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fix a bunch of docs problems
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sckott committed Jun 10, 2020
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<div itemprop="articleBody">

<h1>All modules for which code is available</h1>
<ul><li><a href="pytaxize/itis/itis.html">pytaxize.itis.itis</a></li>
<ul><li><a href="pytaxize/col/col.html">pytaxize.col.col</a></li>
<li><a href="pytaxize/gbif/parse.html">pytaxize.gbif.parse</a></li>
<li><a href="pytaxize/gn/gni.html">pytaxize.gn.gni</a></li>
<li><a href="pytaxize/gn/gnr.html">pytaxize.gn.gnr</a></li>
<li><a href="pytaxize/ids/ids.html">pytaxize.ids.ids</a></li>
<li><a href="pytaxize/itis/itis.html">pytaxize.itis.itis</a></li>
<li><a href="pytaxize/tax.html">pytaxize.tax</a></li>
</ul>

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<h1>Source code for pytaxize.gbif.parse</h1><div class="highlight"><pre>
<span></span><span class="kn">import</span> <span class="nn">json</span>
<span class="kn">from</span> <span class="nn">pytaxize.refactor</span> <span class="kn">import</span> <span class="n">Refactor</span>

<span class="k">try</span><span class="p">:</span>
<span class="kn">import</span> <span class="nn">pandas</span> <span class="k">as</span> <span class="nn">pd</span>
<span class="k">except</span> <span class="ne">ImportError</span><span class="p">:</span>
<span class="n">warnings</span><span class="o">.</span><span class="n">warn</span><span class="p">(</span><span class="s2">&quot;Pandas library not installed, dataframes disabled&quot;</span><span class="p">)</span>
<span class="n">pd</span> <span class="o">=</span> <span class="kc">None</span>

<span class="k">def</span> <span class="nf">parse</span><span class="p">(</span><span class="n">name</span><span class="p">,</span> <span class="n">as_dataframe</span><span class="o">=</span><span class="kc">False</span><span class="p">):</span>
<span class="sd">&quot;&quot;&quot;</span>
<span class="sd"> Parse taxon names using the GBIF name parser.</span>

<span class="sd"> :param name: A character vector of scientific names.</span>
<span class="sd"> Returns a DataFrame containing fields extracted from parsed</span>
<span class="sd"> taxon names. Fields returned are the union of fields extracted from</span>
<span class="sd"> all species names in scientificname</span>
<span class="sd"> :param as_dataframe: (optional) Type: boolean. Return as pandas data frame?</span>
<span class="sd"> default: False</span>

<span class="sd"> Author John Baumgartner (johnbb@student.unimelb.edu.au)</span>

<span class="sd"> References http://dev.gbif.org/wiki/display/POR/Webservice+API,</span>
<span class="sd"> http://tools.gbif.org/nameparser/api.do</span>

<span class="sd"> Usage::</span>

<span class="sd"> from pytaxize import gbif</span>
<span class="sd"> gbif.parse(name=[&#39;x Agropogon littoralis&#39;])</span>
<span class="sd"> names = [&#39;x Agropogon littoralis&#39;, &#39;Helianthus annuus texanus&#39;]</span>
<span class="sd"> gbif.parse(names)</span>
<span class="sd"> gbif.parse(names, as_dataframe=True)</span>
<span class="sd"> &quot;&quot;&quot;</span>
<span class="n">name</span> <span class="o">=</span> <span class="nb">list</span><span class="p">(</span><span class="n">name</span><span class="p">)</span>
<span class="n">url</span> <span class="o">=</span> <span class="s2">&quot;https://api.gbif.org/v0.9/parser/name&quot;</span>
<span class="n">headers</span> <span class="o">=</span> <span class="p">{</span><span class="s2">&quot;content-type&quot;</span><span class="p">:</span> <span class="s2">&quot;application/json&quot;</span><span class="p">}</span>
<span class="n">tt</span> <span class="o">=</span> <span class="n">Refactor</span><span class="p">(</span><span class="n">url</span><span class="p">,</span> <span class="n">payload</span><span class="o">=</span><span class="p">{},</span> <span class="n">request</span><span class="o">=</span><span class="s2">&quot;post&quot;</span><span class="p">)</span><span class="o">.</span><span class="n">json</span><span class="p">(</span>
<span class="n">data</span><span class="o">=</span><span class="n">json</span><span class="o">.</span><span class="n">dumps</span><span class="p">(</span><span class="n">name</span><span class="p">),</span> <span class="n">headers</span><span class="o">=</span><span class="n">headers</span>
<span class="p">)</span>
<span class="k">if</span> <span class="n">as_dataframe</span><span class="p">:</span>
<span class="n">tt</span> <span class="o">=</span> <span class="n">pd</span><span class="o">.</span><span class="n">DataFrame</span><span class="p">(</span><span class="n">tt</span><span class="p">)</span>
<span class="k">return</span> <span class="n">tt</span>
</pre></div>

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