- added sequence resource and corresponding doc

.yardoc/checksums

@@ -1,3 +1,4 @@
-lib/classyfire_api.rb ed7783c1c688d4ee2a91044082a5ac80c3cd3c3e
+lib/classyfire_api.rb 4e5cc4102771d77c67759b9298ae685f0cb612cd
 lib/query_resource.rb 645cfb1688a5c44e67e5227fc0e9a77589731f24
 lib/entity_resource.rb 6c50b4be6a5eb13b44d7080b19c7033b7a37c7cf
+lib/sequence_resource.rb d8c5007781d50d0bc13cbe360b617e2937a19428

README.md

@@ -41,13 +41,31 @@
 > > >
 > > >The output format is "json" (JSON).
 
+> ##2. Sequence##
+>
+> >Sequences are represented by the Sequence model, through which one can access the compound's structure-based classification.
+> >
+> >###GET###
+> >
+> >**/sequence/{fingerprint}**
+> >
+> >A (FASTA) sequence's classification can be retrieved in the JSON. In this example, the sequence has the fingerprint = "8bf70c23ac100cd2c3955081d8613325"
+> > >
+> > >ClassyFireAPI.get_sequence_classification("8bf70c23ac100cd2c3955081d8613325","json")
+> >
+> > Where:
+> >
+> > >The sequence's fingerprint is "8bf70c23ac100cd2c3955081d8613325",
+> > > > The fingerprint is generate by Digest::MD5 from the peptide sequence "APDVQDCPECTLQENPFFSQPGAPILQCMGCCFSRAYPTPLRSKKTMLVQKNVTSESTCCVAKSYNRVTVMGGFKVENHTACHCSTCYYHKS"
+> > >The output format is "json" (JSON).
 
-> ##2. Query##
+
+> ##3. Query##
 >
 > >The Query model represents the chemical structure to be classified. Its attributes are the query label and the query input.
 > > >The query label is an identifier
 > > >
-> > >The query input contains the compound's identifier (optional) and its structural representation, separated by a comma. The chemical structure is represented either in the [Daylight SMILES](http://www.daylight.com/dayhtml/doc/theory/theory.smiles.html) or the [InChI](http://www.iupac.org/home/publications/e-resources/inchi.html) format.
+> > >The query input contains the compound's identifier (optional) and its structural representation, separated by a tab. The chemical structure is represented either in the [Daylight SMILES](http://www.daylight.com/dayhtml/doc/theory/theory.smiles.html) format, the [InChI](http://www.iupac.org/home/publications/e-resources/inchi.html) format. Moreover, the compound can be represented with its [IUPAC name](http://www.chem.qmul.ac.uk/iupac/).
 > >
 > >###POST###
 > >A query can be submitted using the POST method as demonstrated in the following example.

doc/ClassyFireAPI.html

@@ -156,6 +156,30 @@
 <p>Retrieves the classification results for a given query.</p>
 </div></span>
   
+</li>
+
+      
+        <li class="public ">
+  <span class="summary_signature">
+    
+      <a href="#get_sequence_classification-class_method" title="get_sequence_classification (class method)">+ (Text) <strong>get_sequence_classification</strong>(fingerprint, format = &quot;json&quot;) </a>
+    
+
+    
+  </span>
+  
+  
+  
+  
+  
+  
+  
+
+  
+    <span class="summary_desc"><div class='inline'>
+<p>Retrieves the classification results for a given sequence.</p>
+</div></span>
+  
 </li>
 
       
@@ -400,7 +424,7 @@ of a given size.</p>
       
         &mdash;
         <div class='inline'>
-<p>the ID of the query.</p>
+<p>the InChIKey of the entity.</p>
 </div>
       
