</span>
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+ </div>
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+ </div>
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+
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+ <div id="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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+ <div id="attribute-list">
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+ <h3 class="section-bar">Attributes</h3>
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+
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+ <div class="name-list">
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+ <table>
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+ <tr class="top-aligned-row context-row">
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+ <td class="context-item-name">uri</td>
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+ <td class="context-item-value">&nbsp;[R]&nbsp;</td>
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+ <td class="context-item-desc"></td>
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+ </tr>
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+ <tr class="top-aligned-row context-row">
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+ <td class="context-item-name">workflow</td>
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+ <td class="context-item-value">&nbsp;[R]&nbsp;</td>
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+ <td class="context-item-desc"></td>
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+ </tr>
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+ <tr class="top-aligned-row context-row">
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+ <td class="context-item-name">workflow_id</td>
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+ <td class="context-item-value">&nbsp;[R]&nbsp;</td>
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+ <td class="context-item-desc"></td>
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+ </tr>
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+ <tr class="top-aligned-row context-row">
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+ <td class="context-item-name">workflow_version</td>
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+ <td class="context-item-value">&nbsp;[R]&nbsp;</td>
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+ <td class="context-item-desc"></td>
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+ </tr>
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+ </table>
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+ </div>
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+ </div>
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+
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+
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+
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+ <!-- if method_list -->
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+ <div id="methods">
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+ <h3 class="section-bar">Public Class methods</h3>
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+
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+ <div id="method-M000005" class="method-detail">
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+ <a name="M000005"></a>
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+
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+ <div class="method-heading">
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+ <a href="ReadWorkflow.src/M000005.html" target="Code" class="method-signature"
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+ onclick="popupCode('ReadWorkflow.src/M000005.html');return false;">
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+ <span class="method-name">new</span><span class="method-args">(uri)</span>
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+ </a>
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+ </div>
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+
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+ <div class="method-description">
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+ <p>
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+ Requires the URI of the workflow in the repository as a String.
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+ </p>
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+ </div>
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+ </div>
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+
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+
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+ </div>
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+
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+
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+ </div>
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+
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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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+ </div>
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+
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+ </body>
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+ </html>
data/doc/classes/MyExperimentREST/ReadWorkflow.src/M000002.html ADDED
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+ <?xml version="1.0" encoding="iso-8859-1"?>
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+ <!DOCTYPE html
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+ PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN"
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+ "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
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+
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+ <html>
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+ <head>
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+ <title>new (MyExperimentREST::ReadWorkflow)</title>
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+ <meta http-equiv="Content-Type" content="text/html; charset=iso-8859-1" />
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+ <link rel="stylesheet" href="../../.././rdoc-style.css" type="text/css" media="screen" />
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+ </head>
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+ <body class="standalone-code">
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+ <pre><span class="ruby-comment cmt"># File lib/myexperiment-rest/my_experiment_rest.rb, line 18</span>
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+ <span class="ruby-keyword kw">def</span> <span class="ruby-identifier">initialize</span>(<span class="ruby-identifier">uri</span>)
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+ <span class="ruby-ivar">@uri</span> = <span class="ruby-identifier">uri</span>
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+
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+ <span class="ruby-comment cmt"># 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 re">/workflows\/(\d+)[\/\.]/</span>)
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+ <span class="ruby-keyword kw">if</span> <span class="ruby-identifier">uri_id</span> <span class="ruby-operator">!=</span> <span class="ruby-keyword kw">nil</span>
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+ <span class="ruby-ivar">@workflow_id</span> = <span class="ruby-identifier">uri_id</span>[<span class="ruby-value">1</span>]
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+ <span class="ruby-keyword kw">else</span>
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+ <span class="ruby-identifier">raise</span> <span class="ruby-value str">&quot;Could not match workflow id.&quot;</span>
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+ <span class="ruby-keyword kw">end</span>
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+
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+ <span class="ruby-comment cmt"># 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 re">/version=(\d+)/</span>)
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+ <span class="ruby-keyword kw">if</span> <span class="ruby-identifier">uri_version</span> <span class="ruby-operator">!=</span> <span class="ruby-keyword kw">nil</span>
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+ <span class="ruby-ivar">@workflow_version</span> = <span class="ruby-identifier">uri_version</span>[<span class="ruby-value">1</span>]
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+ <span class="ruby-keyword kw">else</span>
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+ <span class="ruby-ivar">@workflow_version</span> = <span class="ruby-value str">''</span>
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+ <span class="ruby-keyword kw">end</span>
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+
