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Module: ClassyFireAPI
&mdash; Documentation by YARD 0.8.7.6
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<span class="title">ClassyFireAPI</span>
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Class List
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Method List
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<div id="content"><h1>Module: ClassyFireAPI
</h1>
<dl class="box">
<dt class="r1 last">Defined in:</dt>
<dd class="r1 last">lib/classyfire_api.rb</dd>
</dl>
<div class="clear"></div>
<h2>Constant Summary</h2>
<dl class="constants">
<dt id="URL-constant" class="">URL =
</dt>
<dd><pre class="code"><span class='tstring'><span class='tstring_beg'>&#39;</span><span class='tstring_content'>http://classyfire.wishartlab.com</span><span class='tstring_end'>&#39;</span></span></pre></dd>
</dl>
<h2>
Class Method Summary
<small>(<a href="#" class="summary_toggle">collapse</a>)</small>
</h2>
<ul class="summary">
<li class="public ">
<span class="summary_signature">
<a href="#get_entity_classification-class_method" title="get_entity_classification (class method)">+ (Text) <strong>get_entity_classification</strong>(inchikey, format = &quot;json&quot;) </a>
</span>
<span class="summary_desc"><div class='inline'>
<p>Retrieves the classification results for a given entity.</p>
</div></span>
</li>
<li class="public ">
<span class="summary_signature">
<a href="#get_query-class_method" title="get_query (class method)">+ (Text) <strong>get_query</strong>(query_id, format = &quot;json&quot;) </a>
</span>
<span class="summary_desc"><div class='inline'>
<p>Retrieves the classification results for a given query.</p>
</div></span>
</li>
<li class="public ">
<span class="summary_signature">
<a href="#query_status-class_method" title="query_status (class method)">+ (String) <strong>query_status</strong>(query_id) </a>
</span>
<span class="summary_desc"><div class='inline'>
<p>Retrieves the status of a query.</p>
</div></span>
</li>
<li class="public ">
<span class="summary_signature">
<a href="#retrieve_classification-class_method" title="retrieve_classification (class method)">+ (String) <strong>retrieve_classification</strong>(input, output) </a>
</span>
<span class="summary_desc"><div class='inline'>
<p>Reads a tab separated file, and use the structure representation to
retrieve the strutcure&#39;s classification from ClassyFire.</p>
</div></span>
</li>
<li class="public ">
<span class="summary_signature">
<a href="#retrieve_entities_json-class_method" title="retrieve_entities_json (class method)">+ (String) <strong>retrieve_entities_json</strong>(input, output) </a>
</span>
<span class="summary_desc"><div class='inline'>
<p>Reads a tab separated file, and use the structure representation to
retrieve the strutcure&#39;s classification from ClassyFire in a JSON
format.</p>
</div></span>
</li>
<li class="public ">
<span class="summary_signature">
<a href="#retrieve_entities_sdf-class_method" title="retrieve_entities_sdf (class method)">+ (String) <strong>retrieve_entities_sdf</strong>(input, output) </a>
</span>
<span class="summary_desc"><div class='inline'>
<p>Reads a tab separated file, and use the structure representation to
retrieve the strutcure&#39;s classification from ClassyFire in a SDF
format.</p>
</div></span>
</li>
<li class="public ">
<span class="summary_signature">
<a href="#submit_queries_from_directory-class_method" title="submit_queries_from_directory (class method)">+ (Object) <strong>submit_queries_from_directory</strong>(folder, slice_length, type = &quot;STRUCTURE&quot;) </a>
</span>
<span class="summary_desc"><div class='inline'>
<p>Takes each file in a folder, and submit the contained structures in bluks
of a given size.</p>
</div></span>
</li>
<li class="public ">
<span class="summary_signature">
<a href="#submit_query-class_method" title="submit_query (class method)">+ (Hash) <strong>submit_query</strong>(label, input, type = &#39;STRUCTURE&#39;) </a>
</span>
<span class="summary_desc"><div class='inline'>
<p>Submits a ClassyFire query, which should be returned in a specific format.</p>
</div></span>
</li>
<li class="public ">
<span class="summary_signature">
<a href="#submit_query_input_in_chunks-class_method" title="submit_query_input_in_chunks (class method)">+ (Object) <strong>submit_query_input_in_chunks</strong>(input_file, slice_length, start, type = &#39;STRUCTURE&#39;) </a>
</span>
<span class="summary_desc"><div class='inline'>
<p>Takes a tab-separated file and submit the contained structures in bulks of
a given size.</p>
</div></span>
</li>
<li class="public ">
<span class="summary_signature">
<a href="#submit_random_subset_of_query_input_in_chunks-class_method" title="submit_random_subset_of_query_input_in_chunks (class method)">+ (Object) <strong>submit_random_subset_of_query_input_in_chunks</strong>(tab_separated_input_file, size, type = &#39;STRUCTURE&#39;) </a>
</span>
<span class="summary_desc"><div class='inline'>
<p>Takes a tab-separated file and submit randomly selected structures in bulks
of a given size.</p>
</div></span>
</li>
</ul>
<div id="class_method_details" class="method_details_list">
<h2>Class Method Details</h2>
<div class="method_details first">
<h3 class="signature first" id="get_entity_classification-class_method">
+ (<tt>Text</tt>) <strong>get_entity_classification</strong>(inchikey, format = &quot;json&quot;)
</h3><div class="docstring">
<div class="discussion">
<p>Retrieves the classification results for a given entity.</p>
</div>
</div>
<div class="tags">
<p class="tag_title">Parameters:</p>
<ul class="param">
<li>
<span class='name'>inchikey</span>
<span class='type'>(<tt>String</tt>)</span>
&mdash;
<div class='inline'>
<p>the ID of the query.</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, &#39;text&#39; (either JSON, CSV, or SDF)</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 61</span>
<span class='kw'>def</span> <span class='const'>ClassyFireAPI</span><span class='period'>.</span><span class='id identifier rubyid_get_entity_classification'>get_entity_classification</span><span class='lparen'>(</span><span class='id identifier rubyid_inchikey'>inchikey</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='id identifier rubyid_inchikey_id'>inchikey_id</span> <span class='op'>=</span> <span class='id identifier rubyid_inchikey'>inchikey</span><span class='period'>.</span><span class='id identifier rubyid_to_s'>to_s</span><span class='period'>.</span><span class='id identifier rubyid_gsub'>gsub</span><span class='lparen'>(</span><span class='tstring'><span class='tstring_beg'>&#39;</span><span class='tstring_content'>InChIKey=</span><span class='tstring_end'>&#39;</span></span><span class='comma'>,</span><span class='tstring'><span class='tstring_beg'>&#39;</span><span class='tstring_end'>&#39;</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_inchikey_id'>inchikey_id</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'>elsif</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'>sdf</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_inchikey_id'>inchikey_id</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'>:sdf</span>
<span class='kw'>elsif</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'>csv</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_inchikey_id'>inchikey_id</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'>:csv</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 ">
<h3 class="signature " id="get_query-class_method">
+ (<tt>Text</tt>) <strong>get_query</strong>(query_id, format = &quot;json&quot;)
</h3><div class="docstring">
<div class="discussion">
<p>Retrieves the classification results for a given query.</p>
<p>the query&#39;s entities in the specified format.</p>
</div>
</div>
<div class="tags">
<p class="tag_title">Parameters:</p>
<ul class="param">
<li>
<span class='name'>query_id</span>
<span class='type'>(<tt>Integer</tt>)</span>
&mdash;
<div class='inline'>
<p>the ID of the query.</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 (either JSON, CSV, or SDF)</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</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 36</span>
<span class='kw'>def</span> <span class='const'>ClassyFireAPI</span><span class='period'>.</span><span class='id identifier rubyid_get_query'>get_query</span><span class='lparen'>(</span><span class='id identifier rubyid_query_id'>query_id</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'>/queries/</span><span class='embexpr_beg'>#{</span><span class='id identifier rubyid_query_id'>query_id</span><span class='embexpr_end'>}</span><span class='tstring_content'>.json</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'>elsif</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'>sdf</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'>/queries/</span><span class='embexpr_beg'>#{</span><span class='id identifier rubyid_query_id'>query_id</span><span class='embexpr_end'>}</span><span class='tstring_content'>.sdf</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'>:sdf</span>
<span class='kw'>elsif</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'>csv</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'>/queries/</span><span class='embexpr_beg'>#{</span><span class='id identifier rubyid_query_id'>query_id</span><span class='embexpr_end'>}</span><span class='tstring_content'>.csv</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'>:csv</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 ">
<h3 class="signature " id="query_status-class_method">
+ (<tt>String</tt>) <strong>query_status</strong>(query_id)
</h3><div class="docstring">
<div class="discussion">
<p>Retrieves the status of a query</p>
</div>
</div>
<div class="tags">
<p class="tag_title">Parameters:</p>
<ul class="param">
<li>
<span class='name'>query_id</span>
<span class='type'>(<tt>Integer</tt>)</span>
&mdash;
<div class='inline'>
<p>the ID of the query</p>
</div>
</li>
</ul>
<p class="tag_title">Returns:</p>
<ul class="return">
<li>
<span class='type'>(<tt>String</tt>)</span>
&mdash;
<div class='inline'>
<p>the query status, &#39;Done&#39; or &#39;In progress&#39;, &#39;string&#39;</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 85</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>
<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'>/queries/</span><span class='embexpr_beg'>#{</span><span class='id identifier rubyid_query_id'>query_id</span><span class='embexpr_end'>}</span><span class='tstring_content'>/status.json</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'>rescue</span> <span class='const'>Exception</span><span class='op'>=&gt;</span><span class='id identifier rubyid_e'>e</span>
<span class='gvar'>$stderr</span><span class='period'>.</span><span class='id identifier rubyid_puts'>puts</span> <span class='id identifier rubyid_e'>e</span><span class='period'>.</span><span class='id identifier rubyid_message'>message</span>
<span class='kw'>nil</span>
<span class='kw'>end</span>
<span class='kw'>end</span></pre>
</td>
</tr>
</table>
</div>
<div class="method_details ">
<h3 class="signature " id="retrieve_classification-class_method">
+ (<tt>String</tt>) <strong>retrieve_classification</strong>(input, output)
</h3><div class="docstring">
<div class="discussion">
<p>Reads a tab separated file, and use the structure representation to
retrieve the strutcure&#39;s classification from ClassyFire.</p>
</div>
</div>
<div class="tags">