     </li>
@@ -629,6 +653,129 @@ specified format.</p>
     </td>
   </tr>
 </table>
+</div>
+    
+      <div class="method_details ">
+  <h3 class="signature " id="get_sequence_classification-class_method">
+  
+    + (<tt>Text</tt>) <strong>get_sequence_classification</strong>(fingerprint, format = &quot;json&quot;) 
+  
+
+  
+
+  
+</h3><div class="docstring">
+  <div class="discussion">
+    
+<p>Retrieves the classification results for a given sequence.</p>
+
+
+  </div>
+</div>
+<div class="tags">
+  <p class="tag_title">Parameters:</p>
+<ul class="param">
+  
+    <li>
+      
+        <span class='name'>the</span>
+      
+      
+        <span class='type'></span>
+      
+      
+      
+        &mdash;
+        <div class='inline'>
+<p>fingerprint [String] the fingerprint (generated from the sequence using
+Digest::MD5).</p>
+</div>
+      
+    </li>
+  
+    <li>
+      
+        <span class='name'>format</span>
+      
+      
+        <span class='type'>(<tt>String</tt>)</span>
+      
+      
+        <em class="default">(defaults to: <tt>&quot;json&quot;</tt>)</em>
+      
+      
+        &mdash;
+        <div class='inline'>
+<p>the format of the query (Only JSON)</p>
+</div>
+      
+    </li>
+  
+</ul>
+
+<p class="tag_title">Returns:</p>
+<ul class="return">
+  
+    <li>
+      
+      
+        <span class='type'>(<tt>Text</tt>)</span>
+      
+      
+      
+        &mdash;
+        <div class='inline'>
+<p>A text file displaying the classification results for the entity in the
+specified format.</p>
+</div>
+      
+    </li>
+  
+</ul>
+
+</div><table class="source_code">
+  <tr>
+    <td>
+      <pre class="lines">
+
+
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+    </td>
+    <td>
+      <pre class="code"><span class="info file"># File 'lib/classyfire_api.rb', line 87</span>
+
+<span class='kw'>def</span> <span class='const'>ClassyFireAPI</span><span class='period'>.</span><span class='id identifier rubyid_get_sequence_classification'>get_sequence_classification</span><span class='lparen'>(</span><span class='id identifier rubyid_fingerprint'>fingerprint</span><span class='comma'>,</span><span class='id identifier rubyid_format'>format</span><span class='op'>=</span><span class='tstring'><span class='tstring_beg'>&quot;</span><span class='tstring_content'>json</span><span class='tstring_end'>&quot;</span></span><span class='rparen'>)</span>
+  <span class='kw'>begin</span>
+    <span class='kw'>if</span> <span class='id identifier rubyid_format'>format</span> <span class='op'>==</span> <span class='tstring'><span class='tstring_beg'>&quot;</span><span class='tstring_content'>json</span><span class='tstring_end'>&quot;</span></span>
+      <span class='const'>RestClient</span><span class='period'>.</span><span class='id identifier rubyid_get'>get</span> <span class='tstring'><span class='tstring_beg'>&quot;</span><span class='embexpr_beg'>#{</span><span class='const'>URL</span><span class='embexpr_end'>}</span><span class='tstring_content'>/entities/</span><span class='embexpr_beg'>#{</span><span class='id identifier rubyid_fingerprint'>fingerprint</span><span class='embexpr_end'>}</span><span class='tstring_content'>.</span><span class='embexpr_beg'>#{</span><span class='id identifier rubyid_format'>format</span><span class='embexpr_end'>}</span><span class='tstring_end'>&quot;</span></span><span class='comma'>,</span> <span class='symbol'>:accept</span> <span class='op'>=&gt;</span> <span class='symbol'>:json</span>
+    <span class='kw'>end</span> 
+  <span class='kw'>rescue</span> <span class='const'>RestClient</span><span class='op'>::</span><span class='const'>ResourceNotFound</span> <span class='op'>=&gt;</span> <span class='id identifier rubyid_e'>e</span>
+    <span class='id identifier rubyid_e'>e</span><span class='period'>.</span><span class='id identifier rubyid_response'>response</span>
+  <span class='kw'>rescue</span>  <span class='const'>RestClient</span><span class='op'>::</span><span class='const'>InternalServerError</span> <span class='op'>=&gt;</span> <span class='id identifier rubyid_e'>e</span>
+    <span class='id identifier rubyid_e'>e</span><span class='period'>.</span><span class='id identifier rubyid_response'>response</span>
+  <span class='kw'>rescue</span> <span class='const'>RestClient</span><span class='op'>::</span><span class='const'>GatewayTimeout</span> <span class='op'>=&gt;</span> <span class='id identifier rubyid_e'>e</span>
+    <span class='id identifier rubyid_e'>e</span><span class='period'>.</span><span class='id identifier rubyid_response'>response</span>
+  <span class='kw'>rescue</span> <span class='const'>RestClient</span><span class='op'>::</span><span class='const'>RequestTimeout</span> <span class='op'>=&gt;</span> <span class='id identifier rubyid_e'>e</span>
+    <span class='id identifier rubyid_e'>e</span><span class='period'>.</span><span class='id identifier rubyid_response'>response</span>
+  <span class='kw'>end</span>
+<span class='kw'>end</span></pre>
+    </td>
+  </tr>
+</table>
 </div>
     
       <div class="method_details ">
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-      <pre class="code"><span class="info file"># File 'lib/classyfire_api.rb', line 85</span>
+      <pre class="code"><span class="info file"># File 'lib/classyfire_api.rb', line 128</span>
 
