- Updated doc

- Updated ClassyFireAPI.submit_query_input_in_chunks
This commit is contained in:
djoumbou 2016-03-10 15:54:39 -07:00
parent 3891deaba4
commit b7c175e327
11 changed files with 83 additions and 62 deletions

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@ -1,4 +1,4 @@
lib/classyfire_api.rb 4e5cc4102771d77c67759b9298ae685f0cb612cd lib/classyfire_api.rb 3449cdc9aef5fb255b1fdc933f7d7653bb1fa960
lib/query_resource.rb 645cfb1688a5c44e67e5227fc0e9a77589731f24 lib/query_resource.rb 645cfb1688a5c44e67e5227fc0e9a77589731f24
lib/entity_resource.rb 6c50b4be6a5eb13b44d7080b19c7033b7a37c7cf lib/entity_resource.rb 6c50b4be6a5eb13b44d7080b19c7033b7a37c7cf
lib/sequence_resource.rb d8c5007781d50d0bc13cbe360b617e2937a19428 lib/sequence_resource.rb d8c5007781d50d0bc13cbe360b617e2937a19428

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@ -327,7 +327,7 @@ of a given size.</p>
<span class="summary_desc"><div class='inline'> <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> </div></span>
</li> </li>
@ -475,7 +475,6 @@ specified format.</p>
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<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='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='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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<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'>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'>begin</span>
@ -739,7 +739,6 @@ specified format.</p>
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<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'>def</span> <span class='const'>ClassyFireAPI</span><span class='period'>.</span><span class='id identifier rubyid_get_sequence_classification'>get_sequence_classification</span><span class='lparen'>(</span><span class='id identifier rubyid_fingerprint'>fingerprint</span><span class='comma'>,</span><span class='id identifier rubyid_format'>format</span><span class='op'>=</span><span class='tstring'><span class='tstring_beg'>&quot;</span><span class='tstring_content'>json</span><span class='tstring_end'>&quot;</span></span><span class='rparen'>)</span>
<span class='kw'>begin</span> <span class='kw'>begin</span>
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<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'>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='kw'>begin</span>
@ -932,8 +932,6 @@ retrieve the strutcure&#39;s classification from ClassyFire.</p>
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@ -994,10 +992,12 @@ retrieve the strutcure&#39;s classification from ClassyFire.</p>
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<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='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_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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<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='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_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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<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='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_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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<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'>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='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"> </h3><div class="docstring">
<div class="discussion"> <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> <p>if there is an error.</p>
@ -1589,6 +1589,24 @@ slice_length [Integer] The maximum number of entries for each query input
&mdash; &mdash;
<div class='inline'> <div class='inline'>
<p>the input of the query.</p> <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> </div>
</li> </li>
@ -1620,7 +1638,6 @@ slice_length [Integer] The maximum number of entries for each query input
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<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'>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='kw'>begin</span>
@ -1722,7 +1740,6 @@ framgments from the index &#39;start&#39;.</p>
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<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='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='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='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='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='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>
<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='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='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='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_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_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='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='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='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_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_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_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='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='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_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_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"> <pre class="lines">
252
253
254 254
255 255
256 256
@ -2000,10 +2018,12 @@ text. is fragmented into n part of #slice_length entries each).</p>
299 299
300 300
301 301
302</pre> 302
303
304</pre>
</td> </td>
<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='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='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>
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0.8.7.6 (ruby-2.3.0). 0.8.7.6 (ruby-2.3.0).
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@ -114,7 +114,7 @@
</div> </div>
<div id="footer"> <div id="footer">
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0.8.7.6 (ruby-2.3.0). 0.8.7.6 (ruby-2.3.0).
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@ -183,7 +183,7 @@
</div> </div>
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0.8.7.6 (ruby-2.3.0). 0.8.7.6 (ruby-2.3.0).
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@ -114,7 +114,7 @@
</div> </div>
<div id="footer"> <div id="footer">
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<a href="http://yardoc.org" title="Yay! A Ruby Documentation Tool" target="_parent">yard</a> <a href="http://yardoc.org" title="Yay! A Ruby Documentation Tool" target="_parent">yard</a>
0.8.7.6 (ruby-2.3.0). 0.8.7.6 (ruby-2.3.0).
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@ -140,7 +140,7 @@
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0.8.7.6 (ruby-2.3.0). 0.8.7.6 (ruby-2.3.0).
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@ -236,7 +236,7 @@ XML format.</p>
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0.8.7.6 (ruby-2.3.0). 0.8.7.6 (ruby-2.3.0).
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@ -236,7 +236,7 @@ XML format.</p>
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0.8.7.6 (ruby-2.3.0). 0.8.7.6 (ruby-2.3.0).
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@ -105,7 +105,7 @@
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0.8.7.6 (ruby-2.3.0). 0.8.7.6 (ruby-2.3.0).
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@ -4,10 +4,11 @@ require 'csv'
module ClassyFireAPI module ClassyFireAPI
URL = 'http://classyfire.wishartlab.com' 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 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 # @return [Hash] A Ruby Hash with the id (and other attributes) of the Query or nil
# if there is an error. # if there is an error.
def ClassyFireAPI.submit_query(label,input, type='STRUCTURE') def ClassyFireAPI.submit_query(label,input, type='STRUCTURE')
@ -160,7 +161,7 @@ module ClassyFireAPI
if sline.length == 1 if sline.length == 1
input <<"#{sline[0]}" input <<"#{sline[0]}"
elsif sline.length >= 2 elsif sline.length >= 2
input <<"#{sline[0]}\t#{sline[2]}" input <<"#{sline[0]}\t#{sline[1]}"
end end
end end