<p class="tag_title">Parameters:</p>
<ul class="param">
<li>
<span class='name'>input</span>
<span class='type'>(<tt>String</tt>)</span>
&mdash;
<div class='inline'>
<p>path to the input file.</p>
</div>
</li>
</ul>
<p class="tag_title">Returns:</p>
<ul class="return">
<li>
<span class='type'>(<tt>String</tt>)</span>
&mdash;
<div class='inline'>
<p>path to the output file.</p>
</div>
</li>
</ul>
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<pre class="code"><span class="info file"># File 'lib/classyfire_api.rb', line 266</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>
<span class='id identifier rubyid_f_input'>f_input</span> <span class='op'>=</span> <span class='const'>File</span><span class='period'>.</span><span class='id identifier rubyid_open'>open</span><span class='lparen'>(</span><span class='id identifier rubyid_absolute_path'>absolute_path</span><span class='comma'>,</span> <span class='tstring'><span class='tstring_beg'>&#39;</span><span class='tstring_content'>r</span><span class='tstring_end'>&#39;</span></span><span class='rparen'>)</span>
<span class='id identifier rubyid_h'>h</span> <span class='op'>=</span> <span class='const'>Hash</span><span class='period'>.</span><span class='id identifier rubyid_new'>new</span>
<span class='id identifier rubyid_directory'>directory</span> <span class='op'>=</span> <span class='id identifier rubyid_absolute_path'>absolute_path</span><span class='period'>.</span><span class='id identifier rubyid_split'>split</span><span class='lparen'>(</span><span class='tstring'><span class='tstring_beg'>&#39;</span><span class='tstring_content'>/</span><span class='tstring_end'>&#39;</span></span><span class='rparen'>)</span><span class='lbracket'>[</span><span class='int'>0</span><span class='op'>...</span><span class='op'>-</span><span class='int'>1</span><span class='rbracket'>]</span><span class='period'>.</span><span class='id identifier rubyid_join'>join</span><span class='lparen'>(</span><span class='tstring'><span class='tstring_beg'>&quot;</span><span class='tstring_content'>/</span><span class='tstring_end'>&quot;</span></span><span class='rparen'>)</span>
<span class='id identifier rubyid_f_output'>f_output</span> <span class='op'>=</span> <span class='const'>File</span><span class='period'>.</span><span class='id identifier rubyid_new'>new</span><span class='lparen'>(</span><span class='id identifier rubyid_output'>output</span><span class='comma'>,</span> <span class='tstring'><span class='tstring_beg'>&#39;</span><span class='tstring_content'>w</span><span class='tstring_end'>&#39;</span></span><span class='rparen'>)</span>
<span class='id identifier rubyid_res'>res</span> <span class='op'>=</span> <span class='const'>String</span><span class='period'>.</span><span class='id identifier rubyid_new'>new</span>
<span class='id identifier rubyid_res'>res</span> <span class='op'>+=</span> <span class='tstring'><span class='tstring_beg'>&quot;</span><span class='tstring_content'>{</span><span class='tstring_end'>&quot;</span></span>
<span class='id identifier rubyid_res'>res</span> <span class='op'>+=</span> <span class='tstring'><span class='tstring_beg'>&#39;</span><span class='tstring_content'>&quot;id&quot;: 1,</span><span class='tstring_end'>&#39;</span></span>
<span class='id identifier rubyid_res'>res</span> <span class='op'>+=</span> <span class='tstring'><span class='tstring_beg'>&#39;</span><span class='tstring_content'>&quot;label&quot;:&quot;</span><span class='tstring_end'>&#39;</span></span> <span class='op'>+</span> <span class='id identifier rubyid_output'>output</span> <span class='op'>+</span> <span class='tstring'><span class='tstring_beg'>&#39;</span><span class='tstring_content'>&quot;,</span><span class='tstring_end'>&#39;</span></span> <span class='op'>+</span> <span class='tstring'><span class='tstring_beg'>&#39;</span><span class='tstring_content'>&quot;classification_status&quot;:&quot;Done&quot;,</span><span class='tstring_end'>&#39;</span></span> <span class='op'>+</span> <span class='tstring'><span class='tstring_beg'>&#39;</span><span class='tstring_content'>&quot;entities&quot;:[</span><span class='tstring_end'>&#39;</span></span>
<span class='id identifier rubyid_f_input'>f_input</span><span class='period'>.</span><span class='id identifier rubyid_each_line'>each_line</span> <span class='kw'>do</span> <span class='op'>|</span><span class='id identifier rubyid_line'>line</span><span class='op'>|</span>
<span class='id identifier rubyid_sline'>sline</span> <span class='op'>=</span> <span class='id identifier rubyid_line'>line</span><span class='period'>.</span><span class='id identifier rubyid_strip'>strip</span><span class='period'>.</span><span class='id identifier rubyid_split'>split</span><span class='lparen'>(</span><span class='tstring'><span class='tstring_beg'>&quot;</span><span class='tstring_content'>\t</span><span class='tstring_end'>&quot;</span></span><span class='rparen'>)</span>
<span class='kw'>if</span> <span class='id identifier rubyid_sline'>sline</span><span class='period'>.</span><span class='id identifier rubyid_length'>length</span> <span class='op'>==</span> <span class='int'>1</span>
<span class='id identifier rubyid_h'>h</span><span class='lbracket'>[</span><span class='id identifier rubyid_sline'>sline</span><span class='lbracket'>[</span><span class='int'>0</span><span class='rbracket'>]</span><span class='rbracket'>]</span> <span class='op'>=</span> <span class='id identifier rubyid_sline'>sline</span><span class='lbracket'>[</span><span class='int'>0</span><span class='rbracket'>]</span>
<span class='kw'>elsif</span> <span class='id identifier rubyid_sline'>sline</span><span class='period'>.</span><span class='id identifier rubyid_length'>length</span> <span class='op'>==</span> <span class='int'>2</span>
<span class='id identifier rubyid_h'>h</span><span class='lbracket'>[</span><span class='id identifier rubyid_sline'>sline</span><span class='lbracket'>[</span><span class='int'>0</span><span class='rbracket'>]</span><span class='rbracket'>]</span> <span class='op'>=</span> <span class='id identifier rubyid_line'>line</span><span class='period'>.</span><span class='id identifier rubyid_strip'>strip</span>
<span class='kw'>end</span>
<span class='kw'>end</span>
<span class='id identifier rubyid_puts'>puts</span> <span class='id identifier rubyid_h'>h</span><span class='period'>.</span><span class='id identifier rubyid_keys'>keys</span><span class='period'>.</span><span class='id identifier rubyid_uniq'>uniq</span><span class='period'>.</span><span class='id identifier rubyid_length'>length</span>
<span class='kw'>if</span> <span class='id identifier rubyid_h'>h</span><span class='period'>.</span><span class='id identifier rubyid_keys'>keys</span><span class='period'>.</span><span class='id identifier rubyid_length'>length</span> <span class='op'>&gt;</span> <span class='int'>0</span>
<span class='id identifier rubyid_i'>i</span> <span class='op'>=</span> <span class='int'>1</span>
<span class='id identifier rubyid_h'>h</span><span class='period'>.</span><span class='id identifier rubyid_keys'>keys</span><span class='period'>.</span><span class='id identifier rubyid_uniq'>uniq</span><span class='lbracket'>[</span><span class='int'>0</span><span class='op'>..</span><span class='op'>-</span><span class='int'>1</span><span class='rbracket'>]</span><span class='period'>.</span><span class='id identifier rubyid_each'>each</span> <span class='kw'>do</span> <span class='op'>|</span><span class='id identifier rubyid_key'>key</span><span class='op'>|</span>
<span class='id identifier rubyid_puts'>puts</span> <span class='id identifier rubyid_i'>i</span>
<span class='id identifier rubyid_puts'>puts</span> <span class='tstring'><span class='tstring_beg'>&quot;</span><span class='embexpr_beg'>#{</span><span class='id identifier rubyid_key'>key</span><span class='embexpr_end'>}</span><span class='tstring_content'> :: </span><span class='embexpr_beg'>#{</span><span class='id identifier rubyid_h'>h</span><span class='lbracket'>[</span><span class='id identifier rubyid_key'>key</span><span class='rbracket'>]</span><span class='embexpr_end'>}</span><span class='tstring_end'>&quot;</span></span>
<span class='kw'>begin</span>
<span class='id identifier rubyid_qs'>qs</span> <span class='op'>=</span> <span class='id identifier rubyid_submit_query'>submit_query</span><span class='lparen'>(</span><span class='id identifier rubyid_key'>key</span><span class='comma'>,</span><span class='id identifier rubyid_h'>h</span><span class='lbracket'>[</span><span class='id identifier rubyid_key'>key</span><span class='rbracket'>]</span><span class='rparen'>)</span>
<span class='id identifier rubyid_qs_decoded'>qs_decoded</span> <span class='op'>=</span> <span class='const'>JSON</span><span class='period'>.</span><span class='id identifier rubyid_parse'>parse</span><span class='lparen'>(</span><span class='id identifier rubyid_qs'>qs</span><span class='rparen'>)</span>
<span class='id identifier rubyid_qr'>qr</span> <span class='op'>=</span> <span class='const'>JSON</span><span class='period'>.</span><span class='id identifier rubyid_parse'>parse</span><span class='lparen'>(</span><span class='id identifier rubyid_get_query'>get_query</span><span class='lparen'>(</span><span class='id identifier rubyid_qs_decoded'>qs_decoded</span><span class='lbracket'>[</span><span class='tstring'><span class='tstring_beg'>&quot;</span><span class='tstring_content'>id</span><span class='tstring_end'>&quot;</span></span><span class='rbracket'>]</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='rparen'>)</span>
<span class='id identifier rubyid_res'>res</span> <span class='op'>+=</span> <span class='id identifier rubyid_qr'>qr</span><span class='lbracket'>[</span><span class='tstring'><span class='tstring_beg'>&quot;</span><span class='tstring_content'>entities</span><span class='tstring_end'>&quot;</span></span><span class='rbracket'>]</span><span class='lbracket'>[</span><span class='int'>0</span><span class='rbracket'>]</span><span class='period'>.</span><span class='id identifier rubyid_to_json'>to_json</span>
<span class='id identifier rubyid_res'>res</span> <span class='op'>+=</span> <span class='tstring'><span class='tstring_beg'>&quot;</span><span class='tstring_content'>,</span><span class='tstring_end'>&quot;</span></span>
<span class='id identifier rubyid_i'>i</span> <span class='op'>+=</span> <span class='int'>1</span>
<span class='kw'>rescue</span> <span class='const'>Exception</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_message'>message</span>
<span class='kw'>end</span>
<span class='kw'>end</span>
<span class='id identifier rubyid_key'>key</span> <span class='op'>=</span> <span class='id identifier rubyid_h'>h</span><span class='period'>.</span><span class='id identifier rubyid_keys'>keys</span><span class='lbracket'>[</span><span class='op'>-</span><span class='int'>1</span><span class='rbracket'>]</span>
<span class='id identifier rubyid_puts'>puts</span> <span class='tstring'><span class='tstring_beg'>&quot;</span><span class='embexpr_beg'>#{</span><span class='id identifier rubyid_key'>key</span><span class='embexpr_end'>}</span><span class='tstring_content'> :: </span><span class='embexpr_beg'>#{</span><span class='id identifier rubyid_h'>h</span><span class='lbracket'>[</span><span class='id identifier rubyid_key'>key</span><span class='rbracket'>]</span><span class='embexpr_end'>}</span><span class='tstring_end'>&quot;</span></span>
