RubyGems - myexperiment-rest - Versions diffs - 0.3.3 → 0.3.4 - Mend

myexperiment-rest 0.3.3 → 0.3.4

Files changed (47) hide show

data/CHANGES +4 -1
data/README +2 -2
data/Rakefile +3 -3
metadata +7 -50
data/doc/rdoc/CHANGES.html +0 -168
data/doc/rdoc/LICENSE.html +0 -127
data/doc/rdoc/MyExperimentREST.html +0 -271
data/doc/rdoc/MyExperimentREST/MyExperimentIOData.html +0 -319
data/doc/rdoc/MyExperimentREST/MyExperimentUser.html +0 -405
data/doc/rdoc/MyExperimentREST/MyExperimentWorkflow.html +0 -369
data/doc/rdoc/MyExperimentREST/SessionCookie.html +0 -216
data/doc/rdoc/MyExperimentREST/Urls.html +0 -175
data/doc/rdoc/MyExperimentREST/User.html +0 -262
data/doc/rdoc/MyExperimentREST/Workflow.html +0 -271
data/doc/rdoc/README.html +0 -145
data/doc/rdoc/created.rid +0 -9
data/doc/rdoc/images/brick.png +0 -0
data/doc/rdoc/images/brick_link.png +0 -0
data/doc/rdoc/images/bug.png +0 -0
data/doc/rdoc/images/bullet_black.png +0 -0
data/doc/rdoc/images/bullet_toggle_minus.png +0 -0
data/doc/rdoc/images/bullet_toggle_plus.png +0 -0
data/doc/rdoc/images/date.png +0 -0
data/doc/rdoc/images/find.png +0 -0
data/doc/rdoc/images/loadingAnimation.gif +0 -0
data/doc/rdoc/images/macFFBgHack.png +0 -0
data/doc/rdoc/images/package.png +0 -0
data/doc/rdoc/images/page_green.png +0 -0
data/doc/rdoc/images/page_white_text.png +0 -0
data/doc/rdoc/images/page_white_width.png +0 -0
data/doc/rdoc/images/plugin.png +0 -0
data/doc/rdoc/images/ruby.png +0 -0
data/doc/rdoc/images/tag_green.png +0 -0
data/doc/rdoc/images/wrench.png +0 -0
data/doc/rdoc/images/wrench_orange.png +0 -0
data/doc/rdoc/images/zoom.png +0 -0
data/doc/rdoc/index.html +0 -142
data/doc/rdoc/js/darkfish.js +0 -116
data/doc/rdoc/js/jquery.js +0 -32
data/doc/rdoc/js/quicksearch.js +0 -114
data/doc/rdoc/js/thickbox-compressed.js +0 -10
data/doc/rdoc/lib/myexperiment-rest/authentication_rb.html +0 -54
data/doc/rdoc/lib/myexperiment-rest/constants_rb.html +0 -52
data/doc/rdoc/lib/myexperiment-rest/user_rb.html +0 -54
data/doc/rdoc/lib/myexperiment-rest/workflow_rb.html +0 -54
data/doc/rdoc/lib/myexperiment-rest_rb.html +0 -64
data/doc/rdoc/rdoc.css +0 -763

data/doc/rdoc/MyExperimentREST/MyExperimentWorkflow.html DELETED

@@ -1,369 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Strict//EN"
-  "http://www.w3.org/TR/xhtml1/DTD/xhtml1-strict.dtd">
-<html xmlns="http://www.w3.org/1999/xhtml" xml:lang="en" lang="en">
-<head>
-  <meta content="text/html; charset=UTF-8" http-equiv="Content-Type" />
-  <title>Class: MyExperimentREST::MyExperimentWorkflow</title>
-  <link rel="stylesheet" href="../rdoc.css" type="text/css" media="screen" />
-  <script src="../js/jquery.js" type="text/javascript" charset="utf-8"></script>
-  <script src="../js/thickbox-compressed.js" type="text/javascript" charset="utf-8"></script>
-  <script src="../js/quicksearch.js" type="text/javascript" charset="utf-8"></script>
-  <script src="../js/darkfish.js" type="text/javascript" charset="utf-8"></script>
-</head>
-<body id="top" class="class">
-  <div id="metadata">
-    <div id="home-metadata">
-      <div id="home-section" class="section">
-        <h3 class="section-header">
-          <a href="../index.html">Home</a>
-          <a href="../index.html#classes">Classes</a>
-          <a href="../index.html#methods">Methods</a>
-        </h3>
-      </div>
-    </div>
-    <div id="file-metadata">
-      <div id="file-list-section" class="section">
-        <h3 class="section-header">In Files</h3>
-        <div class="section-body">
-          <ul>
-            <li><a href="../lib/myexperiment-rest/workflow_rb.html?TB_iframe=true&amp;height=550&amp;width=785"
-              class="thickbox" title="lib/myexperiment-rest/workflow.rb">lib/myexperiment-rest/workflow.rb</a></li>
-          </ul>
-        </div>
-      </div>
-    </div>
-    <div id="class-metadata">
-      <!-- Parent Class -->
