RubyGems - bioportal - Versions diffs - 2.1 - Mend

bioportal 2.1

Files changed (42) hide show

checksums.yaml +7 -0
data/.gitignore +3 -0
data/.ruby-gemset +1 -0
data/BSD-LICENSE +23 -0
data/Gemfile +5 -0
data/Gemfile.lock +30 -0
data/README.rdoc +11 -0
data/Rakefile +24 -0
data/app/helpers/bio_portal_helper.rb +17 -0
data/app/models/bioportal_concept.rb +39 -0
data/app/views/bioportal/_bioportal_visualise.html.erb +2 -0
data/bioportal.gemspec +11 -0
data/generators/bioportal_migration/USAGE +8 -0
data/generators/bioportal_migration/bioportal_migration_generator.rb +7 -0
data/generators/bioportal_migration/templates/migration.rb +16 -0
data/install.rb +1 -0
data/lib/bioportal.rb +178 -0
data/lib/bioportal/engine.rb +5 -0
data/lib/tasks/bioportal_tasks.rake +4 -0
data/rdoc/classes/BioPortal.html +112 -0
data/rdoc/classes/BioPortal/Acts.html +148 -0
data/rdoc/classes/BioPortal/Acts/ClassMethods.html +160 -0
data/rdoc/classes/BioPortal/Acts/InstanceMethods.html +325 -0
data/rdoc/classes/BioPortal/Acts/SingletonMethods.html +105 -0
data/rdoc/classes/BioPortal/RestAPI.html +489 -0
data/rdoc/classes/BioPortalHelper.html +334 -0
data/rdoc/classes/BioportalConcept.html +251 -0
data/rdoc/created.rid +1 -0
data/rdoc/files/BSD-LICENSE.html +134 -0
data/rdoc/files/README.html +213 -0
data/rdoc/files/app/helpers/bio_portal_helper_rb.html +108 -0
data/rdoc/files/app/models/bioportal_concept_rb.html +101 -0
data/rdoc/files/lib/bioportal_rb.html +112 -0
data/rdoc/fr_class_index.html +34 -0
data/rdoc/fr_file_index.html +31 -0
data/rdoc/fr_method_index.html +53 -0
data/rdoc/index.html +24 -0
data/rdoc/rdoc-style.css +208 -0
data/test/bioportal_test.rb +60 -0
data/test/test_helper.rb +18 -0
data/uninstall.rb +1 -0
metadata +84 -0

data/rdoc/classes/BioPortalHelper.html ADDED

@@ -0,0 +1,334 @@
+<?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>Module: BioPortalHelper</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>Module</strong></td>
+          <td class="class-name-in-header">BioPortalHelper</td>
+        </tr>
+        <tr class="top-aligned-row">
+            <td><strong>In:</strong></td>
+            <td>
+                <a href="../files/app/helpers/bio_portal_helper_rb.html">
+                app/helpers/bio_portal_helper.rb
+                </a>
+        <br />
+            </td>
+        </tr>
+        </table>
+    </div>
+  <!-- banner header -->
+  <div id="bodyContent">
+  <div id="contextContent">
+    <div id="description">
+      <p>
+To change this template, choose Tools | Templates and open the template in
+the editor.