<span class='kw'>begin</span>
<span class='id identifier rubyid_qs'>qs</span> <span class='op'>=</span> <span class='id identifier rubyid_submit_query'>submit_query</span><span class='lparen'>(</span><span class='id identifier rubyid_key'>key</span><span class='comma'>,</span><span class='id identifier rubyid_h'>h</span><span class='lbracket'>[</span><span class='id identifier rubyid_key'>key</span><span class='rbracket'>]</span><span class='rparen'>)</span>
<span class='id identifier rubyid_sleep'>sleep</span><span class='lparen'>(</span><span class='float'>0.2</span><span class='rparen'>)</span>
<span class='id identifier rubyid_qs_decoded'>qs_decoded</span> <span class='op'>=</span> <span class='const'>JSON</span><span class='period'>.</span><span class='id identifier rubyid_parse'>parse</span><span class='lparen'>(</span><span class='id identifier rubyid_qs'>qs</span><span class='rparen'>)</span>
<span class='id identifier rubyid_qr'>qr</span> <span class='op'>=</span> <span class='const'>JSON</span><span class='period'>.</span><span class='id identifier rubyid_parse'>parse</span><span class='lparen'>(</span><span class='id identifier rubyid_get_query'>get_query</span><span class='lparen'>(</span><span class='id identifier rubyid_qs_decoded'>qs_decoded</span><span class='lbracket'>[</span><span class='tstring'><span class='tstring_beg'>&quot;</span><span class='tstring_content'>id</span><span class='tstring_end'>&quot;</span></span><span class='rbracket'>]</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='rparen'>)</span>
<span class='comment'># puts qr[&quot;entities&quot;]
</span> <span class='comment'># sleep(0.2)
</span> <span class='comment'># f_output.print qr[&quot;entities&quot;][0],&quot;\n&quot;
</span> <span class='id identifier rubyid_res'>res</span> <span class='op'>+=</span> <span class='id identifier rubyid_qr'>qr</span><span class='lbracket'>[</span><span class='tstring'><span class='tstring_beg'>&quot;</span><span class='tstring_content'>entities</span><span class='tstring_end'>&quot;</span></span><span class='rbracket'>]</span><span class='lbracket'>[</span><span class='int'>0</span><span class='rbracket'>]</span><span class='period'>.</span><span class='id identifier rubyid_to_json'>to_json</span>
<span class='comment'># res += &quot;,&quot;
</span> <span class='kw'>rescue</span> <span class='const'>Exception</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_message'>message</span>
<span class='kw'>end</span>
<span class='kw'>end</span>
<span class='id identifier rubyid_res'>res</span> <span class='op'>+=</span> <span class='tstring'><span class='tstring_beg'>&quot;</span><span class='tstring_content'>]}</span><span class='tstring_end'>&quot;</span></span>
<span class='id identifier rubyid_f_output'>f_output</span><span class='period'>.</span><span class='id identifier rubyid_print'>print</span> <span class='id identifier rubyid_res'>res</span>
<span class='kw'>end</span></pre>
</td>
</tr>
</table>
</div>
<div class="method_details ">
<h3 class="signature " id="retrieve_entities_json-class_method">
+ (<tt>String</tt>) <strong>retrieve_entities_json</strong>(input, output)
</h3><div class="docstring">
<div class="discussion">
<p>Reads a tab separated file, and use the structure representation to
retrieve the strutcure&#39;s classification from ClassyFire in a JSON
format.</p>
</div>
</div>
<div class="tags">
<p class="tag_title">Parameters:</p>
<ul class="param">
<li>
<span class='name'>input</span>
<span class='type'>(<tt>String</tt>)</span>
&mdash;
<div class='inline'>
<p>path to the input file</p>
</div>
</li>
</ul>
<p class="tag_title">Returns:</p>
<ul class="return">
<li>
<span class='type'>(<tt>String</tt>)</span>
&mdash;
<div class='inline'>
<p>path to the output file</p>
</div>
</li>
</ul>
</div><table class="source_code">
<tr>
<td>
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</td>
<td>
<pre class="code"><span class="info file"># File 'lib/classyfire_api.rb', line 335</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>
<span class='id identifier rubyid_f_input'>f_input</span> <span class='op'>=</span> <span class='const'>File</span><span class='period'>.</span><span class='id identifier rubyid_open'>open</span><span class='lparen'>(</span><span class='id identifier rubyid_absolute_path'>absolute_path</span><span class='comma'>,</span> <span class='tstring'><span class='tstring_beg'>&#39;</span><span class='tstring_content'>r</span><span class='tstring_end'>&#39;</span></span><span class='rparen'>)</span>
<span class='id identifier rubyid_h'>h</span> <span class='op'>=</span> <span class='const'>Hash</span><span class='period'>.</span><span class='id identifier rubyid_new'>new</span>
<span class='id identifier rubyid_directory'>directory</span> <span class='op'>=</span> <span class='id identifier rubyid_absolute_path'>absolute_path</span><span class='period'>.</span><span class='id identifier rubyid_split'>split</span><span class='lparen'>(</span><span class='tstring'><span class='tstring_beg'>&#39;</span><span class='tstring_content'>/</span><span class='tstring_end'>&#39;</span></span><span class='rparen'>)</span><span class='lbracket'>[</span><span class='int'>0</span><span class='op'>...</span><span class='op'>-</span><span class='int'>1</span><span class='rbracket'>]</span><span class='period'>.</span><span class='id identifier rubyid_join'>join</span><span class='lparen'>(</span><span class='tstring'><span class='tstring_beg'>&quot;</span><span class='tstring_content'>/</span><span class='tstring_end'>&quot;</span></span><span class='rparen'>)</span>
<span class='id identifier rubyid_f_output'>f_output</span> <span class='op'>=</span> <span class='const'>File</span><span class='period'>.</span><span class='id identifier rubyid_new'>new</span><span class='lparen'>(</span><span class='id identifier rubyid_output'>output</span><span class='comma'>,</span> <span class='tstring'><span class='tstring_beg'>&#39;</span><span class='tstring_content'>w</span><span class='tstring_end'>&#39;</span></span><span class='rparen'>)</span>
<span class='id identifier rubyid_puts'>puts</span>
<span class='id identifier rubyid_res'>res</span> <span class='op'>=</span> <span class='const'>String</span><span class='period'>.</span><span class='id identifier rubyid_new'>new</span>
<span class='id identifier rubyid_res'>res</span> <span class='op'>+=</span> <span class='tstring'><span class='tstring_beg'>&quot;</span><span class='tstring_content'>{</span><span class='tstring_end'>&quot;</span></span>
<span class='id identifier rubyid_res'>res</span> <span class='op'>+=</span> <span class='tstring'><span class='tstring_beg'>&#39;</span><span class='tstring_content'>&quot;id&quot;: 1,</span><span class='tstring_end'>&#39;</span></span>
<span class='id identifier rubyid_res'>res</span> <span class='op'>+=</span> <span class='tstring'><span class='tstring_beg'>&#39;</span><span class='tstring_content'>&quot;label&quot;:&quot;</span><span class='tstring_end'>&#39;</span></span> <span class='op'>+</span> <span class='id identifier rubyid_output'>output</span> <span class='op'>+</span> <span class='tstring'><span class='tstring_beg'>&#39;</span><span class='tstring_content'>&quot;,</span><span class='tstring_end'>&#39;</span></span> <span class='op'>+</span> <span class='tstring'><span class='tstring_beg'>&#39;</span><span class='tstring_content'>&quot;classification_status&quot;:&quot;Done&quot;,</span><span class='tstring_end'>&#39;</span></span> <span class='op'>+</span> <span class='tstring'><span class='tstring_beg'>&#39;</span><span class='tstring_content'>&quot;entities&quot;:[</span><span class='tstring_end'>&#39;</span></span>
<span class='id identifier rubyid_f_input'>f_input</span><span class='period'>.</span><span class='id identifier rubyid_each_line'>each_line</span> <span class='kw'>do</span> <span class='op'>|</span><span class='id identifier rubyid_line'>line</span><span class='op'>|</span>
<span class='id identifier rubyid_sline'>sline</span> <span class='op'>=</span> <span class='id identifier rubyid_line'>line</span><span class='period'>.</span><span class='id identifier rubyid_strip'>strip</span><span class='period'>.</span><span class='id identifier rubyid_split'>split</span><span class='lparen'>(</span><span class='tstring'><span class='tstring_beg'>&quot;</span><span class='tstring_content'>\t</span><span class='tstring_end'>&quot;</span></span><span class='rparen'>)</span>
<span class='id identifier rubyid_h'>h</span><span class='lbracket'>[</span><span class='id identifier rubyid_sline'>sline</span><span class='lbracket'>[</span><span class='int'>0</span><span class='rbracket'>]</span><span class='rbracket'>]</span> <span class='op'>=</span> <span class='id identifier rubyid_sline'>sline</span><span class='lbracket'>[</span><span class='op'>-</span><span class='int'>1</span><span class='rbracket'>]</span>
<span class='kw'>end</span>
<span class='id identifier rubyid_puts'>puts</span> <span class='id identifier rubyid_h'>h</span><span class='period'>.</span><span class='id identifier rubyid_keys'>keys</span><span class='period'>.</span><span class='id identifier rubyid_uniq'>uniq</span><span class='period'>.</span><span class='id identifier rubyid_length'>length</span>
<span class='kw'>if</span> <span class='id identifier rubyid_h'>h</span><span class='period'>.</span><span class='id identifier rubyid_keys'>keys</span><span class='period'>.</span><span class='id identifier rubyid_length'>length</span> <span class='op'>&gt;</span> <span class='int'>0</span>
<span class='id identifier rubyid_i'>i</span> <span class='op'>=</span> <span class='int'>1</span>
<span class='id identifier rubyid_h'>h</span><span class='period'>.</span><span class='id identifier rubyid_keys'>keys</span><span class='period'>.</span><span class='id identifier rubyid_uniq'>uniq</span><span class='lbracket'>[</span><span class='int'>0</span><span class='op'>...</span><span class='op'>-</span><span class='int'>1</span><span class='rbracket'>]</span><span class='period'>.</span><span class='id identifier rubyid_each'>each</span> <span class='kw'>do</span> <span class='op'>|</span><span class='id identifier rubyid_key'>key</span><span class='op'>|</span>
<span class='id identifier rubyid_puts'>puts</span> <span class='id identifier rubyid_i'>i</span>
<span class='comment'># puts &quot;#{key} :: #{h[key]}&quot;
</span> <span class='kw'>begin</span>
<span class='id identifier rubyid_inchikey'>inchikey</span> <span class='op'>=</span> <span class='backtick'>%x(</span><span class='tstring_content'>/Applications/ChemAxon/JChem/bin/molconvert inchikey -s &quot;</span><span class='embexpr_beg'>#{</span><span class='id identifier rubyid_h'>h</span><span class='lbracket'>[</span><span class='id identifier rubyid_key'>key</span><span class='rbracket'>]</span><span class='embexpr_end'>}</span><span class='tstring_content'>&quot;</span><span class='tstring_end'>)</span></span><span class='period'>.</span><span class='id identifier rubyid_strip'>strip</span>
<span class='comment'># puts inchikey
</span> <span class='id identifier rubyid_qr'>qr</span> <span class='op'>=</span> <span class='const'>JSON</span><span class='period'>.</span><span class='id identifier rubyid_parse'>parse</span><span class='lparen'>(</span><span class='const'>ClassyFireAPI</span><span class='period'>.</span><span class='id identifier rubyid_get_entity_classification'>get_entity_classification</span><span class='lparen'>(</span><span class='id identifier rubyid_inchikey'>inchikey</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='rparen'>)</span>