-      <div id="parent-class-section" class="section">
-        <h3 class="section-header">Parent</h3>
-        <p class="link">Object</p>
-      </div>
-      <!-- Method Quickref -->
-      <div id="method-list-section" class="section">
-        <h3 class="section-header">Methods</h3>
-        <ul class="link-list">
-          <li><a href="#method-c-new">::new</a></li>
-          <li><a href="#method-c-parse">::parse</a></li>
-        </ul>
-      </div>
-    </div>
-    <div id="project-metadata">
-      <div id="fileindex-section" class="section project-section">
-        <h3 class="section-header">Files</h3>
-        <ul>
-          <li class="file"><a href="../CHANGES.html">CHANGES</a></li>
-          <li class="file"><a href="../LICENSE.html">LICENSE</a></li>
-          <li class="file"><a href="../README.html">README</a></li>
-        </ul>
-      </div>
-      <div id="classindex-section" class="section project-section">
-        <h3 class="section-header">Class/Module Index
-          <span class="search-toggle"><img src="../images/find.png"
-            height="16" width="16" alt="[+]"
-            title="show/hide quicksearch" /></span></h3>
-        <form action="#" method="get" accept-charset="utf-8" class="initially-hidden">
-        <fieldset>
-          <legend>Quicksearch</legend>
-          <input type="text" name="quicksearch" value=""
-            class="quicksearch-field" />
-        </fieldset>
-        </form>
-        <ul class="link-list">
-          <li><a href="../MyExperimentREST.html">MyExperimentREST</a></li>
-          <li><a href="../MyExperimentREST/MyExperimentIOData.html">MyExperimentREST::MyExperimentIOData</a></li>
-          <li><a href="../MyExperimentREST/MyExperimentUser.html">MyExperimentREST::MyExperimentUser</a></li>
-          <li><a href="../MyExperimentREST/MyExperimentWorkflow.html">MyExperimentREST::MyExperimentWorkflow</a></li>
-          <li><a href="../MyExperimentREST/SessionCookie.html">MyExperimentREST::SessionCookie</a></li>
-          <li><a href="../MyExperimentREST/Urls.html">MyExperimentREST::Urls</a></li>
-          <li><a href="../MyExperimentREST/User.html">MyExperimentREST::User</a></li>
-          <li><a href="../MyExperimentREST/Workflow.html">MyExperimentREST::Workflow</a></li>
-        </ul>
-        <div id="no-class-search-results" style="display: none;">No matching classes.</div>
-      </div>
-    </div>
-  </div>
-  <div id="documentation">
-    <h1 class="class">MyExperimentREST::MyExperimentWorkflow</h1>
-    <div id="description" class="description">
-<p>Contains all available information about a workflow: <em><a
-href="MyExperimentWorkflow.html#attribute-i-content_uri">content_uri</a></em>,
-<em>title</em>, <em>description</em>,<em>inputs</em>, <em>outputs</em> and
-<em><a
-href="MyExperimentWorkflow.html#attribute-i-uploader_uri">uploader_uri</a></em>.</p>
-    </div><!-- description -->
-    <div id="5Buntitled-5D" class="documentation-section">
-      <!-- Attributes -->
-      <div id="attribute-method-details" class="method-section section">
-        <h3 class="section-header">Attributes</h3>
-        <div id="content_uri-attribute-method" class="method-detail">
-          <a name="content_uri"></a>
-          <div class="method-heading attribute-method-heading">
-            <span class="method-name">content_uri</span><span
-              class="attribute-access-type">[R]</span>
-          </div>
-          <div class="method-description">
-          </div>
-        </div>
-        <div id="description-attribute-method" class="method-detail">
-          <a name="description"></a>
-          <div class="method-heading attribute-method-heading">
-            <span class="method-name">description</span><span
-              class="attribute-access-type">[R]</span>
-          </div>
-          <div class="method-description">
