myexperiment-rest 0.2.7 → 0.2.8

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Files changed (89) hide show
  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
  15. data/doc/rdoc/images/brick_link.png +0 -0
  16. data/doc/rdoc/images/bug.png +0 -0
  17. data/doc/rdoc/images/bullet_black.png +0 -0
  18. data/doc/rdoc/images/bullet_toggle_minus.png +0 -0
  19. data/doc/rdoc/images/bullet_toggle_plus.png +0 -0
  20. data/doc/rdoc/images/date.png +0 -0
  21. data/doc/rdoc/images/find.png +0 -0
  22. data/doc/rdoc/images/loadingAnimation.gif +0 -0
  23. data/doc/rdoc/images/macFFBgHack.png +0 -0
  24. data/doc/rdoc/images/package.png +0 -0
  25. data/doc/rdoc/images/page_green.png +0 -0
  26. data/doc/rdoc/images/page_white_text.png +0 -0
  27. data/doc/rdoc/images/page_white_width.png +0 -0
  28. data/doc/rdoc/images/plugin.png +0 -0
  29. data/doc/rdoc/images/ruby.png +0 -0
  30. data/doc/rdoc/images/tag_green.png +0 -0
  31. data/doc/rdoc/images/wrench.png +0 -0
  32. data/doc/rdoc/images/wrench_orange.png +0 -0
  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
data/CHANGES CHANGED
@@ -1,5 +1,8 @@
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  = Changes log for the MyExperiment via REST Gem
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+ == Version 0.2.8
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+ * Added user information for workflow
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+
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  == Version 0.2.7
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  * Minor clean up of get_workflow_data.rb and documentation.
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  * Added libxml-ruby dependency in gem specification.
data/README CHANGED
@@ -1,7 +1,7 @@
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  = MyExperiment Interaction via REST
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  Authors:: Konstantinos Karasavvas
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- Gem Version:: 0.2.7
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+ Gem Version:: 0.2.8
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  Contact:: mailto:kostas.karasavvas@nbic.nl
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  Licence:: MIT (See LICENCE or http://www.opensource.org/licenses/mit-license)
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  Copyright:: (c) 2010 Netherlands Bioinformatics Centre, The Netherlands
data/Rakefile CHANGED
@@ -6,13 +6,13 @@
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  require 'rubygems'
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  require 'rake'
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  require 'rake/clean'
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- require 'rake/gempackagetask'
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- require 'rake/rdoctask'
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  require 'rake/testtask'
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+ require 'rubygems/package_task'
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+ require 'rdoc/task'
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  spec = Gem::Specification.new do |s|
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  s.name = 'myexperiment-rest'
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- s.version = '0.2.7'
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+ s.version = '0.2.8'
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  s.extra_rdoc_files = ['README', 'LICENSE', 'CHANGES']
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  s.summary = 'This is a simple library to access data on myExperiment via its REST API. Currently supports a subset of the workflow information available.'
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  s.description = s.summary
@@ -22,17 +22,17 @@ spec = Gem::Specification.new do |s|
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  s.files = %w(LICENSE README CHANGES Rakefile) + Dir.glob("{bin,lib,doc,spec}/**/*")
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  s.require_path = "lib"
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  s.bindir = "bin"
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- s.add_dependency 'rest-client', '>= 1.6.3'
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- s.add_dependency 'libxml-ruby', '>= 2.0.5'
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+ s.add_dependency 'rest-client', '~> 1.6.3'
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+ s.add_dependency 'libxml-ruby', '~> 2.0.5'
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  end
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- Rake::GemPackageTask.new(spec) do |p|
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+ Gem::PackageTask.new(spec) do |p|
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  p.gem_spec = spec
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  p.need_tar = true
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  p.need_zip = true
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  end
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- Rake::RDocTask.new do |rdoc|
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+ RDoc::Task.new do |rdoc|
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  files =['README', 'LICENSE', 'CHANGES', 'lib/**/*.rb']
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  rdoc.rdoc_files.add(files)
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  rdoc.main = "README" # page to start on
data/bin/get_workflow_data.rb CHANGED
@@ -27,3 +27,10 @@ wkf.inputs.each do |i|
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  puts "--------------------------"
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  end
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+ puts wkf.user.name
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+ puts wkf.user.description
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+ puts wkf.user.email
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+ puts wkf.user.avatar
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+ puts wkf.user.website
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+ puts wkf.user.created_at
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+
data/doc/rdoc/CHANGES.html ADDED
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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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+
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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>File: CHANGES [myexperiment-rest Docs]</title>
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+
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+ <link type="text/css" media="screen" href="./rdoc.css" rel="stylesheet" />
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+
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+ <script src="./js/jquery.js" type="text/javascript"
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+ charset="utf-8"></script>
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+ <script src="./js/thickbox-compressed.js" type="text/javascript"
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+ charset="utf-8"></script>
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+ <script src="./js/quicksearch.js" type="text/javascript"
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+ charset="utf-8"></script>
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+ <script src="./js/darkfish.js" type="text/javascript"
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+ charset="utf-8"></script>
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+ </head>
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+
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+ <body class="file">
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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="project-metadata">
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+
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+
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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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+
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+ </ul>
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+ </div>
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+
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+
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+ <div id="classindex-section" class="section project-section">
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+ <h3 class="section-header">Class 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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+
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+ <li><a href="./MyExperimentREST/TavernaWorkflow.html">MyExperimentREST::TavernaWorkflow</a></li>
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+
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+ <li><a href="./MyExperimentREST/Workflows.html">MyExperimentREST::Workflows</a></li>
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+
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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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+
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+
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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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+
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+ <h1>Changes log for the MyExperiment via REST Gem</h1>
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+
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+ <h2>Version 0.2.8</h2>
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+ <ul><li>
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+ <p>Added user information for workflow</p>
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+ </li></ul>
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+
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+ <h2>Version 0.2.7</h2>
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+ <ul><li>
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+ <p>Minor clean up of get_workflow_data.rb and documentation.</p>
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+ </li><li>
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+ <p>Added libxml-ruby dependency in gem specification.</p>
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+ </li></ul>
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+
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+ <h2>Version 0.2.6</h2>