<span class='id identifier rubyid_qr'>qr</span><span class='lbracket'>[</span><span class='tstring'><span class='tstring_beg'>&#39;</span><span class='tstring_content'>identifier</span><span class='tstring_end'>&#39;</span></span><span class='rbracket'>]</span> <span class='op'>=</span> <span class='id identifier rubyid_key'>key</span>
<span class='id identifier rubyid_res'>res</span> <span class='op'>+=</span> <span class='id identifier rubyid_qr'>qr</span><span class='period'>.</span><span class='id identifier rubyid_to_json'>to_json</span>
<span class='id identifier rubyid_res'>res</span> <span class='op'>+=</span> <span class='tstring'><span class='tstring_beg'>&quot;</span><span class='tstring_content'>,</span><span class='tstring_end'>&quot;</span></span>
<span class='id identifier rubyid_puts'>puts</span> <span class='tstring'><span class='tstring_beg'>&quot;</span><span class='embexpr_beg'>#{</span><span class='id identifier rubyid_key'>key</span><span class='embexpr_end'>}</span><span class='tstring_content'> :: RETURN NIL</span><span class='tstring_end'>&quot;</span></span> <span class='kw'>if</span> <span class='id identifier rubyid_qr'>qr</span><span class='period'>.</span><span class='id identifier rubyid_nil?'>nil?</span> <span class='op'>||</span> <span class='id identifier rubyid_qr'>qr</span><span class='lbracket'>[</span><span class='tstring'><span class='tstring_beg'>&#39;</span><span class='tstring_content'>direct_parent</span><span class='tstring_end'>&#39;</span></span><span class='rbracket'>]</span><span class='lbracket'>[</span><span class='tstring'><span class='tstring_beg'>&#39;</span><span class='tstring_content'>name</span><span class='tstring_end'>&#39;</span></span><span class='rbracket'>]</span><span class='period'>.</span><span class='id identifier rubyid_nil?'>nil?</span>
<span class='kw'>rescue</span> <span class='const'>Exception</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_message'>message</span>
<span class='kw'>end</span>
<span class='id identifier rubyid_i'>i</span> <span class='op'>+=</span> <span class='int'>1</span>
<span class='kw'>end</span>
<span class='id identifier rubyid_key'>key</span> <span class='op'>=</span> <span class='id identifier rubyid_h'>h</span><span class='period'>.</span><span class='id identifier rubyid_keys'>keys</span><span class='lbracket'>[</span><span class='op'>-</span><span class='int'>1</span><span class='rbracket'>]</span>
<span class='comment'># puts &quot;#{key} :: #{h[key]}&quot;
</span> <span class='kw'>begin</span>
<span class='id identifier rubyid_inchikey'>inchikey</span> <span class='op'>=</span> <span class='backtick'>%x(</span><span class='tstring_content'>/Applications/ChemAxon/JChem/bin/molconvert inchikey -s &quot;</span><span class='embexpr_beg'>#{</span><span class='id identifier rubyid_h'>h</span><span class='lbracket'>[</span><span class='id identifier rubyid_key'>key</span><span class='rbracket'>]</span><span class='embexpr_end'>}</span><span class='tstring_content'>&quot;</span><span class='tstring_end'>)</span></span><span class='period'>.</span><span class='id identifier rubyid_strip'>strip</span>
<span class='comment'># puts inchikey
</span> <span class='id identifier rubyid_qr'>qr</span> <span class='op'>=</span> <span class='const'>JSON</span><span class='period'>.</span><span class='id identifier rubyid_parse'>parse</span><span class='lparen'>(</span><span class='const'>ClassyFireAPI</span><span class='period'>.</span><span class='id identifier rubyid_get_entity_classification'>get_entity_classification</span><span class='lparen'>(</span><span class='id identifier rubyid_inchikey'>inchikey</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='rparen'>)</span>
<span class='id identifier rubyid_qr'>qr</span><span class='lbracket'>[</span><span class='tstring'><span class='tstring_beg'>&#39;</span><span class='tstring_content'>identifier</span><span class='tstring_end'>&#39;</span></span><span class='rbracket'>]</span> <span class='op'>=</span> <span class='id identifier rubyid_key'>key</span>
<span class='id identifier rubyid_res'>res</span> <span class='op'>+=</span> <span class='id identifier rubyid_qr'>qr</span><span class='period'>.</span><span class='id identifier rubyid_to_json'>to_json</span>
<span class='id identifier rubyid_puts'>puts</span> <span class='tstring'><span class='tstring_beg'>&quot;</span><span class='embexpr_beg'>#{</span><span class='id identifier rubyid_key'>key</span><span class='embexpr_end'>}</span><span class='tstring_content'> :: RETURN NIL</span><span class='tstring_end'>&quot;</span></span> <span class='kw'>if</span> <span class='id identifier rubyid_qr'>qr</span><span class='period'>.</span><span class='id identifier rubyid_nil?'>nil?</span> <span class='op'>||</span> <span class='id identifier rubyid_qr'>qr</span><span class='lbracket'>[</span><span class='tstring'><span class='tstring_beg'>&#39;</span><span class='tstring_content'>direct_parent</span><span class='tstring_end'>&#39;</span></span><span class='rbracket'>]</span><span class='lbracket'>[</span><span class='tstring'><span class='tstring_beg'>&#39;</span><span class='tstring_content'>name</span><span class='tstring_end'>&#39;</span></span><span class='rbracket'>]</span><span class='period'>.</span><span class='id identifier rubyid_nil?'>nil?</span>
<span class='comment'># res += &quot;,&quot;
</span> <span class='kw'>rescue</span> <span class='const'>Exception</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_message'>message</span>
<span class='kw'>end</span>
<span class='kw'>end</span>
<span class='id identifier rubyid_res'>res</span> <span class='op'>+=</span> <span class='tstring'><span class='tstring_beg'>&quot;</span><span class='tstring_content'>]}</span><span class='tstring_end'>&quot;</span></span>
<span class='id identifier rubyid_f_output'>f_output</span><span class='period'>.</span><span class='id identifier rubyid_print'>print</span> <span class='id identifier rubyid_res'>res</span>
<span class='kw'>end</span></pre>
</td>
</tr>
</table>
</div>
<div class="method_details ">
<h3 class="signature " id="retrieve_entities_sdf-class_method">
+ (<tt>String</tt>) <strong>retrieve_entities_sdf</strong>(input, output)
</h3><div class="docstring">
<div class="discussion">
<p>Reads a tab separated file, and use the structure representation to
retrieve the strutcure&#39;s classification from ClassyFire in a SDF
format.</p>
</div>
</div>
<div class="tags">
<p class="tag_title">Parameters:</p>
<ul class="param">
<li>
<span class='name'>input</span>
<span class='type'>(<tt>String</tt>)</span>
&mdash;
<div class='inline'>
<p>path to the input file</p>
</div>
</li>
</ul>
<p class="tag_title">Returns:</p>
<ul class="return">
<li>
<span class='type'>(<tt>String</tt>)</span>
&mdash;
<div class='inline'>
<p>path to the output file</p>
</div>
</li>
</ul>
</div><table class="source_code">
<tr>
<td>
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</td>
<td>
<pre class="code"><span class="info file"># File 'lib/classyfire_api.rb', line 397</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>
<span class='id identifier rubyid_f_input'>f_input</span> <span class='op'>=</span> <span class='const'>File</span><span class='period'>.</span><span class='id identifier rubyid_open'>open</span><span class='lparen'>(</span><span class='id identifier rubyid_absolute_path'>absolute_path</span><span class='comma'>,</span> <span class='tstring'><span class='tstring_beg'>&#39;</span><span class='tstring_content'>r</span><span class='tstring_end'>&#39;</span></span><span class='rparen'>)</span>
<span class='id identifier rubyid_h'>h</span> <span class='op'>=</span> <span class='const'>Hash</span><span class='period'>.</span><span class='id identifier rubyid_new'>new</span>
<span class='id identifier rubyid_directory'>directory</span> <span class='op'>=</span> <span class='id identifier rubyid_absolute_path'>absolute_path</span><span class='period'>.</span><span class='id identifier rubyid_split'>split</span><span class='lparen'>(</span><span class='tstring'><span class='tstring_beg'>&#39;</span><span class='tstring_content'>/</span><span class='tstring_end'>&#39;</span></span><span class='rparen'>)</span><span class='lbracket'>[</span><span class='int'>0</span><span class='op'>...</span><span class='op'>-</span><span class='int'>1</span><span class='rbracket'>]</span><span class='period'>.</span><span class='id identifier rubyid_join'>join</span><span class='lparen'>(</span><span class='tstring'><span class='tstring_beg'>&quot;</span><span class='tstring_content'>/</span><span class='tstring_end'>&quot;</span></span><span class='rparen'>)</span>
<span class='id identifier rubyid_f_output'>f_output</span> <span class='op'>=</span> <span class='const'>File</span><span class='period'>.</span><span class='id identifier rubyid_new'>new</span><span class='lparen'>(</span><span class='id identifier rubyid_output'>output</span><span class='comma'>,</span> <span class='tstring'><span class='tstring_beg'>&#39;</span><span class='tstring_content'>w</span><span class='tstring_end'>&#39;</span></span><span class='rparen'>)</span>
<span class='id identifier rubyid_res'>res</span> <span class='op'>=</span> <span class='const'>String</span><span class='period'>.</span><span class='id identifier rubyid_new'>new</span>
<span class='id identifier rubyid_f_input'>f_input</span><span class='period'>.</span><span class='id identifier rubyid_each_line'>each_line</span> <span class='kw'>do</span> <span class='op'>|</span><span class='id identifier rubyid_line'>line</span><span class='op'>|</span>
<span class='id identifier rubyid_sline'>sline</span> <span class='op'>=</span> <span class='id identifier rubyid_line'>line</span><span class='period'>.</span><span class='id identifier rubyid_strip'>strip</span><span class='period'>.</span><span class='id identifier rubyid_split'>split</span><span class='lparen'>(</span><span class='tstring'><span class='tstring_beg'>&quot;</span><span class='tstring_content'>\t</span><span class='tstring_end'>&quot;</span></span><span class='rparen'>)</span>
<span class='id identifier rubyid_h'>h</span><span class='lbracket'>[</span><span class='id identifier rubyid_sline'>sline</span><span class='lbracket'>[</span><span class='int'>0</span><span class='rbracket'>]</span><span class='rbracket'>]</span> <span class='op'>=</span> <span class='id identifier rubyid_sline'>sline</span><span class='lbracket'>[</span><span class='op'>-</span><span class='int'>1</span><span class='rbracket'>]</span>
<span class='kw'>end</span>
<span class='id identifier rubyid_puts'>puts</span> <span class='id identifier rubyid_h'>h</span><span class='period'>.</span><span class='id identifier rubyid_keys'>keys</span><span class='period'>.</span><span class='id identifier rubyid_uniq'>uniq</span><span class='period'>.</span><span class='id identifier rubyid_length'>length</span>
<span class='kw'>if</span> <span class='id identifier rubyid_h'>h</span><span class='period'>.</span><span class='id identifier rubyid_keys'>keys</span><span class='period'>.</span><span class='id identifier rubyid_length'>length</span> <span class='op'>&gt;</span> <span class='int'>0</span>
<span class='id identifier rubyid_i'>i</span> <span class='op'>=</span> <span class='int'>1</span>