-          </div>
-        </div>
-        <div id="inputs-attribute-method" class="method-detail">
-          <a name="inputs"></a>
-          <div class="method-heading attribute-method-heading">
-            <span class="method-name">inputs</span><span
-              class="attribute-access-type">[R]</span>
-          </div>
-          <div class="method-description">
-          </div>
-        </div>
-        <div id="outputs-attribute-method" class="method-detail">
-          <a name="outputs"></a>
-          <div class="method-heading attribute-method-heading">
-            <span class="method-name">outputs</span><span
-              class="attribute-access-type">[R]</span>
-          </div>
-          <div class="method-description">
-          </div>
-        </div>
-        <div id="title-attribute-method" class="method-detail">
-          <a name="title"></a>
-          <div class="method-heading attribute-method-heading">
-            <span class="method-name">title</span><span
-              class="attribute-access-type">[R]</span>
-          </div>
-          <div class="method-description">
-          </div>
-        </div>
-        <div id="uploader_uri-attribute-method" class="method-detail">
-          <a name="uploader_uri"></a>
-          <div class="method-heading attribute-method-heading">
-            <span class="method-name">uploader_uri</span><span
-              class="attribute-access-type">[R]</span>
-          </div>
-          <div class="method-description">
-          </div>
-        </div>
-      </div><!-- attribute-method-details -->
-      <!-- Methods -->
-      <div id="public-class-method-details" class="method-section section">
-        <h3 class="section-header">Public Class Methods</h3>
-        <div id="new-method" class="method-detail ">
-          <a name="method-c-new"></a>
-          <div class="method-heading">
-            <span class="method-name">new</span><span
-              class="method-args">(attributes)</span>
-            <span class="method-click-advice">click to toggle source</span>
-          </div>
-          <div class="method-description">
-            <div class="method-source-code" id="new-source">
-<pre>
-<span class="ruby-comment"># File lib/myexperiment-rest/workflow.rb, line 59</span>
-<span class="ruby-keyword">def</span> <span class="ruby-identifier">initialize</span>(<span class="ruby-identifier">attributes</span>)
-  <span class="ruby-ivar">@content_uri</span> = <span class="ruby-identifier">attributes</span>[<span class="ruby-value">:content_uri</span>]
-  <span class="ruby-ivar">@title</span> = <span class="ruby-identifier">attributes</span>[<span class="ruby-value">:title</span>]
-  <span class="ruby-ivar">@description</span> = <span class="ruby-identifier">attributes</span>[<span class="ruby-value">:description</span>]
-  <span class="ruby-ivar">@inputs</span> = <span class="ruby-identifier">attributes</span>[<span class="ruby-value">:inputs</span>]
-  <span class="ruby-ivar">@outputs</span> = <span class="ruby-identifier">attributes</span>[<span class="ruby-value">:outputs</span>]
-  <span class="ruby-ivar">@uploader_uri</span> = <span class="ruby-identifier">attributes</span>[<span class="ruby-value">:uploader_uri</span>]
-<span class="ruby-keyword">end</span></pre>
-            </div><!-- new-source -->
-          </div>
-        </div><!-- new-method -->
-        <div id="parse-method" class="method-detail ">
-          <a name="method-c-parse"></a>
-          <div class="method-heading">
-            <span class="method-name">parse</span><span
-              class="method-args">(xml)</span>
-            <span class="method-click-advice">click to toggle source</span>
-          </div>
-          <div class="method-description">
-            <p>Parse workflow information XML and instantiate a <em><a