 <span class='kw'>def</span> <span class='const'>ClassyFireAPI</span><span class='period'>.</span><span class='id identifier rubyid_query_status'>query_status</span><span class='lparen'>(</span><span class='id identifier rubyid_query_id'>query_id</span><span class='rparen'>)</span>
   <span class='kw'>begin</span>
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-      <pre class="code"><span class="info file"># File 'lib/classyfire_api.rb', line 266</span>
+      <pre class="code"><span class="info file"># File 'lib/classyfire_api.rb', line 309</span>
 
 <span class='kw'>def</span> <span class='const'>ClassyFireAPI</span><span class='period'>.</span><span class='id identifier rubyid_retrieve_classification'>retrieve_classification</span><span class='lparen'>(</span><span class='id identifier rubyid_input'>input</span><span class='comma'>,</span><span class='id identifier rubyid_output'>output</span><span class='rparen'>)</span>
   <span class='id identifier rubyid_absolute_path'>absolute_path</span> <span class='op'>=</span> <span class='const'>File</span><span class='period'>.</span><span class='id identifier rubyid_expand_path'>expand_path</span><span class='lparen'>(</span><span class='id identifier rubyid_input'>input</span><span class='rparen'>)</span>
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-      <pre class="code"><span class="info file"># File 'lib/classyfire_api.rb', line 335</span>
+      <pre class="code"><span class="info file"># File 'lib/classyfire_api.rb', line 378</span>
 
 <span class='kw'>def</span> <span class='const'>ClassyFireAPI</span><span class='period'>.</span><span class='id identifier rubyid_retrieve_entities_json'>retrieve_entities_json</span><span class='lparen'>(</span><span class='id identifier rubyid_input'>input</span><span class='comma'>,</span><span class='id identifier rubyid_output'>output</span><span class='rparen'>)</span>
   <span class='id identifier rubyid_absolute_path'>absolute_path</span> <span class='op'>=</span> <span class='const'>File</span><span class='period'>.</span><span class='id identifier rubyid_expand_path'>expand_path</span><span class='lparen'>(</span><span class='id identifier rubyid_input'>input</span><span class='rparen'>)</span>
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-      <pre class="code"><span class="info file"># File 'lib/classyfire_api.rb', line 397</span>
+      <pre class="code"><span class="info file"># File 'lib/classyfire_api.rb', line 440</span>
 
 <span class='kw'>def</span> <span class='const'>ClassyFireAPI</span><span class='period'>.</span><span class='id identifier rubyid_retrieve_entities_sdf'>retrieve_entities_sdf</span><span class='lparen'>(</span><span class='id identifier rubyid_input'>input</span><span class='comma'>,</span><span class='id identifier rubyid_output'>output</span><span class='rparen'>)</span>
   <span class='id identifier rubyid_absolute_path'>absolute_path</span> <span class='op'>=</span> <span class='const'>File</span><span class='period'>.</span><span class='id identifier rubyid_expand_path'>expand_path</span><span class='lparen'>(</span><span class='id identifier rubyid_input'>input</span><span class='rparen'>)</span>
@@ -1362,19 +1509,19 @@ slice_length [Integer] The maximum number of entries for each query input
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-      <pre class="code"><span class="info file"># File 'lib/classyfire_api.rb', line 184</span>
+      <pre class="code"><span class="info file"># File 'lib/classyfire_api.rb', line 227</span>
 
 <span class='kw'>def</span> <span class='const'>ClassyFireAPI</span><span class='period'>.</span><span class='id identifier rubyid_submit_queries_from_directory'>submit_queries_from_directory</span><span class='lparen'>(</span><span class='id identifier rubyid_folder'>folder</span><span class='comma'>,</span><span class='id identifier rubyid_slice_length'>slice_length</span><span class='comma'>,</span><span class='id identifier rubyid_type'>type</span><span class='op'>=</span><span class='tstring'><span class='tstring_beg'>&quot;</span><span class='tstring_content'>STRUCTURE</span><span class='tstring_end'>&quot;</span></span><span class='rparen'>)</span>
   <span class='kw'>if</span> <span class='const'>File</span><span class='period'>.</span><span class='id identifier rubyid_directory?'>directory?</span><span class='lparen'>(</span><span class='id identifier rubyid_folder'>folder</span><span class='rparen'>)</span>
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-      <pre class="code"><span class="info file"># File 'lib/classyfire_api.rb', line 107</span>
+      <pre class="code"><span class="info file"># File 'lib/classyfire_api.rb', line 150</span>
 
