Add changes for 678e169

_modules/pyobistools/taxa.html

@@ -43,6 +43,9 @@ <h1>Source code for pyobistools.taxa</h1><div class="highlight"><pre>
 
 <span class="kn">from</span> <span class="nn">pyobistools.utils</span> <span class="kn">import</span> <span class="n">removesuffix</span>
 
+<span class="kn">from</span> <span class="nn">pyobistools.validation</span> <span class="kn">import</span> <span class="n">check_scientificname_and_ids</span> <span class="k">as</span> <span class="n">check_names</span>
+
+
 <div class="viewcode-block" id="STANDARD_SPECIES_COLUMNS">
 <a class="viewcode-back" href="../../api/pyobistools/taxa/index.html#pyobistools.taxa.STANDARD_SPECIES_COLUMNS">[docs]</a>
 <span class="n">STANDARD_SPECIES_COLUMNS</span> <span class="o">=</span> <span class="p">{</span>
@@ -138,6 +141,23 @@ <h1>Source code for pyobistools.taxa</h1><div class="highlight"><pre>
 
 
 
+<div class="viewcode-block" id="match_taxa">
+<a class="viewcode-back" href="../../api/pyobistools/taxa/index.html#pyobistools.taxa.match_taxa">[docs]</a>
+<span class="k">def</span> <span class="nf">match_taxa</span><span class="p">(</span><span class="n">names</span><span class="p">,</span> <span class="n">ask</span><span class="o">=</span><span class="kc">True</span><span class="p">,</span> <span class="n">itis_usage</span><span class="o">=</span><span class="kc">False</span><span class="p">):</span>
+<span class="w">    </span><span class="sd">&quot;&quot;&quot;</span>
+<span class="sd">    Wrap the existing functionality in validation in the expected name for this function as per R&#39;s iobis/obistools.</span>
+
+<span class="sd">    @param names    List of scientific names to check against</span>
+<span class="sd">    @param ask      Do we ask the user to resolve multi-match or ambiguous names?</span>
+<span class="sd">    @param itis_usage   Pass through the ITIS check setting for the client function to handle</span>
+
+<span class="sd">    @return structure with appended lsids where WoRMS (or ITIS can resolve them)</span>
+<span class="sd">    &quot;&quot;&quot;</span>
+
+    <span class="k">return</span> <span class="n">check_names</span><span class="o">.</span><span class="n">check_scientificname_and_ids</span><span class="p">(</span><span class="n">names</span><span class="p">,</span> <span class="n">value</span><span class="o">=</span><span class="s1">&#39;names&#39;</span><span class="p">,</span> <span class="n">itis_usage</span><span class="o">=</span><span class="n">itis_usage</span><span class="p">)</span></div>
+
+
+
 <div class="viewcode-block" id="search_worms">
 <a class="viewcode-back" href="../../api/pyobistools/taxa/index.html#pyobistools.taxa.search_worms">[docs]</a>
 <span class="k">def</span> <span class="nf">search_worms</span><span class="p">(</span><span class="n">names</span><span class="p">:</span> <span class="n">t</span><span class="o">.</span><span class="n">List</span><span class="p">[</span><span class="nb">str</span><span class="p">],</span>

_sources/api/pyobistools/taxa/index.rst.txt

@@ -16,6 +16,7 @@ Functions
    pyobistools.taxa._standardize_types
    pyobistools.taxa.remove_suffix
    pyobistools.taxa.add_suffix
+   pyobistools.taxa.match_taxa
    pyobistools.taxa.search_worms
    pyobistools.taxa.search_itis
    pyobistools.taxa.search_obis
@@ -46,6 +47,17 @@ Attributes
    Adds suffixes to a name for searching ITIS
 
 
+.. py:function:: match_taxa(names, ask=True, itis_usage=False)
+
+   Wrap the existing functionality in validation in the expected name for this function as per R's iobis/obistools.
+
+   @param names    List of scientific names to check against
+   @param ask      Do we ask the user to resolve multi-match or ambiguous names?
+   @param itis_usage   Pass through the ITIS check setting for the client function to handle
+
+   @return structure with appended lsids where WoRMS (or ITIS can resolve them)
+
+
 .. py:function:: search_worms(names, kwargs = {})
 
