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diff --git a/rdoc/classes/OpenTox/Dataset.html b/rdoc/classes/OpenTox/Dataset.html new file mode 100644 index 0000000..f6966f7 --- /dev/null +++ b/rdoc/classes/OpenTox/Dataset.html @@ -0,0 +1,331 @@ +<?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: OpenTox::Dataset</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">OpenTox::Dataset</td> + </tr> + <tr class="top-aligned-row"> + <td><strong>In:</strong></td> + <td> + <a href="../../files/lib/opentox-ruby-api-wrapper_rb.html"> + lib/opentox-ruby-api-wrapper.rb + </a> + <br /> + </td> + </tr> + + <tr class="top-aligned-row"> + <td><strong>Parent:</strong></td> + <td> + <a href="OpenTox.html"> + OpenTox + </a> + </td> + </tr> + </table> + </div> + <!-- banner header --> + + <div id="bodyContent"> + + + + <div id="contextContent"> + + + + </div> + + <div id="method-list"> + <h3 class="section-bar">Methods</h3> + + <div class="name-list"> + <a href="#M000016">add</a> + <a href="#M000013">all_compounds_and_features</a> + <a href="#M000014">all_features</a> + <a href="#M000012">compounds</a> + <a href="#M000015">features</a> + <a href="#M000011">name</a> + <a href="#M000010">new</a> + </div> + </div> + + </div> + + + <!-- if includes --> + + <div id="section"> + + + + + + + + + <!-- if method_list --> + <div id="methods"> + <h3 class="section-bar">Public Class methods</h3> + + <div id="method-M000010" class="method-detail"> + <a name="M000010"></a> + + <div class="method-heading"> + <a href="#M000010" class="method-signature"> + <span class="method-name">new</span><span class="method-args">(params)</span> + </a> + </div> + + <div class="method-description"> + <p> +Initialize with <tt>:uri => uri</tt> or <tt>:<a +href="Dataset.html#M000011">name</a> => <a +href="Dataset.html#M000011">name</a></tt> (creates a <a +href="Dataset.html#M000010">new</a> dataset) +</p> + <p><a class="source-toggle" href="#" + onclick="toggleCode('M000010-source');return false;">[Source]</a></p> + <div class="method-source-code" id="M000010-source"> +<pre> +<span class="ruby-comment cmt"># File lib/opentox-ruby-api-wrapper.rb, line 78</span> + <span class="ruby-keyword kw">def</span> <span class="ruby-identifier">initialize</span>(<span class="ruby-identifier">params</span>) + <span class="ruby-keyword kw">if</span> <span class="ruby-identifier">params</span>[<span class="ruby-identifier">:uri</span>] + <span class="ruby-ivar">@uri</span> = <span class="ruby-identifier">params</span>[<span class="ruby-identifier">:uri</span>].<span class="ruby-identifier">to_s</span> + <span class="ruby-keyword kw">elsif</span> <span class="ruby-identifier">params</span>[<span class="ruby-identifier">:name</span>] + <span class="ruby-ivar">@uri</span> = <span class="ruby-constant">RestClient</span>.<span class="ruby-identifier">post</span> <span class="ruby-constant">ENV</span>[<span class="ruby-value str">'OPENTOX_DATASETS'</span>], <span class="ruby-identifier">:name</span> =<span class="ruby-operator">></span> <span class="ruby-identifier">params</span>[<span class="ruby-identifier">:name</span>] + <span class="ruby-constant">RestClient</span>.<span class="ruby-identifier">delete</span> <span class="ruby-ivar">@uri</span> <span class="ruby-operator">+</span> <span class="ruby-value str">'/associations'</span> + <span class="ruby-keyword kw">end</span> + <span class="ruby-keyword kw">end</span> +</pre> + </div> + </div> + </div> + + <h3 class="section-bar">Public Instance methods</h3> + + <div id="method-M000016" class="method-detail"> + <a name="M000016"></a> + + <div class="method-heading"> + <a href="#M000016" class="method-signature"> + <span class="method-name">add</span><span class="method-args">(compound,feature)</span> + </a> + </div> + + <div class="method-description"> + <p> +Add a compound and a feature to a dataset +</p> + <p><a class="source-toggle" href="#" + onclick="toggleCode('M000016-source');return false;">[Source]</a></p> + <div class="method-source-code" id="M000016-source"> +<pre> +<span class="ruby-comment cmt"># File lib/opentox-ruby-api-wrapper.rb, line 118</span> + <span class="ruby-keyword kw">def</span> <span class="ruby-identifier">add</span>(<span class="ruby-identifier">compound</span>,<span class="ruby-identifier">feature</span>) + <span class="ruby-constant">RestClient</span>.