 <span class='kw'>def</span> <span class='const'>ClassyFireAPI</span><span class='period'>.</span><span class='id identifier rubyid_submit_query_input_in_chunks'>submit_query_input_in_chunks</span><span class='lparen'>(</span><span class='id identifier rubyid_input_file'>input_file</span><span class='comma'>,</span><span class='id identifier rubyid_slice_length'>slice_length</span><span class='comma'>,</span> <span class='id identifier rubyid_start'>start</span><span class='comma'>,</span> <span class='id identifier rubyid_type'>type</span><span class='op'>=</span><span class='tstring'><span class='tstring_beg'>&#39;</span><span class='tstring_content'>STRUCTURE</span><span class='tstring_end'>&#39;</span></span><span class='rparen'>)</span>
   <span class='ivar'>@start_time</span> <span class='op'>=</span> <span class='const'>Time</span><span class='period'>.</span><span class='id identifier rubyid_now'>now</span>
@@ -1803,49 +1950,6 @@ text. is fragmented into n part of #slice_length entries each).</p>
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-      <pre class="code"><span class="info file"># File 'lib/classyfire_api.rb', line 209</span>
+      <pre class="code"><span class="info file"># File 'lib/classyfire_api.rb', line 252</span>
 
 <span class='kw'>def</span> <span class='const'>ClassyFireAPI</span><span class='period'>.</span><span class='id identifier rubyid_submit_random_subset_of_query_input_in_chunks'>submit_random_subset_of_query_input_in_chunks</span><span class='lparen'>(</span><span class='id identifier rubyid_tab_separated_input_file'>tab_separated_input_file</span><span class='comma'>,</span><span class='id identifier rubyid_size'>size</span><span class='comma'>,</span> <span class='id identifier rubyid_type'>type</span><span class='op'>=</span><span class='tstring'><span class='tstring_beg'>&#39;</span><span class='tstring_content'>STRUCTURE</span><span class='tstring_end'>&#39;</span></span><span class='rparen'>)</span>
   <span class='ivar'>@start_time</span> <span class='op'>=</span> <span class='const'>Time</span><span class='period'>.</span><span class='id identifier rubyid_now'>now</span>
@@ -1919,7 +2066,7 @@ text. is fragmented into n part of #slice_length entries each).</p>
 </div>
 
     <div id="footer">
-  Generated on Wed Mar  9 19:25:39 2016 by
+  Generated on Wed Mar  9 19:48:06 2016 by
   <a href="http://yardoc.org" title="Yay! A Ruby Documentation Tool" target="_parent">yard</a>
   0.8.7.6 (ruby-2.3.0).
 </div>

doc/EntityResource.html

@@ -114,7 +114,7 @@
 </div>
 
     <div id="footer">
-  Generated on Wed Mar  9 19:25:39 2016 by
+  Generated on Wed Mar  9 19:48:06 2016 by
   <a href="http://yardoc.org" title="Yay! A Ruby Documentation Tool" target="_parent">yard</a>
   0.8.7.6 (ruby-2.3.0).
 </div>

doc/QueryResource.html

@@ -183,7 +183,7 @@
 </div>
 
     <div id="footer">
-  Generated on Wed Mar  9 19:25:39 2016 by
+  Generated on Wed Mar  9 19:48:06 2016 by
   <a href="http://yardoc.org" title="Yay! A Ruby Documentation Tool" target="_parent">yard</a>
   0.8.7.6 (ruby-2.3.0).
 </div>

