RubyGems - myexperiment-rest - Versions diffs - 0.2.6 - Mend

myexperiment-rest 0.2.6

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data/CHANGES +9 -0
data/LICENSE +23 -0
data/README +33 -0
data/Rakefile +45 -0
data/bin/get_workflow_data.rb +31 -0
data/doc/classes/MyExperimentREST.html +113 -0
data/doc/classes/MyExperimentREST/IOData.html +169 -0
data/doc/classes/MyExperimentREST/IOData.src/M000003.html +20 -0
data/doc/classes/MyExperimentREST/ReadWorkflow.html +184 -0
data/doc/classes/MyExperimentREST/ReadWorkflow.src/M000002.html +39 -0
data/doc/classes/MyExperimentREST/ReadWorkflow.src/M000005.html +41 -0
data/doc/classes/MyExperimentREST/TavernaIOData.html +167 -0
data/doc/classes/MyExperimentREST/TavernaIOData.src/M000006.html +20 -0
data/doc/classes/MyExperimentREST/TavernaIOData.src/M000007.html +20 -0
data/doc/classes/MyExperimentREST/TavernaWorkflow.html +209 -0
data/doc/classes/MyExperimentREST/TavernaWorkflow.src/M000005.html +23 -0
data/doc/classes/MyExperimentREST/TavernaWorkflow.src/M000006.html +22 -0
data/doc/classes/MyExperimentREST/Workflow.html +172 -0
data/doc/classes/MyExperimentREST/Workflow.src/M000001.html +21 -0
data/doc/classes/MyExperimentREST/Workflows.html +167 -0
data/doc/classes/MyExperimentREST/Workflows.src/M000004.html +41 -0
data/doc/classes/TestReadWorkflow.html +167 -0
data/doc/classes/TestReadWorkflow.src/M000001.html +18 -0
data/doc/classes/TestReadWorkflow.src/M000002.html +24 -0
data/doc/classes/TestReadWorkflow.src/M000003.html +20 -0
data/doc/classes/TestReadWorkflow.src/M000004.html +20 -0
data/doc/created.rid +1 -0
data/doc/files/bin/get_workflow_data_rb.html +116 -0
data/doc/files/lib/myexperiment-rest/my_experiment_rest_rb.html +110 -0
data/doc/files/lib/myexperiment-rest/myexperiment_rest_rb.html +110 -0
data/doc/files/lib/myexperiment-rest_rb.html +108 -0
data/doc/files/test/test_read_workflow_rb.html +122 -0
data/doc/fr_class_index.html +31 -0
data/doc/fr_file_index.html +29 -0
data/doc/fr_method_index.html +32 -0
data/doc/index.html +24 -0
data/doc/rdoc-style.css +208 -0
data/doc/rdoc/classes/MyExperimentREST.html +117 -0
data/doc/rdoc/classes/MyExperimentREST/TavernaIOData.html +178 -0
data/doc/rdoc/classes/MyExperimentREST/TavernaWorkflow.html +223 -0
data/doc/rdoc/classes/MyExperimentREST/Workflows.html +199 -0
data/doc/rdoc/created.rid +1 -0
data/doc/rdoc/files/CHANGES.html +121 -0
data/doc/rdoc/files/LICENSE.html +133 -0
data/doc/rdoc/files/README.html +148 -0
data/doc/rdoc/files/lib/myexperiment-rest/myexperiment_rest_rb.html +110 -0
data/doc/rdoc/files/lib/myexperiment-rest_rb.html +108 -0
data/doc/rdoc/fr_class_index.html +30 -0
data/doc/rdoc/fr_file_index.html +31 -0
data/doc/rdoc/fr_method_index.html +29 -0
data/doc/rdoc/index.html +24 -0
data/doc/rdoc/rdoc-style.css +208 -0
data/lib/myexperiment-rest.rb +5 -0
data/lib/myexperiment-rest/myexperiment_rest.rb +146 -0
metadata +133 -0

