- Updated doc

- Updated ClassyFireAPI.submit_query_input_in_chunks
2016-03-10 15:54:39 -07:00 · 2016-03-10 15:54:39 -07:00 · b7c175e327
parent 3891deaba4
commit b7c175e327
11 changed files with 83 additions and 62 deletions
--- a/.yardoc/checksums
+++ b/.yardoc/checksums
@ -1,4 +1,4 @@
-lib/classyfire_api.rb 4e5cc4102771d77c67759b9298ae685f0cb612cd
+lib/classyfire_api.rb 3449cdc9aef5fb255b1fdc933f7d7653bb1fa960
 lib/query_resource.rb 645cfb1688a5c44e67e5227fc0e9a77589731f24
 lib/entity_resource.rb 6c50b4be6a5eb13b44d7080b19c7033b7a37c7cf
 lib/sequence_resource.rb d8c5007781d50d0bc13cbe360b617e2937a19428
--- a/.yardoc/objects/root.dat
+++ b/.yardoc/objects/root.dat
--- a/doc/ClassyFireAPI.html
+++ b/doc/ClassyFireAPI.html
@ -327,7 +327,7 @@ of a given size.</p>

  
    <span class="summary_desc"><div class='inline'>
-<p>Submits a ClassyFire query, which should be returned in a specific format.</p>
+<p>Submits a ClassyFire query in a JSON format.</p>
 </div></span>
  
 </li>
@ -475,7 +475,6 @@ specified format.</p>
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@ -494,10 +493,11 @@ specified format.</p>
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-80</pre>
+80
+81</pre>
    </td>
    <td>
-      <pre class="code"><span class="info file"># File 'lib/classyfire_api.rb', line 61</span>
+      <pre class="code"><span class="info file"># File 'lib/classyfire_api.rb', line 62</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>
@ -608,7 +608,6 @@ specified format.</p>
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@ -626,10 +625,11 @@ specified format.</p>
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+54
+55</pre>
    </td>
    <td>
-      <pre class="code"><span class="info file"># File 'lib/classyfire_api.rb', line 36</span>
+      <pre class="code"><span class="info file"># File 'lib/classyfire_api.rb', line 37</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>
@ -739,7 +739,6 @@ specified format.</p>
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@ -753,10 +752,11 @@ specified format.</p>
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+102</pre>
    </td>
    <td>
-      <pre class="code"><span class="info file"># File 'lib/classyfire_api.rb', line 87</span>
+      <pre class="code"><span class="info file"># File 'lib/classyfire_api.rb', line 88</span>

 <span class='kw'>def</span> <span class='const'>ClassyFireAPI</span><span class='period'>.</span><span class='id identifier rubyid_get_sequence_classification'>get_sequence_classification</span><span class='lparen'>(</span><span class='id identifier rubyid_fingerprint'>fingerprint</span><span class='comma'>,</span><span class='id identifier rubyid_format'>format</span><span class='op'>=</span><span class='tstring'><span class='tstring_beg'>&quot;</span><span class='tstring_content'>json</span><span class='tstring_end'>&quot;</span></span><span class='rparen'>)</span>
  <span class='kw'>begin</span>
@ -842,17 +842,17 @@ specified format.</p>
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-135</pre>
+135
+136</pre>
    </td>
    <td>
-      <pre class="code"><span class="info file"># File 'lib/classyfire_api.rb', line 128</span>
+      <pre class="code"><span class="info file"># File 'lib/classyfire_api.rb', line 129</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>
@ -932,8 +932,6 @@ retrieve the strutcure&#39;s classification from ClassyFire.</p>
      <pre class="lines">