doc/SequenceResource.html

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+<!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>
+    <meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
+<title>
+  Class: SequenceResource
+  
+    &mdash; Documentation by YARD 0.8.7.6
+  
+</title>
+
+  <link rel="stylesheet" href="css/style.css" type="text/css" charset="utf-8" />
+
+  <link rel="stylesheet" href="css/common.css" type="text/css" charset="utf-8" />
+
+<script type="text/javascript" charset="utf-8">
+  hasFrames = window.top.frames.main ? true : false;
+  relpath = '';
+  framesUrl = "frames.html#!SequenceResource.html";
+</script>
+
+
+  <script type="text/javascript" charset="utf-8" src="js/jquery.js"></script>
+
+  <script type="text/javascript" charset="utf-8" src="js/app.js"></script>
+
+
+  </head>
+  <body>
+    <div id="header">
+      <div id="menu">
+  
+    <a href="_index.html">Index (S)</a> &raquo;
+    
+    
+    <span class="title">SequenceResource</span>
+  
+
+  <div class="noframes"><span class="title">(</span><a href="." target="_top">no frames</a><span class="title">)</span></div>
+</div>
+
+      <div id="search">
+  
+    <a class="full_list_link" id="class_list_link"
+        href="class_list.html">
+      Class List
+    </a>
+  
+    <a class="full_list_link" id="method_list_link"
+        href="method_list.html">
+      Method List
+    </a>
+  
+    <a class="full_list_link" id="file_list_link"
+        href="file_list.html">
+      File List
+    </a>
+  
+</div>
+      <div class="clear"></div>
+    </div>
+
+    <iframe id="search_frame"></iframe>
+
+    <div id="content"><h1>Class: SequenceResource
+  
+  
+  
+</h1>
+
+<dl class="box">
+  
+    <dt class="r1">Inherits:</dt>
+    <dd class="r1">
+      <span class="inheritName">ActiveResource::Base</span>
+      
+        <ul class="fullTree">
+          <li>Object</li>
+          
+            <li class="next">ActiveResource::Base</li>
+          
+            <li class="next">SequenceResource</li>
+          
+        </ul>
+        <a href="#" class="inheritanceTree">show all</a>
+      
+      </dd>
+    
+  
+  
+    
+  
+    
+  
+  
+  
+    <dt class="r2 last">Defined in:</dt>
+    <dd class="r2 last">lib/sequence_resource.rb</dd>
+  
+</dl>
+<div class="clear"></div>
+
+
+
+
+
+
+
+
+
+  
+
+</div>
+
+    <div id="footer">
+  Generated on Wed Mar  9 19:48:06 2016 by
+  <a href="http://yardoc.org" title="Yay! A Ruby Documentation Tool" target="_parent">yard</a>
+  0.8.7.6 (ruby-2.3.0).
+</div>
+
+  </body>
+</html>

doc/_index.html

@@ -118,6 +118,19 @@
           </ul>
         </ul>
       
+        
+        <ul id="alpha_S" class="alpha">
+          <li class="letter">S</li>
+          <ul>
+            
+              <li>
+                <span class='object_link'><a href="SequenceResource.html" title="SequenceResource (class)">SequenceResource</a></span>
+                
+              </li>
+            
+          </ul>
+        </ul>
+      
     </td>
   </tr>
 </table>
@@ -127,7 +140,7 @@
 </div>
 
     <div id="footer">
-  Generated on Wed Mar  9 19:25:38 2016 by
+  Generated on Wed Mar  9 19:48:06 2016 by
   <a href="http://yardoc.org" title="Yay! A Ruby Documentation Tool" target="_parent">yard</a>
   0.8.7.6 (ruby-2.3.0).
 </div>

doc/class_list.html

@@ -50,7 +50,7 @@
 
       <ul id="full_list" class="class">
         <li><span class='object_link'><a href="top-level-namespace.html" title="Top Level Namespace (root)">Top Level Namespace</a></span></li>
-<li><span class='object_link'><a href="ClassyFireAPI.html" title="ClassyFireAPI (module)">ClassyFireAPI</a></span><small class='search_info'>Top Level Namespace</small></li><li><span class='object_link'><a href="EntityResource.html" title="EntityResource (class)">EntityResource</a></span> &lt; Base<small class='search_info'>Top Level Namespace</small></li><li><span class='object_link'><a href="QueryResource.html" title="QueryResource (class)">QueryResource</a></span> &lt; Base<small class='search_info'>Top Level Namespace</small></li>
+<li><span class='object_link'><a href="ClassyFireAPI.html" title="ClassyFireAPI (module)">ClassyFireAPI</a></span><small class='search_info'>Top Level Namespace</small></li><li><span class='object_link'><a href="EntityResource.html" title="EntityResource (class)">EntityResource</a></span> &lt; Base<small class='search_info'>Top Level Namespace</small></li><li><span class='object_link'><a href="QueryResource.html" title="QueryResource (class)">QueryResource</a></span> &lt; Base<small class='search_info'>Top Level Namespace</small></li><li><span class='object_link'><a href="SequenceResource.html" title="SequenceResource (class)">SequenceResource</a></span> &lt; Base<small class='search_info'>Top Level Namespace</small></li>
 
       </ul>
     </div>

doc/file.README.html

@@ -131,7 +131,34 @@ InChIKey=LABTWGUMFABVFG-ONEGZZNKSA-N.</p>
 </blockquote>
 </blockquote>
 