-href="MyExperimentWorkflow.html">MyExperimentWorkflow</a></em> object</p>
-            <div class="method-source-code" id="parse-source">
-<pre>
-<span class="ruby-comment"># File lib/myexperiment-rest/workflow.rb, line 69</span>
-<span class="ruby-keyword">def</span> <span class="ruby-keyword">self</span>.<span class="ruby-identifier">parse</span>(<span class="ruby-identifier">xml</span>)
-  <span class="ruby-identifier">wkf_inputs</span> = []
-  <span class="ruby-identifier">wkf_outputs</span> = []
-  <span class="ruby-identifier">doc</span> = <span class="ruby-constant">LibXML</span><span class="ruby-operator">::</span><span class="ruby-constant">XML</span><span class="ruby-operator">::</span><span class="ruby-constant">Document</span>.<span class="ruby-identifier">string</span>(<span class="ruby-identifier">xml</span>)
-  <span class="ruby-identifier">doc</span>.<span class="ruby-identifier">find</span>(<span class="ruby-string">&quot;//workflow/components/dataflows/dataflow[@role='top']/sources/source&quot;</span>).<span class="ruby-identifier">each</span> <span class="ruby-keyword">do</span> <span class="ruby-operator">|</span><span class="ruby-identifier">element</span><span class="ruby-operator">|</span>
-    <span class="ruby-identifier">wkf_inputs</span> <span class="ruby-operator">&lt;&lt;</span> <span class="ruby-constant">MyExperimentIOData</span>.<span class="ruby-identifier">from_xml</span>(<span class="ruby-identifier">element</span>)
-  <span class="ruby-keyword">end</span>
-  <span class="ruby-identifier">doc</span>.<span class="ruby-identifier">find</span>(<span class="ruby-string">&quot;//workflow/components/dataflows/dataflow[@role='top']/sinks/sink&quot;</span>).<span class="ruby-identifier">each</span> <span class="ruby-keyword">do</span> <span class="ruby-operator">|</span><span class="ruby-identifier">element</span><span class="ruby-operator">|</span>
-    <span class="ruby-identifier">wkf_outputs</span> <span class="ruby-operator">&lt;&lt;</span> <span class="ruby-constant">MyExperimentIOData</span>.<span class="ruby-identifier">from_xml</span>(<span class="ruby-identifier">element</span>)
-  <span class="ruby-keyword">end</span>
-  <span class="ruby-identifier">new</span>(<span class="ruby-value">:content_uri</span> =<span class="ruby-operator">&gt;</span> <span class="ruby-identifier">doc</span>.<span class="ruby-identifier">find_first</span>(<span class="ruby-string">&quot;/workflow/content-uri&quot;</span>).<span class="ruby-identifier">content</span>,
-      <span class="ruby-value">:title</span> =<span class="ruby-operator">&gt;</span> <span class="ruby-identifier">doc</span>.<span class="ruby-identifier">find_first</span>(<span class="ruby-string">&quot;/workflow/title&quot;</span>).<span class="ruby-identifier">content</span>,
-      <span class="ruby-value">:description</span> =<span class="ruby-operator">&gt;</span> <span class="ruby-identifier">doc</span>.<span class="ruby-identifier">find_first</span>(<span class="ruby-string">&quot;/workflow/description&quot;</span>).<span class="ruby-identifier">content</span>,
-      <span class="ruby-value">:inputs</span> =<span class="ruby-operator">&gt;</span> <span class="ruby-identifier">wkf_inputs</span>,
-      <span class="ruby-value">:outputs</span> =<span class="ruby-operator">&gt;</span> <span class="ruby-identifier">wkf_outputs</span>,
-      <span class="ruby-value">:uploader_uri</span> =<span class="ruby-operator">&gt;</span> <span class="ruby-identifier">doc</span>.<span class="ruby-identifier">find_first</span>(<span class="ruby-string">&quot;/workflow/uploader&quot;</span>).<span class="ruby-identifier">attributes</span>[<span class="ruby-string">'uri'</span>])
-<span class="ruby-keyword">end</span></pre>
-            </div><!-- parse-source -->
-          </div>
-        </div><!-- parse-method -->
-      </div><!-- public-class-method-details -->
