Mercurial > repos > yating-l > hubarchivecreator

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  <div class="section" id="module-hubArchiveCreator">
<span id="auto-generated-documentation"></span><h1>Auto Generated Documentation<a class="headerlink" href="#module-hubArchiveCreator" title="Permalink to this headline">¶</a></h1>
<p>This Galaxy tool permits to prepare your files to be ready for
Assembly Hub visualization.
Program test arguments:
hubArchiveCreator.py -g test-data/augustusDbia3.gff3 -f test-data/dbia3.fa -d . -u ./tools -o output.html</p>
<dl class="function">
<dt id="hubArchiveCreator.configure_logger_dev">
<code class="descclassname">hubArchiveCreator.</code><code class="descname">configure_logger_dev</code><span class="sig-paren">(</span><em>log_stdout=None</em><span class="sig-paren">)</span><a class="reference internal" href="_modules/hubArchiveCreator.html#configure_logger_dev"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#hubArchiveCreator.configure_logger_dev" title="Permalink to this definition">¶</a></dt>
<dd><dl class="docutils">
<dt>Dev Logger is defined as following:</dt>
<dd><ul class="first last simple">
<li>Dev needs to have WARN, ERROR and CRITICAL but well formatted / without traceback, in stdout</li>
<li>Still access to full, brute and traceback in stderr for errors</li>
<li>And further access to debug if needed</li>
</ul>
</dd>
</dl>
</dd></dl>

<dl class="function">
<dt id="hubArchiveCreator.configure_logger_stderr">
<code class="descclassname">hubArchiveCreator.</code><code class="descname">configure_logger_stderr</code><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="reference internal" href="_modules/hubArchiveCreator.html#configure_logger_stderr"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#hubArchiveCreator.configure_logger_stderr" title="Permalink to this definition">¶</a></dt>
<dd><p>Configure what should be logged in stderr</p>
</dd></dl>

<dl class="function">
<dt id="hubArchiveCreator.configure_logger_user">
<code class="descclassname">hubArchiveCreator.</code><code class="descname">configure_logger_user</code><span class="sig-paren">(</span><em>log_stdout=None</em><span class="sig-paren">)</span><a class="reference internal" href="_modules/hubArchiveCreator.html#configure_logger_user"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#hubArchiveCreator.configure_logger_user" title="Permalink to this definition">¶</a></dt>
<dd><dl class="docutils">
<dt>User Logger is defined as following:</dt>
<dd><ul class="first last">
<li><dl class="first docutils">
<dt>User needs to have WARN, ERROR and CRITICAL but well formatted / without traceback</dt>
<dd><p class="first last">in STDOUT</p>
</dd>
</dl>
</li>
<li><dl class="first docutils">
<dt>Still access to full, brute and traceback for errors</dt>
<dd><p class="first last">in STDERR</p>
</dd>
</dl>
</li>
<li><dl class="first docutils">
<dt>And further access to debug if needed</dt>
<dd><p class="first last">in .log</p>
</dd>
</dl>
</li>
</ul>
</dd>
</dl>
</dd></dl>

<dl class="function">
<dt id="hubArchiveCreator.create_ordered_datatype_objects">
<code class="descclassname">hubArchiveCreator.</code><code class="descname">create_ordered_datatype_objects</code><span class="sig-paren">(</span><em>ExtensionClass</em>, <em>array_inputs</em>, <em>inputs_data</em><span class="sig-paren">)</span><a class="reference internal" href="_modules/hubArchiveCreator.html#create_ordered_datatype_objects"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#hubArchiveCreator.create_ordered_datatype_objects" title="Permalink to this definition">¶</a></dt>
<dd><p>Function which executes the creation all the necessary files / folders for a special Datatype, for TrackHub
and update the dictionary of datatype</p>
<table class="docutils field-list" frame="void" rules="none">
<col class="field-name" />
<col class="field-body" />
<tbody valign="top">
<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first simple">
<li><strong>ExtensionClass</strong> (<em>Datatype</em>) &#8211; </li>
<li><strong>array_inputs</strong> (<em>list[string]</em>) &#8211; </li>
<li><strong>inputs_data</strong> (<a class="reference external" href="https://docs.python.org/2/library/stdtypes.html#dict" title="(in Python v2.7)"><em>dict</em></a>) &#8211; </li>
</ul>
</td>
</tr>
<tr class="field-even field"><th class="field-name">Return type:</th><td class="field-body"><p class="first last"><a class="reference external" href="https://docs.python.org/2/library/stdtypes.html#dict" title="(in Python v2.7)">dict</a></p>
</td>
</tr>
</tbody>
</table>
</dd></dl>

<dl class="function">
<dt id="hubArchiveCreator.sanitize_name_input">
<code class="descclassname">hubArchiveCreator.</code><code class="descname">sanitize_name_input</code><span class="sig-paren">(</span><em>string_to_sanitize</em><span class="sig-paren">)</span><a class="reference internal" href="_modules/hubArchiveCreator.html#sanitize_name_input"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#hubArchiveCreator.sanitize_name_input" title="Permalink to this definition">¶</a></dt>
<dd><p>Sanitize the string passed in parameter by replacing &#8216;/&#8217; and &#8216; &#8216; by &#8216;_&#8217;</p>
<table class="docutils field-list" frame="void" rules="none">
<col class="field-name" />
<col class="field-body" />
<tbody valign="top">
<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><strong>string_to_sanitize</strong> &#8211; </td>
</tr>
</tbody>
</table>
<p>:return :</p>
<table class="docutils field-list" frame="void" rules="none">
<col class="field-name" />
<col class="field-body" />
<tbody valign="top">
<tr class="field-odd field"><th class="field-name">Example:</th><td class="field-body"></td>
</tr>
</tbody>
</table>
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="gp">&gt;&gt;&gt; </span><span class="n">sanitize_name_input</span><span class="p">(</span><span class="s1">&#39;this/is an//example&#39;</span><span class="p">)</span>
<span class="go">this_is_an__example</span>
</pre></div>
</div>
</dd></dl>

<dl class="function">
<dt id="hubArchiveCreator.sanitize_name_inputs">
<code class="descclassname">hubArchiveCreator.</code><code class="descname">sanitize_name_inputs</code><span class="sig-paren">(</span><em>inputs_data</em><span class="sig-paren">)</span><a class="reference internal" href="_modules/hubArchiveCreator.html#sanitize_name_inputs"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#hubArchiveCreator.sanitize_name_inputs" title="Permalink to this definition">¶</a></dt>
<dd><p>Sanitize value of the keys &#8220;name&#8221; of the dictionary passed in parameter.</p>
<p>Because sometimes output from Galaxy, or even just file name, from user inputs, have spaces.
Also, it can contain &#8216;/&#8217; character and could break the use of os.path function.</p>
<table class="docutils field-list" frame="void" rules="none">
<col class="field-name" />
<col class="field-body" />
<tbody valign="top">
<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><strong>inputs_data</strong> &#8211; dict[string, dict[string, string]]</td>
</tr>
</tbody>
</table>
</dd></dl>

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author	yating-l
date	Wed, 21 Dec 2016 12:13:04 -0500
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