-<h2 id="label-2.+Query">2. Query</h2>
+<h2 id="label-2.+Sequence">2. Sequence</h2>
+
+<blockquote>
+<p>Sequences are represented by the Sequence model, through which one can
+access the compound&#39;s structure-based classification.</p>
+
+<h3 id="label-GET">GET</h3>
+
+<p><strong>/sequence/fingerprint</strong></p>
+
+<p>A (FASTA) sequence&#39;s classification can be retrieved in the JSON. In
+this example, the sequence has the fingerprint =
+“8bf70c23ac100cd2c3955081d8613325”</p>
+
+<blockquote>
+<p>ClassyFireAPI.get_sequence_classification(“8bf70c23ac100cd2c3955081d8613325”,“json”)</p>
+</blockquote>
+
+<p>Where:</p>
+
+<blockquote>
+<p>The sequence&#39;s fingerprint is “8bf70c23ac100cd2c3955081d8613325”,</p>
+
+<p>The output format is “json” (JSON).</p>
+</blockquote>
+</blockquote>
+
+<h2 id="label-3.+Query">3. Query</h2>
 
 <blockquote>
 <p>The Query model represents the chemical structure to be classified. Its
@@ -141,12 +168,13 @@ attributes are the query label and the query input.</p>
 <p>The query label is an identifier</p>
 
 <p>The query input contains the compound&#39;s identifier (optional) and its
-structural representation, separated by a comma. The chemical structure is
+structural representation, separated by a tab. The chemical structure is
 represented either in the <a
 href="http://www.daylight.com/dayhtml/doc/theory/theory.smiles.html">Daylight
-SMILES</a> or the <a
+SMILES</a> format, the <a
 href="http://www.iupac.org/home/publications/e-resources/inchi.html">InChI</a>
-format.</p>
+format. Moreover, the compound can be represented with its <a
+href="http://www.chem.qmul.ac.uk/iupac/">IUPAC name</a>.</p>
 </blockquote>
 
 <h3 id="label-POST">POST</h3>
@@ -155,12 +183,9 @@ format.</p>
 following example.</p>
 
 <blockquote>
-<p>ClassyFireAPI.submit_query(“curl_test”,“MOL1tCCCOCCnMOL2tCOCC=CCCC”,“STRUCTURE”)</p>
+<p>ClassyFireAPI.submit_query(“curl_test”,“MOL1tCCCOCCnMOL2tCOCC=CCCC”,“STRUCTURE”)
-</blockquote>
+where the parameters are:</p>
 
-<p>where the parameters are:</p>
-
-<blockquote>
 <p>The query label: curl_test,</p>
 
 <p>The entity identifiers: MOL1,MOL2</p>
@@ -197,14 +222,14 @@ XML format.</p>
 
 <h1 id="label-Who+do+I+talk+to-3F"><strong>Who do I talk to?</strong></h1>
 <ul><li>
-<p>Repo owner or admin</p>
+<p>Yannick Djoumbou Feunang: djoumbou@ualberta.ca</p>
 </li><li>
 <p>Other community or team contact</p>
 </li></ul>
 </div></div>
 
     <div id="footer">
-  Generated on Wed Mar  9 19:25:39 2016 by
+  Generated on Wed Mar  9 19:48:06 2016 by
   <a href="http://yardoc.org" title="Yay! A Ruby Documentation Tool" target="_parent">yard</a>
   0.8.7.6 (ruby-2.3.0).
 </div>

doc/index.html

@@ -131,7 +131,34 @@ InChIKey=LABTWGUMFABVFG-ONEGZZNKSA-N.</p>
 </blockquote>
 </blockquote>
 
-<h2 id="label-2.+Query">2. Query</h2>
+<h2 id="label-2.+Sequence">2. Sequence</h2>
+
+<blockquote>
+<p>Sequences are represented by the Sequence model, through which one can
+access the compound&#39;s structure-based classification.</p>
+
+<h3 id="label-GET">GET</h3>
+
+<p><strong>/sequence/fingerprint</strong></p>
+
+<p>A (FASTA) sequence&#39;s classification can be retrieved in the JSON. In
+this example, the sequence has the fingerprint =
+“8bf70c23ac100cd2c3955081d8613325”</p>
+
+<blockquote>
+<p>ClassyFireAPI.get_sequence_classification(“8bf70c23ac100cd2c3955081d8613325”,“json”)</p>
+</blockquote>
+
+<p>Where:</p>
+
+<blockquote>
+<p>The sequence&#39;s fingerprint is “8bf70c23ac100cd2c3955081d8613325”,</p>
+
+<p>The output format is “json” (JSON).</p>
+</blockquote>
+</blockquote>
+
+<h2 id="label-3.+Query">3. Query</h2>
 
 <blockquote>
 <p>The Query model represents the chemical structure to be classified. Its
@@ -141,12 +168,13 @@ attributes are the query label and the query input.</p>
 <p>The query label is an identifier</p>
 