<span class='id identifier rubyid_h'>h</span><span class='period'>.</span><span class='id identifier rubyid_keys'>keys</span><span class='period'>.</span><span class='id identifier rubyid_uniq'>uniq</span><span class='lbracket'>[</span><span class='int'>0</span><span class='op'>...</span><span class='op'>-</span><span class='int'>1</span><span class='rbracket'>]</span><span class='period'>.</span><span class='id identifier rubyid_each'>each</span> <span class='kw'>do</span> <span class='op'>|</span><span class='id identifier rubyid_key'>key</span><span class='op'>|</span>
<span class='id identifier rubyid_puts'>puts</span> <span class='id identifier rubyid_i'>i</span>
<span class='comment'># puts &quot;#{key} :: #{h[key]}&quot;
</span> <span class='kw'>begin</span>
<span class='id identifier rubyid_inchikey'>inchikey</span> <span class='op'>=</span> <span class='backtick'>%x(</span><span class='tstring_content'>/Applications/ChemAxon/JChem/bin/molconvert inchikey -s &quot;</span><span class='embexpr_beg'>#{</span><span class='id identifier rubyid_h'>h</span><span class='lbracket'>[</span><span class='id identifier rubyid_key'>key</span><span class='rbracket'>]</span><span class='embexpr_end'>}</span><span class='tstring_content'>&quot;</span><span class='tstring_end'>)</span></span><span class='period'>.</span><span class='id identifier rubyid_strip'>strip</span>
<span class='comment'># puts inchikey
</span> <span class='id identifier rubyid_qr'>qr</span> <span class='op'>=</span> <span class='const'>ClassyFireAPI</span><span class='period'>.</span><span class='id identifier rubyid_get_entity_classification'>get_entity_classification</span><span class='lparen'>(</span><span class='id identifier rubyid_inchikey'>inchikey</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'>sdf</span><span class='tstring_end'>&quot;</span></span><span class='rparen'>)</span>
<span class='kw'>if</span> <span class='id identifier rubyid_qr'>qr</span><span class='period'>.</span><span class='id identifier rubyid_include?'>include?</span><span class='lparen'>(</span><span class='tstring'><span class='tstring_beg'>&quot;</span><span class='tstring_content'>The page you were looking for doesn&#39;t exist</span><span class='tstring_end'>&quot;</span></span><span class='rparen'>)</span>
<span class='id identifier rubyid_puts'>puts</span> <span class='tstring'><span class='tstring_beg'>&quot;</span><span class='tstring_content'>The page you were looking for doesn&#39;t exist</span><span class='tstring_end'>&quot;</span></span>
<span class='kw'>elsif</span> <span class='id identifier rubyid_qr'>qr</span><span class='period'>.</span><span class='id identifier rubyid_empty?'>empty?</span>
<span class='kw'>else</span>
<span class='id identifier rubyid_input'>input</span> <span class='op'>=</span> <span class='id identifier rubyid_qr'>qr</span><span class='period'>.</span><span class='id identifier rubyid_split'>split</span><span class='lparen'>(</span><span class='tstring'><span class='tstring_beg'>&quot;</span><span class='tstring_content'>\n</span><span class='tstring_end'>&quot;</span></span><span class='rparen'>)</span><span class='lbracket'>[</span><span class='int'>1</span><span class='op'>..</span><span class='op'>-</span><span class='int'>1</span><span class='rbracket'>]</span><span class='period'>.</span><span class='id identifier rubyid_join'>join</span><span class='lparen'>(</span><span class='tstring'><span class='tstring_beg'>&quot;</span><span class='tstring_content'>\n</span><span class='tstring_end'>&quot;</span></span><span class='rparen'>)</span>
<span class='id identifier rubyid_puts'>puts</span> <span class='id identifier rubyid_input'>input</span>
<span class='id identifier rubyid_f_output'>f_output</span><span class='period'>.</span><span class='id identifier rubyid_puts'>puts</span> <span class='tstring'><span class='tstring_beg'>&quot;</span><span class='embexpr_beg'>#{</span><span class='id identifier rubyid_key'>key</span><span class='embexpr_end'>}</span><span class='tstring_content'>\n</span><span class='tstring_end'>&quot;</span></span>
<span class='id identifier rubyid_f_output'>f_output</span><span class='period'>.</span><span class='id identifier rubyid_puts'>puts</span> <span class='id identifier rubyid_input'>input</span>
<span class='kw'>end</span>
<span class='kw'>rescue</span> <span class='const'>Exception</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_message'>message</span>
<span class='kw'>end</span>
<span class='id identifier rubyid_i'>i</span> <span class='op'>+=</span> <span class='int'>1</span>
<span class='kw'>end</span>
<span class='id identifier rubyid_key'>key</span> <span class='op'>=</span> <span class='id identifier rubyid_h'>h</span><span class='period'>.</span><span class='id identifier rubyid_keys'>keys</span><span class='lbracket'>[</span><span class='op'>-</span><span class='int'>1</span><span class='rbracket'>]</span>
<span class='comment'># puts &quot;#{key} :: #{h[key]}&quot;
</span> <span class='kw'>begin</span>
<span class='id identifier rubyid_inchikey'>inchikey</span> <span class='op'>=</span> <span class='backtick'>%x(</span><span class='tstring_content'>/Applications/ChemAxon/JChem/bin/molconvert inchikey -s &quot;</span><span class='embexpr_beg'>#{</span><span class='id identifier rubyid_h'>h</span><span class='lbracket'>[</span><span class='id identifier rubyid_key'>key</span><span class='rbracket'>]</span><span class='embexpr_end'>}</span><span class='tstring_content'>&quot;</span><span class='tstring_end'>)</span></span><span class='period'>.</span><span class='id identifier rubyid_strip'>strip</span>
<span class='comment'># puts inchikey
</span> <span class='id identifier rubyid_qr'>qr</span> <span class='op'>=</span> <span class='const'>ClassyFireAPI</span><span class='period'>.</span><span class='id identifier rubyid_get_entity_classification'>get_entity_classification</span><span class='lparen'>(</span><span class='id identifier rubyid_inchikey'>inchikey</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'>sdf</span><span class='tstring_end'>&quot;</span></span><span class='rparen'>)</span>
<span class='kw'>if</span> <span class='id identifier rubyid_qr'>qr</span><span class='period'>.</span><span class='id identifier rubyid_include?'>include?</span><span class='lparen'>(</span><span class='tstring'><span class='tstring_beg'>&quot;</span><span class='tstring_content'>The page you were looking for doesn&#39;t exist</span><span class='tstring_end'>&quot;</span></span><span class='rparen'>)</span>
<span class='id identifier rubyid_puts'>puts</span> <span class='tstring'><span class='tstring_beg'>&quot;</span><span class='tstring_content'>The page you were looking for doesn&#39;t exist</span><span class='tstring_end'>&quot;</span></span>
<span class='kw'>elsif</span> <span class='id identifier rubyid_qr'>qr</span><span class='period'>.</span><span class='id identifier rubyid_empty?'>empty?</span>
<span class='kw'>else</span>
<span class='id identifier rubyid_input'>input</span> <span class='op'>=</span> <span class='id identifier rubyid_qr'>qr</span><span class='period'>.</span><span class='id identifier rubyid_split'>split</span><span class='lparen'>(</span><span class='tstring'><span class='tstring_beg'>&quot;</span><span class='tstring_content'>\n</span><span class='tstring_end'>&quot;</span></span><span class='rparen'>)</span><span class='lbracket'>[</span><span class='int'>1</span><span class='op'>..</span><span class='op'>-</span><span class='int'>1</span><span class='rbracket'>]</span><span class='period'>.</span><span class='id identifier rubyid_join'>join</span><span class='lparen'>(</span><span class='tstring'><span class='tstring_beg'>&quot;</span><span class='tstring_content'>\n</span><span class='tstring_end'>&quot;</span></span><span class='rparen'>)</span>
<span class='id identifier rubyid_puts'>puts</span> <span class='id identifier rubyid_input'>input</span>
<span class='id identifier rubyid_f_output'>f_output</span><span class='period'>.</span><span class='id identifier rubyid_puts'>puts</span> <span class='tstring'><span class='tstring_beg'>&quot;</span><span class='embexpr_beg'>#{</span><span class='id identifier rubyid_key'>key</span><span class='embexpr_end'>}</span><span class='tstring_content'>\n</span><span class='tstring_end'>&quot;</span></span>
<span class='id identifier rubyid_f_output'>f_output</span><span class='period'>.</span><span class='id identifier rubyid_puts'>puts</span> <span class='id identifier rubyid_input'>input</span>
<span class='kw'>end</span>
<span class='kw'>rescue</span> <span class='const'>Exception</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_message'>message</span>
<span class='kw'>end</span>
<span class='kw'>end</span>
<span class='comment'># f_output.print res
</span><span class='kw'>end</span></pre>
</td>
</tr>
</table>
</div>
<div class="method_details ">
<h3 class="signature " id="submit_queries_from_directory-class_method">
+ (<tt>Object</tt>) <strong>submit_queries_from_directory</strong>(folder, slice_length, type = &quot;STRUCTURE&quot;)
</h3><div class="docstring">
<div class="discussion">
<p>Takes each file in a folder, and submit the contained structures in bluks
of a given size.</p>
<p>For &#39;STRUCTURE&#39; or &#39;IUPAC_NAME&#39;query types, each line must
contain either</p>
<pre class="code ruby"><code class="ruby">1) Only a structural represenation: SMILES, InChI for the &#39;STRUCTURE&#39; query_type or a IUPAC name
for the &#39;IUPAC NAME&#39; query type.
2) a tab-separated pair of an ID and the corresponding sructure representation: SMILES, InChI for the
&#39;STRUCTURE&#39; query_type or a IUPAC name for the &#39;IUPAC NAME&#39; query type.</code></pre>
<p>For &#39;FASTA&#39; query type, just submit the query as a standard FASTA
text. @param: input_file [String] The path to the folder. @param:
slice_length [Integer] The maximum number of entries for each query input
(each file is fragmented into n part of #slice_length entries each),
&#39;integer&#39;</p>
</div>
</div>
<div class="tags">
<p class="tag_title">Parameters:</p>
<ul class="param">
<li>
<span class='name'>type</span>
<span class='type'>(<tt>String</tt>)</span>
<em class="default">(defaults to: <tt>&quot;STRUCTURE&quot;</tt>)</em>
&mdash;
<div class='inline'>
<p>the query_type &#39;STRUCTURE&#39; (default) or &#39;IUPAC_NAME&#39; or
&#39;FASTA&#39;</p>
</div>
</li>
</ul>
</div><table class="source_code">
<tr>
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<pre class="code"><span class="info file"># File 'lib/classyfire_api.rb', line 184</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>
<span class='const'>Dir</span><span class='period'>.</span><span class='id identifier rubyid_foreach'>foreach</span><span class='lparen'>(</span><span class='id identifier rubyid_folder'>folder</span><span class='rparen'>)</span> <span class='kw'>do</span> <span class='op'>|</span><span class='id identifier rubyid_filename'>filename</span><span class='op'>|</span>