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+ <span class="ruby-comment cmt"># 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-value str">'http://www.myexperiment.org/workflow.xml'</span>, {<span class="ruby-identifier">:params</span> =<span class="ruby-operator">&gt;</span> {<span class="ruby-value str">'id'</span> =<span class="ruby-operator">&gt;</span> <span class="ruby-node">&quot;#{@workflow_id}&quot;</span>, <span class="ruby-value str">'version'</span> =<span class="ruby-operator">&gt;</span> <span class="ruby-node">&quot;#{@workflow_version}&quot;</span>,<span class="ruby-value str">'elements'</span> =<span class="ruby-operator">&gt;</span> <span class="ruby-value str">'title,description,components'</span>} } )
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+
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+ <span class="ruby-ivar">@workflow</span> = <span class="ruby-identifier">populate_workflow</span>(<span class="ruby-identifier">response</span>)
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+ <span class="ruby-keyword kw">end</span></pre>
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+ </body>
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+ </html>
data/doc/classes/MyExperimentREST/ReadWorkflow.src/M000005.html ADDED
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+ <?xml version="1.0" encoding="iso-8859-1"?>
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+ <!DOCTYPE html
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+ PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN"
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+ "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
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+
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+ <html>
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+ <head>
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+ <title>new (MyExperimentREST::ReadWorkflow)</title>
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+ <meta http-equiv="Content-Type" content="text/html; charset=iso-8859-1" />
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+ <link rel="stylesheet" href="../../.././rdoc-style.css" type="text/css" media="screen" />
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+ </head>
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+ <body class="standalone-code">
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+ <pre><span class="ruby-comment cmt"># File lib/myexperiment-rest/myexperiment_rest.rb, line 18</span>
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+ <span class="ruby-keyword kw">def</span> <span class="ruby-identifier">initialize</span>(<span class="ruby-identifier">uri</span>)
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+ <span class="ruby-ivar">@uri</span> = <span class="ruby-identifier">uri</span>
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+
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+ <span class="ruby-comment cmt"># 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 re">/workflows\/(\d+)/</span>)
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+ <span class="ruby-keyword kw">if</span> <span class="ruby-identifier">uri_id</span> <span class="ruby-operator">!=</span> <span class="ruby-keyword kw">nil</span>
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+ <span class="ruby-ivar">@workflow_id</span> = <span class="ruby-identifier">uri_id</span>[<span class="ruby-value">1</span>]
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+ <span class="ruby-keyword kw">else</span>
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+ <span class="ruby-identifier">raise</span> <span class="ruby-value str">&quot;Could not match workflow id.&quot;</span>
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+ <span class="ruby-keyword kw">end</span>
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+
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+ <span class="ruby-comment cmt"># 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 re">/version=(\d+)/</span>)
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+ <span class="ruby-keyword kw">if</span> <span class="ruby-identifier">uri_version</span> <span class="ruby-operator">!=</span> <span class="ruby-keyword kw">nil</span>
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+ <span class="ruby-ivar">@workflow_version</span> = <span class="ruby-identifier">uri_version</span>[<span class="ruby-value">1</span>]
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+ <span class="ruby-keyword kw">else</span>
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+ <span class="ruby-ivar">@workflow_version</span> = <span class="ruby-value str">''</span>
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+ <span class="ruby-keyword kw">end</span>
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+
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+ <span class="ruby-comment cmt"># 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-value str">'http://www.myexperiment.org/workflow.xml'</span>, {<span class="ruby-identifier">:params</span> =<span class="ruby-operator">&gt;</span> {<span class="ruby-value str">'id'</span> =<span class="ruby-operator">&gt;</span> <span class="ruby-node">&quot;#{@workflow_id}&quot;</span>,
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+ <span class="ruby-value str">'version'</span> =<span class="ruby-operator">&gt;</span> <span class="ruby-node">&quot;#{@workflow_version}&quot;</span>,
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+ <span class="ruby-value str">'elements'</span> =<span class="ruby-operator">&gt;</span> <span class="ruby-value str">'title,description,content-uri,components'</span>} } )
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+
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+ <span class="ruby-ivar">@workflow</span> = <span class="ruby-identifier">populate_workflow</span>(<span class="ruby-identifier">response</span>)
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+ <span class="ruby-keyword kw">end</span></pre>
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+ </body>
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+ </html>
data/doc/classes/MyExperimentREST/TavernaIOData.html ADDED
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+ <?xml version="1.0" encoding="iso-8859-1"?>
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+ <!DOCTYPE html
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+ PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN"
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+ "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
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+
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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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+ <title>Class: MyExperimentREST::TavernaIOData</title>
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+ <meta http-equiv="Content-Type" content="text/html; charset=iso-8859-1" />
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+ <meta http-equiv="Content-Script-Type" content="text/javascript" />
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+ <link rel="stylesheet" href="../.././rdoc-style.css" type="text/css" media="screen" />
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+ <script type="text/javascript">
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+ // <![CDATA[
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+
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+ function popupCode( url ) {
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+ window.open(url, "Code", "resizable=yes,scrollbars=yes,toolbar=no,status=no,height=150,width=400")
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+ }
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+
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+ function toggleCode( id ) {
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+ if ( document.getElementById )
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+ elem = document.getElementById( id );
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+ else if ( document.all )
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+ elem = eval( "document.all." + id );
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+ else
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+ return false;
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+
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+ elemStyle = elem.style;
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+
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+ if ( elemStyle.display != "block" ) {
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+ elemStyle.display = "block"
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+ } else {
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+ elemStyle.display = "none"
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+ }
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+
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+ return true;
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+ }
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+
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+ // Make codeblocks hidden by default
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+ document.writeln( "<style type=\"text/css\">div.method-source-code { display: none }</style>" )
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+