<span class="ruby-identifier">put</span> <span class="ruby-ivar">@uri</span>, <span class="ruby-identifier">:compound_uri</span> =<span class="ruby-operator">></span> <span class="ruby-identifier">compound</span>.<span class="ruby-identifier">uri</span>, <span class="ruby-identifier">:feature_uri</span> =<span class="ruby-operator">></span> <span class="ruby-identifier">feature</span>.<span class="ruby-identifier">uri</span> + <span class="ruby-keyword kw">end</span> +</pre> + </div> + </div> + </div> + + <div id="method-M000013" class="method-detail"> + <a name="M000013"></a> + + <div class="method-heading"> + <a href="#M000013" class="method-signature"> + <span class="method-name">all_compounds_and_features</span><span class="method-args">()</span> + </a> + </div> + + <div class="method-description"> + <p> +Get all <a href="Dataset.html#M000012">compounds</a> and <a +href="Dataset.html#M000015">features</a> from a dataset, returns a hash +with compound_uris as keys and arrays of <a +href="Dataset.html#M000015">features</a> as values +</p> + <p><a class="source-toggle" href="#" + onclick="toggleCode('M000013-source');return false;">[Source]</a></p> + <div class="method-source-code" id="M000013-source"> +<pre> +<span class="ruby-comment cmt"># File lib/opentox-ruby-api-wrapper.rb, line 98</span> + <span class="ruby-keyword kw">def</span> <span class="ruby-identifier">all_compounds_and_features</span> + <span class="ruby-identifier">compounds</span> = {} + <span class="ruby-constant">Crack</span><span class="ruby-operator">::</span><span class="ruby-constant">XML</span>.<span class="ruby-identifier">parse</span>(<span class="ruby-constant">RestClient</span>.<span class="ruby-identifier">get</span> <span class="ruby-ivar">@uri</span> <span class="ruby-operator">+</span> <span class="ruby-value str">'/compounds/features'</span>)[<span class="ruby-value str">'dataset'</span>][<span class="ruby-value str">'compound'</span>].<span class="ruby-identifier">each</span> <span class="ruby-keyword kw">do</span> <span class="ruby-operator">|</span><span class="ruby-identifier">c</span><span class="ruby-operator">|</span> + <span class="ruby-identifier">features</span> = <span class="ruby-identifier">c</span>[<span class="ruby-value str">'feature_uri'</span>].<span class="ruby-identifier">collect</span>{ <span class="ruby-operator">|</span><span class="ruby-identifier">f</span><span class="ruby-operator">|</span> <span class="ruby-constant">Feature</span>.<span class="ruby-identifier">new</span> <span class="ruby-identifier">:uri</span> =<span class="ruby-operator">></span> <span class="ruby-identifier">f</span> } + <span class="ruby-identifier">compounds</span>[<span class="ruby-identifier">c</span>[<span class="ruby-value str">'uri'</span>]] = <span class="ruby-identifier">features</span> + <span class="ruby-keyword kw">end</span> + <span class="ruby-identifier">compounds</span> + <span class="ruby-keyword kw">end</span> +</pre> + </div> + </div> + </div> + + <div id="method-M000014" class="method-detail"> + <a name="M000014"></a> + + <div class="method-heading"> + <a href="#M000014" class="method-signature"> + <span class="method-name">all_features</span><span class="method-args">()</span> + </a> + </div> + + <div class="method-description"> + <p> +Get all <a href="Dataset.html#M000015">features</a> from a dataset +</p> + <p><a class="source-toggle" href="#" + onclick="toggleCode('M000014-source');return false;">[Source]</a></p> + <div class="method-source-code" id="M000014-source"> +<pre> +<span class="ruby-comment cmt"># File lib/opentox-ruby-api-wrapper.rb, line 108</span> + <span class="ruby-keyword kw">def</span> <span class="ruby-identifier">all_features</span> + <span class="ruby-constant">RestClient</span>.<span class="ruby-identifier">get</span>(<span class="ruby-ivar">@uri</span> <span class="ruby-operator">+</span> <span class="ruby-value str">'/features'</span>).<span class="ruby-identifier">split</span>(<span class="ruby-value str">"\n"</span>).<span class="ruby-identifier">collect</span>{<span class="ruby-operator">|</span><span class="ruby-identifier">f</span><span class="ruby-operator">|</span> <span class="ruby-constant">Feature</span>.