+</p>
+    </div>
+   </div>
+    <div id="method-list">
+      <h3 class="section-bar">Methods</h3>
+      <div class="name-list">
+      <a href="#M000011">bioportal_form_complete</a>&nbsp;&nbsp;
+      <a href="#M000006">link_to_concept_id</a>&nbsp;&nbsp;
+      <a href="#M000010">link_to_download_ontology</a>&nbsp;&nbsp;
+      <a href="#M000007">link_to_ontology</a>&nbsp;&nbsp;
+      <a href="#M000008">link_to_ontology_version</a>&nbsp;&nbsp;
+      <a href="#M000009">link_to_ontology_version_visualize</a>&nbsp;&nbsp;
+      <a href="#M000005">visualise_ontology</a>&nbsp;&nbsp;
+      </div>
+    </div>
+  </div>
+    <!-- if includes -->
+    <div id="section">
+    <div id="constants-list">
+      <h3 class="section-bar">Constants</h3>
+      <div class="name-list">
+        <table summary="Constants">
+        <tr class="top-aligned-row context-row">
+          <td class="context-item-name">BIOPORTAL_BASE_URL</td>
+          <td>=</td>
+          <td class="context-item-value">&quot;http://bioportal.bioontology.org&quot;</td>
+        </tr>
+        <tr class="top-aligned-row context-row">
+          <td class="context-item-name">BIOPORTAL_REST_BASE_URL</td>
+          <td>=</td>
+          <td class="context-item-value">&quot;http://rest.bioontology.org&quot;</td>
+        </tr>
+        </table>
+      </div>
+    </div>
+    <!-- if method_list -->
+    <div id="methods">
+      <h3 class="section-bar">Public Instance methods</h3>
+      <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">bioportal_form_complete</span><span class="method-args">(options,html_options={})</span>
+          </a>
+        </div>
+        <div class="method-description">
+          <p>
+options include
+</p>
+<pre>
+ - name - the name thats used as a prefix to the element names
+ - ontology_ids - arrays of ontology_ids (an element of &quot;all&quot; indicates all ontologies)
+ - no_javascript_include - if present will not include the javascript_include_tag for the bioportal_form_complete.js
+ - value - uri,shortid or name. defaults to name
+</pre>
+          <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 app/helpers/bio_portal_helper.rb, line 48</span>
+48:   <span class="ruby-keyword kw">def</span> <span class="ruby-identifier">bioportal_form_complete</span> <span class="ruby-identifier">options</span>,<span class="ruby-identifier">html_options</span>={}
+49:     <span class="ruby-identifier">options</span>[<span class="ruby-identifier">:value</span>]<span class="ruby-operator">||=</span><span class="ruby-value str">&quot;name&quot;</span>
+50:     <span class="ruby-identifier">result</span> = <span class="ruby-value str">&quot;&quot;</span>
+51:     <span class="ruby-identifier">result</span> <span class="ruby-operator">+=</span> <span class="ruby-identifier">javascript_include_tag</span>(<span class="ruby-value str">&quot;bioportal_form_complete.js&quot;</span>) <span class="ruby-keyword kw">unless</span> <span class="ruby-identifier">options</span>[<span class="ruby-identifier">:no_javascript_include</span>]
+52:
+53:     <span class="ruby-identifier">html_options</span>[<span class="ruby-identifier">:class</span>]=<span class="ruby-node">&quot;bp_form_complete-#{options[:ontology_ids].join(',')}-#{options[:value]}&quot;</span>
+54:     <span class="ruby-identifier">name</span> = <span class="ruby-identifier">options</span>[<span class="ruby-identifier">:name</span>]
+55:     <span class="ruby-identifier">result</span> <span class="ruby-operator">+=</span> <span class="ruby-identifier">text_field_tag</span> <span class="ruby-identifier">name</span>,<span class="ruby-keyword kw">nil</span>,<span class="ruby-identifier">html_options</span>
+56:     <span class="ruby-keyword kw">return</span> <span class="ruby-identifier">result</span>
+57:   <span class="ruby-keyword kw">end</span>
+</pre>
+          </div>
+        </div>
+      </div>
+      <div id="method-M000006" class="method-detail">
+        <a name="M000006"></a>
+        <div class="method-heading">
+          <a href="#M000006" class="method-signature">
+          <span class="method-name">link_to_concept_id</span><span class="method-args">(name,concept_id,ontology_version_id,options={})</span>
+          </a>
+        </div>
+        <div class="method-description">
+          <p><a class="source-toggle" href="#"
+            onclick="toggleCode('M000006-source');return false;">[Source]</a></p>
+          <div class="method-source-code" id="M000006-source">
+<pre>
+    <span class="ruby-comment cmt"># File app/helpers/bio_portal_helper.rb, line 19</span>