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@ -994,10 +992,12 @@ retrieve the strutcure&#39;s classification from ClassyFire.</p>
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-371</pre>
+371
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+373</pre>
    </td>
    <td>
-      <pre class="code"><span class="info file"># File 'lib/classyfire_api.rb', line 309</span>
+      <pre class="code"><span class="info file"># File 'lib/classyfire_api.rb', line 311</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>
@ -1133,8 +1133,6 @@ format.</p>
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@ -1186,10 +1184,12 @@ format.</p>
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+431
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+433</pre>
    </td>
    <td>
-      <pre class="code"><span class="info file"># File 'lib/classyfire_api.rb', line 378</span>
+      <pre class="code"><span class="info file"># File 'lib/classyfire_api.rb', line 380</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>
@ -1316,8 +1316,6 @@ format.</p>
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@ -1375,10 +1373,12 @@ format.</p>
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+499
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+501</pre>
    </td>
    <td>
-      <pre class="code"><span class="info file"># File 'lib/classyfire_api.rb', line 440</span>
+      <pre class="code"><span class="info file"># File 'lib/classyfire_api.rb', line 442</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>
@ -1509,8 +1509,6 @@ slice_length [Integer] The maximum number of entries for each query input
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@ -1518,10 +1516,12 @@ slice_length [Integer] The maximum number of entries for each query input
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+236
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+238</pre>
    </td>
    <td>
-      <pre class="code"><span class="info file"># File 'lib/classyfire_api.rb', line 227</span>
+      <pre class="code"><span class="info file"># File 'lib/classyfire_api.rb', line 229</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>
@ -1550,7 +1550,7 @@ slice_length [Integer] The maximum number of entries for each query input
 </h3><div class="docstring">
  <div class="discussion">
    
-<p>Submits a ClassyFire query, which should be returned in a specific format.</p>
+<p>Submits a ClassyFire query in a JSON format.</p>

 <p>if there is an error.</p>

@ -1589,6 +1589,24 @@ slice_length [Integer] The maximum number of entries for each query input
        &mdash;
        <div class='inline'>
 <p>the input of the query.</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 type of the query.</p>
 </div>
      
    </li>
@ -1620,7 +1638,6 @@ slice_length [Integer] The maximum number of entries for each query input
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@ -1635,10 +1652,11 @@ slice_length [Integer] The maximum number of entries for each query input
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+28
+29</pre>
    </td>
    <td>
-      <pre class="code"><span class="info file"># File 'lib/classyfire_api.rb', line 13</span>
+      <pre class="code"><span class="info file"># File 'lib/classyfire_api.rb', line 14</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>
@ -1722,7 +1740,6 @@ framgments from the index &#39;start&#39;.</p>
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@ -1784,10 +1801,12 @@ framgments from the index &#39;start&#39;.</p>
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+212
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+214</pre>
    </td>
    <td>
-      <pre class="code"><span class="info file"># File 'lib/classyfire_api.rb', line 150</span>
+      <pre class="code"><span class="info file"># File 'lib/classyfire_api.rb', line 151</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>
@ -1802,7 +1821,7 @@ framgments from the index &#39;start&#39;.</p>
    <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='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>

@ -1817,6 +1836,7 @@ framgments from the index &#39;start&#39;.</p>
  <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'>if</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='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>
@ -1827,6 +1847,7 @@ framgments from the index &#39;start&#39;.</p>
      <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='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>
@ -1844,7 +1865,6 @@ framgments from the index &#39;start&#39;.</p>
        <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>
@ -1950,8 +1970,6 @@ text. is fragmented into n part of #slice_length entries each).</p>
      <pre class="lines">


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@ -2000,10 +2018,12 @@ text. is fragmented into n part of #slice_length entries each).</p>
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-302</pre>
+302
+303
+304</pre>
    </td>
    <td>
-      <pre class="code"><span class="info file"># File 'lib/classyfire_api.rb', line 252</span>
+      <pre class="code"><span class="info file"># File 'lib/classyfire_api.rb', line 254</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>
@ -2066,7 +2086,7 @@ text. is fragmented into n part of #slice_length entries each).</p>
 </div>

    <div id="footer">
-  Generated on Wed Mar  9 19:55:20 2016 by
+  Generated on Thu Mar 10 15:54:06 2016 by
  <a href="http://yardoc.org" title="Yay! A Ruby Documentation Tool" target="_parent">yard</a>
  0.8.7.6 (ruby-2.3.0).
 </div>
--- a/doc/EntityResource.html
+++ b/doc/EntityResource.html
@ -114,7 +114,7 @@
 </div>