data/doc/rdoc/classes/MyExperimentREST/Workflows.html ADDED Viewed

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+<?xml version="1.0" encoding="iso-8859-1"?>
+<!DOCTYPE html
+     PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN"
+     "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
+<html xmlns="http://www.w3.org/1999/xhtml" xml:lang="en" lang="en">
+<head>
+  <title>Class: MyExperimentREST::Workflows</title>
+  <meta http-equiv="Content-Type" content="text/html; charset=iso-8859-1" />
+  <meta http-equiv="Content-Script-Type" content="text/javascript" />
+  <link rel="stylesheet" href="../.././rdoc-style.css" type="text/css" media="screen" />
+  <script type="text/javascript">
+  // <![CDATA[
+  function popupCode( url ) {
+    window.open(url, "Code", "resizable=yes,scrollbars=yes,toolbar=no,status=no,height=150,width=400")
+  }
+  function toggleCode( id ) {
+    if ( document.getElementById )
+      elem = document.getElementById( id );
+    else if ( document.all )
+      elem = eval( "document.all." + id );
+    else
+      return false;
+    elemStyle = elem.style;
+    if ( elemStyle.display != "block" ) {
+      elemStyle.display = "block"
+    } else {
+      elemStyle.display = "none"
+    }
+    return true;
+  }
+  // Make codeblocks hidden by default
+  document.writeln( "<style type=\"text/css\">div.method-source-code { display: none }</style>" )
+  // ]]>
+  </script>
+</head>
+<body>
+    <div id="classHeader">
+        <table class="header-table">
+        <tr class="top-aligned-row">
+          <td><strong>Class</strong></td>
+          <td class="class-name-in-header">MyExperimentREST::Workflows</td>
+        </tr>
+        <tr class="top-aligned-row">
+            <td><strong>In:</strong></td>
+            <td>
+                <a href="../../files/lib/myexperiment-rest/myexperiment_rest_rb.html">
+                lib/myexperiment-rest/myexperiment_rest.rb
+                </a>
+        <br />
+            </td>
+        </tr>
+        <tr class="top-aligned-row">
+            <td><strong>Parent:</strong></td>
+            <td>
+                Object
+            </td>
+        </tr>
+        </table>
+    </div>
+  <!-- banner header -->
+  <div id="bodyContent">
+  <div id="contextContent">
+    <div id="description">
+      <p>
+Connects to myExperiment REST API and creates a <em><a
+href="TavernaWorkflow.html">TavernaWorkflow</a></em> object.
+</p>
+    </div>
+   </div>
+    <div id="method-list">
+      <h3 class="section-bar">Methods</h3>
+      <div class="name-list">
+      <a href="#M000001">read</a>&nbsp;&nbsp;
+      </div>
+    </div>
+  </div>
+    <!-- if includes -->
+    <div id="includes">
+      <h3 class="section-bar">Included Modules</h3>
+      <div id="includes-list">
+        <span class="include-name">LibXML</span>
+      </div>
+    </div>
+    <div id="section">
+    <div id="attribute-list">
+      <h3 class="section-bar">Attributes</h3>
+      <div class="name-list">
+        <table>
+        <tr class="top-aligned-row context-row">
+          <td class="context-item-name">uri</td>
+          <td class="context-item-value">&nbsp;[R]&nbsp;</td>
+          <td class="context-item-desc"></td>
+        </tr>
+        </table>
+      </div>
+    </div>
+    <!-- if method_list -->
+    <div id="methods">
+      <h3 class="section-bar">Public Instance methods</h3>
+      <div id="method-M000001" class="method-detail">
+        <a name="M000001"></a>
+        <div class="method-heading">
+          <a href="#M000001" class="method-signature">
+          <span class="method-name">read</span><span class="method-args">(uri)</span>
+          </a>
+        </div>
+        <div class="method-description">
+          <p>
+Requires the URI of the workflow in the repository as a String.
+</p>
+          <p><a class="source-toggle" href="#"
+            onclick="toggleCode('M000001-source');return false;">[Source]</a></p>
+          <div class="method-source-code" id="M000001-source">
+<pre>
+    <span class="ruby-comment cmt"># File lib/myexperiment-rest/myexperiment_rest.rb, line 19</span>
+19:     <span class="ruby-keyword kw">def</span> <span class="ruby-identifier">read</span>(<span class="ruby-identifier">uri</span>)
+20:
+21:       <span class="ruby-identifier">workflow_id</span> = <span class="ruby-value str">''</span>
+22:       <span class="ruby-identifier">workflow_version</span> = <span class="ruby-value str">''</span>
+23:
+24:       <span class="ruby-comment cmt"># Get workflow id</span>
+25:       <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>)
+26:       <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>
+27:         <span class="ruby-identifier">workflow_id</span> = <span class="ruby-identifier">uri_id</span>[<span class="ruby-value">1</span>]
+28:       <span class="ruby-keyword kw">else</span>
+29:         <span class="ruby-identifier">raise</span> <span class="ruby-value str">&quot;Could not match workflow id.&quot;</span>
+30:       <span class="ruby-keyword kw">end</span>
+31:
+32:       <span class="ruby-comment cmt"># Get workflow version if it exists</span>
+33:       <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>)
+34:       <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>
+35:         <span class="ruby-identifier">workflow_version</span> = <span class="ruby-identifier">uri_version</span>[<span class="ruby-value">1</span>]
+36:       <span class="ruby-keyword kw">end</span>
+37:
+38:       <span class="ruby-comment cmt"># Get workflow resource information -- if version is empty it returns the current version</span>
+39:       <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>,
+40:                                                                                          <span class="ruby-value str">'version'</span> =<span class="ruby-operator">&gt;</span> <span class="ruby-node">&quot;#{workflow_version}&quot;</span>,
+41:                                                                                          <span class="ruby-value str">'elements'</span> =<span class="ruby-operator">&gt;</span> <span class="ruby-value str">'title,description,content-uri,components'</span>} } )
+42:
+43:       <span class="ruby-identifier">populate_workflow</span>(<span class="ruby-identifier">response</span>)
+44:     <span class="ruby-keyword kw">end</span>
+</pre>
+          </div>
+        </div>
+      </div>
+    </div>
+  </div>
+<div id="validator-badges">
+  <p><small><a href="http://validator.w3.org/check/referer">[Validate]</a></small></p>
+</div>
+</body>
+</html>