+19:   <span class="ruby-keyword kw">def</span> <span class="ruby-identifier">link_to_concept_id</span> <span class="ruby-identifier">name</span>,<span class="ruby-identifier">concept_id</span>,<span class="ruby-identifier">ontology_version_id</span>,<span class="ruby-identifier">options</span>={},<span class="ruby-identifier">html_options</span>={}
+20:     <span class="ruby-identifier">options</span>[<span class="ruby-identifier">:popup</span>]<span class="ruby-operator">||=</span><span class="ruby-keyword kw">true</span>
+21:     <span class="ruby-identifier">link_to</span>(<span class="ruby-identifier">h</span>(<span class="ruby-identifier">name</span>),<span class="ruby-constant">BIOPORTAL_BASE_URL</span><span class="ruby-operator">+</span><span class="ruby-value str">&quot;/visualize/&quot;</span><span class="ruby-operator">+</span><span class="ruby-identifier">ontology_version_id</span>.<span class="ruby-identifier">to_s</span><span class="ruby-operator">+</span><span class="ruby-value str">&quot;/?conceptid=&quot;</span><span class="ruby-operator">+</span><span class="ruby-constant">URI</span>.<span class="ruby-identifier">encode</span>(<span class="ruby-identifier">concept_id</span>),<span class="ruby-identifier">options</span>,<span class="ruby-identifier">html_options</span>)
+22:   <span class="ruby-keyword kw">end</span>
+</pre>
+          </div>
+        </div>
+      </div>
+      <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">link_to_download_ontology</span><span class="method-args">(name,ontology_version_id,options={})</span>
+          </a>
+        </div>
+        <div class="method-description">
+          <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 app/helpers/bio_portal_helper.rb, line 39</span>
+39:   <span class="ruby-keyword kw">def</span> <span class="ruby-identifier">link_to_download_ontology</span> <span class="ruby-identifier">name</span>,<span class="ruby-identifier">ontology_version_id</span>,<span class="ruby-identifier">options</span>={},<span class="ruby-identifier">html_options</span>={}
+40:     <span class="ruby-identifier">link_to</span>(<span class="ruby-identifier">h</span>(<span class="ruby-identifier">name</span>),<span class="ruby-constant">BIOPORTAL_REST_BASE_URL</span><span class="ruby-operator">+</span><span class="ruby-value str">&quot;/bioportal/ontologies/download/&quot;</span><span class="ruby-operator">+</span><span class="ruby-identifier">ontology_version_id</span>,<span class="ruby-identifier">options</span>,<span class="ruby-identifier">html_options</span>)
+41:   <span class="ruby-keyword kw">end</span>
+</pre>
+          </div>
+        </div>
+      </div>
+      <div id="method-M000007" class="method-detail">
+        <a name="M000007"></a>
+        <div class="method-heading">
+          <a href="#M000007" class="method-signature">
+          <span class="method-name">link_to_ontology</span><span class="method-args">(name,ontology_id,options={})</span>
+          </a>
+        </div>
+        <div class="method-description">
+          <p><a class="source-toggle" href="#"
+            onclick="toggleCode('M000007-source');return false;">[Source]</a></p>
+          <div class="method-source-code" id="M000007-source">
+<pre>
+    <span class="ruby-comment cmt"># File app/helpers/bio_portal_helper.rb, line 24</span>
+24:   <span class="ruby-keyword kw">def</span> <span class="ruby-identifier">link_to_ontology</span> <span class="ruby-identifier">name</span>,<span class="ruby-identifier">ontology_id</span>,<span class="ruby-identifier">options</span>={},<span class="ruby-identifier">html_options</span>={}
+25:     <span class="ruby-identifier">options</span>[<span class="ruby-identifier">:popup</span>]<span class="ruby-operator">||=</span><span class="ruby-keyword kw">true</span>
+26:     <span class="ruby-identifier">link_to</span>(<span class="ruby-identifier">h</span>(<span class="ruby-identifier">name</span>),<span class="ruby-constant">BIOPORTAL_BASE_URL</span><span class="ruby-operator">+</span><span class="ruby-value str">&quot;/virtual/&quot;</span><span class="ruby-operator">+</span><span class="ruby-identifier">ontology_id</span>.<span class="ruby-identifier">to_s</span>,<span class="ruby-identifier">options</span>,<span class="ruby-identifier">html_options</span>)
+27:   <span class="ruby-keyword kw">end</span>
+</pre>
+          </div>
+        </div>
+      </div>
+      <div id="method-M000008" class="method-detail">
+        <a name="M000008"></a>
+        <div class="method-heading">