    <div id="footer">
-  Generated on Wed Mar  9 19:55:20 2016 by
+  Generated on Thu Mar 10 15:54:06 2016 by
  <a href="http://yardoc.org" title="Yay! A Ruby Documentation Tool" target="_parent">yard</a>
  0.8.7.6 (ruby-2.3.0).
 </div>
--- a/doc/QueryResource.html
+++ b/doc/QueryResource.html
@ -183,7 +183,7 @@
 </div>

    <div id="footer">
-  Generated on Wed Mar  9 19:55:20 2016 by
+  Generated on Thu Mar 10 15:54:06 2016 by
  <a href="http://yardoc.org" title="Yay! A Ruby Documentation Tool" target="_parent">yard</a>
  0.8.7.6 (ruby-2.3.0).
 </div>
--- a/doc/SequenceResource.html
+++ b/doc/SequenceResource.html
@ -114,7 +114,7 @@
 </div>

    <div id="footer">
-  Generated on Wed Mar  9 19:55:20 2016 by
+  Generated on Thu Mar 10 15:54:06 2016 by
  <a href="http://yardoc.org" title="Yay! A Ruby Documentation Tool" target="_parent">yard</a>
  0.8.7.6 (ruby-2.3.0).
 </div>
--- a/doc/_index.html
+++ b/doc/_index.html
@ -140,7 +140,7 @@
 </div>

    <div id="footer">
-  Generated on Wed Mar  9 19:55:19 2016 by
+  Generated on Thu Mar 10 15:54:06 2016 by
  <a href="http://yardoc.org" title="Yay! A Ruby Documentation Tool" target="_parent">yard</a>
  0.8.7.6 (ruby-2.3.0).
 </div>
--- a/doc/file.README.html
+++ b/doc/file.README.html
@ -236,7 +236,7 @@ XML format.</p>
 </div></div>

    <div id="footer">
-  Generated on Wed Mar  9 19:55:20 2016 by
+  Generated on Thu Mar 10 15:54:06 2016 by
  <a href="http://yardoc.org" title="Yay! A Ruby Documentation Tool" target="_parent">yard</a>
  0.8.7.6 (ruby-2.3.0).
 </div>
--- a/doc/index.html
+++ b/doc/index.html
@ -236,7 +236,7 @@ XML format.</p>
 </div></div>

    <div id="footer">
-  Generated on Wed Mar  9 19:55:20 2016 by
+  Generated on Thu Mar 10 15:54:06 2016 by
  <a href="http://yardoc.org" title="Yay! A Ruby Documentation Tool" target="_parent">yard</a>
  0.8.7.6 (ruby-2.3.0).
 </div>
--- a/doc/top-level-namespace.html
+++ b/doc/top-level-namespace.html
@ -105,7 +105,7 @@
 </div>

    <div id="footer">
-  Generated on Wed Mar  9 19:55:20 2016 by
+  Generated on Thu Mar 10 15:54:06 2016 by
  <a href="http://yardoc.org" title="Yay! A Ruby Documentation Tool" target="_parent">yard</a>
  0.8.7.6 (ruby-2.3.0).
 </div>
--- a/lib/classyfire_api.rb
+++ b/lib/classyfire_api.rb
@ -4,10 +4,11 @@ require 'csv'
 module ClassyFireAPI
  URL = 'http://classyfire.wishartlab.com'

-  # Submits a ClassyFire query, which should be returned in a specific format.
+  # Submits a ClassyFire query in a JSON format.
  #
  # @param label [String] the label of the query.
-  # @param input[String] the input of the query.
+  # @param input [String] the input of the query.
+  # @param type [String] the type of the query.
  # @return [Hash] A Ruby Hash with the id (and other attributes) of the Query or nil
  # if there is an error.
  def ClassyFireAPI.submit_query(label,input, type='STRUCTURE')
@ -160,7 +161,7 @@ module ClassyFireAPI
      if sline.length == 1
        input <<"#{sline[0]}"
      elsif sline.length >= 2
-        input <<"#{sline[0]}\t#{sline[2]}"
+        input <<"#{sline[0]}\t#{sline[1]}"
      end
    end