 <p>The query input contains the compound&#39;s identifier (optional) and its
-structural representation, separated by a comma. The chemical structure is
+structural representation, separated by a tab. The chemical structure is
 represented either in the <a
 href="http://www.daylight.com/dayhtml/doc/theory/theory.smiles.html">Daylight
-SMILES</a> or the <a
+SMILES</a> format, the <a
 href="http://www.iupac.org/home/publications/e-resources/inchi.html">InChI</a>
-format.</p>
+format. Moreover, the compound can be represented with its <a
+href="http://www.chem.qmul.ac.uk/iupac/">IUPAC name</a>.</p>
 </blockquote>
 
 <h3 id="label-POST">POST</h3>
@@ -155,12 +183,9 @@ format.</p>
 following example.</p>
 
 <blockquote>
-<p>ClassyFireAPI.submit_query(“curl_test”,“MOL1tCCCOCCnMOL2tCOCC=CCCC”,“STRUCTURE”)</p>
+<p>ClassyFireAPI.submit_query(“curl_test”,“MOL1tCCCOCCnMOL2tCOCC=CCCC”,“STRUCTURE”)
-</blockquote>
+where the parameters are:</p>
 
-<p>where the parameters are:</p>
-
-<blockquote>
 <p>The query label: curl_test,</p>
 
 <p>The entity identifiers: MOL1,MOL2</p>
@@ -197,14 +222,14 @@ XML format.</p>
 
 <h1 id="label-Who+do+I+talk+to-3F"><strong>Who do I talk to?</strong></h1>
 <ul><li>
-<p>Repo owner or admin</p>
+<p>Yannick Djoumbou Feunang: djoumbou@ualberta.ca</p>
 </li><li>
 <p>Other community or team contact</p>
 </li></ul>
 </div></div>
 
     <div id="footer">
-  Generated on Wed Mar  9 19:25:38 2016 by
+  Generated on Wed Mar  9 19:48:06 2016 by
   <a href="http://yardoc.org" title="Yay! A Ruby Documentation Tool" target="_parent">yard</a>
   0.8.7.6 (ruby-2.3.0).
 </div>

doc/method_list.html

@@ -64,54 +64,60 @@
   
 
   <li class="r1 ">
+    <span class='object_link'><a href="ClassyFireAPI.html#get_sequence_classification-class_method" title="ClassyFireAPI.get_sequence_classification (method)">get_sequence_classification</a></span>
+    <small>ClassyFireAPI</small>
+  </li>
+  
+
+  <li class="r2 ">
     <span class='object_link'><a href="ClassyFireAPI.html#query_status-class_method" title="ClassyFireAPI.query_status (method)">query_status</a></span>
     <small>ClassyFireAPI</small>
   </li>
   
 
-  <li class="r2 ">
+  <li class="r1 ">
     <span class='object_link'><a href="ClassyFireAPI.html#retrieve_classification-class_method" title="ClassyFireAPI.retrieve_classification (method)">retrieve_classification</a></span>
     <small>ClassyFireAPI</small>
   </li>
   
 
-  <li class="r1 ">
+  <li class="r2 ">
     <span class='object_link'><a href="ClassyFireAPI.html#retrieve_entities_json-class_method" title="ClassyFireAPI.retrieve_entities_json (method)">retrieve_entities_json</a></span>
     <small>ClassyFireAPI</small>
   </li>
   
 
-  <li class="r2 ">
+  <li class="r1 ">
     <span class='object_link'><a href="ClassyFireAPI.html#retrieve_entities_sdf-class_method" title="ClassyFireAPI.retrieve_entities_sdf (method)">retrieve_entities_sdf</a></span>
     <small>ClassyFireAPI</small>
   </li>
   
 
-  <li class="r1 ">
+  <li class="r2 ">
     <span class='object_link'><a href="ClassyFireAPI.html#submit_queries_from_directory-class_method" title="ClassyFireAPI.submit_queries_from_directory (method)">submit_queries_from_directory</a></span>
     <small>ClassyFireAPI</small>
   </li>
   
 
-  <li class="r2 ">
+  <li class="r1 ">
     <span class='object_link'><a href="ClassyFireAPI.html#submit_query-class_method" title="ClassyFireAPI.submit_query (method)">submit_query</a></span>
     <small>ClassyFireAPI</small>
   </li>
   
 
-  <li class="r1 ">
+  <li class="r2 ">
     <span class='object_link'><a href="ClassyFireAPI.html#submit_query_input_in_chunks-class_method" title="ClassyFireAPI.submit_query_input_in_chunks (method)">submit_query_input_in_chunks</a></span>
     <small>ClassyFireAPI</small>
   </li>
   