+          <a href="#M000008" class="method-signature">
+          <span class="method-name">link_to_ontology_version</span><span class="method-args">(name,ontology_version_id,options={})</span>
+          </a>
+        </div>
+        <div class="method-description">
+          <p><a class="source-toggle" href="#"
+            onclick="toggleCode('M000008-source');return false;">[Source]</a></p>
+          <div class="method-source-code" id="M000008-source">
+<pre>
+    <span class="ruby-comment cmt"># File app/helpers/bio_portal_helper.rb, line 29</span>
+29:   <span class="ruby-keyword kw">def</span> <span class="ruby-identifier">link_to_ontology_version</span> <span class="ruby-identifier">name</span>,<span class="ruby-identifier">ontology_version_id</span>,<span class="ruby-identifier">options</span>={},<span class="ruby-identifier">html_options</span>={}
+30:     <span class="ruby-identifier">options</span>[<span class="ruby-identifier">:popup</span>]<span class="ruby-operator">||=</span><span class="ruby-keyword kw">true</span>
+31:     <span class="ruby-identifier">link_to</span>(<span class="ruby-identifier">h</span>(<span class="ruby-identifier">name</span>),<span class="ruby-constant">BIOPORTAL_BASE_URL</span><span class="ruby-operator">+</span><span class="ruby-value str">&quot;/ontologies/&quot;</span><span class="ruby-operator">+</span><span class="ruby-identifier">ontology_version_id</span>.<span class="ruby-identifier">to_s</span>,<span class="ruby-identifier">options</span>,<span class="ruby-identifier">html_options</span>)
+32:   <span class="ruby-keyword kw">end</span>
+</pre>
+          </div>
+        </div>
+      </div>
+      <div id="method-M000009" class="method-detail">
+        <a name="M000009"></a>
+        <div class="method-heading">
+          <a href="#M000009" class="method-signature">
+          <span class="method-name">link_to_ontology_version_visualize</span><span class="method-args">(name,ontology_version_id,options={})</span>
+          </a>
+        </div>
+        <div class="method-description">
+          <p><a class="source-toggle" href="#"
+            onclick="toggleCode('M000009-source');return false;">[Source]</a></p>
+          <div class="method-source-code" id="M000009-source">
+<pre>
+    <span class="ruby-comment cmt"># File app/helpers/bio_portal_helper.rb, line 34</span>
+34:   <span class="ruby-keyword kw">def</span> <span class="ruby-identifier">link_to_ontology_version_visualize</span> <span class="ruby-identifier">name</span>,<span class="ruby-identifier">ontology_version_id</span>,<span class="ruby-identifier">options</span>={},<span class="ruby-identifier">html_options</span>={}
+35:     <span class="ruby-identifier">options</span>[<span class="ruby-identifier">:popup</span>]<span class="ruby-operator">||=</span><span class="ruby-keyword kw">true</span>
+36:     <span class="ruby-identifier">link_to</span>(<span class="ruby-identifier">h</span>(<span class="ruby-identifier">name</span>),<span class="ruby-constant">BIOPORTAL_BASE_URL</span><span class="ruby-operator">+</span><span class="ruby-value str">&quot;/visualize/&quot;</span><span class="ruby-operator">+</span><span class="ruby-identifier">ontology_version_id</span>.<span class="ruby-identifier">to_s</span>,<span class="ruby-identifier">options</span>,<span class="ruby-identifier">html_options</span>)
+37:   <span class="ruby-keyword kw">end</span>
+</pre>
+          </div>
+        </div>
+      </div>
+      <div id="method-M000005" class="method-detail">
+        <a name="M000005"></a>
+        <div class="method-heading">
+          <a href="#M000005" class="method-signature">
+          <span class="method-name">visualise_ontology</span><span class="method-args">(model,options={})</span>
+          </a>
+        </div>
+        <div class="method-description">
+          <p><a class="source-toggle" href="#"
+            onclick="toggleCode('M000005-source');return false;">[Source]</a></p>
+          <div class="method-source-code" id="M000005-source">
+<pre>
+    <span class="ruby-comment cmt"># File app/helpers/bio_portal_helper.rb, line 10</span>
+10:   <span class="ruby-keyword kw">def</span> <span class="ruby-identifier">visualise_ontology</span> <span class="ruby-identifier">model</span>,<span class="ruby-identifier">options</span>={}
+11:     <span class="ruby-identifier">options</span>[<span class="ruby-identifier">:show_concept</span>]<span class="ruby-operator">||=</span><span class="ruby-keyword kw">false</span>