data/doc/rdoc/created.rid ADDED Viewed

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1	+ Wed, 20 Jul 2011 19:32:01 +0200

data/doc/rdoc/files/CHANGES.html ADDED Viewed

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+<?xml version="1.0" encoding="iso-8859-1"?>
+<!DOCTYPE html
+     PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN"
+     "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
+<html xmlns="http://www.w3.org/1999/xhtml" xml:lang="en" lang="en">
+<head>
+  <title>File: CHANGES</title>
+  <meta http-equiv="Content-Type" content="text/html; charset=iso-8859-1" />
+  <meta http-equiv="Content-Script-Type" content="text/javascript" />
+  <link rel="stylesheet" href=".././rdoc-style.css" type="text/css" media="screen" />
+  <script type="text/javascript">
+  // <![CDATA[
+  function popupCode( url ) {
+    window.open(url, "Code", "resizable=yes,scrollbars=yes,toolbar=no,status=no,height=150,width=400")
+  }
+  function toggleCode( id ) {
+    if ( document.getElementById )
+      elem = document.getElementById( id );
+    else if ( document.all )
+      elem = eval( "document.all." + id );
+    else
+      return false;
+    elemStyle = elem.style;
+    if ( elemStyle.display != "block" ) {
+      elemStyle.display = "block"
+    } else {
+      elemStyle.display = "none"
+    }
+    return true;
+  }
+  // Make codeblocks hidden by default
+  document.writeln( "<style type=\"text/css\">div.method-source-code { display: none }</style>" )
+  // ]]>
+  </script>
+</head>
+<body>
+  <div id="fileHeader">
+    <h1>CHANGES</h1>
+    <table class="header-table">
+    <tr class="top-aligned-row">
+      <td><strong>Path:</strong></td>
+      <td>CHANGES
+      </td>
+    </tr>
+    <tr class="top-aligned-row">
+      <td><strong>Last Update:</strong></td>
+      <td>Wed Jul 20 19:30:21 +0200 2011</td>
+    </tr>
+    </table>
+  </div>
+  <!-- banner header -->
+  <div id="bodyContent">
+  <div id="contextContent">
+    <div id="description">
+      <h1>Changes log for the MyExperiment via REST Gem</h1>
+<h2>Version 0.2.6</h2>
+<ul>
+<li>Added dependency in gem specification.
+</li>
+</ul>
+<h2>Version 0.2.5</h2>
+<ul>
+<li>Abstracted the TavernaWorkflow class better so that it can be properly
+reused.
+</li>
+<li>API slightly changed; added input_type ([T2_FLOW | MY_EXPERIMENT])
+</li>
+</ul>
+    </div>
+   </div>
+  </div>
+    <!-- if includes -->
+    <div id="section">
+    <!-- if method_list -->
+  </div>
+<div id="validator-badges">
+  <p><small><a href="http://validator.w3.org/check/referer">[Validate]</a></small></p>
+</div>
+</body>
+</html>