<span class='id identifier rubyid_puts'>puts</span> <span class='tstring'><span class='tstring_beg'>&quot;</span><span class='tstring_content'>Filename: </span><span class='embexpr_beg'>#{</span><span class='id identifier rubyid_filename'>filename</span><span class='embexpr_end'>}</span><span class='tstring_end'>&quot;</span></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_folder'>folder</span><span class='op'>+</span><span class='tstring'><span class='tstring_beg'>&quot;</span><span class='tstring_content'>/</span><span class='tstring_end'>&quot;</span></span><span class='op'>+</span><span class='id identifier rubyid_filename'>filename</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='rparen'>)</span> <span class='kw'>unless</span> <span class='id identifier rubyid_filename'>filename</span> <span class='op'>==</span> <span class='tstring'><span class='tstring_beg'>&quot;</span><span class='tstring_content'>.</span><span class='tstring_end'>&quot;</span></span> <span class='op'>||</span> <span class='id identifier rubyid_filename'>filename</span> <span class='op'>==</span> <span class='tstring'><span class='tstring_beg'>&quot;</span><span class='tstring_content'>..</span><span class='tstring_end'>&quot;</span></span> <span class='op'>||</span> <span class='id identifier rubyid_filename'>filename</span> <span class='op'>==</span> <span class='tstring'><span class='tstring_beg'>&quot;</span><span class='tstring_content'>.DS_Store</span><span class='tstring_end'>&quot;</span></span>
<span class='kw'>end</span>
<span class='kw'>else</span>
<span class='gvar'>$stderr</span><span class='period'>.</span><span class='id identifier rubyid_puts'>puts</span> <span class='tstring'><span class='tstring_beg'>&quot;</span><span class='embexpr_beg'>#{</span><span class='id identifier rubyid_folder'>folder</span><span class='embexpr_end'>}</span><span class='tstring_content'> is not a folder.</span><span class='tstring_end'>&quot;</span></span>
<span class='kw'>end</span>
<span class='kw'>end</span></pre>
</td>
</tr>
</table>
</div>
<div class="method_details ">
<h3 class="signature " id="submit_query-class_method">
+ (<tt>Hash</tt>) <strong>submit_query</strong>(label, input, type = &#39;STRUCTURE&#39;)
</h3><div class="docstring">
<div class="discussion">
<p>Submits a ClassyFire query, which should be returned in a specific format.</p>
<p>if there is an error.</p>
</div>
</div>
<div class="tags">
<p class="tag_title">Parameters:</p>
<ul class="param">
<li>
<span class='name'>label</span>
<span class='type'>(<tt>String</tt>)</span>
&mdash;
<div class='inline'>
<p>the label of the query.</p>
</div>
</li>
<li>
<span class='name'>input</span>
<span class='type'>(<tt>String</tt>)</span>
&mdash;
<div class='inline'>
<p>the input of the query.</p>
</div>
</li>
</ul>
<p class="tag_title">Returns:</p>
<ul class="return">
<li>
<span class='type'>(<tt>Hash</tt>)</span>
&mdash;
<div class='inline'>
<p>A Ruby Hash with the id (and other attributes) of the Query or nil</p>
</div>
</li>
</ul>
</div><table class="source_code">
<tr>
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</td>
<td>
<pre class="code"><span class="info file"># File 'lib/classyfire_api.rb', line 13</span>
<span class='kw'>def</span> <span class='const'>ClassyFireAPI</span><span class='period'>.</span><span class='id identifier rubyid_submit_query'>submit_query</span><span class='lparen'>(</span><span class='id identifier rubyid_label'>label</span><span class='comma'>,</span><span class='id identifier rubyid_input'>input</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='kw'>begin</span>
<span class='id identifier rubyid_q'>q</span> <span class='op'>=</span> <span class='const'>RestClient</span><span class='period'>.</span><span class='id identifier rubyid_post'>post</span> <span class='const'>URL</span><span class='op'>+</span><span class='tstring'><span class='tstring_beg'>&#39;</span><span class='tstring_content'>/queries</span><span class='tstring_end'>&#39;</span></span><span class='comma'>,</span> <span class='lbrace'>{</span><span class='symbol'>:label</span> <span class='op'>=&gt;</span> <span class='id identifier rubyid_label'>label</span><span class='comma'>,</span> <span class='symbol'>:query_input</span> <span class='op'>=&gt;</span> <span class='id identifier rubyid_input'>input</span><span class='comma'>,</span> <span class='symbol'>:query_type</span> <span class='op'>=&gt;</span> <span class='id identifier rubyid_type'>type</span><span class='rbrace'>}</span><span class='period'>.</span><span class='id identifier rubyid_to_json'>to_json</span><span class='comma'>,</span> <span class='symbol'>:accept</span> <span class='op'>=&gt;</span> <span class='symbol'>:json</span><span class='comma'>,</span> <span class='symbol'>:content_type</span> <span class='op'>=&gt;</span> <span class='symbol'>:json</span>
<span class='kw'>rescue</span> <span class='const'>RestClient</span><span class='op'>::</span><span class='const'>BadRequest</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'>rescue</span> <span class='const'>RestClient</span><span class='op'>::</span><span class='const'>UnprocessableEntity</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='id identifier rubyid_q'>q</span>
<span class='kw'>end</span></pre>
</td>
</tr>
</table>
</div>
<div class="method_details ">
<h3 class="signature " id="submit_query_input_in_chunks-class_method">
+ (<tt>Object</tt>) <strong>submit_query_input_in_chunks</strong>(input_file, slice_length, start, type = &#39;STRUCTURE&#39;)
</h3><div class="docstring">
<div class="discussion">
<p>Takes a tab-separated file and submit the contained structures in bulks of
a given size</p>
<p>For &#39;STRUCTURE&#39; or &#39;IUPAC_NAME&#39;query types, each line must
contain either</p>
<pre class="code ruby"><code class="ruby">1) Only a structural represenation: SMILES, InChI for the &#39;STRUCTURE&#39; query_type or a IUPAC name
for the &#39;IUPAC NAME&#39; query type.
2) a tab-separated pair of an ID and the corresponding sructure representation: SMILES, InChI for the
&#39;STRUCTURE&#39; query_type or a IUPAC name for the &#39;IUPAC NAME&#39; query type.</code></pre>
<p>For &#39;FASTA&#39; query type, just submit the query as a standard FASTA
text. @param: slice_length [Integer] The maximum number of entries for each
query input (the whole file is fragmented into n part of #slice_length
entries each). @param: start [Integer] The starting index. Submit
framgments from the index &#39;start&#39;.</p>
</div>
</div>
<div class="tags">
<p class="tag_title">Parameters:</p>
<ul class="param">
<li>
<span class='name'>input_file</span>
<span class='type'>(<tt>Text</tt>)</span>
&mdash;
<div class='inline'>
<p>The path to the input file.</p>
</div>
</li>
</ul>
</div><table class="source_code">
<tr>
<td>
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</td>
<td>
<pre class="code"><span class="info file"># File 'lib/classyfire_api.rb', line 107</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>
<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_file'>input_file</span><span class='rparen'>)</span>
<span class='id identifier rubyid_f'>f</span> <span class='op'>=</span> <span class='const'>File</span><span class='period'>.</span><span class='id identifier rubyid_open'>open</span><span class='lparen'>(</span><span class='id identifier rubyid_absolute_path'>absolute_path</span><span class='comma'>,</span> <span class='tstring'><span class='tstring_beg'>&#39;</span><span class='tstring_content'>r</span><span class='tstring_end'>&#39;</span></span><span class='rparen'>)</span>
<span class='id identifier rubyid_input'>input</span> <span class='op'>=</span> <span class='lbracket'>[</span><span class='rbracket'>]</span>
<span class='id identifier rubyid_lines'>lines</span> <span class='op'>=</span> <span class='const'>File</span><span class='period'>.</span><span class='id identifier rubyid_readlines'>readlines</span><span class='lparen'>(</span><span class='id identifier rubyid_absolute_path'>absolute_path</span><span class='rparen'>)</span>
<span class='id identifier rubyid_lines'>lines</span><span class='period'>.</span><span class='id identifier rubyid_uniq'>uniq</span><span class='period'>.</span><span class='id identifier rubyid_each'>each</span> <span class='kw'>do</span> <span class='op'>|</span><span class='id identifier rubyid_line'>line</span><span class='op'>|</span>
<span class='id identifier rubyid_sline'>sline</span> <span class='op'>=</span> <span class='id identifier rubyid_line'>line</span><span class='period'>.</span><span class='id identifier rubyid_strip'>strip</span><span class='period'>.</span><span class='id identifier rubyid_split'>split</span><span class='lparen'>(</span><span class='tstring'><span class='tstring_beg'>&quot;</span><span class='tstring_content'>\t</span><span class='tstring_end'>&quot;</span></span><span class='rparen'>)</span>
<span class='kw'>if</span> <span class='id identifier rubyid_sline'>sline</span><span class='period'>.</span><span class='id identifier rubyid_length'>length</span> <span class='op'>==</span> <span class='int'>1</span>
<span class='id identifier rubyid_input'>input</span> <span class='op'>&lt;&lt;</span><span class='tstring'><span class='tstring_beg'>&quot;</span><span class='embexpr_beg'>#{</span><span class='id identifier rubyid_sline'>sline</span><span class='lbracket'>[</span><span class='int'>0</span><span class='rbracket'>]</span><span class='embexpr_end'>}</span><span class='tstring_end'>&quot;</span></span>
<span class='kw'>elsif</span> <span class='id identifier rubyid_sline'>sline</span><span class='period'>.</span><span class='id identifier rubyid_length'>length</span> <span class='op'>&gt;=</span> <span class='int'>2</span>
<span class='id identifier rubyid_input'>input</span> <span class='op'>&lt;&lt;</span><span class='tstring'><span class='tstring_beg'>&quot;</span><span class='embexpr_beg'>#{</span><span class='id identifier rubyid_sline'>sline</span><span class='lbracket'>[</span><span class='int'>0</span><span class='rbracket'>]</span><span class='embexpr_end'>}</span><span class='tstring_content'>\t</span><span class='embexpr_beg'>#{</span><span class='id identifier rubyid_sline'>sline</span><span class='lbracket'>[</span><span class='int'>2</span><span class='rbracket'>]</span><span class='embexpr_end'>}</span><span class='tstring_end'>&quot;</span></span>
<span class='kw'>end</span>
<span class='kw'>end</span>
<span class='id identifier rubyid_query_ids'>query_ids</span> <span class='op'>=</span> <span class='lbracket'>[</span><span class='rbracket'>]</span>
<span class='id identifier rubyid_subdivised_groups'>subdivised_groups</span> <span class='op'>=</span> <span class='id identifier rubyid_input'>input</span><span class='period'>.</span><span class='id identifier rubyid_uniq'>uniq</span><span class='period'>.</span><span class='id identifier rubyid_each_slice'>each_slice</span><span class='lparen'>(</span><span class='id identifier rubyid_slice_length'>slice_length</span><span class='rparen'>)</span><span class='period'>.</span><span class='id identifier rubyid_to_a'>to_a</span>
<span class='id identifier rubyid_puts'>puts</span> <span class='tstring'><span class='tstring_beg'>&quot;</span><span class='tstring_content'>nr of subdivised_groups: </span><span class='embexpr_beg'>#{</span><span class='id identifier rubyid_subdivised_groups'>subdivised_groups</span><span class='period'>.</span><span class='id identifier rubyid_length'>length</span><span class='embexpr_end'>}</span><span class='tstring_end'>&quot;</span></span>
<span class='id identifier rubyid_puts'>puts</span> <span class='id identifier rubyid_subdivised_groups'>subdivised_groups</span><span class='lbracket'>[</span><span class='int'>0</span><span class='rbracket'>]</span>
<span class='id identifier rubyid_sleeping_time'>sleeping_time</span> <span class='op'>=</span> <span class='int'>120</span>
<span class='id identifier rubyid_initial_nr_of_jobs'>initial_nr_of_jobs</span> <span class='op'>=</span> <span class='int'>60</span>