+12:     <span class="ruby-identifier">concept_id</span>=<span class="ruby-keyword kw">nil</span>
+13:     <span class="ruby-identifier">concept_id</span>=<span class="ruby-identifier">model</span>.<span class="ruby-identifier">concept_uri</span> <span class="ruby-keyword kw">if</span> <span class="ruby-identifier">options</span>[<span class="ruby-identifier">:show_concept</span>] <span class="ruby-operator">&amp;&amp;</span> <span class="ruby-operator">!</span><span class="ruby-identifier">model</span>.<span class="ruby-identifier">concept_uri</span>.<span class="ruby-identifier">nil?</span>
+14:     <span class="ruby-identifier">ontology_id</span>=<span class="ruby-identifier">model</span>.<span class="ruby-identifier">ontology_version_id</span>
+15:     <span class="ruby-identifier">ontology_id</span> <span class="ruby-operator">||=</span> <span class="ruby-identifier">model</span>.<span class="ruby-identifier">ontology_id</span>
+16:     <span class="ruby-identifier">render</span>(<span class="ruby-identifier">:partial=</span><span class="ruby-operator">&gt;</span><span class="ruby-value str">&quot;bioportal/bioportal_visualise&quot;</span>,<span class="ruby-identifier">:locals=</span><span class="ruby-operator">&gt;</span>{<span class="ruby-identifier">:ontology_id=</span><span class="ruby-operator">&gt;</span><span class="ruby-identifier">ontology_id</span>,<span class="ruby-identifier">:concept_id=</span><span class="ruby-operator">&gt;</span><span class="ruby-identifier">concept_id</span>})
+17:   <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/rdoc/classes/BioportalConcept.html ADDED

@@ -0,0 +1,251 @@
+<?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: BioportalConcept</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">BioportalConcept</td>
+        </tr>
+        <tr class="top-aligned-row">
+            <td><strong>In:</strong></td>
+            <td>
+                <a href="../files/app/models/bioportal_concept_rb.html">
+                app/models/bioportal_concept.rb
+                </a>
+        <br />
+            </td>
+        </tr>
+        <tr class="top-aligned-row">
+            <td><strong>Parent:</strong></td>
+            <td>
+                ActiveRecord::Base
+            </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="#M000003">bioportal_base_rest_url</a>&nbsp;&nbsp;
+      <a href="#M000004">check_cached_concept</a>&nbsp;&nbsp;
+      <a href="#M000001">get_concept</a>&nbsp;&nbsp;
+      <a href="#M000002">get_ontology</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"><a href="BioPortal/RestAPI.html">BioPortal::RestAPI</a></span>
+      </div>
+    </div>
+    <div id="section">
+    <!-- if method_list -->
+    <div id="methods">
+      <h3 class="section-bar">Public Instance methods</h3>
+      <div id="method-M000003" class="method-detail">
+        <a name="M000003"></a>
+        <div class="method-heading">
+          <a href="#M000003" class="method-signature">
+          <span class="method-name">bioportal_base_rest_url</span><span class="method-args">()</span>
+          </a>
+        </div>
+        <div class="method-description">
+          <p>
+the base url is defined by the associated class - this overrides the method
+in the RestAPI mixin
+</p>
+          <p><a class="source-toggle" href="#"
+            onclick="toggleCode('M000003-source');return false;">[Source]</a></p>
+          <div class="method-source-code" id="M000003-source">
+<pre>
+    <span class="ruby-comment cmt"># File app/models/bioportal_concept.rb, line 29</span>
+29:   <span class="ruby-keyword kw">def</span> <span class="ruby-identifier">bioportal_base_rest_url</span>
+30:     <span class="ruby-identifier">conceptable</span>.<span class="ruby-identifier">bioportal_base_rest_url</span>
+31:   <span class="ruby-keyword kw">end</span>
+</pre>
+          </div>
+        </div>
+      </div>
+      <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">get_concept</span><span class="method-args">(options={})</span>
+          </a>
+        </div>
+        <div class="method-description">
+          <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 app/models/bioportal_concept.rb, line 8</span>
+ 8:   <span class="ruby-keyword kw">def</span> <span class="ruby-identifier">get_concept</span> <span class="ruby-identifier">options</span>={}
+ 9:     <span class="ruby-identifier">options</span>[<span class="ruby-identifier">:refresh</span>]<span class="ruby-operator">||=</span><span class="ruby-keyword kw">false</span>
+10:
+11:     <span class="ruby-identifier">refresh</span>=<span class="ruby-identifier">options</span>.<span class="ruby-identifier">delete</span>(<span class="ruby-identifier">:refresh</span>)
+12:
+13:     <span class="ruby-identifier">concept</span> = <span class="ruby-constant">YAML</span><span class="ruby-operator">::</span><span class="ruby-identifier">load</span>(<span class="ruby-identifier">cached_concept_yaml</span>) <span class="ruby-keyword kw">unless</span> (<span class="ruby-identifier">refresh</span> <span class="ruby-operator">||</span> <span class="ruby-identifier">cached_concept_yaml</span>.<span class="ruby-identifier">nil?</span>)
+14:     <span class="ruby-keyword kw">unless</span> <span class="ruby-identifier">concept</span>
+15:       <span class="ruby-identifier">concept</span> = <span class="ruby-keyword kw">super</span>(<span class="ruby-keyword kw">self</span>.<span class="ruby-identifier">ontology_version_id</span>,<span class="ruby-keyword kw">self</span>.<span class="ruby-identifier">concept_uri</span>,<span class="ruby-identifier">options</span>)
+16:       <span class="ruby-identifier">update_attribute</span>(<span class="ruby-identifier">:cached_concept_yaml</span>, <span class="ruby-identifier">concept</span>.<span class="ruby-identifier">to_yaml</span>)
+17:     <span class="ruby-keyword kw">end</span>
+18:
+19:     <span class="ruby-keyword kw">return</span> <span class="ruby-identifier">concept</span>
+20:   <span class="ruby-keyword kw">end</span>
+</pre>
+          </div>
+        </div>
+      </div>
+      <div id="method-M000002" class="method-detail">
+        <a name="M000002"></a>
+        <div class="method-heading">
+          <a href="#M000002" class="method-signature">
+          <span class="method-name">get_ontology</span><span class="method-args">(options={})</span>
+          </a>
+        </div>
+        <div class="method-description">
+          <p><a class="source-toggle" href="#"
+            onclick="toggleCode('M000002-source');return false;">[Source]</a></p>
+          <div class="method-source-code" id="M000002-source">
+<pre>
+    <span class="ruby-comment cmt"># File app/models/bioportal_concept.rb, line 22</span>
+22:   <span class="ruby-keyword kw">def</span> <span class="ruby-identifier">get_ontology</span> <span class="ruby-identifier">options</span>={}
+23:     <span class="ruby-identifier">ontology</span> = <span class="ruby-identifier">get_ontology_details</span> <span class="ruby-keyword kw">self</span>.<span class="ruby-identifier">ontology_version_id</span>,<span class="ruby-identifier">options</span>
+24:
+25:     <span class="ruby-keyword kw">return</span> <span class="ruby-identifier">ontology</span>
+26:   <span class="ruby-keyword kw">end</span>
+</pre>
+          </div>
+        </div>
+      </div>
+      <h3 class="section-bar">Protected Instance methods</h3>
+      <div id="method-M000004" class="method-detail">
+        <a name="M000004"></a>
+        <div class="method-heading">
+          <a href="#M000004" class="method-signature">
+          <span class="method-name">check_cached_concept</span><span class="method-args">()</span>
+          </a>
+        </div>
+        <div class="method-description">
+          <p>
+invoked before_save, and if the ontology_id, ontology_version_id or
+concept_uri has changed then the cached concept will be cleared
+</p>
+          <p><a class="source-toggle" href="#"
+            onclick="toggleCode('M000004-source');return false;">[Source]</a></p>
+          <div class="method-source-code" id="M000004-source">
+<pre>
+    <span class="ruby-comment cmt"># File app/models/bioportal_concept.rb, line 36</span>
+36:   <span class="ruby-keyword kw">def</span> <span class="ruby-identifier">check_cached_concept</span>
+37:     <span class="ruby-identifier">changed_fields</span> = <span class="ruby-identifier">changes</span>.<span class="ruby-identifier">keys</span>
+38:
+39:     <span class="ruby-keyword kw">if</span> <span class="ruby-operator">!</span>(<span class="ruby-identifier">changed_fields</span> <span class="ruby-operator">&amp;</span> [<span class="ruby-value str">&quot;ontology_id&quot;</span>,<span class="ruby-value str">&quot;ontology_version_id&quot;</span>,<span class="ruby-value str">&quot;concept_uri&quot;</span>]).<span class="ruby-identifier">empty?</span>
+40:       <span class="ruby-keyword kw">self</span>.<span class="ruby-identifier">cached_concept_yaml</span>=<span class="ruby-keyword kw">nil</span>
+41:     <span class="ruby-keyword kw">end</span>
+42:   <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>