data/doc/rdoc/files/LICENSE.html ADDED Viewed

@@ -0,0 +1,133 @@
+<?xml version="1.0" encoding="iso-8859-1"?>
+<!DOCTYPE html
+     PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN"
+     "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
+<html xmlns="http://www.w3.org/1999/xhtml" xml:lang="en" lang="en">
+<head>
+  <title>File: LICENSE</title>
+  <meta http-equiv="Content-Type" content="text/html; charset=iso-8859-1" />
+  <meta http-equiv="Content-Script-Type" content="text/javascript" />
+  <link rel="stylesheet" href=".././rdoc-style.css" type="text/css" media="screen" />
+  <script type="text/javascript">
+  // <![CDATA[
+  function popupCode( url ) {
+    window.open(url, "Code", "resizable=yes,scrollbars=yes,toolbar=no,status=no,height=150,width=400")
+  }
+  function toggleCode( id ) {
+    if ( document.getElementById )
+      elem = document.getElementById( id );
+    else if ( document.all )
+      elem = eval( "document.all." + id );
+    else
+      return false;
+    elemStyle = elem.style;
+    if ( elemStyle.display != "block" ) {
+      elemStyle.display = "block"
+    } else {
+      elemStyle.display = "none"
+    }
+    return true;
+  }
+  // Make codeblocks hidden by default
+  document.writeln( "<style type=\"text/css\">div.method-source-code { display: none }</style>" )
+  // ]]>
+  </script>
+</head>
+<body>
+  <div id="fileHeader">
+    <h1>LICENSE</h1>
+    <table class="header-table">
+    <tr class="top-aligned-row">
+      <td><strong>Path:</strong></td>
+      <td>LICENSE
+      </td>
+    </tr>
+    <tr class="top-aligned-row">
+      <td><strong>Last Update:</strong></td>
+      <td>Wed Apr 06 16:45:13 +0200 2011</td>
+    </tr>
+    </table>
+  </div>
+  <!-- banner header -->
+  <div id="bodyContent">
+  <div id="contextContent">
+    <div id="description">
+      <h2>myexperiment-rest</h2>
+<p>
+The MIT License
+</p>
+<p>
+Copyright (c) 2010 - Netherlands Bioinformatics Centre
+</p>
+<p>
+Permission is hereby granted, free of charge, to any person obtaining a
+copy of this software and associated documentation files (the
+&quot;Software&quot;), to deal in the Software without restriction,
+including without limitation the rights to use, copy, modify, merge,
+publish, distribute, sublicense, and/or sell copies of the Software, and to
+permit persons to whom the Software is furnished to do so, subject to the
+following conditions:
+</p>
+<p>
+The above copyright notice and this permission notice shall be included in
+all copies or substantial portions of the Software.
+</p>
+<p>
+THE SOFTWARE IS PROVIDED &quot;AS IS&quot;, WITHOUT WARRANTY OF ANY KIND,
+EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF
+MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN
+NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM,
+DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR
+OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE
+USE OR OTHER DEALINGS IN THE SOFTWARE.
+</p>
+    </div>
+   </div>
+  </div>
+    <!-- if includes -->
+    <div id="section">
+    <!-- if method_list -->
+  </div>
+<div id="validator-badges">
+  <p><small><a href="http://validator.w3.org/check/referer">[Validate]</a></small></p>
+</div>
+</body>
+</html>