<span class='id identifier rubyid_i'>i</span> <span class='op'>=</span> <span class='id identifier rubyid_start'>start</span>
<span class='kw'>while</span> <span class='id identifier rubyid_i'>i</span> <span class='op'>&lt;</span> <span class='id identifier rubyid_initial_nr_of_jobs'>initial_nr_of_jobs</span>
<span class='id identifier rubyid_title'>title</span> <span class='op'>=</span> <span class='const'>File</span><span class='period'>.</span><span class='id identifier rubyid_basename'>basename</span><span class='lparen'>(</span><span class='id identifier rubyid_absolute_path'>absolute_path</span><span class='rparen'>)</span><span class='period'>.</span><span class='id identifier rubyid_split'>split</span><span class='lparen'>(</span><span class='tstring'><span class='tstring_beg'>&quot;</span><span class='tstring_content'>.</span><span class='tstring_end'>&quot;</span></span><span class='rparen'>)</span><span class='lbracket'>[</span><span class='int'>0</span><span class='rbracket'>]</span> <span class='op'>+</span> <span class='tstring'><span class='tstring_beg'>&quot;</span><span class='tstring_content'>_yannick</span><span class='tstring_end'>&quot;</span></span> <span class='op'>+</span> <span class='tstring'><span class='tstring_beg'>&quot;</span><span class='tstring_content'>_part_</span><span class='embexpr_beg'>#{</span><span class='id identifier rubyid_i'>i</span><span class='embexpr_end'>}</span><span class='tstring_end'>&quot;</span></span>
<span class='kw'>begin</span>
<span class='id identifier rubyid_puts'>puts</span> <span class='tstring'><span class='tstring_beg'>&quot;</span><span class='tstring_content'>submitting </span><span class='embexpr_beg'>#{</span><span class='id identifier rubyid_title'>title</span><span class='embexpr_end'>}</span><span class='tstring_end'>&quot;</span></span>
<span class='id identifier rubyid_q'>q</span> <span class='op'>=</span> <span class='id identifier rubyid_submit_query'>submit_query</span><span class='lparen'>(</span><span class='id identifier rubyid_title'>title</span><span class='comma'>,</span><span class='id identifier rubyid_subdivised_groups'>subdivised_groups</span><span class='lbracket'>[</span><span class='id identifier rubyid_i'>i</span><span class='op'>-</span><span class='int'>1</span><span class='rbracket'>]</span><span class='period'>.</span><span class='id identifier rubyid_join'>join</span><span class='lparen'>(</span><span class='tstring'><span class='tstring_beg'>&quot;</span><span class='tstring_content'>\n</span><span class='tstring_end'>&quot;</span></span><span class='rparen'>)</span><span class='comma'>,</span><span class='id identifier rubyid_type'>type</span><span class='rparen'>)</span>
<span class='id identifier rubyid_query_ids'>query_ids</span> <span class='op'>&lt;&lt;</span> <span class='const'>JSON</span><span class='period'>.</span><span class='id identifier rubyid_parse'>parse</span><span class='lparen'>(</span><span class='id identifier rubyid_q'>q</span><span class='rparen'>)</span><span class='lbracket'>[</span><span class='tstring'><span class='tstring_beg'>&#39;</span><span class='tstring_content'>id</span><span class='tstring_end'>&#39;</span></span><span class='rbracket'>]</span>
<span class='kw'>rescue</span> <span class='const'>Exception</span> <span class='op'>=&gt;</span> <span class='id identifier rubyid_e'>e</span>
<span class='id identifier rubyid_puts'>puts</span> <span class='id identifier rubyid_e'>e</span><span class='period'>.</span><span class='id identifier rubyid_message'>message</span>
<span class='id identifier rubyid_puts'>puts</span> <span class='id identifier rubyid_e'>e</span><span class='period'>.</span><span class='id identifier rubyid_backtrace'>backtrace</span><span class='period'>.</span><span class='id identifier rubyid_inspect'>inspect</span>
<span class='kw'>end</span>
<span class='id identifier rubyid_i'>i</span> <span class='op'>=</span> <span class='id identifier rubyid_i'>i</span> <span class='op'>+</span> <span class='int'>1</span>
<span class='kw'>end</span>
<span class='id identifier rubyid_puts'>puts</span> <span class='tstring'><span class='tstring_beg'>&quot;</span><span class='tstring_content'>Going to sleep at </span><span class='embexpr_beg'>#{</span><span class='const'>Time</span><span class='period'>.</span><span class='id identifier rubyid_now'>now</span> <span class='op'>-</span> <span class='ivar'>@start_time</span><span class='embexpr_end'>}</span><span class='tstring_content'> for </span><span class='embexpr_beg'>#{</span><span class='id identifier rubyid_sleeping_time'>sleeping_time</span><span class='embexpr_end'>}</span><span class='tstring_content'> s.</span><span class='tstring_end'>&quot;</span></span>
<span class='id identifier rubyid_sleep'>sleep</span><span class='lparen'>(</span><span class='id identifier rubyid_sleeping_time'>sleeping_time</span><span class='rparen'>)</span>
<span class='id identifier rubyid_puts'>puts</span> <span class='tstring'><span class='tstring_beg'>&quot;</span><span class='tstring_content'>Waking up at </span><span class='embexpr_beg'>#{</span><span class='const'>Time</span><span class='period'>.</span><span class='id identifier rubyid_now'>now</span> <span class='op'>-</span> <span class='ivar'>@start_time</span><span class='embexpr_end'>}</span><span class='tstring_end'>&quot;</span></span>
<span class='kw'>while</span> <span class='id identifier rubyid_i'>i</span> <span class='op'>&lt;</span> <span class='id identifier rubyid_subdivised_groups'>subdivised_groups</span><span class='period'>.</span><span class='id identifier rubyid_length'>length</span>
<span class='id identifier rubyid_k'>k</span> <span class='op'>=</span> <span class='int'>0</span>
<span class='kw'>for</span> <span class='id identifier rubyid_k'>k</span> <span class='kw'>in</span> <span class='lparen'>(</span><span class='id identifier rubyid_i'>i</span><span class='op'>..</span><span class='lparen'>(</span><span class='id identifier rubyid_i'>i</span><span class='op'>+</span><span class='int'>80</span><span class='rparen'>)</span><span class='rparen'>)</span>
<span class='id identifier rubyid_title'>title</span> <span class='op'>=</span> <span class='const'>File</span><span class='period'>.</span><span class='id identifier rubyid_basename'>basename</span><span class='lparen'>(</span><span class='id identifier rubyid_absolute_path'>absolute_path</span><span class='rparen'>)</span><span class='period'>.</span><span class='id identifier rubyid_split'>split</span><span class='lparen'>(</span><span class='tstring'><span class='tstring_beg'>&quot;</span><span class='tstring_content'>.</span><span class='tstring_end'>&quot;</span></span><span class='rparen'>)</span><span class='lbracket'>[</span><span class='int'>0</span><span class='rbracket'>]</span> <span class='op'>+</span> <span class='tstring'><span class='tstring_beg'>&quot;</span><span class='tstring_content'>_yannick</span><span class='tstring_end'>&quot;</span></span> <span class='op'>+</span> <span class='tstring'><span class='tstring_beg'>&quot;</span><span class='tstring_content'>_part_</span><span class='embexpr_beg'>#{</span><span class='id identifier rubyid_k'>k</span><span class='embexpr_end'>}</span><span class='tstring_end'>&quot;</span></span>
<span class='id identifier rubyid_i'>i</span> <span class='op'>=</span> <span class='id identifier rubyid_i'>i</span> <span class='op'>+</span> <span class='int'>1</span>
<span class='kw'>begin</span>
<span class='id identifier rubyid_puts'>puts</span> <span class='tstring'><span class='tstring_beg'>&quot;</span><span class='tstring_content'>submitting </span><span class='embexpr_beg'>#{</span><span class='id identifier rubyid_title'>title</span><span class='embexpr_end'>}</span><span class='tstring_end'>&quot;</span></span>
<span class='id identifier rubyid_q'>q</span> <span class='op'>=</span> <span class='id identifier rubyid_submit_query'>submit_query</span><span class='lparen'>(</span><span class='id identifier rubyid_title'>title</span><span class='comma'>,</span><span class='id identifier rubyid_subdivised_groups'>subdivised_groups</span><span class='lbracket'>[</span><span class='id identifier rubyid_k'>k</span><span class='op'>-</span><span class='int'>1</span><span class='rbracket'>]</span><span class='period'>.</span><span class='id identifier rubyid_join'>join</span><span class='lparen'>(</span><span class='tstring'><span class='tstring_beg'>&quot;</span><span class='tstring_content'>\n</span><span class='tstring_end'>&quot;</span></span><span class='rparen'>)</span><span class='comma'>,</span><span class='id identifier rubyid_type'>type</span><span class='rparen'>)</span>
<span class='kw'>rescue</span> <span class='const'>Exception</span> <span class='op'>=&gt;</span> <span class='id identifier rubyid_e'>e</span>
<span class='id identifier rubyid_puts'>puts</span> <span class='id identifier rubyid_e'>e</span><span class='period'>.</span><span class='id identifier rubyid_message'>message</span>
<span class='id identifier rubyid_puts'>puts</span> <span class='id identifier rubyid_e'>e</span><span class='period'>.</span><span class='id identifier rubyid_backtrace'>backtrace</span><span class='period'>.</span><span class='id identifier rubyid_inspect'>inspect</span>
<span class='kw'>end</span>
<span class='kw'>end</span>
<span class='id identifier rubyid_i'>i</span> <span class='op'>=</span> <span class='id identifier rubyid_k'>k</span>
<span class='id identifier rubyid_puts'>puts</span> <span class='tstring'><span class='tstring_beg'>&quot;</span><span class='tstring_content'>Going to sleep at </span><span class='embexpr_beg'>#{</span><span class='const'>Time</span><span class='period'>.</span><span class='id identifier rubyid_now'>now</span> <span class='op'>-</span> <span class='ivar'>@start_time</span><span class='embexpr_end'>}</span><span class='tstring_content'> for </span><span class='embexpr_beg'>#{</span><span class='id identifier rubyid_sleeping_time'>sleeping_time</span><span class='embexpr_end'>}</span><span class='tstring_content'> s.</span><span class='tstring_end'>&quot;</span></span>
<span class='id identifier rubyid_sleep'>sleep</span><span class='lparen'>(</span><span class='id identifier rubyid_sleeping_time'>sleeping_time</span><span class='rparen'>)</span>
<span class='id identifier rubyid_puts'>puts</span> <span class='tstring'><span class='tstring_beg'>&quot;</span><span class='tstring_content'>Waking up at </span><span class='embexpr_beg'>#{</span><span class='const'>Time</span><span class='period'>.</span><span class='id identifier rubyid_now'>now</span> <span class='op'>-</span> <span class='ivar'>@start_time</span><span class='embexpr_end'>}</span><span class='tstring_end'>&quot;</span></span>
<span class='kw'>end</span>
<span class='kw'>end</span></pre>
</td>
</tr>
</table>
</div>
<div class="method_details ">
<h3 class="signature " id="submit_random_subset_of_query_input_in_chunks-class_method">
+ (<tt>Object</tt>) <strong>submit_random_subset_of_query_input_in_chunks</strong>(tab_separated_input_file, size, type = &#39;STRUCTURE&#39;)
</h3><div class="docstring">
<div class="discussion">
<p>Takes a tab-separated file and submit randomly selected structures in bulks
of a given size.</p>
<p>For &#39;STRUCTURE&#39; or &#39;IUPAC_NAME&#39;query types, each line must
contain either</p>
<pre class="code ruby"><code class="ruby">1) Only a structural represenation: SMILES, InChI for the &#39;STRUCTURE&#39; query_type or a IUPAC name
for the &#39;IUPAC NAME&#39; query type.