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+ // ]]>
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+ </script>
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+
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+ </head>
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+ <body>
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+
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+
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+
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+ <div id="classHeader">
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+ <table class="header-table">
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+ <tr class="top-aligned-row">
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+ <td><strong>Class</strong></td>
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+ <td class="class-name-in-header">MyExperimentREST::TavernaIOData</td>
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+ </tr>
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+ <tr class="top-aligned-row">
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+ <td><strong>In:</strong></td>
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+ <td>
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+ <a href="../../files/lib/myexperiment-rest/myexperiment_rest_rb.html">
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+ lib/myexperiment-rest/myexperiment_rest.rb
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+ </a>
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+ <br />
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+ </td>
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+ </tr>
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+
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+ <tr class="top-aligned-row">
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+ <td><strong>Parent:</strong></td>
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+ <td>
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+ Object
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+ </td>
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+ </tr>
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+ </table>
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+ </div>
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+ <!-- banner header -->
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+
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+ <div id="bodyContent">
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+
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+
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+
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+ <div id="contextContent">
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+
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+ <div id="description">
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+ <p>
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+ Contains all available information about an input or output: name,
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+ descriptions and examples. The last two are lists.
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+ </p>
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+
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+ </div>
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+
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+
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+ </div>
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+
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+ <div id="method-list">
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+ <h3 class="section-bar">Methods</h3>
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+
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+ <div class="name-list">
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+ <a href="#M000006">new</a>&nbsp;&nbsp;
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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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+
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+ <!-- if includes -->
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+
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+ <div id="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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+ <div id="attribute-list">
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+ <h3 class="section-bar">Attributes</h3>
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+
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+ <div class="name-list">
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+ <table>
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+ <tr class="top-aligned-row context-row">
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+ <td class="context-item-name">descriptions</td>
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+ <td class="context-item-value">&nbsp;[R]&nbsp;</td>
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+ <td class="context-item-desc"></td>
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+ </tr>
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+ <tr class="top-aligned-row context-row">
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+ <td class="context-item-name">examples</td>
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+ <td class="context-item-value">&nbsp;[R]&nbsp;</td>
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+ <td class="context-item-desc"></td>
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+ </tr>
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+ <tr class="top-aligned-row context-row">
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+ <td class="context-item-name">name</td>
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+ <td class="context-item-value">&nbsp;[R]&nbsp;</td>
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+ <td class="context-item-desc"></td>
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+ </tr>
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+ </table>
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+ <div id="methods">
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+ <h3 class="section-bar">Public Class methods</h3>
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+ <div id="method-M000006" class="method-detail">
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+ <a name="M000006"></a>
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+
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+ <div class="method-heading">
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+ <a href="TavernaIOData.src/M000006.html" target="Code" class="method-signature"
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+ onclick="popupCode('TavernaIOData.src/M000006.html');return false;">
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+ <span class="method-name">new</span><span class="method-args">(name, descriptions, examples)</span>
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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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+ </div>
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+
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+ </body>
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+ </html>
data/doc/classes/MyExperimentREST/TavernaIOData.src/M000006.html ADDED
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+ <?xml version="1.0" encoding="iso-8859-1"?>
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+ <head>
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+ <title>new (MyExperimentREST::TavernaIOData)</title>
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+ <meta http-equiv="Content-Type" content="text/html; charset=iso-8859-1" />
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+ <link rel="stylesheet" href="../../.././rdoc-style.css" type="text/css" media="screen" />
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+ </head>
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+ <body class="standalone-code">
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+ <pre><span class="ruby-comment cmt"># File lib/myexperiment-rest/myexperiment_rest.rb, line 136</span>
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+ <span class="ruby-keyword kw">def</span> <span class="ruby-identifier">initialize</span>(<span class="ruby-identifier">name</span>, <span class="ruby-identifier">descriptions</span>, <span class="ruby-identifier">examples</span>)
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+ <span class="ruby-ivar">@name</span> = <span class="ruby-identifier">name</span>
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+ <span class="ruby-ivar">@descriptions</span> = <span class="ruby-identifier">descriptions</span>
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+ <span class="ruby-ivar">@examples</span> = <span class="ruby-identifier">examples</span>
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+ <span class="ruby-keyword kw">end</span></pre>
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+ </body>
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+ </html>