 
-  <li class="r2 ">
+  <li class="r1 ">
     <span class='object_link'><a href="ClassyFireAPI.html#submit_random_subset_of_query_input_in_chunks-class_method" title="ClassyFireAPI.submit_random_subset_of_query_input_in_chunks (method)">submit_random_subset_of_query_input_in_chunks</a></span>
     <small>ClassyFireAPI</small>
   </li>
   
 
-  <li class="r1 ">
+  <li class="r2 ">
     <span class='object_link'><a href="QueryResource.html#to_param-instance_method" title="QueryResource#to_param (method)">#to_param</a></span>
     <small>QueryResource</small>
   </li>

doc/top-level-namespace.html

@@ -89,7 +89,7 @@
     
   
     
-      <strong class="classes">Classes:</strong> <span class='object_link'><a href="EntityResource.html" title="EntityResource (class)">EntityResource</a></span>, <span class='object_link'><a href="QueryResource.html" title="QueryResource (class)">QueryResource</a></span>
+      <strong class="classes">Classes:</strong> <span class='object_link'><a href="EntityResource.html" title="EntityResource (class)">EntityResource</a></span>, <span class='object_link'><a href="QueryResource.html" title="QueryResource (class)">QueryResource</a></span>, <span class='object_link'><a href="SequenceResource.html" title="SequenceResource (class)">SequenceResource</a></span>
     
   
 </p>
@@ -105,7 +105,7 @@
 </div>
 
     <div id="footer">
-  Generated on Wed Mar  9 19:25:39 2016 by
+  Generated on Wed Mar  9 19:48:06 2016 by
   <a href="http://yardoc.org" title="Yay! A Ruby Documentation Tool" target="_parent">yard</a>
   0.8.7.6 (ruby-2.3.0).
 </div>

lib/classyfire_api.rb

@@ -55,7 +55,7 @@ module ClassyFireAPI
 
   # Retrieves the classification results for a given entity.
   #
-  # @param inchikey [String] the ID of the query.
+  # @param inchikey [String] the InChIKey of the entity.
   # @param format [String] the format of the query, 'text' (either JSON, CSV, or SDF)
   # @return [Text] A text file displaying the classification results for the entity in the specified format.
   def ClassyFireAPI.get_entity_classification(inchikey,format="json")
@@ -79,6 +79,49 @@ module ClassyFireAPI
     end
   end
 
+  # Retrieves the classification results for a given sequence.
+  #
+  # @param the fingerprint [String] the fingerprint (generated from the sequence using Digest::MD5).
+  # @param format [String] the format of the query (Only JSON)
+  # @return [Text] A text file displaying the classification results for the entity in the specified format.
+   def ClassyFireAPI.get_sequence_classification(fingerprint,format="json")
+    begin
+      if format == "json"
+        RestClient.get "#{URL}/entities/#{fingerprint}.#{format}", :accept => :json
+      end 
+    rescue RestClient::ResourceNotFound => e
+      e.response
+    rescue  RestClient::InternalServerError => e
+      e.response
+    rescue RestClient::GatewayTimeout => e
+      e.response
+    rescue RestClient::RequestTimeout => e
+      e.response
+    end
+  end
+
+  def ClassyFireAPI.get_entity_classification(inchikey,format="json")
+    inchikey_id = inchikey.to_s.gsub('InChIKey=','')
+    begin
+      if format == "json"
+        RestClient.get "#{URL}/entities/#{inchikey_id}.#{format}", :accept => :json
+      elsif format == "sdf"
+        RestClient.get "#{URL}/entities/#{inchikey_id}.#{format}", :accept => :sdf
+      elsif format == "csv"
+        RestClient.get "#{URL}/entities/#{inchikey_id}.#{format}", :accept => :csv
+      end 
+    rescue RestClient::ResourceNotFound => e
+      e.response
+    rescue  RestClient::InternalServerError => e
+      e.response
+    rescue RestClient::GatewayTimeout => e
+      e.response
+    rescue RestClient::RequestTimeout => e
+      e.response
+    end
+  end
+
+
   # Retrieves the status of a query
   # @param query_id [Integer] the ID of the query
   # @return [String] the query status, 'Done' or 'In progress', 'string'

lib/sequence_resource.rb

@@ -0,0 +1,6 @@
+require 'active_resource'
+
+class SequenceResource < ActiveResource::Base
+  self.site ='http://classyfire.wishartlab.com'
+  self.element_name = "sequence"
+end