-    </div><!-- 5Buntitled-5D -->
-  </div><!-- documentation -->
-  <div id="validator-badges">
-    <p><small><a href="http://validator.w3.org/check/referer">[Validate]</a></small></p>
-    <p><small>Generated with the <a href="http://deveiate.org/projects/Darkfish-Rdoc/">Darkfish
-      Rdoc Generator</a> 2</small>.</p>
-  </div>
-</body>
-</html>

data/doc/rdoc/MyExperimentREST/SessionCookie.html DELETED

@@ -1,216 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Strict//EN"
-  "http://www.w3.org/TR/xhtml1/DTD/xhtml1-strict.dtd">
-<html xmlns="http://www.w3.org/1999/xhtml" xml:lang="en" lang="en">
-<head>
-  <meta content="text/html; charset=UTF-8" http-equiv="Content-Type" />
-  <title>Class: MyExperimentREST::SessionCookie</title>
-  <link rel="stylesheet" href="../rdoc.css" type="text/css" media="screen" />
-  <script src="../js/jquery.js" type="text/javascript" charset="utf-8"></script>
-  <script src="../js/thickbox-compressed.js" type="text/javascript" charset="utf-8"></script>
-  <script src="../js/quicksearch.js" type="text/javascript" charset="utf-8"></script>
-  <script src="../js/darkfish.js" type="text/javascript" charset="utf-8"></script>
-</head>
-<body id="top" class="class">
-  <div id="metadata">
-    <div id="home-metadata">
-      <div id="home-section" class="section">
-        <h3 class="section-header">
-          <a href="../index.html">Home</a>
-          <a href="../index.html#classes">Classes</a>
-          <a href="../index.html#methods">Methods</a>
-        </h3>
-      </div>
-    </div>
-    <div id="file-metadata">
-      <div id="file-list-section" class="section">
-        <h3 class="section-header">In Files</h3>
-        <div class="section-body">
-          <ul>
-            <li><a href="../lib/myexperiment-rest/authentication_rb.html?TB_iframe=true&amp;height=550&amp;width=785"
-              class="thickbox" title="lib/myexperiment-rest/authentication.rb">lib/myexperiment-rest/authentication.rb</a></li>
-          </ul>
-        </div>
-      </div>
-    </div>
-    <div id="class-metadata">
-      <!-- Parent Class -->
-      <div id="parent-class-section" class="section">
-        <h3 class="section-header">Parent</h3>
-        <p class="link">Object</p>
-      </div>
-      <!-- Method Quickref -->
-      <div id="method-list-section" class="section">
-        <h3 class="section-header">Methods</h3>
-        <ul class="link-list">
-          <li><a href="#method-c-create_session_cookie">::create_session_cookie</a></li>
-        </ul>
-      </div>
-    </div>
-    <div id="project-metadata">
-      <div id="fileindex-section" class="section project-section">
-        <h3 class="section-header">Files</h3>
-        <ul>
-          <li class="file"><a href="../CHANGES.html">CHANGES</a></li>
-          <li class="file"><a href="../LICENSE.html">LICENSE</a></li>
-          <li class="file"><a href="../README.html">README</a></li>
-        </ul>
-      </div>
-      <div id="classindex-section" class="section project-section">
-        <h3 class="section-header">Class/Module Index
-          <span class="search-toggle"><img src="../images/find.png"
-            height="16" width="16" alt="[+]"
-            title="show/hide quicksearch" /></span></h3>
-        <form action="#" method="get" accept-charset="utf-8" class="initially-hidden">
-        <fieldset>
-          <legend>Quicksearch</legend>
-          <input type="text" name="quicksearch" value=""
-            class="quicksearch-field" />
-        </fieldset>
-        </form>
-        <ul class="link-list">
-          <li><a href="../MyExperimentREST.html">MyExperimentREST</a></li>
-          <li><a href="../MyExperimentREST/MyExperimentIOData.html">MyExperimentREST::MyExperimentIOData</a></li>
-          <li><a href="../MyExperimentREST/MyExperimentUser.html">MyExperimentREST::MyExperimentUser</a></li>