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+ <ul><li>
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+ <p>Added rest-client dependency version in gem specification.</p>
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+ </li></ul>
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+
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+ <h2>Version 0.2.5</h2>
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+ <ul><li>
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+ <p>Abstracted the TavernaWorkflow class better so that it can be properly
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+ reused.</p>
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+ </li><li>
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+ <p>API slightly changed; added input_type ([T2_FLOW | MY_EXPERIMENT])</p>
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+ </li></ul>
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+
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+ </div>
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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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+ </body>
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+ </html>
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data/doc/rdoc/LICENSE.html ADDED
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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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+
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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>File: LICENSE [myexperiment-rest Docs]</title>
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+
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+ <link type="text/css" media="screen" href="./rdoc.css" rel="stylesheet" />
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+
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+ <script src="./js/jquery.js" type="text/javascript"
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+ charset="utf-8"></script>
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+ <script src="./js/thickbox-compressed.js" type="text/javascript"
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+ charset="utf-8"></script>
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+ <script src="./js/quicksearch.js" type="text/javascript"
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+ charset="utf-8"></script>
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+ <script src="./js/darkfish.js" type="text/javascript"
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+ charset="utf-8"></script>
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+ </head>
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+
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+ <body class="file">
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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="project-metadata">
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+
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+
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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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+ <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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+
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+ </ul>
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+ </div>
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+
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+
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+ <div id="classindex-section" class="section project-section">
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+ <h3 class="section-header">Class 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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+ <li><a href="./MyExperimentREST/TavernaUser.html">MyExperimentREST::TavernaUser</a></li>
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+
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+ <li><a href="./MyExperimentREST/TavernaWorkflow.html">MyExperimentREST::TavernaWorkflow</a></li>
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+
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+ <li><a href="./MyExperimentREST/Workflows.html">MyExperimentREST::Workflows</a></li>
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+
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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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+
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+
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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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+
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+ <h2>myexperiment-rest</h2>
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+
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+ <p>The MIT License</p>
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+
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+ <p>Copyright © 2010 - Netherlands Bioinformatics Centre</p>
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+
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+ <p>Permission is hereby granted, free of charge, to any person obtaining a
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+ copy of this software and associated documentation files (the
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+ “Software”), to deal in the Software without restriction, including
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+ without limitation the rights to use, copy, modify, merge, publish,
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+ distribute, sublicense, and/or sell copies of the Software, and to permit
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+ persons to whom the Software is furnished to do so, subject to the
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+ following conditions:</p>
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+
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+ <p>The above copyright notice and this permission notice shall be included in
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+ all copies or substantial portions of the Software.</p>
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+
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+ <p>THE SOFTWARE IS PROVIDED “AS IS”, WITHOUT WARRANTY OF ANY KIND, EXPRESS
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+ OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
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+ FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
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+ AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
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+ LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
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+ FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER
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+ DEALINGS IN THE SOFTWARE.</p>
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+
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+ </div>
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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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+ </body>
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+ </html>
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+
data/doc/rdoc/MyExperimentREST.html ADDED
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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>Module: MyExperimentREST</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="module">
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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_rb.html?TB_iframe=true&amp;height=550&amp;width=785"
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+ class="thickbox" title="lib/myexperiment-rest.rb">lib/myexperiment-rest.rb</a></li>
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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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+ <!-- Namespace Contents -->
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+ <div id="namespace-list-section" class="section">
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+ <h3 class="section-header">Namespace</h3>
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+ <ul class="link-list">
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+
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+ <li><span class="type">CLASS</span> <a href="MyExperimentREST/TavernaIOData.html">MyExperimentREST::TavernaIOData</a></li>
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+
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+ <li><span class="type">CLASS</span> <a href="MyExperimentREST/TavernaUser.html">MyExperimentREST::TavernaUser</a></li>
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+
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+ <li><span class="type">CLASS</span> <a href="MyExperimentREST/TavernaWorkflow.html">MyExperimentREST::TavernaWorkflow</a></li>
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+ <li><span class="type">CLASS</span> <a href="MyExperimentREST/Workflows.html">MyExperimentREST::Workflows</a></li>
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+ </ul>
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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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+ <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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+ <li class="file"><a href="./README.html">README</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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+ <ul class="link-list">
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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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+ <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="documentation">
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+ <h1 class="module">MyExperimentREST</h1>
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+ <div id="description" class="description">
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+
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+ </div><!-- description -->
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+ <!-- Methods -->
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