2) a tab-separated pair of an ID and the corresponding sructure representation: SMILES, InChI for the
&#39;STRUCTURE&#39; query_type or a IUPAC name for the &#39;IUPAC NAME&#39; query type.</code></pre>
<p>For &#39;FASTA&#39; query type, just submit the query as a standard FASTA
text. is fragmented into n part of #slice_length entries each).</p>
</div>
</div>
<div class="tags">
<p class="tag_title">Parameters:</p>
<ul class="param">
<li>
<span class='name'>tab_separated_input_file</span>
<span class='type'>(<tt>Text</tt>)</span>
&mdash;
<div class='inline'>
<p>The path to the input file.</p>
</div>
</li>
<li>
<span class='name'>size</span>
<span class='type'>(<tt>Integer</tt>)</span>
&mdash;
<div class='inline'>
<p>The maximum number of entries for each query input (the whole file</p>
</div>
</li>
<li>
<span class='name'>type</span>
<span class='type'>(<tt>String</tt>)</span>
<em class="default">(defaults to: <tt>&#39;STRUCTURE&#39;</tt>)</em>
&mdash;
<div class='inline'>
<p>The query_type, &#39;STRUCTURE&#39; (default) or &#39;IUPAC_NAME&#39; or
&#39;FASTA&#39;.</p>
</div>
</li>
</ul>
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<pre class="code"><span class="info file"># File 'lib/classyfire_api.rb', line 209</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>
<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_tab_separated_input_file'>tab_separated_input_file</span><span class='rparen'>)</span>
<span class='id identifier rubyid_f'>f</span> <span class='op'>=</span> <span class='const'>File</span><span class='period'>.</span><span class='id identifier rubyid_open'>open</span><span class='lparen'>(</span><span class='id identifier rubyid_absolute_path'>absolute_path</span><span class='comma'>,</span> <span class='tstring'><span class='tstring_beg'>&#39;</span><span class='tstring_content'>r</span><span class='tstring_end'>&#39;</span></span><span class='rparen'>)</span>
<span class='id identifier rubyid_input'>input</span> <span class='op'>=</span> <span class='lbracket'>[</span><span class='rbracket'>]</span>
<span class='id identifier rubyid_f'>f</span><span class='period'>.</span><span class='id identifier rubyid_each_line'>each_line</span> <span class='kw'>do</span> <span class='op'>|</span><span class='id identifier rubyid_line'>line</span><span class='op'>|</span>
<span class='id identifier rubyid_sline'>sline</span> <span class='op'>=</span> <span class='id identifier rubyid_line'>line</span><span class='period'>.</span><span class='id identifier rubyid_strip'>strip</span><span class='period'>.</span><span class='id identifier rubyid_split'>split</span><span class='lparen'>(</span><span class='tstring'><span class='tstring_beg'>&quot;</span><span class='tstring_content'>\t</span><span class='tstring_end'>&quot;</span></span><span class='rparen'>)</span>
<span class='kw'>if</span> <span class='id identifier rubyid_sline'>sline</span><span class='period'>.</span><span class='id identifier rubyid_length'>length</span> <span class='op'>==</span> <span class='int'>1</span>
<span class='id identifier rubyid_input'>input</span> <span class='op'>&lt;&lt;</span><span class='tstring'><span class='tstring_beg'>&quot;</span><span class='embexpr_beg'>#{</span><span class='id identifier rubyid_sline'>sline</span><span class='lbracket'>[</span><span class='int'>0</span><span class='rbracket'>]</span><span class='embexpr_end'>}</span><span class='tstring_end'>&quot;</span></span>
<span class='kw'>elsif</span> <span class='id identifier rubyid_sline'>sline</span><span class='period'>.</span><span class='id identifier rubyid_length'>length</span> <span class='op'>==</span> <span class='int'>2</span>
<span class='id identifier rubyid_input'>input</span> <span class='op'>&lt;&lt;</span><span class='tstring'><span class='tstring_beg'>&quot;</span><span class='embexpr_beg'>#{</span><span class='id identifier rubyid_sline'>sline</span><span class='lbracket'>[</span><span class='int'>0</span><span class='rbracket'>]</span><span class='embexpr_end'>}</span><span class='tstring_content'>\t</span><span class='embexpr_beg'>#{</span><span class='id identifier rubyid_sline'>sline</span><span class='lbracket'>[</span><span class='int'>1</span><span class='rbracket'>]</span><span class='embexpr_end'>}</span><span class='tstring_end'>&quot;</span></span>
<span class='kw'>end</span>
<span class='kw'>end</span>
<span class='id identifier rubyid_query_ids'>query_ids</span> <span class='op'>=</span> <span class='lbracket'>[</span><span class='rbracket'>]</span>
<span class='id identifier rubyid_indexes'>indexes</span> <span class='op'>=</span> <span class='lbracket'>[</span><span class='rbracket'>]</span>
<span class='id identifier rubyid_r'>r</span> <span class='op'>=</span> <span class='int'>1</span>
<span class='kw'>while</span> <span class='id identifier rubyid_r'>r</span> <span class='op'>&lt;=</span> <span class='lparen'>(</span><span class='id identifier rubyid_size'>size</span><span class='rparen'>)</span>
<span class='id identifier rubyid_s'>s</span> <span class='op'>=</span> <span class='id identifier rubyid_rand'>rand</span><span class='lparen'>(</span><span class='int'>0</span><span class='op'>..</span><span class='lparen'>(</span><span class='id identifier rubyid_input'>input</span><span class='period'>.</span><span class='id identifier rubyid_length'>length</span> <span class='op'>-</span> <span class='int'>1</span><span class='rparen'>)</span><span class='rparen'>)</span>
<span class='kw'>unless</span> <span class='id identifier rubyid_indexes'>indexes</span><span class='period'>.</span><span class='id identifier rubyid_include?'>include?</span><span class='lparen'>(</span><span class='id identifier rubyid_s'>s</span><span class='rparen'>)</span>
<span class='id identifier rubyid_indexes'>indexes</span><span class='op'>&lt;&lt;</span><span class='id identifier rubyid_s'>s</span>
<span class='id identifier rubyid_r'>r</span> <span class='op'>+=</span> <span class='int'>1</span>
<span class='kw'>end</span>
<span class='kw'>end</span>
<span class='id identifier rubyid_random_subset'>random_subset</span> <span class='op'>=</span> <span class='id identifier rubyid_indexes'>indexes</span><span class='period'>.</span><span class='id identifier rubyid_map'>map</span><span class='lbrace'>{</span><span class='op'>|</span><span class='id identifier rubyid_x'>x</span><span class='op'>|</span> <span class='id identifier rubyid_input'>input</span><span class='lbracket'>[</span><span class='id identifier rubyid_x'>x</span><span class='rbracket'>]</span><span class='rbrace'>}</span>
<span class='id identifier rubyid_subdivised_groups'>subdivised_groups</span> <span class='op'>=</span> <span class='id identifier rubyid_random_subset'>random_subset</span><span class='period'>.</span><span class='id identifier rubyid_each_slice'>each_slice</span><span class='lparen'>(</span><span class='int'>100</span><span class='rparen'>)</span><span class='period'>.</span><span class='id identifier rubyid_to_a'>to_a</span>
<span class='id identifier rubyid_sleeping_time'>sleeping_time</span> <span class='op'>=</span> <span class='int'>120</span>
<span class='id identifier rubyid_i'>i</span> <span class='op'>=</span> <span class='int'>0</span>
<span class='kw'>while</span> <span class='id identifier rubyid_i'>i</span> <span class='op'>&lt;</span> <span class='id identifier rubyid_subdivised_groups'>subdivised_groups</span><span class='period'>.</span><span class='id identifier rubyid_length'>length</span>
<span class='id identifier rubyid_k'>k</span> <span class='op'>=</span> <span class='int'>0</span>
<span class='kw'>for</span> <span class='id identifier rubyid_k'>k</span> <span class='kw'>in</span> <span class='lparen'>(</span><span class='id identifier rubyid_i'>i</span><span class='op'>..</span><span class='lparen'>(</span><span class='id identifier rubyid_i'>i</span> <span class='op'>+</span> <span class='int'>5</span><span class='rparen'>)</span><span class='rparen'>)</span>
<span class='id identifier rubyid_title'>title</span> <span class='op'>=</span> <span class='const'>File</span><span class='period'>.</span><span class='id identifier rubyid_basename'>basename</span><span class='lparen'>(</span><span class='id identifier rubyid_absolute_path'>absolute_path</span><span class='rparen'>)</span><span class='period'>.</span><span class='id identifier rubyid_split'>split</span><span class='lparen'>(</span><span class='tstring'><span class='tstring_beg'>&quot;</span><span class='tstring_content'>.</span><span class='tstring_end'>&quot;</span></span><span class='rparen'>)</span><span class='lbracket'>[</span><span class='int'>0</span><span class='rbracket'>]</span> <span class='op'>+</span> <span class='tstring'><span class='tstring_beg'>&quot;</span><span class='tstring_content'>_yannick</span><span class='tstring_end'>&quot;</span></span> <span class='op'>+</span> <span class='tstring'><span class='tstring_beg'>&quot;</span><span class='tstring_content'>_part_</span><span class='embexpr_beg'>#{</span><span class='id identifier rubyid_k'>k</span><span class='op'>+</span><span class='int'>1</span><span class='embexpr_end'>}</span><span class='tstring_end'>&quot;</span></span>
<span class='id identifier rubyid_i'>i</span> <span class='op'>=</span> <span class='id identifier rubyid_i'>i</span> <span class='op'>+</span> <span class='int'>1</span>
<span class='kw'>begin</span>
<span class='id identifier rubyid_puts'>puts</span> <span class='tstring'><span class='tstring_beg'>&quot;</span><span class='tstring_content'>submitting </span><span class='embexpr_beg'>#{</span><span class='id identifier rubyid_title'>title</span><span class='embexpr_end'>}</span><span class='tstring_end'>&quot;</span></span>
<span class='id identifier rubyid_q'>q</span> <span class='op'>=</span> <span class='id identifier rubyid_submit_query'>submit_query</span><span class='lparen'>(</span><span class='id identifier rubyid_title'>title</span><span class='comma'>,</span><span class='id identifier rubyid_subdivised_groups'>subdivised_groups</span><span class='lbracket'>[</span><span class='id identifier rubyid_k'>k</span><span class='rbracket'>]</span><span class='period'>.</span><span class='id identifier rubyid_join'>join</span><span class='lparen'>(</span><span class='tstring'><span class='tstring_beg'>&quot;</span><span class='tstring_content'>\n</span><span class='tstring_end'>&quot;</span></span><span class='rparen'>)</span><span class='comma'>,</span><span class='id identifier rubyid_type'>type</span><span class='rparen'>)</span>
<span class='kw'>rescue</span> <span class='const'>Exception</span> <span class='op'>=&gt;</span> <span class='id identifier rubyid_e'>e</span>
<span class='id identifier rubyid_puts'>puts</span> <span class='id identifier rubyid_e'>e</span><span class='period'>.</span><span class='id identifier rubyid_message'>message</span>
<span class='id identifier rubyid_puts'>puts</span> <span class='id identifier rubyid_e'>e</span><span class='period'>.</span><span class='id identifier rubyid_backtrace'>backtrace</span><span class='period'>.</span><span class='id identifier rubyid_inspect'>inspect</span>
<span class='kw'>end</span>
<span class='kw'>end</span>
<span class='id identifier rubyid_i'>i</span> <span class='op'>=</span> <span class='id identifier rubyid_k'>k</span>
<span class='id identifier rubyid_puts'>puts</span> <span class='tstring'><span class='tstring_beg'>&quot;</span><span class='tstring_content'>Going to sleep at </span><span class='embexpr_beg'>#{</span><span class='const'>Time</span><span class='period'>.</span><span class='id identifier rubyid_now'>now</span> <span class='op'>-</span> <span class='ivar'>@start_time</span><span class='embexpr_end'>}</span><span class='tstring_content'> for </span><span class='embexpr_beg'>#{</span><span class='id identifier rubyid_sleeping_time'>sleeping_time</span><span class='embexpr_end'>}</span><span class='tstring_content'> s.</span><span class='tstring_end'>&quot;</span></span>
<span class='id identifier rubyid_sleep'>sleep</span><span class='lparen'>(</span><span class='id identifier rubyid_sleeping_time'>sleeping_time</span><span class='rparen'>)</span>
<span class='id identifier rubyid_puts'>puts</span> <span class='tstring'><span class='tstring_beg'>&quot;</span><span class='tstring_content'>Waking up at </span><span class='embexpr_beg'>#{</span><span class='const'>Time</span><span class='period'>.</span><span class='id identifier rubyid_now'>now</span> <span class='op'>-</span> <span class='ivar'>@start_time</span><span class='embexpr_end'>}</span><span class='tstring_end'>&quot;</span></span>
<span class='kw'>end</span>
<span class='kw'>end</span></pre>
</td>
</tr>
</table>
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