-          <li><a href="../MyExperimentREST/MyExperimentWorkflow.html">MyExperimentREST::MyExperimentWorkflow</a></li>
-          <li><a href="../MyExperimentREST/SessionCookie.html">MyExperimentREST::SessionCookie</a></li>
-          <li><a href="../MyExperimentREST/Urls.html">MyExperimentREST::Urls</a></li>
-          <li><a href="../MyExperimentREST/User.html">MyExperimentREST::User</a></li>
-          <li><a href="../MyExperimentREST/Workflow.html">MyExperimentREST::Workflow</a></li>
-        </ul>
-        <div id="no-class-search-results" style="display: none;">No matching classes.</div>
-      </div>
-    </div>
-  </div>
-  <div id="documentation">
-    <h1 class="class">MyExperimentREST::SessionCookie</h1>
-    <div id="description" class="description">
-<p>Connects to myExperiment REST API and creates a session cookie object that
-can be used for basic authentication.</p>
-    </div><!-- description -->
-    <div id="5Buntitled-5D" class="documentation-section">
-      <!-- Methods -->
-      <div id="public-class-method-details" class="method-section section">
-        <h3 class="section-header">Public Class Methods</h3>
-        <div id="create_session_cookie-method" class="method-detail ">
-          <a name="method-c-create_session_cookie"></a>
-          <div class="method-heading">
-            <span class="method-name">create_session_cookie</span><span
-              class="method-args">(username, password)</span>
-            <span class="method-click-advice">click to toggle source</span>
-          </div>
-          <div class="method-description">
-            <p>Returns a session cookie as a string.</p>
-            <div class="method-source-code" id="create_session_cookie-source">
-<pre>
-<span class="ruby-comment"># File lib/myexperiment-rest/authentication.rb, line 12</span>
-<span class="ruby-keyword">def</span> <span class="ruby-keyword">self</span>.<span class="ruby-identifier">create_session_cookie</span>(<span class="ruby-identifier">username</span>, <span class="ruby-identifier">password</span>)
-  <span class="ruby-keyword">begin</span>
-    <span class="ruby-comment"># Create a session cookie</span>
-    <span class="ruby-identifier">response</span> = <span class="ruby-constant">RestClient</span>.<span class="ruby-identifier">post</span>(<span class="ruby-node">&quot;#{Urls::MYEXPERIMENT_URL}/#{Urls::SESSION_URL}&quot;</span>,
-                                     <span class="ruby-node">&quot;&lt;session&gt;&lt;username&gt;#{username}&lt;/username&gt;&lt;password&gt;#{password}&lt;/password&gt;&lt;/session&gt;&quot;</span>,
-                                     {<span class="ruby-value">:content_type</span> =<span class="ruby-operator">&gt;</span> <span class="ruby-string">'application/xml'</span>} )
-    <span class="ruby-identifier">response</span>.<span class="ruby-identifier">cookies</span>
-  <span class="ruby-keyword">rescue</span> <span class="ruby-constant">Exception</span> =<span class="ruby-operator">&gt;</span> <span class="ruby-identifier">e</span>
-    <span class="ruby-identifier">raise</span> <span class="ruby-string">&quot;REST call to acquire workflow resource failed!\n&quot;</span> <span class="ruby-operator">+</span> <span class="ruby-identifier">e</span>
-  <span class="ruby-keyword">end</span>
-<span class="ruby-keyword">end</span></pre>
-            </div><!-- create_session_cookie-source -->
-          </div>
-        </div><!-- create_session_cookie-method -->
-      </div><!-- public-class-method-details -->
-    </div><!-- 5Buntitled-5D -->
-  </div><!-- documentation -->
-  <div id="validator-badges">
-    <p><small><a href="http://validator.w3.org/check/referer">[Validate]</a></small></p>
-    <p><small>Generated with the <a href="http://deveiate.org/projects/Darkfish-Rdoc/">Darkfish
-      Rdoc Generator</a> 2</small>.</p>
-  </div>
-</body>
-</html>