<span class="ruby-identifier">new</span>(<span class="ruby-identifier">:uri</span> =<span class="ruby-operator">></span> <span class="ruby-identifier">f</span>)} + <span class="ruby-keyword kw">end</span> +</pre> + </div> + </div> + </div> + + <div id="method-M000012" class="method-detail"> + <a name="M000012"></a> + + <div class="method-heading"> + <a href="#M000012" class="method-signature"> + <span class="method-name">compounds</span><span class="method-args">()</span> + </a> + </div> + + <div class="method-description"> + <p> +Get all <a href="Dataset.html#M000012">compounds</a> from a dataset +</p> + <p><a class="source-toggle" href="#" + onclick="toggleCode('M000012-source');return false;">[Source]</a></p> + <div class="method-source-code" id="M000012-source"> +<pre> +<span class="ruby-comment cmt"># File lib/opentox-ruby-api-wrapper.rb, line 93</span> + <span class="ruby-keyword kw">def</span> <span class="ruby-identifier">compounds</span> + <span class="ruby-constant">RestClient</span>.<span class="ruby-identifier">get</span>(<span class="ruby-ivar">@uri</span> <span class="ruby-operator">+</span> <span class="ruby-value str">'/compounds'</span>).<span class="ruby-identifier">split</span>(<span class="ruby-value str">"\n"</span>).<span class="ruby-identifier">collect</span>{ <span class="ruby-operator">|</span><span class="ruby-identifier">c</span><span class="ruby-operator">|</span> <span class="ruby-constant">Compound</span>.<span class="ruby-identifier">new</span>(<span class="ruby-identifier">:uri</span> =<span class="ruby-operator">></span> <span class="ruby-identifier">c</span>) } + <span class="ruby-keyword kw">end</span> +</pre> + </div> + </div> + </div> + + <div id="method-M000015" class="method-detail"> + <a name="M000015"></a> + + <div class="method-heading"> + <a href="#M000015" class="method-signature"> + <span class="method-name">features</span><span class="method-args">(compound)</span> + </a> + </div> + + <div class="method-description"> + <p> +Get all <a href="Dataset.html#M000015">features</a> for a compound +</p> + <p><a class="source-toggle" href="#" + onclick="toggleCode('M000015-source');return false;">[Source]</a></p> + <div class="method-source-code" id="M000015-source"> +<pre> +<span class="ruby-comment cmt"># File lib/opentox-ruby-api-wrapper.rb, line 113</span> + <span class="ruby-keyword kw">def</span> <span class="ruby-identifier">features</span>(<span class="ruby-identifier">compound</span>) + <span class="ruby-constant">RestClient</span>.<span class="ruby-identifier">get</span>(<span class="ruby-ivar">@uri</span> <span class="ruby-operator">+</span> <span class="ruby-value str">'/compound/'</span> <span class="ruby-operator">+</span> <span class="ruby-identifier">uri_escape</span>(<span class="ruby-identifier">compound</span>.<span class="ruby-identifier">uri</span>) <span class="ruby-operator">+</span> <span class="ruby-value str">'/features'</span>).<span class="ruby-identifier">split</span>(<span class="ruby-value str">"\n"</span>).<span class="ruby-identifier">collect</span>{<span class="ruby-operator">|</span><span class="ruby-identifier">f</span><span class="ruby-operator">|</span> <span class="ruby-constant">Feature</span>.<span class="ruby-identifier">new</span>(<span class="ruby-identifier">:uri</span> =<span class="ruby-operator">></span> <span class="ruby-identifier">f</span>) } + <span class="ruby-keyword kw">end</span> +</pre> + </div> + </div> + </div> + + <div id="method-M000011" class="method-detail"> + <a name="M000011"></a> + + <div class="method-heading"> + <a href="#M000011" class="method-signature"> + <span class="method-name">name</span><span class="method-args">()</span> + </a> + </div> + + <div class="method-description"> + <p> +Get the dataset <a href="Dataset.html#M000011">name</a> +</p> + <p><a class="source-toggle" href="#" + onclick="toggleCode('M000011-source');return false;">[Source]</a></p> + <div class="method-source-code" id="M000011-source"> +<pre> +<span class="ruby-comment cmt"># File lib/opentox-ruby-api-wrapper.rb, line 88</span> + <span class="ruby-keyword kw">def</span> <span class="ruby-identifier">name</span> + <span class="ruby-constant">RestClient</span>.<span class="ruby-identifier">get</span> <span class="ruby-ivar">@uri</span> <span class="ruby-operator">+</span> <span class="ruby-value str">'/name'</span> + <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>
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