    Searches WoRMS for records based on a list of scientific names and returns

api/pyobistools/taxa/index.html

@@ -49,16 +49,19 @@ <h3>Functions<a class="headerlink" href="#functions" title="Link to this heading
 <tr class="row-odd"><td><p><a class="reference internal" href="#pyobistools.taxa.add_suffix" title="pyobistools.taxa.add_suffix"><code class="xref py py-obj docutils literal notranslate"><span class="pre">add_suffix</span></code></a>(name)</p></td>
 <td><p>Adds suffixes to a name for searching ITIS</p></td>
 </tr>
-<tr class="row-even"><td><p><a class="reference internal" href="#pyobistools.taxa.search_worms" title="pyobistools.taxa.search_worms"><code class="xref py py-obj docutils literal notranslate"><span class="pre">search_worms</span></code></a>(names[, kwargs])</p></td>
+<tr class="row-even"><td><p><a class="reference internal" href="#pyobistools.taxa.match_taxa" title="pyobistools.taxa.match_taxa"><code class="xref py py-obj docutils literal notranslate"><span class="pre">match_taxa</span></code></a>(names[, ask, itis_usage])</p></td>
+<td><p>Wrap the existing functionality in validation in the expected name for this function as per R's iobis/obistools.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pyobistools.taxa.search_worms" title="pyobistools.taxa.search_worms"><code class="xref py py-obj docutils literal notranslate"><span class="pre">search_worms</span></code></a>(names[, kwargs])</p></td>
 <td><p>Searches WoRMS for records based on a list of scientific names and returns</p></td>
 </tr>
-<tr class="row-odd"><td><p><a class="reference internal" href="#pyobistools.taxa.search_itis" title="pyobistools.taxa.search_itis"><code class="xref py py-obj docutils literal notranslate"><span class="pre">search_itis</span></code></a>(names[, kwargs])</p></td>
+<tr class="row-even"><td><p><a class="reference internal" href="#pyobistools.taxa.search_itis" title="pyobistools.taxa.search_itis"><code class="xref py py-obj docutils literal notranslate"><span class="pre">search_itis</span></code></a>(names[, kwargs])</p></td>
 <td><p>Searches ITIS for records based on a list of scientific names and returns</p></td>
 </tr>
-<tr class="row-even"><td><p><a class="reference internal" href="#pyobistools.taxa.search_obis" title="pyobistools.taxa.search_obis"><code class="xref py py-obj docutils literal notranslate"><span class="pre">search_obis</span></code></a>(names[, kwargs])</p></td>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pyobistools.taxa.search_obis" title="pyobistools.taxa.search_obis"><code class="xref py py-obj docutils literal notranslate"><span class="pre">search_obis</span></code></a>(names[, kwargs])</p></td>
 <td><p>Searches OBIS for records based on a list of scientific names and returns</p></td>
 </tr>
-<tr class="row-odd"><td><p><a class="reference internal" href="#pyobistools.taxa.search" title="pyobistools.taxa.search"><code class="xref py py-obj docutils literal notranslate"><span class="pre">search</span></code></a>(names[, worms_kwargs, itis_kwargs, ...])</p></td>
+<tr class="row-even"><td><p><a class="reference internal" href="#pyobistools.taxa.search" title="pyobistools.taxa.search"><code class="xref py py-obj docutils literal notranslate"><span class="pre">search</span></code></a>(names[, worms_kwargs, itis_kwargs, ...])</p></td>
 <td><p>Search a list of scientific names in WoRMS, ITIS and OBIS and return the resulting</p></td>
 </tr>
 </tbody>
@@ -118,6 +121,16 @@ <h3>Attributes<a class="headerlink" href="#attributes" title="Link to this headi
 </dl>
 </dd></dl>
 
+<dl class="py function">
+<dt class="sig sig-object py" id="pyobistools.taxa.match_taxa">
+<span class="sig-prename descclassname"><span class="pre">pyobistools.taxa.</span></span><span class="sig-name descname"><span class="pre">match_taxa</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">names</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">ask</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">True</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">itis_usage</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">False</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../../../_modules/pyobistools/taxa.html#match_taxa"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pyobistools.taxa.match_taxa" title="Link to this definition">¶</a></dt>
+<dd><p>Wrap the existing functionality in validation in the expected name for this function as per R’s iobis/obistools.</p>
+<p>&#64;param names    List of scientific names to check against
+&#64;param ask      Do we ask the user to resolve multi-match or ambiguous names?
+&#64;param itis_usage   Pass through the ITIS check setting for the client function to handle</p>
+<p>&#64;return structure with appended lsids where WoRMS (or ITIS can resolve them)</p>
+</dd></dl>
+
 <dl class="py function">
 <dt class="sig sig-object py" id="pyobistools.taxa.search_worms">
 <span class="sig-prename descclassname"><span class="pre">pyobistools.taxa.</span></span><span class="sig-name descname"><span class="pre">search_worms</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">names</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">kwargs</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">{}</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../../../_modules/pyobistools/taxa.html#search_worms"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pyobistools.taxa.search_worms" title="Link to this definition">¶</a></dt>

genindex.html

@@ -117,6 +117,8 @@ <h2 id="F">F</h2>
 <h2 id="M">M</h2>
 <table style="width: 100%" class="indextable genindextable"><tr>
   <td style="width: 33%; vertical-align: top;"><ul>
+      <li><a href="api/pyobistools/taxa/index.html#pyobistools.taxa.match_taxa">match_taxa() (in module pyobistools.taxa)</a>
+</li>
       <li>
     module