RubyGems - bioportal - Versions diffs - 2.1 - Mend

bioportal 2.1

This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.

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>